Science.gov

Sample records for abundance analysis relative

  1. Humidity affects relative ion abundance in direct analysis in real time mass spectrometry of hexamethylene triperoxide diamine.

    PubMed

    Newsome, G Asher; Ackerman, Luke K; Johnson, Kevin J

    2014-12-16

    Unstable explosive hexamethylene triperoxide diamine (HMTD) is dangerous in quantity and benefits from the minimal sampling handling associated with atmospheric pressure chemical ionization for mass spectral analysis. Seasonal variation observed in HMTD mass spectra suggested a humidity dependence. Therefore, direct analysis in real time (DART) ionization mass spectra were acquired at a range of humidity values. An enclosure was designed to fit around the ion source and mass spectrometer inlet at atmospheric pressure. The enclosure was supplied with controlled amounts of humidified air from a test atmosphere generator to create programmable conditions for ambient analysis. The relative abundance and fragmentation of analyte ions were observed to change reliably with changing humidity values and, to a lesser degree, temperature. Humidity at such plasma-based ion sources should be regulated to avoid ∼90% shifts in relative ion abundance and provide stability and reproducibility of HMTD analysis.

  2. RELATIVE ABUNDANCE MEASUREMENTS IN PLUMES AND INTERPLUMES

    SciTech Connect

    Guennou, C.; Hahn, M.; Savin, D. W.

    2015-07-10

    We present measurements of relative elemental abundances in plumes and interplumes. Plumes are bright, narrow structures in coronal holes that extend along open magnetic field lines far out into the corona. Previous work has found that in some coronal structures the abundances of elements with a low first ionization potential (FIP) <10 eV are enhanced relative to their photospheric abundances. This coronal-to-photospheric abundance ratio, commonly called the FIP bias, is typically 1 for elements with a high-FIP (>10 eV). We have used Extreme Ultraviolet Imaging Spectrometer observations made on 2007 March 13 and 14 over a ≈24 hr period to characterize abundance variations in plumes and interplumes. To assess their elemental composition, we used a differential emission measure analysis, which accounts for the thermal structure of the observed plasma. We used lines from ions of iron, silicon, and sulfur. From these we estimated the ratio of the iron and silicon FIP bias relative to that for sulfur. From the results, we have created FIP-bias-ratio maps. We find that the FIP-bias ratio is sometimes higher in plumes than in interplumes and that this enhancement can be time dependent. These results may help to identify whether plumes or interplumes contribute to the fast solar wind observed in situ and may also provide constraints on the formation and heating mechanisms of plumes.

  3. Abundance coefficients, a new method for measuring microorganism relative abundance

    USGS Publications Warehouse

    Forester, R.M.

    1977-01-01

    A new method of measuring the relative abundance of microorganisms by using a set of interrelated coefficients, termed 'abundance coefficients' or 'AC', is proposed. These coefficients provide a means of recording abundance for geometric density categories, and each density measurement represents an approximation of the Poisson parameter ??t. The AC is the natural logarithm of a 'characteristic value,' which is a particular number for each geometric density category. The 'characteristic values' are based upon a probabilistic error statement derived from the Poisson formula, and they present evidence for separation of the geometric category boundaries by e = 2.71828. The proposed AC provide a means for recording species abundance in a manner suitable for arithmetic manipulation, for population structure studies, and for the determination of practical limits for defining the presence or absence of a species. Further, these coefficients provide for both intrasample and intersample abundance comparisons. ?? 1977 Plenum Publishing Corporation.

  4. Identification of hydrologic indicators related to fish diversity and abundance: A data mining approach for fish community analysis

    NASA Astrophysics Data System (ADS)

    Yang, Yi-Chen E.; Cai, Ximing; Herricks, Edwin E.

    2008-04-01

    This paper develops a new approach to identify hydrologic indicators related to fish community and generate a quantitative function between an ecological target index and the identified hydrologic indicators. The approach is based on genetic programming (GP), a data mining method. Using the Shannon Index (a fish community diversity index) or the number of individuals (total abundance) of a fish community, as an ecological target, the GP identified the most ecologically relevant hydrologic indicators (ERHIs) from 32 indicators of hydrologic alteration, for the case study site, the upper Illinois River. Robustness analysis showed that different GP runs found a similar set of ERHIs; each of the identified ERHI from different GP runs had a consistent relationship with the target index. By comparing the GP results with those from principal component analysis and autecology matrix, the three approaches identified a small number (six) of common ERHIs. Particularly, the timing of low flow (Dmin) seems to be more relevant to the diversity of the fish community, while the magnitude of the low flow (Qb) is more relevant to the total fish abundance; large rising rates result in a significant improvement of fish diversity, which is counterintuitive and against previous findings. The quantitative function developed by GP was further used to construct an indicator impact matrix (IIM), which was demonstrated as a potentially useful tool for streamflow restoration design.

  5. Use of a Hierarchical Oligonucleotide Primer Extension Approach for Multiplexed Relative Abundance Analysis of Methanogens in Anaerobic Digestion Systems

    PubMed Central

    Chuang, Hui-Ping; Hsu, Mao-Hsuan; Chen, Wei-Yu

    2013-01-01

    In this study, we established a rapid multiplex method to detect the relative abundances of amplified 16S rRNA genes from known cultivatable methanogens at hierarchical specificities in anaerobic digestion systems treating industrial wastewater and sewage sludge. The method was based on the hierarchical oligonucleotide primer extension (HOPE) technique and combined with a set of 27 primers designed to target the total archaeal populations and methanogens from 22 genera within 4 taxonomic orders. After optimization for their specificities and detection sensitivity under the conditions of multiple single-nucleotide primer extension reactions, the HOPE approach was applied to analyze the methanogens in 19 consortium samples from 7 anaerobic treatment systems (i.e., 513 reactions). Among the samples, the methanogen populations detected with order-level primers accounted for >77.2% of the PCR-amplified 16S rRNA genes detected using an Archaea-specific primer. The archaeal communities typically consisted of 2 to 7 known methanogen genera within the Methanobacteriales, Methanomicrobiales, and Methanosarcinales and displayed population dynamic and spatial distributions in anaerobic reactor operations. Principal component analysis of the HOPE data further showed that the methanogen communities could be clustered into 3 distinctive groups, in accordance with the distribution of the Methanosaeta, Methanolinea, and Methanomethylovorans, respectively. This finding suggested that in addition to acetotrophic and hydrogenotrophic methanogens, the methylotrophic methanogens might play a key role in the anaerobic treatment of industrial wastewater. Overall, the results demonstrated that the HOPE approach is a specific, rapid, and multiplexing platform to determine the relative abundances of targeted methanogens in PCR-amplified 16S rRNA gene products. PMID:24077716

  6. Statistical analysis of polychaete population density: dynamics of dominant species and scaling properties in relative abundance fluctuations

    NASA Astrophysics Data System (ADS)

    Quiroz-Martinez, B.; Schmitt, F. G.; Dauvin, J.-C.

    2012-01-01

    We consider here the dynamics of two polychaete populations based on a 20 yr temporal benthic survey of two muddy fine sand communities in the Bay of Morlaix, Western English Channel. These populations display high temporal variability, which is analyzed here using scaling approaches. We find that population densities have heavy tailed probability density functions. We analyze the dynamics of relative species abundance in two different communities of polychaetes by estimating in a novel way a "mean square drift" coefficient which characterizes their fluctuations in relative abundance over time. We show the usefulness of using new tools to approach and model such highly variable population dynamics in marine ecosystems.

  7. Low abundance materials at the mars pathfinder landing site: An investigation using spectral mixture analysis and related techniques

    USGS Publications Warehouse

    Bell, J.F.; Farrand, W. H.; Johnson, J. R.; Morris, R.V.

    2002-01-01

    Recalibrated and geometrically registered multispectral images from the Imager for Mars Pathfinder (IMP) were analyzed using Spectral Mixture Analysis (SMA) and related techniques. SMA models a multispectral image scene as a linear combination of end-member spectra, and anomalous materials which do not fit the model are detected as model residuals. While most of the IMP data studied here are modeled generally well using "Bright Dust," "Gray Rock," and "Shade" image endmembers, additional anomalous materials were detected through careful analysis of root mean square (RMS) error images resulting from SMA. For example, analysis of SMA fraction and RMS images indicates spectral differences within a previously monolithologic Dark Soil class. A type of Dark Soil that has high fractional abundances in rock fraction images (Gray Rock Soil) was identified. Other anomalous materials identified included a previously noted "Black Rock" lithology, a class of possibly indurated, compacted, or partially cemented soils ("Intermediate Soil"), and a unit referred to as "Anomalous Patches" on at least one rock. The Black Rock lithology has a strong 900-1000-nm absorption, and modeling of the derived image endmembers using a laboratory reference endmember modeling (REM) approach produced best-fit model spectra that are most consistent with the presence of high-Ca pyroxenes and/or olivine, crystalline ferric oxide minerals, or mixtures of these materials as important components of the Black Rock endmember. More unique mineralogic identifications could not be obtained using our initial REM analyses. Both Intermediate Soil and Anomalous Patches units exhibit a relatively narrow 860-950-nm absorption that is consistent with the presence of either low-Ca pyroxenes or a cementing crystalline ferric oxide mineral. ?? 2002 Elsevier Science (USA).

  8. Microsatellites in Brassica unigenes: relative abundance, marker design, and use in comparative physical mapping and genome analysis.

    PubMed

    Parida, Swarup K; Yadava, Devendra K; Mohapatra, Trilochan

    2010-01-01

    Microsatellites present in the transcribed regions of the genome have the potential to reveal functional diversity. Unigene sequence databases are the sources of such genic microsatellites with unique flanking sequences and genomic locations even in complex polyploids. The present study was designed to assay the unigenes of Brassica napus and B. rapa for various microsatellite repeats, and to design markers and use them in comparative genome analysis and study of evolution. The average frequency of microsatellites in Brassica unigenes was one in every 7.25 kb of sequence, as compared with one in every 8.57 kb of sequence in Arabidopsis thaliana. Trinucleotide motifs coding for serine and the dinucleotide motif GA were most abundant. We designed 2374 and 347 unigene-based microsatellite (UGMS) markers including 541 and 58 class I types in B. napus and B. rapa, respectively, and evaluated their use across diverse species and genera. Most of these markers (93.3%) gave successful amplification of target microsatellite motifs, which was confirmed by sequencing. Interspecific polymorphism between B. napus and B. rapa detected in silico for the UGMS markers was 4.16 times higher in 5' untranslated regions than in coding sequences. Physical anchoring of Brassica UGMS markers on the A. thaliana genome indicated their significance in studying the evolutionary history of A. thaliana genomic duplications in relation to speciation. Comparative physical mapping identified 85% of Brassica unigenes as single copy and gave clues for the presence of conserved primordial gene order. Complex chromosomal rearrangements such as inversions, tandem and segmental duplications, and insertions/deletions were evident between A. thaliana and B. rapa genomes. The results obtained have encouraging implications for the use of UGMS markers in comparative genome analysis and for understanding evolutionary complexities in the family Brassicaceae.

  9. Correlation of mRNA expression and protein abundance affected by multiple sequence features related to translational efficiency in Desulfovibrio vulgaris: A quantitative analysis

    SciTech Connect

    Nie, Lei; Wu, Gang; Zhang, Weiwen

    2006-12-01

    The modest correlation between mRNA expression and protein abundance in large scale datasets is explained in part by experimental challenges, such as technological limitations, and in part by fundamental biological factors in the transcription and translation processes. Among various factors affecting the mRNA-protein correlation, the roles of biological factors related to translation are poorly understood. In this study, using experimental mRNA expression and protein abundance data collected from Desulfovibrio vulgaris by DNA microarray and LC-MS/MS proteomic analysis, we quantitatively examined the effects of several translational-efficiency-related sequence features on mRNA-protein correlation. Three classes of sequence features were investigated according to different translational stages: (1) initiation: Shine-Dalgarno sequences, start codon identity and start codon context; (2) elongation: codon usage and amino acid usage; and (3) termination: stop codon identity and stop codon context. Surprisingly, although it is widely accepted that translation initiation is a rate-limiting step for translation, our results showed that the mRNA-protein correlation was affected the most by the features at elongation stages, codon usage and amino acid composition (7.4-12.6% and 5.3-9.3% of the total variation of mRNA-protein correlation, respectively), followed by stop codon context and the Shine-Dalgarno sequence (2.5-4.2% and 2.3%, respectively). Taken together, all sequence features contributed to 18.4-21.8% of the total variation of mRNA-protein correlation. As the first comprehensive quantitative analysis of the mRNA-protein correlation in bacterial D. vulgaris, our results suggest that the traditional view of the relative importance of various sequence features in prokaryotic protein translation might be questionable.

  10. Chemical abundance analysis of 19 barium stars

    NASA Astrophysics Data System (ADS)

    Yang, Guo-Chao; Liang, Yan-Chun; Spite, Monique; Chen, Yu-Qin; Zhao, Gang; Zhang, Bo; Liu, Guo-Qing; Liu, Yu-Juan; Liu, Nian; Deng, Li-Cai; Spite, Francois; Hill, Vanessa; Zhang, Cai-Xia

    2016-01-01

    We aim at deriving accurate atmospheric parameters and chemical abundances of 19 barium (Ba) stars, including both strong and mild Ba stars, based on the high signal-to-noise ratio and high resolution Echelle spectra obtained from the 2.16 m telescope at Xinglong station of National Astronomical Observatories, Chinese Academy of Sciences. The chemical abundances of the sample stars were obtained from an LTE, plane-parallel and line-blanketed atmospheric model by inputting the atmospheric parameters (effective temperatures Teff, surface gravities log g, metallicity [Fe/H] and microturbulence velocity ξt) and equivalent widths of stellar absorption lines. These samples of Ba stars are giants as indicated by atmospheric parameters, metallicities and kinematic analysis about UVW velocity. Chemical abundances of 17 elements were obtained for these Ba stars. Their Na, Al, α- and iron-peak elements (O, Na, Mg, Al, Si, Ca, Sc, Ti, V, Cr, Mn, Ni) are similar to the solar abundances. Our samples of Ba stars show obvious overabundances of neutron-capture (n-capture) process elements relative to the Sun. Their median abundances of [Ba/Fe], [La/Fe] and [Eu/Fe] are 0.54, 0.65 and 0.40, respectively. The Y I and Zr I abundances are lower than Ba, La and Eu, but higher than the α- and iron-peak elements for the strong Ba stars and similar to the iron-peak elements for the mild stars. There exists a positive correlation between Ba intensity and [Ba/Fe]. For the n-capture elements (Y, Zr, Ba, La), there is an anti-correlation between their [X/Fe] and [Fe/H]. We identify nine of our sample stars as strong Ba stars with [Ba/Fe] >0.6 where seven of them have Ba intensity Ba=2-5, one has Ba=1.5 and another one has Ba=1.0. The remaining ten stars are classified as mild Ba stars with 0.17<[Ba/Fe] <0.54.

  11. ABUNDANT OR RARE? A HYBRID APPROACH FOR DETERMINING SPECIES RELATIVE ABUNDANCE AT AN ECOREGOIONAL SCALE

    EPA Science Inventory

    Everyone knows what abundant and rare species are, but quantifying the concept proves elusive. As part of an EPA/USGS project to assess near-coastal species vulnerability to climate change affects, we designed a hybrid approach to determine species relative abundance at an ecoreg...

  12. ABUNDANT OR RARE? A HYBRID APPROACH FOR DETERMINING SPECIES RELATIVE ABUNDANCE AT AN ECOREGOIONAL SCALE - 2014

    EPA Science Inventory

    Everyone knows what abundant and rare species are, but quantifying the concept proves elusive. As part of an EPA/USGS project to assess near-coastal species vulnerability to climate change affects, we designed a hybrid approach to determine species relative abundance at an ecoreg...

  13. Genetic diversity in aspen and its relation to arthropod abundance.

    PubMed

    Zhang, Chunxia; Vornam, Barbara; Volmer, Katharina; Prinz, Kathleen; Kleemann, Frauke; Köhler, Lars; Polle, Andrea; Finkeldey, Reiner

    2014-01-01

    The ecological consequences of biodiversity have become a prominent public issue. Little is known on the effect of genetic diversity on ecosystem services. Here, a diversity experiment was established with European and North American aspen (Populus tremula, P. tremuloides) planted in plots representing either a single deme only or combinations of two, four and eight demes. The goals of this study were to explore the complex inter- and intraspecific genetic diversity of aspen and to then relate three measures for diversity (deme diversity, genetic diversity determined as Shannon index or as expected heterozygosity) to arthropod abundance. Microsatellite and AFLP markers were used to analyze the genetic variation patterns within and between the aspen demes and deme mixtures. Large differences were observed regarding the genetic diversity within demes. An analysis of molecular variance revealed that most of the total genetic diversity was found within demes, but the genetic differentiation among demes was also high. The complex patterns of genetic diversity and differentiation resulted in large differences of the genetic variation within plots. The average diversity increased from plots with only one deme to plots with two, four, and eight demes, respectively and separated plots with and without American aspen. To test whether intra- and interspecific diversity impacts on ecosystem services, arthropod abundance was determined. Increasing genetic diversity of aspen was related to increasing abundance of arthropods. However, the relationship was mainly driven by the presence of American aspen suggesting that species identity overrode the effect of intraspecific variation of European aspen.

  14. Genetic diversity in aspen and its relation to arthropod abundance

    PubMed Central

    Zhang, Chunxia; Vornam, Barbara; Volmer, Katharina; Prinz, Kathleen; Kleemann, Frauke; Köhler, Lars; Polle, Andrea; Finkeldey, Reiner

    2015-01-01

    The ecological consequences of biodiversity have become a prominent public issue. Little is known on the effect of genetic diversity on ecosystem services. Here, a diversity experiment was established with European and North American aspen (Populus tremula, P. tremuloides) planted in plots representing either a single deme only or combinations of two, four and eight demes. The goals of this study were to explore the complex inter- and intraspecific genetic diversity of aspen and to then relate three measures for diversity (deme diversity, genetic diversity determined as Shannon index or as expected heterozygosity) to arthropod abundance. Microsatellite and AFLP markers were used to analyze the genetic variation patterns within and between the aspen demes and deme mixtures. Large differences were observed regarding the genetic diversity within demes. An analysis of molecular variance revealed that most of the total genetic diversity was found within demes, but the genetic differentiation among demes was also high. The complex patterns of genetic diversity and differentiation resulted in large differences of the genetic variation within plots. The average diversity increased from plots with only one deme to plots with two, four, and eight demes, respectively and separated plots with and without American aspen. To test whether intra- and interspecific diversity impacts on ecosystem services, arthropod abundance was determined. Increasing genetic diversity of aspen was related to increasing abundance of arthropods. However, the relationship was mainly driven by the presence of American aspen suggesting that species identity overrode the effect of intraspecific variation of European aspen. PMID:25674097

  15. Abundance Analysis of 10 Kepler Planetary Hosts

    NASA Astrophysics Data System (ADS)

    Vaz, Zachary A.; Schuler, Simon C.; Williams, Drake; Cunha, Katia M. L.; Smith, Verne V.; Ghezzi, Luan; Teske, Johanna

    2016-01-01

    This study aims to identify possible connections between the detailed chemical abundances of stars and the existence of small planets discovered by NASA's Kepler spacecraft. We have analyzed high quality Keck/HIRES spectra of the planetary hosts Kepler-65, Kepler-93, Kepler-97, Kepler-98, Kepler-102, Kepler 128, Kepler-406, Kepler-408, Kepler-409, and Kepler-411 and derived the abundances of up to 17 elements for these stars. Results from previous studies have suggested that stellar abundance patterns or "signatures" may indicate the presence of planets, possibly terrestrial planets in particular. Should such patterns exist, they could be used to identify stars with small planets. Here we present the results of our abundance analysis of 10 stars with a variety of exoplanet systems discovered by Kepler and address the hypothesis that chemical abundance signatures can indicate the presence of small planets.This work is generously supported by NASA through a Kepler Participating Scientist grant to SCS (Grant #NNX13AH78G).

  16. Radio Bursts as Diagnostics of Relative Abundances in Solar Particles

    NASA Astrophysics Data System (ADS)

    Cane, H. V.; Richardson, I. G.; von Rosenvinge, T. T.

    2008-05-01

    Based solely on the presence of associated low frequency type III radio bursts with specific characteristics, Cane et al. (2002) suggested that large solar energetic particle events are likely to include contributions from particles accelerated in the associated flares. Studies using ACE/SIS observations of O and Fe intensity-time profiles have supported this suggestion. Nevertheless, some researchers have argued that particles cannot be flare accelerated if the relative abundances differ from those in the small particle events that are widely accepted to be composed of flare particles. However, based on the radio data, the flare particles in large events are not released at the time of the flare soft X-ray onset but are delayed, either because they are accelerated later or released later. These changed conditions are expected to alter the relative abundances (electrons to protons, heavy to light ions) compared to those associated with small flares. From a comprehensive analysis of the characteristics of the coronal mass ejections (CMEs), flares and radio bursts (at metric and longer wavelengths) associated with the ~340 proton events at >25 MeV that occurred during solar cycle 23, we confirm earlier results (Cane et al. 1986) that the timing of the type III bursts is a reasonable discriminator for the relative abundances at the start of solar particle events. In contrast, the speeds of the associated CMEs do not discriminate events, nor does the presence of meter wavelength type II bursts. Cane, H. V., R. E. McGuire, and T. T. von Rosenvinge (1986), Two classes of solar energetic particle events associated with impulsive and long-duration soft X-ray flares, Astrophys. J., 301, 448. Cane, H. V., W. C. Erickson, and N. P. Prestage (2002), Solar flares, type III radio bursts, coronal mass ejections, and energetic particles, J. Geophys. Res., 107(A10), 1315, doi:10.1029/2001JA000320.

  17. Relative resource abundance explains butterfly biodiversity in island communities

    PubMed Central

    Yamamoto, Naoaki; Yokoyama, Jun; Kawata, Masakado

    2007-01-01

    Ecologists have long been intrigued by the factors that control the pattern of biodiversity, i.e., the distribution and abundance of species. Previous studies have demonstrated that coexisting species partition their resources and/or that the compositional similarity between communities is determined by environmental factors, lending support to the niche-assembly model. However, no attempt has been made to test whether the relative amount of resources that reflects relative niche space controls relative species abundance in communities. Here, we demonstrate that the relative abundance of butterfly species in island communities is significantly related to the relative biomasses of their host plants but not to the geographic distance between communities. In the studied communities, the biomass of particular host plant species positively affected the abundance of the butterfly species that used them, and consequently, influenced the relative abundance of the butterfly communities. This indicated that the niche space of butterflies (i.e., the amount of resources) strongly influences butterfly biodiversity patterns. We present this field evidence of the niche-apportionment model that propose that the relative amount of niche space explains the pattern of the relative abundance of the species in communities. PMID:17553963

  18. Relative nuclei abundance inside the International Space Station

    NASA Astrophysics Data System (ADS)

    Larsson, Oscar

    2012-07-01

    The Sileye3/Alteino experiment was first operational on-board the International Space Station, ISS, 27 April 2002. From 2006 through 2009 it was activated for long duration measurements of relative particle abundance as part of the ESA ALTCRISS project. Measuring the relative abundance of different nuclei species inside the ISS gives important clues as to how the known cosmic ray spectrum outside the space station changes when traversing the hull, i.e. giving indications as to how the hadronic interactions in the hull gives rise to changes in the expected radiation environment for the astronauts, which is of great interest for risk assessments for future long duration deep space missions. In our work the relative abundance for nuclei species with energies above ≃ 60 MeV/n and 5 ≤ Z ≤ 26 are presented for different places and detector orientations inside the ISS, also with and without shielding of the detector. What can be seen when comparing with the relative abundance of nuclei in the cosmic rays, is a significant difference in abundance for odd Z nuclei, whereas even numbered are in better agreement. Odd Z nuclei are much more abundant inside the ISS. This is an update from our previous report with increased statistics and with relative abundance on more nuclei.

  19. Relative nuclear abundances inside ISS with ALTEA-Space experiment

    NASA Astrophysics Data System (ADS)

    Zaconte, Veronica; Casolino, Marco; di Fino, Luca; La Tessa, Chiara; Larosa, Marianna; Narici, Livio; Picozza, Piergiorgio; Rinaldi, Adele; Sannita, Walter G.

    ALTEA (Anomalous Long Term Effects on Astronauts) is a multidisciplinary project aimed at studying the cosmic rays and their effects on the astronauts during the space missions, with a focus on the Light Flashes phenomenon. The ALTEA-Space is the main space experiment of the ALTEA project and its goal is the characterization of the radiation environment inside the International Space Station (ISS). It includes a stack of six silicon telescope particle detectors arranged in a 3D structure, capable to determine the energy loss and the trajectory of the cosmic ray ions. ALTEA-Space is on board the ISS since July 2006 and collected data continuously between August 2006 and July 2007. The first analysis has been performed on particles that release almost constant energy inside the detectors and provides spectra of the quasi relativistic radiation making possible the identification of ions from Boron to Iron. Relative nuclear abundances and absolute fluxes for all discriminated elements are presented, both total and divided into the different geomagnetic regions (polar, equatorial and South Atlantic Anomaly). Abundances are compared with literature values and with data from previous experiments.

  20. Rank abundance relations in evolutionary dynamics of random replicators

    NASA Astrophysics Data System (ADS)

    Yoshino, Yoshimi; Galla, Tobias; Tokita, Kei

    2008-09-01

    We present a nonequilibrium statistical mechanics description of rank abundance relations (RAR) in random community models of ecology. Specifically, we study a multispecies replicator system with quenched random interaction matrices. We here consider symmetric interactions as well as asymmetric and antisymmetric cases. RARs are obtained analytically via a generating functional analysis, describing fixed-point states of the system in terms of a small set of order parameters, and in dependence on the symmetry or otherwise of interactions and on the productivity of the community. Our work is an extension of Tokita [Phys. Rev. Lett. 93, 178102 (2004)], where the case of symmetric interactions was considered within an equilibrium setup. The species abundance distribution in our model come out as truncated normal distributions or transformations thereof and, in some case, are similar to left-skewed distributions observed in ecology. We also discuss the interaction structure of the resulting food-web of stable species at stationarity, cases of heterogeneous cooperation pressures as well as effects of finite system size and of higher-order interactions.

  1. Rank abundance relations in evolutionary dynamics of random replicators.

    PubMed

    Yoshino, Yoshimi; Galla, Tobias; Tokita, Kei

    2008-09-01

    We present a nonequilibrium statistical mechanics description of rank abundance relations (RAR) in random community models of ecology. Specifically, we study a multispecies replicator system with quenched random interaction matrices. We here consider symmetric interactions as well as asymmetric and antisymmetric cases. RARs are obtained analytically via a generating functional analysis, describing fixed-point states of the system in terms of a small set of order parameters, and in dependence on the symmetry or otherwise of interactions and on the productivity of the community. Our work is an extension of Tokita [Phys. Rev. Lett. 93, 178102 (2004)], where the case of symmetric interactions was considered within an equilibrium setup. The species abundance distribution in our model come out as truncated normal distributions or transformations thereof and, in some case, are similar to left-skewed distributions observed in ecology. We also discuss the interaction structure of the resulting food-web of stable species at stationarity, cases of heterogeneous cooperation pressures as well as effects of finite system size and of higher-order interactions.

  2. Relative abundance of desert tortoises on the Nevada Test Site

    SciTech Connect

    Rautenstrauch, K.R.; O`Farrell, T.P.

    1993-12-31

    Seven hundred fifty-nine transects having a total length of 1,191 km were walked during 1981--1986 to determine the distribution and relative abundance of desert tortoises (Gopherus agassizii) on the Nevada Test Site (NTS). The abundance of tortoises on NTS was low to very low relative to other populations in the Mojave Desert. Sign of tortoises was found from 880 to 1,570 m elevation and was more abundant above 1,200 m than has been reported previously for Nevada. Tortoises were more abundant on NTS on the upper alluvial fans and slopes of mountains than in valley bottoms. They also were more common on or near limestone and dolomite mountains than on mountains of volcanic origin.

  3. Chemical abundance analysis of symbiotic giants - III. Metallicity and CNO abundance patterns in 24 southern systems

    NASA Astrophysics Data System (ADS)

    Gałan, Cezary; Mikołajewska, Joanna; Hinkle, Kenneth H.; Joyce, Richard R.

    2016-01-01

    The elemental abundances of symbiotic giants are essential to address the role of chemical composition in the evolution of symbiotic binaries, to map their parent population, and to trace their mass transfer history. However, the number of symbiotic giants with fairly well determined photospheric composition is still insufficient for statistical analyses. This is the third in a series of papers on the chemical composition of symbiotic giants determined from high-resolution (R ˜ 50 000), near-infrared spectra. Here we present results for 24 S-type systems. Spectrum synthesis methods employing standard local thermal equilibrium analysis and atmosphere models were used to obtain photospheric abundances of CNO and elements around the iron peak (Fe, Ti, Ni, and Sc). Our analysis reveals metallicities distributed in a wide range from slightly supersolar ([Fe/H] ˜ +0.35 dex) to significantly subsolar ([Fe/H] ˜ -0.8 dex) but principally with near-solar and slightly subsolar metallicity ([Fe/H] ˜ -0.4 to -0.3 dex). The enrichment in 14N isotope, found in all these objects, indicates that the giants have experienced the first dredge-up. This was confirmed in a number of objects by the low 12C/13C ratio (5-23). We found that the relative abundance of [Ti/Fe] is generally large in red symbiotic systems.

  4. Capitalizing on opportunistic data for monitoring relative abundances of species.

    PubMed

    Giraud, Christophe; Calenge, Clément; Coron, Camille; Julliard, Romain

    2016-06-01

    With the internet, a massive amount of information on species abundance can be collected by citizen science programs. However, these data are often difficult to use directly in statistical inference, as their collection is generally opportunistic, and the distribution of the sampling effort is often not known. In this article, we develop a general statistical framework to combine such "opportunistic data" with data collected using schemes characterized by a known sampling effort. Under some structural assumptions regarding the sampling effort and detectability, our approach makes it possible to estimate the relative abundance of several species in different sites. It can be implemented through a simple generalized linear model. We illustrate the framework with typical bird datasets from the Aquitaine region in south-western France. We show that, under some assumptions, our approach provides estimates that are more precise than the ones obtained from the dataset with a known sampling effort alone. When the opportunistic data are abundant, the gain in precision may be considerable, especially for rare species. We also show that estimates can be obtained even for species recorded only in the opportunistic scheme. Opportunistic data combined with a relatively small amount of data collected with a known effort may thus provide access to accurate and precise estimates of quantitative changes in relative abundance over space and/or time. PMID:26496390

  5. Empirical oxygen abundances and physical conditions for relatively low abundance H II regions

    SciTech Connect

    Skillman, E.D. )

    1989-12-01

    The utility of the emission-line ratio (3727 + 4959 + 5007 A)/H-beta as an estimate of the total oxygen abundance in H II regions of low abundance (less than 10 percent of the solar value) is discussed. Using both observational data where the 4363A line is measured and model H II regions it is concluded that, for low abundance systems, total oxygen abundances can be determined with an accuracy of + or - 0.2 dex in the absence of a 4363A measurement. An attempt is made to study the average behavior of the stellar effective temperature (Teff) and ionization parameter (U) with changing abundance in low abundance systems. It is shown that some diagnostic methods which are viable for high abundance systems are not capable of uniquely determining Teff and U in low abundance systems. The most promising method of determining Teff and U requires measuring emission lines of forbidden O II, O III, S II, and S III. 53 refs.

  6. Abundance recovery error analysis using simulated AVIRIS data

    NASA Technical Reports Server (NTRS)

    Stoner, William W.; Harsanyi, Joseph C.; Farrand, William H.; Wong, Jennifer A.

    1992-01-01

    Measurement noise and imperfect atmospheric correction translate directly into errors in the determination of the surficial abundance of materials from imaging spectrometer data. The effects of errors on abundance recovery were investigated previously using Monte Carlo simulation methods by Sabol et. al. The drawback of the Monte Carlo approach is that thousands of trials are needed to develop good statistics on the probable error in abundance recovery. This computational burden invariably limits the number of scenarios of interest that can practically be investigated. A more efficient approach is based on covariance analysis. The covariance analysis approach expresses errors in abundance as a function of noise in the spectral measurements and provides a closed form result eliminating the need for multiple trials. Monte Carlo simulation and covariance analysis are used to predict confidence limits for abundance recovery for a scenario which is modeled as being derived from Airborne Visible/Infrared Imaging Spectrometer (AVIRIS).

  7. Changes in the Relative Abundance of Two Saccharomyces Species from Oak Forests to Wine Fermentations

    PubMed Central

    Dashko, Sofia; Liu, Ping; Volk, Helena; Butinar, Lorena; Piškur, Jure; Fay, Justin C.

    2016-01-01

    Saccharomyces cerevisiae and its sibling species Saccharomyces paradoxus are known to inhabit temperate arboreal habitats across the globe. Despite their sympatric distribution in the wild, S. cerevisiae is predominantly associated with human fermentations. The apparent ecological differentiation of these species is particularly striking in Europe where S. paradoxus is abundant in forests and S. cerevisiae is abundant in vineyards. However, ecological differences may be confounded with geographic differences in species abundance. To compare the distribution and abundance of these two species we isolated Saccharomyces strains from over 1200 samples taken from vineyard and forest habitats in Slovenia. We isolated numerous strains of S. cerevisiae and S. paradoxus, as well as a small number of Saccharomyces kudriavzevii strains, from both vineyard and forest environments. We find S. cerevisiae less abundant than S. paradoxus on oak trees both within and outside the vineyard, but more abundant on grapevines and associated substrates. Analysis of the uncultured microbiome shows, that both S. cerevisiae and S. paradoxus are rare species in soil and bark samples, but can be much more common in grape must. In contrast to S. paradoxus, European strains of S. cerevisiae have acquired multiple traits thought to be important for life in the vineyard and dominance of wine fermentations. We conclude, that S. cerevisiae and S. paradoxus currently share both vineyard and non-vineyard habitats in Slovenia and we discuss factors relevant to their global distribution and relative abundance. PMID:26941733

  8. Changes in the Relative Abundance of Two Saccharomyces Species from Oak Forests to Wine Fermentations.

    PubMed

    Dashko, Sofia; Liu, Ping; Volk, Helena; Butinar, Lorena; Piškur, Jure; Fay, Justin C

    2016-01-01

    Saccharomyces cerevisiae and its sibling species Saccharomyces paradoxus are known to inhabit temperate arboreal habitats across the globe. Despite their sympatric distribution in the wild, S. cerevisiae is predominantly associated with human fermentations. The apparent ecological differentiation of these species is particularly striking in Europe where S. paradoxus is abundant in forests and S. cerevisiae is abundant in vineyards. However, ecological differences may be confounded with geographic differences in species abundance. To compare the distribution and abundance of these two species we isolated Saccharomyces strains from over 1200 samples taken from vineyard and forest habitats in Slovenia. We isolated numerous strains of S. cerevisiae and S. paradoxus, as well as a small number of Saccharomyces kudriavzevii strains, from both vineyard and forest environments. We find S. cerevisiae less abundant than S. paradoxus on oak trees both within and outside the vineyard, but more abundant on grapevines and associated substrates. Analysis of the uncultured microbiome shows, that both S. cerevisiae and S. paradoxus are rare species in soil and bark samples, but can be much more common in grape must. In contrast to S. paradoxus, European strains of S. cerevisiae have acquired multiple traits thought to be important for life in the vineyard and dominance of wine fermentations. We conclude, that S. cerevisiae and S. paradoxus currently share both vineyard and non-vineyard habitats in Slovenia and we discuss factors relevant to their global distribution and relative abundance. PMID:26941733

  9. Relating mesocarnivore relative abundance to anthropogenic land-use with a hierarchical spatial count model

    USGS Publications Warehouse

    Crimmins, Shawn M.; Walleser, Liza R.; Hertel, Dan R.; McKann, Patrick C.; Rohweder, Jason J.; Thogmartin, Wayne E.

    2016-01-01

    There is growing need to develop models of spatial patterns in animal abundance, yet comparatively few examples of such models exist. This is especially true in situations where the abundance of one species may inhibit that of another, such as the intensively-farmed landscape of the Prairie Pothole Region (PPR) of the central United States, where waterfowl production is largely constrained by mesocarnivore nest predation. We used a hierarchical Bayesian approach to relate the distribution of various land-cover types to the relative abundances of four mesocarnivores in the PPR: coyote Canis latrans, raccoon Procyon lotor, red fox Vulpes vulpes, and striped skunk Mephitis mephitis. We developed models for each species at multiple spatial resolutions (41.4 km2, 10.4 km2, and 2.6 km2) to address different ecological and management-related questions. Model results for each species were similar irrespective of resolution. We found that the amount of row-crop agriculture was nearly ubiquitous in our best models, exhibiting a positive relationship with relative abundance for each species. The amount of native grassland land-cover was positively associated with coyote and raccoon relative abundance, but generally absent from models for red fox and skunk. Red fox and skunk were positively associated with each other, suggesting potential niche overlap. We found no evidence that coyote abundance limited that of other mesocarnivore species, as might be expected under a hypothesis of mesopredator release. The relationships between relative abundance and land-cover types were similar across spatial resolutions. Our results indicated that mesocarnivores in the PPR are most likely to occur in portions of the landscape with large amounts of agricultural land-cover. Further, our results indicated that track-survey data can be used in a hierarchical framework to gain inferences regarding spatial patterns in animal relative abundance.

  10. Assessing relative abundance and reproductive success of shrubsteppe raptors

    USGS Publications Warehouse

    Lehman, Robert N.; Carpenter, L.B.; Steenhof, Karen; Kochert, Michael N.

    1998-01-01

    From 1991-1994, we quantified relative abundance and reproductive success of the Ferruginous Hawk (Buteo regalis), Northern Harrier (Circus cyaneus), Burrowing Owl (Speotytoc unicularia), and Short-eared Owl (Asio flammeus) on the shrubsteppe plateaus (benchlands) in and near the Snake River Birds of Prey National Conservation Area in southwestern Idaho. To assess relative abundance, we searched randomly selected plots using four sampling methods: point counts, line transects, and quadrats of two sizes. On a persampling-effort basis, transects were slightly more effective than point counts and quadrats for locating raptor nests (3.4 pairs detected/100 h of effort vs. 2.2-3.1 pairs). Random sampling using quadrats failed to detect a Short-eared Owl population increase from 1993 to 1994. To evaluate nesting success, we tried to determine reproductive outcome for all nesting attempts located during random, historical, and incidental nest searches. We compared nesting success estimates based on all nesting attempts, on attempts found during incubation, and the Mayfield model. Most pairs used to evaluate success were pairs found incidentally. Visits to historical nesting areas yielded the highest number of pairs per sampling effort (14.6/100 h), but reoccupancy rates for most species decreased through time. Estimates based on all attempts had the highest sample sizes but probably overestimated success for all species except the Ferruginous Hawk. Estimates of success based on nesting attempts found during incubation had the lowest sample sizes. All three methods yielded biased nesting snccess estimates for the Northern Harrier and Short-eared Owl. The estimate based on pairs found during incubation probably provided the least biased estimate for the Burrowing Owl. Assessments of nesting success were hindered by difficulties in confirming egg laying and nesting success for all species except the Ferruginous hawk.

  11. Relative foraminiferan abundance as an indicator of seagrass sediment health:

    NASA Astrophysics Data System (ADS)

    Cajandig, P.; Quiros, A.; Nolan, H.; Tallman, R.; Cooper, N.; Ayala, J.; Courtier, C.

    2013-12-01

    Authors: Patrick Cajandig*, Jose Ayala**, Nathaniel Cooper**, Catherine Courtier**, Hannah Nolan**, Rachelle Tallman**, T.E. Angela L. Quiros** * Davis High-School CA, **University of California Santa Cruz, Ecology and Evolutionary Biology Department Seagrasses are a key component in coastal ecosystems. Found in shallow marine environments, they make a large contribution to coastal ecosystem health by sustaining water quality, stabilizing the sea bottom, and providing habitat as well as food for other organisms. Seagrasses accumulate tiny grains of sediment, increasing water clarity. Just like barren hills are prone to erosion compared to vegetated, rooted down hills, we find a similar situation in the ocean. Seagrasses have broad roots that extend vertically and horizontally to help stabilize the seabed. Seagrasses support a whole ecosystem, because some organisms feed off of the seagrass alone, while others feed off the inhabitants of the seagrass. The quality of sediment is a vital part of seagrass health, just like nutrient rich soils are important to land plants. But what in seagrass sediment is a good indication of health? We hypothesize that seagrass health measures such as percent cover and seagrass species diversity are related to the abundance of foraminiferans relative to other seagrass sediment components. My mentor, T. E. Angela L. Quiros, from the University of California, Santa Cruz (UCSC), collected the sediment samples from seagrass beds in the Philippines. Samples were dried and brought to UCSC for sediment sieving. We used different sized sieves to sort the sediment. These sieves ranged from coarse to very fine sieves (Phi -2.0 (coarse) through +3.0 (fine) going in 0.5 intervals on a log scale). We weighed the sediment that was caught in each tray and separated them into bags of different size classes. To analyze each sample, we subsampled four size classes (Phi's -2.0, -1.5,-1.0, 0.0), and used a dissecting scope to identify and then weigh the

  12. Neutral theory and relative species abundance in ecology

    NASA Astrophysics Data System (ADS)

    Volkov, Igor; Banavar, Jayanth R.; Hubbell, Stephen P.; Maritan, Amos

    2003-08-01

    The theory of island biogeography asserts that an island or a local community approaches an equilibrium species richness as a result of the interplay between the immigration of species from the much larger metacommunity source area and local extinction of species on the island (local community). Hubbell generalized this neutral theory to explore the expected steady-state distribution of relative species abundance (RSA) in the local community under restricted immigration. Here we present a theoretical framework for the unified neutral theory of biodiversity and an analytical solution for the distribution of the RSA both in the metacommunity (Fisher's log series) and in the local community, where there are fewer rare species. Rare species are more extinction-prone, and once they go locally extinct, they take longer to re-immigrate than do common species. Contrary to recent assertions, we show that the analytical solution provides a better fit, with fewer free parameters, to the RSA distribution of tree species on Barro Colorado Island, Panama, than the lognormal distribution.

  13. Abundance of Hepatic Transporters in Caucasians: A Meta-Analysis

    PubMed Central

    Burt, Howard J.; Riedmaier, Arian Emami; Harwood, Matthew D.; Crewe, H. Kim; Gill, Katherine L.

    2016-01-01

    This study aimed to derive quantitative abundance values for key hepatic transporters suitable for in vitro–in vivo extrapolation within a physiologically based pharmacokinetic modeling framework. A meta-analysis was performed whereby data on abundance measurements, sample preparation methods, and donor demography were collated from the literature. To define values for a healthy Caucasian population, a subdatabase was created whereby exclusion criteria were applied to remove samples from non-Caucasian individuals, those with underlying disease, or those with subcellular fractions other than crude membrane. Where a clinically relevant active genotype was known, only samples from individuals with an extensive transporter phenotype were included. Authors were contacted directly when additional information was required. After removing duplicated samples, the weighted mean, geometric mean, standard deviation, coefficient of variation, and between-study homogeneity of transporter abundances were determined. From the complete database containing 24 transporters, suitable abundance data were available for 11 hepatic transporters from nine studies after exclusion criteria were applied. Organic anion transporting polypeptides OATP1B1 and OATP1B3 showed the highest population abundance in healthy adult Caucasians. For several transporters, the variability in abundance was reduced significantly once the exclusion criteria were applied. The highest variability was observed for OATP1B3 > OATP1B1 > multidrug resistance protein 2 > multidrug resistance gene 1. No relationship was found between transporter expression and donor age. To our knowledge, this study provides the first in-depth analysis of current quantitative abundance data for a wide range of hepatic transporters, with the aim of using these data for in vitro–in vivo extrapolation, and highlights the significance of investigating the background of tissue(s) used in quantitative transporter proteomic studies. Similar

  14. Abundance of Hepatic Transporters in Caucasians: A Meta-Analysis.

    PubMed

    Burt, Howard J; Riedmaier, Arian Emami; Harwood, Matthew D; Crewe, H Kim; Gill, Katherine L; Neuhoff, Sibylle

    2016-10-01

    This study aimed to derive quantitative abundance values for key hepatic transporters suitable for in vitro-in vivo extrapolation within a physiologically based pharmacokinetic modeling framework. A meta-analysis was performed whereby data on abundance measurements, sample preparation methods, and donor demography were collated from the literature. To define values for a healthy Caucasian population, a subdatabase was created whereby exclusion criteria were applied to remove samples from non-Caucasian individuals, those with underlying disease, or those with subcellular fractions other than crude membrane. Where a clinically relevant active genotype was known, only samples from individuals with an extensive transporter phenotype were included. Authors were contacted directly when additional information was required. After removing duplicated samples, the weighted mean, geometric mean, standard deviation, coefficient of variation, and between-study homogeneity of transporter abundances were determined. From the complete database containing 24 transporters, suitable abundance data were available for 11 hepatic transporters from nine studies after exclusion criteria were applied. Organic anion transporting polypeptides OATP1B1 and OATP1B3 showed the highest population abundance in healthy adult Caucasians. For several transporters, the variability in abundance was reduced significantly once the exclusion criteria were applied. The highest variability was observed for OATP1B3 > OATP1B1 > multidrug resistance protein 2 > multidrug resistance gene 1. No relationship was found between transporter expression and donor age. To our knowledge, this study provides the first in-depth analysis of current quantitative abundance data for a wide range of hepatic transporters, with the aim of using these data for in vitro-in vivo extrapolation, and highlights the significance of investigating the background of tissue(s) used in quantitative transporter proteomic studies. Similar

  15. Distribution and relative abundance of forest birds in relation to burn severity in southeastern Arizona

    USGS Publications Warehouse

    Kirkpatrick, C.; Conway, C.J.; Jones, P.B.

    2006-01-01

    The frequency of wild and prescribed fires in montane forests of the southwestern United States has increased after a century of fire suppression and subsequent fuels accumulation. To assess the effects of recent fires (median time since fire = 6 yr) on the montane forest bird community, we surveyed birds in 8 Sky Island mountain ranges in southeastern Arizona, USA, and examined how the distribution (i.e., presence-absence) of 65 species and relative abundance of 16 species correlated with evidence of severe and less severe fire at >1,500 survey points. We detected associations between fire and bird presence-absence for 17% of the 65 species analyzed and between fire and bird relative abundance for 25% of the 16 species analyzed. Most species (73%) were positively associated with burned areas and displayed stronger associations (i.e., more extreme odds ratios) with survey points that had evidence of severe as opposed to less severe fire. Positive associations with severe fire were strong (>3 to 1 odds) for western wood-pewee (Contopus sordidulus) and house wren (Troglodytes aedon), and negative associations with severe fire were strong for warbling vireo (Vireo gilvus) and red-breasted nuthatch (Sitta canadensis). Although recent fires appear to have had a positive effect on the distribution and relative abundance of several montane forest bird species in the region, these species are not the open-woodland birds that we would have expected to have benefited from fire based on previous research. Nevertheless, our results confirm associations between fire and bird presence-absence and relative abundance reported previously for 7 species of birds. Our results also provide new information for Grace's warbler (Dendroica graciae) and greater pewee (C. pertinax), 2 species for which fire data were formerly lacking. Managers can use these data to make and test predictions about the effects of future fires, both severe and less severe, on montane forest birds in the

  16. THE IMPACT OF ENHANCED He AND CNONa ABUNDANCES ON GLOBULAR CLUSTER RELATIVE AGE-DATING METHODS

    SciTech Connect

    MarIn-Franch, Antonio; Aparicio, Antonio; Cassisi, Santi; Pietrinferni, Adriano E-mail: antapaj@iac.e E-mail: pietrinferni@oa-teramo.inaf.i

    2010-05-10

    The impact that unrecognized differences in the chemical patterns of Galactic globular clusters (GGCs) have on their relative age determinations is studied. The two most widely used relative age-dating methods, horizontal and vertical, together with the more recent relative MS-fitting method, were carefully analyzed on a purely theoretical basis. The BaSTI library was adopted to perform the present analysis. We find that relative ages derived using the horizontal and vertical methods are largely dependent on the initial He content and heavy element distribution. Unrecognized cluster-to-cluster chemical abundance differences can lead to an error in the derived relative ages as large as {approx}0.5 (or {approx}6 Gyr if an age of 12.8 Gyr is adopted for normalization) and even larger for some extreme cases. It is shown that the relative MS-fitting method is by far the age-dating technique for which undetected cluster-to-cluster differences in the He abundance have less impact. Present results are used in order to pose constraints on the maximum possible spread in the He and CNONa elements abundances on the basis of the estimates-taken from the literature-of the GGCs relative age dispersion obtained with the various relative age-dating techniques. Finally, it is shown that the age-metallicity relation found for young GGCs by the GC Treasury program is a real age sequence and cannot be produced by variations in the He and/or heavy element distribution.

  17. Regulation of relative abundance of arterivirus subgenomic mRNAs.

    PubMed

    Pasternak, Alexander O; Spaan, Willy J M; Snijder, Eric J

    2004-08-01

    The subgenomic (sg) mRNAs of arteriviruses (order Nidovirales) form a 5'- and 3'-coterminal nested set with the viral genome. Their 5' common leader sequence is derived from the genomic 5'-proximal region. Fusion of sg RNA leader and "body" segments involves a discontinuous transcription step. Presumably during minus-strand synthesis, the nascent RNA strand is transferred from one site in the genomic template to another, a process guided by conserved transcription-regulating sequences (TRSs) at these template sites. Subgenomic RNA species are produced in different but constant molar ratios, with the smallest RNAs usually being most abundant. Factors thought to influence sg RNA synthesis are size differences between sg RNA species, differences in sequence context between body TRSs, and the mutual influence (or competition) between strand transfer reactions occurring at different body TRSs. Using an Equine arteritis virus infectious cDNA clone, we investigated how body TRS activity affected sg RNA synthesis from neighboring body TRSs. Flanking sequences were standardized by head-to-tail insertion of several copies of an RNA7 body TRS cassette. A perfect gradient of sg RNA abundance, progressively favoring smaller RNA species, was observed. Disruption of body TRS function by mutagenesis did not have a significant effect on the activity of other TRSs. However, deletion of body TRS-containing regions enhanced synthesis of sg RNAs from upstream TRSs but not of those produced from downstream TRSs. The results of this study provide considerable support for the proposed discontinuous extension of minus-strand RNA synthesis as a crucial step in sg RNA synthesis. PMID:15254182

  18. Chemical Abundance Analysis of the Symbiotic Red Giants

    NASA Astrophysics Data System (ADS)

    Galan, Cezary; Mikolajewska, Joanna; Hinkle, Kenneth H.

    2015-01-01

    The study of symbiotic stars - the long period, interacting binary systems - composed of red giant donor and a hot, compact companion is important for our understanding of binary stellar evolution in systems where mass loss or transfer take place involving RGB/AGB stars. The elemental abundances of symbiotic giants can track the mass exchange history and can determine their parent stellar population. However, the number of these objects with fairly well determined photospheric composition is insufficient for statistical considerations. Here we present the detailed chemical abundance analysis obtained for the first time for 14 M-type symbiotic giants. The analysis is based on the high resolution (R ˜ 50000), high S/N ˜ 100, near-IR spectra (at H- and K-band regions) obtained with Phoenix/Gemini South spectrometer. Spectrum synthesis employing standard LTE analysis and atmosphere models was used to obtain photospheric abundances of CNO and elements around the iron peak (Sc, Ti, Fe, and Ni). Our analysis reveals mostly slightly sub-solar or near-solar metallicities. We obtained significantly subsolar metallicities for RW Hya, RT Ser, and Hen 3-1213 and slightly super-solar metallicity in V455 Sco. The very low ^{12}C/^{13}C isotopic ratios, ˜6-11, and significant enrichment in nitrogen ^{14}N isotope in almost all giants in our sample indicate that they have experienced the first dredge-up.

  19. Abundance analysis of s-process enhanced barium stars

    NASA Astrophysics Data System (ADS)

    Mahanta, Upakul; Karinkuzhi, Drisya; Goswami, Aruna; Duorah, Kalpana

    2016-08-01

    Detailed chemical composition studies of stars with enhanced abundances of neutron-capture elements can provide observational constraints for neutron-capture nucleosynthesis studies and clues for understanding their contribution to the Galactic chemical enrichment. We present abundance results from high-resolution spectral analyses of a sample of four chemically peculiar stars characterized by s-process enhancement. High-Resolution spectra (R ˜42000) of these objects spanning a wavelength range from 4000 to 6800 Å, are taken from the ELODIE archive. We have estimated the stellar atmospheric parameters, the effective temperature Teff, the surface gravity log g, and metallicity [Fe/H] from local thermodynamic equilibrium analysis using model atmospheres. We report estimates of elemental abundances for several neutron-capture elements, Sr, Y, Zr, Ba, La, Ce, Pr, Nd, Sm, Eu and Dy. While HD 49641 and HD 58368 show [Ba/Fe] ≥ 1.16 the other two objects HD 119650 and HD 191010 are found to be mild barium stars with [Ba/Fe] ˜ 0.4. The derived abundances of the elements are interpreted on the basis of existing theories for understanding their origin and evolution.

  20. Lifting a veil on diversity: a Bayesian approach to fitting relative-abundance models.

    PubMed

    Golicher, Duncan J; O'Hara, Robert B; Ruíz-Montoya, Lorena; Cayuela, Luis

    2006-02-01

    Bayesian methods incorporate prior knowledge into a statistical analysis. This prior knowledge is usually restricted to assumptions regarding the form of probability distributions of the parameters of interest, leaving their values to be determined mainly through the data. Here we show how a Bayesian approach can be applied to the problem of drawing inference regarding species abundance distributions and comparing diversity indices between sites. The classic log series and the lognormal models of relative- abundance distribution are apparently quite different in form. The first is a sampling distribution while the other is a model of abundance of the underlying population. Bayesian methods help unite these two models in a common framework. Markov chain Monte Carlo simulation can be used to fit both distributions as small hierarchical models with shared common assumptions. Sampling error can be assumed to follow a Poisson distribution. Species not found in a sample, but suspected to be present in the region or community of interest, can be given zero abundance. This not only simplifies the process of model fitting, but also provides a convenient way of calculating confidence intervals for diversity indices. The method is especially useful when a comparison of species diversity between sites with different sample sizes is the key motivation behind the research. We illustrate the potential of the approach using data on fruit-feeding butterflies in southern Mexico. We conclude that, once all assumptions have been made transparent, a single data set may provide support for the belief that diversity is negatively affected by anthropogenic forest disturbance. Bayesian methods help to apply theory regarding the distribution of abundance in ecological communities to applied conservation. PMID:16705973

  1. Neutral theory predicts the relative abundance and diversity of genetic elements in a broad array of eukaryotic genomes.

    PubMed

    Serra, François; Becher, Verónica; Dopazo, Hernán

    2013-01-01

    It is universally true in ecological communities, terrestrial or aquatic, temperate or tropical, that some species are very abundant, others are moderately common, and the majority are rare. Likewise, eukaryotic genomes also contain classes or "species" of genetic elements that vary greatly in abundance: DNA transposons, retrotransposons, satellite sequences, simple repeats and their less abundant functional sequences such as RNA or genes. Are the patterns of relative species abundance and diversity similar among ecological communities and genomes? Previous dynamical models of genomic diversity have focused on the selective forces shaping the abundance and diversity of transposable elements (TEs). However, ideally, models of genome dynamics should consider not only TEs, but also the diversity of all genetic classes or "species" populating eukaryotic genomes. Here, in an analysis of the diversity and abundance of genetic elements in >500 eukaryotic chromosomes, we show that the patterns are consistent with a neutral hypothesis of genome assembly in virtually all chromosomes tested. The distributions of relative abundance of genetic elements are quite precisely predicted by the dynamics of an ecological model for which the principle of functional equivalence is the main assumption. We hypothesize that at large temporal scales an overarching neutral or nearly neutral process governs the evolution of abundance and diversity of genetic elements in eukaryotic genomes. PMID:23798991

  2. Neutral Theory Predicts the Relative Abundance and Diversity of Genetic Elements in a Broad Array of Eukaryotic Genomes

    PubMed Central

    Serra, François; Becher, Verónica; Dopazo, Hernán

    2013-01-01

    It is universally true in ecological communities, terrestrial or aquatic, temperate or tropical, that some species are very abundant, others are moderately common, and the majority are rare. Likewise, eukaryotic genomes also contain classes or “species” of genetic elements that vary greatly in abundance: DNA transposons, retrotransposons, satellite sequences, simple repeats and their less abundant functional sequences such as RNA or genes. Are the patterns of relative species abundance and diversity similar among ecological communities and genomes? Previous dynamical models of genomic diversity have focused on the selective forces shaping the abundance and diversity of transposable elements (TEs). However, ideally, models of genome dynamics should consider not only TEs, but also the diversity of all genetic classes or “species” populating eukaryotic genomes. Here, in an analysis of the diversity and abundance of genetic elements in >500 eukaryotic chromosomes, we show that the patterns are consistent with a neutral hypothesis of genome assembly in virtually all chromosomes tested. The distributions of relative abundance of genetic elements are quite precisely predicted by the dynamics of an ecological model for which the principle of functional equivalence is the main assumption. We hypothesize that at large temporal scales an overarching neutral or nearly neutral process governs the evolution of abundance and diversity of genetic elements in eukaryotic genomes. PMID:23798991

  3. Relative coronal abundances derived from X-ray observations 3: The effect of cascades on the relative intensity of Fe (XVII) line fluxes, and a revised iron abundance

    NASA Technical Reports Server (NTRS)

    Walker, A. B. C., Jr.; Rugge, H. R.; Weiss, K.

    1974-01-01

    Permitted lines in the optically thin coronal X-ray spectrum were analyzed to find the distribution of coronal material, as a function of temperature, without special assumptions concerning coronal conditions. The resonance lines of N, O, Ne, Na, Mg, Al, Si, S, and Ar which dominate the quiet coronal spectrum below 25A were observed. Coronal models were constructed and the relative abundances of these elements were determined. The intensity in the lines of the 2p-3d transitions near 15A was used in conjunction with these coronal models, with the assumption of coronal excitation, to determine the Fe XVII abundance. The relative intensities of the 2p-3d Fe XVII lines observed in the corona agreed with theoretical prediction. Using a more complete theoretical model, and higher resolution observations, a revised calculation of iron abundance relative to hydrogen of 0.000026 was made.

  4. High-resolution abundance analysis of HD 140283

    NASA Astrophysics Data System (ADS)

    Siqueira-Mello, C.; Andrievsky, S. M.; Barbuy, B.; Spite, M.; Spite, F.; Korotin, S. A.

    2015-12-01

    Context. HD 140283 is a reference subgiant that is metal poor and confirmed to be a very old star. The element abundances of this type of old star can constrain the nature and nucleosynthesis processes that occurred in its (even older) progenitors. The present study may shed light on nucleosynthesis processes yielding heavy elements early in the Galaxy. Aims: A detailed analysis of a high-quality spectrum is carried out, with the intent of providing a reference on stellar lines and abundances of a very old, metal-poor subgiant. We aim to derive abundances from most available and measurable spectral lines. Methods: The analysis is carried out using high-resolution (R = 81 000) and high signal-to-noise ratio (800 analysis in non-LTE (NLTE) is based on the MULTI code. We present LTE abundances for 26 elements, and NLTE calculations for the species C i, O i, Na i, Mg i, Al i, K i, Ca i, Sr ii, and Ba ii lines. Results: The abundance analysis provided an extensive line list suitable for metal-poor subgiant stars. The results for Li, CNO, α-, and iron peak elements are in good agreement with literature. The newly NLTE Ba abundance, along with a NLTE Eu correction and a 3D Ba correction from literature, leads to [Eu/Ba] = + 0.59 ± 0.18. This result confirms a dominant r-process contribution, possibly together with a very small contribution from the main s-process, to the neutron-capture elements in HD 140283. Overabundances of the lighter heavy elements and the high abundances derived for Ba, La, and Ce favour the operation of the weak r-process in HD 140283

  5. Determining the Local Abundance of Martian Methane and its 13-C/l2-C and D/H Isotopic Ratios for Comparison with Related Gas and Soil Analysis on the 2011 Mars Science Laboratory (MSL) Mission

    NASA Technical Reports Server (NTRS)

    Webster, Christopher R.; Mahaffy, Paul R.

    2011-01-01

    Understanding the origin of Martian methane will require numerous complementary measurements from both in situ and remote sensing investigations and laboratory work to correlate planetary surface geophysics with atmospheric dynamics and chemistry. Three instruments (Quadrupole Mass Spectrometer (QMS), Gas Chromatograph (GC) and Tunable Laser Spectrometer (TLS)) with sophisticated sample handling and processing capability make up the Sample Analysis at Mars (SAM) analytical chemistry suite on NASA s 2011 Mars Science Laboratory (MSL) Mission. Leveraging off the SAM sample and gas processing capability that includes methane enrichment, TLS has unprecedented sensitivity for measuring absolute methane (parts-per-trillion), water, and carbon dioxide abundances in both the Martian atmosphere and evolved from heated soil samples. In concert with a wide variety of associated trace gases (e.g. SO2, H2S, NH3, higher hydrocarbons, organics, etc.) and other isotope ratios measured by SAM, TLS will focus on determining the absolute abundances of methane, water and carbon dioxide, and their isotope ratios: 13C/12C and D/H in methane; 13C/12C and 18O/17O/16O in carbon dioxide; and 18O/17O/16O and D/H in water. Measurements near the MSL landing site will be correlated with satellite (Mars Express, Mars 2016) and ground-based observations.

  6. Estimating Culicoides sonorensis biting midge abundance using digital image analysis.

    PubMed

    Osborne, C J; Mayo, C E; Mullens, B A; Maclachlan, N J

    2014-12-01

    ImageJ is an open-source software tool used for a variety of scientific objectives including cell counting, shape analysis and image correction. This technology has previously been used to estimate mosquito abundance in surveillance efforts. However, the utility of this application for estimating abundance or parity in the surveillance of Culicoides spp. (Diptera: Ceratopogonidae) has not yet been tested. Culicoides sonorensis (Wirth and Jones), a biting midge often measuring 2.0-2.5 mm in length, is an economically important vector of ruminant arboviruses in California. Current surveillance methods use visual sorting for the characteristics of midges and are very time-intensive for large studies. This project tested the utility of ImageJ as a tool to assist in gross trap enumeration as well as in parity analysis of C. sonorensis in comparison with traditional visual methods of enumeration using a dissecting microscope. Results confirmed that automated counting of midges is a reliable means of approximating midge numbers under certain conditions. Further evaluation confirmed accurate and time-efficient parity analysis in comparison with hand sorting. The ImageJ software shows promise as a tool that can assist and expedite C. sonorensis surveillance. Further, these methods may be useful in other insect surveillance activities.

  7. Relative changes in krill abundance inferred from Antarctic fur seal.

    PubMed

    Huang, Tao; Sun, Liguang; Stark, John; Wang, Yuhong; Cheng, Zhongqi; Yang, Qichao; Sun, Song

    2011-01-01

    Antarctic krill Euphausia superba is a predominant species in the Southern Ocean, it is very sensitive to climate change, and it supports large stocks of fishes, seabirds, seals and whales in Antarctic marine ecosystems. Modern krill stocks have been estimated directly by net hauls and acoustic surveys; the historical krill density especially the long-term one in the Southern Ocean, however, is unknown. Here we inferred the relative krill population changes along the West Antarctic Peninsula (WAP) over the 20th century from the trophic level change of Antarctic fur seal Arctocephalus gazella using stable carbon (δ(13)C) and nitrogen (δ(15)N) isotopes of archival seal hairs. Since Antarctic fur seals feed preferentially on krill, the variation of δ(15)N in seal hair indicates a change in the proportion of krill in the seal's diets and thus the krill availability in local seawater. For the past century, enriching fur seal δ(15)N values indicated decreasing krill availability. This is agreement with direct observation for the past ∼30 years and suggests that the recently documented decline in krill populations began in the early parts of the 20th century. This novel method makes it possible to infer past krill population changes from ancient tissues of krill predators.

  8. Relative Changes in Krill Abundance Inferred from Antarctic Fur Seal

    PubMed Central

    Huang, Tao; Sun, Liguang; Stark, John; Wang, Yuhong; Cheng, Zhongqi; Yang, Qichao; Sun, Song

    2011-01-01

    Antarctic krill Euphausia superba is a predominant species in the Southern Ocean, it is very sensitive to climate change, and it supports large stocks of fishes, seabirds, seals and whales in Antarctic marine ecosystems. Modern krill stocks have been estimated directly by net hauls and acoustic surveys; the historical krill density especially the long-term one in the Southern Ocean, however, is unknown. Here we inferred the relative krill population changes along the West Antarctic Peninsula (WAP) over the 20th century from the trophic level change of Antarctic fur seal Arctocephalus gazella using stable carbon (δ13C) and nitrogen (δ15N) isotopes of archival seal hairs. Since Antarctic fur seals feed preferentially on krill, the variation of δ15N in seal hair indicates a change in the proportion of krill in the seal's diets and thus the krill availability in local seawater. For the past century, enriching fur seal δ15N values indicated decreasing krill availability. This is agreement with direct observation for the past ∼30 years and suggests that the recently documented decline in krill populations began in the early parts of the 20th century. This novel method makes it possible to infer past krill population changes from ancient tissues of krill predators. PMID:22087294

  9. Seasonal abundance of soil arthropods in relation to meteorological and edaphic factors in the agroecosystems of Faisalabad, Punjab, Pakistan.

    PubMed

    Shakir, Muhammad Mussadiq; Ahmed, Sohail

    2015-05-01

    Soil arthropods are an important component of agroecosystems, contributing significantly to their biodiversity and functioning. However, seasonal patterns, population dynamics, and significant roles of these soil arthropods in improvement of soil structures and functions are influenced by many factors. The objective of the current study was to investigate soil arthropod abundance in relation to a blend of meteorological and edaphic factors and to find out the difference in abundance among various crops (sugarcane, cotton, wheat, alfalfa fodder, and citrus orchards). The arthropod sampling was done by pitfall traps and Tullgren extractions on fortnightly intervals. Soil temperature and relative humidity were noted on the field sites while analysis for soil pH, organic matter, and soil moisture contents were done in the laboratory. The rainfall data was obtained from an observatory. Results showed that significant differences were found in soil arthropod abundance across different sampling months and crops. Out of total 13,673 soil arthropods sampled, 38 % belonged to Collembola, followed by 15 % Hymenoptera, 15 % Acarina, 11 % Myriapods, 6 % Coleoptera, 5 % Orthoptera, and 5 % Araneae. Mean abundance per sample was highest in summer months as compared to winter. Overall abundance per sample was significantly different between all crops (p < 0.05). Cluster analysis revealed four categories of soil arthropods according to abundance, i.e., highly abundant (Collembola, Acarina, Myripoda, Hymenoptera), moderately abundant (Orthoptera, Aranae, Coleoptera), least abundant (Dermaptera, Hemiptera, Diptera), and rare (Blattaria, Isoptera, Diplura, Lepidoptera). Soil temperature and soil organic matter showed significant positive correlation with abundance, while relative humidity was significantly negatively correlated. Soil moisture and soil pH showed no significant correlations while no correlation was found with total rainfall. PCA analysis revealed that soil surface

  10. Seasonal abundance of soil arthropods in relation to meteorological and edaphic factors in the agroecosystems of Faisalabad, Punjab, Pakistan

    NASA Astrophysics Data System (ADS)

    Shakir, Muhammad Mussadiq; Ahmed, Sohail

    2015-05-01

    Soil arthropods are an important component of agroecosystems, contributing significantly to their biodiversity and functioning. However, seasonal patterns, population dynamics, and significant roles of these soil arthropods in improvement of soil structures and functions are influenced by many factors. The objective of the current study was to investigate soil arthropod abundance in relation to a blend of meteorological and edaphic factors and to find out the difference in abundance among various crops (sugarcane, cotton, wheat, alfalfa fodder, and citrus orchards). The arthropod sampling was done by pitfall traps and Tullgren extractions on fortnightly intervals. Soil temperature and relative humidity were noted on the field sites while analysis for soil pH, organic matter, and soil moisture contents were done in the laboratory. The rainfall data was obtained from an observatory. Results showed that significant differences were found in soil arthropod abundance across different sampling months and crops. Out of total 13,673 soil arthropods sampled, 38 % belonged to Collembola, followed by 15 % Hymenoptera, 15 % Acarina, 11 % Myriapods, 6 % Coleoptera, 5 % Orthoptera, and 5 % Araneae. Mean abundance per sample was highest in summer months as compared to winter. Overall abundance per sample was significantly different between all crops ( p < 0.05). Cluster analysis revealed four categories of soil arthropods according to abundance, i.e., highly abundant (Collembola, Acarina, Myripoda, Hymenoptera), moderately abundant (Orthoptera, Aranae, Coleoptera), least abundant (Dermaptera, Hemiptera, Diptera), and rare (Blattaria, Isoptera, Diplura, Lepidoptera). Soil temperature and soil organic matter showed significant positive correlation with abundance, while relative humidity was significantly negatively correlated. Soil moisture and soil pH showed no significant correlations while no correlation was found with total rainfall. PCA analysis revealed that soil surface

  11. Seasonal abundance of soil arthropods in relation to meteorological and edaphic factors in the agroecosystems of Faisalabad, Punjab, Pakistan.

    PubMed

    Shakir, Muhammad Mussadiq; Ahmed, Sohail

    2015-05-01

    Soil arthropods are an important component of agroecosystems, contributing significantly to their biodiversity and functioning. However, seasonal patterns, population dynamics, and significant roles of these soil arthropods in improvement of soil structures and functions are influenced by many factors. The objective of the current study was to investigate soil arthropod abundance in relation to a blend of meteorological and edaphic factors and to find out the difference in abundance among various crops (sugarcane, cotton, wheat, alfalfa fodder, and citrus orchards). The arthropod sampling was done by pitfall traps and Tullgren extractions on fortnightly intervals. Soil temperature and relative humidity were noted on the field sites while analysis for soil pH, organic matter, and soil moisture contents were done in the laboratory. The rainfall data was obtained from an observatory. Results showed that significant differences were found in soil arthropod abundance across different sampling months and crops. Out of total 13,673 soil arthropods sampled, 38 % belonged to Collembola, followed by 15 % Hymenoptera, 15 % Acarina, 11 % Myriapods, 6 % Coleoptera, 5 % Orthoptera, and 5 % Araneae. Mean abundance per sample was highest in summer months as compared to winter. Overall abundance per sample was significantly different between all crops (p < 0.05). Cluster analysis revealed four categories of soil arthropods according to abundance, i.e., highly abundant (Collembola, Acarina, Myripoda, Hymenoptera), moderately abundant (Orthoptera, Aranae, Coleoptera), least abundant (Dermaptera, Hemiptera, Diptera), and rare (Blattaria, Isoptera, Diplura, Lepidoptera). Soil temperature and soil organic matter showed significant positive correlation with abundance, while relative humidity was significantly negatively correlated. Soil moisture and soil pH showed no significant correlations while no correlation was found with total rainfall. PCA analysis revealed that soil surface

  12. The relative abundance of desert tortoises on the Nevada Test Site within ecological landform units

    SciTech Connect

    Woodward, R.; Rautenstrauch, K.R.; Hall, D.B.; Ostler, W.K.

    1998-09-01

    Sign-survey transects were sampled in 1996 to better determine the relative abundance of desert tortoises on the Nevada Test Site (NTS). These transects were sampled within ecological land-form units (ELUs), which are small, ecologically homogeneous units of land. Two-hundred and six ELUs were sampled by walking 332 transects totaling 889 kilometers (km). These ELUs covered 528 km{sup 2}. Two-hundred and eight-one sign were counted. An average of 0.32 sign was found per km walked. Seventy percent of the area sampled had a very low abundance of tortoises, 29% had a low abundance, and 1% had a moderate abundance. A revised map of the relative abundance of desert tortoise on the NTS is presented. Within the 1,330 km{sup 2} of desert tortoise habitat on the NTS, 49% is classified as having no tortoises or a very low abundance, 18% has a low or moderate abundance, 12% is unclassified land being used by the Yucca Mountain Site Characterization Project, and the remaining 21% still has an unknown abundance of desert tortoises. Based on the results of this work, the amount of tortoise habitat previously classified as having an unknown or low-moderate abundance, and on which clearance surveys and on-site monitoring was required, has been reduced by 20%.

  13. The Relative Abundance of Desert Tortoises on the Nevada Test Site within Ecological Landform Units

    SciTech Connect

    Woodward, Roy; Rautenstrauch, Kurt R.; Hall, Derek B.; Ostler, W. Kent

    1998-09-01

    Sign-survey transects were sampled in 1996 to better determine the relative abundance of desert tortoises on the Nevada Test Site (NTS). These transects were sampled within ecological land-form units (ELUs), which are small, ecologically homogeneous units of land. Two-hundred and six ELUs were sampled by walking 332 transects totaling 889 kilometers (km) (552 miles [mi]). These ELUs covered 528 km{sup 2} (204 mi{sup 2}). Two-hundred and eighty-one sign were counted. An average of 0.32 sign was found per km walked. Seventy percent of the area sampled had a very low abundance of tortoises, 29 percent had a low abundance, and 1 percent had a moderate abundance. A revised map of the relative abundance of desert tortoise on the NTS is presented. Within the 1,330 km{sup 2} (514 mi{sup 2}) of desert tortoise habitat on the NTS, 49 percent is classified as having no tortoises or a very low abundance, 18 percent has a low or moderate abundance, 12 percent is unclassified land being used by the Yucca Mountain Site Characterization Project, and the remaining 21 percent still has an unknown abundance of desert tortoises. Based on the results of this work, the amount of tortoise habitat previously classified as having an unknown or low-moderate abundance, and on which clearance surveys and on-site monitoring was required, has been reduced by 20 percent.

  14. Evidence for seasonal patterns in the relative abundance of avian influenza virus subtypes in blue-winged teal (Anas discors)

    USGS Publications Warehouse

    Ramey, Andrew M.; Poulson, Rebecca L.; González-Reiche, Ana S.; Wilcox, Benjamin R.; Walther, Patrick; Link, Paul; Carter, Deborah L.; Newsome, George M.; Müller, Maria L.; Berghaus, Roy D.; Perez, Daniel R.; Hall, Jeffrey S.; Stallknecht, David E.

    2014-01-01

    Seasonal dynamics of influenza A viruses (IAVs) are driven by host density and population immunity. Through an analysis of subtypic data for IAVs isolated from Blue-winged Teal (Anas discors), we present evidence for seasonal patterns in the relative abundance of viral subtypes in spring and summer/autumn.

  15. Accurate measurement of the relative abundance of different DNA species in complex DNA mixtures.

    PubMed

    Jeong, Sangkyun; Yu, Hyunjoo; Pfeifer, Karl

    2012-06-01

    A molecular tool that can compare the abundances of different DNA sequences is necessary for comparing intergenic or interspecific gene expression. We devised and verified such a tool using a quantitative competitive polymerase chain reaction approach. For this approach, we adapted a competitor array, an artificially made plasmid DNA in which all the competitor templates for the target DNAs are arranged with a defined ratio, and melting analysis for allele quantitation for accurate quantitation of the fractional ratios of competitively amplified DNAs. Assays on two sets of DNA mixtures with explicitly known compositional structures of the test sequences were performed. The resultant average relative errors of 0.059 and 0.021 emphasize the highly accurate nature of this method. Furthermore, the method's capability of obtaining biological data is demonstrated by the fact that it can illustrate the tissue-specific quantitative expression signatures of the three housekeeping genes G6pdx, Ubc, and Rps27 by using the forms of the relative abundances of their transcripts, and the differential preferences of Igf2 enhancers for each of the multiple Igf2 promoters for the transcription.

  16. Accurate Measurement of the Relative Abundance of Different DNA Species in Complex DNA Mixtures

    PubMed Central

    Jeong, Sangkyun; Yu, Hyunjoo; Pfeifer, Karl

    2012-01-01

    A molecular tool that can compare the abundances of different DNA sequences is necessary for comparing intergenic or interspecific gene expression. We devised and verified such a tool using a quantitative competitive polymerase chain reaction approach. For this approach, we adapted a competitor array, an artificially made plasmid DNA in which all the competitor templates for the target DNAs are arranged with a defined ratio, and melting analysis for allele quantitation for accurate quantitation of the fractional ratios of competitively amplified DNAs. Assays on two sets of DNA mixtures with explicitly known compositional structures of the test sequences were performed. The resultant average relative errors of 0.059 and 0.021 emphasize the highly accurate nature of this method. Furthermore, the method's capability of obtaining biological data is demonstrated by the fact that it can illustrate the tissue-specific quantitative expression signatures of the three housekeeping genes G6pdx, Ubc, and Rps27 by using the forms of the relative abundances of their transcripts, and the differential preferences of Igf2 enhancers for each of the multiple Igf2 promoters for the transcription. PMID:22334570

  17. Geographic patterns in relative abundances and population trends of breeding and wintering loggerhead shrikes in North America

    USGS Publications Warehouse

    Sauer, J.R.; Orsillo, S.; Peterjohn, B.G.; Yosef, Reuven; Lohrer, Fred E.

    1995-01-01

    In North America, the Breeding Bird Survey and the Christmas Bird Count provide data that are collected at sites visited each year, and the site-specific data can be placed in a Geographic Information System and smoothed to produce contour maps of relative abundance and trend for the United States and southern Canada. We develop these contour maps for Loggerhead Shrike (Lanius ludovicianus) data from both surveys, and compare the patterns derived from each survey to evaluate the consistency of trends and relative abundances within physiographic strata. Patterns in relative abundance seem to be associated with strata, especially in the breeding season, but trends are often heterogeneous within strata. Because of limitations of the surveys and observed geographic patterns of shrike trends in the survey data, we suggest that there is no natural scale for the analysis of shrike-habitat associations.

  18. The relative abundances of the elements silicon through nickel in the low energy galactic cosmic rays

    NASA Technical Reports Server (NTRS)

    Garcia-Munoz, M.; Mason, G. M.; Simpson, J. A.

    1978-01-01

    Measurements of the relative abundances of the elements Si through Ni in galactic cosmic rays in the energy interval 72 to 450 MeV/nucleon are reported based on data collected by a cosmic-ray telescope on the IMP 8 satellite. The measured abundances are compared with propagation calculations using various distributions of path lengths. It is found that the measurements favor an exponential distribution of path lengths truncated at short path lengths. The source abundances of Si, Ca, Fe, and Ni derived by extrapolating the measured abundances back to the source are shown to be comparable to the solar-system abundances. The relevance of the measurements of Sc through Mn to the Mn-54 radioactive decay is examined.

  19. Changes in transcript abundance relating to colony collapse disorder in honey bees (Apis mellifera).

    PubMed

    Johnson, Reed M; Evans, Jay D; Robinson, Gene E; Berenbaum, May R

    2009-09-01

    Colony collapse disorder (CCD) is a mysterious disappearance of honey bees that has beset beekeepers in the United States since late 2006. Pathogens and other environmental stresses, including pesticides, have been linked to CCD, but a causal relationship has not yet been demonstrated. Because the gut acts as a primary interface between the honey bee and its environment as a site of entry for pathogens and toxins, we used whole-genome microarrays to compare gene expression between guts of bees from CCD colonies originating on both the east and west coasts of the United States and guts of bees from healthy colonies sampled before the emergence of CCD. Considerable variation in gene expression was associated with the geographical origin of bees, but a consensus list of 65 transcripts was identified as potential markers for CCD status. Overall, elevated expression of pesticide response genes was not observed. Genes involved in immune response showed no clear trend in expression pattern despite the increased prevalence of viruses and other pathogens in CCD colonies. Microarray analysis revealed unusual ribosomal RNA fragments that were conspicuously more abundant in the guts of CCD bees. The presence of these fragments may be a possible consequence of picorna-like viral infection, including deformed wing virus and Israeli acute paralysis virus, and may be related to arrested translation. Ribosomal fragment abundance and presence of multiple viruses may prove to be useful diagnostic markers for colonies afflicted with CCD.

  20. Detecting horizontally transferred and essential genes based on dinucleotide relative abundance.

    PubMed

    Baran, Robert H; Ko, Hanseok

    2008-10-01

    Various methods have been developed to detect horizontal gene transfer in bacteria, based on anomalous nucleotide composition, assuming that compositional features undergo amelioration in the host genome. Evolutionary theory predicts the inevitability of false positives when essential sequences are strongly conserved. Foreign genes could become more detectable on the basis of their higher order compositions if such features ameliorate more rapidly and uniformly than lower order features. This possibility is tested by comparing the heterogeneities of bacterial genomes with respect to strand-independent first- and second-order features, (i) G + C content and (ii) dinucleotide relative abundance, in 1 kb segments. Although statistical analysis confirms that (ii) is less inhomogeneous than (i) in all 12 species examined, extreme anomalies with respect to (ii) in the Escherichia coli K12 genome are typically co-located with essential genes.

  1. Relative abundance of an invasive alien plant affects insect-flower interaction networks in Ireland

    NASA Astrophysics Data System (ADS)

    Stout, Jane C.; Casey, Leanne M.

    2014-02-01

    Invasive alien flowering plants may affect native plant pollinator interactions and have knock on impacts on populations of native plants and animals. The magnitude of these impacts, however, may be modified by the relative abundance of the invasive plant and the number of flowers it presents.We tested this by examining the structure of insect-flower interaction networks in six sites with increasing levels of invasion by Rhododendron ponticum in Ireland.Neither flower-visiting insect abundance, species richness nor diversity were related to R. ponticum flower abundance, but the composition of insect communities was. The total number of flowers in a site increased with the relative abundance of R. ponticum flowers but the number of co-flowering native plant species in these sites was low (<6), making interaction networks relatively small.As a result, changes in interaction network properties (connectance, interaction evenness and network level specialisation), which correlated with R. ponticum flower abundance, were a result of the small network size rather than due to changes in the resilience of networks.Overall, we conclude that the impacts of invasive alien plants on native plant-pollinator interactions are not only species specific, but site specific, according to the abundance of flowers produced by both the invasive and the native plants.

  2. Relative abundance of mesopredators and size of oak patches in the cross-timbers ecoregion

    USGS Publications Warehouse

    Disney, M.R.; Hellgren, E.C.; Davis, C.A.; Leslie, David M.; Engle, David M.

    2008-01-01

    Mesopredators (e.g., raccoon Procyon lotor, Virginia opossum Didelphis virginiana, striped skunk Mephitis mephitis) have received considerable attention because of links to population declines in birds via increased nest predation, especially in landscapes fragmented by anthropogenic forces. Relationships of abundance of mesopredators to size of habitat patches have received less attention than relationships to other metrics of fragmentation, particularly edge characteristics. We tested the hypothesis that relative abundance of mesopredators (e.g., raccoons and Virginia opossums) was related negatively to size of forest patch. We delineated 15 patches of oak (Quercus) forest ranging from 0.2 to 55.3 ha within a grassland-woodland mosaic in the cross-timbers ecoregion of Oklahoma. Scent stations and live traps within these patches were used to index relative abundance of mesopredators in summers 2003 and 2004. Both indices of relative abundance were related weakly and negatively to area of forest patch. However, rate of capture and visitation to scent station were not correlated consistently throughout the study. Our results suggested that the two methods to index abundance provided separate information on functional and numerical responses to size of patch. Our evidence that mesopredators within the cross timbers were more likely to be in smaller patches of oak forest may have implications to success of avian nesting in these patches.

  3. Life history traits predict relative abundance in an assemblage of forest caterpillars.

    PubMed

    Lind, Eric M; Barbosa, Pedro

    2010-11-01

    Species in a given trophic level occur in vastly unequal abundance, a pattern commonly documented but poorly explained for most taxa. Theoretical predictions of species density such as those arising from the metabolic theory of ecology hold well at large spatial and temporal scales but are not supported in many communities sampled at a relatively small scale. At these scales ecological factors may be more important than the inherent limits to energy use set by allometric scaling of mass. These factors include the amount of resources available, and the ability of individuals to convert these resources successfully into population growth. While previous studies have demonstrated the limits of macroecological theory in explaining local abundance, few studies have tested alternative generalized mechanisms determining abundance at the community scale. Using an assemblage of forest moth species found co-occurring as caterpillars on a single host plant species, we tested whether species abundance on that plant could be explained by mass allometry, intrinsic population growth, diet breadth, or some combination of these traits. We parameterized life history traits of the caterpillars in association with the host plant in both field and laboratory settings, so that the population growth estimate was specific to the plant on which abundance was measured. Using a generalized least-squares regression method incorporating phylogenetic relatedness, we found no relationship between abundance and mass but found that abundance was best explained by both intrinsic population growth rate and diet breadth. Species population growth potential was most affected by survivorship and larval development time on the host plant. Metabolic constraints may determine upper limits to local abundance levels for species, but local community abundance is strongly predicted by the potential for population increase and the resources available to that species in the environment.

  4. [Mammals' camera-trapping in Sierra Nanchititla, Mexico: relative abundance and activity patterns].

    PubMed

    Monroy-Vilchis, Octavio; Zarco-González, Martha M; Rodríguez-Soto, Clarita; Soria-Díaz, Leroy; Urios, Vicente

    2011-03-01

    Species conservation and their management depend on the availability of their population behavior and changes in time. This way, population studies include aspects such as species abundance and activity pattern, among others, with the advantage that nowadays new technologies can be applied, in addition to common methods. In this study, we used camera-traps to obtain the index of relative abundance and to establish activity pattern of medium and large mammals in Sierra Nanchititla, Mexico. The study was conducted from December 2003 to May 2006, with a total sampling effort of 4 305 trap-days. We obtained 897 photographs of 19 different species. Nasua narica, Sylvilagus floridanus and Urocyon cinereoargenteus were the most abundant, in agreement with the relative abundance index (RAI, number of independent records/100 trap-days), and according to previous studies with indirect methods in the area. The activity patterns of the species showed that 67% of them are nocturnal, except Odocoileus virginianus, Nasua narica and others. Some species showed differences with previously reported patterns, which are related with seasonality, resources availability, organism sex, principally. The applied method contributed with reliable data about relative abundance and activity patterns. PMID:21516657

  5. Iron Abundance in the Prototype PG 1159 Star, GW Vir Pulsator PG 1159-035, and Related Objects

    NASA Technical Reports Server (NTRS)

    Werner, K.; Rauch, T.; Kruk, J. W.; Kurucz, R. L.

    2011-01-01

    We performed an iron abundance determination of the hot, hydrogen deficient post-AGB star PG 1159-035. which is the prototype of the PG 1159 spectral class and the GW Vir pulsators, and of two related objects (PG 1520+525, PG 1144+005), based on the first detection of Fe VIII lines in stellar photospheres. In another PG 1159 star. PG 1424+535. we detect Fe VII lines. In all four stars, each within T(sub eff) = 110,000-150,000 K, we find a solar iron abundance. This result agrees with our recent abundance analysis of the hottest PG 1159 stars (T(sub eff) = 150,000-200,000 K) that exhibit Fe x lines. On the whole, we find that the PG 1159 stars are not significantly iron deficient, in contrast to previous notions.

  6. Early recruitment equals long-term relative abundance in an alpine saxicolous lichen guild.

    PubMed

    Hestmark, Geir; Skogesal, Olav; Skullerud, Øystein

    2007-01-01

    The relative abundance within a guild of six species of the lichen-forming fungal genus Umbilicaria was studied during primary colonization of rock surfaces in a chronosequence of ca. 245 y in an alpine glacier foreland in southern Norway. Although the density of the guild grew from zero to more than 1000 thalli/m2 and the species differ substantially in life history traits such as initial growth rate, maximal size, maturation rate and propagule types, the relative abundance among the species remained almost unchanged through those years. The relative abundance of species is correlated with their life history parameters, such as initial growth rate and size-related maturation. The pattern of relative abundance was also similar in the saxicolous communities outside the foreland, which are potentially several thousand years old. Outside the foreland however the density of the guild is only 1/10 of that in the oldest parts of the foreland, due to soil formation and vegetation growth that have covered many of the low profile rock habitats. Thus the areas affected by the disturbance of glacier expansions and retreats provide temporary opportunities for large increases in the population sizes of the members of the saxicolous community. The observations support the view that pre-emption of habitat rather than competitive exclusion is common in saxicolous lichen communities and that "succession" consists in the addition but rarely the loss of species.

  7. Long-Term Changes in Species Composition and Relative Abundances of Sharks at a Provisioning Site

    PubMed Central

    Brunnschweiler, Juerg M.; Abrantes, Kátya G.; Barnett, Adam

    2014-01-01

    Diving with sharks, often in combination with food baiting/provisioning, has become an important product of today’s recreational dive industry. Whereas the effects baiting/provisioning has on the behaviour and abundance of individual shark species are starting to become known, there is an almost complete lack of equivalent data from multi-species shark diving sites. In this study, changes in species composition and relative abundances were determined at the Shark Reef Marine Reserve, a multi-species shark feeding site in Fiji. Using direct observation sampling methods, eight species of sharks (bull shark Carcharhinus leucas, grey reef shark Carcharhinus amblyrhynchos, whitetip reef shark Triaenodon obesus, blacktip reef shark Carcharhinus melanopterus, tawny nurse shark Nebrius ferrugineus, silvertip shark Carcharhinus albimarginatus, sicklefin lemon shark Negaprion acutidens, and tiger shark Galeocerdo cuvier) displayed inter-annual site fidelity between 2003 and 2012. Encounter rates and/or relative abundances of some species changed over time, overall resulting in more individuals (mostly C. leucas) of fewer species being encountered on average on shark feeding dives at the end of the study period. Differences in shark community composition between the years 2004–2006 and 2007–2012 were evident, mostly because N. ferrugineus, C. albimarginatus and N. acutidens were much more abundant in 2004–2006 and very rare in the period of 2007–2012. Two explanations are offered for the observed changes in relative abundances over time, namely inter-specific interactions and operator-specific feeding protocols. Both, possibly in combination, are suggested to be important determinants of species composition and encounter rates, and relative abundances at this shark provisioning site in Fiji. This study, which includes the most species from a spatially confined shark provisioning site to date, suggests that long-term provisioning may result in competitive exclusion

  8. Long-term changes in species composition and relative abundances of sharks at a provisioning site.

    PubMed

    Brunnschweiler, Juerg M; Abrantes, Kátya G; Barnett, Adam

    2014-01-01

    Diving with sharks, often in combination with food baiting/provisioning, has become an important product of today's recreational dive industry. Whereas the effects baiting/provisioning has on the behaviour and abundance of individual shark species are starting to become known, there is an almost complete lack of equivalent data from multi-species shark diving sites. In this study, changes in species composition and relative abundances were determined at the Shark Reef Marine Reserve, a multi-species shark feeding site in Fiji. Using direct observation sampling methods, eight species of sharks (bull shark Carcharhinus leucas, grey reef shark Carcharhinus amblyrhynchos, whitetip reef shark Triaenodon obesus, blacktip reef shark Carcharhinus melanopterus, tawny nurse shark Nebrius ferrugineus, silvertip shark Carcharhinus albimarginatus, sicklefin lemon shark Negaprion acutidens, and tiger shark Galeocerdo cuvier) displayed inter-annual site fidelity between 2003 and 2012. Encounter rates and/or relative abundances of some species changed over time, overall resulting in more individuals (mostly C. leucas) of fewer species being encountered on average on shark feeding dives at the end of the study period. Differences in shark community composition between the years 2004-2006 and 2007-2012 were evident, mostly because N. ferrugineus, C. albimarginatus and N. acutidens were much more abundant in 2004-2006 and very rare in the period of 2007-2012. Two explanations are offered for the observed changes in relative abundances over time, namely inter-specific interactions and operator-specific feeding protocols. Both, possibly in combination, are suggested to be important determinants of species composition and encounter rates, and relative abundances at this shark provisioning site in Fiji. This study, which includes the most species from a spatially confined shark provisioning site to date, suggests that long-term provisioning may result in competitive exclusion among shark

  9. Long-term changes in species composition and relative abundances of sharks at a provisioning site.

    PubMed

    Brunnschweiler, Juerg M; Abrantes, Kátya G; Barnett, Adam

    2014-01-01

    Diving with sharks, often in combination with food baiting/provisioning, has become an important product of today's recreational dive industry. Whereas the effects baiting/provisioning has on the behaviour and abundance of individual shark species are starting to become known, there is an almost complete lack of equivalent data from multi-species shark diving sites. In this study, changes in species composition and relative abundances were determined at the Shark Reef Marine Reserve, a multi-species shark feeding site in Fiji. Using direct observation sampling methods, eight species of sharks (bull shark Carcharhinus leucas, grey reef shark Carcharhinus amblyrhynchos, whitetip reef shark Triaenodon obesus, blacktip reef shark Carcharhinus melanopterus, tawny nurse shark Nebrius ferrugineus, silvertip shark Carcharhinus albimarginatus, sicklefin lemon shark Negaprion acutidens, and tiger shark Galeocerdo cuvier) displayed inter-annual site fidelity between 2003 and 2012. Encounter rates and/or relative abundances of some species changed over time, overall resulting in more individuals (mostly C. leucas) of fewer species being encountered on average on shark feeding dives at the end of the study period. Differences in shark community composition between the years 2004-2006 and 2007-2012 were evident, mostly because N. ferrugineus, C. albimarginatus and N. acutidens were much more abundant in 2004-2006 and very rare in the period of 2007-2012. Two explanations are offered for the observed changes in relative abundances over time, namely inter-specific interactions and operator-specific feeding protocols. Both, possibly in combination, are suggested to be important determinants of species composition and encounter rates, and relative abundances at this shark provisioning site in Fiji. This study, which includes the most species from a spatially confined shark provisioning site to date, suggests that long-term provisioning may result in competitive exclusion among shark

  10. Relative abundance and size of coastal sharks derived from commercial shark longline catch and effort data.

    PubMed

    Carlson, J K; Hale, L F; Morgan, A; Burgess, G

    2012-04-01

    In the north-west Atlantic Ocean, stock assessments conducted for some commercially harvested coastal sharks indicate declines from 64 to 80% with respect to virgin population levels. While the status of commercially important species is available, abundance trend information for other coastal shark species in the north-west Atlantic Ocean are unavailable. Using a generalized linear modelling (GLM) approach, a relative abundance index was derived from 1994 to 2009 using observer data collected in a commercial bottom longline fishery. Trends in abundance and average size were estimated for bull shark Carcharhinus leucas, spinner shark Carcharhinus brevipinna, tiger shark Galeocerdo cuvier and lemon shark Negaprion brevirostris. Increases in relative abundance for all shark species ranged from 14% for C. brevipinna, 12% for C. leucas, 6% for N. brevirostris and 3% for G. cuvier. There was no significant change in the size at capture over the time period considered for all species. While the status of shark populations should not be based exclusively on abundance trend information, but ultimately on stock assessment models, results from this study provide some cause for optimism on the status of these coastal shark species.

  11. The relative abundance of mountain pine beetle fungal associates through the beetle life cycle in pine trees.

    PubMed

    Khadempour, Lily; LeMay, Valerie; Jack, David; Bohlmann, Jörg; Breuil, Colette

    2012-11-01

    The mountain pine beetle (MPB) is a native bark beetle of western North America that attacks pine tree species, particularly lodgepole pine. It is closely associated with the ophiostomatoid ascomycetes Grosmannia clavigera, Leptographium longiclavatum, Ophiostoma montium, and Ceratocystiopsis sp.1, with which it is symbiotically associated. To develop a better understanding of interactions between beetles, fungi, and host trees, we used target-specific DNA primers with qPCR to assess the changes in fungal associate abundance over the stages of the MPB life cycle that occur in galleries under the bark of pine trees. Multivariate analysis of covariance identified statistically significant changes in the relative abundance of the fungi over the life cycle of the MPB. Univariate analysis of covariance identified a statistically significant increase in the abundance of Ceratocystiopsis sp.1 through the beetle life cycle, and pair-wise analysis showed that this increase occurs after the larval stage. In contrast, the abundance of O. montium and Leptographium species (G. clavigera, L. longiclavatum) did not change significantly through the MPB life cycle. From these results, the only fungus showing a significant increase in relative abundance has not been formally described and has been largely ignored by other MPB studies. Although our results were from only one site, in previous studies we have shown that the fungi described were all present in at least ten sites in British Columbia. We suggest that the role of Ceratocystiopsis sp.1 in the MPB system should be explored, particularly its potential as a source of nutrients for teneral adults.

  12. Simultaneous modeling of habitat suitability, occupancy, and relative abundance: African elephants in Zimbabwe

    USGS Publications Warehouse

    Martin, Julien; Chamaille-Jammes, Simon; Nichols, James D.; Fritz, Herve; Hines, James E.; Fonnesbeck, Christopher J.; MacKenzie, Darryl I.; Bailey, Larissa L.

    2010-01-01

    The recent development of statistical models such as dynamic site occupancy models provides the opportunity to address fairly complex management and conservation problems with relatively simple models. However, surprisingly few empirical studies have simultaneously modeled habitat suitability and occupancy status of organisms over large landscapes for management purposes. Joint modeling of these components is particularly important in the context of management of wild populations, as it provides a more coherent framework to investigate the population dynamics of organisms in space and time for the application of management decision tools. We applied such an approach to the study of water hole use by African elephants in Hwange National Park, Zimbabwe. Here we show how such methodology may be implemented and derive estimates of annual transition probabilities among three dry-season states for water holes: (1) unsuitable state (dry water holes with no elephants); (2) suitable state (water hole with water) with low abundance of elephants; and (3) suitable state with high abundance of elephants. We found that annual rainfall and the number of neighboring water holes influenced the transition probabilities among these three states. Because of an increase in elephant densities in the park during the study period, we also found that transition probabilities from low abundance to high abundance states increased over time. The application of the joint habitat–occupancy models provides a coherent framework to examine how habitat suitability and factors that affect habitat suitability influence the distribution and abundance of organisms. We discuss how these simple models can further be used to apply structured decision-making tools in order to derive decisions that are optimal relative to specified management objectives. The modeling framework presented in this paper should be applicable to a wide range of existing data sets and should help to address important ecological

  13. Abundance analysis of an extended sample of open clusters: A search for chemical inhomogeneities

    NASA Astrophysics Data System (ADS)

    Reddy, Arumalla B. S.; Giridhar, Sunetra; Lambert, David L.

    We have initiated a program to explore the presence of chemical inhomogeneities in the Galactic disk using the open clusters as ideal probes. We have analyzed high-dispersion echelle spectra (R ≥ 55,000) of red giant members for eleven open clusters to derive abundances for many elements. The membership to the cluster has been confirmed through their radial velocities and proper motions. The spread in temperatures and gravities being very small among the red giants, nearly the same stellar lines were employed thereby reducing the random errors. The errors of average abundance for the cluster were generally in 0.02 to 0.07 dex range. Our present sample covers galactocentric distances of 8.3 to 11.3 kpc and an age range of 0.2 to 4.3 Gyrs. Our earlier analysis of four open clusters (Reddy A.B.S. et al., 2012, MNRAS, 419,1350) indicate that abundances relative to Fe for elements from Na to Eu are equal within measurement uncertainties to published abundances for thin disk giants in the field. This supports the view that field stars come from disrupted open clusters. In the enlarged sample of eleven open clusters we find cluster to cluster abundance variations for some s- and r- process elements, with certain elements such as Zr and Ba showing large variation. These differences mark the signatures that these clusters had formed under different environmental conditions (Type II SN, Type Ia SN, AGB stars or a mixture of any of these) unique to the time and site of formation. These eleven clusters support the widely held impression that there is an abundance gradient such that the metallicity [Fe/H] at the solar galactocentric distance decreases outwards at about -0.1 dex per kpc.

  14. Lactobacillus and Pediococcus species richness and relative abundance in the vagina of rhesus monkeys (Macaca mulatta)

    PubMed Central

    Gravett, Michael G.; Jin, Ling; Pavlova, Sylvia I.; Tao, Lin

    2012-01-01

    Background The rhesus monkey is an important animal model to study human vaginal health to which lactic acid bacteria play a significant role. However, the vaginal lactic acid bacterial species richness and relative abundance in rhesus monkeys is largely unknown. Methods Vaginal swab samples were aseptically obtained from 200 reproductive aged female rhesus monkeys. Following Rogosa agar plating, single bacterial colonies representing different morphotypes were isolated and analyzed for whole-cell protein profile, species-specifc PCR, and 16S rRNA gene sequence. Results A total of 510 Lactobacillus strains of 17 species and one Pediococcus acidilactici were identified. The most abundant species was L. reuteri, which colonized the vaginas of 86% monkeys. L. johnsonii was the second most abundant species, which colonized 36% of monkeys. The majority of monkeys were colonized by multiple Lactobacillus species. Conclusions The vaginas of rhesus monkeys are frequently colonized by multiple Lactobacillus species, dominated by L. reuteri. PMID:22429090

  15. Leaf selection by two Bornean colobine monkeys in relation to plant chemistry and abundance.

    PubMed

    Matsuda, Ikki; Tuuga, Augustine; Bernard, Henry; Sugau, John; Hanya, Goro

    2013-01-01

    Focusing on the chemical basis of dietary selection while investigating the nutritional ecology of animals helps understand their feeding biology. It is also important to consider food abundance/biomass while studying the mechanism of animal food selection. We studied leaf selection in two Bornean folivorous primates in relation to plant chemistry and abundance: proboscis monkeys inhabiting a secondary riverine forest and red leaf monkeys inhabiting a primary forest. Both species tended to prefer leaves containing higher protein levels, although more abundant plant species were chosen within the preferred species, probably to maximise energy gain per unit time. However, the two species showed clear differences in their detailed feeding strategy. Red leaf monkeys strictly chose to consume young leaves to adapt to the poor nutritional environment of the primary forest, whereas proboscis monkeys were not highly selective because of the better quality of its common food in the riverine forest. PMID:23695180

  16. Cerulean Warbler abundance and occurrence relative to large-scale edge and habitat characteristics

    SciTech Connect

    Wood, P.B.; Bosworth, S.B.; Dettmers, R.

    2006-02-15

    We examined Cerulean Warbler (Dendroica cerulea) abundance and occurrence in southwestern West Virginia, where the coal-mining technique of mountaintop removal mining-valley fill converts large contiguous tracts of deciduous forest to forest patches surrounded by early successional habitats. Our study objectives were to quantify abundance and occurrence of Cerulean Warblers relative to (1) distance from the edge of extensive reclaimed grasslands and (2) habitat structure and landscape characteristics. Cerulean Warbler abundance increased with distance from the edge and edge effects extended 340 m into the forest. Percent occurrence did not vary with distance from mine edge, suggesting a degree of tolerance to the extensive edge occurring at the interface of forest and reclaimed lands. Abundance and occurrence were greater on ridges and midslopes than in bottomlands; consequently, disturbances such as mountaintop mining in which ridges are removed may have a greater impact on populations compared to other sources of fragmentation where ridges are not disturbed. It was found that, in addition to outright loss of forested habitat, mountaintop mining-valley fill alters the spatial configuration of forested habitats, creating edge and area effects that negatively affect Cerulean Warbler abundance and occurrence in the reclaimed mine landscape.

  17. Species richness and relative abundance of birds in natural and anthropogenic fragments of Brazilian Atlantic forest.

    PubMed

    dos Anjos, Luiz

    2004-06-01

    Bird communities were studied in two types of fragmented habitat of Atlantic forest in the State of Paraná, southern Brazil; one consisted of forest fragments that were created as a result of human activities (forest remnants), the other consisted of a set of naturally occurring forest fragments (forest patches). Using quantitative data obtained by the point counts method in 3 forest patches and 3 forest remnants during one year, species richness and relative abundance were compared in those habitats, considering species groups according to their general feeding habits. Insectivores, omnivores, and frugivores presented similar general tendencies in both habitats (decrease of species number with decreasing size and increasing isolation of forest fragment). However, these tendencies were different, when considering the relative abundance data: the trunk insectivores presented the highest value in the smallest patch while the lowest relative abundance was in the smallest remnant. In the naturally fragmented landscape, time permitted that the loss of some species of trunk insectivores be compensated for the increase in abundance of other species. In contrast, the remnants essentially represented newly formed islands that are not yet at equilibrium and where future species losses would make them similar to the patches.

  18. Quantitative Analysis of Age Specific Variation in the Abundance of Human Female Parotid Salivary Proteins

    PubMed Central

    Ambatipudi, Kiran S.; Lu, Bingwen; Hagen, Fred K; Melvin, James E.; Yates, John R.

    2010-01-01

    Summary Human saliva is a protein-rich, easily accessible source of potential local and systemic biomarkers to monitor changes that occur under pathological conditions; however little is known about the changes in abundance associated with normal aging. In this study, we performed a comprehensive proteomic profiling of pooled saliva collected from the parotid glands of healthy female subjects, divided into two age groups 1 and 2 (20–30 and 55–65 years old, respectively). Hydrophobic charge interaction chromatography was used to separate high from low abundant proteins prior to characterization of the parotid saliva using multidimensional protein identification technology (MudPIT). Collectively, 532 proteins were identified in the two age groups. Of these proteins, 266 were identified exclusively in one age group, while 266 proteins were common to both groups. The majority of the proteins identified in the two age groups belonged to the defense and immune response category. Of note, several defense related proteins (e.g. lysozyme, lactoferrin and histatin-1) were significantly more abundant in group 2 as determined by G-test. Selected representative mass spectrometric findings were validated by western blot analysis. Our study reports the first quantitative analysis of differentially regulated proteins in ductal saliva collected from young and older female subjects. This study supports the use of high-throughput proteomics as a robust discovery tool. Such results provide a foundation for future studies to identify specific salivary proteins which may be linked to age-related diseases specific to women. PMID:19764810

  19. Measurement of Relative Abundances of Ultra-Heavy Cosmic Rays with CALET on the ISS

    NASA Astrophysics Data System (ADS)

    Rauch, Brian; Calet Collaboration

    2016-03-01

    The CALorimetric Electron Telescope (CALET) is a Japanese-Italian-US astroparticle observatory that was launched from the Tanegashima Space Center on the H-IIB Launch Vehicle No.5 (H-IIB F5) aboard the KOUNOTORI5 (HTV5 cargo transfer vehicle) to the International Space Station (ISS) on August 19, 2015. The HTV5 arrived at the ISS on August 24, and CALET was installed on port 9 of the Japanese Experiment Module ``Kibo'' Exposed Facility (JEM-EF), where CALET underwent the planned turn on and checkout procedures. CALET has completed its commissioning phase and its main calorimeter (CAL) is observing the highest energy cosmic electrons from 1 GeV to 20 TeV, along with cosmic ray nuclei through iron up to 1,000 TeV and gamma-rays above 10 GeV. In a five-year mission CALET will also have the exposure to measure the relative abundances of the ultra-heavy (UH) cosmic rays with ~4 × the statistics of the TIGER instrument for the full CAL acceptance. Rigidity cutoffs based on the earth's geomagnetic field in the 51.6° inclination ISS orbit can provide an energy independent UH measurement with expanded acceptance with ~10 × the TIGER statistics. An overview of the anticipated performance and preliminary CALET UH analysis data will be presented. This research was supported by NASA at Washington University under Grant Number NNX11AE02G.

  20. Penguin tissue as a proxy for relative krill abundance in East Antarctica during the Holocene.

    PubMed

    Huang, Tao; Sun, Liguang; Long, Nanye; Wang, Yuhong; Huang, Wen

    2013-09-30

    Antarctic krill (Euphausia superba) is a key component of the Southern Ocean food web. It supports a large number of upper trophic-level predators, and is also a major fishery resource. Understanding changes in krill abundance has long been a priority for research and conservation in the Southern Ocean. In this study, we performed stable isotope analyses on ancient Adélie penguin tissues and inferred relative krill abundance during the Holocene epoch from paleodiets of Adélie penguin (Pygoscelis adeliae), using inverse of δ¹⁵N (ratio of ¹⁵N/¹⁴N) value as a proxy. We find that variations in krill abundance during the Holocene are in accord with episodes of regional climate changes, showing greater krill abundance in cold periods. Moreover, the low δ¹⁵N values found in modern Adélie penguins indicate relatively high krill availability, which supports the hypothesis of krill surplus in modern ages due to recent hunt for krill-eating seals and whales by humans.

  1. Penguin tissue as a proxy for relative krill abundance in East Antarctica during the Holocene

    PubMed Central

    Huang, Tao; Sun, Liguang; Long, Nanye; Wang, Yuhong; Huang, Wen

    2013-01-01

    Antarctic krill (Euphausia superba) is a key component of the Southern Ocean food web. It supports a large number of upper trophic-level predators, and is also a major fishery resource. Understanding changes in krill abundance has long been a priority for research and conservation in the Southern Ocean. In this study, we performed stable isotope analyses on ancient Adélie penguin tissues and inferred relative krill abundance during the Holocene epoch from paleodiets of Adélie penguin (Pygoscelis adeliae), using inverse of δ15N (ratio of 15N/14N) value as a proxy. We find that variations in krill abundance during the Holocene are in accord with episodes of regional climate changes, showing greater krill abundance in cold periods. Moreover, the low δ15N values found in modern Adélie penguins indicate relatively high krill availability, which supports the hypothesis of krill surplus in modern ages due to recent hunt for krill-eating seals and whales by humans. PMID:24076768

  2. Weed management practices affect the diversity and relative abundance of physic nut mites.

    PubMed

    Saraiva, Althiéris de Sousa; Sarmento, Renato A; Erasmo, Eduardo A L; Pedro-Neto, Marçal; de Souza, Danival José; Teodoro, Adenir V; Silva, Daniella G

    2015-03-01

    Crop management practices determine weed community, which in turn may influence patterns of diversity and abundance of associated arthropods. This study aimed to evaluate whether local weed management practices influence the diversity and relative abundance of phytophagous and predatory mites, as well as mites with undefined feeding habits--of the families Oribatidae and Acaridae--in a physic nut (Jatropha curcas L.) plantation subjected to (1) within-row herbicide spraying and between-row mowing; (2) within-row herbicide spraying and no between-row mowing; (3) within-row weeding and between-row mowing; (4) within-row weeding and no between-row mowing; and (5) unmanaged (control). The herbicide used was glyphosate. Herbicide treatments resulted in higher diversity and relative abundance of predatory mites and mites with undefined feeding habit on physic nut shrubs. This was probably due to the toxic effects of the herbicide on mites or to removal of weeds. Within-row herbicide spraying combined with between-row mowing was the treatment that most contributed to this effect. Our results show that within-row weeds harbor important species of predatory mites and mites with undefined feeding habit. However, the dynamics of such mites in the system can be changed according to the weed management practice applied. Among the predatory mites of the family Phytoseiidae Amblydromalus sp. was the most abundant, whereas Brevipalpus phoenicis was the most frequent phytophagous mite and an unidentified oribatid species was the most frequent mite with undefined feeding habit.

  3. Decline in relative abundance of bottlenose dolphins exposed to long-term disturbance.

    PubMed

    Bejder, Lars; Samuels, Amy; Whitehead, Hal; Gales, Nick; Mann, Janet; Connor, Richard; Heithaus, Mike; Watson-Capps, Jana; Flaherty, Cindy; Krützen, Michael

    2006-12-01

    Studies evaluating effects of human activity on wildlife typically emphasize short-term behavioral responses from which it is difficult to infer biological significance or formulate plans to mitigate harmful impacts. Based on decades of detailed behavioral records, we evaluated long-term impacts of vessel activity on bottlenose dolphins (Tursiops sp.) in Shark Bay, Australia. We compared dolphin abundance within adjacent 36-km2 tourism and control sites, over three consecutive 4.5-year periods wherein research activity was relatively constant but tourism levels increased from zero, to one, to two dolphin-watching operators. A nonlinear logistic model demonstrated that there was no difference in dolphin abundance between periods with no tourism and periods in which one operator offered tours. As the number of tour operators increased to two, there was a significant average decline in dolphin abundance (14.9%; 95% CI=-20.8 to -8.23), approximating a decline of one per seven individuals. Concurrently, within the control site, the average increase in dolphin abundance was not significant (8.5%; 95% CI=-4.0 to +16.7). Given the substantially greater presence and proximity of tour vessels to dolphins relative to research vessels, tour-vessel activity contributed more to declining dolphin numbers within the tourism site than research vessels. Although this trend may not jeopardize the large, genetically diverse dolphin population of Shark Bay, the decline is unlikely to be sustainable for local dolphin tourism. A similar decline would be devastating for small, closed, resident, or endangered cetacean populations. The substantial effect of tour vessels on dolphin abundance in a region of low-level tourism calls into question the presumption that dolphin-watching tourism is benign.

  4. Modeled distribution and abundance of a pelagic seabird reveal trends in relation to fisheries

    USGS Publications Warehouse

    Renner, Martin; Parrish, Julia K.; Piatt, John F.; Kuletz, Kathy J.; Edwards, Ann E.; Hunt, George L.

    2013-01-01

    The northern fulmar Fulmarus glacialis is one of the most visible and widespread seabirds in the eastern Bering Sea and Aleutian Islands. However, relatively little is known about its abundance, trends, or the factors that shape its distribution. We used a long-term pelagic dataset to model changes in fulmar at-sea distribution and abundance since the mid-1970s. We used an ensemble model, based on a weighted average of generalized additive model (GAM), multivariate adaptive regression splines (MARS), and random forest models to estimate the pelagic distribution and density of fulmars in the waters of the Aleutian Archipelago and Bering Sea. The most important predictor variables were colony effect, sea surface temperature, distribution of fisheries, location, and primary productivity. We calculated a time series from the ratio of observed to predicted values and found that fulmar at-sea abundance declined from the 1970s to the 2000s at a rate of 0.83% (± 0.39% SE) per annum. Interpolating fulmar densities on a spatial grid through time, we found that the center of fulmar distribution in the Bering Sea has shifted north, coinciding with a northward shift in fish catches and a warming ocean. Our study shows that fisheries are an important, but not the only factor, shaping fulmar distribution and abundance trends in the eastern Bering Sea and Aleutian Islands.

  5. Nature's starships. I. Observed abundances and relative frequencies of amino acids in meteorites

    SciTech Connect

    Cobb, Alyssa K.; Pudritz, Ralph E. E-mail: pudritz@physics.mcmaster.ca

    2014-03-10

    The class of meteorites called carbonaceous chondrites are examples of material from the solar system which have been relatively unchanged from the time of their initial formation. These meteorites have been classified according to the temperatures and physical conditions of their parent planetesimals. We collate available data on amino acid abundance in these meteorites and plot the concentrations of different amino acids for each meteorite within various meteorite subclasses. We plot average concentrations for various amino acids across meteorites separated by subclass and petrologic type. We see a predominance in the abundance and variety of amino acids in CM2 and CR2 meteorites. The range in temperature corresponding to these subclasses indicates high degrees of aqueous alteration, suggesting aqueous synthesis of amino acids. Within the CM2 and CR2 subclasses, we identify trends in relative frequencies of amino acids to investigate how common amino acids are as a function of their chemical complexity. These two trends (total abundance and relative frequencies) can be used to constrain formation parameters of amino acids within planetesimals. Our organization of the data supports an onion shell model for the temperature structure of planetesimals. The least altered meteorites (type 3) and their amino acids originated near cooler surface regions. The most active amino acid synthesis likely took place at intermediate depths (type 2). The most altered materials (type 1) originated furthest toward parent body cores. This region is likely too hot to either favor amino acid synthesis or for amino acids to be retained after synthesis.

  6. The relative importance of disturbance and exotic-plant abundance in California coastal sage scrub

    USGS Publications Warehouse

    Fleming, G.M.; Diffendorfer, J.E.; Zedler, P.H.

    2009-01-01

    Many ecosystems of conservation concern require some level of disturbance to sustain their species composition and ecological function. However, inappropriate disturbance regimes could favor invasion or expansion of exotic species. In southern California coastal sage scrub (CSS) fire is a natural disturbance, but because of human influence, frequencies may now be unnaturally high. Other anthropogenic disturbances such as grazing also occur in reserve areas. Managers charged with imposing or tolerating fire or other disturbance within their reserves are concerned that habitat quality may be degraded by an increasing abundance of exotic plants. We used vegetation monitoring data from Camp Pendleton, California, USA, to assess the correlation between past disturbances (frequent fire, agriculture, or grazing and mechanical disturbances) and current exotic species abundance in CSS. We found that disturbance history was only modestly related to exotic abundance overall, but fire frequency showed the strongest association. We also examined whether cover and richness of various native plant life forms (woody species, perennial herbs, and annual herbs) were more strongly influenced by disturbance history or by exotic-plant abundance. Native plant responses varied among life forms, but woody species and annual herbs were generally more strongly and negatively associated with exotic abundance than with disturbance. Effective CSS conservation will require developing means to curb the negative impacts of exotic plants, which may abound with or without severe or recent disturbance. Additionally, more focus should be given to understory herbs showing sensitivity to invasion. Though understudied, native herbs comprise the greatest portion of plant diversity in CSS and are critical to preservation of the community as a whole. ?? 2009 by the Ecological Society of America.

  7. A Metastable Equilibrium Model for the Relative Abundances of Microbial Phyla in a Hot Spring

    PubMed Central

    Dick, Jeffrey M.; Shock, Everett L.

    2013-01-01

    Many studies link the compositions of microbial communities to their environments, but the energetics of organism-specific biomass synthesis as a function of geochemical variables have rarely been assessed. We describe a thermodynamic model that integrates geochemical and metagenomic data for biofilms sampled at five sites along a thermal and chemical gradient in the outflow channel of the hot spring known as “Bison Pool” in Yellowstone National Park. The relative abundances of major phyla in individual communities sampled along the outflow channel are modeled by computing metastable equilibrium among model proteins with amino acid compositions derived from metagenomic sequences. Geochemical conditions are represented by temperature and activities of basis species, including pH and oxidation-reduction potential quantified as the activity of dissolved hydrogen. By adjusting the activity of hydrogen, the model can be tuned to closely approximate the relative abundances of the phyla observed in the community profiles generated from BLAST assignments. The findings reveal an inverse relationship between the energy demand to form the proteins at equal thermodynamic activities and the abundance of phyla in the community. The distance from metastable equilibrium of the communities, assessed using an equation derived from energetic considerations that is also consistent with the information-theoretic entropy change, decreases along the outflow channel. Specific divergences from metastable equilibrium, such as an underprediction of the relative abundances of phototrophic organisms at lower temperatures, can be explained by considering additional sources of energy and/or differences in growth efficiency. Although the metabolisms used by many members of these communities are driven by chemical disequilibria, the results support the possibility that higher-level patterns of chemotrophic microbial ecosystems are shaped by metastable equilibrium states that depend on both the

  8. Abundances relative to carbon of the elements silicon to nickel in the galactic cosmic radiation

    NASA Technical Reports Server (NTRS)

    Cartwright, B.; Garcia-Munoz, M.; Simpson, J. A.

    1974-01-01

    Discussion of the abundances relative to carbon of the elements from silicon to nickel in the galactic cosmic radiation as measured by cosmic ray telescopes on the IMP-5 and IMP-7 satellites, in energy ranges between 40 and 450 MeV/nucleon depending on the species. The IMP-7 measurements are still to be considered only preliminary and do not yet fully exploit the resolution capabilities of that instrument. Calculations of the abundances to be expected in this charge range if the cosmic radiation traverses 6 g/sq cm of material after acceleration are presented, and the consequences which follow both for propagation models and for the chemical composition of the sources of the cosmic radiation are discussed.

  9. Mosquito species diversity and abundance in relation to land use in a riceland agroecosystem in Mwea, Kenya.

    PubMed

    Muturi, Ephantus J; Shililu, Josephat; Jacob, Benjamin; Gu, Weidong; Githure, John; Novak, Robert

    2006-06-01

    We conducted an entomological survey to determine the mosquito species diversity and abundance in relation to land use in the Mwea rice scheme, Kenya. Adult mosquitoes were collected by indoor spraying of houses and outdoors by CDC light traps in three villages representing planned (Mbuinjeru) and unplanned (Kiamachiri) rice agroecosystems and a non-irrigated agroecosystem (Murinduko). During the 12-month sampling period, a total of 98,708 mosquitoes belonging to five genera and 25 species were collected. The five most common species collected during this study were Anopheles arabiensis Patton (52.5%), Culex quinquefasciatus Say (36.7%), Anopheles pharoensis Theobald (5.2%), Anopheles coustani Laveran (1.4%), and Anopheles funestus Giles (1.3%). Anopheles arabiensis, Cx quinquefasciatus, and An. pharoensis were more abundant in rice agroecosystems than in the non-irrigated agroecosystem, and in planned than in the unplanned rice agroecosystems. In contrast, An. funestus was more abundant in the non-irrigated agroecosystem. The mosquito species diversity (H) and evenness (E(H)) in the non-irrigated agroecosystem (Shannon diversity Index, H = 1.507, EH = 0.503) was significantly higher than in the rice agroecosystems (H) = 0.968, E(H) = 0.313, unplanned; and H= 1.040, E(H) = 0.367 planned). Results of lag cross correlation analysis revealed a strong relationship between rainfall and the abundance of An. arabiensis, and C. quinquefasciatus in the non-irrigated agroecosystem but not in the rice agroecosystems. It is inferred from the data that different levels of habitat perturbations with regard to rice cultivation have different effects on mosquito diversity and abundance. This provides an understanding of how mosquito diversity is impacted by different habitat management and rice cropping strategies.

  10. Weed management practices affect the diversity and relative abundance of physic nut mites.

    PubMed

    Saraiva, Althiéris de Sousa; Sarmento, Renato A; Erasmo, Eduardo A L; Pedro-Neto, Marçal; de Souza, Danival José; Teodoro, Adenir V; Silva, Daniella G

    2015-03-01

    Crop management practices determine weed community, which in turn may influence patterns of diversity and abundance of associated arthropods. This study aimed to evaluate whether local weed management practices influence the diversity and relative abundance of phytophagous and predatory mites, as well as mites with undefined feeding habits--of the families Oribatidae and Acaridae--in a physic nut (Jatropha curcas L.) plantation subjected to (1) within-row herbicide spraying and between-row mowing; (2) within-row herbicide spraying and no between-row mowing; (3) within-row weeding and between-row mowing; (4) within-row weeding and no between-row mowing; and (5) unmanaged (control). The herbicide used was glyphosate. Herbicide treatments resulted in higher diversity and relative abundance of predatory mites and mites with undefined feeding habit on physic nut shrubs. This was probably due to the toxic effects of the herbicide on mites or to removal of weeds. Within-row herbicide spraying combined with between-row mowing was the treatment that most contributed to this effect. Our results show that within-row weeds harbor important species of predatory mites and mites with undefined feeding habit. However, the dynamics of such mites in the system can be changed according to the weed management practice applied. Among the predatory mites of the family Phytoseiidae Amblydromalus sp. was the most abundant, whereas Brevipalpus phoenicis was the most frequent phytophagous mite and an unidentified oribatid species was the most frequent mite with undefined feeding habit. PMID:25528451

  11. The relative contribution of climate to changes in lesser prairie-chicken abundance

    USGS Publications Warehouse

    Ross, Beth E.; Haukos, David A.; Hagen, Christian A.; Pitman, James

    2016-01-01

    Managing for species using current weather patterns fails to incorporate the uncertainty associated with future climatic conditions; without incorporating potential changes in climate into conservation strategies, management and conservation efforts may fall short or waste valuable resources. Understanding the effects of climate change on species in the Great Plains of North America is especially important, as this region is projected to experience an increased magnitude of climate change. Of particular ecological and conservation interest is the lesser prairie-chicken (Tympanuchus pallidicinctus), which was listed as “threatened” under the U.S. Endangered Species Act in May 2014. We used Bayesian hierarchical models to quantify the effects of extreme climatic events (extreme values of the Palmer Drought Severity Index [PDSI]) relative to intermediate (changes in El Niño Southern Oscillation) and long-term climate variability (changes in the Pacific Decadal Oscillation) on trends in lesser prairie-chicken abundance from 1981 to 2014. Our results indicate that lesser prairie-chicken abundance on leks responded to environmental conditions of the year previous by positively responding to wet springs (high PDSI) and negatively to years with hot, dry summers (low PDSI), but had little response to variation in the El Niño Southern Oscillation and the Pacific Decadal Oscillation. Additionally, greater variation in abundance on leks was explained by variation in site relative to broad-scale climatic indices. Consequently, lesser prairie-chicken abundance on leks in Kansas is more strongly influenced by extreme drought events during summer than other climatic conditions, which may have negative consequences for the population as drought conditions intensify throughout the Great Plains.

  12. 454 pyrosequencing to describe microbial eukaryotic community composition, diversity and relative abundance: a test for marine haptophytes.

    PubMed

    Egge, Elianne; Bittner, Lucie; Andersen, Tom; Audic, Stéphane; de Vargas, Colomban; Edvardsen, Bente

    2013-01-01

    Next generation sequencing of ribosomal DNA is increasingly used to assess the diversity and structure of microbial communities. Here we test the ability of 454 pyrosequencing to detect the number of species present, and assess the relative abundance in terms of cell numbers and biomass of protists in the phylum Haptophyta. We used a mock community consisting of equal number of cells of 11 haptophyte species and compared targeting DNA and RNA/cDNA, and two different V4 SSU rDNA haptophyte-biased primer pairs. Further, we tested four different bioinformatic filtering methods to reduce errors in the resulting sequence dataset. With sequencing depth of 11000-20000 reads and targeting cDNA with Haptophyta specific primers Hap454 we detected all 11 species. A rarefaction analysis of expected number of species recovered as a function of sampling depth suggested that minimum 1400 reads were required here to recover all species in the mock community. Relative read abundance did not correlate to relative cell numbers. Although the species represented with the largest biomass was also proportionally most abundant among the reads, there was generally a weak correlation between proportional read abundance and proportional biomass of the different species, both with DNA and cDNA as template. The 454 sequencing generated considerable spurious diversity, and more with cDNA than DNA as template. With initial filtering based only on match with barcode and primer we observed 100-fold more operational taxonomic units (OTUs) at 99% similarity than the number of species present in the mock community. Filtering based on quality scores, or denoising with PyroNoise resulted in ten times more OTU99% than the number of species. Denoising with AmpliconNoise reduced the number of OTU99% to match the number of species present in the mock community. Based on our analyses, we propose a strategy to more accurately depict haptophyte diversity using 454 pyrosequencing. PMID:24069303

  13. 454 pyrosequencing to describe microbial eukaryotic community composition, diversity and relative abundance: a test for marine haptophytes.

    PubMed

    Egge, Elianne; Bittner, Lucie; Andersen, Tom; Audic, Stéphane; de Vargas, Colomban; Edvardsen, Bente

    2013-01-01

    Next generation sequencing of ribosomal DNA is increasingly used to assess the diversity and structure of microbial communities. Here we test the ability of 454 pyrosequencing to detect the number of species present, and assess the relative abundance in terms of cell numbers and biomass of protists in the phylum Haptophyta. We used a mock community consisting of equal number of cells of 11 haptophyte species and compared targeting DNA and RNA/cDNA, and two different V4 SSU rDNA haptophyte-biased primer pairs. Further, we tested four different bioinformatic filtering methods to reduce errors in the resulting sequence dataset. With sequencing depth of 11000-20000 reads and targeting cDNA with Haptophyta specific primers Hap454 we detected all 11 species. A rarefaction analysis of expected number of species recovered as a function of sampling depth suggested that minimum 1400 reads were required here to recover all species in the mock community. Relative read abundance did not correlate to relative cell numbers. Although the species represented with the largest biomass was also proportionally most abundant among the reads, there was generally a weak correlation between proportional read abundance and proportional biomass of the different species, both with DNA and cDNA as template. The 454 sequencing generated considerable spurious diversity, and more with cDNA than DNA as template. With initial filtering based only on match with barcode and primer we observed 100-fold more operational taxonomic units (OTUs) at 99% similarity than the number of species present in the mock community. Filtering based on quality scores, or denoising with PyroNoise resulted in ten times more OTU99% than the number of species. Denoising with AmpliconNoise reduced the number of OTU99% to match the number of species present in the mock community. Based on our analyses, we propose a strategy to more accurately depict haptophyte diversity using 454 pyrosequencing.

  14. Detailed abundance analysis of the brightest star in Segue 2, the least massive galaxy

    NASA Astrophysics Data System (ADS)

    Roederer, Ian U.; Kirby, Evan N.

    2014-05-01

    We present the first high-resolution spectroscopic observations of one red giant star in the ultra-faint dwarf galaxy Segue 2, which has the lowest total mass (including dark matter) estimated for any known galaxy. These observations were made using the Magellan Inamori Kyocera Echelle (MIKE) spectrograph on the Magellan II Telescope at Las Campanas Observatory. We perform a standard abundance analysis of this star, SDSS J021933.13+200830.2, and present abundances of 21 species of 18 elements as well as upper limits for 25 additional species. We derive [Fe/H] = -2.9, in excellent agreement with previous estimates from medium-resolution spectroscopy. Our main result is that this star bears the chemical signatures commonly found in field stars of similar metallicity. The heavy elements produced by neutron-capture reactions are present, but they are deficient at levels characteristic of stars in other ultra-faint dwarf galaxies and a few luminous dwarf galaxies. The otherwise normal abundance patterns suggest that the gas from which this star formed was enriched by metals from multiple Type II supernovae reflecting a relatively well-sampled IMF. This adds to the growing body of evidence indicating that Segue 2 may have been substantially more massive in the past.

  15. Relating the Diversity, Abundance, and Activity of Ammonia-Oxidizing Archaeal Communities to Nitrification Rates in the Coastal Ocean

    NASA Astrophysics Data System (ADS)

    Tolar, B. B.; Smith, J. M.; Chavez, F.; Francis, C.

    2015-12-01

    Ammonia oxidation, the rate-limiting first step of nitrification, is an important link between reduced (ammonia) and oxidized (nitrate) nitrogen, and controls the relative distribution of these forms of inorganic nitrogen. This process is catalyzed via the ammonia monooxygenase enzyme of both ammonia-oxidizing Bacteria (AOB) and Archaea (AOA); the α subunit of this enzyme is encoded by the amoA gene and has been used as the molecular marker to detect this process. In the ocean, AOA are typically 10-1000 times more and are likely more active than AOB, and thus are key players in the marine nitrogen cycle. Monterey Bay is a dynamic site to study nitrification, as seasonal upwelling brings deep water and nutrients into surface waters, which can promote phytoplankton blooms and impact biogeochemical processes such as the nitrogen cycle. We have sampled two sites within Monterey Bay bimonthly for two years as part of the ongoing Monterey Bay Time Series (MBTS) to quantify AOA genes, transcripts, and nitrification rates. Two ecotypes of AOA are routinely found in Monterey Bay - the 'shallow' water column A (WCA) and 'deep' water column B (WCB) clades, which are thought to have distinct physiological properties and can be distinguished based on the amoA gene sequence. Previous work has shown a strong relationship between nitrification rates in Monterey Bay with the abundance of WCA amoA genes and transcripts. Additionally, we found a correlation between the relative abundance of Marine Group I (MGI) Thaumarchaeota 16S rRNA reads (as % of total) and the absolute abundance of AOA amoA genes (determined via qPCR) in Monterey Bay and the California Current System. AOA 16S rRNA gene abundances in turn correlated significantly with changes in nitrification rate with depth, while the relative abundance of genes and transcripts binned to a single AOA (Nitrosopumilus maritimus) was not significantly correlated to nitrification rate. Further analysis of the sequenced AOA

  16. Parametric scaling from species relative abundances to absolute abundances in the computation of biological diversity: a first proposal using Shannon's entropy.

    PubMed

    Ricotta, Carlo

    2003-01-01

    Traditional diversity measures such as the Shannon entropy are generally computed from the species' relative abundance vector of a given community to the exclusion of species' absolute abundances. In this paper, I first mention some examples where the total information content associated with a given community may be more adequate than Shannon's average information content for a better understanding of ecosystem functioning. Next, I propose a parametric measure of statistical information that contains both Shannon's entropy and total information content as special cases of this more general function.

  17. Relating river geomorphology to the abundance of periphyton in New Zealand rivers

    NASA Astrophysics Data System (ADS)

    Hoyle, Jo; Hicks, Murray; Kilroy, Cathy

    2013-04-01

    Aquatic plants (including both periphyton and macrophytes) are a natural component of stream and river systems. However, abundant growth of instream plants can have detrimental impacts on the values of rivers. For example, periphyton in rivers provides basal resources for food webs and provides an important ecological service by removing dissolved nutrients and contaminants from the water column. However, high abundance of periphyton can have negative effects on habitat quality, water chemistry and biodiversity, and can reduce recreation and aesthetic values. The abundance of periphyton in rivers is influenced by a number of factors, but two key factors can be directly influenced by human activities: flow regimes and nutrient concentrations. Establishing quantitative relationships between periphyton abundance and these factors has proven to be difficult but remains an urgent priority due to the need to manage the ecological impacts of water abstraction and eutrophication of rivers worldwide. This need is particularly strong in New Zealand, where there is increasing demand for water for industry, power generation and agriculture. However, we currently have limited ability to predict the effects of changes in the mid-range flow regime on the presence/absence, abundance and composition of aquatic plants. Current water allocation limits are based on simple flow statistics, such as multiples of the median flow, but these are regional averages and can be quite unreliable on a site-specific basis. This stems largely from our limited ability to transform flow data into ecologically meaningful physical processes that directly affect plants (e.g., drag, abrasion, bed movement). The research we will present examines whether geomorphic variables, such as frequency of bed movement, are useful co-predictors in periphyton abundance-flow relationships. We collected topographic survey data and bed sediment data for 20 study reaches in the Manawatu-Wanganui region of New Zealand

  18. Relative abundance of tau and neurofilament epitopes in hippocampal neurofibrillary tangles.

    PubMed Central

    Schmidt, M. L.; Lee, V. M.; Trojanowski, J. Q.

    1990-01-01

    Neurofibrillary tangles (NFTs) derive, in part, from normal neuronal cytoskeletal proteins, ie, large portions of tau (tau) but only restricted segments of the peripheral domains of the high- and middle-molecular weight neurofilament subunits. To learn more about the events leading to the incorporation of tau and neurofilament epitopes into NFTs, the relative abundance of tau and NF determinants in these lesions was quantitatively analyzed in hippocampi from Alzheimer disease (AD) patients and age-matched controls using monoclonal antibodies specific for tau or for NF proteins. Immunostained NFTs appeared qualitatively the same in both AD and controls, ie, every epitope found in AD NFTs occurred also in the NFTs of the control patients. However, in hippocampi with only a few tangles, tau epitopes, but no NF epitopes, were detected in NFTs. In contrast, both tau and NF epitopes were present in those tangles that were found in hippocampi with abundant NFTs. Nevertheless, the number of tau-positive NFTs generally exceeded the number of NF-positive NFTs. These findings indicate that tau epitopes are more abundant than NF epitopes in NFTs and that the formation of NFTs may be linked to a derangement in the normal metabolism of tau that is more extensive than alterations in NF protein metabolism. Images Figure 1 PMID:1693468

  19. Spectral Properties of Cool Stars: Extended Abundance Analysis of 1,617 Planet-search Stars

    NASA Astrophysics Data System (ADS)

    Brewer, John M.; Fischer, Debra A.; Valenti, Jeff A.; Piskunov, Nikolai

    2016-08-01

    We present a catalog of uniformly determined stellar properties and abundances for 1,617 F, G, and K stars using an automated spectral synthesis modeling procedure. All stars were observed using the HIRES spectrograph at Keck Observatory. Our procedure used a single line list to fit model spectra to observations of all stars to determine effective temperature, surface gravity, metallicity, projected rotational velocity, and the abundances of 15 elements (C, N, O, Na, Mg, Al, Si, Ca, Ti, V, Cr, Mn, Fe, Ni, and Y). Sixty percent of the sample had Hipparcos parallaxes and V-band photometry, which we combined with the spectroscopic results to obtain mass, radius, and luminosity. Additionally, we used the luminosity, effective temperature, metallicity and α-element enhancement to interpolate in the Yonsei-Yale isochrones to derive mass, radius, gravity, and age ranges for those stars. Finally, we determined new relations between effective temperature and macroturbulence for dwarfs and subgiants. Our analysis achieved precisions of 25 K in {T}{eff}, 0.01 dex in [M/H], 0.028 dex for {log}g, and 0.5 km s-1 in v\\sin i based on multiple observations of the same stars. The abundance results were similarly precise, between ˜0.01 and ˜0.04 dex, though trends with respect to {T}{eff} remained for which we derived empirical corrections. The trends, though small, were much larger than our uncertainties and are shared with published abundances. We show that changing our model atmosphere grid accounts for most of the trend in [M/H] between 5000 and 5500 K, indicating a possible problem with the atmosphere models or opacities.

  20. Spectral Properties of Cool Stars: Extended Abundance Analysis of 1,617 Planet-search Stars

    NASA Astrophysics Data System (ADS)

    Brewer, John M.; Fischer, Debra A.; Valenti, Jeff A.; Piskunov, Nikolai

    2016-08-01

    We present a catalog of uniformly determined stellar properties and abundances for 1,617 F, G, and K stars using an automated spectral synthesis modeling procedure. All stars were observed using the HIRES spectrograph at Keck Observatory. Our procedure used a single line list to fit model spectra to observations of all stars to determine effective temperature, surface gravity, metallicity, projected rotational velocity, and the abundances of 15 elements (C, N, O, Na, Mg, Al, Si, Ca, Ti, V, Cr, Mn, Fe, Ni, and Y). Sixty percent of the sample had Hipparcos parallaxes and V-band photometry, which we combined with the spectroscopic results to obtain mass, radius, and luminosity. Additionally, we used the luminosity, effective temperature, metallicity and α-element enhancement to interpolate in the Yonsei–Yale isochrones to derive mass, radius, gravity, and age ranges for those stars. Finally, we determined new relations between effective temperature and macroturbulence for dwarfs and subgiants. Our analysis achieved precisions of 25 K in {T}{eff}, 0.01 dex in [M/H], 0.028 dex for {log}g, and 0.5 km s‑1 in v\\sin i based on multiple observations of the same stars. The abundance results were similarly precise, between ˜0.01 and ˜0.04 dex, though trends with respect to {T}{eff} remained for which we derived empirical corrections. The trends, though small, were much larger than our uncertainties and are shared with published abundances. We show that changing our model atmosphere grid accounts for most of the trend in [M/H] between 5000 and 5500 K, indicating a possible problem with the atmosphere models or opacities.

  1. Environmental controls on microbial abundance and activity on the greenland ice sheet: a multivariate analysis approach.

    PubMed

    Stibal, Marek; Telling, Jon; Cook, Joe; Mak, Ka Man; Hodson, Andy; Anesio, Alexandre M

    2012-01-01

    Microbes in supraglacial ecosystems have been proposed to be significant contributors to regional and possibly global carbon cycling, and quantifying the biogeochemical cycling of carbon in glacial ecosystems is of great significance for global carbon flow estimations. Here we present data on microbial abundance and productivity, collected along a transect across the ablation zone of the Greenland ice sheet (GrIS) in summer 2010. We analyse the relationships between the physical, chemical and biological variables using multivariate statistical analysis. Concentrations of debris-bound nutrients increased with distance from the ice sheet margin, as did both cell numbers and activity rates before reaching a peak (photosynthesis) or a plateau (respiration, abundance) between 10 and 20 km from the margin. The results of productivity measurements suggest an overall net autotrophy on the GrIS and support the proposed role of ice sheet ecosystems in carbon cycling as regional sinks of CO(2) and places of production of organic matter that can be a potential source of nutrients for downstream ecosystems. Principal component analysis based on chemical and biological data revealed three clusters of sites, corresponding to three 'glacier ecological zones', confirmed by a redundancy analysis (RDA) using physical data as predictors. RDA using data from the largest 'bare ice zone' showed that glacier surface slope, a proxy for melt water flow, accounted for most of the variation in the data. Variation in the chemical data was fully explainable by the determined physical variables. Abundance of phototrophic microbes and their proportion in the community were identified as significant controls of the carbon cycling-related microbial processes.

  2. READSCAN: a fast and scalable pathogen discovery program with accurate genome relative abundance estimation

    PubMed Central

    Rashid, Mamoon; Pain, Arnab

    2013-01-01

    Summary: READSCAN is a highly scalable parallel program to identify non-host sequences (of potential pathogen origin) and estimate their genome relative abundance in high-throughput sequence datasets. READSCAN accurately classified human and viral sequences on a 20.1 million reads simulated dataset in <27 min using a small Beowulf compute cluster with 16 nodes (Supplementary Material). Availability: http://cbrc.kaust.edu.sa/readscan Contact: arnab.pain@kaust.edu.sa or raeece.naeem@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23193222

  3. The swift fox in rangeland and cropland in western Kansas: Relative abundance, mortality, and body size

    USGS Publications Warehouse

    Matlack, R.S.; Gipson, P.S.; Kaufman, D.W.

    2000-01-01

    We assessed suitability of cropland and shortgrass rangeland for swift foxes (Vulpes velox) in western Kansas. Relative abundance and survival were similar for foxes in rangeland and cropland. Mortality resulting from non-traumatic causes, coyotes, and motor vehicles differed significantly between habitats. Predation by coyotes, motor vehicles, and non-traumatic causes were responsible for 45%, 36%, and 18%, respectively, of 11 deaths in rangeland and 20%, 10%, and 70%, respectively, of 10 deaths in cropland. Swift foxes in rangeland were larger and in better condition than those in cropland. Males were larger than females based on mass, standardized mass (mass/body length), body length, hindfoot length, and ear length.

  4. [Diversity and relative abundance of corals, octocorals and sponges at Jaragua National Park, Dominican Republic].

    PubMed

    Weil, Ernesto

    2006-06-01

    The Jaragua National Park is located in a remote area to the SW coast of the Dominican Republic. Fishing and mining are the major human activities. The main reef formations of the Park include: (a) long bank reefs (spur and groove) growing as bands over the platform and running in a SW-NW direction at 12-25 m depth, (b) well developed, deep, fringing reefs at the platform edge (drop-off) areas which could extend from 10 to 45 m depth, and (c) small patch reefs and poorly developed coral-octocoral-sponge-algal communities in shallow platforms near shore, rocky bottoms, and over the submerged walls of the uplifted reef. Nine reef localities were surveyed between Cabo Beata and Bahia Honda using Scuba diving to inventory the diversity and relative abundance of scleractinian corals, octocorals and sponges. Fringing reefs were surveyed starting at the bottom (30 m) and swimming in a zig-zag pattern (50 m on each side) to shallower areas. Bank reefs were surveyed by swimming in zig-zag across the spur-groove formation along 500 m. Sponges were the most diverse group with 83 species in 50 genera followed by the scleractinian corals with 56 species in 26 genera and the octocorals with 47 species in 15 genera. New records included eight coral species, 29 octocoral species and 59 sponges. The diversity, species composition and abundance of particular groups varied across the different localities. Northern reefs within the park and the Los Frailes Island offshore had the highest live cover, relative abundance and diversity for the three groups. In general, the Jaragua National Park had the highest diversity of corals, octocorals and sponges reported for the Dominican Republic and rank amongst the highest reported for the northern Caribbean. It is recommended that the area be protected and that fishing activities be regulated or eliminated altogether.

  5. The Relative Abundance of Isolated Clusters as a Probe of Dark Energy

    NASA Astrophysics Data System (ADS)

    Lee, Jounghun

    2012-06-01

    Those galaxy clusters that do not belong to superclusters are referred to as isolated clusters. Their relative abundance at a given epoch may be a powerful constraint of the dark energy equation of state since it depends strongly on how fast the structures grow on the largest scale in the universe. We note that the mass function of isolated clusters can be separately evaluated through modification of the recently developed Corasaniti-Achitouv (CA) theory according to which the stochastic collapse barrier is quantified by two coefficients: the drifting average coefficient (β) and the diffusion coefficient (DB ). Regarding β in the CA formalism as an adjustable parameter and assuming that the formation of isolated clusters corresponds to the case of DB = 0, we determine the mass function of isolated clusters by fitting the numerical results from the MICE simulations to the modified CA formula. It is found that the best-fit value of β changes with redshift and that the CA mass function with DB = 0 agrees very well with the numerical results at various redshifts. Defining the relative abundance of isolated clusters, ξ I , as the ratio of the cumulative mass function of isolated clusters to that of non-isolated clusters at a given epoch, we finally show how sensitively ξ I changes with the dark energy equation of state. It is also discussed how ξ I can help break the degeneracy between the dark energy equation of state and the other key cosmological parameters.

  6. How should detection probability be incorporated into estimates of relative abundance?

    USGS Publications Warehouse

    MacKenzie, D.I.; Kendall, W.L.

    2002-01-01

    Determination of the relative abundance of two populations, separated by time or space, is of interest in many ecological situations. We focus on two estimators of relative abundance, which assume that the probability that an individual is detected at least once in the survey is either equal or unequal for the two populations. We present three methods for incorporating the collected information into our inference. The first method, proposed previously, is a traditional hypothesis test for evidence that detection probabilities are unequal. However, we feel that, a priori, it is more likely that detection probabilities are actually different; hence, the burden of proof should be shifted, requiring evidence that detection probabilities are practically equivalent. The second method we present, equivalence testing, is one approach to doing so. Third, we suggest that model averaging could be used by combining the two estimators according to derived model weights. These differing approaches are applied to a mark-recapture experiment on Nuttail's cottontail rabbit (Sylvilagus nuttallii) conducted in central Oregon during 1974 and 1975, which has been previously analyzed by other authors.

  7. Mantle rare gas relative abundances in a steady-state mass transport model

    NASA Technical Reports Server (NTRS)

    Porcelli, D.; Wasserburg, G. J.

    1994-01-01

    A model for He and Xe was presented previously which incorporates mass transfer of rare gases from an undegassed lower mantle (P) and the atmosphere into a degassed upper mantle (D). We extend the model to include Ne and Ar. Model constraints on rare gas relative abundances within P are derived. Discussions of terrestrial volatile acquisition have focused on the rare gas abundance pattern of the atmosphere relative to meteoritic components, and the pattern of rare gases still trapped in the Ear,th is important in identifying volatile capture and loss processes operating during Earth formation. The assumptions and principles of the model are discussed in Wasserburg and Porcelli (this volume). For P, the concentrations in P of the decay/nuclear products 4 He, 21 Ne, 40 Ar, and 136 Xe can be calculated from the concentrations of the parent elements U, Th, K, and Pu. The total concentration of the daughter element in P is proportional to the isotopic shifts in P. For Ar, ((40)Ar/(36)Ar)p - ((40)Ar/(36)Ar)o =Delta (exp 40) p= 40 Cp/(exp 36)C where(i)C(sub j) the concentration of isotope i in j. In D, isotope compositions are the result of mixing rare gases from P, decay/nuclear products generated in the upper mantle, and subducted rare gases (for Ar and Xe).

  8. Relationship between air temperature and diacid relative abundances in lower troposphere aerosols

    NASA Astrophysics Data System (ADS)

    Sempere, R.; Kawamura, K.; Poggiale, J.

    2013-12-01

    Aerosol samples were collected in western Pacific, Arctic, as well as in urban area in Europe and Japan at differents seasons covering a large range of temperature. They were analyzed for total carbon (TC), water-soluble organic carbon (WSOC) along with the molecular distributions of C2-C10 a, w-dicarboxylic acids, and related polar compounds, mainly, w-oxocarboxylic acids (C2-C9) and a-dicarbonyls (C2-C3). Oxalic acid (C2) was usually the most abundant followed by malonic (C3) and succinic (C4) acids. We observed that relative abundance of oxalic acid (C2) and succinic acid (C4)/ total diacids were correlated with air temperature. These findings suggest that the intensity of photochemical oxidation reactions and thus the variation in sunlight intensity characterized here by air temperature, significantly control the molecular distribution of water-soluble organic compounds during the long-range transport of anthropogenic and/or biogenic higher molecular weight organic compounds.

  9. Relative elemental abundance and heating constraints determined for the solar corona from SERTS measurements

    NASA Technical Reports Server (NTRS)

    Falconer, David A.

    1994-01-01

    Intensities of EUV spectral lines were measured as a function of radius off the solar limb by two flights of Goddard's Solar EUV Rocket Telescope and Spectrograph (SERTS) for three quiet sun regions. The density scale height, line-ratio densities, line-ratio temperatures, and emission measures were determined. The line-ratio temperature determined from the ionization balances of Arnaud and Rothenflug (1985) were more self-consistent than the line-ratio temperatures obtained from the values of Arnaud and Raymond (1992). Limits on the filling factor were determined from the emission measure and the line-ratio densities for all three regions. The relative abundances of silicon, aluminum, and chromium to iron were determined. Results did agree with standard coronal relative elemental abundances for one observation, but did not agree for another. Aluminum was overabundant while silicon was underabundant. Heating was required above 1.15 solar radii for all three regions studied. For two regions, local nonconductive heating is needed for any filling factor, and in all three regions for filling factor of 0.1.

  10. Mapping of replication initiation sites in human ribosomal DNA by nascent-strand abundance analysis.

    PubMed Central

    Yoon, Y; Sanchez, J A; Brun, C; Huberman, J A

    1995-01-01

    New techniques for mapping mammalian DNA replication origins are needed. We have modified the existing nascent-strand size analysis technique (L. Vassilev and E.M. Johnson, Nucleic Acids Res. 17:7693-7705, 1989) to provide an independent means of studying replication initiation sites. We call the new method nascent-strand abundance analysis. We confirmed the validity of this method with replicating simian virus 40 DNA as a model. We then applied nascent-strand abundance and nascent-strand size analyses to mapping of initiation sites in human (HeLa) ribosomal DNA (rDNA), a region previously examined exclusively by two-dimensional gel electrophoresis methods (R.D. Little, T.H.K. Platt, and C.L. Schildkraut, Mol. Cell. Biol. 13:6600-6613, 1993). Our results partly confirm those obtained by two-dimensional gel electrophoresis techniques. Both studies suggest that replication initiates at relatively high frequency a few kilobase pairs upstream of the transcribed region and that many additional low-frequency initiation sites are distributed through most of the remainder of the ribosomal DNA repeat unit. PMID:7739533

  11. Analysis of Carbohydrate and Fatty Acid Marker Abundance in Ricin Toxin Preparations for Forensic Information

    SciTech Connect

    Colburn, Heather A.; Wunschel, David S.; Kreuzer-Martin, Helen W.; Moran, James J.; Antolick, Kathryn C.; Melville, Angela M.

    2010-07-15

    One challenge in the forensic analysis of ricin samples is determining the method and extent of sample preparation. Ricin purification from the source castor seeds is essentially a protein purification through removal of the non-protein fractions of the seed. Two major, non-protein constituents in the seed are the castor oil and carbohydrates. Ricinoleic acid is a relatively unique fatty acid in nature and is the most abundant component of castor oil, which comprises roughly half the seed weight. The carbohydrate component comprises roughly half of the remaining “mash” left after oil and hull removal. We used derivatization of carbohydrate and fatty acid markers followed by identification and quantification using gas chromatography/mass spectrometry (GC/MS) to assess compositional changes in ricin samples purified by different methods. The loss of ricinoleic acid indicated steps for oil removal had occurred. Changes to the carbohydrate content of the sample were also observed following protein precipitation. The differential loss of arabinose relative to mannose indicated removal of the major carbohydrate fraction of the seed and enrichment of the protein content. Taken together, these changes in fatty acid and carbohydrate abundance are indicative of the preparation method used for each sample.

  12. Changes in Relative Thylakoid Protein Abundance Induced by Fluctuating Light in the Diatom Thalassiosira pseudonana.

    PubMed

    Grouneva, Irina; Muth-Pawlak, Dorota; Battchikova, Natalia; Aro, Eva-Mari

    2016-05-01

    One of the hallmarks of marine diatom biology is their ability to cope with rapid changes in light availability due to mixing of the water column and the lens effect. We investigated how irradiance fluctuations influence the relative abundance of key photosynthetic proteins in the centric diatom Thalassiosira pseudonana by means of mass-spectrometry-based approaches for relative protein quantitation. Most notably, fluctuating-light conditions lead to a substantial overall up-regulation of light-harvesting complex proteins as well as several subunits of photosystems II and I. Despite an initial delay in growth under FL, there were no indications of FL-induced photosynthesis limitation, in contrast to other photosynthetic organisms. Our findings further strengthen the notion that diatoms use a qualitatively different mechanism of photosynthetic regulation in which chloroplast-mitochondria interaction has overtaken crucial regulatory processes of photosynthetic light reactions that are typical for the survival of land plants, green algae, and cyanobacteria. PMID:27025989

  13. Population dynamics of some Pakistan mosquitoes: changes in adult relative abundance over time and space.

    PubMed

    Reisen, W K; Milby, M M

    1986-02-01

    Time series and spatial changes in the relative abundance of 14 mosquito species were described from weekly or biweekly collections at nine localities in Punjab province, Pakistan, from January 1976 to June 1980. Comparisons between indoor aspirator catches and outdoor mechanical sweeper collections enabled mosquito resting habits to be classified as: (1) endophilic (Anopheles culicifacies, An. fluviatilis, An. stephensi, An. subpictus); (2) partially exophilic (An. annularis, An. pulcherrimus, An. nigerrimus, Culex bitaeniorhynchus, Cx, pseudovishnui, Cx, quinquefasciatus, Cx. tritaeniorhynchus), or exophilic (Cx. fuscocephala, Aedes caspius, Mansonia uniformis). Temporal abundance patterns were grouped by seasonality, overwintering strategies and the magnitude of fluctuation. Seasonal patterns were: (1) unimodal-spring (Cx. quinquefasciatus, Ae. capius); (2) unimodal-monsoon (An. nigerrimus, An. subpictus, Cx. bitaeniorhynchus, Cx. fuscocephala); (3) bimodal-spring dominant (An. annularis, An. culcifacies, An. stephensi), and (4) bimodal-monsoon/post-monsoon dominant (An. fluviatilis, An. pulcherrimus, Cx. pseudovishnui, Cx. tritaeniorhynchus, Ma. uniformis). Mosquito overwintering strategies included: (1) adults with slowed reproductive activity (An. annularis, An. culicifacies, An. fluviatilis, An. pulcherrimus, An. stephensi, Cx. quinquefasciatus); (2) females with interrupted reproductive activity (An. nigerrimus, Cx. fuscocephala, Cx. pseudovishnui, Cx. tritaeniorhynchus); (3) immature stages (Ae. caspius, Ma. uniformis) and (4) annual extinction and re-introduction (An. subpictus). The magnitude of seasonal change was classified by the number of standard deviations from the overall mean exhibited by the annual maxima or minima: (1) stationary, less than 1 standard deviation (An. culicifacies, An. fluviatilis, Cx. bitaeniorhynchus, Ae. caspius), (2) fluctuating moderately, one to two standard deviations (An. annularis, An. nigerrimus, An. pulcherrimus, An

  14. Bacterial pathogen gene abundance and relation to recreational water quality at seven Great Lakes beaches.

    PubMed

    Oster, Ryan J; Wijesinghe, Rasanthi U; Haack, Sheridan K; Fogarty, Lisa R; Tucker, Taaja R; Riley, Stephen C

    2014-12-16

    Quantitative assessment of bacterial pathogens, their geographic variability, and distribution in various matrices at Great Lakes beaches are limited. Quantitative PCR (qPCR) was used to test for genes from E. coli O157:H7 (eaeO157), shiga-toxin producing E. coli (stx2), Campylobacter jejuni (mapA), Shigella spp. (ipaH), and a Salmonella enterica-specific (SE) DNA sequence at seven Great Lakes beaches, in algae, water, and sediment. Overall, detection frequencies were mapA>stx2>ipaH>SE>eaeO157. Results were highly variable among beaches and matrices; some correlations with environmental conditions were observed for mapA, stx2, and ipaH detections. Beach seasonal mean mapA abundance in water was correlated with beach seasonal mean log10 E. coli concentration. At one beach, stx2 gene abundance was positively correlated with concurrent daily E. coli concentrations. Concentration distributions for stx2, ipaH, and mapA within algae, sediment, and water were statistically different (Non-Detect and Data Analysis in R). Assuming 10, 50, or 100% of gene copies represented viable and presumably infective cells, a quantitative microbial risk assessment tool developed by Michigan State University indicated a moderate probability of illness for Campylobacter jejuni at the study beaches, especially where recreational water quality criteria were exceeded. Pathogen gene quantification may be useful for beach water quality management.

  15. Statistical analysis from recent abundance determinations in HgMn stars

    NASA Astrophysics Data System (ADS)

    Ghazaryan, S.; Alecian, G.

    2016-08-01

    To better understand the hot chemically peculiar group of HgMn stars, we have considered a compilation of a large number of recently published data obtained for these stars from spectroscopy. We compare these data to the previous compilation by Smith. We confirm the main trends of the abundance peculiarities, namely the increasing overabundances with increasing atomic number of heavy elements, and their large spread from star to star. For all the measured elements, we have looked for correlations between abundances and effective temperature (Teff). In addition to the known correlation for Mn, some other elements are found to show some connection between their abundances and Teff. We have also checked if multiplicity is a determinant parameter for abundance peculiarities determined for these stars. A statistical analysis using a Kolmogorov-Smirnov test shows that the abundances anomalies in the atmosphere of HgMn stars do not present significant dependence on the multiplicity.

  16. Merkel cell carcinoma subgroups by Merkel cell polyomavirus DNA relative abundance and oncogene expression

    PubMed Central

    Bhatia, Kishor; Goedert, James J.; Modali, Rama; Preiss, Liliana; Ayers, Leona W.

    2010-01-01

    Merkel cell polyomavirus (MCPyV) was recently discovered in Merkel cell carcinoma (MCC), a clinically and pathologically heterogeneous malignancy of dermal neuroendocrine cells. To investigate this heterogeneity, we developed a tissue microarray (TMA) to characterize immunohistochemical staining of candidate tumor cell proteins and a quantitative PCR assay to detect MCPyV and measure viral loads. MCPyV was detected in 19 of 23 (74%) primary MCC tumors, but 8 of these had less than 1 viral copy per 300 cells. Viral abundance of 0.06–1.2viral copies/cell was directly related to presence of retinoblastoma gene product (pRb) and terminal deoxyribonucleotidyl transferase (TdT) by immunohistochemical staining (P≤0.003). Higher viral abundance tumors tended to be associated with less p53 expression, younger age at diagnosis, and longer survival (P≤0.08). These data suggest that MCC may arise through different oncogenic pathways, including ones independent of pRb and MCPyV. PMID:19551862

  17. Stream salamander species richness and abundance in relation to environmental factors in Shenandoah National Park, Virginia

    USGS Publications Warehouse

    Grant, E.H.C.; Jung, R.E.; Rice, K.C.

    2005-01-01

    Stream salamanders are sensitive to acid mine drainage and may be sensitive to acidification and low acid neutralizing capacity (ANC) of a watershed. Streams in Shenandoah National Park, Virginia, are subject to episodic acidification from precipitation events. We surveyed 25 m by 2 m transects located on the stream bank adjacent to the water channel in Shenandoah National Park for salamanders using a stratified random sampling design based on elevation, aspect and bedrock geology. We investigated the relationships of four species (Eurycea bislineata, Desmognathus fuscus, D. monticola and Gyrinophilus porphyriticus) to habitat and water quality variables. We did not find overwhelming evidence that stream salamanders are affected by the acid-base status of streams in Shenandoah National Park. Desmognathus fuscus and D. monticola abundance was greater both in streams that had a higher potential to neutralize acidification, and in higher elevation (>700 m) streams. Neither abundance of E. bislineata nor species richness were related to any of the habitat variables. Our sampling method preferentially detected the adult age class of the study species and did not allow us to estimate population sizes. We suggest that continued monitoring of stream salamander populations in SNP will determine the effects of stream acidification on these taxa.

  18. Relative abundance and species richness of cerambycid beetles in partial cut and uncut bottomland hardwood forests

    USGS Publications Warehouse

    Newell, P.; King, S.

    2009-01-01

    Partial cutting techniques are increasingly advocated and used to create habitat for priority wildlife. However, partial cutting may or may not benefit species dependent on deadwood; harvesting can supplement coarse woody debris in the form of logging slash, but standing dead trees may be targeted for removal. We sampled cerambycid beetles during the spring and summer of 2006 and 2007 with canopy malaise traps in 1- and 2-year-old partial cut and uncut bottomland hardwood forests of Louisiana. We captured a total of 4195 cerambycid beetles representing 65 species. Relative abundance was higher in recent partial cuts than in uncut controls and with more dead trees in a plot. Total species richness and species composition were not different between treatments. The results suggest partial cuts with logging slash left on site increase the abundance of cerambycid beetles in the first few years after partial cutting and that both partial cuts and uncut forest should be included in the bottomland hardwood forest landscape.

  19. Distribution, species composition and relative abundances of sandflies in North Waziristan Agency, Pakistan.

    PubMed

    Ali, N; Ullah, A; Wahid, S; Khisroon, M; Rasheed, S B

    2016-03-01

    This study was conducted to investigate the diversity of sandflies (Psychodidae: Phlebotominae) and the incidence of leishmaniasis in three villages of North Waziristan Agency, Pakistan. Sandflies were sampled monthly during 2012, at dusk and dawn, in selected indoor habitats including both bedrooms and animal sheds using a knock-down spray catch method. A total of 3687 sandflies were collected, including 1444 individuals in Drezanda, 1193 in Damdil and 1050 in Dattakhel. This study revealed 14 species of two genera, Phlebotomus (Phlebotomus sergenti, Phlebotomus papatasi, Phlebotomus caucasicus, Phlebotomus kazeruni, Phlebotomus alexandri and Phlebotomus salehi) and Sergentomyia (Sergentomyia dentate, Sergentomyia baghdadis, Sergentomyia babu, Sergentomyia theodori, Sergentomyia sumbarica, Sergentomyia dreyfussitur kestanica, Sergentomyia hogsoni pawlowskyi and Sergentomyia fallax afghanica) (both: Diptera: Psychodidae). Phlebotomus sergenti was the most abundant species (42.1%), followed by S. dentata (17.7%) and S. baghdadis (17.4%). The number of males collected represented about twice that of female flies, and the maximum number was collected in July, followed by August. The determination of the species composition of sandfly populations, seasonal variations, relative abundances and estimations of infection in the vector population may provide information about the dynamics of leishmaniasis transmission that is useful in planning vector control activities.

  20. Influence of culture medium composition on relative mRNA abundances in domestic cat embryos.

    PubMed

    Hribal, R; Jewgenow, K; Braun, B C; Comizzoli, P

    2013-04-01

    Different culture conditions have been used to produce domestic cat embryos. As part of the in vitro procedures, the medium composition significantly affects the quality of the embryo development also. Quality assessments based on cleavage kinetics and blastomere symmetry are useful, but embryos also can differ in their relative gene expression patterns despite similar morphological characteristics. The aim of this study was to compare cat embryos produced with two different in vitro culture systems routinely used in two different laboratories [Smithsonian Conservation Biology Institute, Washington D.C., USA (SCBI) and Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany (IZW)]. Specifically, relative mRNA expression patterns of critical genes for pre-implantation embryo development were assessed in both conditions. Embryos were produced in parallel in both culture systems by IVF using frozen-thawed ejaculated semen in the United States and fresh epididymal sperm in Germany. Success of embryo development in vitro was recorded as well as relative mRNA abundances [DNA methyltransferases 1 and 3A (DNMT1, DNMT3A), gap junction protein alpha 1 (GJA1), octamer-binding transcription factor 4 [OCT4], insulin-like growth factors 1 and 2 receptors (IGF1R, IGF2R), beta-actin (ACTB)] in pools of days 4-5 morulae by semi-quantitative RT-PCR assay. Percentages of cleaved embryos were similar (p > 0.05) between both culture systems, regardless of the location. OCT4 mRNA abundance was higher (p < 0.05) in embryos derived in the SCBI culture system compared with those from the IZW system when epididymal sperm was used for IVF. No clear correlation between the expression pattern and the culture system could be found for all other genes. It is suggested that OCT4 expression might be affected by the media composition in some conditions and can be the indicator of a better embryo quality.

  1. Ion Mobility Mass Spectrometry Direct Isotope Abundance Analysis

    SciTech Connect

    Manuel J. Manard, Stephan Weeks, Kevin Kyle

    2010-05-27

    The nuclear forensics community is currently engaged in the analysis of illicit nuclear or radioactive material for the purposes of non-proliferations and attribution. One technique commonly employed for gathering nuclear forensics information is isotope analysis. At present, the state-of-the-art methodology for obtaining isotopic distributions is thermal ionization mass spectrometry (TIMS). Although TIMS is highly accurate at determining isotope distributions, the technique requires an elementally pure sample to perform the measurement. The required radiochemical separations give rise to sample preparation times that can be in excess of one to two weeks. Clearly, the nuclear forensics community is in need of instrumentation and methods that can expedite their decision making process in the event of a radiological release or nuclear detonation. Accordingly, we are developing instrumentation that couples a high resolution IM drift cell to the front end of a MS. The IM cell provides a means of separating ions based upon their collision cross-section and mass-to-charge ratio (m/z). Two analytes with the same m/z, but with different collision cross-sections (shapes) would exit the cell at different times, essentially enabling the cell to function in a similar manner to a gas chromatography (GC) column. Thus, molecular and atomic isobaric interferences can be effectively removed from the ion beam. The mobility selected chemical species could then be introduced to a MS for high-resolution mass analysis to generate isotopic distributions of the target analytes. The outcome would be an IM/MS system capable of accurately measuring isotopic distributions while concurrently eliminating isobaric interferences and laboratory radiochemical sample preparation. The overall objective of this project is developing instrumentation and methods to produce near real-time isotope distributions with a modular mass spectrometric system that performs the required gas-phase chemistry and

  2. Relative abundance, age, growth, and fecundity of grubby Myoxocephalus aenaeus in Niantic River and Niantic Bay, Long Island Sound

    NASA Astrophysics Data System (ADS)

    Roseman, Edward F.; Tomichek, Christine A.; Maynard, Tracy; Burton, Jennifer A.

    2005-04-01

    Grubby ( Myoxocephalus aenaeus, Cottidae) is a common benthic fish of inshore waters and estuaries of eastern Long Island Sound; however, little information exists on their life history or population demographics. This study utilised a long-term data series (1976-2002) to assess grubby life history and population demographics and explores trends in the Niantic River and Niantic Bay populations. In addition, we examined the age, size, and fecundity of adult grubby in 2001-02 to determine the population characteristics in the region. Mean grubby catch per unit effort (CPUE) in Niantic Bay ranged from 0.4 per trawl in 1976 to 2.9 per trawl in 1984 while river CPUE ranged from 0.4 per trawl in 1977 to 7.6 per trawl in 1989. Catch of grubby in bottom trawls varied seasonally with highest CPUE occurring in winter. Highest entrainment of grubby larvae occurred in 2001 while the lowest entrainment observed was in 1991. Four age classes, 0+ through III+, were derived from otolith analysis (N = 51) although length frequency analysis suggested the possibility of older fish in the population. The total number of eggs in ovaries ranged from 286 to 16 451 for grubby (N = 64) between 52 mm and 155 mm TL. Results of this study indicated a decline in abundance of adult grubby over the 26-year period, possibly related to concurrent declines in eelgrass ( Zostera marina) abundance and/or increased water temperature.

  3. Relative abundance, age, growth, and fecundity of grubby Myoxocephalus aenaeus in Niantic River and Niantic Bay, Long Island Sound

    USGS Publications Warehouse

    Roseman, E.F.; Tomichek, C.A.; Maynard, T.; Burton, J.A.

    2005-01-01

    Grubby (Myoxocephalus aenaeus, Cottidae) is a common benthic fish of inshore waters and estuaries of eastern Long Island Sound; however, little information exists on their life history or population demographics. This study utilised a long-term data series (1976-2002) to assess grubby life history and population demographics and explores trends in the Niantic River and Niantic Bay populations. In addition, we examined the age, size, and fecundity of adult grubby in 2001-02 to determine the population characteristics in the region. Mean grubby catch per unit effort (CPUE) in Niantic Bay ranged from 0.4 per trawl in 1976 to 2.9 per trawl in 1984 while river CPUE ranged from 0.4 per trawl in 1977 to 7.6 per trawl in 1989. Catch of grubby in bottom trawls varied seasonally with highest CPUE occurring in winter. Highest entrainment of grubby larvae occurred in 2001 while the lowest entrainment observed was in 1991. Four age classes, 0+ through III+, were derived from otolith analysis (N = 51) although length frequency analysis suggested the possibility of older fish in the population. The total number of eggs in ovaries ranged from 286 to 16 451 for grubby (N = 64) between 52 mm and 155 mm TL. Results of this study indicated a decline in abundance of adult grubby over the 26-year period, possibly related to concurrent declines in eelgrass (Zostera marina) abundance and/or increased water temperature. ?? 2005 Elsevier B.V. All rights reserved.

  4. Relating large-scale climate variability to local species abundance: ENSO forcing and shrimp in Breton Sound, Louisiana, USA

    USGS Publications Warehouse

    Piazza, Bryan P.; LaPeyre, Megan K.; Keim, B.D.

    2010-01-01

    Climate creates environmental constraints (filters) that affect the abundance and distribution of species. In estuaries, these constraints often result from variability in water flow properties and environmental conditions (i.e. water flow, salinity, water temperature) and can have significant effects on the abundance and distribution of commercially important nekton species. We investigated links between large-scale climate variability and juvenile brown shrimp Farfantepenaeus aztecus abundance in Breton Sound estuary, Louisiana (USA). Our goals were to (1) determine if a teleconnection exists between local juvenile brown shrimp abundance and the El Niño Southern Oscillation (ENSO) and (2) relate that linkage to environmental constraints that may affect juvenile brown shrimp recruitment to, and survival in, the estuary. Our results identified a teleconnection between winter ENSO conditions and juvenile brown shrimp abundance in Breton Sound estuary the following spring. The physical connection results from the impact of ENSO on winter weather conditions in Breton Sound (air pressure, temperature, and precipitation). Juvenile brown shrimp abundance effects lagged ENSO by 3 mo: lower than average abundances of juvenile brown shrimp were caught in springs following winter El Niño events, and higher than average abundances of brown shrimp were caught in springs following La Niña winters. Salinity was the dominant ENSO-forced environmental filter for juvenile brown shrimp. Spring salinity was cumulatively forced by winter river discharge, winter wind forcing, and spring precipitation. Thus, predicting brown shrimp abundance requires incorporating climate variability into models.

  5. A landscape analysis of cougar distribution and abundance in Montana, USA.

    PubMed

    Riley, S J; Malecki, R A

    2001-09-01

    Recent growth in the distribution and abundance of cougars (Puma concolor) throughout western North America has created opportunities, challenges, and problems for wildlife managers and raises questions about what factors affect cougar populations. We present an analysis of factors thought to affect cougar distribution and abundance across the broad geographical scales on which most population management decisions are made. Our objectives were to: (1) identify and evaluate landscape parameters that can be used to predict the capability of habitats to support cougars, and (2) evaluate factors that may account for the recent expansion in cougar numbers. Habitat values based on terrain ruggedness and forested cover explained 73% of the variation in a cougar abundance index. Indices of cougar abundance also were spatially and temporally correlated with ungulate abundance. An increase in the number and total biomass of ungulate prey species is hypothesized to account for recent increases in cougars. Cougar populations in Montana are coping with land development by humans when other components of habitat and prey populations are sufficient. Our analysis provides a better understanding of what may have influenced recent growth in cougar distribution and abundance in Montana and, when combined with insights about stakeholder acceptance capacity, offers a basis for cougar management at broad scales. Long-term conservation of cougars necessitates a better understanding of ecosystem functions that affect prey distribution and abundance, more accurate estimates of cougar populations, and management abilities to integrate these components with human values.

  6. The relative abundances of Sn, Te, Xe, Ba and Ce. Ph.D. Thesis

    NASA Technical Reports Server (NTRS)

    Krombel, K. E.

    1983-01-01

    Elements with even atomic number (Z) in the interval 50 or = Z or = 58 were resolved in the cosmic radiation using the Heavy Nuclei Experiment on the HEAO-3 satellite. Their relative abundances were compared with the results expected from pure r-process material, pure s-process material, and solar system material, both with and without a modification due to possible first ionization potential effects. Such effects may be the result of the preferential acceleration, and hence enhancement in the cosmic rays, of those elements having low first ionization potentials. Measurements were found to be inconsistent with pure r-process material at the greater than 98% confidence level whether or not the first ionization potential adjustments are made.

  7. Fossil plant relative abundances indicate sudden loss of Late Triassic biodiversity in East Greenland.

    PubMed

    McElwain, Jennifer C; Wagner, Peter J; Hesselbo, Stephen P

    2009-06-19

    The pace of Late Triassic (LT) biodiversity loss is uncertain, yet it could help to decipher causal mechanisms of mass extinction. We investigated relative abundance distributions (RADs) of six LT plant assemblages from the Kap Stewart Group, East Greenland, to determine the pace of collapse of LT primary productivity. RADs displayed not simply decreases in the number of taxa, but decreases in the number of common taxa. Likelihood tests rejected a hypothesis of continuously declining diversity. Instead, the RAD shift occurred over the upper two-to-four fossil plant assemblages and most likely over the last three (final 13 meters), coinciding with increased atmospheric carbon dioxide concentration and global warming. Thus, although the LT event did not induce mass extinction of plant families, it accompanied major and abrupt change in their ecology and diversity.

  8. Two classes of intrahepatic cholangiocarcinoma defined by relative abundance of mutations and copy number alterations

    PubMed Central

    Kim, Young-Ho; Hong, Eun-Kyung; Kong, Sun-Young; Han, Sung-Sik; Kim, Seoung-Hoon; Rhee, Je-Keun; Hwang, Soo-Kyung; Park, Sang-Jae; Kim, Tae-Min

    2016-01-01

    Intrahepatic cholangiocarcinoma (ICC) is a biliary tree-origin epithelial malignancy in liver with unfavorable clinical outcomes. Systematic genome analyses may advance our understanding of ICC pathogenesis also improving current diagnostic and therapeutic modalities. In this study, we analyzed 17 ICC tumor-vs-matched normal pairs using either whole-exome (n = 7), transcriptome sequencing (n = 7) or both platforms (n = 3). For somatic mutations, we identified recurrent mutations of previously reported genes such as KRAS, TP53, APC as well as epigenetic regulators and those of TGFβ signaling pathway. According to the abundance of somatic mutations and DNA copy number alterations (CNA), ten ICC exome cases were distinguished into two classes as those primarily driven by either somatic mutations (M class) or CNAs (C class). Compared to M class ICCs (92–147 somatic mutations; n = 5) with a relative deficit of CNAs, C class ICCs (54–84 mutations; n = 5) harbor recurrent focal CNAs including deletions involving CDKN2A, ROBO1, ROBO2, RUNX3, and SMAD4. We also show that transcriptome sequencing can be used for expression-based ICC categorization but the somatic mutation calling from the transcriptome can be heavily influenced by the gene expression level and potentially, by posttranscriptional modification such as nonsense mediated decay. Along with a substantial level of mutational heterogeneity of ICC genomes, our study reveals previously unrecognized two ICC classes defined by relative abundance of somatic mutations over CNAs or vice versa, which should be considered in the selection of genotyping platforms and sensitive screening of targets for ICC therapeutics. PMID:27009864

  9. Two classes of intrahepatic cholangiocarcinoma defined by relative abundance of mutations and copy number alterations.

    PubMed

    Kim, Young-Ho; Hong, Eun-Kyung; Kong, Sun-Young; Han, Sung-Sik; Kim, Seoung-Hoon; Rhee, Je-Keun; Hwang, Soo-Kyung; Park, Sang-Jae; Kim, Tae-Min

    2016-04-26

    Intrahepatic cholangiocarcinoma (ICC) is a biliary tree-origin epithelial malignancy in liver with unfavorable clinical outcomes. Systematic genome analyses may advance our understanding of ICC pathogenesis also improving current diagnostic and therapeutic modalities. In this study, we analyzed 17 ICC tumor-vs-matched normal pairs using either whole-exome (n = 7), transcriptome sequencing (n = 7) or both platforms (n = 3). For somatic mutations, we identified recurrent mutations of previously reported genes such as KRAS, TP53, APC as well as epigenetic regulators and those of TGFβ signaling pathway. According to the abundance of somatic mutations and DNA copy number alterations (CNA), ten ICC exome cases were distinguished into two classes as those primarily driven by either somatic mutations (M class) or CNAs (C class). Compared to M class ICCs (92-147 somatic mutations; n = 5) with a relative deficit of CNAs, C class ICCs (54-84 mutations; n = 5) harbor recurrent focal CNAs including deletions involving CDKN2A, ROBO1, ROBO2, RUNX3, and SMAD4. We also show that transcriptome sequencing can be used for expression-based ICC categorization but the somatic mutation calling from the transcriptome can be heavily influenced by the gene expression level and potentially, by posttranscriptional modification such as nonsense mediated decay. Along with a substantial level of mutational heterogeneity of ICC genomes, our study reveals previously unrecognized two ICC classes defined by relative abundance of somatic mutations over CNAs or vice versa, which should be considered in the selection of genotyping platforms and sensitive screening of targets for ICC therapeutics.

  10. Predicted CALET measurements of ultra-heavy cosmic ray relative abundances

    NASA Astrophysics Data System (ADS)

    Rauch, B. F.

    2014-05-01

    The CALorimetric Electron Telescope (CALET) is an imaging calorimeter under construction for launch to the ISS in 2014 for a planned 5 year mission. CALET consists of a charge detection module (CHD) with two segmented planes of 1 cm thick plastic scintillator, an imaging calorimeter (IMC) with a total of 3 radiation lengths (X∘) of tungsten plates read out with 8 planes of interleaved scintillating fibers, and a total absorption calorimeter (TASC) with 27 X∘ of lead tungstate (PWO) logs. The primary objectives of the instrument are to measure electron energy spectra from 1 GeV to 20 TeV, to detect gamma-rays above 10 GeV, and to measure the energy spectra of nuclei from protons through iron up to 1,000 TeV. In this paper we describe how the geomagnetic field at the 51.6° inclination orbit of the ISS can be used to allow CALET to measure the rare ultra-heavy (UH) cosmic ray (CR) abundances, which provide important clues for the CR source and acceleration mechanism. The CHD scintillator response is relatively insensitive to energy above minimum ionization, and the angle-dependent rigidity as a function of geomagnetic latitude can be exploited to discriminate particles above this energy threshold. Such events require corrections for trajectory in instrument that can be made with only the top 4 layers of the IMC, which allows for considerably greater geometric acceptance than for events that require passage through the TASC for energy determination. Using this approach CALET will be able to measure UH CR relative abundances over its expected mission with superior statistics to previous space instruments.

  11. Two classes of intrahepatic cholangiocarcinoma defined by relative abundance of mutations and copy number alterations.

    PubMed

    Kim, Young-Ho; Hong, Eun-Kyung; Kong, Sun-Young; Han, Sung-Sik; Kim, Seoung-Hoon; Rhee, Je-Keun; Hwang, Soo-Kyung; Park, Sang-Jae; Kim, Tae-Min

    2016-04-26

    Intrahepatic cholangiocarcinoma (ICC) is a biliary tree-origin epithelial malignancy in liver with unfavorable clinical outcomes. Systematic genome analyses may advance our understanding of ICC pathogenesis also improving current diagnostic and therapeutic modalities. In this study, we analyzed 17 ICC tumor-vs-matched normal pairs using either whole-exome (n = 7), transcriptome sequencing (n = 7) or both platforms (n = 3). For somatic mutations, we identified recurrent mutations of previously reported genes such as KRAS, TP53, APC as well as epigenetic regulators and those of TGFβ signaling pathway. According to the abundance of somatic mutations and DNA copy number alterations (CNA), ten ICC exome cases were distinguished into two classes as those primarily driven by either somatic mutations (M class) or CNAs (C class). Compared to M class ICCs (92-147 somatic mutations; n = 5) with a relative deficit of CNAs, C class ICCs (54-84 mutations; n = 5) harbor recurrent focal CNAs including deletions involving CDKN2A, ROBO1, ROBO2, RUNX3, and SMAD4. We also show that transcriptome sequencing can be used for expression-based ICC categorization but the somatic mutation calling from the transcriptome can be heavily influenced by the gene expression level and potentially, by posttranscriptional modification such as nonsense mediated decay. Along with a substantial level of mutational heterogeneity of ICC genomes, our study reveals previously unrecognized two ICC classes defined by relative abundance of somatic mutations over CNAs or vice versa, which should be considered in the selection of genotyping platforms and sensitive screening of targets for ICC therapeutics. PMID:27009864

  12. Elemental and Molecular Relative Abundances in the Ejecta of Eta Carinae

    NASA Technical Reports Server (NTRS)

    Kober, G. V.; Gull, T. R.; Nielsen, K.; Bruhweiler, F.; Verner, K.; Stahl, O.; Weis, K.; Bomans, D.

    2006-01-01

    We are measuring relative elemental abundances for the ejecta in the line of sight from Eta Carinae using high dispersion spectroscopy with the HST/STIS and the VLT/UVES. While multiple velocity components have been identified, we focus on the -513 and -146 km/s components originating from the Homunculus and the Little Homunculus. Complicating factors are the complex nebular structures in the immediate vicinity of the bright, massive star: the very bright emission structures, Weigelt blobs B, C and D, the broad, clumpy structures of the extended wind apparently not photoionized by Eta Car B, and general scattered starlight from the extended wind and the dusty core of the circumstellar material. We have used the 3050 to 3160A region of overlap between STIS and UVES to intercompare equivalent widths of absorption lines to estimate the 'contributing factor', namely the amount of light originating from the star compared to nebular structures. While the extracted STIS spectra are from 0.1" wide aperture, the UVES spectra are limited by the 1" seeing conditions. Curiously we find that the scattering contribution in the UVES spectra changes with time, apparently with orbital phase of the 5.54-year period. This indicates that the dust may be modified by changes in the central source with phase. The noticeable drop in scattered light appears to occur about 1.7 years (phase 0.35) after the spectroscopic minimum. Relative abundances of iron peak elements and some molecules will be estimated. Observations in this study were accomplished with HST through STSci and with VLT through ESO and funded under STIS GTO resources.

  13. Abundance of Woody Riparian Species in the Western USA in Relation to Phenology, Climate, and Flow Regime

    NASA Astrophysics Data System (ADS)

    Auble, G. T.; Friedman, J. M.; Scott, M. L.; Shafroth, P. B.; Merigliano, M. M.; Freehling, M. D.; Evans, R. E.; Griffin, E. R.

    2004-12-01

    We randomly selected 475 long-term U.S. Geological Survey stream gaging stations in 17 western states to relate the presence and abundance of woody species to environmental factors. Along a 1.3-km reach near each station we measured the cover of all species on a list of the 44 most abundant large woody riparian species in the region. We used logistic regression to fit the response of four abundant species to growing degree days and mean precipitation. Then we related relative abundance of these 4 species to timing of the flood peak in sites where the likelihood of occurrence was greater than 0.5. The exotics Tamarix ramosissima (saltcedar) and Elaeagnus angustifolia (Russian-olive) are now the third and fourth most frequently occurring large woody riparian species in the western U.S. and the second and fifth most abundant. In climatically suitable areas, species differences in reproductive phenology produce different relations of abundance to flow regime. Because of its limited period of seed release and viability in early summer, cottonwood (Populus deltoides) is disadvantaged where floods occur in the spring or fall. Abundances of saltcedar, because of its long period of seed release; Russian-olive, because of seed dormancy; and Salix exigua, because of the importance of vegetative spread, are much less sensitive to flood timing.

  14. ANALYSIS OF RICIN TOXIN PREPARATIONS FOR CARBOHYDRATE AND FATTY ACID ABUNDANCE AND ISOTOPE RATIO INFORMATION

    SciTech Connect

    Wunschel, David S.; Kreuzer-Martin, Helen W.; Antolick, Kathryn C.; Colburn, Heather A.; Moran, James J.; Melville, Angela M.

    2009-12-01

    This report describes method development and preliminary evaluation for analyzing castor samples for signatures of purifying ricin. Ricin purification from the source castor seeds is essentially a problem of protein purification using common biochemical methods. Indications of protein purification will likely manifest themselves as removal of the non-protein fractions of the seed. Two major, non-protein, types of biochemical constituents in the seed are the castor oil and various carbohydrates. The oil comprises roughly half the seed weight while the carbohydrate component comprises roughly half of the remaining “mash” left after oil and hull removal. Different castor oil and carbohydrate components can serve as indicators of specific toxin processing steps. Ricinoleic acid is a relatively unique fatty acid in nature and is the most abundant component of castor oil. The loss of ricinoleic acid indicates a step to remove oil from the seeds. The relative amounts of carbohydrates and carbohydrate-like compounds, including arabinose, xylose, myo-inositol fucose, rhamnose, glucosamine and mannose detected in the sample can also indicate specific processing steps. For instance, the differential loss of arabinose relative to mannose and N-acetyl glucosamine indicates enrichment for the protein fraction of the seed using protein precipitation. The methods developed in this project center on fatty acid and carbohydrate extraction from castor samples followed by derivatization to permit analysis by gas chromatography-mass spectrometry (GC-MS). Method descriptions herein include: the source and preparation of castor materials used for method evaluation, the equipment and description of procedure required for chemical derivatization, and the instrument parameters used in the analysis. Two types of derivatization methods describe analysis of carbohydrates and one procedure for analysis of fatty acids. Two types of GC-MS analysis is included in the method development, one

  15. An Abundance Analysis of R-Coronae Stars in the Galaxy and the Large Magellanic Cloud

    NASA Astrophysics Data System (ADS)

    Pollard, K. R.; Cottrell, P. L.; Lawson, W. A.

    1994-05-01

    High-resolution echelle spectra have been obtained of one galactic and two Large Magellanic Cloud (LMC) R Coronae Borealis (RCB) stars with the Anglo-Australian Telescope. An analysis of these data using He- and C- rich models and the WIDTH6 model atmosphere code of Kurucz indicates that the galactic RCB star SU Tau and the two LMC stars, HV 12842 and W Men (HV 966), have similar atmospheric parameters to the warmer galactic RCB and hydrogen-deficient carbon (HdC) stars such as R CrB and XX Cam. The newly analysed RCB stars have T_eff_ ~ 7000 K, log g = 0.5 to 1.0, microturbulent velocities between 7 and 8 km s^-1^ and C/He ratios ranging from 0.0034 to 0.011. An abundance analysis has been performed on these stars for a wide range of species. Special emphasis has been placed on H, He, Li, C, N, O, Fe and the s-process elements. Specific values for [H/He], [Li/Fe] and [Fe/total] (expressed relative to the total abundance of all species) in SU Tau, HV 12842 and W Men are -5,4, -6.2 and -6.5; +2.6, +2.4 and +2.1; and -0.4, -0.7 and -0.7 respectively. The analysis of RCB stars in the LMC provides us with the opportunity to study the metallicity dependence of RCB star evolution.

  16. The Advanced Spectral Library (ASTRAL): Abundance Analysis of the CP Star HR 465

    NASA Astrophysics Data System (ADS)

    Carpenter, Kenneth G.; Nielsen, Krister E.; Kober, Gladys V.

    2016-01-01

    We present the results of a spectrum analysis of the prototypical A-type magnetic CP star HR465. Synthetic spectra, using an non-LTE atmosphere model, were generated to fit high-resolution ultraviolet spectra (1200-3100 A) obtained as a part of the "Advanced Spectral Library (ASTRAL) Project: Hot Stars" program (GO-13346: Ayres PI). The ultraviolet data were supplemented by high resolution optical data recorded at the Nordic Optical Telescope with the SOFIN spectrograph. The optical data was used as a complement to the high line density ultraviolet spectrum and primarily used to derive accurate iron-group element abundances.HR 465 has previously been analyzed using IUE spectra. We revisit the object with this high quality data. Large parts of the spectrum have been synthesized with an ATLAS model (Teff=10750K, logg=4.0) and we present abundance results for more than 50 elements. We can confirm some of the abundance characteristics previously derived from IUE data, where elements heavier than Z=30 show significant abundance enhancements compared to solar values, while some of the lighter elements show abundance deficiencies. We will place these results in context of other AP stars, and the large number of element abundances will also help us to put some constraint on stellar abundance and evolution theories.

  17. Hierarchical spatial models for predicting pygmy rabbit distribution and relative abundance

    USGS Publications Warehouse

    Wilson, T.L.; Odei, J.B.; Hooten, M.B.; Edwards, T.C.

    2010-01-01

    Conservationists routinely use species distribution models to plan conservation, restoration and development actions, while ecologists use them to infer process from pattern. These models tend to work well for common or easily observable species, but are of limited utility for rare and cryptic species. This may be because honest accounting of known observation bias and spatial autocorrelation are rarely included, thereby limiting statistical inference of resulting distribution maps. We specified and implemented a spatially explicit Bayesian hierarchical model for a cryptic mammal species (pygmy rabbit Brachylagus idahoensis). Our approach used two levels of indirect sign that are naturally hierarchical (burrows and faecal pellets) to build a model that allows for inference on regression coefficients as well as spatially explicit model parameters. We also produced maps of rabbit distribution (occupied burrows) and relative abundance (number of burrows expected to be occupied by pygmy rabbits). The model demonstrated statistically rigorous spatial prediction by including spatial autocorrelation and measurement uncertainty. We demonstrated flexibility of our modelling framework by depicting probabilistic distribution predictions using different assumptions of pygmy rabbit habitat requirements. Spatial representations of the variance of posterior predictive distributions were obtained to evaluate heterogeneity in model fit across the spatial domain. Leave-one-out cross-validation was conducted to evaluate the overall model fit. Synthesis and applications. Our method draws on the strengths of previous work, thereby bridging and extending two active areas of ecological research: species distribution models and multi-state occupancy modelling. Our framework can be extended to encompass both larger extents and other species for which direct estimation of abundance is difficult. ?? 2010 The Authors. Journal compilation ?? 2010 British Ecological Society.

  18. Bee Abundance and Nutritional Status in Relation to Grassland Management Practices in an Agricultural Landscape.

    PubMed

    Smith, Griffin W; Debinski, Diane M; Scavo, Nicole A; Lange, Corey J; Delaney, John T; Moranz, Raymond A; Miller, James R; Engle, David M; Toth, Amy L

    2016-04-01

    Grasslands provide important resources for pollinators in agricultural landscapes. Managing grasslands with fire and grazing has the potential to benefit plant and pollinator communities, though there is uncertainty about the ideal approach. We examined the relationships among burning and grazing regimes, plant communities, and Bombus species and Apis mellifera L. abundance and nutritional indicators at the Grand River Grasslands in southern Iowa and northern Missouri. Treatment regimes included burn-only, grazed-and-burned, and patch-burn graze (pastures subdivided into three temporally distinct fire patches with free access by cattle). The premise of the experimental design was that patch-burn grazing would increase habitat heterogeneity, thereby providing more diverse and abundant floral resources for pollinators. We predicted that both bee abundance and individual bee nutritional indicators (bee size and lipid content) would be positively correlated with floral resource abundance. There were no significant differences among treatments with respect to bee abundance. However, some of the specific characteristics of the plant community showed significant relationships with bee response variables. Pastures with greater abundance of floral resources had greater bee abundance but lower bee nutritional indicators. Bee nutritional variables were positively correlated with vegetation height, but, in some cases, negatively correlated with stocking rate. These results suggest grassland site characteristics such as floral resource abundance and stocking rate are of potential importance to bee pollinators and suggest avenues for further research to untangle the complex interactions between grassland management, plant responses, and bee health.

  19. Relative importance of phosphorus, fish biomass, and watershed land use as drivers of phytoplankton abundance in shallow lakes.

    PubMed

    Gorman, Matt W; Zimmer, Kyle D; Herwig, Brian R; Hanson, Mark A; Wright, Robert G; Vaughn, Sean R; Younk, Jerry A

    2014-01-01

    Phytoplankton abundance in shallow lakes is potentially influenced by ambient phosphorus concentrations, nutrient loading accentuated by human activities in lake watersheds, and abundance of planktivorous and benthivorous fish. However, few studies have simultaneously assessed the relative importance of these factors influencing phytoplankton abundance over large spatial scales. We assessed relative influences of watershed characteristics, total phosphorus concentrations, and fish biomass on phytoplankton abundance in 70 shallow lakes in western Minnesota (USA) during summer 2005 and 2006. Our independent variables included total phosphorus (TP), benthivore biomass, planktivore biomass, summed planktivore and benthivore biomass (summed fish), areal extent of agriculture in the watershed, region (prairie versus parkland lakes), and year. Predictive models containing from one to three independent variables were compared using an information theoretic approach. The most parsimonious model consisted of TP and summed fish, and had over 10,000-fold greater support compared to models using just TP or summed fish, or models comprised of other variables. We also found no evidence that relative importance of predictor variables differed between regions or years, and parameter estimates of TP and summed fish were temporally and spatially consistent. TP and summed fish were only weakly correlated, and the model using both variables was a large improvement over using either variable alone. This indicates these two variables can independently increase phytoplankton abundance, which emphasizes the importance of managing both nutrients and fish when trying to control phytoplankton abundance in shallow lakes.

  20. STUDIES ON THE SPECIES COMPOSITION AND RELATIVE ABUNDANCE OF MOSQUITOES OF MPIGI DISTRICT, CENTRAL UGANDA

    PubMed Central

    Mayanja, Martin; Mutebi, John-Paul; Crabtree, Mary B.; Ssenfuka, Fred; Muwawu, Teddy; Lutwama, Julius J.

    2015-01-01

    Prediction of arboviral disease outbreaks and planning for appropriate control interventions require knowledge of the mosquito vectors involved. Although mosquito surveys have been conducted in different regions of Uganda since the mid 30’s such studies have not been carried out in Mpigi District. In October 2011, we conducted mosquito collections in Mpigi district to determine species composition and relative abundance of the different species. The survey was conducted in four villages, Njeru, Ddela, Kiwumu and Nsumbain Kammengo sub-county, Mpigi district, Uganda. CDC light traps baited with dry ice (carbon dioxide) were used to capture adult mosquitoes. A total of 54,878 mosquitoes comprising 46 species from eight genera were collected. The dominant species at all sites was Coquilletidia (Coquilletidia) fuscopennata Theobald (n=38,059, 69%), followed by Coquillettidia (Coquillettidia) metallica Theobald (n=4,265, 7.8%). The number of species collected varied from 17 in the genus Culex to 1 in the genus Lutzia. Of the 46 species identified, arboviruses had previously been isolated from 28 (60.9%) suggesting a high potential for arboviral transmission and/or maintenance in Mpigi District. PMID:26346305

  1. The relative abundance of hemocyte types in a polyphagous moth larva depends on diet.

    PubMed

    Vogelweith, Fanny; Moret, Yannick; Monceau, Karine; Thiéry, Denis; Moreau, Jérôme

    2016-05-01

    Hemocytes are crucial cells of the insect immune system because of their involvement in multiple immune responses including coagulation, phagocytosis and encapsulation. There are various types of hemocytes, each having a particular role in immunity, such that variation in their relative abundance affects the outcome of the immune response. This study aims to characterize these various types of hemocytes in larvae of the grapevine pest insect Eupoecilia ambiguella, and to assess variation in their concentration as a function of larval diet and immune challenge. Four types of hemocytes were found in the hemolymph of 5th instar larvae: granulocytes, oenocytoids, plasmatocytes and spherulocytes. We found that the total concentration of hemocytes and the concentration of each hemocyte type varied among diets and in response to the immune challenge. Irrespective of the diet, the concentration of granulocytes increased following a bacterial immune challenge, while the concentration of plasmatocytes and spherulocytes differentially varied between larval diets. The concentration of oenocytoids did not vary among diets before the immune challenge but varied between larval diets in response to the challenge. These results suggest that the resistance of insect larvae to different natural enemies critically depends on the effect of larval diet on the larvae's investment into the different types of hemocytes.

  2. Intake of Meat Proteins Substantially Increased the Relative Abundance of Genus Lactobacillus in Rat Feces

    PubMed Central

    Zhu, Yingying; Lin, Xisha; Li, He; Li, Yingqiu; Shi, Xuebin; Zhao, Fan; Xu, Xinglian; Li, Chunbao; Zhou, Guanghong

    2016-01-01

    Diet has been shown to have a critical influence on gut bacteria and host health, and high levels of red meat in diet have been shown to increase colonic DNA damage and thus be harmful to gut health. However, previous studies focused more on the effects of meat than of meat proteins. In order to investigate whether intake of meat proteins affects the composition and metabolic activities of gut microbiota, feces were collected from growing rats that were fed with either meat proteins (from beef, pork or fish) or non-meat proteins (casein or soy) for 14 days. The resulting composition of gut microbiota was profiled by sequencing the V4-V5 region of the 16S ribosomal RNA genes and the short chain fatty acids (SCFAs) were analyzed using gas chromatography. The composition of gut microbiota and SCFA levels were significantly different between the five diet groups. At a recommended dose of 20% protein in the diet, meat protein-fed rats had a higher relative abundance of the beneficial genus Lactobacillus, but lower levels of SCFAs and SCFA-producing bacteria including Fusobacterium, Bacteroides and Prevotella, compared with the soy protein-fed group. Further work is needed on the regulatory pathways linking dietary protein intake to gut microbiota. PMID:27042829

  3. Intake of Meat Proteins Substantially Increased the Relative Abundance of Genus Lactobacillus in Rat Feces.

    PubMed

    Zhu, Yingying; Lin, Xisha; Li, He; Li, Yingqiu; Shi, Xuebin; Zhao, Fan; Xu, Xinglian; Li, Chunbao; Zhou, Guanghong

    2016-01-01

    Diet has been shown to have a critical influence on gut bacteria and host health, and high levels of red meat in diet have been shown to increase colonic DNA damage and thus be harmful to gut health. However, previous studies focused more on the effects of meat than of meat proteins. In order to investigate whether intake of meat proteins affects the composition and metabolic activities of gut microbiota, feces were collected from growing rats that were fed with either meat proteins (from beef, pork or fish) or non-meat proteins (casein or soy) for 14 days. The resulting composition of gut microbiota was profiled by sequencing the V4-V5 region of the 16S ribosomal RNA genes and the short chain fatty acids (SCFAs) were analyzed using gas chromatography. The composition of gut microbiota and SCFA levels were significantly different between the five diet groups. At a recommended dose of 20% protein in the diet, meat protein-fed rats had a higher relative abundance of the beneficial genus Lactobacillus, but lower levels of SCFAs and SCFA-producing bacteria including Fusobacterium, Bacteroides and Prevotella, compared with the soy protein-fed group. Further work is needed on the regulatory pathways linking dietary protein intake to gut microbiota. PMID:27042829

  4. Relative abundance and flight phenology of two pheromone types of Acrobasis nuxvorella (Lepidoptera: Pyralidae).

    PubMed

    Hartfield, E A; Harris, M K; Medina, R F

    2011-08-01

    Two synthetic sex pheromones have been developed and are currently used to detect the flight of the pecan nut casebearer, Acrobasis nuxvorella Neunzig, the most damaging pest of pecan [Carya illinoinensis (Wangenh.) K. Koch]. One pheromone (referred to as standard) is attractive to moths in the southern United States, but not in Mexico. The other pheromone (referred to as Mexican) is attractive to moths in the southern United States and in Mexico. These two pheromones have been implemented by producers as an important tool in monitoring the activity of this pest and have allowed for more efficient pesticide use. In the future, these pheromones could be used as a means of population reduction through pheromone based control methods. Trapping data taken over a 3-yr period were used to determine if phenological differences exist between pheromone types of pecan nut casebearer. The relative abundance of each pheromone type at several locations in the United States also was evaluated. Results of this study indicate that no phenological differences exist between the two pheromone types studied in the United States and that significantly more males are attracted to field-deployed pheromone traps baited with the standard pheromone than to traps baited with the Mexican pheromone. PMID:22251690

  5. Intake of Meat Proteins Substantially Increased the Relative Abundance of Genus Lactobacillus in Rat Feces.

    PubMed

    Zhu, Yingying; Lin, Xisha; Li, He; Li, Yingqiu; Shi, Xuebin; Zhao, Fan; Xu, Xinglian; Li, Chunbao; Zhou, Guanghong

    2016-01-01

    Diet has been shown to have a critical influence on gut bacteria and host health, and high levels of red meat in diet have been shown to increase colonic DNA damage and thus be harmful to gut health. However, previous studies focused more on the effects of meat than of meat proteins. In order to investigate whether intake of meat proteins affects the composition and metabolic activities of gut microbiota, feces were collected from growing rats that were fed with either meat proteins (from beef, pork or fish) or non-meat proteins (casein or soy) for 14 days. The resulting composition of gut microbiota was profiled by sequencing the V4-V5 region of the 16S ribosomal RNA genes and the short chain fatty acids (SCFAs) were analyzed using gas chromatography. The composition of gut microbiota and SCFA levels were significantly different between the five diet groups. At a recommended dose of 20% protein in the diet, meat protein-fed rats had a higher relative abundance of the beneficial genus Lactobacillus, but lower levels of SCFAs and SCFA-producing bacteria including Fusobacterium, Bacteroides and Prevotella, compared with the soy protein-fed group. Further work is needed on the regulatory pathways linking dietary protein intake to gut microbiota.

  6. Ontogenetic changes in heterogeneity of parasite communities of fish: disentangling the relative role of compositional versus abundance variability.

    PubMed

    Timi, J T; Lanfranchi, A L

    2013-03-01

    In order to determine how much of the variability in parasite assemblages is driven by differences in composition or in abundance we used multivariate dispersions (average distance from infracommunities to their size class centroid in the multivariate space) as a measurement of β-diversity in infracommunities of Conger orbignianus, applying a set of dissimilarity measures with different degrees of emphasis on composition versus relative abundance information. To evaluate comparatively the rate of such changes, we also analysed the effect of host size by regressing differences in β-diversity among size classes against differences in mean fish size. Multivariate dispersions varied along an ontogenetic gradient, its significance depending on the measurement used. Larger fish showed higher richness and abundance; however, smaller fish displayed lower variations in abundance but higher in composition. This could be caused by stochastic encounters at low densities due to the overdispersion of parasites in previous hosts. As fish grow, the composition of their parasite assemblages becomes homogenized by repeated exposure, with abundance thus arising as the main source of variability. Both variables act at different rates, with the exponential decay in the compositional variability as differences in fish size increase being about twice as steep as the decay in abundance variability, indicating that compositional homogeneity is reached faster than abundance heterogeneity as fish grow. Discerning between both variables is crucial in order to understand how community structure is formed by size-dependent variability of host populations.

  7. NOTE: On the Deuterium Abundance on Mars and Some Related Problems

    NASA Astrophysics Data System (ADS)

    Krasnopolsky, Vladimir

    2000-12-01

    Strong fractionation of deuterium in photolysis of H 2O and above the hygropause reduces the production of HD relative to H 2 on Mars by a factor of 3.7 total. The model by Y. L. Yung et al. (1988, Icarus76, 146-159) for deuterium fractionation in chemical reactions on Mars corrected for this factor results in (HD/H 2)/(HDO/H 2O)=0.43. This value may fit the deuterium abundance observed by V. A. Krasnopolsky et al. (1998, Science 280, 1576-1580) if the eddy diffusion coefficient does not depend on solar activity: K=1.4×10 13n-1/2 cm 2 s -1 (model 2). The Mariner 9 observations show very low variability of atomic oxygen at the 1.2 n bar pressure level (h˜125 km) with solar activity. This requires eddy diffusion to be proportional to the solar activity index F10.7: K=( F10.7 cm/30)×10 13n-1/2 cm 2 s -1 (model 1). The fractionation factor for escape of hydrogen isotopes is equal to 0.016 and 0.135 for models 1 and 2. These values have been averaged over the solar cycle. The three-reservoir model for hydrogen isotope fractionation suggested by Krasnopolsky et al. (1998) involves a reservoir composed primarily of water ice in the polar caps that isotopically interacts with the atmosphere. Assuming that water ice is half of the total volume of the polar caps and the polar-layered deposits, the total loss of water from Mars is equal to 65 and 120 m for models 1 and 2, respectively. Along with thermal and nonthermal escape, these values may include the loss of water by oxidation of regolith, if the released hydrogen escaped with isotopic fractionation. Although the solar-wind α particles are the main source of He on Mars, capture of the solar-wind H + and D + ions by Mars has a negligible effect on the thermospheric abundances of H and D. Improved observations of minor components in Mars' thermosphere may resolve the problem of eddy diffusion at various solar activity and choosing between the models.

  8. Pintail and mallard survival in California relative to habitat, abundance, and hunting

    USGS Publications Warehouse

    Fleskes, J.P.; Yee, J.L.; Yarris, G.S.; Miller, M.R.; Casazza, M.L.

    2007-01-01

    The influence of habitat, waterfowl abundance, and hunting on winter survival of waterfowl is not well understood. We studied late August-March survival of 163 after-hatch-year (AHY) and 128 hatch-year (HY) female mallards (Anas platyrhynchos) radiotagged in Sacramento Valley (SACV) and 885 AHY female northern pintails (A. acuta) radiotagged throughout the Central Valley of California, USA, relative to flooded habitat (HAB), January abundance of each species (JMAL or JPIN), hunter-days (HDY), and a hunting pressure index (HPI) that combined these variables. From EARLY (1987-1994) to LATE (1998-2000), HAB increased 39%, JPIN increased 45%, JMAL increased 53%, HDY increased 21%, duck-hunting season increased from 59 days to 100 days, and the female daily bag limit doubled to 2 for mallards but remained 1 for pintails. Survival (?? SE) was greater during LATE versus EARLY for pintails radiotagged in each region (SACV: 93.2 ?? 2.1% vs. 87.6 ?? 3.0%; Suisun Marsh: 86.6 ?? 3.2% vs. 77.0 ?? 3.7%; San Joaquin Valley: 86.6 ?? 3.1% vs. 76.9 ?? 4.1%) but not for SACV mallards (AHY: 70.6 ?? 7.2% to 74.4 ?? 7.7% vs. 80.1 ?? 7.2% to 82.8 ?? 5.6%; HY: 48.7 ?? 9.1% [1999-2000 only] vs. 63.5 ?? 8.8% to 67.6 ?? 8.0%). Most pintail (72%) and mallard (91%) deaths were from hunting, and lower HPI and higher JPIN or JMAL were associated with reduced mortality. Increased HAB was associated with reduced winter mortality for pintails but not for SACV mallards. Pintail survival rates that we measured were within the range reported for other North American wintering areas, and during LATE were higher than most, even though our study duration was 68-110 days longer. Winter survival rates of SACV mallards were also within the reported range. However, with higher bag limits and longer seasons, mallard survival during LATE was lower than in most other wintering areas, especially during 1999-2000, when high winds on opening weekend resulted in high hunting mortality. Habitat conservation and

  9. Quantitative determination of mineral types and abundances from reflectance spectra using principal components analysis

    NASA Technical Reports Server (NTRS)

    Smith, M. O.; Adams, J. B.; Johnson, P. E.

    1985-01-01

    A procedure was developed for analyzing remote reflectance spectra, including multispectral images, that quantifies parameters such as types of mineral mixtures, the abundances of mixed minerals, and particle sizes. Principal components analysis reduced the spectral dimensionality and allowed testing the uniqueness and validity of spectral mixing models. By analyzing variations in the overall spectral reflectance curves, the type of spectral mixture was identified, mineral abundances quantified and the effects of particle size identified. The results demonstrate an advantage in classification accuracy over classical forms of analysis that ignore effects of particle-size or mineral-mixture systematics on spectra. The approach is applicable to remote sensing data of planetary surfaces for quantitative determinations of mineral abundances.

  10. Relation of desert pupfish abundance to selected environmental variables in natural and manmade habitats in the Salton Sea basin

    USGS Publications Warehouse

    Martin, B.A.; Saiki, M.K.

    2005-01-01

    We assessed the relation between abundance of desert pupfish, Cyprinodon macularius, and selected biological and physicochemical variables in natural and manmade habitats within the Salton Sea Basin. Field sampling in a natural tributary, Salt Creek, and three agricultural drains captured eight species including pupfish (1.1% of the total catch), the only native species encountered. According to Bray-Curtis resemblance functions, fish species assemblages differed mostly between Salt Creek and the drains (i.e., the three drains had relatively similar species assemblages). Pupfish numbers and environmental variables varied among sites and sample periods. Canonical correlation showed that pupfish abundance was positively correlated with abundance of western mosquitofish, Gambusia affinis, and negatively correlated with abundance of porthole livebearers, Poeciliopsis gracilis, tilapias (Sarotherodon mossambica and Tilapia zillii), longjaw mudsuckers, Gillichthys mirabilis, and mollies (Poecilia latipinnaandPoecilia mexicana). In addition, pupfish abundance was positively correlated with cover, pH, and salinity, and negatively correlated with sediment factor (a measure of sediment grain size) and dissolved oxygen. Pupfish abundance was generally highest in habitats where water quality extremes (especially high pH and salinity, and low dissolved oxygen) seemingly limited the occurrence of nonnative fishes. This study also documented evidence of predation by mudsuckers on pupfish. These findings support the contention of many resource managers that pupfish populations are adversely influenced by ecological interactions with nonnative fishes. ?? Springer 2005.

  11. Relating species abundance distributions to species-area curves in two Mediterranean-type shrublands

    USGS Publications Warehouse

    Keeley, J.E.

    2003-01-01

    Based on both theoretical and empirical studies there is evidence that different species abundance distributions underlie different species-area relationships. Here I show that Australian and Californian shrubland communities (at the scale from 1 to 1000 m2) exhibit different species-area relationships and different species abundance patterns. The species-area relationship in Australian heathlands best fits an exponential model and species abundance (based on both density and cover) follows a narrow log normal distribution. In contrast, the species-area relationship in Californian shrublands is best fit with the power model and, although species abundance appears to fit a log normal distribution, the distribution is much broader than in Australian heathlands. I hypothesize that the primary driver of these differences is the abundance of small-stature annual species in California and the lack of annuals in Australian heathlands. Species-area is best fit by an exponential model in Australian heathlands because the bulk of the species are common and thus the species-area curves initially rise rapidly between 1 and 100 m2. Annuals in Californian shrublands generate very broad species abundance distributions with many uncommon or rare species. The power function is a better model in these communities because richness increases slowly from 1 to 100 m2 but more rapidly between 100 and 1000 m2 due to the abundance of rare or uncommon species that are more likely to be encountered at coarser spatial scales. The implications of this study are that both the exponential and power function models are legitimate representations of species-area relationships in different plant communities. Also, structural differences in community organization, arising from different species abundance distributions, may lead to different species-area curves, and this may be tied to patterns of life form distribution.

  12. Relating species abundance distributions to species-area curves in two Mediterranean-type shrublands

    USGS Publications Warehouse

    Keeley, Jon E.

    2003-01-01

    Based on both theoretical and empirical studies there is evidence that different species abundance distributions underlie different species-area relationships. Here I show that Australian and Californian shrubland communities (at the scale from 1 to 1000 m2) exhibit different species-area relationships and different species abundance patterns. The species-area relationship in Australian heathlands best fits an exponential model and species abundance (based on both density and cover) follows a narrow log normal distribution. In contrast, the species-area relationship in Californian shrublands is best fit with the power model and, although species abundance appears to fit a log normal distribution, the distribution is much broader than in Australian heathlands. I hypothesize that the primary driver of these differences is the abundance of small-stature annual species in California and the lack of annuals in Australian heathlands. Species-area is best fit by an exponential model in Australian heathlands because the bulk of the species are common and thus the species-area curves initially rise rapidly between 1 and 100 m2. Annuals in Californian shrublands generate very broad species abundance distributions with many uncommon or rare species. The power function is a better model in these communities because richness increases slowly from 1 to 100 m2 but more rapidly between 100 and 1000 m2due to the abundance of rare or uncommon species that are more likely to be encountered at coarser spatial scales. The implications of this study are that both the exponential and power function models are legitimate representations of species-area relationships in different plant communities. Also, structural differences in community organization, arising from different species abundance distributions, may lead to different species-area curves, and this may be tied to patterns of life form distribution.

  13. Species richness and relative abundance of breeding birds in forests of the Mississippi Alluvial Valley

    USGS Publications Warehouse

    Nelms, C.O.; Twedt, D.J.; Smith, Winston Paul

    1993-01-01

    In 1992, the Vicksburg Field Research Station of the National Wetlands Research Center initiated research on the ecology of migratory birds within forests of the Mississippi Alluvial Valley (MAV). The MAV was historically a nearly contiguous bottomland hardwood forest, however, only remnants remain. These remnants are fragmented and often influenced by drainage projects, silviculture, agriculture, and urban development. Our objectives are to assess species richness and relative abundance, and to relate these to the size, quality, and composition of forest stands. Species richness and relative abundance were estimated for 53 randomly selected forest sites using 1 to 8 point counts per site, depending on the size of the forest fragment. However, statistical comparisons among sites will be restricted to an equal number ofpoint counts within the sites being compared. Point counts, lasting five minutes, were conducted from 11 May to 29 June 1992, foltowing Ralph, Sauer, and Droege (Point Count Standards; memo dated 9 March 1992). Vegetation was measured at the first three points on each site using a modification of the methods employed by Martin and Roper (Condor 90: 5 1-57; 1988). During 252 counts, 7 1 species were encountered, but only 62 species were encountered within a 50-m radius of point center. The mean number of species encountered within 50 m of a point, was 7.3 (s.d. = 2.7) and the mean number of individuals was 11.2 (s.d. = 4.2). The mean number of species detected at any distance was 9.6 (s.d, = 2.8) and the mean number of individuals was 15.6 (s.d. = 7.9). The most frequently encountered warblers in the MAV were Prothonotary Warbler and Northern Parula. Rarely encountered warblers were American Redstart and Worm-eating Warbler. The genera, Quercus, Ulmus, Carya, and Celtis were each encountered at 80 or more of the 152 points at which vegetation was sampled. Species most frequentlyencountered were: sugarberry (Celtis laevagata), water hickory (Caqa

  14. 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

    infiltration variables, and moderate effects on biocrust properties. Biocrust total cover and composition were again the most influential of biocrust community properties on infiltration, especially in the case of the composition effect on steady state infiltration under ponding. The key difference was that the Australian biocrusts primarily decreased infiltration. On dune runoff zones, later successional biocrusts (lichens, mosses, dark cyanobacterial crusts) of any type decreased infiltration rates compared to early successional crusts. On swale run-on zones, lichens impeded infiltration and mosses did not. These results highlight the importance of biocrusts as key players in the redistribution of water, and demonstrate the modulating role played by animal ecosystem engineers through their localized surface disturbances. Our studies highlight the central role of the relative abundance of mosses compared to other biocrust organisms as an underappreciated, and perhaps a key, determinant of biocrust hydrology.

  15. ANOMALOUS RELATIVE AR/CA CORONAL ABUNDANCES OBSERVED BY THE HINODE/EUV IMAGING SPECTROMETER NEAR SUNSPOTS

    SciTech Connect

    Doschek, G. A.; Warren, H. P.; Feldman, U.

    2015-07-20

    In determining the element abundance of argon (a high first ionization potential; FIP element) relative to calcium (a low FIP element) in flares, unexpectedly high intensities of two Ar xiv lines (194.40, 187.96 Å) relative to a Ca xiv line (193.87 Å) intensity were found in small (a few arcseconds) regions near sunspots in flare spectra recorded by the Extreme-ultraviolet Imaging Spectrometer on the Hinode spacecraft. In the most extreme case the Ar xiv line intensity relative to the Ca xiv intensity was 7 times the value expected from the photospheric abundance ratio, which is about 30 times the abundance of argon relative to calcium in active regions, i.e., the measured Ar/Ca abundance ratio is about 10 instead of 0.37 as in active regions. The Ar xiv and Ca xiv lines are formed near 3.4 MK and have very similar contribution functions. This is the first observation of the inverse FIP effect in the Sun. Other regions show increases of 2–3 over photospheric abundances, or just photospheric abundances. This phenomenon appears to occur rarely and only over small areas of flares away from the regions containing multi-million degree plasma, but more work is needed to quantify the occurrences and their locations. In the bright hot regions of flares the Ar/Ca abundance ratio is coronal, i.e., the same as in active regions. In this Letter we show three examples of the inverse FIP effect.

  16. Influence of relative NK–DC abundance on placentation and its relation to epigenetic programming in the offspring

    PubMed Central

    Freitag, N; Zwier, M V; Barrientos, G; Tirado-González, I; Conrad, M L; Rose, M; Scherjon, S A; Plösch, T; Blois, S M

    2014-01-01

    Normal placentation relies on an efficient maternal adaptation to pregnancy. Within the decidua, natural killer (NK) cells and dendritic cells (DC) have a critical role in modulating angiogenesis and decidualization associated with pregnancy. However, the contribution of these immune cells to the placentation process and subsequently fetal development remains largely elusive. Using two different mouse models, we here show that optimal placentation and fetal development is sensitive to disturbances in NK cell relative abundance at the fetal–maternal interface. Depletion of NK cells during early gestation compromises the placentation process by causing alteration in placental function and structure. Embryos derived from NK-depleted dams suffer from intrauterine growth restriction (IUGR), a phenomenon that continued to be evident in the offspring on post-natal day 4. Further, we demonstrate that IUGR was accompanied by an overall reduction of global DNA methylation levels and epigenetic changes in the methylation of specific hepatic gene promoters. Thus, temporary changes within the NK cell pool during early gestation influence placental development and function, subsequently affecting hepatic gene methylation and fetal metabolism. PMID:25165878

  17. Purification, characterization and structural analysis of an abundant beta-1,3-glucanase from banana fruit.

    PubMed

    Peumans, W J; Barre, A; Derycke, V; Rougé, P; Zhang, W; May, G D; Delcour, J A; Van Leuven, F; Van Damme, E J

    2000-02-01

    An abundant, catalytically active beta-1,3-endoglucanase (EC 3.2.1. 39) has been isolated from the pulp of ripe bananas. Biochemical analysis of the purified protein, molecular modelling, and molecular cloning of the corresponding gene indicate that this banana enzyme closely resembles previously characterized plant beta-glucanases with respect to its amino-acid sequence, structure and biological activity. The results described in this paper demonstrate both the occurrence of an abundant active beta-1,3-endoglucanases in fruits and also readdress the question of the possible involvement of these enzymes in the ripening and/or softening process.

  18. An elemental abundance analysis of the superficially normal A star Vega

    NASA Technical Reports Server (NTRS)

    Adelman, Saul J.; Gulliver, Austin F.

    1990-01-01

    An elemental abundance analysis of Vega has been performed using high-signal-to-noise 2.4 A/mm Reticon observations of the region 4313-4809 A. Vega is found to be a metal-poor star with a mean underabundance of 0.60 dex. The He/H ratio of 0.03 as derived from He I 4472 A suggests that the superficial helium convection zone has disappeared and that radiative diffusion is producing the photospheric abundance anomalies.

  19. An elemental abundance analysis of the superficially normal A star Vega

    SciTech Connect

    Adelman, S.J.; Gulliver, A.F. Brandon Univ. )

    1990-01-01

    An elemental abundance analysis of Vega has been performed using high-signal-to-noise 2.4 A/mm Reticon observations of the region 4313-4809 A. Vega is found to be a metal-poor star with a mean underabundance of 0.60 dex. The He/H ratio of 0.03 as derived from He I 4472 A suggests that the superficial helium convection zone has disappeared and that radiative diffusion is producing the photospheric abundance anomalies. 45 refs.

  20. Costs of Foraging Predispose Animals to Obesity-Related Mortality when Food Is Constantly Abundant

    PubMed Central

    McNamara, John M.; Houston, Alasdair I.; Higginson, Andrew D.

    2015-01-01

    Obesity is an important medical problem affecting humans and animals in the developed world, but the evolutionary origins of the behaviours that cause obesity are poorly understood. The potential role of occasional gluts of food in determining fat-storage strategies for avoiding mortality have been overlooked, even though animals experienced such conditions in the recent evolutionary past and may follow the same strategies in the modern environment. Humans, domestic, and captive animals in the developed world are exposed to a surplus of calorie-rich food, conditions characterised as ‘constant-glut’. Here, we use a mathematical model to demonstrate that obesity-related mortality from poor health in a constant-glut environment should equal the average mortality rate in the ‘pre-modern’ environment when predation risk was more closely linked with foraging. It should therefore not be surprising that animals exposed to abundant food often over-eat to the point of ill-health. Our work suggests that individuals tend to defend a given excessive level of reserves because this level was adaptive when gluts were short-lived. The model predicts that mortality rate in constant-glut conditions can increase as the assumed health cost of being overweight decreases, meaning that any adaptation that reduced such health costs would have counter-intuitively led to an increase in mortality in the modern environment. Taken together, these results imply that efforts to reduce the incidence of obesity that are focussed on altering individual behaviour are likely to be ineffective because modern, constant-glut conditions trigger previously adaptive behavioural responses. PMID:26545121

  1. NEON AND CNO ABUNDANCES FOR EXTREME HELIUM STARS-A NON-LTE ANALYSIS

    SciTech Connect

    Pandey, Gajendra; Lambert, David L. E-mail: dll@astro.as.utexas.edu

    2011-02-01

    A non-LTE (NLTE) abundance analysis was carried out for three extreme helium stars (EHes): BD+10{sup 0} 2179, BD-9{sup 0} 4395, and LS IV+6{sup 0} 002, from their optical spectra with NLTE model atmospheres. NLTE TLUSTY model atmospheres were computed with H, He, C, N, O, and Ne treated in NLTE. Model atmosphere parameters were chosen from consideration of fits to observed He I line profiles and ionization equilibria of C and N ions. The program SYNSPEC was then used to determine the NLTE abundances for Ne as well as H, He, C, N, and O. LTE neon abundances from Ne I lines in the EHes: LSE 78, V1920 Cyg, HD 124448, and PV Tel, are derived from published models and an estimate of the NLTE correction applied to obtain the NLTE Ne abundance. We show that the derived abundances of these key elements, including Ne, are well matched with semi-quantitative predictions for the EHe resulting from a cold merger (i.e., no nucleosynthesis during the merger) of an He white dwarf with a C-O white dwarf.

  2. Neon and CNO Abundances for Extreme Helium Stars—A Non-LTE Analysis

    NASA Astrophysics Data System (ADS)

    Pandey, Gajendra; Lambert, David L.

    2011-02-01

    A non-LTE (NLTE) abundance analysis was carried out for three extreme helium stars (EHes): BD+10° 2179, BD-9° 4395, and LS IV+6° 002, from their optical spectra with NLTE model atmospheres. NLTE TLUSTY model atmospheres were computed with H, He, C, N, O, and Ne treated in NLTE. Model atmosphere parameters were chosen from consideration of fits to observed He I line profiles and ionization equilibria of C and N ions. The program SYNSPEC was then used to determine the NLTE abundances for Ne as well as H, He, C, N, and O. LTE neon abundances from Ne I lines in the EHes: LSE 78, V1920 Cyg, HD 124448, and PV Tel, are derived from published models and an estimate of the NLTE correction applied to obtain the NLTE Ne abundance. We show that the derived abundances of these key elements, including Ne, are well matched with semi-quantitative predictions for the EHe resulting from a cold merger (i.e., no nucleosynthesis during the merger) of an He white dwarf with a C-O white dwarf.

  3. Evaluating abundance and trends in a Hawaiian avian community using state-space analysis

    USGS Publications Warehouse

    Camp, Richard J.; Brinck, Kevin W.; Gorresen, P.M.; Paxton, Eben

    2015-01-01

    Estimating population abundances and patterns of change over time are important in both ecology and conservation. Trend assessment typically entails fitting a regression to a time series of abundances to estimate population trajectory. However, changes in abundance estimates from year-to-year across time are due to both true variation in population size (process variation) and variation due to imperfect sampling and model fit. State-space models are a relatively new method that can be used to partition the error components and quantify trends based only on process variation. We compare a state-space modelling approach with a more traditional linear regression approach to assess trends in uncorrected raw counts and detection-corrected abundance estimates of forest birds at Hakalau Forest National Wildlife Refuge, Hawai‘i. Most species demonstrated similar trends using either method. In general, evidence for trends using state-space models was less strong than for linear regression, as measured by estimates of precision. However, while the state-space models may sacrifice precision, the expectation is that these estimates provide a better representation of the real world biological processes of interest because they are partitioning process variation (environmental and demographic variation) and observation variation (sampling and model variation). The state-space approach also provides annual estimates of abundance which can be used by managers to set conservation strategies, and can be linked to factors that vary by year, such as climate, to better understand processes that drive population trends.

  4. Exoproteome analysis reveals higher abundance of proteins linked to alkaline stress in persistent Listeria monocytogenes strains.

    PubMed

    Rychli, Kathrin; Grunert, Tom; Ciolacu, Luminita; Zaiser, Andreas; Razzazi-Fazeli, Ebrahim; Schmitz-Esser, Stephan; Ehling-Schulz, Monika; Wagner, Martin

    2016-02-01

    The foodborne pathogen Listeria monocytogenes, responsible for listeriosis a rare but severe infection disease, can survive in the food processing environment for month or even years. So-called persistent L. monocytogenes strains greatly increase the risk of (re)contamination of food products, and are therefore a great challenge for food safety. However, our understanding of the mechanism underlying persistence is still fragmented. In this study we compared the exoproteome of three persistent strains with the reference strain EGDe under mild stress conditions using 2D differential gel electrophoresis. Principal component analysis including all differentially abundant protein spots showed that the exoproteome of strain EGDe (sequence type (ST) 35) is distinct from that of the persistent strain R479a (ST8) and the two closely related ST121 strains 4423 and 6179. Phylogenetic analyses based on multilocus ST genes showed similar grouping of the strains. Comparing the exoproteome of strain EGDe and the three persistent strains resulted in identification of 22 differentially expressed protein spots corresponding to 16 proteins. Six proteins were significantly increased in the persistent L. monocytogenes exoproteomes, among them proteins involved in alkaline stress response (e.g. the membrane anchored lipoprotein Lmo2637 and the NADPH dehydrogenase NamA). In parallel the persistent strains showed increased survival under alkaline stress, which is often provided during cleaning and disinfection in the food processing environments. In addition, gene expression of the proteins linked to stress response (Lmo2637, NamA, Fhs and QoxA) was higher in the persistent strain not only at 37 °C but also at 10 °C. Invasion efficiency of EGDe was higher in intestinal epithelial Caco2 and macrophage-like THP1 cells compared to the persistent strains. Concurrently we found higher expression of proteins involved in virulence in EGDe e.g. the actin-assembly-inducing protein ActA and the

  5. CD −24°17504 REVISITED: A NEW COMPREHENSIVE ELEMENT ABUNDANCE ANALYSIS

    SciTech Connect

    Jacobson, Heather R.; Frebel, Anna

    2015-07-20

    With [Fe/H] ∼ −3.3, CD −24°17504 is a canonical metal-poor main-sequence turn-off star. Though it has appeared in numerous literature studies, the most comprehensive abundance analysis for the star based on high-resolution, high signal-to-noise ratio (S/N) spectra is nearly 15 years old. We present a new detailed abundance analysis for 21 elements based on combined archival Keck-HIRES and Very Large Telescope-UVES spectra of the star that is higher in both spectral resolution and S/N than previous data. Our results are very similar to those of an earlier comprehensive study of the star, but we present for the first time a carbon abundance from the CH G-band feature as well as improved upper limits for neutron-capture species such as Y, Ba, and Eu. In particular, we find that CD −24°17504 has [Fe/H] = −3.41, [C/Fe] = +1.10, [Sr/H] = −4.68, and [Ba/H] ≤ −4.46, making it a carbon-enhanced metal-poor star with neutron-capture element abundances among the lowest measured in Milky Way halo stars.

  6. Landscape Level Variation in Tick Abundance Relative to Seasonal Migration in Red Deer

    PubMed Central

    Qviller, Lars; Risnes-Olsen, Nina; Bærum, Kim Magnus; Meisingset, Erling L.; Loe, Leif Egil; Ytrehus, Bjørnar; Viljugrein, Hildegunn; Mysterud, Atle

    2013-01-01

    Partial migration is common among northern ungulates, typically involving an altitudinal movement for seasonally migratory individuals. The main driving force behind migration is the benefit of an extended period of access to newly emerged, high quality forage along the green up gradient with increasing altitude; termed the forage maturation hypothesis. Any other limiting factor spatially correlated with this gradient may provide extra benefits or costs to migration, without necessarily being the cause of it. A common ectoparasite on cervids in Europe is the sheep tick (Ixodes ricinus), but it has not been tested whether migration may lead to the spatial separation from these parasites and thus potentially provide an additional benefit to migration. Further, if there is questing of ticks in winter ranges in May before spring migration, deer migration may also play a role for the distribution of ticks. We quantified the abundance of questing sheep tick within winter and summer home ranges of migratory (n = 42) and resident red deer (Cervus elaphus) individuals (n = 32) in two populations in May and August 2009–2012. Consistent with predictions, there was markedly lower abundance of questing ticks in the summer areas of migrating red deer (0.6/20 m2), both when compared to the annual home range of resident deer (4.9/20 m2) and the winter home ranges of migrants (5.8/20 m2). The reduced abundances within summer home ranges of migrants were explained by lower abundance of ticks with increasing altitude and distance from the coast. The lower abundance of ticks in summer home ranges of migratory deer does not imply that ticks are the main driver of migration (being most likely the benefits expected from forage maturation), but it suggests that ticks may add to the value of migration in some ecosystems and that it may act to spread ticks long distances in the landscape. PMID:23951125

  7. Non-LTE analysis of copper abundances for the two distinct halo populations in the solar neighborhood

    NASA Astrophysics Data System (ADS)

    Yan, H. L.; Shi, J. R.; Nissen, P. E.; Zhao, G.

    2016-01-01

    Context. Two distinct halo populations were found in the solar neighborhood by a series of works. They can be clearly separated by [α/Fe] and several other elemental abundance ratios including [Cu/Fe]. Very recently, a non-local thermodynamic equilibrium (non-LTE) study revealed that relatively large departures exist between LTE and non-LTE results in copper abundance analysis. The study also showed that non-LTE effects of neutral copper vary with stellar parameters and thus affect the [Cu/Fe] trend. Aims: We aim to derive the copper abundances for the stars from the sample of Nissen & Schuster (2010) with both LTE and non-LTE calculations. Based on our results, we study the non-LTE effects of copper and investigate whether the high-α population can still be distinguished from the low-α population in the non-LTE [Cu/Fe] results. Methods: Our differential abundance ratios are derived from the high-resolution spectra collected from VLT/UVES and NOT/FIES spectrographs. Applying the MAFAGS opacity sampling atmospheric models and spectrum synthesis method, we derive the non-LTE copper abundances based on the new atomic model with current atomic data obtained from both laboratory and theoretical calculations. Results: The copper abundances determined from non-LTE calculations are increased by 0.01 to 0.2 dex depending on the stellar parameters compared with the LTE results. The non-LTE [Cu/Fe] trend is much flatter than the LTE one in the metallicity range -1.6 < [ Fe / H ] < -0.8. Taking non-LTE effects into consideration, the high- and low-α stars still show distinguishable copper abundances, which appear even more clear in a diagram of non-LTE [Cu/Fe] versus [Fe/H]. Conclusions: The non-LTE effects are strong for copper, especially in metal-poor stars. Our results confirmed that there are two distinct halo populations in the solar neighborhood. The dichotomy in copper abundance is a peculiar feature of each population, suggesting that they formed in different

  8. Longitudinal patterns in flathead catfish relative abundance and length at age within a large river: Effects of an urban gradient

    USGS Publications Warehouse

    Paukert, C.P.; Makinster, A.S.

    2009-01-01

    We investigated the spatial variation of flathead catfish (Pylodictis olivaris) relative abundance and growth in the 274 km long Kansas River to determine if population dynamics of catfish are related to urbanization. Electrofishing was conducted at 462 random sites throughout the river in summer, 2005-2006 to collect fish. Relative abundance of age 1 fish (???200mm), subadult (>200-400mm) and adult fish (>400 mm) ranged from 0.34 to 14.67 fish h-1, mean length at age 1 was 165 (range: 128-195) mm total length (TL) and mean length at age 3 was 376 mm TL (range: 293-419mm TL). The proportion of land use within 200 m of the river edge was between 0 and 0.54 urban. River reaches with high relative abundance of age 1 flathead catfish had high relative abundance of subadult and adult catfish. River reaches with fast flathead catfish growth to age 1 had fast growth to age 3. High urban land use and riprap in the riparian area were evident in river reaches near the heavily populated Kansas City and Topeka, Kansas, USA. Reaches with increased number of log jams and islands had decreased riparian agriculture. Areas of low urbanization had faster flathead catfish growth (r = 0.67, p = 0.005). Relative abundance of flathead catfish was higher in more agricultural areas (r = -0.57, p = 0.02). Changes in land use in riverine environments may alter population dynamics of a fish species within a river. Spatial differences in population dynamics need to be considered when evaluating riverine fish populations. Published in 2008 by John Wiley & Sons Ltd.

  9. Variation in local abundance and species richness of stream fishes in relation to dispersal barriers: Implications for management and conservation

    USGS Publications Warehouse

    Nislow, K.H.; Hudy, M.; Letcher, B.H.; Smith, E.P.

    2011-01-01

    1.Barriers to immigration, all else being equal, should in principle depress local abundance and reduce local species richness. These issues are particularly relevant to stream-dwelling species when improperly designed road crossings act as barriers to migration with potential impacts on the viability of upstream populations. However, because abundance and richness are highly spatially and temporally heterogeneous and the relative importance of immigration on demography is uncertain, population- and community-level effects can be difficult to detect. 2.In this study, we tested the effects of potential barriers to upstream movements on the local abundance and species richness of a diverse assemblage of resident stream fishes in the Monongahela National Forest, West Virginia, U.S.A. Fishes were sampled using simple standard techniques above- and below road crossings that were either likely or unlikely to be barriers to upstream fish movements (based on physical dimensions of the crossing). We predicted that abundance of resident fishes would be lower in the upstream sections of streams with predicted impassable barriers, that the strength of the effect would vary among species and that variable effects on abundance would translate into lower species richness. 3.Supporting these predictions, the statistical model that best accounted for variation in abundance and species richness included a significant interaction between location (upstream or downstream of crossing) and type (passable or impassable crossing). Stream sections located above predicated impassable culverts had fewer than half the number of species and less than half the total fish abundance, while stream sections above and below passable culverts had essentially equivalent richness and abundance. 4.Our results are consistent with the importance of immigration and population connectivity to local abundance and species richness of stream fishes. In turn, these results suggest that when measured at

  10. Relations between fish abundances, summer temperatures, and forest harvest in a northern Minnesota stream system from 1997 to 2007

    USGS Publications Warehouse

    Merten, Eric C.; Hemstad, Nathaniel A.; Eggert, S.L.; Johnson, L.B.; Kolka, Randall K.; Newman, Raymond M.; Vondracek, Bruce C.

    2010-01-01

    Short-term effects of forest harvest on fish habitat have been well documented, including sediment inputs, leaf litter reductions, and stream warming. However, few studies have considered changes in local climate when examining postlogging changes in fish communities. To address this need, we examined fish abundances between 1997 and 2007 in a basin in a northern hardwood forest. Streams in the basin were subjected to experimental riparian forest harvest in fall 1997. We noted a significant decrease for fish index of biotic integrity and abundance of Salvelinus fontinalis and Phoxinus eos over the study period. However, for P. eos and Culaea inconstans, the temporal patterns in abundances were related more to summer air temperatures than to fine sediment or spring precipitation when examined using multiple regressions. Univariate regressions suggested that summer air temperatures influenced temporal patterns in fish communities more than fine sediment or spring precipitation.

  11. Relations between fish abundances, summer temperatures, and forest harvest in a northern Minnesota stream system from 1997 to 2007

    USGS Publications Warehouse

    Merten, Eric C.; Hemstad, Nathaniel A.; Eggert, L.S.; Johnson, L.B.; Kolka, R.K.; Newman, Raymond M.; Vondracek, Bruce C.

    2015-01-01

    Short-term effects of forest harvest on fish habitat have been well documented, including sediment inputs, leaf litter reductions, and stream warming. However, few studies have considered changes in local climate when examining postlogging changes in fish communities. To address this need, we examined fish abundances between 1997 and 2007 in a basin in a northern hardwood forest. Streams in the basin were subjected to experimental riparian forest harvest in fall 1997. We noted a significant decrease for fish index of biotic integrity and abundance of Salvelinus fontinalis and Phoxinus eos over the study period. However, for P. eos and Culaea inconstans, the temporal patterns in abundances were related more to summer air temperatures than to fine sediment or spring precipitation when examined using multiple regressions. Univariate regressions suggested that summer air temperatures influenced temporal patterns in fish communities more than fine sediment or spring precipitation.

  12. Climate-related variability in abundance of mesozooplankton in the northern Gulf of Alaska 1998-2009

    NASA Astrophysics Data System (ADS)

    Sousa, Leandra; Coyle, Kenneth O.; Barry, Ronald P.; Weingartner, Thomas J.; Hopcroft, Russell R.

    2016-10-01

    Significant changes in fisheries resources have occurred in the Gulf of Alaska (GOA) in the mid 1970s, with an increase in groundfish and a decrease in crab and shrimp populations. Increased fishing pressure and such events suggest that the GOA is susceptible to climate variation; however the mechanistic links between ecosystem change and climate remain unclear. At-sea surveys were undertaken during the month of May from 1998 to 2009 to collect data on zooplankton abundance and water mass properties in the northern GOA. Significant changes in temperature, salinity and zooplankton abundance were identified during this period. The euphausiid Thysanoessa inermis and the copepod Calanus marshallae had increased abundances in years when there was a strong phytoplankton spring bloom preceded by anomalously cold winters. The euphausiid Euphausia pacifica and the copepods Pseudocalanus spp., Neocalanus plumchrus/flemingeri, and Oithona spp. were more resilient to relatively high mean water temperatures. High zooplankton abundances in years of substantial cross-shelf mixing suggest that iron and nutrient transport between the shelf and oceanic domains are essential for sustaining high zooplankton populations via phytoplankton blooms. The abundance of zooplankton in the northern GOA is highly influenced by advective processes and changes in temperature. Further understanding of biological and physical mechanisms that control the GOA ecosystem are of major importance to predict the response of zooplankton communities to environmental changes.

  13. Stratigraphy of small shield volcanoes on Venus: Criteria for determining stratigraphic relationships and assessment of relative age and temporal abundance

    NASA Astrophysics Data System (ADS)

    Ivanov, Mikhail A.; Head, James W.

    2004-10-01

    Small volcanic edifices, shields with a diameter less than about 20 km, are common and sometimes very abundant features on the plains of Venus. Typically, they form tight or loose clusters of features known as shield fields. Small shields are interpreted to be formed due to small-scale eruptions through numerous and distinct sources, a mode of formation apparently significantly different from the mechanism thought to be responsible for the emplacement of the vast regional plains of Venus. Did the eruption style of small shields occur repeatedly throughout the visible part of the geologic record of Venus? Or was this style more concentrated in a specific epoch or epochs of geologic history? Do the clusters of shields represent localized development of sources over a thermal anomaly such as a plume, or do they represent exposures or kipukas of a more regional unit or units? A major step toward answering these questions is an understanding of small shield stratigraphy. Multiple criteria have been developed to assess the stratigraphic relationships of individual small shields and that of shield fields with the adjacent units. In our analysis, we expanded and developed the previous criteria and added detailed criteria to describe specific patterns of deformation within shield fields, cross-cutting, and embayment relationships between shield fields and surrounding units. We also used secondary characteristics of shield fields such as radar albedo difference, changes in shield density and size, etc. In our study, we applied these criteria and analyzed in detail stratigraphic relationships of shield fields in a random sample of features (64 fields) and in the global geotraverse along 30°N (77 fields). The total number of analyzed shield fields (141) represents about 22% of the general population of these features catalogued by Crumpler and Aubele [2000]. The majority of the fields (98, or ~69%) predate emplacement of material of vast regional plains with wrinkle ridges

  14. In-depth analysis of low abundant proteins in bovine colostrum using different fractionation techniques.

    PubMed

    Nissen, Asger; Bendixen, Emøke; Ingvartsen, Klaus Lønne; Røntved, Christine Maria

    2012-09-01

    Bovine colostrum is well known for its large content of bioactive components and its importance for neonatal survival. Unfortunately, the colostrum proteome is complicated by a wide dynamic range, because of a few dominating proteins that hamper sensitivity and proteome coverage achieved on low abundant proteins. Moreover, the composition of colostrum is complex and the proteins are located within different physical fractions that make up the colostrum. To gain a more exhaustive picture of the bovine colostrum proteome and gather information on protein location, we performed an extensive pre-analysis fractionation of colostrum prior to 2D-LC-MS/MS analysis. Physical and chemical properties of the proteins and colostrum were used alone or in combination for the separation of proteins. ELISA was used to quantify and verify the presence of proteins in colostrum. In total, 403 proteins were identified in the nonfractionated colostrum (NF) and seven fractions (F1-F7) using six different fractionation techniques. Fractionation contributed with 69 additional proteins in the fluid phase compared with NF. Different fractionation techniques each resulted in detection of unique subsets of proteins. Whey production by high-speed centrifugation contributed most to detection of low abundant proteins. Hence, prefractionation of colostrum prior to 2D-LC-MS/MS analysis expanded our knowledge on the presence and location of low abundant proteins in bovine colostrum. PMID:22848049

  15. Molecular identification and relative abundance of cryptic Lophodermium species in natural populations of Scots pine, Pinus sylvestris L.

    PubMed

    Reignoux, Sabrina N A; Green, Sarah; Ennos, Richard A

    2014-01-01

    The multi-locus phylogenetic species recognition approach and population genetic analysis of Amplified Fragment Length Polymorphism (AFLP) markers were used to delineate Lophodermium taxa inhabiting needles of Scots pine (Pinus sylvestris) in native pinewoods within Scotland. These analyses revealed three major lineages corresponding to the morphological species Lophodermium seditiosum and Lophodermium conigenum, fruiting on broken branches, and Lophodermium pinastri, fruiting on naturally fallen needles. Within L. pinastri three well supported sister clades were found representing cryptic taxa designated L. pinastri I, L. pinastri II, and L. pinastri III. Significant differences in mean growth rate in culture were found among the cryptic taxa. Taxon-specific primers based on ITS sequences were designed and used to classify over 500 Lophodermium isolates, derived from fallen needles of P. sylvestris in three Scottish and one French pinewood site, into the three L. pinastri cryptic taxa. Highly significant differences in the relative abundance of the three taxa were found among the Scottish pinewood sites, and between the French and all of the Scottish sites.

  16. Abundance of diurnal raptors in relation to prairie dog colonies: Implications for bird-aircraft strike hazard

    USGS Publications Warehouse

    Merriman, J.W.; Boal, C.W.; Bashore, T.L.; Zwank, P.J.; Wester, D.B.

    2007-01-01

    Some diurnal raptors are frequently observed at prairie dog (Cynomys sp.) colonies. As a result, some military installations have conducted prairie dog control activities to reduce the bird-aircraft strike hazard (BASH) potential of low-flying aircraft. To evaluate the validity of this management strategy, we assessed raptor associations with prairie dog colonies at 2 short-grass prairie study areas: southern Lubbock County, Texas, USA, and Melrose Bombing and Gunnery Range in east-central New Mexico, USA. We quantified diurnal raptors (i.e., Falconiformes) at plots occupied (colony plots) and unoccupied (noncolony plots) by black-tailed prairie dogs (Cynomys ludovicianus) at both sites throughout 2002. We compared the number of individual birds of a given species at colony and noncolony plots within each study area by season. Ferruginous hawks (Buteo regalis) and northern harriers (Circus cyaneus) were more abundant at colony plots, whereas Swainson's hawks (B. swainsoni) and American kestrels (Falco sparverius) were more abundant at noncolony plots. Red-tailed hawk (B. jamaicensis) abundance did not differ between the 2 plot types. Our results suggest prairie dog control as a method of reducing BASH potential may be effective at some sites but may be ineffective or even increase the BASH potential at others. Thus, bird-avoidance models assessing the BASH potential should be conducted on a site-specific basis using information on relative and seasonal abundances of individual raptor species and the relative strike risks they pose to aircraft.

  17. Temporal Patterns in the Abundance of a Critically Endangered Marsupial Relates to Disturbance by Roads and Agriculture

    PubMed Central

    Yeatman, Georgina J.; Wayne, Adrian F.; Mills, Harriet R.; Prince, Jane

    2016-01-01

    The aim of this study was to investigate how landscape disturbance associated with roads, agriculture and forestry influenced temporal patterns in woylie (Bettongia penicillata) abundance before, during and after periods of rapid population change. Data were collected from an area of approximately 140,000 ha of forest within the Upper Warren region in south-western Australia. Woylie abundance was measured using cage trapping at 22 grid and five transect locations with varying degrees of landscape disturbance between 1994 and 2012. We found evidence that the distribution and abundance of woylies over time appears to be related to the degree of fragmentation by roads and proximity to agriculture. Sites furthest from agriculture supported a greater abundance of woylies and had slower rates of population decline. Sites with fewer roads had a greater abundance of woylies generally and a greater rate of increase in abundance after the implementation of invasive predator control. The results of this study suggest that landscape disturbance is less important at peak population densities, but during times of environmental and population change, sites less dissected by roads and agriculture better support woylie populations. This may be due to the role these factors play in increasing the vulnerability of woylies to introduced predators, population fragmentation, weed species invasion, mortality from road collisions or a reduction in available habitat. Strategies that reduce the impact of disturbance on woylie populations could include the rationalisation of forest tracks and consolidation of contiguous habitat through the acquisition of private property. Reducing the impact of disturbance in the Upper Warren region could improve the resilience of this critically important woylie population during future environmental change. PMID:27501320

  18. Temporal Patterns in the Abundance of a Critically Endangered Marsupial Relates to Disturbance by Roads and Agriculture.

    PubMed

    Yeatman, Georgina J; Wayne, Adrian F; Mills, Harriet R; Prince, Jane

    2016-01-01

    The aim of this study was to investigate how landscape disturbance associated with roads, agriculture and forestry influenced temporal patterns in woylie (Bettongia penicillata) abundance before, during and after periods of rapid population change. Data were collected from an area of approximately 140,000 ha of forest within the Upper Warren region in south-western Australia. Woylie abundance was measured using cage trapping at 22 grid and five transect locations with varying degrees of landscape disturbance between 1994 and 2012. We found evidence that the distribution and abundance of woylies over time appears to be related to the degree of fragmentation by roads and proximity to agriculture. Sites furthest from agriculture supported a greater abundance of woylies and had slower rates of population decline. Sites with fewer roads had a greater abundance of woylies generally and a greater rate of increase in abundance after the implementation of invasive predator control. The results of this study suggest that landscape disturbance is less important at peak population densities, but during times of environmental and population change, sites less dissected by roads and agriculture better support woylie populations. This may be due to the role these factors play in increasing the vulnerability of woylies to introduced predators, population fragmentation, weed species invasion, mortality from road collisions or a reduction in available habitat. Strategies that reduce the impact of disturbance on woylie populations could include the rationalisation of forest tracks and consolidation of contiguous habitat through the acquisition of private property. Reducing the impact of disturbance in the Upper Warren region could improve the resilience of this critically important woylie population during future environmental change. PMID:27501320

  19. Relative abundance of the helium isotopes He-3 and He-4 in the cosmic radiation

    NASA Technical Reports Server (NTRS)

    Jordan, S. P.; Meyer, P.

    1984-01-01

    The geomagnetic field near the equator is used to measure the He-3/He-4 abundance ratio near 6 GeV/nucleon. This ratio is found to be 0.24 + or - 0.05, under the assumption that the helium rigidity spectrum has the form dI/dR = about R exp(-2.65). If all He-3 is of secondary origin, this implies an interstellar mean escape-path length of about 15 g/sq cm, a value considerably larger than that determined from observations of heavier elements but compatible with measurements of the helium isotopic ratio at lower energies.

  20. Breeding chorus indices are weakly related to estimated abundance of boreal chorus frogs

    USGS Publications Warehouse

    Corn, P.S.; Muths, E.; Kissel, A.M.; Scherer, R. D.

    2011-01-01

    Call surveys used to monitor breeding choruses of anuran amphibians generate index values that are frequently used to represent the number of male frogs present, but few studies have quantified this relationship. We compared abundance of male Boreal Chorus Frogs (Pseudacris maculata), estimated using capture–recapture methods in two populations in Colorado, to call index values derived from automated recordings. Single index values, such as might result from large monitoring efforts, were unrelated to population size. A synthetic call saturation index (CSI), the daily proportion of the maximum possible sum of index values derived from multiple recordings, was greater in larger populations, but the relationship was not highly predictive.

  1. First high-precision differential abundance analysis of extremely metal-poor stars

    NASA Astrophysics Data System (ADS)

    Reggiani, Henrique; Meléndez, Jorge; Yong, David; Ramírez, Ivan; Asplund, Martin

    2016-02-01

    Context. Studies of extremely metal-poor stars indicate that chemical abundance ratios [X/Fe] have a root mean square scatter as low as 0.05 dex (12%). It remains unclear whether this reflects observational uncertainties or intrinsic astrophysical scatter arising from physical conditions in the interstellar medium at early times. Aims: We measure differential chemical abundance ratios in extremely metal-poor stars to investigate the limits of precision and to understand whether cosmic scatter or observational errors are dominant. Methods: We used high-resolution (R ~ 95 000) and high signal-to-noise (S/N = 700 at 5000 Å) HIRES/Keck spectra to determine high-precision differential abundances between two extremely metal-poor stars through a line-by-line differential approach. We determined stellar parameters for the star G64-37 with respect to the standard star G64-12. We performed EW measurements for the two stars for the lines recognized in both stars and performed spectral synthesis to study the carbon abundances. Results: The differential approach allowed us to obtain errors of σ(Teff) = 27 K, σ(log g) = 0.06 dex, σ( [Fe/H] ) = 0.02 dex and σ(vt) = 0.06 km s-1. We estimated relative chemical abundances with a precision as low as σ([X/Fe]) ≈ 0.01 dex. The small uncertainties demonstrate that there are genuine abundance differences larger than the measurement errors. The observed Li difference cannot be explained by the difference in mass because the less massive star has more Li. Conclusions: It is possible to achieve an abundance precision around ≈ 0.01-0.05 dex for extremely metal-poor stars, which opens new windows on the study of the early chemical evolution of the Galaxy. Table A.1 is also available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/586/A67

  2. Geostatistical Analysis of Spatial Variability of Mineral Abundance and Kd in Frenchman Flat, NTS, Alluvium

    SciTech Connect

    Carle, S F; Zavarin, M; Pawloski, G A

    2002-11-01

    characterize the spatial variation of minerals. The models must also be plausible from a geological perspective. Spatial variation of mineral abundance is caused not only by random processes but also by ordered geologic processes such as alluvial fan progradation, provenance, and in-situ alteration. Much of the spatial variation of sorbing mineral abundances is attributable to different ''chemofacies'' within which zonal mean abundances are relatively uniform. The chemofacies are, in large part, associated with the alluvial layers interpreted by Warren et al. (2002).

  3. Proteomic analysis of an unculturable bacterial endosymbiont (Blochmannia) reveals high abundance of chaperonins and biosynthetic enzymes

    PubMed Central

    Fan, Yongliang; Thompson, J. Will; Dubois, Laura G.; Moseley, M. Arthur; Wernegreen, Jennifer J.

    2013-01-01

    Many insect groups have coevolved with bacterial endosymbionts that live within specialized host cells. As a salient example, ants in the tribe Camponotini rely on Blochmannia, an intracellular bacterial mutualist that synthesizes amino acids and recycles nitrogen for the host. We performed a shotgun, label-free, LC/MS/MS quantitative proteomic analysis to investigate the proteome of Blochmannia associated with Camponotus chromaiodes. We identified more than 330 Blochmannia proteins, or 54% coverage of the predicted proteome, as well as 244 Camponotus proteins. Using the average intensity of the top 3 “best flier” peptides along with spiking of a surrogate standard at a known concentration, we estimated the concentration (fmol/μg) of those proteins with confident identification. The estimated dynamic range of Blochmannia protein abundance spanned three orders of magnitude and covered diverse functional categories, with particularly high representation of metabolism, information transfer, and chaperones. GroEL, the most abundant protein, totaled 6% of Blochmannia protein abundance. Biosynthesis of essential amino acids, fatty acids, and nucleotides, and sulfate assimilation had disproportionately high coverage in the proteome, further supporting a nutritional role of the symbiosis. This first quantitative proteomic analysis of an ant endosymbiont illustrates a promising approach to study the functional basis of intimate symbioses. PMID:23205679

  4. Transcript Abundance of Photorhabdus Insect-Related (Pir) Toxin in Manduca sexta and Galleria mellonella Infections

    PubMed Central

    Castagnola, Anaïs; Mulley, Geraldine; Davis, Nathaniel; Waterfield, Nicholas; Stock, S. Patricia

    2016-01-01

    In this study, we assessed pirAB toxin transcription in Photorhabdus luminescens laumondii (strain TT01) (Enterobacteriaceae) by comparing mRNA abundance under in vivo and in vitro conditions. In vivo assays considered both natural and forced infections with two lepidopteran hosts: Galleria mellonella and Manduca sexta. Three portals of entry were utilized for the forced infection assays: (a) integument; (b) the digestive route (via mouth and anus); and (c) the tracheal route (via spiracles). We also assessed plu4093-2 transcription during the course of a natural infection; this is when the bacteria are delivered by Heterorhabditis bacteriophora nematodes. Transcript abundance in G. mellonella was higher than in M. sexta at two of the observed time points: 15 and 18 h. Expression of pirAB plu4093-2 reached above endogenous control levels at 22 h in G. mellonella but not in M. sexta. Overall, pirAB plu4093-2 transcripts were not as highly expressed in M. sexta as in G. mellonella, from 15 to 22 h. This is the first study to directly compare pirAB plu4093-2 toxin transcript production considering different portals of entry. PMID:27690103

  5. MEASUREMENTS OF THE RELATIVE ABUNDANCES OF HIGH-ENERGY COSMIC-RAY NUCLEI IN THE TeV/NUCLEON REGION

    SciTech Connect

    Ahn, H. S.; Ganel, O.; Han, J. H.; Kim, K. C.; Lee, M. H.; Malinin, A.; Allison, P. S.; Beatty, J. J.; Brandt, T. J.; Bagliesi, M. G.; Bigongiari, G.; Maestro, P.; Marrocchesi, P. S.; Barbier, L.; Childers, J. T.; DuVernois, M. A.; Conklin, N. B.; Coutu, S.; Jeon, J. A.; Lee, J.

    2010-06-01

    We present measurements of the relative abundances of cosmic-ray nuclei in the energy range of 500-3980 GeV/nucleon from the second flight of the Cosmic Ray Energetics And Mass balloon-borne experiment. Particle energy was determined using a sampling tungsten/scintillating-fiber calorimeter, while particle charge was identified precisely with a dual-layer silicon charge detector installed for this flight. The resulting element ratios C/O, N/O, Ne/O, Mg/O, Si/O, and Fe/O at the top of atmosphere are 0.919 {+-} 0.123{sup stat} {+-} 0.030{sup syst}, 0.076 {+-} 0.019{sup stat} {+-} 0.013{sup syst}, 0.115 {+-} 0.031{sup stat} {+-} 0.004{sup syst}, 0.153 {+-} 0.039{sup stat} {+-} 0.005{sup syst}, 0.180 {+-} 0.045{sup stat} {+-} 0.006{sup syst}, and 0.139 {+-} 0.043{sup stat} {+-} 0.005{sup syst}, respectively, which agree with measurements at lower energies. The source abundance of N/O is found to be 0.054 {+-} 0.013{sup stat} {+-} 0.009{sup syst+0.010esc} {sub -0.017}. The cosmic-ray source abundances are compared to local Galactic (LG) abundances as a function of first ionization potential and as a function of condensation temperature. At high energies the trend that the cosmic-ray source abundances at large ionization potential or low condensation temperature are suppressed compared to their LG abundances continues. Therefore, the injection mechanism must be the same at TeV/nucleon energies as at the lower energies measured by HEAO-3, CRN, and TRACER. Furthermore, the cosmic-ray source abundances are compared to a mixture of 80% solar system abundances and 20% massive stellar outflow (MSO) as a function of atomic mass. The good agreement with TIGER measurements at lower energies confirms the existence of a substantial fraction of MSO material required in the {approx}TeV per nucleon region.

  6. RVC-CAL library for endmember and abundance estimation in hyperspectral image analysis

    NASA Astrophysics Data System (ADS)

    Lazcano López, R.; Madroñal Quintín, D.; Juárez Martínez, E.; Sanz Álvaro, C.

    2015-10-01

    Hyperspectral imaging (HI) collects information from across the electromagnetic spectrum, covering a wide range of wavelengths. Although this technology was initially developed for remote sensing and earth observation, its multiple advantages - such as high spectral resolution - led to its application in other fields, as cancer detection. However, this new field has shown specific requirements; for instance, it needs to accomplish strong time specifications, since all the potential applications - like surgical guidance or in vivo tumor detection - imply real-time requisites. Achieving this time requirements is a great challenge, as hyperspectral images generate extremely high volumes of data to process. Thus, some new research lines are studying new processing techniques, and the most relevant ones are related to system parallelization. In that line, this paper describes the construction of a new hyperspectral processing library for RVC-CAL language, which is specifically designed for multimedia applications and allows multithreading compilation and system parallelization. This paper presents the development of the required library functions to implement two of the four stages of the hyperspectral imaging processing chain--endmember and abundances estimation. The results obtained show that the library achieves speedups of 30%, approximately, comparing to an existing software of hyperspectral images analysis; concretely, the endmember estimation step reaches an average speedup of 27.6%, which saves almost 8 seconds in the execution time. It also shows the existence of some bottlenecks, as the communication interfaces among the different actors due to the volume of data to transfer. Finally, it is shown that the library considerably simplifies the implementation process. Thus, experimental results show the potential of a RVC-CAL library for analyzing hyperspectral images in real-time, as it provides enough resources to study the system performance.

  7. Golden alga presence and abundance are inversely related to salinity in a high-salinity river ecosystem, Pecos River, USA

    USGS Publications Warehouse

    Israël, Natascha M.D.; VanLandeghem, Matthew M.; Denny, Shawn; Ingle, John; Patino, Reynaldo

    2014-01-01

    Prymnesium parvum (golden alga, GA) is a toxigenic harmful alga native to marine ecosystems that has also affected brackish inland waters. The first toxic bloom of GA in the western hemisphere occurred in the Pecos River, one of the saltiest rivers in North America. Environmental factors (water quality) associated with GA occurrence in this basin, however, have not been examined. Water quality and GA presence and abundance were determined at eight sites in the Pecos River basin with or without prior history of toxic blooms. Sampling was conducted monthly from January 2012 to July 2013. Specific conductance (salinity) varied spatiotemporally between 4408 and 73,786 mS/cm. Results of graphical, principal component (PCA), and zero-inflated Poisson (ZIP) regression analyses indicated that the incidence and abundance of GA are reduced as salinity increases spatiotemporally. LOWESS regression and correlation analyses of archived data for specific conductance and GA abundance at one of the study sites retrospectively confirmed the negative association between these variables. Results of PCA also suggested that at <15,000 mS/cm, GA was present at a relatively wide range of nutrient (nitrogen and phosphorus) concentrations whereas at higher salinity, GA was observed only at mid-to-high nutrient levels. Generally consistent with earlier studies, results of ZIP regression indicated that GA presence is positively associated with organic phosphorus and in samples where GA is present, GA abundance is positively associated with organic nitrogen and negatively associated with inorganic nitrogen. This is the first report of an inverse relation between salinity and GA presence and abundance in riverine waters and of interaction effects of salinity and nutrients in the field. These observations contribute to a more complete understanding of environmental conditions that influence GA distribution in inland waters.

  8. The surface nitrogen abundance of a massive star in relation to its oscillations, rotation, and magnetic field

    SciTech Connect

    Aerts, C.; Molenberghs, G.; Kenward, M. G.; Neiner, C.

    2014-02-01

    We have composed a sample of 68 massive stars in our galaxy whose projected rotational velocity, effective temperature, and gravity are available from high-precision spectroscopic measurements. The additional seven observed variables considered here are their surface nitrogen abundance, rotational frequency, magnetic field strength, and the amplitude and frequency of their dominant acoustic and gravity modes of oscillation. A multiple linear regression to estimate the nitrogen abundance combined with principal component analysis, after addressing the incomplete and truncated nature of the data, reveals that the effective temperature and the frequency of the dominant acoustic oscillation mode are the only two significant predictors for the nitrogen abundance, while the projected rotational velocity and the rotational frequency have no predictive power. The dominant gravity mode and the magnetic field strength are correlated with the effective temperature but have no predictive power for the nitrogen abundance. Our findings are completely based on observations and their proper statistical treatment and call for a new strategy in evaluating the outcome of stellar evolution computations.

  9. Effects of FGF10 on bovine oocyte meiosis progression, apoptosis, embryo development and relative abundance of developmentally important genes in vitro.

    PubMed

    Pomini Pinto, R F; Fontes, P K; Loureiro, B; Sousa Castilho, A C; Sousa Ticianelli, J; Montanari Razza, E; Satrapa, R A; Buratini, J; Moraes Barros, C

    2015-02-01

    Fibroblast growth factor (FGF10) acts at the cumulus oocyte complex, increasing the expression of cumulus cell expansion-related genes and oocyte competency genes. We tested the hypothesis that addition of FGF10 to the maturation medium improves oocyte maturation, decreases the percentage of apoptotic oocytes and increases development to the blastocyst stage while increasing the relative abundance of developmentally important genes (COX2, CDX2 and PLAC8). In all experiments, oocytes were matured for 22 h in TCM-199 supplemented with 0, 2.5, 10 or 50 ng/ml FGF10. In Experiment 1, after maturation, oocytes were stained with Hoechst to evaluate meiosis progression (metaphase I, intermediary phases and extrusion of the first polar body) and submitted to the TUNEL assay to evaluate apoptosis. In Experiment 2, oocytes were fertilized and cultured to the blastocyst stage. Blastocysts were frozen for analysis of COX2, CDX2 and PLAC8 relative abundance. In Experiment 1, 2.5 ng/ml FGF10 increased (p < 0.05) the percentage of oocytes with extrusion of the first polar body (35%) compared to 0, 10 and 50 ng/ml FGF10 (21, 14 and 12%, respectively) and FGF10 decreased the percentage of oocytes that were TUNEL positive in all doses studied. In Experiment 2, there was no difference in the percentage of oocytes becoming blastocysts between treatments and control. Real-time RT-PCR showed a tendency of 50 ng/ml FGF10 to increase the relative abundance of COX2 and PLAC8 and of 10 ng/ml FGF10 to increase CDX2. In conclusion, the addition of FGF10 to the oocyte maturation medium improves oocyte maturation in vitro, decreases the percentage of apoptotic oocytes and tends to increase the relative abundance of developmentally important genes. PMID:25495767

  10. Distribution and relative abundance of the crayfishes Procambarus alleni (Faxon) and P. fallax (Hagen) in southern Florida

    USGS Publications Warehouse

    Hendrix, A.N.; Loftus, W.F.

    2000-01-01

    The Everglades crayfish (Procambarus alleni Faxon) is the only species reported from Everglades National Park (ENP) and Big Cypress National Preserve (BICY). However, we identified a second species, Procambarus fallax (Hagen), from those locations. Reexamination of archived samples showed that P. fallax had been collected as early as 1985 but had been misidentified or overlooked; therefore, we provide methods for distinguishing live and preserved specimens of these morphologically similar species. Species relative abundance varied predictably with hydroperiod (length of inundation) both in recent collections and in archived samples. Procambarus fallax relative abundance was highest in sites characterized by long hydroperiod and prolonged inundation, whereas P. alleni was the lone species in short hydroperiod marshes.

  11. Mesozooplankton abundance in relation to the chlorophyll maximum in the Neuse River Estuary, North Carolina, USA: Implications for trophic dynamics

    NASA Astrophysics Data System (ADS)

    Kimmel, David G.; McGlaughon, Benjamin D.; Leonard, Jeremy; Paerl, Hans W.; Taylor, J. Christopher; Cira, Emily K.; Wetz, Michael S.

    2015-05-01

    Estuaries often have distinct zones of high chlorophyll a concentrations, known as chlorophyll maximum (CMAX). The persistence of these features is often attributed to physical (mixing and light availability) and chemical (nutrient availability) features, but the role of mesozooplankton grazing is rarely explored. We measured the spatial and temporal variability of the CMAX and mesozooplankton community in the eutrophic Neuse River Estuary, North Carolina. We also conducted grazing experiments to determine the relative impact of mesozooplankton grazing on the CMAX during the phytoplankton growing season (spring through late summer). The CMAX was consistently located upriver of the zone of maximum zooplankton abundance, with an average spatial separation of 18 km. Grazing experiments in the CMAX region revealed negligible effect of mesozooplankton on chlorophyll a during March, and no effect during June or August. These results suggest that the spatial separation of the peak in chlorophyll a concentration and mesozooplankton abundance results in minimal impact of mesozooplankton grazing, contributing to persistence of the CMAX for prolonged time periods. In the Neuse River Estuary, the low mesozooplankton abundance in the CMAX region is attributed to lack of a low salinity tolerant species, predation by the ctenophore Mnemiopsis leidyi, and/or physiologic impacts on mesozooplankton growth rates due to temperature (in the case of low wintertime abundances). The consequences of this lack of overlap result in exacerbation of the effects of eutrophication; namely a lack of trophic transfer to mesozooplankton in this region and the sinking of phytodetritus to the benthos that fuels hypoxia.

  12. Persistent disturbance by commercial navigation afters the relative abundance of channel-dwelling fishes in a large river

    USGS Publications Warehouse

    Gutreuter, S.; Vallazza, J.M.; Knights, B.C.

    2006-01-01

    We provide the first evidence for chronic effects of disturbance by commercial vessels on the spatial distribution and abundance of fishes in the channels of a large river. Most of the world's large rivers are intensively managed to satisfy increasing demands for commercial shipping, but little research has been conducted to identify and alleviate any adverse consequences of commercial navigation. We used a combination of a gradient sampling design incorporating quasicontrol areas with Akaike's information criterion (AIC)-weighted model averaging to estimate effects of disturbances by commercial vessels on fishes in the upper Mississippi River. Species density, which mainly measured species evenness, decreased with increasing disturbance frequency. The most abundant species - gizzard shad (Dorosoma cepedianum) and freshwater drum (Aplodinotus grunniens) - and the less abundant shovelnose sturgeon (Scaphirhynchus platorhynchus) and flathead catfish (Pylodictis olivaris) were seemingly unaffected by traffic disturbance. In contrast, the relative abundance of the toothed herrings (Hiodon spp.), redhorses (Moxostoma spp.), buffaloes (Ictiobus spp.), channel catfish (Ictalurus punctatus), sauger (Sander canadensis), and white bass (Morone chrysops) decreased with increasing traffic in the navigation channel. We hypothesized that the combination of alteration of hydraulic features within navigation channels and rehabilitation of secondary channels might benefit channel-dependent species. ?? 2006 NRC.

  13. Relative Abundance of and Composition within Fungal Orders Differ between Cheatgrass (Bromus tectorum) and Sagebrush (Artemisia tridentata)-Associated Soils

    PubMed Central

    Weber, Carolyn F.; King, Gary M.; Aho, Ken

    2015-01-01

    Nonnative Bromus tectorum (cheatgrass) is decimating sagebrush steppe, one of the largest ecosystems in the Western United States, and is causing regional-scale shifts in the predominant plant-fungal interactions. Sagebrush, a native perennial, hosts arbuscular mycorrhizal fungi (AMF), whereas cheatgrass, a winter annual, is a relatively poor host of AMF. This shift is likely intertwined with decreased carbon (C)-sequestration in cheatgrass-invaded soils and alterations in overall soil fungal community composition and structure, but the latter remain unresolved. We examined soil fungal communities using high throughput amplicon sequencing (ribosomal large subunit gene) in the 0–4 cm and 4–8 cm depth intervals of six cores from cheatgrass- and six cores from sagebrush-dominated soils. Sagebrush core surfaces (0–4 cm) contained higher nitrogen and total C than cheatgrass core surfaces; these differences mirrored the presence of glomalin related soil proteins (GRSP), which has been associated with AMF activity and increased C-sequestration. Fungal richness was not significantly affected by vegetation type, depth or an interaction of the two factors. However, the relative abundance of seven taxonomic orders was significantly affected by vegetation type or the interaction between vegetation type and depth. Teloschistales, Spizellomycetales, Pezizales and Cantharellales were more abundant in sagebrush libraries and contain mycorrhizal, lichenized and basal lineages of fungi. Only two orders (Coniochaetales and Sordariales), which contain numerous economically important pathogens and opportunistic saprotrophs, were more abundant in cheatgrass libraries. Pleosporales, Agaricales, Helotiales and Hypocreales were most abundant across all libraries, but the number of genera detected within these orders was as much as 29 times lower in cheatgrass relative to sagebrush libraries. These compositional differences between fungal communities associated with cheatgrass- and

  14. Analysis of the c-src gene product structure, abundance, and protein kinase activity in human neuroblastoma and glioblastoma cells.

    PubMed

    O'Shaughnessy, J; Deseau, V; Amini, S; Rosen, N; Bolen, J B

    1987-01-01

    We have compared in different human neuroblastoma cell lines and human glioblastoma cells the expression level, structure, and tyrosine-specific protein kinase activity of pp60c-src. Our results show that not all human neuroblastoma cell lines express pp60c-src molecules with amino-terminal structural alterations. In neuroblastoma cells which possess pp60c-src with altered gel migration, the diminished polyacrylamide gel mobility of pp60c-src was found not to be dependent upon amino-terminal phosphorylations since extensive treatment of these molecules with phosphatase did not significantly change their gel migration properties. Similar differences in gel migration were observed when RNA from the various neuroblastoma and glioblastoma cells was translated in vitro using either rabbit reticulocyte or wheat germ lysates. White the level of c-src mRNA in the different cells analyzed was found to be similar, the abundance of pp60c-src in these same cells was found to vary by as much as 12-fold. This suggests that the abundance of pp60c-src in human neuroendocrine tumors is regulated through post-transcriptional and/or post-translational events which may be related to the stage of neuronal differentiation of the cells. Based upon determination of pp60c-src abundance by immunoblot analysis, we demonstrate that pp60c-src molecules derived from human neuroblastoma and glioblastoma cells have very similar in vitro protein kinase activities.

  15. Data-poor management of African lion hunting using a relative index of abundance.

    PubMed

    Edwards, Charles T T; Bunnefeld, Nils; Balme, Guy A; Milner-Gulland, E J

    2014-01-01

    Sustainable management of terrestrial hunting requires managers to set quotas restricting offtake. This often takes place in the absence of reliable information on the population size, and as a consequence, quotas are set in an arbitrary fashion, leading to population decline and revenue loss. In this investigation, we show how an indirect measure of abundance can be used to set quotas in a sustainable manner, even in the absence of information on population size. Focusing on lion hunting in Africa, we developed a simple algorithm to convert changes in the number of safari days required to kill a lion into a quota for the following year. This was tested against a simulation model of population dynamics, accounting for uncertainties in demography, observation, and implementation. Results showed it to reliably set sustainable quotas despite these uncertainties, providing a robust foundation for the conservation of hunted species.

  16. The abundance of fecal Faecalibacterium prausnitzii in relation to obesity and gender in Chinese adults.

    PubMed

    Feng, Jie; Tang, Huang; Li, Min; Pang, Xiaoyan; Wang, Linghua; Zhang, Menghui; Zhao, Yufeng; Zhang, Xiaojun; Shen, Jian

    2014-01-01

    The influence of gender and obesity on the abundance of human colonic Feacalibacterium prausnitzii is currently unclear. We collected fecal samples from 54 obese and 54 sex- and age-matched normal-weight Chinese adults and quantified the fecal F. prausnitzii as percentage of 16S rRNA gene copies of F. prausnitzii accounting to that of total gut bacteria with quantitative PCR. The fecal F. prausnitzii amount was not significantly different between obese and lean subjects. Men possessed significantly lower level of fecal F. prausnitzii than women, and the significant and positive correlation of fecal F. prausnitzii quantity with fasting glucose level was observed in men, not in women. Our results suggest that the gender effect, in addition to other factors including the geographic location, ethnicity, diet and gut transit times of study subjects, has to be considered when studying the relationship between gut F. prausnitzii and diseases.

  17. Relationship between Reproductive Allocation and Relative Abundance among 32 Species of a Tibetan Alpine Meadow: Effects of Fertilization and Grazing

    PubMed Central

    Niu, Kechang; Schmid, Bernhard; Choler, Philippe; Du, Guozhen

    2012-01-01

    Background Understanding the relationship between species traits and species abundance is an important goal in ecology and biodiversity science. Although theoretical studies predict that traits related to performance (e.g. reproductive allocation) are most directly linked to species abundance within a community, empirical investigations have rarely been done. It also remains unclear how environmental factors such as grazing or fertilizer application affect the predicted relationship. Methodology We conducted a 3-year field experiment in a Tibetan alpine meadow to assess the relationship between plant reproductive allocation (RA) and species relative abundance (SRA) on control, grazed and fertilized plots. Overall, the studied plant community contained 32 common species. Principal Findings At the treatment level, (i) RA was negatively correlated with SRA on control plots and during the first year on fertilized plots. (ii) No negative RA–SRA correlations were observed on grazed plots and during the second and third year on fertilized plots. (iii) Seed size was positively correlated with SRA on control plots. At the plot level, the correlation between SRA and RA were not affected by treatment, year or species composition. Conclusions/Significance Our study shows that the performance-related trait RA can negatively affect SRA within communities, which is possibly due to the tradeoffs between clonal growth (for space occupancy) and sexual reproduction. We propose that if different species occupy different positions along these tradeoffs it will contribute to biodiversity maintenance in local communities or even at lager scale. PMID:22536385

  18. Abundance of thraustochytrids and bacteria in the equatorial Indian Ocean, in relation to transparent exopolymeric particles (TEPs).

    PubMed

    Damare, Varada; Raghukumar, Seshagiri

    2008-07-01

    Thraustochytrid protists are often abundant in coastal waters. However, their population dynamics and substrate preferences in the oceanic water column are poorly understood. We studied the abundance and distribution of thraustochytrids, bacteria and TEPs in the equatorial Indian Ocean waters during September 2003, October 2004 and September 2006. Thraustochytrids and bacteria were abundant, suggesting high biological productivity of the region. Thraustochytrids were positively related to bacteria during October 2004 but not at other times, suggesting overlapping or varying substrate preferences at different times. Thraustochytrid and bacteria were positively related to TEPs only in a few stations during October 2004, but were mostly positively related to TEPs generated from in situ water in a roller table experiment. TEPs from natural samples during October 2004 had a much greater affinity to the lectin Concanavalin A than to Limulin compared with those in September 2006 and from the roller tank experiments. The chemical composition of TEPs might explain their relationship with thraustochytrids. Thraustochytrids averaged a higher biomass than bacteria in two of the three cruises, but were less frequent and more patchily distributed compared with bacteria.

  19. Variations in Abundance Enhancements in Impulsive Solar Energetic-Particle Events and Related CMEs and Flares

    NASA Astrophysics Data System (ADS)

    Reames, Donald V.; Cliver, Edward W.; Kahler, Stephen W.

    2014-12-01

    We study event-to-event variations in the abundance enhancements of the elements He through Pb for Fe-rich impulsive solar energetic-particle (SEP) events, and their relationship with properties of associated coronal mass ejections (CMEs) and solar flares. Using a least-squares procedure we fit the power-law enhancement of element abundances as a function of their mass-to-charge ratio A/ Q to determine both the power and the coronal temperature (which determines Q) in each of 111 impulsive SEP events identified previously. Individual SEP events with the steepest element enhancements, e.g. ˜ ( A/ Q)6, tend to be smaller, lower-fluence events with steeper energy spectra that are associated with B- and C-class X-ray flares, with cooler (˜ 2.5 MK) coronal plasma, and with narrow (< 100∘), slower (< 700 km s-1) CMEs. On the other hand, higher-fluence SEP events have flatter energy spectra, less-dramatic heavy-element enhancements, e.g. ˜ ( A/ Q)3, and come from somewhat hotter coronal plasma (˜ 3.2 MK) associated with C-, M-, and even X-class X-ray flares and with wider CMEs. Enhancements in 3He/4He are uncorrelated with those in heavy elements. However, events with 3He/4He≥0.1 are even more strongly associated with narrow, slow CMEs, with cooler coronal plasma, and with B- and C-class X-ray flares than are other Fe-rich impulsive SEP events with smaller enhancements of 3He.

  20. How to link the relative abundances of gas species in coma of comets to their initial chemical composition?

    NASA Astrophysics Data System (ADS)

    Marboeuf, Ulysse; Schmitt, Bernard

    2014-11-01

    Comets are expected to be the most primitive objects in the Solar System. The chemical composition of these objects is frequently assumed to be directly provided by the observations of the abundances of volatile molecules in the coma. The present work aims to determine the relationship between the chemical composition of the coma, the outgassing profile of volatile molecules and the internal chemical composition, and water ice structure of the nucleus, and physical assumptions on comets. To do this, we have developed a quasi 3D model of a cometary nucleus which takes into account all phase changes and water ice structures (amorphous, crystalline, clathrate, and a mixture of them); we have applied this model to the Comet 67P/Churyumov-Gerasimenko, the target of the Rosetta mission. We find that the outgassing profile of volatile molecules is a strong indicator of the physical and thermal properties (water ice structure, thermal inertia, abundances, distribution, physical differentiation) of the solid nucleus. Day/night variations of the rate of production of species helps to distinguish the clathrate structure from other water ice structures in nuclei, implying different thermodynamic conditions of cometary ice formation in the protoplanetary disc. The relative abundance (to H2O) of volatile molecules released from the nucleus interior varies by some orders of magnitude as a function of the distance to the Sun, the volatility of species, their abundance and distribution between the "trapped" and "condensed" states, the structure of water ice, and the thermal inertia and other physical assumptions (dust mantle, …) on the nucleus. For the less volatile molecules such as CO2 and H2S, the relative (to H2O) abundance of species in coma remain similar to the primitive composition of the nucleus (relative deviation less than 25%) only around the perihelion passage (in the range -3 to -2 to +2-3 AU), whatever is the water ice structure and chemical composition, and under

  1. Detailed abundance analysis of five field blue horizontal-branch stars

    NASA Astrophysics Data System (ADS)

    Kafando, I.; LeBlanc, F.; Robert, C.

    2016-06-01

    Previous studies have shown that hot blue horizontal-branch (BHB) stars in globular clusters present abundance anomalies of certain chemical elements in their atmosphere; some metals are overabundant while helium is underabundant. Vertical stratification of chemical species, including iron, is also found in the atmosphere of a number of these objects. The aim of our work is to do a detailed abundance analysis of BHB stars found in the field. We studied the stars HD 128801, HD 143459, HD 213781, and HZ 27, using our high-resolution spectra in the visible region obtained with ESPaDOnS at the Canada-France-Hawaii Telescope, and also Feige 86, using existing Ultraviolet and Visual Echelle Spectrograph visible spectra from the ESO archives. We searched for vertical stratification of the elements identified in our five stars, with the ZEEMAN2 code and stellar model atmospheres of PHOENIX. We confirm here the star rotational and radial velocities previously found, along with their average abundances. For the three cooler stars in our sample (HD 128801, HD 143459, and HZ 27), most elements detected are underabundant. For the two hotter stars (Feige 86 and HD 213781), the abundances of most elements are near or above their solar value. Of all the elements studied, only phosphorus is clearly found to be vertically stratified in the atmosphere of HD 213781. Marginal indications of vertical stratification of iron is observed for Feige 86. The chemical properties of the five field BHB stars are consistent with those of their globular-cluster counterparts.

  2. A spectroscopic study of southern (candidate) γ Doradus stars. II. Detailed abundance analysis and fundamental parameters

    NASA Astrophysics Data System (ADS)

    Bruntt, H.; De Cat, P.; Aerts, C.

    2008-02-01

    Context: The γ Doradus stars are a recent class of variable main sequence F-type stars located on the red edge of the Cepheid instability strip. They pulsate in gravity modes, and this makes them particularly interesting for detailed asteroseismic analysis, which can provide fundamental knowledge of properties near the convective cores of intermediate-mass main sequence stars. Aims: To improve current understanding of γ Dor stars through theoretical modelling, additional constraints are needed. Our aim is to estimate the fundamental atmospheric parameters and determine the chemical composition of these stars. Detailed analyses of single stars have previously suggested links to Am and λ Boo stars, so we wish to explore this interesting connection between chemical peculiarity and pulsation. Methods: We analysed a sample of γ Dor stars for the first time, including nine bona fide and three candidate members of the class. We determined the fundamental atmospheric parameters and compared the abundance pattern with other A-type stars. We used the semi-automatic software package VWA for the analysis. This code relies on the calculation of synthetic spectra and thus takes line-blending into account. This is important because of the fast rotation in some of the sample stars, and we made a thorough analysis of how VWA performs when increasing v sin i. We obtained good results in agreement with previously derived fundamental parameters and abundances in a few selected reference stars with properties similar to the γ Dor stars. Results: We find that the abundance pattern in the γ Dor stars is not distinct from the constant A- and F-type stars we analysed. Appendices A and B are only available in electronic form at http://www.aanda.org

  3. Vegetation affects the relative abundances of dominant soil bacterial taxa and soil respiration rates in an upland grassland soil.

    PubMed

    Thomson, Bruce C; Ostle, Nick; McNamara, Niall; Bailey, Mark J; Whiteley, Andrew S; Griffiths, Robert I

    2010-02-01

    Plant-derived organic matter inputs are thought to be a key driver of soil bacterial community composition and associated soil processes. We sought to investigate the role of acid grassland vegetation on soil bacterial community structure by assessing bacterial diversity in combination with other soil variables in temporally and spatially distinct samples taken from a field-based plant removal experiment. Removal of aboveground vegetation resulted in reproducible differences in soil properties, soil respiration and bacterial diversity. Vegetated soils had significantly increased carbon and nitrogen concentrations and exhibited higher rates of respiration. Molecular analyses revealed that the soils were broadly dominated by Alphaproteobacterial and Acidobacterial lineages, with increased abundances of Alphaproteobacteria in vegetated soils and more Acidobacteria in bare soils. This field-based study contributes to a growing body of evidence documenting the effect of soil nutrient status on the relative abundances of dominant soil bacterial taxa, with Proteobacterial taxa dominating over Acidobacteria in soils exhibiting higher rates of C turnover. Furthermore, we highlight the role of aboveground vegetation in mediating this effect by demonstrating that plant removal can alter the relative abundances of dominant soil taxa with concomitant changes in soil CO(2)-C efflux.

  4. The CagA toxin of Helicobacter pylori: abundant production but relatively low amount translocated

    PubMed Central

    Jiménez-Soto, Luisa F.; Haas, Rainer

    2016-01-01

    CagA is one of the most studied pathogenicity factors of the bacterial pathogen Helicobacter pylori. It is injected into host cells via the H. pylori cag-Type IV secretion system. Due to its association with gastric cancer, CagA is classified as oncogenic protein. At the same time CagA represents the 4th most abundant protein produced by H. pylori, suggesting that high amounts of toxin are required to cause the physiological changes or damage observed in cells. We were able to quantify the injection of CagA into gastric AGS epithelial cells in vitro by the adaptation of a novel protease-based approach to remove the tightly adherent extracellular bacteria. After one hour of infection only 1.5% of the total CagA available was injected by the adherent bacteria, whereas after 3 hours 7.5% was found within the host cell. Thus, our data show that only a surprisingly small amount of the CagA available in the infection is finally injected under in vitro infection conditions. PMID:26983895

  5. 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

  6. 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.

  7. Bacterial and archaeal symbionts in the South China Sea sponge Phakellia fusca: community structure, relative abundance, and ammonia-oxidizing populations.

    PubMed

    Han, Minqi; Liu, Fang; Zhang, Fengli; Li, Zhiyong; Lin, Houwen

    2012-12-01

    Many biologically active natural products have been isolated from Phakellia fusca, an indigenous sponge in the South China Sea; however, the microbial symbionts of Phakellia fusca remain unknown. The present investigations on sponge microbial community are mainly based on qualitative analysis, while quantitative analysis, e.g., relative abundance, is rarely carried out, and little is known about the roles of microbial symbionts. In this study, the community structure and relative abundance of bacteria, actinobacteria, and archaea associated with Phakellia fusca were revealed by 16S rRNA gene library-based sequencing and quantitative real time PCR (qRT-PCR). The ammonia-oxidizing populations were investigated based on amoA gene and anammox-specific 16S rRNA gene libraries. As a result, it was found that bacterial symbionts of sponge Phakellia fusca consist of Proteobacteria including Gamma-, Alpha-, and Delta-proteobacteria, Cyanobacteria with Gamma-proteobacteria as the predominant components. In particular, the diversity of actinobacterial symbionts in Phakellia fusca is high, which is composed of Corynebacterineae, Acidimicrobidae, Frankineae, Micrococcineae, and Streptosporangineae. All the observed archaea in sponge Phakellia fusca belong to Crenarchaeota, and the detected ammonia-oxidizing populations are ammonia-oxidizing archaea, suggesting the nitrification function of sponge archaeal symbionts. According to qRT-PCR analysis, bacterial symbionts dominated the microbial community, while archaea represented the second predominant symbionts, followed by actinobacteria. The revealed diverse prokaryotic symbionts of Phakellia fusca are valuable for the understanding and in-depth utilization of Phakellia fusca microbial symbionts. This study extends our knowledge of the community, especially the relative abundance of microbial symbionts in sponges.

  8. Abundance and productivity of bacterioplankton in relation to seasonal upwelling in the northwest Indian Ocean

    NASA Astrophysics Data System (ADS)

    Wiebinga, Cas J.; Veldhuis, Marcel J. W.; De Baar, Hein J. W.

    1997-03-01

    The role of bacterioplankton in the Somali Current, the Gulf of Aden and the Red Sea was studied during the SW- (May-August 1992) and NE-monsoon (January-February 1993). The diversity in physical and biological characteristics of the regions and seasons is reflected in a broad range of both phyto- and bacterioplankton production. During the SW-monsoon, the Somali current showed highest bacterial production (up to 849 mgC m -2 day -1) in regions with enrichment of the surface waters by upwelling of cold, nutrient-rich, deep water. In contrast, the Gulf of Aden and the Red Sea were most productive during the NE-monsoon (average 225 mgC m -2 day -1). Depth profiles of the upper 300 m in general showed a subsurface maximum in bacterial abundance and production at 20-70 m depth. Heterotrophic activity and primary production were closely correlated, indicating the dependence of bacterioplankton on local phytoplankton-derived organic carbon and their ability to adapt quickly to changes in the environment. The bacterial carbon demand in the upper 300 m of the water column was largely supplied by phytoplankton production in the euphotic zone. Bacterial production was 18 ± 7% (average ± S.D.) of primary production. Assuming an assimilation efficiency of 50% for marine bacteria, they consumed up to half of the carbon produced by the phytoplankton. Cycling of carbon within the euphotic zone appears to be achieved by intense grazing by (micro)zooplankton and subsequent remineralization.

  9. Natural landscape and stream segment attributes influencing the distribution and relative abundance of riverine smallmouth bass in Missouri

    USGS Publications Warehouse

    Brewer, S.K.; Rabeni, C.F.; Sowa, S.P.; Annis, G.

    2007-01-01

    Protecting and restoring fish populations on a regional basis are most effective if the multiscale factors responsible for the relative quality of a fishery are known. We spatially linked Missouri's statewide historical fish collections to environmental features in a geographic information system, which was used as a basis for modeling the importance of landscape and stream segment features in supporting a population of smallmouth bass Micropterus dolomieu. Decision tree analyses were used to develop probability-based models to predict statewide occurrence and within-range relative abundances. We were able to identify the range of smallmouth bass throughout Missouri and the probability of occurrence within that range by using a few broad landscape variables: the percentage of coarse-textured soils in the watershed, watershed relief, and the percentage of soils with low permeability in the watershed. The within-range relative abundance model included both landscape and stream segment variables. As with the statewide probability of occurrence model, soil permeability was particularly significant. The predicted relative abundance of smallmouth bass in stream segments containing low percentages of permeable soils was further influenced by channel gradient, stream size, spring-flow volume, and local slope. Assessment of model accuracy with an independent data set showed good concordance. A conceptual framework involving naturally occurring factors that affect smallmouth bass potential is presented as a comparative model for assessing transferability to other geographic areas and for studying potential land use and biotic effects. We also identify the benefits, caveats, and data requirements necessary to improve predictions and promote ecological understanding. ?? Copyright by the American Fisheries Society 2007.

  10. Long-term Prairie Falcon population changes in relation to prey abundance, weather, land uses, and habitat conditions

    USGS Publications Warehouse

    Steenhof, K.; Kochert, M.N.; Carpenter, L.B.; Lehman, R.N.

    1999-01-01

    We studied a nesting population of Prairie Falcons (Falco mexicanus) in the Snake River Birds of Prey National Conservation Area (NCA) from 1974-1997 to identify factors that influence abundance and reproduction. Our sampling period included two major droughts and associated crashes in Townsend's ground squirrel (Spermophilus townsendii) populations. The number of Prairie Falcon pairs found on long-term survey segments declined significantly from 1976-1997. Early declines were most severe at the eastern end of the NCA, where fires and agriculture have changed native shrubsteppe habitat. More recent declines occurred in the portion of canyon near the Orchard Training Area (OTA), where the Idaho Army National Guard conducts artillery firing and tank maneuvers. Overall Prairie Falcon reproductive rates were tied closely to annual indexes of ground squirrel abundance, but precipitation before and during the breeding season was related inversely to some measures of reproduction. Most reproductive parameters showed no significant trends over time, but during the 1990s, nesting success and productivity were lower in the stretch of canyon near the OTA than in adjacent areas. Extensive shrub loss, by itself, did not explain the pattern of declines in abundance and reproduction that we observed. Recent military training activities likely have interacted with fire and livestock grazing to create less than favorable foraging opportunities for Prairie Falcons in a large part of the NCA. To maintain Prairie Falcon populations in the NCA, managers should suppress wildfires, restore native plant communities, and regulate potentially incompatible land uses.

  11. Long-term prairie falcon population changes in relation to prey abundance, weather, land uses, and habitat conditions

    USGS Publications Warehouse

    Steenhof, Karen; Kochert, Michael N.; Carpenter, L.B.; Lehman, Robert N.

    1999-01-01

    We studied a nesting population of Prairie Falcons( Falco mexicanus) in the Snake River Birds of Prey National Conservation Area (NCA) from 1974-1997 to identify factors that influence abundance and reproduction. Our sampling period included two major droughts and associated crashes in Townsenda??s ground squirrel (Spermophilus townsendii) populations. The number of Prairie Falcon pairs found on long-term survey segments declined significantly from 1976-1997. Early declines were most severe at the eastern end of the NCA, where fires and agriculture have changed native shrubsteppe habitat. More recent declines occurred in the portion of canyon near the Orchard Training Area (OTA), where the Idaho Army National Guard conducts artillery firing and tank maneuvers. Overall Prairie Falcon reproductive rates were tied closely to annual indexes of ground squirrel abundance, but precipitation before and during the breeding season was related inversely to some measures of reproduction. Most reproductive parameters showed no significant trends over time, but during the 199Os, nesting success and productivity were lower in the stretch of canyon near the OTA than in adjacent areas. Extensive shrub loss, by itself, did not explain the pattern of declines in abundance and reproduction that we observed. Recent military training activities likely have interacted with fire and livestock grazing to create less than favorable foraging opportunities for Prairie Falcons in a large part of the NCA. To maintain Prairie Falcon populations in the NCA, managers should suppress wildfires, restore native plant communities, and regulate potentially incompatible land uses.

  12. Accurate abundance analysis of late-type stars: advances in atomic physics

    NASA Astrophysics Data System (ADS)

    Barklem, Paul S.

    2016-05-01

    The measurement of stellar properties such as chemical compositions, masses and ages, through stellar spectra, is a fundamental problem in astrophysics. Progress in the understanding, calculation and measurement of atomic properties and processes relevant to the high-accuracy analysis of F-, G-, and K-type stellar spectra is reviewed, with particular emphasis on abundance analysis. This includes fundamental atomic data such as energy levels, wavelengths, and transition probabilities, as well as processes of photoionisation, collisional broadening and inelastic collisions. A recurring theme throughout the review is the interplay between theoretical atomic physics, laboratory measurements, and astrophysical modelling, all of which contribute to our understanding of atoms and atomic processes, as well as to modelling stellar spectra.

  13. Spectroscopic survey of γ Doradus stars - I. Comprehensive atmospheric parameters and abundance analysis of γ Doradus stars

    NASA Astrophysics Data System (ADS)

    Kahraman Aliçavuş, F.; Niemczura, E.; De Cat, P.; Soydugan, E.; Kołaczkowski, Z.; Ostrowski, J.; Telting, J. H.; Uytterhoeven, K.; Poretti, E.; Rainer, M.; Suárez, J. C.; Mantegazza, L.; Kilmartin, P.; Pollard, K. R.

    2016-05-01

    We present a spectroscopic survey of known and candidate γ Doradus stars. The high-resolution, high signal-to-noise spectra of 52 objects were collected by five different spectrographs. The spectral classification, atmospheric parameters (Teff, log g, ξ), vsin i and chemical composition of the stars were derived. The stellar spectral and luminosity classes were found between G0-A7 and IV-V, respectively. The initial values for Teff and log g were determined from the photometric indices and spectral energy distribution. Those parameters were improved by the analysis of hydrogen lines. The final values of Teff, log g and ξ were derived from the iron lines analysis. The Teff values were found between 6000 K and 7900 K, while log g values range from 3.8 to 4.5 dex. Chemical abundances and vsin i values were derived by the spectrum synthesis method. The vsin i values were found between 5 and 240 km s-1. The chemical abundance pattern of γ Doradus stars were compared with the pattern of non-pulsating stars. It turned out that there is no significant difference in abundance patterns between these two groups. Additionally, the relations between the atmospheric parameters and the pulsation quantities were checked. A strong correlation between the vsin i and the pulsation periods of γ Doradus variables was obtained. The accurate positions of the analysed stars in the Hertzsprung-Russell diagram have been shown. Most of our objects are located inside or close to the blue edge of the theoretical instability strip of γ Doradus.

  14. Enzymatic activities and prokaryotic abundance in relation to organic matter along a West-East Mediterranean transect (TRANSMED cruise).

    PubMed

    Zaccone, R; Boldrin, A; Caruso, G; La Ferla, R; Maimone, G; Santinelli, C; Turchetto, M

    2012-07-01

    The distribution of extracellular enzymatic activities (EEA) [leucine aminopeptidase (LAP), ß-glucosidase (GLU), alkaline phosphatase (AP)], as well as that of prokaryotic abundance (PA) and biomass (PB), dissolved organic carbon (DOC), particulate organic carbon and particulate total nitrogen (POC, PTN), was determined in the epi-, meso-, and bathypelagic waters of the Mediterranean Sea along a West-East transect and at one Atlantic station located outside the Strait of Gibraltar. This study represents a synoptical evaluation of the microbial metabolism during early summer. Decreasing trends with depth were observed for most of the parameters (PA, PB, AP, DOC, POC, PTN). Significant differences between the western and eastern basins of the Mediterranean Sea were found, displaying higher rates of LAP and GLU and lower C/N ratios more in the eastern than in the western areas. Conversely, in the epipelagic layer, PA and PB were found to be higher in the western than in the eastern basins. PB was significantly related to DOC concentration (all data, n = 145, r = 0.53, P < 0.01), while significant correlations of EEA with POC and PTN were found in the epipelagic layer, indicating an active response of microbial metabolism to organic substrates. Specific enzyme activities normalized to cell abundance pointed out high values of LAP and GLU in the bathypelagic layer, especially in the eastern basin, while cell-specific AP was high in the epi- and bathypelagic zone of the eastern basin indicating a rapid regeneration of inorganic P for both prokaryotes and phytoplankton needs. Low activity and abundance characterized the Atlantic station, while opposite trends of these parameters were observed along the Mediterranean transect, showing the uncoupling between abundance and activity data. In the east Mediterranean Sea, decomposition processes increased probably in response to mesoscale structures which lead to organic matter downwelling. PMID:22349935

  15. Abundance and diversity of ammonia-oxidizing bacteria in relation to ammonium in a chinese shallow eutrophic urban lake

    PubMed Central

    Qiu, Shanlian; Chen, Guoyuan; Zhou, Yiyong

    2010-01-01

    The measures of most-probable-number and restriction fragment length polymorphism analysis were used to analyze the abundance and diversity of ammonia-oxidizing bacteria in sediment of a Chinese shallow eutrophic urban lake (Lake Yuehu). Among the 5 sampling sites, ammonia concentration in interstitial water was positively proportional not only to the content of organic matter, but also to ammonia-oxidizing bacteria numbers (at a magnitude of 105 cells g-1 dry weight) in sediment significantly. Furthermore, the diversity of ammonia-oxidizing bacteria were determined by means of PCR primers targeting the amoA gene with five gene libraries created and restriction pattern analysis. The 13 restriction patterns were recorded with 4 ones being common among all sampling sites. The 8 restriction patterns including 4 unique ones were found at the site with the highest NH4+ concentrations in interstitial water, while, there were only common patterns without unique ones at the site with the lowest NH4+ concentrations in interstitial water. Phylogenetic analysis showed that the amoA fragments retrieved belong to Nitrosomonas oligotropha & ureae lineage, N. europaea lineage, N. communis lineage and Nitrosospira lineage, most of which were affiliated with the genus Nitrosomonas. The N. oligotropha & ureae-like bacteria were the dominant species. Thus, the abundance and diversity of sediment AOB is closely linked to ammonium status in eutrophic lakes. PMID:24031484

  16. Meta-analysis: abundance, behavior, and hydraulic energy shape biotic effects on sediment transport in streams.

    PubMed

    Albertson, L K; Allen, D C

    2015-05-01

    An increasing number of studies have emphasized the need to bridge the disciplines of ecology and geomorphology. A large number of case studies show that organisms can affect erosion, but a comprehensive understanding of biological impacts on sediment transport conditions is still lacking. We use meta-analysis to synthesize published data to quantify the effects of the abundance, body size, and behavior of organisms on erosion in streams. We also explore the influence of current velocity, discharge, and sediment grain size on the strength of biotic effects on erosion. We found that species that both increase erosion (destabilizers) and decrease erosion (stabilizers) can alter incipient sediment motion, sediment suspension, and sediment deposition above control conditions in which the organisms were not present. When abundance was directly manipulated, these biotic effects were consistently stronger in the higher abundance treatment, increasing effect sizes by 66%. Per capita effect size and per capita biomass were also consistently positively correlated. Fish and crustaceans were the most studied organisms, but aquatic insects increased the effect size by 550 x compared to other types of organisms after accounting for biomass. In streams with lower discharge and smaller grain sizes, we consistently found stronger biotic effects. Taken collectively, these findings provide synthetic evidence that biology can affect physical processes in streams, and these effects can be mediated by hydraulic energy. We suggest that future studies focus on understudied organisms, such as biofilms, conducting experiments under realistic field conditions, and developing hypotheses for the effect of biology on erosion and velocity currents in the context of restoration to better understand the forces that mediate physical disturbances in stream ecosystems. PMID:26236846

  17. Meta-analysis: abundance, behavior, and hydraulic energy shape biotic effects on sediment transport in streams.

    PubMed

    Albertson, L K; Allen, D C

    2015-05-01

    An increasing number of studies have emphasized the need to bridge the disciplines of ecology and geomorphology. A large number of case studies show that organisms can affect erosion, but a comprehensive understanding of biological impacts on sediment transport conditions is still lacking. We use meta-analysis to synthesize published data to quantify the effects of the abundance, body size, and behavior of organisms on erosion in streams. We also explore the influence of current velocity, discharge, and sediment grain size on the strength of biotic effects on erosion. We found that species that both increase erosion (destabilizers) and decrease erosion (stabilizers) can alter incipient sediment motion, sediment suspension, and sediment deposition above control conditions in which the organisms were not present. When abundance was directly manipulated, these biotic effects were consistently stronger in the higher abundance treatment, increasing effect sizes by 66%. Per capita effect size and per capita biomass were also consistently positively correlated. Fish and crustaceans were the most studied organisms, but aquatic insects increased the effect size by 550 x compared to other types of organisms after accounting for biomass. In streams with lower discharge and smaller grain sizes, we consistently found stronger biotic effects. Taken collectively, these findings provide synthetic evidence that biology can affect physical processes in streams, and these effects can be mediated by hydraulic energy. We suggest that future studies focus on understudied organisms, such as biofilms, conducting experiments under realistic field conditions, and developing hypotheses for the effect of biology on erosion and velocity currents in the context of restoration to better understand the forces that mediate physical disturbances in stream ecosystems.

  18. Estimating number of species and relative abundances in stream-fish communities: effects of sampling effort and discontinuous spatial distributions

    USGS Publications Warehouse

    Angermeier, Paul L.; Smogor, Roy A.

    1995-01-01

    We sampled fishes and measured microhabitat in series of contiguous habitat units (riffles, runs, pools) in three Virginia streams. We used Monte Carlo simulations to construct hypothetical series of habitat units, then examined how number of species, similarity in relative abundances, and number of microhabitats accumulated with increasing number of habitat units (i.e., sampling effort). Proportions of all species and microhabitats represented were relatively low and variable at low sampling effort, but increased asymptotically and became less variable with greater sampling effort. To facilitate comparisons among streams, we fitted simulation results to negative exponential curves. The curves indicated that 90% of the species present were usually found by sampling 5 to 14 habitat units (stream length of 22–67 stream widths). Estimates of species relative abundances required less sampling effort for a given accuracy than estimates of number of species. Rates of species accumulation (with effort) varied among streams and reflected discontinuity in species distributions among habitat units. Most discontinuity seemed to be due to low population density rather than to habitat selectivity. Results from an Illinois stream corroborated our findings from Virginia, and suggested that greater sampling effort is needed to characterize fish community structure in more homogeneous stream reaches.

  19. Abundance quantification by independent component analysis of hyperspectral imagery for oil spill coverage calculation

    NASA Astrophysics Data System (ADS)

    Han, Zhongzhi; Wan, Jianhua; Zhang, Jie; Zhang, Hande

    2016-08-01

    The estimation of oil spill coverage is an important part of monitoring of oil spills at sea. The spatial resolution of images collected by airborne hyper-spectral remote sensing limits both the detection of oil spills and the accuracy of estimates of their size. We consider at-sea oil spills with zonal distribution in this paper and improve the traditional independent component analysis algorithm. For each independent component we added two constraint conditions: non-negativity and constant sum. We use priority weighting by higher-order statistics, and then the spectral angle match method to overcome the order nondeterminacy. By these steps, endmembers can be extracted and abundance quantified simultaneously. To examine the coverage of a real oil spill and correct our estimate, a simulation experiment and a real experiment were designed using the algorithm described above. The result indicated that, for the simulation data, the abundance estimation error is 2.52% and minimum root mean square error of the reconstructed image is 0.030 6. We estimated the oil spill rate and area based on eight hyper-spectral remote sensing images collected by an airborne survey of Shandong Changdao in 2011. The total oil spill area was 0.224 km2, and the oil spill rate was 22.89%. The method we demonstrate in this paper can be used for the automatic monitoring of oil spill coverage rates. It also allows the accurate estimation of the oil spill area.

  20. Direct mutation analysis by high-throughput sequencing: from germline to low-abundant, somatic variants

    PubMed Central

    Gundry, Michael; Vijg, Jan

    2011-01-01

    DNA mutations are the source of genetic variation within populations. The majority of mutations with observable effects are deleterious. In humans mutations in the germ line can cause genetic disease. In somatic cells multiple rounds of mutations and selection lead to cancer. The study of genetic variation has progressed rapidly since the completion of the draft sequence of the human genome. Recent advances in sequencing technology, most importantly the introduction of massively parallel sequencing (MPS), have resulted in more than a hundred-fold reduction in the time and cost required for sequencing nucleic acids. These improvements have greatly expanded the use of sequencing as a practical tool for mutation analysis. While in the past the high cost of sequencing limited mutation analysis to selectable markers or small forward mutation targets assumed to be representative for the genome overall, current platforms allow whole genome sequencing for less than $5,000. This has already given rise to direct estimates of germline mutation rates in multiple organisms including humans by comparing whole genome sequences between parents and offspring. Here we present a brief history of the field of mutation research, with a focus on classical tools for the measurement of mutation rates. We then review MPS, how it is currently applied and the new insight into human and animal mutation frequencies and spectra that has been obtained from whole genome sequencing. While great progress has been made, we note that the single most important limitation of current MPS approaches for mutation analysis is the inability to address low-abundance mutations that turn somatic tissues into mosaics of cells. Such mutations are at the basis of intra-tumor heterogeneity, with important implications for clinical diagnosis, and could also contribute to somatic diseases other than cancer, including aging. Some possible approaches to gain access to low-abundance mutations are discussed, with a

  1. Diversity and abundance of mosquito species in relation to their larval habitats in Mizoram, North Eastern Himalayan region.

    PubMed

    Vanlalruia, Khawling; Senthilkumar, Nachimuthu; Gurusubramanian, Guruswami

    2014-09-01

    The abundance, richness and diversity of anopheline and culicid mosquitoes associated with their habitats, season, and physico-chemical quality of water were surveyed along six districts of Mizoram, North Eastern Himalayan region. The productivity of permanent and temporary habitat types was quantified by carrying out weekly larval sampling using a standard dipping method for a period of three years. Diversity was estimated using the Shannon index (H'), Evenness index (Heve), similarity measures cluster analysis and MANOVA. In total, 5 genera and 20 species of mosquitoes were identified: Culex quinquefasciatus, Anopheles barbirostris and Anopheles vagus were the most abundant and widely-distributed species, representing 39.71%, 29.39% and 14.52% of total mosquito individuals sampled, respectively. Anopheles sp. diversity was lowest in Lunglei district (H'=0.48) and highest in Aizawl (H'=2.03), whereas Culex sp. diversity was lowest in Lawngtlai (H'=0.38), and highest in Aizawl (H'=2.99) and Kolasib (H'=2.13). This represents the first update on the diversity and geographic distribution of the mosquitoes of Mizoram. Mosquito larvae were present in both temporary and permanent habitats suitable for breeding with monthly variations dependent on rainfall intensity, temperature, humidity and location. Early instars were more abundant significantly (P<0.0001) than late instars among the habitat types in all study sites. The productivity of mosquito larvae was significantly (P<0.0001) higher in ponds especially in permanent than semi-permanent and temporary. Weekly rainfall intensity led to an increase or decrease in anopheline and culicid larval abundance depending on the location. Mosquito diversity was highest in monsoon season (July-September) and lowest in January-March. A. barbirostris, A. vagus and C. quinquefasciatus appear the most likely habitat generalist as it demonstrates both widespread distribution. Abundance and diversity of culicine and anopheline larvae

  2. High-resolution abundance analysis of very metal-poor r-I stars

    NASA Astrophysics Data System (ADS)

    Siqueira Mello, C.; Hill, V.; Barbuy, B.; Spite, M.; Spite, F.; Beers, T. C.; Caffau, E.; Bonifacio, P.; Cayrel, R.; François, P.; Schatz, H.; Wanajo, S.

    2014-05-01

    Context. Moderately r-process-enriched stars (r-I; +0.3 ≤ [Eu/Fe] ≤ +1.0) are at least four times as common as those that are greatly enriched in r-process elements (r-II; [Eu/Fe] > +1.0), and the abundances in their atmospheres are important tools for obtaining a better understanding of the nucleosynthesis processes responsible for the origin of the elements beyond the iron peak. Aims: The main aim of this work is to derive abundances for a sample of seven metal-poor stars with -3.4 ≤ [Fe/H] ≤ -2.4 classified as r-I stars, to understand the role of these stars for constraining the astrophysical nucleosynthesis event(s) that is (are) responsible for the production of the r-process, and to investigate whether they differ, in any significant way, from the r-II stars. Methods: We carried out a detailed abundance analysis based on high-resolution spectra obtained with the VLT/UVES spectrograph, using spectra in the wavelength ranges 3400-4500 Å, 6800-8200 Å, and 8700-10 000 Å, with resolving power R ~ 40 000 (blue arm) and R ~ 55 000 (red arm). The OSMARCS LTE 1D model atmosphere grid was employed, along with the spectrum synthesis code Turbospectrum. Results: We have derived abundances of the light elements Li, C, and N, the α-elements Mg, Si, S, Ca, and Ti, the odd-Z elements Al, K, and Sc, the iron-peak elements V, Cr, Mn, Fe, Co, and Ni, and the trans-iron elements from the first peak (Sr, Y, Zr, Mo, Ru, and Pd), the second peak (Ba, La, Ce, Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, and Yb), the third peak (Os and Ir, as upper limits), and the actinides (Th) regions. The results are compared with values for these elements for r-II and "normal" very and extremely metal-poor stars reported in the literature, ages based on radioactive chronometry are explored using different models, and a number of conclusions about the r-process and the r-I stars are presented. Hydrodynamical models were used for some elements, and general behaviors for the 3D corrections

  3. Immune modulatory function of abundant immune-related microRNAs in microvesicles from bovine colostrum.

    PubMed

    Sun, Qi; Chen, Xi; Yu, Jianxiong; Zen, Ke; Zhang, Chen-Yu; Li, Liang

    2013-03-01

    Colostrum provides essential nutrients and immunologically active factors that are beneficial to newborns. Our previous work demonstrated that milk contains large amounts of miRNA that is largely stored in milk-derived microvesicles (MVs). In the present study, we found that the MVs from colostrum contain significantly higher levels of several immune-related miRNAs. We hypothesized that the colostrum MVs may transfer the immune-related miRNAs into cells, which contribute to its immune modulatory feature. We isolated colostrum MVs by ultracentrifugation and demonstrated several immune modulation features associated with miRNAs. We also provide evidence that the physical structure of milk-derived MVs is essential for transfer miRNAs and following immune modulation effect. Moreover, we found that colostrum powder-derived MVs also contains higher levels of immune-related miRNAs that display similar immune modulation effects. Taken together, these results show that MV-containing immunerelated miRNAs may be a novel mechanism by which colostrum modulates body immune response. PMID:23483481

  4. Reef sharks exhibit site-fidelity and higher relative abundance in marine reserves on the Mesoamerican Barrier Reef.

    PubMed

    Bond, Mark E; Babcock, Elizabeth A; Pikitch, Ellen K; Abercrombie, Debra L; Lamb, Norlan F; Chapman, Demian D

    2012-01-01

    Carcharhinid sharks can make up a large fraction of the top predators inhabiting tropical marine ecosystems and have declined in many regions due to intense fishing pressure. There is some support for the hypothesis that carcharhinid species that complete their life-cycle within coral reef ecosystems, hereafter referred to as "reef sharks", are more abundant inside no-take marine reserves due to a reduction in fishing pressure (i.e., they benefit from marine reserves). Key predictions of this hypothesis are that (a) individual reef sharks exhibit high site-fidelity to these protected areas and (b) their relative abundance will generally be higher in these areas compared to fished reefs. To test this hypothesis for the first time in Caribbean coral reef ecosystems we combined acoustic monitoring and baited remote underwater video (BRUV) surveys to measure reef shark site-fidelity and relative abundance, respectively. We focused on the Caribbean reef shark (Carcharhinus perezi), the most common reef shark in the Western Atlantic, at Glover's Reef Marine Reserve (GRMR), Belize. Acoustically tagged sharks (N = 34) were detected throughout the year at this location and exhibited strong site-fidelity. Shark presence or absence on 200 BRUVs deployed at GRMR and three other sites (another reserve site and two fished reefs) showed that the factor "marine reserve" had a significant positive effect on reef shark presence. We rejected environmental factors or site-environment interactions as predominant drivers of this pattern. These results are consistent with the hypothesis that marine reserves can benefit reef shark populations and we suggest new hypotheses to determine the underlying mechanism(s) involved: reduced fishing mortality or enhanced prey availability.

  5. Reef Sharks Exhibit Site-Fidelity and Higher Relative Abundance in Marine Reserves on the Mesoamerican Barrier Reef

    PubMed Central

    Bond, Mark E.; Babcock, Elizabeth A.; Pikitch, Ellen K.; Abercrombie, Debra L.; Lamb, Norlan F.; Chapman, Demian D.

    2012-01-01

    Carcharhinid sharks can make up a large fraction of the top predators inhabiting tropical marine ecosystems and have declined in many regions due to intense fishing pressure. There is some support for the hypothesis that carcharhinid species that complete their life-cycle within coral reef ecosystems, hereafter referred to as “reef sharks”, are more abundant inside no-take marine reserves due to a reduction in fishing pressure (i.e., they benefit from marine reserves). Key predictions of this hypothesis are that (a) individual reef sharks exhibit high site-fidelity to these protected areas and (b) their relative abundance will generally be higher in these areas compared to fished reefs. To test this hypothesis for the first time in Caribbean coral reef ecosystems we combined acoustic monitoring and baited remote underwater video (BRUV) surveys to measure reef shark site-fidelity and relative abundance, respectively. We focused on the Caribbean reef shark (Carcharhinus perezi), the most common reef shark in the Western Atlantic, at Glover's Reef Marine Reserve (GRMR), Belize. Acoustically tagged sharks (N = 34) were detected throughout the year at this location and exhibited strong site-fidelity. Shark presence or absence on 200 BRUVs deployed at GRMR and three other sites (another reserve site and two fished reefs) showed that the factor “marine reserve” had a significant positive effect on reef shark presence. We rejected environmental factors or site-environment interactions as predominant drivers of this pattern. These results are consistent with the hypothesis that marine reserves can benefit reef shark populations and we suggest new hypotheses to determine the underlying mechanism(s) involved: reduced fishing mortality or enhanced prey availability. PMID:22412965

  6. Reef sharks exhibit site-fidelity and higher relative abundance in marine reserves on the Mesoamerican Barrier Reef.

    PubMed

    Bond, Mark E; Babcock, Elizabeth A; Pikitch, Ellen K; Abercrombie, Debra L; Lamb, Norlan F; Chapman, Demian D

    2012-01-01

    Carcharhinid sharks can make up a large fraction of the top predators inhabiting tropical marine ecosystems and have declined in many regions due to intense fishing pressure. There is some support for the hypothesis that carcharhinid species that complete their life-cycle within coral reef ecosystems, hereafter referred to as "reef sharks", are more abundant inside no-take marine reserves due to a reduction in fishing pressure (i.e., they benefit from marine reserves). Key predictions of this hypothesis are that (a) individual reef sharks exhibit high site-fidelity to these protected areas and (b) their relative abundance will generally be higher in these areas compared to fished reefs. To test this hypothesis for the first time in Caribbean coral reef ecosystems we combined acoustic monitoring and baited remote underwater video (BRUV) surveys to measure reef shark site-fidelity and relative abundance, respectively. We focused on the Caribbean reef shark (Carcharhinus perezi), the most common reef shark in the Western Atlantic, at Glover's Reef Marine Reserve (GRMR), Belize. Acoustically tagged sharks (N = 34) were detected throughout the year at this location and exhibited strong site-fidelity. Shark presence or absence on 200 BRUVs deployed at GRMR and three other sites (another reserve site and two fished reefs) showed that the factor "marine reserve" had a significant positive effect on reef shark presence. We rejected environmental factors or site-environment interactions as predominant drivers of this pattern. These results are consistent with the hypothesis that marine reserves can benefit reef shark populations and we suggest new hypotheses to determine the underlying mechanism(s) involved: reduced fishing mortality or enhanced prey availability. PMID:22412965

  7. MGA: A gamma-ray spectrum analysis code for determining plutonium isotopic abundances. Volume 3, FORTRAN listing of the GA code

    SciTech Connect

    Gunnink, R

    1991-09-01

    Nondestructive measurements of x-ray and gamma-ray emissions can be used to determine the abundances of various actinides in a sample. Volume 1 of this report describes the methods and algorithms we have developed to determine the relative isotopic abundances of actinides in a sample, by analyzing gamma-ray spectra obtained using germanium detector systems. Volume 2 is a guide to using the MGA (Multiple Group Analysis) computer program we have written to perform plutonium isotopic analyses. This report contains a listing of the FORTRAN instructions of the code.

  8. Sexual versus Asexual Reproduction: Distinct Outcomes in Relative Abundance of Parthenogenetic Mealybugs following Recent Colonization.

    PubMed

    Tabata, Jun; Ichiki, Ryoko T; Tanaka, Hirotaka; Kageyama, Daisuke

    2016-01-01

    Asexual reproduction, including parthenogenesis in which embryos develop within a female without fertilization, is assumed to confer advantages over sexual reproduction, which includes a "cost of males." Sexual reproduction largely predominates in animals, however, indicating that this cost is outweighed by the genetic and/or ecological benefits of sexuality, including the acquisition of advantageous mutations occurring in different individuals and the elimination of deleterious mutations. But the evolution of sexual reproduction remains unclear, because we have limited examples that demonstrate the relative success of sexual lineages in the face of competition from asexual lineages in the same environment. Here we investigated a sympatric occurrence of sexual and asexual reproduction in the pineapple mealybug, Dysmicoccus brevipes. This pest invaded southwestern Japan, including Okinawa and Ishigaki Islands, in the 1930s in association with imported pineapple plants. Our recent censuses demonstrated that on Okinawa sexually reproducing individuals can coexist with and even dominate asexual individuals in the presence of habitat and resource competition, which is considered to be severe for this nearly immobile insect. Molecular phylogeny based on partial DNA sequences in the mitochondrial and nuclear genomes, as well as the endosymbiotic bacterial genome, revealed that the asexual lineage diverged from a common sexual ancestor in the relatively recent past. In contrast, only the asexual lineage exhibiting obligate apomictic thelytoky was discovered on Ishigaki. Co-existence of the two lineages cannot be explained by the results of laboratory experiments, which showed that the intrinsic rate of increase in the sexual lineage was not obviously superior to that of the asexual lineage. Differences in biotic and/or abiotic selective forces operating on the two islands might be the cause of this discrepancy. This biological system offers a unique opportunity to assess

  9. Sexual versus Asexual Reproduction: Distinct Outcomes in Relative Abundance of Parthenogenetic Mealybugs following Recent Colonization

    PubMed Central

    Tabata, Jun; Ichiki, Ryoko T.; Tanaka, Hirotaka; Kageyama, Daisuke

    2016-01-01

    Asexual reproduction, including parthenogenesis in which embryos develop within a female without fertilization, is assumed to confer advantages over sexual reproduction, which includes a “cost of males.” Sexual reproduction largely predominates in animals, however, indicating that this cost is outweighed by the genetic and/or ecological benefits of sexuality, including the acquisition of advantageous mutations occurring in different individuals and the elimination of deleterious mutations. But the evolution of sexual reproduction remains unclear, because we have limited examples that demonstrate the relative success of sexual lineages in the face of competition from asexual lineages in the same environment. Here we investigated a sympatric occurrence of sexual and asexual reproduction in the pineapple mealybug, Dysmicoccus brevipes. This pest invaded southwestern Japan, including Okinawa and Ishigaki Islands, in the 1930s in association with imported pineapple plants. Our recent censuses demonstrated that on Okinawa sexually reproducing individuals can coexist with and even dominate asexual individuals in the presence of habitat and resource competition, which is considered to be severe for this nearly immobile insect. Molecular phylogeny based on partial DNA sequences in the mitochondrial and nuclear genomes, as well as the endosymbiotic bacterial genome, revealed that the asexual lineage diverged from a common sexual ancestor in the relatively recent past. In contrast, only the asexual lineage exhibiting obligate apomictic thelytoky was discovered on Ishigaki. Co-existence of the two lineages cannot be explained by the results of laboratory experiments, which showed that the intrinsic rate of increase in the sexual lineage was not obviously superior to that of the asexual lineage. Differences in biotic and/or abiotic selective forces operating on the two islands might be the cause of this discrepancy. This biological system offers a unique opportunity to

  10. Sexual versus Asexual Reproduction: Distinct Outcomes in Relative Abundance of Parthenogenetic Mealybugs following Recent Colonization.

    PubMed

    Tabata, Jun; Ichiki, Ryoko T; Tanaka, Hirotaka; Kageyama, Daisuke

    2016-01-01

    Asexual reproduction, including parthenogenesis in which embryos develop within a female without fertilization, is assumed to confer advantages over sexual reproduction, which includes a "cost of males." Sexual reproduction largely predominates in animals, however, indicating that this cost is outweighed by the genetic and/or ecological benefits of sexuality, including the acquisition of advantageous mutations occurring in different individuals and the elimination of deleterious mutations. But the evolution of sexual reproduction remains unclear, because we have limited examples that demonstrate the relative success of sexual lineages in the face of competition from asexual lineages in the same environment. Here we investigated a sympatric occurrence of sexual and asexual reproduction in the pineapple mealybug, Dysmicoccus brevipes. This pest invaded southwestern Japan, including Okinawa and Ishigaki Islands, in the 1930s in association with imported pineapple plants. Our recent censuses demonstrated that on Okinawa sexually reproducing individuals can coexist with and even dominate asexual individuals in the presence of habitat and resource competition, which is considered to be severe for this nearly immobile insect. Molecular phylogeny based on partial DNA sequences in the mitochondrial and nuclear genomes, as well as the endosymbiotic bacterial genome, revealed that the asexual lineage diverged from a common sexual ancestor in the relatively recent past. In contrast, only the asexual lineage exhibiting obligate apomictic thelytoky was discovered on Ishigaki. Co-existence of the two lineages cannot be explained by the results of laboratory experiments, which showed that the intrinsic rate of increase in the sexual lineage was not obviously superior to that of the asexual lineage. Differences in biotic and/or abiotic selective forces operating on the two islands might be the cause of this discrepancy. This biological system offers a unique opportunity to assess

  11. 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.

  12. Ion Energy Distributions and their Relative Abundance in Inductively Coupled Plasmas

    NASA Technical Reports Server (NTRS)

    Kim, J. S.; Rao, M. V. V. S.; Cappelli, M. A.; Sharma, S. P.; Arnold, James O. (Technical Monitor)

    1998-01-01

    Study of kinetics of ions and neutrals produced in high density inductively coupled plasma (ICP) discharges is of great importance for achieving a high degree of plasma assisted deposition and etching. In this paper, we present the ion energy distributions (IEDs) of various ions arriving at the grounded lower electrode. The ions were energy as well as mass analyzed by a combination of electrostatic analyzer-quadrupole mass spectrometer for pure Ar and CF4/Ar mixtures. The measurements have been made at gas pressures ranging from 30 to 100 mTorr. In addition, the IEDs were measured when the wafer-supporting electrode was also rf-powered and the effect of the self-bias was observed in the energy distributions of ions. The shapes of the IEDs are discussed an related to the sheath properties and measured electrical waveforms, as a function of pressure and applied power. Relative ion intensities were obtained by integration of each ion kinetic energy distribution function over its energy range.

  13. Stocking of hatchery-reared striped bass in the Patuxent River, Maryland: survival, relative abundance, and cost-effectiveness

    USGS Publications Warehouse

    Dorazio, R.M.; Florence, B.M.; Wooley, C.M.

    1991-01-01

    Hatchery-reared fingerlings of striped bass Morone saxatilis were tagged, stocked, and recovered in the Patuxent River, Maryland, to estimate their survival and abundance relative to wild young of the year and to compare the costs and benefits of stocking phase-I (35–50 mm, total length) and phase-II (150–200 mm) fish. About 100,000 phase-I fingerlings were tagged and released each year during midsummer 1988 and 1989. Both tagged and untagged (wild) young of the year were recovered by alongshore seining in the river through 80 d poststocking. Mortality rates of wild and hatchery-reared young of the year were not significantly different-about 3%/d. Wild young of the year were more abundant in 1989 than in 1988. In 1988, phase-I fingerlings composed 56% of all young-of-the-year striped bass in the river. In 1989 wild young-of-the-year striped bass outnumbered hatchery-reared fingerlings by about 11 to 1. Whether phase-I or phase-II stocking was more cost-effective depended on the relative magnitudes of fingerling survival and on hatchery production costs. The range of phase-II survival (5–50%) observed among different hatcheries and years of production was too broad to support generalizations about cost-effectiveness, given the fivefold difference in the unit costs of phase-I and phase-II production.

  14. Relative Abundance of Integral Plasma Membrane Proteins in Arabidopsis Leaf and Root Tissue Determined by Metabolic Labeling and Mass Spectrometry

    PubMed Central

    Bernfur, Katja; Larsson, Olaf; Larsson, Christer; Gustavsson, Niklas

    2013-01-01

    Metabolic labeling of proteins with a stable isotope (15N) in intact Arabidopsis plants was used for accurate determination by mass spectrometry of differences in protein abundance between plasma membranes isolated from leaves and roots. In total, 703 proteins were identified, of which 188 were predicted to be integral membrane proteins. Major classes were transporters, receptors, proteins involved in membrane trafficking and cell wall-related proteins. Forty-one of the integral proteins, including nine of the 13 isoforms of the PIP (plasma membrane intrinsic protein) aquaporin subfamily, could be identified by peptides unique to these proteins, which made it possible to determine their relative abundance in leaf and root tissue. In addition, peptides shared between isoforms gave information on the proportions of these isoforms. A comparison between our data for protein levels and corresponding data for mRNA levels in the widely used database Genevestigator showed an agreement for only about two thirds of the proteins. By contrast, localization data available in the literature for 21 of the 41 proteins show a much better agreement with our data, in particular data based on immunostaining of proteins and GUS-staining of promoter activity. Thus, although mRNA levels may provide a useful approximation for protein levels, detection and quantification of isoform-specific peptides by proteomics should generate the most reliable data for the proteome. PMID:23990937

  15. Relation between occupancy and abundance for a territorial species, the California spotted owl.

    PubMed

    Tempel, Douglas J; Gutiérrez, R J

    2013-10-01

    Land and resource managers often use detection-nondetection surveys to monitor the populations of species that may be affected by factors such as habitat alteration, climate change, and biological invasions. Relative to mark-recapture studies, using detection-nondetection surveys is more cost-effective, and recent advances in statistical analyses allow the incorporation of detection probability, covariates, and multiple seasons. We examined the efficacy of using detection-nondetection data (relative to mark-recapture data) for monitoring population trends of a territorial species, the California Spotted Owl (Strix occidentalis occidentalis). We estimated and compared the finite annual rates of population change (λt ) and the resulting realized population change (Δt ) from both occupancy and mark-recapture data collected over 18 years (1993-2010). We used multiseason, robust-design occupancy models to estimate that territory occupancy declined during our study (Δt = 0.702, 95% CI 0.552-0.852) due to increasing territory extinction rates (ε(1993) = 0.019 [SE 0.012]; ε(2009) = 0.134 [SE 0.043]) and decreasing colonization rates (γ(1993) = 0.323 [SE 0.124]; γ(2009) = 0.242 [SE 0.058]). We used Pradel's temporal-symmetry model for mark-recapture data to estimate that the population trajectory closely matched the trends in territory occupancy (Δt = 0.725, 95% CI 0.445-1.004). Individual survival was constant during our study (φ(1993) = 0.816 [SE 0.020]; φ(2009) = 0.815 [SE 0.019]), whereas recruitment declined slightly (f(1993) = 0.195 [SE 0.032]; f(2009) = 0.160 [SE 0.023]). Thus, we concluded that detection-nondetection data can provide reliable inferences on population trends, especially when funds preclude more intensive mark-recapture studies. PMID:23678946

  16. Relation between occupancy and abundance for a territorial species, the California spotted owl.

    PubMed

    Tempel, Douglas J; Gutiérrez, R J

    2013-10-01

    Land and resource managers often use detection-nondetection surveys to monitor the populations of species that may be affected by factors such as habitat alteration, climate change, and biological invasions. Relative to mark-recapture studies, using detection-nondetection surveys is more cost-effective, and recent advances in statistical analyses allow the incorporation of detection probability, covariates, and multiple seasons. We examined the efficacy of using detection-nondetection data (relative to mark-recapture data) for monitoring population trends of a territorial species, the California Spotted Owl (Strix occidentalis occidentalis). We estimated and compared the finite annual rates of population change (λt ) and the resulting realized population change (Δt ) from both occupancy and mark-recapture data collected over 18 years (1993-2010). We used multiseason, robust-design occupancy models to estimate that territory occupancy declined during our study (Δt = 0.702, 95% CI 0.552-0.852) due to increasing territory extinction rates (ε(1993) = 0.019 [SE 0.012]; ε(2009) = 0.134 [SE 0.043]) and decreasing colonization rates (γ(1993) = 0.323 [SE 0.124]; γ(2009) = 0.242 [SE 0.058]). We used Pradel's temporal-symmetry model for mark-recapture data to estimate that the population trajectory closely matched the trends in territory occupancy (Δt = 0.725, 95% CI 0.445-1.004). Individual survival was constant during our study (φ(1993) = 0.816 [SE 0.020]; φ(2009) = 0.815 [SE 0.019]), whereas recruitment declined slightly (f(1993) = 0.195 [SE 0.032]; f(2009) = 0.160 [SE 0.023]). Thus, we concluded that detection-nondetection data can provide reliable inferences on population trends, especially when funds preclude more intensive mark-recapture studies.

  17. A rapid ambient ionization-mass spectrometry approach to monitoring the relative abundance of isomeric glycerophospholipids

    NASA Astrophysics Data System (ADS)

    Kozlowski, Rachel L.; Mitchell, Todd W.; Blanksby, Stephen J.

    2015-04-01

    Glycerophospholipids with two, non-equivalent fatty acyl chains can adopt one of two isomeric forms depending on the relative position of substitutions on the glycerol backbone. These so-called sn-positional isomers can have distinct biophysical and biochemical behaviors making it desirable to uniquely assign their regiochemistries. Unambiguous assignment of such similar molecular structures in complex biological extracts is a significant challenge to current analytical technologies. We have recently reported a novel mass spectrometric method that combines collision- and ozone-induced dissociation in series (CID/OzID) to yield product ions characteristic of acyl chain substitution patterns in glycerophospholipids. Here phosphatidylcholines are examined using the CID/OzID protocol combined with desorption electrospray ionization (DESI) to facilitate the rapid exploration of sample arrays comprised of a wide variety of synthetic and biological sources. Comparison of the spectra acquired from different extracts reveals that the sn-positional isomers PC 16:0/18:1 and PC 18:1/16:0 (where the 18:1 chain is present at the sn-2 and sn-1 position of the glycerol backbone, respectively) are most often found together in lipids of either natural or synthetic origin. Moreover, the proportions of the two isomers vary significantly between extracts from different organisms or even between adjacent tissues from the same organism.

  18. Seasonal and long-term changes in relative abundance of bull sharks from a tourist shark feeding site in Fiji.

    PubMed

    Brunnschweiler, Juerg M; Baensch, Harald

    2011-01-01

    Shark tourism has become increasingly popular, but remains controversial because of major concerns originating from the need of tour operators to use bait or chum to reliably attract sharks. We used direct underwater sampling to document changes in bull shark Carcharhinus leucas relative abundance at the Shark Reef Marine Reserve, a shark feeding site in Fiji, and the reproductive cycle of the species in Fijian waters. Between 2003 and 2009, the total number of C. leucas counted on each day ranged from 0 to 40. Whereas the number of C. leucas counted at the feeding site increased over the years, shark numbers decreased over the course of a calendar year with fewest animals counted in November. Externally visible reproductive status information indicates that the species' seasonal departure from the feeding site may be related to reproductive activity. PMID:21346792

  19. Abundant toxin-related genes in the genomes of beneficial symbionts from deep-sea hydrothermal vent mussels.

    PubMed

    Sayavedra, Lizbeth; Kleiner, Manuel; Ponnudurai, Ruby; Wetzel, Silke; Pelletier, Eric; Barbe, Valerie; Satoh, Nori; Shoguchi, Eiichi; Fink, Dennis; Breusing, Corinna; Reusch, Thorsten Bh; Rosenstiel, Philip; Schilhabel, Markus B; Becher, Dörte; Schweder, Thomas; Markert, Stephanie; Dubilier, Nicole; Petersen, Jillian M

    2015-01-01

    Bathymodiolus mussels live in symbiosis with intracellular sulfur-oxidizing (SOX) bacteria that provide them with nutrition. We sequenced the SOX symbiont genomes from two Bathymodiolus species. Comparison of these symbiont genomes with those of their closest relatives revealed that the symbionts have undergone genome rearrangements, and up to 35% of their genes may have been acquired by horizontal gene transfer. Many of the genes specific to the symbionts were homologs of virulence genes. We discovered an abundant and diverse array of genes similar to insecticidal toxins of nematode and aphid symbionts, and toxins of pathogens such as Yersinia and Vibrio. Transcriptomics and proteomics revealed that the SOX symbionts express the toxin-related genes (TRGs) in their hosts. We hypothesize that the symbionts use these TRGs in beneficial interactions with their host, including protection against parasites. This would explain why a mutualistic symbiont would contain such a remarkable 'arsenal' of TRGs.

  20. Relation of age-0 largemouth bass abundance to hydrilla coverage and water level at Lochloosa and Orange Lakes, Florida

    USGS Publications Warehouse

    Tate, W.B.; Allen, M.S.; Myers, R.A.; Nagid, E.J.; Estes, J.R.

    2003-01-01

    Changes in electrofishing catch per hour (CPH) of age-0 largemouth bass Micropterus salmoides were examined in relation to aquatic macrophytes and seasonal water elevation at Lochloosa and Orange lakes, Florida, during the 1990s. At Lochloosa Lake, stepwise multiple regression revealed a significant positive relationship between the mean CPH of age-0 largemouth bass and the percentage of areal coverage by hydrilla Hydrilla verticallata. At Orange Lake, mean CPH was directly associated with the percentage of areal coverage by hydrilla and inversely related to summer water levels. Thus, the influence of vegetation on age-0 largemouth bass abundance was similar at both lakes, but the effects of water levels were not. Further investigations into the effects of fluctuations in water levels on age-0 largemouth bass in natural lakes are needed.

  1. Seasonal and Long-Term Changes in Relative Abundance of Bull Sharks from a Tourist Shark Feeding Site in Fiji

    PubMed Central

    Brunnschweiler, Juerg M.; Baensch, Harald

    2011-01-01

    Shark tourism has become increasingly popular, but remains controversial because of major concerns originating from the need of tour operators to use bait or chum to reliably attract sharks. We used direct underwater sampling to document changes in bull shark Carcharhinus leucas relative abundance at the Shark Reef Marine Reserve, a shark feeding site in Fiji, and the reproductive cycle of the species in Fijian waters. Between 2003 and 2009, the total number of C. leucas counted on each day ranged from 0 to 40. Whereas the number of C. leucas counted at the feeding site increased over the years, shark numbers decreased over the course of a calendar year with fewest animals counted in November. Externally visible reproductive status information indicates that the species' seasonal departure from the feeding site may be related to reproductive activity. PMID:21346792

  2. Seasonal and long-term changes in relative abundance of bull sharks from a tourist shark feeding site in Fiji.

    PubMed

    Brunnschweiler, Juerg M; Baensch, Harald

    2011-01-27

    Shark tourism has become increasingly popular, but remains controversial because of major concerns originating from the need of tour operators to use bait or chum to reliably attract sharks. We used direct underwater sampling to document changes in bull shark Carcharhinus leucas relative abundance at the Shark Reef Marine Reserve, a shark feeding site in Fiji, and the reproductive cycle of the species in Fijian waters. Between 2003 and 2009, the total number of C. leucas counted on each day ranged from 0 to 40. Whereas the number of C. leucas counted at the feeding site increased over the years, shark numbers decreased over the course of a calendar year with fewest animals counted in November. Externally visible reproductive status information indicates that the species' seasonal departure from the feeding site may be related to reproductive activity.

  3. Abundant toxin-related genes in the genomes of beneficial symbionts from deep-sea hydrothermal vent mussels.

    PubMed

    Sayavedra, Lizbeth; Kleiner, Manuel; Ponnudurai, Ruby; Wetzel, Silke; Pelletier, Eric; Barbe, Valerie; Satoh, Nori; Shoguchi, Eiichi; Fink, Dennis; Breusing, Corinna; Reusch, Thorsten Bh; Rosenstiel, Philip; Schilhabel, Markus B; Becher, Dörte; Schweder, Thomas; Markert, Stephanie; Dubilier, Nicole; Petersen, Jillian M

    2015-01-01

    Bathymodiolus mussels live in symbiosis with intracellular sulfur-oxidizing (SOX) bacteria that provide them with nutrition. We sequenced the SOX symbiont genomes from two Bathymodiolus species. Comparison of these symbiont genomes with those of their closest relatives revealed that the symbionts have undergone genome rearrangements, and up to 35% of their genes may have been acquired by horizontal gene transfer. Many of the genes specific to the symbionts were homologs of virulence genes. We discovered an abundant and diverse array of genes similar to insecticidal toxins of nematode and aphid symbionts, and toxins of pathogens such as Yersinia and Vibrio. Transcriptomics and proteomics revealed that the SOX symbionts express the toxin-related genes (TRGs) in their hosts. We hypothesize that the symbionts use these TRGs in beneficial interactions with their host, including protection against parasites. This would explain why a mutualistic symbiont would contain such a remarkable 'arsenal' of TRGs. PMID:26371554

  4. Experimental and Temporal Observations on the Occurrence and Abundance of Pyrogenic PAH Relative to Atmospheric Oxygen Levels

    NASA Astrophysics Data System (ADS)

    Schuneman, P. J.; Uhle, M. E.

    2004-12-01

    The Phanerozoic record of atmospheric O2 is based on a global mass balance of several dynamic geochemical cycles, with error margins reflecting such complexity. The potential for accurately determining the record of atmospheric O2 may significantly improve with the proposed method, which relies on a direct relationship between atmospheric oxygen, fuels, and fire products. The interaction between combustion and atmospheric-oxygen level during biomass burning events is investigated by comparing the occurrence and abundance of pyrogenic polycyclic aromatic hydrocarbons (PAH) from experimentally-produced, modern, Triassic, and Carboniferous chars. The combustion process consumes O2 directly from the atmosphere and thermally alters organic matter to produce chars. PAH that develop through combustion, and are preserved within chars, are expected to be more abundant at times of elevated atmospheric O2, which facilitates biomass burning efficiency. To investigate the hypothesized relationship in the geologic record, PAH have been extracted from chars of three periods - modern, Triassic, and Carboniferous - relating to 21%, 15%, and 35% atmospheric O2, respectively (Berner and Canfield, 1989). Surface samples of modern chars that developed in controlled burns set by National Park Service personnel in a mixed conifer-deciduous forest were collected at Zion National Park, Utah. Triassic fusain from Petrified Forest National Park, AZ, and Carboniferous fusain from Joggins Fossil Cliffs, Nova Scotia, were collected from floodplain- and coastal plain-deposited mudstone and sandstone. Target PAH shown to be uniquely pyrogenic include: phenanthrene, anthracene, fluoranthene, pyrene, benz(a)anthracene, chrysene, benzo(b)fluoranthene, benzo(k)fluoranthene, benzo(a)pyrene, indeno(1,2,3-cd)pyrene, and benzo(ghi)perylene. The abundance of PAH from modern chars at Zion National Park, Triassic fusain from Petrified Forest National Park, and Carboniferous fusain from Joggins Fossil Cliffs

  5. A Comparison of Anammox Bacterial Abundance and Community Structures in Three Different Emerged Plants-Related Sediments.

    PubMed

    Chu, Jinyu; Zhang, Jinping; Zhou, Xiaohong; Liu, Biao; Li, Yimin

    2015-09-01

    Quantitative polymerase chain reaction (qPCR) assays and 16S rRNA gene clone libraries were used to document the abundance, diversity and community structure of anaerobic ammonia-oxidising (anammox) bacteria in the rhizosphere and non-rhizosphere sediments of three emergent macrophyte species (Iris pseudacorus, Thalia dealbata and Typha orientalis). The qPCR results confirmed the existence of anammox bacteria (AMX) with observed log number of gene copies per dry gram sediment ranging from 5.00 to 6.78. AMX was more abundant in T. orientalis-associated sediments than in the other two plant species. The I. pseudacorus- and T. orientalis-associated sediments had higher Shannon diversity values, indicating higher AMX diversity in these sediments. Based on the 16S rRNA gene, Candidatus 'Brocadia', Candidatus 'Kuenenia', Candidatus 'Jettenia' and new clusters were observed with the predominant Candidatus 'Kuenenia' cluster. The I. pseudacorus-associated sediments contained all the sequences of the C. 'Jettenia' cluster. Sequences obtained from T. orientalis-associated sediments contributed more than 90 % sequences in the new cluster, whereas none was found from I. pseudacorus. The new cluster was distantly related to known sequences; thus, this cluster was grouped outside the known clusters, indicating that the new cluster may be a new Planctomycetales genus. Further studies should be undertaken to confirm this finding. PMID:26077223

  6. A Comparison of Anammox Bacterial Abundance and Community Structures in Three Different Emerged Plants-Related Sediments.

    PubMed

    Chu, Jinyu; Zhang, Jinping; Zhou, Xiaohong; Liu, Biao; Li, Yimin

    2015-09-01

    Quantitative polymerase chain reaction (qPCR) assays and 16S rRNA gene clone libraries were used to document the abundance, diversity and community structure of anaerobic ammonia-oxidising (anammox) bacteria in the rhizosphere and non-rhizosphere sediments of three emergent macrophyte species (Iris pseudacorus, Thalia dealbata and Typha orientalis). The qPCR results confirmed the existence of anammox bacteria (AMX) with observed log number of gene copies per dry gram sediment ranging from 5.00 to 6.78. AMX was more abundant in T. orientalis-associated sediments than in the other two plant species. The I. pseudacorus- and T. orientalis-associated sediments had higher Shannon diversity values, indicating higher AMX diversity in these sediments. Based on the 16S rRNA gene, Candidatus 'Brocadia', Candidatus 'Kuenenia', Candidatus 'Jettenia' and new clusters were observed with the predominant Candidatus 'Kuenenia' cluster. The I. pseudacorus-associated sediments contained all the sequences of the C. 'Jettenia' cluster. Sequences obtained from T. orientalis-associated sediments contributed more than 90 % sequences in the new cluster, whereas none was found from I. pseudacorus. The new cluster was distantly related to known sequences; thus, this cluster was grouped outside the known clusters, indicating that the new cluster may be a new Planctomycetales genus. Further studies should be undertaken to confirm this finding.

  7. Macroscale intraspecific variation and environmental heterogeneity: analysis of cold and warm zone abundance, mortality, and regeneration distributions of four eastern US tree species.

    PubMed

    Prasad, Anantha M

    2015-11-01

    I test for macroscale intraspecific variation of abundance, mortality, and regeneration of four eastern US tree species (Tsuga canadensis,Betula lenta,Liriodendron tulipifera, and Quercus prinus) by splitting them into three climatic zones based on plant hardiness zones (PHZs). The primary goals of the analysis are to assess the differences in environmental heterogeneity and demographic responses among climatic zones, map regional species groups based on decision tree rules, and evaluate univariate and multivariate patterns of species demography with respect to environmental variables. I use the Forest Inventory Analysis (FIA) data to derive abundance, mortality, and regeneration indices and split the range into three climatic zones based on USDA PHZs: (1) cold adapted, leading region; (2) middle, well-adapted region; and (3) warm adapted, trailing region. I employ decision tree ensemble methods to assess the importance of environmental predictors on the abundance of the species between the cold and warm zones and map zonal variations in species groups. Multivariate regression trees are used to simultaneously explore abundance, mortality, and regeneration in tandem to assess species vulnerability. Analyses point to the relative importance of climate in the warm adapted, trailing zone (especially moisture) compared to the cold adapted, leading zone. Higher mortality and lower regeneration patterns in the warm trailing zone point to its vulnerability to growing season temperature and precipitation changes that could figure more prominently in the future. This study highlights the need to account for intraspecific variation of demography in order to understand environmental heterogeneity and differential adaptation. It provides a methodology for assessing the vulnerability of tree species by delineating climatic zones based on easily available PHZ data, and FIA derived abundance, mortality, and regeneration indices as a proxy for overall growth and fitness. Based on

  8. Measurement of isotope abundance variations in nature by gravimetric spiking isotope dilution analysis (GS-IDA).

    PubMed

    Chew, Gina; Walczyk, Thomas

    2013-04-01

    Subtle variations in the isotopic composition of elements carry unique information about physical and chemical processes in nature and are now exploited widely in diverse areas of research. Reliable measurement of natural isotope abundance variations is among the biggest challenges in inorganic mass spectrometry as they are highly sensitive to methodological bias. For decades, double spiking of the sample with a mix of two stable isotopes has been considered the reference technique for measuring such variations both by multicollector-inductively coupled plasma mass spectrometry (MC-ICPMS) and multicollector-thermal ionization mass spectrometry (MC-TIMS). However, this technique can only be applied to elements having at least four stable isotopes. Here we present a novel approach that requires measurement of three isotope signals only and which is more robust than the conventional double spiking technique. This became possible by gravimetric mixing of the sample with an isotopic spike in different proportions and by applying principles of isotope dilution for data analysis (GS-IDA). The potential and principle use of the technique is demonstrated for Mg in human urine using MC-TIMS for isotopic analysis. Mg is an element inaccessible to double spiking methods as it consists of three stable isotopes only and shows great potential for metabolically induced isotope effects waiting to be explored.

  9. Rapid Determination of Bacterial Abundance, Biovolume, Morphology, and Growth by Neural Network-Based Image Analysis

    PubMed Central

    Blackburn, Nicholas; Hagström, Åke; Wikner, Johan; Cuadros-Hansson, Rocio; Bjørnsen, Peter Koefoed

    1998-01-01

    Annual bacterial plankton dynamics at several depths and locations in the Baltic Sea were studied by image analysis. Individual bacteria were classified by using an artificial neural network which also effectively identified nonbacterial objects. Cell counts and frequencies of dividing cells were determined, and the data obtained agreed well with visual observations and previously published values. Cell volumes were measured accurately by comparison with bead standards. The survey included 690 images from a total of 138 samples. Each image contained approximately 200 bacteria. The images were analyzed automatically at a rate of 100 images per h. Bacterial abundance exhibited coherent patterns with time and depth, and there were distinct subsurface peaks in the summer months. Four distinct morphological classes were resolved by the image analyzer, and the dynamics of each could be visualized. The bacterial growth rates estimated from frequencies of dividing cells were different from the bacterial growth rates estimated by the thymidine incorporation method. With minor modifications, the image analysis technique described here can be used to analyze other planktonic classes. PMID:9726867

  10. Relative Abundances and Energy Spectra of C, N, and 0 as Measured by the Advanced Thin Ionization Calorimeter Balloon Experiment

    NASA Technical Reports Server (NTRS)

    Fazely, A. R.; Gunasingha, R. M.; Adams, J. H.; Ahn, E. J.; Ahn, H. S.; Bashindzhagyan, G.; Case, G.; Chang, J.; Christl, M.; Ellison, S.

    2003-01-01

    We present results on the spectra and the relative abundances of C, N, and 0 nuclei in the cosmic radiation as measured from the Advanced Thin Ionization Calorimeter Balloon Experiment (ATIC) . The ATIC detector has completed two successful balloon flights from McMurdo, Antarctica lasting a total of more than 35 days. ATIC is designed as a multiple, long duration balloon flight, investigation of the cosmic ray spectra from below 50 GeV to near 100 TeV total energy, using a fully active Bismuth Germanate calorimeter. It is equipped with a large area mosaic of silicon detector pixels capable of charge identification from H to Fe. As a redundancy check for the charge identification and a particle tracking system, three projective layers of x-y scintillator hodoscopes were employed, above, in the middle and below a 0.75 nuclear interaction length graphite target.

  11. [Relative abundance, population structure, habitat preferences and activity patterns of Tapirus bairdii (Perissodactyla: Tapiridae), in Chimalapas forest, Oaxaca, Mexico].

    PubMed

    Lira-Torres, Iván; Briones-Salas, Miguel; Sánchez-Rojas, Gerardo

    2014-12-01

    Baird's tapir (Tapirus bairdii) is endangered primarily because of habitat loss and fragmentation, and overhunting throughout its distribution range. One of the priority land areas for the conservation of this species is the Northern part of its range in the Chimalapas forest, Oaxaca. The aim of this research was to determine the relative abundance, population struc- ture, habitat preferences and activity patterns of Baird's tapir (Tapirus bairdii) in the Chimalapas forest, Oaxaca, Mexico, through the non-invasive technique of camera-trap sampling. A total of five sampling sessions were undertaken among 2009-2013, and used a total of 30 camera-traps in each period. The determinant factor of the sampling design was the hunting between two study areas. A total sampling effort of 9000 trap-days allowed to estimate an index of relative abundance (IRA) of 6.77 tapir photographs/1,000 trap-days (n = 61). IRA varied significantly between sampling stations (Mann-Whitney, p < 0.01). The frequency of Baird's tapir photos was higher in the dry season in tropical rain forest without hunting (χ2, p < 0.5). In the rainy season, the tropical rain forest and secondary vegetation habitats showed higher photo frequency than expected from random (χ2, p < 0.5). Considering population structure, a 95.08% of adult animals was obtained in photographic records (n = 58). Three types of activity pattern were observed, with more nocturnal records (88.33%; Kruskal-Wallis, p < 0.05). The Chimalapas forest appears to be the second most important terrestrial priority ecoregion, just after the Mayan Forest (Campeche, Chiapas, Quintana Roo), for the conservation of tapir populations, not only for Mexico but also for Central America. PMID:25720176

  12. Geographic distribution and relative abundance of the invasive glassy-winged sharpshooter: effects of temperature and egg parasitoids.

    PubMed

    Gutierrez, Andrew Paul; Ponti, Luigi; Hoddle, Mark; Almeida, Rodrigo P P; Irvin, Nicola A

    2011-08-01

    The capacity to predict the geographic distribution and relative abundance of invasive species is pivotal to developing policy for eradication or control and management. Commonly used methods fall under the ambit of ecological niche models (ENMs). These methods were reviewed and shortcomings identified. Weather-driven physiologically based demographic models (PBDMs) are proposed that resolve many of the deficiencies of ENMs. The PBDM approach is used to analyze the invasiveness of the polyphagous glassy-winged sharpshooter (Homalodisca vitripennis [Germar]), a pest native to the southeastern United States and northeastern Mexico that extended its range into California in 1989. Glassy-winged sharpshooter vectors the pathogenic bacterium, Xylella fastidiosa (Wells) that causes Pierce's disease in grape and scorch-like diseases in other plants. PBDMs for glassy-winged sharpshooter and its egg parasitoids (Gonatocerus ashmeadi Girault and G. triguttatus Girault) were developed and linked to a PBDM for grape published by Wermelinger et al. (1991). Daily weather data from 108 locations across California for the period 1995-2006 were used to drive the PBDM system, and GRASS GIS was used to map the simulation results. The geographic distribution of glassy-winged sharpshooter, as observed, is predicted to be largely restricted to the warm areas of southern California, with the action of the two egg parasitoids reducing its abundance >90%. The average indispensable mortality contributed by G. triguttatus is <1%. A temperature-dependent developmental rate model for X. fastidiosa was developed that suggests its geographic range is also limited to the warm inland areas of southern California. Biological control of glassy-winged sharpshooter further decreases the pathogen's relative range. Climate warming scenarios of +2°C and +3°C suggest that the distribution and severity of glassy-winged sharpshooter and X. fastidiosa will increase in the agriculturally rich central valley

  13. [Relative abundance, population structure, habitat preferences and activity patterns of Tapirus bairdii (Perissodactyla: Tapiridae), in Chimalapas forest, Oaxaca, Mexico].

    PubMed

    Lira-Torres, Iván; Briones-Salas, Miguel; Sánchez-Rojas, Gerardo

    2014-12-01

    Baird's tapir (Tapirus bairdii) is endangered primarily because of habitat loss and fragmentation, and overhunting throughout its distribution range. One of the priority land areas for the conservation of this species is the Northern part of its range in the Chimalapas forest, Oaxaca. The aim of this research was to determine the relative abundance, population struc- ture, habitat preferences and activity patterns of Baird's tapir (Tapirus bairdii) in the Chimalapas forest, Oaxaca, Mexico, through the non-invasive technique of camera-trap sampling. A total of five sampling sessions were undertaken among 2009-2013, and used a total of 30 camera-traps in each period. The determinant factor of the sampling design was the hunting between two study areas. A total sampling effort of 9000 trap-days allowed to estimate an index of relative abundance (IRA) of 6.77 tapir photographs/1,000 trap-days (n = 61). IRA varied significantly between sampling stations (Mann-Whitney, p < 0.01). The frequency of Baird's tapir photos was higher in the dry season in tropical rain forest without hunting (χ2, p < 0.5). In the rainy season, the tropical rain forest and secondary vegetation habitats showed higher photo frequency than expected from random (χ2, p < 0.5). Considering population structure, a 95.08% of adult animals was obtained in photographic records (n = 58). Three types of activity pattern were observed, with more nocturnal records (88.33%; Kruskal-Wallis, p < 0.05). The Chimalapas forest appears to be the second most important terrestrial priority ecoregion, just after the Mayan Forest (Campeche, Chiapas, Quintana Roo), for the conservation of tapir populations, not only for Mexico but also for Central America.

  14. VARIATION IN JUVENILE COHO SALMON SUMMER ABUNDANCE: HIERARCHICAL ANALYSIS OF HABITAT EFFECTS

    EPA Science Inventory

    Varying habitat conditions found across a stream network during the summer months may limit the abundance of salmonids such as coho (Oncorhynchus kisutch). We examined the abundance of juvenile coho salmon across a stream network in an Oregon coast range basin from 2002 through ...

  15. A thorough analysis of the metal abundance gradient history in the Galactic disk by improving the statistics of well studied open clusters

    NASA Astrophysics Data System (ADS)

    Claria, Juan J.; Piatti, Andres E.; Ahumada, Andrea V.; Parisi, Maria Celeste; Palma, Tali

    2008-02-01

    Open clusters (OCs) have long been used as tracers of the evolution of the Galactic disk (GD). Although the number of studied OCs has recently increased significantly, nearly 60% of the ~ 1700 Galactic OCs known to exist are still unstudied objects. We want to examine how the abundance gradient in the GD evolved in time and along different Galactic positions by comparing the abundance gradients corresponding to various groups of open clusters (OCs) of different ages and positions. The greater the number of OCs with well determined distances, ages and metallicities, the more precise and detailed the analysis of the metal abundance gradient in the GD as well as its evolution over time. We then propose to observe some selected OCs with the Washington system C and T_1 filters mainly to determine their basic parameters for the first time, with the aim of: (1) Improving the statistics of well-studied OCs. (2) Showing how the radial abundance gradient has evolved in course of time and along different Galactic longitudes by dividing the whole sample of known OCs into age-position groups. We believe this is crucial in constraining the initial conditions and evolution of the gas and stars in the GD. (3) Shedding light on the controversial existence of an abundance gradient perpendicular to the Galactic plane and on the blurry age-metallicity relation (AMR).

  16. Population size and relative abundance of adult Alabama shad reaching jim woodruff lock and dam, Apalachicola River, Florida

    USGS Publications Warehouse

    Ely, Patrick C.; Young, S.P.; Isely, J.J.

    2008-01-01

    We estimated the population size of migrating Alabama shad Alosa alabamae below Jim Woodruff Lock and Dam in the Apalachicola River (located in the central panhandle of northwestern Florida) using mark-recapture and relative abundance techniques. After adjustment for tag loss, emigration, and mortality, the population size was estimated as 25,935 (95% confidence interval, 17,715-39,535) in 2005, 2,767 (838-5,031) in 2006, and 8,511 (5,211-14,674) in 2007. The cumulative catch rate from boat electrofishing averaged 20.47 Alabama shad per hour in 2005, 6.10 per hour in 2006, and 13.17 per hour in 2007. The relationship between population size (N) and electrofishing catch per unit effort (CPUE) was modeled by the equation N = -9008.2 + (electrofishing CPUE X 1616.4). Additionally, in 2007 the hook-and-line catch rate averaged 1.94 Alabama shad per rod hour. A predictive model relating the population size and hook-and-line CPUE of spawning American shad A. sapidissima was applied to Alabama shad hook-and-line CPUE and produced satisfactory results. Recent spawning populations of Alabama shad in the Apalachicola River are low relative to American shad populations in other southeastern U.S. rivers. ?? Copyright by the American Fisheries Society 2008.

  17. Relative abundance and treatment reduction of viruses during wastewater treatment processes--identification of potential viral indicators.

    PubMed

    Kitajima, Masaaki; Iker, Brandon C; Pepper, Ian L; Gerba, Charles P

    2014-08-01

    Waterborne pathogenic viruses discharged from wastewater treatment plants (WWTPs) pose potential public health risks. In the present study, we investigated the relative abundance, occurrence, and reduction of eleven different viruses at two WWTPs in southern Arizona over a 12-month period, from August 2011 to July 2012. Influent and effluent samples from the two WWTPs were collected monthly. Viruses were concentrated using an electronegative filter method and quantified using TaqMan-based quantitative PCR (qPCR) assays for each of the virus types (i.e., genogroup I, II and IV noroviruses, sapovirus, enterovirus, group A rotavirus, Aichi virus, pepper mild mottle virus, adenovirus, and JC and BK polyomaviruses), with murine norovirus internal control for the monitoring of extraction-RT-qPCR efficiencies. The pepper mild mottle virus, a plant virus, was found to be the most prevalent virus in both influent and effluent wastewater (annual mean concentration of 3.7-4.4×10(6) copies/L and 4.6-6.3×10(5) copies/L in influent and effluent wastewater, respectively), showing a low reduction by the treatment processes (0.76-0.99 annual mean log10 reduction), and no significant seasonal change in concentration. Aichi virus, a human enteric virus, was also found in greater abundance, and showed lower reduction during wastewater treatment than other human enteric viruses. Our results suggest that these viruses could be used as potential indicators of wastewater reclamation system performance, with respect to virus occurrence and removal. PMID:24836386

  18. Relative abundances of chondrule primary textural types in ordinary chondrites and their bearing on conditions of chondrule formation

    NASA Astrophysics Data System (ADS)

    Gooding, J. L.; Keil, K.

    1981-03-01

    A petrographic survey of > 1600 chondrules in thin-sections of 12 different mildly to highly unequilibrated H-, L-, and Li-chondrites, as well as morphological and textural study of 141 whole chondrules separated from 11 of the same chondrites, was used to determine the relative abundances of definable chondrule primary textural types. Percentage abundances of various chondrule types are remarkably similar in all chondrites studied and are ˜47-52 porphyritic olivine-pyroxene (POP), 15-27 porphyritic olivine (P 0), 9-11 porphyritic pyroxene (PP), 34 barred olivine (BO), 7-9 radial pyroxene (RP), 2-5 granular olivine-pyroxene (GOP), 3-5 cryptocrystalline (C), and ≥ 1 metallic (M). Neither chondrule size nor shape is strongly correlated with textural type. Compound and cratered chondrules, which are interpreted as products of collisions between plastic chondrules, comprise ˜2-28% of non-porphyritic (RP, GOP, C) but only ˜2-9% of porphyritic (POP, PO, PP, BO) chondrules, leading to a model-dependent implication that non-porphyritic chondrules evolved at number densities (chondrules per unit volume of space) which were 102 to 104 times greater than those which prevailed during porphyritic chondrule formation (total range of ˜1 to ˜106 m-3. Distinctive "rims" of fine-grained sulfides and/or silicates occur on both porphyritic and non-porphyritic types and appear to post-date chondrule formation. Apparently, either the same process(es) contributed chondrules to all unequilibrated ordinary chondrites or, if genetically different, the various chondrule types were well mixed before incorporation into chondrites. Melting of pre-existing materials is the mechanism favored for chondrule formation.

  19. The distribution and relative abundance of ammonia-oxidizing bacteria in lakes of the McMurdo Dry Valley, Antarctica

    USGS Publications Warehouse

    Voytek, M.A.; Priscu, J.C.; Ward, B.B.

    1999-01-01

    Marked differences in the concentrations of major ions and cations, macronutrient chemistry and general trophic status exist among the lakes of the McMurdo dry valleys in Antarctica. These differences have been attributed to both variations in stream inputs and in situ lake processes (Priscu, 1995; Lizotte et al., 1996, Spigel and Priscu, 1996). This study examines the role of nitrifying bacteria in nitrogen transformations in these lakes. Applying two polymerase chain reaction (PCR) assays targeting the 16S rRNA genes of ammonia-oxidizing bacteria and the active site of the ammonia monooxygenase gene (amoA), the distribution of ammonia-oxidizers was examined in six Antarctic lakes: Lake Bonney, Lake Hoare, Lake Fryxell and Lake Joyce in the Taylor Valley, Lake Miers in the the Miers Valley and Lake Vanda in the Wright Valley. Using a two stage amplification procedure, ammonia-oxidizers from both the beta and gamma- subclasses of the Proteobacteria were detected and their relative abundances were determined in samples collected from all sites. Ammonia-oxidizers were detected in all lakes sampled. Members of the gamma subclass were only present in the saline lakes. In general, nitrifiers were most abundant at depths above the pycnocline and were usually associated with lower concentrations of NH4 and elevated concentrations of NO3 or NO2. The distribution of nitrifiers suggests that the primary N2O peak observed in most of the lakes was produced via nitrification. Preliminary data on the rate of nitrification (Priscu et al., 1996) support the occurrence of nitrification and the presence of nitrifiers at the depth intervals where nitrifiers were detected. In all lakes, except Lake Miers, the data indicate that nitrifying bacteria have an important role in the vertical distribution of nitrogen compounds in these systems.

  20. Bayesian change point analysis of abundance trends for pelagic fishes in the upper San Francisco Estuary.

    PubMed

    Thomson, James R; Kimmerer, Wim J; Brown, Larry R; Newman, Ken B; Mac Nally, Ralph; Bennett, William A; Feyrer, Frederick; Fleishman, Erica

    2010-07-01

    We examined trends in abundance of four pelagic fish species (delta smelt, longfin smelt, striped bass, and threadfin shad) in the upper San Francisco Estuary, California, USA, over 40 years using Bayesian change point models. Change point models identify times of abrupt or unusual changes in absolute abundance (step changes) or in rates of change in abundance (trend changes). We coupled Bayesian model selection with linear regression splines to identify biotic or abiotic covariates with the strongest associations with abundances of each species. We then refitted change point models conditional on the selected covariates to explore whether those covariates could explain statistical trends or change points in species abundances. We also fitted a multispecies change point model that identified change points common to all species. All models included hierarchical structures to model data uncertainties, including observation errors and missing covariate values. There were step declines in abundances of all four species in the early 2000s, with a likely common decline in 2002. Abiotic variables, including water clarity, position of the 2 per thousand isohaline (X2), and the volume of freshwater exported from the estuary, explained some variation in species' abundances over the time series, but no selected covariates could explain statistically the post-2000 change points for any species. PMID:20666259

  1. Bayesian change point analysis of abundance trends for pelagic fishes in the upper San Francisco Estuary

    USGS Publications Warehouse

    Thompson, James R.; Kimmerer, Wim J.; Brown, Larry R.; Newman, Ken B.; Mac Nally, Ralph; Bennett, William A.; Feyrer, Frederick; Fleishman, Erica

    2010-01-01

    We examined trends in abundance of four pelagic fish species (delta smelt, longfin smelt, striped bass, and threadfin shad) in the upper San Francisco Estuary, California, USA, over 40 years using Bayesian change point models. Change point models identify times of abrupt or unusual changes in absolute abundance (step changes) or in rates of change in abundance (trend changes). We coupled Bayesian model selection with linear regression splines to identify biotic or abiotic covariates with the strongest associations with abundances of each species. We then refitted change point models conditional on the selected covariates to explore whether those covariates could explain statistical trends or change points in species abundances. We also fitted a multispecies change point model that identified change points common to all species. All models included hierarchical structures to model data uncertainties, including observation errors and missing covariate values. There were step declines in abundances of all four species in the early 2000s, with a likely common decline in 2002. Abiotic variables, including water clarity, position of the 2‰ isohaline (X2), and the volume of freshwater exported from the estuary, explained some variation in species' abundances over the time series, but no selected covariates could explain statistically the post-2000 change points for any species.

  2. DERIVING PLASMA DENSITIES AND ELEMENTAL ABUNDANCES FROM SERTS DIFFERENTIAL EMISSION MEASURE ANALYSIS

    SciTech Connect

    Schmelz, J. T.; Kimble, J. A.; Saba, J. L. R.

    2012-09-20

    We use high-resolution spectral emission line data obtained by the SERTS instrument during three rocket flights to demonstrate a new approach for constraining electron densities of solar active region plasma. We apply differential emission measure (DEM) forward-fitting techniques to characterize the multithermal solar plasma producing the observed EUV spectra, with constraints on the high-temperature plasma from the Yohkoh Soft X-ray Telescope. In this iterative process, we compare line intensities predicted by an input source distribution to observed line intensities for multiple iron ion species, and search a broad range of densities to optimize {chi}{sup 2} simultaneously for the many available density-sensitive lines. This produces a density weighted by the DEM, which appears to be useful for characterizing the bulk of the emitting plasma over a significant range of temperature. This 'DEM-weighted density' technique is complementary to the use of density-sensitive line ratios and less affected by uncertainties in atomic data and ionization fraction for any specific line. Once the DEM shape and the DEM-weighted density have been established from the iron lines, the relative elemental abundances can be determined for other lines in the spectrum. We have also identified spectral lines in the SERTS wavelength range that may be problematic.

  3. Deriving Plasma Densities and Elemental Abundances from SERTS Differential Emission Measure Analysis

    NASA Technical Reports Server (NTRS)

    Schmelz, J. T.; Kimble, J. A.; Saba, J. L. R.

    2012-01-01

    We use high-resolution spectral emission line data obtained by the SERTS instrument during three rocket flights to demonstrate a new approach for constraining electron densities of solar active region plasma.We apply differential emission measure (DEM) forward-fitting techniques to characterize the multithermal solar plasma producing the observed EUV spectra, with constraints on the high-temperature plasma from the Yohkoh Soft X-ray Telescope. In this iterative process, we compare line intensities predicted by an input source distribution to observed line intensities for multiple iron ion species, and search a broad range of densities to optimize chi-square simultaneously for the many available density-sensitive lines. This produces a density weighted by the DEM, which appears to be useful for characterizing the bulk of the emitting plasma over a significant range of temperature. This "DEM-weighted density" technique is complementary to the use of density-sensitive line ratios and less affected by uncertainties in atomic data and ionization fraction for any specific line. Once the DEM shape and the DEM-weighted density have been established from the iron lines, the relative elemental abundances can be determined for other lines in the spectrum. We have also identified spectral lines in the SERTS wavelength range that may be problematic

  4. Detailed Abundance Analysis of a Metal-poor Giant in the Galactic Center

    NASA Astrophysics Data System (ADS)

    Ryde, N.; Fritz, T. K.; Rich, R. M.; Thorsbro, B.; Schultheis, M.; Origlia, L.; Chatzopoulos, S.

    2016-11-01

    We report the first results from our program to examine the metallicity distribution of the Milky Way nuclear star cluster connected to Sgr A*, with the goal of inferring the star formation and enrichment history of this system, as well as its connection and relationship with the central 100 pc of the bulge/bar system. We present the first high-resolution (R ∼ 24,000), detailed abundance analysis of a K = 10.2 metal-poor, alpha-enhanced red giant projected at 1.5 pc from the Galactic center, using NIRSPEC on Keck II. A careful analysis of the dynamics and color of the star locates it at about {26}-16+54 pc line-of-sight distance in front of the nuclear cluster. It probably belongs to one of the nuclear components (cluster or disk), not to the bar/bulge or classical disk. A detailed spectroscopic synthesis, using a new line list in the K band, finds [Fe/H] ∼ ‑1.0 and [α/Fe] ∼ +0.4, consistent with stars of similar metallicity in the bulge. As known giants with comparable [Fe/H] and alpha enhancement are old, we conclude that this star is most likely to be a representative of the ∼10 Gyr old population. This is also the most metal-poor-confirmed red giant yet discovered in the vicinity of the nuclear cluster of the Galactic center. We consider recent reports in the literature of a surprisingly large number of metal-poor giants in the Galactic center, but the reported gravity of {log}g∼ 4 for these stars calls into question their reported metallicities.

  5. Long-term Records of Pacific Salmon Abundance From Sediment Core Analysis: Relationships to Past Climatic Change, and Implications for the Future

    NASA Astrophysics Data System (ADS)

    Finney, B.

    2002-12-01

    The response of Pacific salmon to future climatic change is uncertain, but will have large impacts on the economy, culture and ecology of the North Pacific Rim. Relationships between sockeye salmon populations and climatic change can be determined by analyzing sediment cores from lakes where sockeye return to spawn. Sockeye salmon return to their natal lake system to spawn and subsequently die following 2 - 3 years of feeding in the North Pacific Ocean. Sockeye salmon abundance can be reconstructed from stable nitrogen isotope analysis of lake sediment cores as returning sockeye transport significant quantities of N, relatively enriched in N-15, from the ocean to freshwater systems. Temporal changes in the input of salmon-derived N, and hence salmon abundance, can be quantified through downcore analysis of N isotopes. Reconstructions of sockeye salmon abundance from lakes in several regions of Alaska show similar temporal patterns, with variability occurring on decadal to millennial timescales. Over the past 2000 years, shifts in sockeye salmon abundance far exceed the historical decadal-scale variability. A decline occurred from about 100 BC - 800 AD, but salmon were consistently more abundant 1200 - 1900 AD. Declines since 1900 AD coincide with the period of extensive commercial fishing. Correspondence between these records and paleoclimatic data suggest that changes in salmon abundance are related to large scale climatic changes over the North Pacific. For example, the increase in salmon abundance c.a. 1200 AD corresponds to a period of glacial advance in southern Alaska, and a shift to drier conditions in western North America. Although the regionally coherent patterns in reconstructed salmon abundance are consistent with the hypothesis that climate is an important driver, the relationships do not always follow patterns observed in the 20th century. A main feature of recorded climate variability in this region is the alternation between multi-decade periods of

  6. THE C+N+O ABUNDANCE OF {omega} CENTAURI GIANT STARS: IMPLICATIONS FOR THE CHEMICAL-ENRICHMENT SCENARIO AND THE RELATIVE AGES OF DIFFERENT STELLAR POPULATIONS

    SciTech Connect

    Marino, A. F.; Milone, A. P.; Aparicio, A.; Piotto, G.; Cassisi, S.; D'Antona, F.; Anderson, J.; Bedin, L. R.; Renzini, A.; Villanova, S. E-mail: milone@iac.es E-mail: giampaolo.piotto@unipd.it E-mail: dantona@oa-roma.inaf.it E-mail: luigi.bedin@oapd.inaf.it E-mail: svillanova@astro-udec.cl

    2012-02-10

    We present a chemical-composition analysis of 77 red-giant stars in Omega Centauri. We have measured abundances for carbon and nitrogen, and combined our results with abundances of O, Na, La, and Fe that we determined in our previous work. Our aim is to better understand the peculiar chemical-enrichment history of this cluster by studying how the total C+N+O content varies among the different metallicity stellar groups, and among stars at different places along the Na-O anticorrelation. We find that the (anti)correlations among the light elements that would be expected on theoretical grounds for matter that has been nuclearly processed via high-temperature proton captures. The overall [(C+N+O)/Fe] increases by {approx}0.5 dex from [Fe/H] {approx}-2.0 to [Fe/H] {approx}-0.9. Our results provide insight into the chemical-enrichment history of the cluster, and the measured CNO variations provide important corrections for estimating the relative ages of the different stellar populations.

  7. Sand fly (Diptera: Psychodidae) abundance and species diversity in relation to environmental factors in parts of coastal plains of southern India.

    PubMed

    Srinivasan, R; Jambulingam, P; Vanamail, P

    2013-07-01

    Abundance pattern of sand flies in relation to several environmental factors, such as type of areas, dwellings, landforms, land usage pattern, and surface soil pH, was assessed in 81 areas or villages of Puducherry district, Puducherry Union Territory, located on the coastal plain of southern India, for three seasons, between November 2006 and October 2008, adopting hand-catch method. In total, 1,319 sand fly specimens comprising 12 species under two genera, viz., Phlebotomus and Sergentomyia, were collected. Among them, Phlebotomus (Euphlebotomus) argentipes Annandale & Brunetti, the vector of visceral leishmaniasis in India, was the predominant species in all habitats surveyed. The hierarchical cluster analysis showed that the density of sand flies was 10-fold higher in high-density group and fivefold higher in medium-density group, compared with the no or low-density group. Sand fly density was found to be influenced significantly with the type of areas, dwellings, landforms, land usage pattern, and surface soil pH in different groups. Rural areas located on fluvial landform with alkaline surface soil pH, supporting rice cultivation and luxuriant vegetation, are the most influencing factors that favor sand fly abundance and diversity in this district. PMID:23926773

  8. Sand fly (Diptera: Psychodidae) abundance and species diversity in relation to environmental factors in parts of coastal plains of southern India.

    PubMed

    Srinivasan, R; Jambulingam, P; Vanamail, P

    2013-07-01

    Abundance pattern of sand flies in relation to several environmental factors, such as type of areas, dwellings, landforms, land usage pattern, and surface soil pH, was assessed in 81 areas or villages of Puducherry district, Puducherry Union Territory, located on the coastal plain of southern India, for three seasons, between November 2006 and October 2008, adopting hand-catch method. In total, 1,319 sand fly specimens comprising 12 species under two genera, viz., Phlebotomus and Sergentomyia, were collected. Among them, Phlebotomus (Euphlebotomus) argentipes Annandale & Brunetti, the vector of visceral leishmaniasis in India, was the predominant species in all habitats surveyed. The hierarchical cluster analysis showed that the density of sand flies was 10-fold higher in high-density group and fivefold higher in medium-density group, compared with the no or low-density group. Sand fly density was found to be influenced significantly with the type of areas, dwellings, landforms, land usage pattern, and surface soil pH in different groups. Rural areas located on fluvial landform with alkaline surface soil pH, supporting rice cultivation and luxuriant vegetation, are the most influencing factors that favor sand fly abundance and diversity in this district.

  9. Abundant toxin-related genes in the genomes of beneficial symbionts from deep-sea hydrothermal vent mussels

    PubMed Central

    Sayavedra, Lizbeth; Kleiner, Manuel; Ponnudurai, Ruby; Wetzel, Silke; Pelletier, Eric; Barbe, Valerie; Satoh, Nori; Shoguchi, Eiichi; Fink, Dennis; Breusing, Corinna; Reusch, Thorsten BH; Rosenstiel, Philip; Schilhabel, Markus B; Becher, Dörte; Schweder, Thomas; Markert, Stephanie; Dubilier, Nicole; Petersen, Jillian M

    2015-01-01

    Bathymodiolus mussels live in symbiosis with intracellular sulfur-oxidizing (SOX) bacteria that provide them with nutrition. We sequenced the SOX symbiont genomes from two Bathymodiolus species. Comparison of these symbiont genomes with those of their closest relatives revealed that the symbionts have undergone genome rearrangements, and up to 35% of their genes may have been acquired by horizontal gene transfer. Many of the genes specific to the symbionts were homologs of virulence genes. We discovered an abundant and diverse array of genes similar to insecticidal toxins of nematode and aphid symbionts, and toxins of pathogens such as Yersinia and Vibrio. Transcriptomics and proteomics revealed that the SOX symbionts express the toxin-related genes (TRGs) in their hosts. We hypothesize that the symbionts use these TRGs in beneficial interactions with their host, including protection against parasites. This would explain why a mutualistic symbiont would contain such a remarkable ‘arsenal’ of TRGs. DOI: http://dx.doi.org/10.7554/eLife.07966.001 PMID:26371554

  10. Genome-wide survey and analysis of microsatellites in the Pacific oyster genome: abundance, distribution, and potential for marker development

    NASA Astrophysics Data System (ADS)

    Wang, Jiafeng; Qi, Haigang; Li, Li; Zhang, Guofan

    2014-01-01

    Microsatellites are a ubiquitous component of the eukaryote genome and constitute one of the most popular sources of molecular markers for genetic studies. However, no data are currently available regarding microsatellites across the entire genome in oysters, despite their importance to the aquaculture industry. We present the first genome-wide investigation of microsatellites in the Pacific oyster Crassostrea gigas by analysis of the complete genome, resequencing, and expression data. The Pacific oyster genome is rich in microsatellites. A total of 604 653 repeats were identified, in average of one locus per 815 base pairs (bp). A total of 12 836 genes had coding repeats, and 7 332 were expressed normally, including genes with a wide range of molecular functions. Compared with 20 different species of animals, microsatellites in the oyster genome typically exhibited 1) an intermediate overall frequency; 2) relatively uniform contents of (A)n and (C)n repeats and abundant long (C)n repeats (≥24 bp); 3) large average length of (AG)n repeats; and 4) scarcity of trinucleotide repeats. The microsatellite-flanking regions exhibited a high degree of polymorphism with a heterozygosity rate of around 2.0%, but there was no correlation between heterozygosity and microsatellite abundance. A total of 19 462 polymorphic microsatellites were discovered, and dinucleotide repeats were the most active, with over 26% of loci found to harbor allelic variations. In all, 7 451 loci with high potential for marker development were identified. Better knowledge of the microsatellites in the oyster genome will provide information for the future design of a wide range of molecular markers and contribute to further advancements in the field of oyster genetics, particularly for molecular-based selection and breeding.

  11. Relative importance of phenotypic trait matching and species' abundances in determining plant-avian seed dispersal interactions in a small insular community.

    PubMed

    González-Castro, Aarón; Yang, Suann; Nogales, Manuel; Carlo, Tomás A

    2015-03-05

    Network theory has provided a general way to understand mutualistic plant-animal interactions at the community level. However, the mechanisms responsible for interaction patterns remain controversial. In this study we use a combination of statistical models and probability matrices to evaluate the relative importance of species morphological and nutritional (phenotypic) traits and species abundance in determining interactions between fleshy-fruited plants and birds that disperse their seeds. The models included variables associated with species abundance, a suite of variables associated with phenotypic traits (fruit diameter, bird bill width, fruit nutrient compounds), and the species identity of the avian disperser. Results show that both phenotypic traits and species abundance are important determinants of pairwise interactions. However, when considered separately, fruit diameter and bill width were more important in determining seed dispersal interactions. The effect of fruit compounds was less substantial and only important when considered together with abundance-related variables and/or the factor 'animal species'.

  12. Secondary ion mass spectrometry combined with alpha track detection for isotope abundance ratio analysis of individual uranium-bearing particles.

    PubMed

    Esaka, Fumitaka; Magara, Masaaki

    2014-03-01

    Secondary ion mass spectrometry (SIMS) was used in combination with alpha track detection for the efficient analysis of uranium-bearing particles with higher (235)U abundances in environmental samples. A polycarbonate film containing particles was prepared and placed in contact with a CR-39 plastic detector. After exposure for 28 days, the detector was etched in a NaOH solution and each uranium-bearing particle was identified through observation of the alpha tracks recorded in the detector. A portion of the film containing each uranium-bearing particle was cut out and put onto a glassy carbon planchet. The films on the planchet were decomposed through plasma ashing for subsequent uranium abundance ratio analysis with SIMS. The alpha track-SIMS analysis of 10 uranium-bearing particles in a sample taken from a nuclear facility enabled n((235)U)/n((238)U) abundance ratios in the range 0.0072-0.25 to be detected, which were significantly higher than those obtained by SIMS without alpha track detection. The duration of the whole analytical process for analysis of 10 particles was about 32 days. The detection efficiency was calculated to be 27.1±6.5%, based on the analysis of the particles in uranium reference materials. The detection limits, defined as the diameter of the particle which produces alpha tracks more than one for a 28-days exposure, were estimated to be 0.8, 0.9, 1.1, 2.1 and 3.0 μm for the particles having the same uranium abundance ratios with NBL CRM U850, U500, U350, U050 and U010 reference materials, respectively. The use of alpha track detection for subsequent SIMS analysis is an inexpensive and an efficient way to measure uranium-bearing particles with higher (235)U abundances. PMID:24468381

  13. Indexing the relative abundance of age-0 white sturgeons in an impoundment of the lower Columbia River from highly skewed trawling data

    USGS Publications Warehouse

    Counihan, T.D.; Miller, A.I.; Parsley, M.J.

    1999-01-01

    The development of recruitment monitoring programs for age-0 white sturgeons Acipenser transmontanus is complicated by the statistical properties of catch-per-unit-effort (CPUE) data. We found that age-0 CPUE distributions from bottom trawl surveys violated assumptions of statistical procedures based on normal probability theory. Further, no single data transformation uniformly satisfied these assumptions because CPUE distribution properties varied with the sample mean (??(CPUE)). Given these analytic problems, we propose that an additional index of age-0 white sturgeon relative abundance, the proportion of positive tows (Ep), be used to estimate sample sizes before conducting age-0 recruitment surveys and to evaluate statistical hypothesis tests comparing the relative abundance of age-0 white sturgeons among years. Monte Carlo simulations indicated that Ep was consistently more precise than ??(CPUE), and because Ep is binomially rather than normally distributed, surveys can be planned and analyzed without violating the assumptions of procedures based on normal probability theory. However, we show that Ep may underestimate changes in relative abundance at high levels and confound our ability to quantify responses to management actions if relative abundance is consistently high. If data suggest that most samples will contain age-0 white sturgeons, estimators of relative abundance other than Ep should be considered. Because Ep may also obscure correlations to climatic and hydrologic variables if high abundance levels are present in time series data, we recommend ??(CPUE) be used to describe relations to environmental variables. The use of both Ep and ??(CPUE) will facilitate the evaluation of hypothesis tests comparing relative abundance levels and correlations to variables affecting age-0 recruitment. Estimated sample sizes for surveys should therefore be based on detecting predetermined differences in Ep, but data necessary to calculate ??(CPUE) should also be

  14. Lithium Abundance in Planet Search Stars

    NASA Astrophysics Data System (ADS)

    Myles, Justin; Yale Exoplanets

    2016-01-01

    Since most lithium in the universe is primordial and is destroyed in stars, lithium abundance can be used as a stellar age indicator. Some research seems to show that planet formation may also affect lithium abundance in exoplanet host stars (EHS). However, small and heterogenous samples have made both of these phenomena unclear. Further study of lithium abundance in EHS is needed to better understand possible physical roles of lithium in planet formation theory. We use a large homogenous sample with accurate stellar parameters on which we will use equivalent width analysis to determine precise lithium abundances. From these abundance values we determine an age vs. abundance relation. Additionally, we aim to explore correlation between lithium abundance and planet formation.

  15. Composition and Relative Abundance of Fish Species in the Lower White Salmon River, Washington, Prior to the Removal of Condit Dam

    USGS Publications Warehouse

    Allen, M. Brady; Connolly, Patrick J.

    2011-01-01

    Information about the composition and relative abundance of fish species was collected by a rotary screw trap and backpack electrofishing in the lower White Salmon River, Washington. The information was collected downstream of Condit Dam, which is at river kilometer (rkm) 5.2, and is proposed for removal in October 2011. A rotary screw trap was installed in the White Salmon River at rkm 1.5 and operated from March through June during 2006-09. All captured fish were identified to species and enumerated. Daily subsets of fish were weighed, measured, and fin clipped for a genetic analysis by the U.S. Fish and Wildlife Service. *Fall Chinook salmon (Oncorhynchus tshawytscha) were captured in the highest numbers (n=18, 640), and were composed of two stocks: tule and upriver bright. Almost all captured fall Chinook salmon were age-0, with only 16 (0.09 percent) being age-1 or older. *Tule fall Chinook salmon, the native stock, generally out-migrated from mid-March through early April. The tule stock was the more abundant fall Chinook salmon subspecies, comprising 85 percent of those captured in the trap. *Upriver bright fall Chinook salmon comprised 15 percent of the Chinook salmon catch and generally out-migrated from late May to early June. *Coho salmon (O. kisutch) and steelhead trout (O. mykiss) were captured by the rotary screw trap in all years. Coho salmon were caught in low numbers (n=661) and 69 percent were age-0 fish. Steelhead were slightly more abundant (n=679) than coho salmon and 84 percent were age-1 or older fish. Trap efficiency estimates varied widely (range, 0-10 percent) by species, fish size, and time of year. However, if we use only the estimates from efficiency tests where more than 300 wild age-0 Chinook salmon were released, there was a mean trapping efficiency of 1.4 percent (n=4, median, 1.3 percent, range, 0.3-2.4 percent) during the tule out-migration period, and a mean trapping efficiency of 0.8 percent (n=2, range, 0.3-1.2 percent) during

  16. Chemical abundances and kinematics of 257 G-, K-type field giants. Setting a base for further analysis of giant-planet properties orbiting evolved stars

    NASA Astrophysics Data System (ADS)

    Adibekyan, V. Zh.; Benamati, L.; Santos, N. C.; Alves, S.; Lovis, C.; Udry, S.; Israelian, G.; Sousa, S. G.; Tsantaki, M.; Mortier, A.; Sozzetti, A.; De Medeiros, J. R.

    2015-06-01

    We performed a uniform and detailed abundance analysis of 12 refractory elements (Na, Mg, Al, Si, Ca, Ti, Cr, Ni, Co, Sc, Mn, and V) for a sample of 257 G- and K-type evolved stars from the CORALIE planet search programme. To date, only one of these stars is known to harbour a planetary companion. We aimed to characterize this large sample of evolved stars in terms of chemical abundances and kinematics, thus setting a solid base for further analysis of planetary properties around giant stars. This sample, being homogeneously analysed, can be used as a comparison sample for other planet-related studies, as well as for different type of studies related to stellar and Galaxy astrophysics. The abundances of the chemical elements were determined using an local thermodynamic equilibrium (LTE) abundance analysis relative to the Sun, with the spectral synthesis code MOOG and a grid of Kurucz ATLAS9 atmospheres. To separate the Galactic stellar populations, both a purely kinematical approach and a chemical method were applied. We confirm the overabundance of Na in giant stars compared to the field FGK dwarfs. This enhancement might have a stellar evolutionary character, but departures from LTE may also produce a similar enhancement. Our chemical separation of stellar populations also suggests a `gap' in metallicity between the thick-disc and high-α metal-rich stars, as previously observed in dwarfs sample from HARPS. The present sample, as most of the giant star samples, also suffers from the B - V colour cut-off, which excludes low-log g stars with high metallicities, and high-log g star with low [Fe/H]. For future studies of planet occurrence dependence on stellar metallicity around these evolved stars, we suggest to use a subsample of stars in a `cut-rectangle' in the log g-[Fe/H] diagram to overcome the aforementioned issue.

  17. Feeding habits of the endangered Ozark big-eared bat (Corynorhinus townsendii ingens) relative to prey abundance

    USGS Publications Warehouse

    Leslie,, David M.; Clark, B.S.

    2002-01-01

    Feeding habits of the endangered Ozark big-cared bat (Corynorhinus townsendii ingens) in eastern Oklahoma, USA, were studied from July 1987 through July 1988. Diets were determined from microscopic analysis of fecal pellets and compared with arthropods collected in Malaise traps. Although lepidopterans comprised only 21.5% of the available prey, they occured in > 90% of the pellets examined and accounted for > 85% of the volume of prey consumed. Dipterans, coleopterans, and homopterans occured in 18.3%, 10,6%, and 6.7% of the feces, respectively, but each accounted for < 5% of the volume of prey consumed. Trichopterans, hymenopterans, and neuropterans also were found in feces but in trace amounts. Our results support the classification of C. t. ingens as a moth specialist, but additional insights are needed to fully understand how its feeding tactics conform to the allotonic frequency hypothesis (i.e., avoiding detection by cared moths). Conservation of this highly endangered North American bat will require, in part, maintenance of habitats capable of supporting abundant populations of Lepidoptera.

  18. Vertical distribution and abundance of Calanus pacificus and Pseudocalanus newmani in relation to chlorophyll a concentrations in Dabob Bay, Washington

    NASA Astrophysics Data System (ADS)

    Pierson, James J.; Leising, Andrew W.; Halsband-Lenk, Claudia; Ferm, Nissa

    2005-11-01

    Recent evidence suggests that diatoms may induce reproductive failure in planktonic copepods, either through ingestion of diatoms by females or contact of embryos with diatom extracts. Therefore, the co-location of copepods and diatoms in situ may affect copepod reproductive success. As part of a study to determine the effect of diatoms on copepod reproductive effort, we measured the abundance and nighttime vertical distribution of two species of copepods, Calanus pacificus and Pseudocalanus newmani, as well as vertical distribution of chlorophyll a, during winter-spring in Dabob Bay, Washington State, USA, in 2002 and 2003, with limited observations in the summer of both years. Populations of both species declined throughout the winter-spring but rebounded by summer. While C. pacificus females, males, and CV copepodites were not strongly co-located with chlorophyll a concentrations, those same stages of P. newmani were consistently found within the layer containing the chlorophyll maximum. Our limited data on vertical migration show that female and CI-CII copepodites of C. pacificus exhibited normal diel vertical migration behavior, but adult P. newmani exhibited reverse diel migration. Overall, these data suggest that the patterns of reproductive success observed for the two species may be related to their different vertical distributions and may affect their population dynamics.

  19. Abundances of polycyclic aromatic hydrocarbons (PAHs) in 14 chinese and american coals and their relation to coal rank and weathering

    USGS Publications Warehouse

    Wang, R.; Liu, Gaisheng; Zhang, Jiahua; Chou, C.-L.; Liu, J.

    2010-01-01

    The abundances of 16 polycyclic aromatic hydrocarbons (PAHs) on the priority list of the United States Environmental Protection Agency (U.S. EPA) have been determined in 14 Chinese and American coals. The ranks of the samples range from lignite, bituminous coal, anthracite, to natural coke. Soxhlet extraction was conducted on each coal for 48 h. The extract was analyzed on a gas chromatograph-mass spectrometer (GC-MS). The results show that the total PAH content ranged from 0.31 to 57.6 ??g/g of coal (on a dry basis). It varied with coal rank and is highest in the maturity range of bituminous coal rank. High-molecular-weight (HMW) PAHs are predominant in low-rank coals, but low-molecular-weight (LMW) PAHs are predominant in high-rank coals. The low-sulfur coals have a higher PAH content than high-sulfur coals. It may be explained by an increasing connection between disulfide bonds and PAHs in high-sulfur coal. In addition, it leads us to conclude that the PAH content of coals may be related to the depositional environment. ?? 2010 American Chemical Society.

  20. Species diversity and relative abundance of lactic acid bacteria in the milk of rhesus monkeys (Macaca mulatta)

    PubMed Central

    Jin, L.; Hinde, K.; Tao, L.

    2013-01-01

    Background Mother’s milk is a source of bacteria that influences the development of the infant commensal gut microbiota. To date, the species diversity and relative abundance of lactic acid bacteria in the milk of non-human primates have not been described. Methods Milk samples were aseptically obtained from 54 female rhesus monkeys (Macaca mulatta) at peak lactation. Following GM17 and MRS agar plating, single bacterial colonies were isolated based on difference in morphotypes, then grouped based on whole-cell protein profiles on SDS–PAGE. Bacterial DNA was isolated and the sequence the 16S rRNA gene was analyzed. Results A total of 106 strains of 19 distinct bacterial species, belonging to five genera, Bacillus, Enterococcus, Lactobacillus, Pediococcus, and Streptococcus, were identified. Conclusions Maternal gut and oral commensal bacteria may be translocated to the mammary gland during lactation and present in milk. This pathway can be an important source of commensal bacteria to the infant gut and oral cavity. PMID:20946146

  1. Effects of fish density and relative abundance on competition between larval lake herring and lake whitefish for zooplankton

    USGS Publications Warehouse

    Todd, Thomas N.; Davis, Bruce M.

    1995-01-01

    Competition for zooplankton between larval lake herring (Coregonus artedi) and lake whitefish (C. clupeaformis) was compared in mesocosm experiments in a small lake. Both species were combined in test enclosures at relative abundances of 1:1 or 1:4 lake herring to lake whitefish at densities of 500; 1, 000; and 2, 000 fish per cage, and were allowed to feed ad libitum on available zooplankton. After 60 days, at 500 fish per cage and a 1:1 ratio, lake whitfish were significantly larger than lake herring. At 1, 000 and 2, 000 fish per cage, lake herring and lake whitefish exhibited similar depressed growth rates. Survival was lower (30-50%) in the nets with 2, 000 fish than in the lower fish densities. We suspect that diet similarities of juvenile lake herring and lake whitefish in addition to the larger size and more aggressive behavior of larval lake whitefish resulted in the depressed growth and poorer survival for lake herring.

  2. Investigation of the relative abundance of heavy versus light nuclei in primary cosmic rays using underground muon bundles

    SciTech Connect

    Sundaralingam, N.

    1993-06-08

    We study multiple muon events (muon bundles) recorded underground at a depth of 2090 mwe. To penetrate to this depth, the muons must have energies above 0.8 TeV at the Earth`s surface; the primary cosmic ray nuclei which give rise to the observed muon bundles have energies at incidence upon the upper atmosphere of 10 to 10{sup 5}TeV. The events are detected using the Soudan 2 experiment`s fine grained tracking calorimeter which is surrounded by a 14 m {times}10 m {times} 31 m proportional tube array (the ``active shield``). Muon bundles which have at least one muon traversing the calorimeter, are reconstructed using tracks in the calorimeter together with hit patterns in the proportional tube shield. All ionization pulses are required to be coincident within 3 microseconds. A goal of this study is to investigate the relative nuclear abundances in the primary cosmic radiation around the ``knee`` region (10{sup 3} {minus} 10{sup 4} TeV) of the incident energy spectrum. Four models for the nuclear composition of cosmic rays are considered: The Linsley model, the Constant Mass Composition model (CMC), the Maryland model and the Proton-poor model. A Monte Carlo which incorporates one model at a time is used to simulate events which are then reconstructed using the same computer algorithms that are used for the data. Identical cuts and selections are applied to the data and to the simulated events.

  3. Lowland tapir (Tapirus terrestris) distribution, activity patterns and relative abundance in the Greater Madidi-Tambopata Landscape.

    PubMed

    Wallace, Robert; Ayala, Guido; Viscarra, Maria

    2012-12-01

    Lowland tapir distribution is described in northwestern Bolivia and southeastern Peru within the Greater Madidi-Tambopata Landscape, a priority Tapir Conservation Unit, using 1255 distribution points derived from camera trapping efforts, field research and interviews with park guards from 5 national protected areas and hunters from 19 local communities. A total of 392 independent camera trapping events from 14 camera trap surveys at 11 sites demonstrated the nocturnal and crepuscular activity patterns (86%) of the lowland tapir and provide 3 indices of relative abundance for spatial and temporal comparison. Capture rates for lowland tapirs were not significantly different between camera trapping stations placed on river beaches versus those placed in the forest. Lowland tapir capture rates were significantly higher in the national protected areas of the region versus indigenous territories and unprotected portions of the landscape. Capture rates through time suggested that lowland tapir populations are recovering within the Tuichi Valley, an area currently dedicated towards ecotourism activities, following the creation (1995) and subsequent implementation (1997) of the Madidi National Park in Bolivia. Based on our distributional data and published conservative estimates of population density, we calculated that this transboundary landscape holds an overall lowland tapir population of between 14 540 and 36 351 individuals, of which at least 24.3% are under protection from national and municipal parks. As such, the Greater Madidi-Tambopata Landscape should be considered a lowland tapir population stronghold and priority conservation efforts are discussed in order to maintain this population. PMID:23253372

  4. Lowland tapir (Tapirus terrestris) distribution, activity patterns and relative abundance in the Greater Madidi-Tambopata Landscape.

    PubMed

    Wallace, Robert; Ayala, Guido; Viscarra, Maria

    2012-12-01

    Lowland tapir distribution is described in northwestern Bolivia and southeastern Peru within the Greater Madidi-Tambopata Landscape, a priority Tapir Conservation Unit, using 1255 distribution points derived from camera trapping efforts, field research and interviews with park guards from 5 national protected areas and hunters from 19 local communities. A total of 392 independent camera trapping events from 14 camera trap surveys at 11 sites demonstrated the nocturnal and crepuscular activity patterns (86%) of the lowland tapir and provide 3 indices of relative abundance for spatial and temporal comparison. Capture rates for lowland tapirs were not significantly different between camera trapping stations placed on river beaches versus those placed in the forest. Lowland tapir capture rates were significantly higher in the national protected areas of the region versus indigenous territories and unprotected portions of the landscape. Capture rates through time suggested that lowland tapir populations are recovering within the Tuichi Valley, an area currently dedicated towards ecotourism activities, following the creation (1995) and subsequent implementation (1997) of the Madidi National Park in Bolivia. Based on our distributional data and published conservative estimates of population density, we calculated that this transboundary landscape holds an overall lowland tapir population of between 14 540 and 36 351 individuals, of which at least 24.3% are under protection from national and municipal parks. As such, the Greater Madidi-Tambopata Landscape should be considered a lowland tapir population stronghold and priority conservation efforts are discussed in order to maintain this population.

  5. Coronal Abundances and Their Variation

    NASA Technical Reports Server (NTRS)

    Saba, Julia L. R.

    1996-01-01

    This contract supported the investigation of elemental abundances in the solar corona, principally through analysis of high-resolution soft X-ray spectra from the Flat Crystal Spectrometer on NASA's Solar Maximum Mission. The goals of the study were a characterization of the mean values of relative abundances of elements accessible in the FCS data, and information on the extent and circumstances of their variability. This is the Final Report, summarizing the data analysis and reporting activities which occurred during the period of performance, June 1993 - December 1996.

  6. Coronal abundances and their variation

    NASA Technical Reports Server (NTRS)

    Saba, Julia L. R.

    1994-01-01

    This contract supports the investigation of elemental abundances in the solar corona, principally through analysis of high-resolution soft x-ray spectra from the Flat Crystal Spectrometer (FCS) on the Solar Maximum Mission. The goals of the study are a characterization of the mean values of relative abundances of elements accessible in the FCS data, and information on the extent and circumstances of their variability. This report is a summation of the data analysis and reporting activities which occurred during the first ten months of the contract, 15 Jun. 1993 to 15 Apr. 1994.

  7. Project VeSElkA: results of abundance analysis I - HD 71030, HD 95608, HD 116235 and HD 186568

    NASA Astrophysics Data System (ADS)

    LeBlanc, F.; Khalack, V.; Yameogo, B.; Thibeault, C.; Gallant, I.

    2015-11-01

    A portion of main-sequence stars, called chemically peculiar (CP) stars, show important abundance anomalies mainly due to atomic diffusion of the species within these stars. Certain CP stars have hydrodynamically stable atmospheres where atomic diffusion may dominate and lead to vertical abundance stratification there. Recently, Project VeSElkA (a word meaning rainbow in Ukrainian and standing for `Vertical Stratification of Element Abundances') was initiated with the goal to detect vertical stratification of chemical abundances in selected CP stars using high-resolution spectra with large signal-to-noise ratios. The first extensive and detailed series of results from atomic-line analysis is presented here for four stars of Project VeSElkA: HD 71030, HD 95608, HD 116235 and HD 186568. These stars were recently observed with ESPaDOnS at Canada-France-Hawaii Telescope. Strong evidence of iron stratification in the atmospheres of HD 95608 and HD 116235 was found. Chromium also shows a steep abundance gradient in the upper atmospheres of these two stars. No evidence of stratification is found for HD 71030 and HD 186568.

  8. Container Type Influences the Relative Abundance, Body Size, and Susceptibility of Ochlerotatus triseriatus (Diptera: Culicidae) to La Crosse Virus.

    PubMed

    Bara, Jeffrey J; Muturi, Ephantus J

    2015-05-01

    Ochlerotatus triseriatus (Say), the primary vector of La Crosse virus (LAC), develops in a variety of natural and artificial aquatic containers where it often co-occurs with larvae of other mosquito species. We conducted a field study at two woodlots (South Farms and Trelease Woods) in Urbana, IL, to examine how container type influences vector abundance, body size, and susceptibility to LAC. Mosquito pupae were collected from tree holes, plastic bins, and waste tires, and eclosing adults were identified to species morphologically. Oc. triseriatus and Ochlerotatus japonicus (Theobald) females were orally challenged with LAC and midgut infection rate, disseminated infection rate, and body titer were determined by reverse-transcriptase real-time PCR. Oc. triseriatus was the dominant species collected in tree holes while Oc. japonicus and Culex restuans (Theobald) were mostly dominant in artificial containers. Female Oc. triseriatus and Oc. japonicus collected from plastic bins were significantly larger than those collected from tree holes or waste tires. Oc. japonicus females from South Farms were also significantly larger than those from Trelease Woods. Oc. triseriatus females collected from plastic bins and waste tires were significantly more susceptible to LAC infection relative to females collected from tree holes. In addition, Oc. triseriatus females from waste tires had significantly higher LAC titer relative to Oc. triseriatus from tree holes. For each container type and study site, wing length was not correlated to infection or dissemination rates. These findings suggest that the container type in which Oc.triseriatus develop may contribute to the spatial and temporal dynamics of LAC transmission.

  9. Relative abundance and the species-specific reinforcement of male mating preference in the Chrysochus (Coleoptera: Chrysomelidae) hybrid zone.

    PubMed

    Peterson, Merrill A; Honchak, Barbara M; Locke, Stefanie E; Beeman, Timothy E; Mendoza, Jessica; Green, Jabin; Buckingham, Kati J; White, Michael A; Monsen, Kirsten J

    2005-12-01

    Most studies of reinforcement have focused on the evolution of either female choice or male mating cues, following the long-held view in sexual selection theory that mating mistakes are typically more costly for females than for males. However, factors such as conspecific sperm precedence can buffer females against the cost of mating mistakes, suggesting that in some hybrid zones mating mistakes may be more costly for males than for females. Thus, the historical bias in reinforcement research may underestimate its frequency. In this study, we present evidence that reinforcement has driven the evolution of male choice in a hybrid zone between the highly promiscuous leaf beetles Chrysochus cobaltinus and C. auratus, the hybrids of which have extremely low fitness. In addition, there is evidence for male choice in these beetles and that male mating mistakes may be costly, due to reduced opportunities to mate with conspecific females. The present study combines laboratory and field methods to quantify the strength of sexual isolation, test the hypothesis of reproductive character displacement, and assess the link between relative abundance and the strength of selection against hybridization. We document that, while sexual isolation is weak, it is sufficient to produce positive assortative mating. In addition, reproductive character displacement was only detected in the relatively rare species. The strong postzygotic barriers in this system are sufficient to generate the bimodality that characterizes this hybrid zone, but the weak sexual isolation is not, calling into question whether strong prezygotic isolation is necessary for the maintenance of bimodality. Growing evidence that the cost of mating mistakes is sufficient to shape the evolution of male mate choice suggests that the reinforcement of male mate choice may prove to be a widespread occurrence.

  10. CHEMICAL ABUNDANCE ANALYSIS OF A NEUTRON-CAPTURE ENHANCED RED GIANT IN THE BULGE PLAUT FIELD

    SciTech Connect

    Johnson, Christian I.; Rich, R. Michael; McWilliam, Andrew E-mail: rmr@astro.ucla.edu E-mail: andy@obs.carnegiescience.edu

    2013-09-20

    We present chemical abundances for 27 elements ranging from oxygen to erbium in the metal-poor ([Fe/H] = –1.67) bulge red giant branch star 2MASS 18174532-3353235. The results are based on equivalent width and spectrum synthesis analyses of a high-resolution (R ∼ 30, 000) spectrum obtained with the Magellan-MIKE spectrograph. While the light (Z ∼< 30) element abundance patterns match those of similar metallicity bulge and halo stars, the strongly enhanced heavy element abundances are more similar to 'r-II' halo stars (e.g., CS 22892-052) typically found at [Fe/H] ∼< – 2.5. We find that the heaviest elements (Z ≥ 56) closely follow the scaled-solar r-process abundance pattern. We do not find evidence supporting significant s-process contributions; however, the intermediate mass elements (e.g., Y and Zr) appear to have been produced through a different process than the heaviest elements. The light and heavy element abundance patterns of 2MASS 18174532-3353235 are in good agreement with the more metal-poor r-process enhanced stars CS 22892-052 and BD +17{sup o}3248. 2MASS 18174532-3353235 also shares many chemical characteristics with the similar metallicity but comparatively α-poor Ursa Minor dwarf galaxy giant COS 82. Interestingly, the Mo and Ru abundances of 2MASS 18174532-3353235 are also strongly enhanced and follow a similar trend recently found to be common in moderately metal-poor main-sequence turn-off halo stars.

  11. Abundant Topological Outliers in Social Media Data and Their Effect on Spatial Analysis

    PubMed Central

    Zipf, Alexander

    2016-01-01

    Twitter and related social media feeds have become valuable data sources to many fields of research. Numerous researchers have thereby used social media posts for spatial analysis, since many of them contain explicit geographic locations. However, despite its widespread use within applied research, a thorough understanding of the underlying spatial characteristics of these data is still lacking. In this paper, we investigate how topological outliers influence the outcomes of spatial analyses of social media data. These outliers appear when different users contribute heterogeneous information about different phenomena simultaneously from similar locations. As a consequence, various messages representing different spatial phenomena are captured closely to each other, and are at risk to be falsely related in a spatial analysis. Our results reveal indications for corresponding spurious effects when analyzing Twitter data. Further, we show how the outliers distort the range of outcomes of spatial analysis methods. This has significant influence on the power of spatial inferential techniques, and, more generally, on the validity and interpretability of spatial analysis results. We further investigate how the issues caused by topological outliers are composed in detail. We unveil that multiple disturbing effects are acting simultaneously and that these are related to the geographic scales of the involved overlapping patterns. Our results show that at some scale configurations, the disturbances added through overlap are more severe than at others. Further, their behavior turns into a volatile and almost chaotic fluctuation when the scales of the involved patterns become too different. Overall, our results highlight the critical importance of thoroughly considering the specific characteristics of social media data when analyzing them spatially. PMID:27611199

  12. Abundant Topological Outliers in Social Media Data and Their Effect on Spatial Analysis.

    PubMed

    Westerholt, Rene; Steiger, Enrico; Resch, Bernd; Zipf, Alexander

    2016-01-01

    Twitter and related social media feeds have become valuable data sources to many fields of research. Numerous researchers have thereby used social media posts for spatial analysis, since many of them contain explicit geographic locations. However, despite its widespread use within applied research, a thorough understanding of the underlying spatial characteristics of these data is still lacking. In this paper, we investigate how topological outliers influence the outcomes of spatial analyses of social media data. These outliers appear when different users contribute heterogeneous information about different phenomena simultaneously from similar locations. As a consequence, various messages representing different spatial phenomena are captured closely to each other, and are at risk to be falsely related in a spatial analysis. Our results reveal indications for corresponding spurious effects when analyzing Twitter data. Further, we show how the outliers distort the range of outcomes of spatial analysis methods. This has significant influence on the power of spatial inferential techniques, and, more generally, on the validity and interpretability of spatial analysis results. We further investigate how the issues caused by topological outliers are composed in detail. We unveil that multiple disturbing effects are acting simultaneously and that these are related to the geographic scales of the involved overlapping patterns. Our results show that at some scale configurations, the disturbances added through overlap are more severe than at others. Further, their behavior turns into a volatile and almost chaotic fluctuation when the scales of the involved patterns become too different. Overall, our results highlight the critical importance of thoroughly considering the specific characteristics of social media data when analyzing them spatially.

  13. Abundant Topological Outliers in Social Media Data and Their Effect on Spatial Analysis.

    PubMed

    Westerholt, Rene; Steiger, Enrico; Resch, Bernd; Zipf, Alexander

    2016-01-01

    Twitter and related social media feeds have become valuable data sources to many fields of research. Numerous researchers have thereby used social media posts for spatial analysis, since many of them contain explicit geographic locations. However, despite its widespread use within applied research, a thorough understanding of the underlying spatial characteristics of these data is still lacking. In this paper, we investigate how topological outliers influence the outcomes of spatial analyses of social media data. These outliers appear when different users contribute heterogeneous information about different phenomena simultaneously from similar locations. As a consequence, various messages representing different spatial phenomena are captured closely to each other, and are at risk to be falsely related in a spatial analysis. Our results reveal indications for corresponding spurious effects when analyzing Twitter data. Further, we show how the outliers distort the range of outcomes of spatial analysis methods. This has significant influence on the power of spatial inferential techniques, and, more generally, on the validity and interpretability of spatial analysis results. We further investigate how the issues caused by topological outliers are composed in detail. We unveil that multiple disturbing effects are acting simultaneously and that these are related to the geographic scales of the involved overlapping patterns. Our results show that at some scale configurations, the disturbances added through overlap are more severe than at others. Further, their behavior turns into a volatile and almost chaotic fluctuation when the scales of the involved patterns become too different. Overall, our results highlight the critical importance of thoroughly considering the specific characteristics of social media data when analyzing them spatially. PMID:27611199

  14. The Impact of Land Abandonment on Species Richness and Abundance in the Mediterranean Basin: A Meta-Analysis

    PubMed Central

    Plieninger, Tobias; Hui, Cang; Gaertner, Mirijam; Huntsinger, Lynn

    2014-01-01

    Land abandonment is common in the Mediterranean Basin, a global biodiversity hotspot, but little is known about its impacts on biodiversity. To upscale existing case-study insights to the Pan-Mediterranean level, we conducted a meta-analysis of the effects of land abandonment on plant and animal species richness and abundance in agroforestry, arable land, pastures, and permanent crops of the Mediterranean Basin. In particular, we investigated (1) which taxonomic groups (arthropods, birds, lichen, vascular plants) are more affected by land abandonment; (2) at which spatial and temporal scales the effect of land abandonment on species richness and abundance is pronounced; (3) whether previous land use and current protected area status affect the magnitude of changes in the number and abundance of species; and (4) how prevailing landforms and climate modify the impacts of land abandonment. After identifying 1240 potential studies, 154 cases from 51 studies that offered comparisons of species richness and abundance and had results relevant to our four areas of investigation were selected for meta-analysis. Results are that land abandonment showed slightly increased (effect size  = 0.2109, P<0.0001) plant and animal species richness and abundance overall, though results were heterogeneous, with differences in effect size between taxa, spatial-temporal scales, land uses, landforms, and climate. In conclusion, there is no “one-size-fits-all” conservation approach that applies to the diverse contexts of land abandonment in the Mediterranean Basin. Instead, conservation policies should strive to increase awareness of this heterogeneity and the potential trade-offs after abandonment. The strong role of factors at the farm and landscape scales that was revealed by the analysis indicates that purposeful management at these scales can have a powerful impact on biodiversity. PMID:24865979

  15. MyGIsFOS: an automated code for parameter determination and detailed abundance analysis in cool stars

    NASA Astrophysics Data System (ADS)

    Sbordone, L.; Caffau, E.; Bonifacio, P.; Duffau, S.

    2014-04-01

    Context. The current and planned high-resolution, high-multiplexity stellar spectroscopic surveys, as well as the swelling amount of underutilized data present in public archives, have led to an increasing number of efforts to automate the crucial but slow process of retrieving stellar parameters and chemical abundances from spectra. Aims: We present MyGIsFOS1, a code designed to derive atmospheric parameters and detailed stellar abundances from medium- to high-resolution spectra of cool (FGK) stars. We describe the general structure and workings of the code, present analyses of a number of well-studied stars representative of the parameter space MyGIsFOS is designed to cover, and give examples of the exploitation of MyGIsFOS very fast analysis to assess uncertainties through Monte Carlo tests. Methods: MyGIsFOS aims to reproduce a "traditional" manual analysis by fitting spectral features for different elements against a precomputed grid of synthetic spectra. The lines of Fe i and Fe ii can be employed to determine temperature, gravity, microturbulence, and metallicity by iteratively minimizing the dependence of Fe i abundance from line lower energy and equivalent width, and imposing Fe i-Fe ii ionization equilibrium. Once parameters are retrieved, detailed chemical abundances are measured from lines of other elements. Results: MyGIsFOS replicates closely the results obtained in similar analyses on a set of well-known stars. It is also quite fast, performing a full parameter determination and detailed abundance analysis in about two minutes per star on a mainstream desktop computer. Currently, its preferred field of application are high-resolution and/or large spectral coverage data (e.g., UVES, X-shooter, HARPS, Sophie). My God It's Full Of Stars, http://mygisfos.obspm.fr

  16. The impact of land abandonment on species richness and abundance in the Mediterranean Basin: a meta-analysis.

    PubMed

    Plieninger, Tobias; Hui, Cang; Gaertner, Mirijam; Huntsinger, Lynn

    2014-01-01

    Land abandonment is common in the Mediterranean Basin, a global biodiversity hotspot, but little is known about its impacts on biodiversity. To upscale existing case-study insights to the Pan-Mediterranean level, we conducted a meta-analysis of the effects of land abandonment on plant and animal species richness and abundance in agroforestry, arable land, pastures, and permanent crops of the Mediterranean Basin. In particular, we investigated (1) which taxonomic groups (arthropods, birds, lichen, vascular plants) are more affected by land abandonment; (2) at which spatial and temporal scales the effect of land abandonment on species richness and abundance is pronounced; (3) whether previous land use and current protected area status affect the magnitude of changes in the number and abundance of species; and (4) how prevailing landforms and climate modify the impacts of land abandonment. After identifying 1240 potential studies, 154 cases from 51 studies that offered comparisons of species richness and abundance and had results relevant to our four areas of investigation were selected for meta-analysis. Results are that land abandonment showed slightly increased (effect size  = 0.2109, P<0.0001) plant and animal species richness and abundance overall, though results were heterogeneous, with differences in effect size between taxa, spatial-temporal scales, land uses, landforms, and climate. In conclusion, there is no "one-size-fits-all" conservation approach that applies to the diverse contexts of land abandonment in the Mediterranean Basin. Instead, conservation policies should strive to increase awareness of this heterogeneity and the potential trade-offs after abandonment. The strong role of factors at the farm and landscape scales that was revealed by the analysis indicates that purposeful management at these scales can have a powerful impact on biodiversity.

  17. The impact of land abandonment on species richness and abundance in the Mediterranean Basin: a meta-analysis.

    PubMed

    Plieninger, Tobias; Hui, Cang; Gaertner, Mirijam; Huntsinger, Lynn

    2014-01-01

    Land abandonment is common in the Mediterranean Basin, a global biodiversity hotspot, but little is known about its impacts on biodiversity. To upscale existing case-study insights to the Pan-Mediterranean level, we conducted a meta-analysis of the effects of land abandonment on plant and animal species richness and abundance in agroforestry, arable land, pastures, and permanent crops of the Mediterranean Basin. In particular, we investigated (1) which taxonomic groups (arthropods, birds, lichen, vascular plants) are more affected by land abandonment; (2) at which spatial and temporal scales the effect of land abandonment on species richness and abundance is pronounced; (3) whether previous land use and current protected area status affect the magnitude of changes in the number and abundance of species; and (4) how prevailing landforms and climate modify the impacts of land abandonment. After identifying 1240 potential studies, 154 cases from 51 studies that offered comparisons of species richness and abundance and had results relevant to our four areas of investigation were selected for meta-analysis. Results are that land abandonment showed slightly increased (effect size  = 0.2109, P<0.0001) plant and animal species richness and abundance overall, though results were heterogeneous, with differences in effect size between taxa, spatial-temporal scales, land uses, landforms, and climate. In conclusion, there is no "one-size-fits-all" conservation approach that applies to the diverse contexts of land abandonment in the Mediterranean Basin. Instead, conservation policies should strive to increase awareness of this heterogeneity and the potential trade-offs after abandonment. The strong role of factors at the farm and landscape scales that was revealed by the analysis indicates that purposeful management at these scales can have a powerful impact on biodiversity. PMID:24865979

  18. Abundance analysis of the supergiant stars HD 80057 and HD 80404 based on their UVES Spectra

    NASA Astrophysics Data System (ADS)

    Tanrıverdi, T.; Baştürk, Ö.

    2016-08-01

    This study presents elemental abundances of the early A-type supergiant HD 80057 and the late A-type supergiant HD 80404. High resolution and high signal-to-noise ratio spectra published by the UVES Paranal Observatory Project (Bagnulo et al., 2003)1

  19. Influence of species, size and relative abundance on the outcomes of competitive interactions between brook trout and juvenile coho salmon

    USGS Publications Warehouse

    Thornton, Emily J; Duda, Jeff; Quinn, Thomas P

    2016-01-01

    Resource competition between animals is influenced by a number of factors including the species, size and relative abundance of competing individuals. Stream-dwelling animals often experience variably available food resources, and some employ territorial behaviors to increase their access to food. We investigated the factors that affect dominance between resident, non-native brook trout and recolonizing juvenile coho salmon in the Elwha River, WA, USA, to see if brook trout are likely to disrupt coho salmon recolonization via interference competition. During dyadic laboratory feeding trials, we hypothesized that fish size, not species, would determine which individuals consumed the most food items, and that species would have no effect. We found that species, not size, played a significant role in dominance; coho salmon won 95% of trials, even when only 52% the length of their brook trout competitors. As the pairs of competing fish spent more time together during a trial sequence, coho salmon began to consume more food, and brook trout began to lose more, suggesting that the results of early trials influenced fish performance later. In group trials, we hypothesized that group composition and species would not influence fish foraging success. In single species groups, coho salmon consumed more than brook trout, but the ranges overlapped. Brook trout consumption remained constant through all treatments, but coho salmon consumed more food in treatments with fewer coho salmon, suggesting that coho salmon experienced more intra- than inter-specific competition and that brook trout do not pose a substantial challenge. Based on our results, we think it is unlikely that competition from brook trout will disrupt Elwha River recolonization by coho salmon.

  20. ON THE RELATIVE ABUNDANCE OF LiH AND LiH{sup +} MOLECULES IN THE EARLY UNIVERSE: NEW RESULTS FROM QUANTUM REACTIONS

    SciTech Connect

    Bovino, Stefano; Tacconi, Mario; Gianturco, Franco A.; Galli, Daniele; Palla, Francesco

    2011-04-20

    The relative efficiencies of the chemical pathways that can lead to the destruction of LiH and LiH{sup +} molecules, conjectured to be present in the primordial gas and to control molecular cooling processes in the gravitational collapse of the post-recombination era, are revisited by using accurate quantum calculations for the several reactions involved. The new rates are employed to survey the behavior of the relative abundance of these molecules at redshifts of interest for early universe conditions. We find significant differences with respect to previous calculations, the present ones yielding LiH abundances higher than LiH{sup +} at all redshifts.

  1. Single-step analysis of low abundance phosphoamino acids via on-line sample preconcentration with chemical derivatization by capillary electrophoresis.

    PubMed

    Ptolemy, Adam S; Britz-McKibbin, Philip

    2005-09-01

    New strategies for rapid, sensitive and high-throughput analysis of low abundance metabolites in biological samples are required for future metabolomic research. In this report, a direct method for sub-micromolar analyses of phosphoamino acids was developed using on-line sample preconcentration with 9-fluorenylmethyloxycarbonyl chloride (FMOC) derivatization by capillary electrophoresis (CE) and UV detection. Analyte focusing by dynamic pH junction and FMOC labeling efficiency were influenced by several experimental factors including buffer pH, ionic strength, sample injection length and FMOC concentration. About a 200-fold enhancement in concentration sensitivity was achieved under optimal conditions relative to conventional off-line derivatization, as reflected by a detection limit (S/N approximately 3) of 0.1 microM. In-capillary sample preconcentration with chemical labeling by CE offers a unique single-step analytical platform for high-throughput screening of low abundance metabolites without intrinsic chromophores.

  2. Single-step analysis of low abundance phosphoamino acids via on-line sample preconcentration with chemical derivatization by capillary electrophoresis.

    PubMed

    Ptolemy, Adam S; Britz-McKibbin, Philip

    2005-09-01

    New strategies for rapid, sensitive and high-throughput analysis of low abundance metabolites in biological samples are required for future metabolomic research. In this report, a direct method for sub-micromolar analyses of phosphoamino acids was developed using on-line sample preconcentration with 9-fluorenylmethyloxycarbonyl chloride (FMOC) derivatization by capillary electrophoresis (CE) and UV detection. Analyte focusing by dynamic pH junction and FMOC labeling efficiency were influenced by several experimental factors including buffer pH, ionic strength, sample injection length and FMOC concentration. About a 200-fold enhancement in concentration sensitivity was achieved under optimal conditions relative to conventional off-line derivatization, as reflected by a detection limit (S/N approximately 3) of 0.1 microM. In-capillary sample preconcentration with chemical labeling by CE offers a unique single-step analytical platform for high-throughput screening of low abundance metabolites without intrinsic chromophores. PMID:16096672

  3. Carbon isotope analysis in urea at high 13C-abundances using the 13/12CO2-breath test device FANci2.

    PubMed

    Schmidt, G

    2002-09-01

    The increasing application of 13C-labelled urea in medicine requires simple and reasonable methods for measuring highly enriched C in urea. The combination: ultimate organic analysis--mass spectrometry so far prescribed is complicated and expensive. For medical diagnosis, however, isotope selective nondispersive infrared spectrometers (NDIRS) have been available for many years. One of these tools is FANci2 which is very reasonable and easily to be operated. By means of such devices also urea highly enriched in 13C can be analysed, provided that the samples are first diluted with a defined amount of urea of natural isotopic composition and then transformed into carbon dioxide by means of urease. The relative abundance of 13C in this carbon dioxide, measured by nondispersive infrared spectrometry, is then a measure of the 13C abundance in the initial urea sample. Comparison of results of such measurements with those attained by mass spectrometry proves that this procedure is feasible and yields precis results.

  4. Abundance, composition, and distribution of crustacean zooplankton in relation to hypolimnetic oxygen depletion in west-central Lake Erie

    USGS Publications Warehouse

    Heberger, Roy F.; Reynolds, James B.

    1977-01-01

    Samples of crustacean zooplankton were collected monthly in west-central Lake Erie in April and June to October 1968, and in July and August 1970, before and during periods of hypolimnetic dissolved oxygen (DO) depletion. The water column at offshore stations was thermally stratified from June through September 1968, and the hypolimnion contained no DO in mid-August of 1968 or 1970. Composition, abundance, and vertical distribution of crustacean zooplankton changed coincidentally with oxygen depletion. From July to early August, zooplankton abundance dropped 79% in 1968 and 50% in 1970. The declines were attributed largely to a sharp decrease in abundance of planktonic Cyclops bicuspidatus thomasi. Zooplankton composition shifted from mainly cyclopoid copepods in July to mainly cladocerans and copepod nauplii in middle to late August. We believe that mortality of adults and dormancy of copepodites in response to anoxia was the probable reason for the late summer decline in planktonic C. b. thomasi.

  5. Culicoides monitoring in Belgium in 2011: analysis of spatiotemporal abundance, species diversity and Schmallenberg virus detection.

    PubMed

    DE Regge, N; DE Deken, R; Fassotte, C; Losson, B; Deblauwe, I; Madder, M; Vantieghem, P; Tomme, M; Smeets, F; Cay, A B

    2015-09-01

    In 2011, Culicoides (Diptera: Ceratopogonidae) were collected at 16 locations covering four regions of Belgium with Onderstepoort Veterinary Institute (OVI) traps and at two locations with Rothamsted suction traps (RSTs). Quantification of the collections and morphological identification showed important variations in abundance and species diversity between individual collection sites, even for sites located in the same region. However, consistently higher numbers of Culicoides midges were collected at some sites compared with others. When species abundance and diversity were analysed at regional level, between-site variation disappeared. Overall, species belonging to the subgenus Avaritia together with Culicoides pulicaris (subgenus Culicoides) were the most abundant, accounting for 80% and 96% of all midges collected with RSTs and OVI traps, respectively. Culicoides were present during most of the year, with Culicoides obsoletus complex midges found from 9 February until 27 December. Real-time reverse-transcription polymerase chain reaction screening for Schmallenberg virus in the heads of collected midges resulted in the first detection of the virus in August 2011 and identified C. obsoletus complex, Culicoides chiopterus and Culicoides dewulfi midges as putative vector species. At Libramont in the south of Belgium, no positive pools were identified. PMID:25761054

  6. Relative abundance of tissue mRNA and association of the single nucleotide polymorphism of the goat NGF gene with prolificacy.

    PubMed

    Naicy, Thomas; Venkatachalapathy, R Thirupathy; Aravindakshan, T V; Raghavan, K C; Mini, M; Shyama, K

    2016-10-01

    Nerve Growth Factor (NGF) promotes the development of pre-antral ovarian follicles through ovarian innervations and regulation of ovarian response to gonadotropins. The present study was conducted to study the tissue gene expression profile, to characterize the genetic variants, find associations of the NGF gene with prolificacy in the prolific Malabari and less prolific Attappady Black goats because NGF has an important role in reproduction by augmenting ovarian folliculogenesis. Relative abundance of NGF mRNA was greatest in reproductive tissues signifying its role in reproduction. The PCR-SSCP analysis of a 251bp fragment of Exon 3 of the NGF gene from the 277 goats revealed four diplotypes (EE, EF, FF and EG) with respective frequencies of 0.76, 0.22, 0.01 and 0.01. Sequencing of the representative samples revealed one synonymous and one novel non synonymous mutations (g.705G>A and g.715C>T). Statistical analysis indicated that the SNP g.705G>A was associated with litter size in Attappady Black goats (P<0.05) and a PCR-RFLP was designed using the restriction enzyme, BpiI, for rapid screening of the SNP. The results of the present study suggest that the NGF gene is a primary candidate gene affecting prolificacy in goats and may be used for Marker Assisted Selection (MAS) in goats, especially in lowly prolific Attappady Black goats. PMID:27576174

  7. A novel method to prioritize RNAseq data for post-hoc analysis based on absolute changes in transcript abundance.

    PubMed

    McNutt, Patrick; Gut, Ian; Hubbard, Kyle; Beske, Phil

    2015-06-01

    . These findings suggest that the large ΔT genes are not a product of random or stochastic phenomenon, but rather represent biologically meaningful changes in the transcriptional program. They furthermore imply that high abundance transcripts are associated with particularly cellular states, and as cells change in response to internal or external conditions, the relative distribution of the abundant transcripts changes accordingly. Thus, prioritization of DEGs based on the concept of metabolic cost is a simple yet powerful method to identify biologically important transcriptional changes and provide novel insights into cellular behaviors. PMID:25781714

  8. Abundance analysis of SDSS J134338.67+484426.6; an extremely metal-poor star from the MARVELS pre-survey

    NASA Astrophysics Data System (ADS)

    Susmitha Rani, A.; Sivarani, T.; Beers, T. C.; Fleming, S.; Mahadevan, S.; Ge, J.

    2016-05-01

    We present an elemental-abundance analysis of an extremely metal-poor (EMP; [Fe/H] <-3.0) star, SDSS J134338.67+484426.6, identified during the course of the Multi-object Apache Point Observatory Radial Velocity Exoplanet Large-area Survey spectroscopic pre-survey of some 20 000 stars to identify suitable candidates for exoplanet searches. This star, with an apparent magnitude V = 12.14, is the lowest metallicity star found in the pre-survey, and is one of only ˜20 known EMP stars that are this bright or brighter. Our high-resolution spectroscopic analysis shows that this star is a subgiant with [Fe/H] = -3.42, having `normal' carbon and no enhancement of neutron-capture abundances. Strontium is underabundant, [Sr/Fe] = -0.47, but the derived lower limit on [Sr/Ba] indicates that Sr is likely enhanced relative to Ba. This star belongs to the sparsely populated class of α-poor EMP stars that exhibit low ratios of [Mg/Fe], [Si/Fe], and [Ca/Fe] compared to typical halo stars at similar metallicity. The observed variations in radial velocity from several epochs of (low- and high-resolution) spectroscopic follow-up indicate that SDSS J134338.67+484426.6 is a possible long-period binary. We also discuss the abundance trends in EMP stars for r-process elements, and compare with other magnesium-poor stars.

  9. Distribution and Abundance of Human Specific Bacteroides and Relation to Traditional Indicators in an Urban Tropical Catchment

    NASA Astrophysics Data System (ADS)

    Nshimyimana, J.; Shanahan, P.; Thompson, J. R.; Ekklesia, E.; Chua Hock Chye, L.

    2012-12-01

    The Singapore government through its Public Utilities Board is interested in opening Kranji Reservoir to recreational use. However, water courses within the Kranji Reservoir catchment contain human fecal indicator bacteria above recreational water quality criteria; their sources and distribution are unknown. The primary goals of this study were to determine the distribution of fecal indicator bacteria in drainages and water bodies in the Kranji reservoir catchment area. Total coliforms, E. coli, and the DNA-based HF marker (targeting a human specific strain of Bacteroides) were quantified in 27 samples collected in January 2009 and 54 samples collected in July 2009. Correlation of HF marker cell equivalents (CE) and E. coli abundance (colony forming units (CFU) or Most Probable Number (MPN)) to different land-use categories revealed potential sources of fecal contamination to the Kranji reservoir. Notably, areas designated as farming/agricultural were associated with the highest levels of E. coli (geometric mean 30,500 CFU/100 ml) and HF marker (1.23±1.13x106 CE/100 ml ± S.D.) while in general lower HF marker and E. coli levels were observed in residential areas, undeveloped areas, and within the Kranji reservoir (i.e. Kranji Reservoir had 2 to 17 MPN/100 ml of E. coli and 103 to 105 HF marker CE/100 ml). A partial survey of potential point sources for fecal contamination within the farming area revealed a wastewater effluent stream with HF marker levels exceeding 107 CE/100ml. As observed in previous studies, total coliforms and E. coli levels were weakly (R<0.4), or anti- correlated to HF marker concentrations across different land uses. Weak correspondence between traditional indicators (E. coli, total coliforms) and molecular indicators (HF marker) may be explained by differences in the ability of the respective organisms to grow or survive under aerated tropical conditions. The HF marker sequence matches that of Bacteroides dorei, an obligate anaerobe that

  10. RELATIVE ABUNDANCE AND SPECIES COMPOSITION OF MOSQUITO POPULATIONS (DIPTERA:CULICIDAE) IN A LA CROSSE VIRUS- ENDEMIC AREA IN WESTERN NORTH CAROLINA

    EPA Science Inventory

    Container surveys were conducted in 5 communities on the Cherokee Indian Reservation, an area of western North Carolina endemic for transmission of La Crosse (LAC) virus, to determine the potential for peridomestic mosquito breeding, the relative abundance of mosquito species, an...

  11. {sup 39}Ar Detection at the 10{sup -16} Isotopic Abundance Level with Atom Trap Trace Analysis

    SciTech Connect

    Jiang, W.; Williams, W.; Bailey, K.; O'Connor, T. P.; Mueller, P.; Davis, A. M.; Hu, S.-M.; Sun, Y. R.; Lu, Z.-T.; Purtschert, R.; Sturchio, N. C.

    2011-03-11

    Atom trap trace analysis, a laser-based atom counting method, has been applied to analyze atmospheric {sup 39}Ar (half-life=269 yr), a cosmogenic isotope with an isotopic abundance of 8x10{sup -16}. In addition to the superior selectivity demonstrated in this work, the counting rate and efficiency of atom trap trace analysis have been improved by 2 orders of magnitude over prior results. The significant applications of this new analytical capability lie in radioisotope dating of ice and water samples and in the development of dark matter detectors.

  12. 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

  13. Preliminary Results of Detailed Chemical Abundance Analysis of Milky Way Satellite Galaxy Reticulum II Discovered in the Dark Energy Survey

    NASA Astrophysics Data System (ADS)

    Nagasawa, Daniel; Marshall, Jennifer L.; Li, Ting; Dark Energy Survey Milky Way Science Group

    2016-01-01

    We present preliminary results from abundance analysis of stars in Milky Way satellite galaxies found in the Dark Energy Survey (DES). DES has discovered 16 candidate satellite galaxies of the Milky Way in its first two years of operation. Since January 2015, three candidates have subsequently been revealed to be dark matter-dominated by spectroscopic follow-up studies of their kinematics, confirming their status as satellite galaxies. Spectroscopic follow-up of the remaining 13 candidates is underway. We have analyzed high resolution VLT/GIRAFFE spectra of member stars in one of these satellite galaxies, Reticulum II. Using equivalent width measurement and spectral synthesis methods, we measure the abundances of Iron and other species in order to begin to understand the chemical content of these Milky Way satellites.

  14. Distribution and abundance of stream fishes in relation to barriers: implications for monitoring stream recovery after barrier removal

    USGS Publications Warehouse

    Zydlewski, Joseph; Coghlan Jr., Stephen M.; Gardner, C.; Saunders, R.

    2011-01-01

    Dams are ubiquitous in coastal regions and have altered stream habitats and the distribution and abundance of stream fishes in those habitats by disrupting hydrology, temperature regime and habitat connectivity. Dam removal is a common restoration tool, but often the response of the fish assemblage is not monitored rigorously. Sedgeunkedunk Stream, a small tributary to the Penobscot River (Maine, USA), has been the focus of a restoration effort that includes the removal of two low-head dams. In this study, we quantified fish assemblage metrics along a longitudinal gradient in Sedgeunkedunk Stream and also in a nearby reference stream. By establishing pre-removal baseline conditions and associated variability and the conditions and variability immediately following removal, we can characterize future changes in the system associated with dam removal. Over 2 years prior to dam removal, species richness and abundance in Sedgeunkedunk Stream were highest downstream of the lowest dam, lowest immediately upstream of that dam and intermediate farther upstream; patterns were similar in the reference stream. Although seasonal and annual variation in metrics within each site was substantial, the overall upstream-to-downstream pattern along the stream gradient was remarkably consistent prior to dam removal. Immediately after dam removal, we saw significant decreases in richness and abundance downstream of the former dam site and a corresponding increase in fish abundance upstream of the former dam site. No such changes occurred in reference sites. Our results show that by quantifying baseline conditions in a small stream before restoration, the effects of stream restoration efforts on fish assemblages can be monitored successfully. These data set the stage for the long-term assessment of Sedgeunkedunk Stream and provide a simple methodology for assessment in other restoration projects.

  15. Dimensional Analysis and General Relativity

    ERIC Educational Resources Information Center

    Lovatt, Ian

    2009-01-01

    Newton's law of gravitation is a central topic in the first-year physics curriculum. A lecturer can go beyond the physical details and use the history of gravitation to discuss the development of scientific ideas; unfortunately, the most recent chapter in this history, general relativity, is not covered in first-year courses. This paper discusses…

  16. Relative abundance and distribution of fishes and crayfish at Ash Meadows National Wildlife Refuge, Nye County, Nevada, 2007-08

    USGS Publications Warehouse

    Scoppettone, G. Gary; Rissler, Peter; Johnson, Danielle; Hereford, Mark

    2011-01-01

    swamp crayfish and western mosquitofish was in water with temperature greater than 26 degrees C near the springhead, and in shallow (depths less than 10 centimeters) grassy marshes. Among 177 sampling stations within the range of Warm Springs Amargosa pupfish, red swamp crayfish were collected at 96 stations and western mosquitofish were collected at 49 stations. Removal of convict cichlid (Amatitlania nigrofasciata) from Fairbanks Spring was followed by a substantial increase in Ash Meadows Amargosa pupfish (Cyprinodon nevadensis mionectes) captures from 910 pre-removal to 3,056 post-removal. Red swamp crayfish was continually removed from Bradford 1 Spring, which seemed to cause an increase in the speckled dace population. Restoration of Kings Pool and Jackrabbit Springs promoted the success of native fishes with the greatest densities in restored reaches. Ongoing restoration of Carson Slough and its tributaries, as well as control and elimination of invasive species, is expected to increase abundance and distribution of Ash Meadows' native fish populations. Further analysis of data from this study will help determine the habitat characteristic(s) that promote native species and curtail non-native species.

  17. Changes in tumorigenesis- and angiogenesis-related gene transcript abundance profiles in ovarian cancer detected by tailored high density cDNA arrays.

    PubMed Central

    Martoglio, A. M.; Tom, B. D.; Starkey, M.; Corps, A. N.; Charnock-Jones, D. S.; Smith, S. K.

    2000-01-01

    BACKGROUND: Complementary DNA array analysis of gene expression has a potential application for clinical diagnosis of disease processes. However, accessibility, affordability, reproducibility of results, and management of the data generated remain issues of concern. Use of cDNA arrays tailored for studies of specific pathways, tissues, or disease states may render a cost- and time-effective method to define potential hallmark genotype alterations. MATERIALS AND METHODS: We produced a 332-membered human cDNA array on nylon membranes tailored for studies of angiogenesis and tumorigenesis in reproductive disease. We tested the system for reproducibility using a novel statistical approach for analysis of array data and employed the arrays to investigate gene expression alterations in ovarian cancer. RESULTS: Intra-assay analysis and removal of agreement outliers was shown to be a critical step prior to interpretation of cDNA array data. The system revealed highly reproducible results, with intermembrane coefficient of reproducibility of +/- 0.98. Comparison of placental and ovarian sample data confirmed expected differences in angiogenic profiles and tissue-specific markers, such as human placental lactogen (hPL). Analysis of expression profiles of five normal ovary and four poorly differentiated serous papillary ovarian adenocarcinoma samples revealed an overall increase in angiogenesis-related markers, including vascular endothelial growth factor (VEGF) and angiopoietin-1 in the diseased tissue. These were accompanied by increases in immune response mediators (e.g. HLA-DR, Ron), apoptotic and neoplastic markers (e.g. BAD protein, b-myb), and novel potential markers of ovarian cancer, such as cofilin, moesin, and neuron-restrictive silencer factor (REST) protein. CONCLUSIONS: In-house production of tailored cDNA arrays, coupled to comprehensive analysis of resulting hybridization profiles, provides an accessible, reliable, and highly effective method of applying array

  18. Temporal changes in euphausiid distribution and abundance in North Atlantic cold-core rings in relation to the surrounding waters

    NASA Astrophysics Data System (ADS)

    Endo, Yoshinari; Wiebe, Peter H.

    2007-02-01

    The species composition of euphausiids was investigated in relationship to the hydrographic conditions in the North Atlantic cold-core rings (CCR) and adjacent waters to elucidate species succession in evolving water masses. Using data, dating back to the 1970s, from as many CCRs as possible and selecting typical cases where no major physical perturbations occurred, a general pattern of euphausiid succession and change in vertical distribution in rings with time was obtained. This pattern was related to the general distribution of euphausiids in the northwestern North Atlantic Ocean, aiming at providing basic information on probable response of North Atlantic marine ecosystem to global warming. Of the 34 euphausiid species identified, 5 were cold-water species, 17 were warm-water species, 6 were wide-ranging warm-water species, 1 was transitional, 4 were cosmopolitan and the remaining was Thysanoessa parva. Among cold-water species, Euphausia krohni and Nematoscelis megalops were dominant in CCRs. E. krohni became rare in rings older than 6 months, whereas N. megalops survived longer, being abundant in some rings of 9 months or older, by staying within its preferred temperature range as the CCR elevated isotherms sank to depths where they are normally found in the Sargasso Sea and because it is an omnivore-carnivore. Among warm-water species, epipelagic species appeared first in rings, corresponding to the physical change occurring most rapidly in the surface layers. Mesopelagic species appeared later. Cold-water species made up 65-85% of the total euphausiid population in number in younger rings (1-5 months old), while warm-water species contributed only 2-7%. Wide-ranging warm-water species made up about up to one fourth of the total in rings 5 and 7 months old. Warm-water species, mainly E. brevis, increased in older rings (9 months old or older) and made up 50% of the total in the oldest ring. The contribution of cold-water species decreased to 14% in older

  19. The Pathogen of the Great Barrier Reef Sponge Rhopaloeides odorabile Is a New Strain of Pseudoalteromonas agarivorans Containing Abundant and Diverse Virulence-Related Genes.

    PubMed

    Choudhury, Jayanta D; Pramanik, Arnab; Webster, Nicole S; Llewellyn, Lyndon E; Gachhui, Ratan; Mukherjee, Joydeep

    2015-08-01

    Sponge diseases have increased dramatically, yet the causative agents of disease outbreaks have eluded identification. We undertook a polyphasic taxonomic analysis of the only confirmed sponge pathogen and identified it as a novel strain of Pseudoalteromonas agarivorans. 16S ribosomal RNA (rRNA) and gyraseB (gyrB) gene sequences along with phenotypic characteristics demonstrated that strain NW4327 was most closely related to P. agarivorans. DNA-DNA hybridization and in silico genome comparisons established NW4327 as a novel strain of P. agarivorans. Genes associated with type IV pili, mannose-sensitive hemagglutinin pili, and curli formation were identified in NW4327. One gene cluster encoding ATP-binding cassette (ABC) transporter, HlyD and TolC, and two clusters related to the general secretion pathway indicated the presence of type I secretion system (T1SS) and type II secretion system (T2SS), respectively. A contiguous gene cluster of at least 19 genes related to type VI secretion system (T6SS) which included all 13 core genes was found. The absence of T1SS and T6SS in nonpathogenic P. agarivorans S816 established NW4327 as the virulent strain. Serine proteases and metalloproteases of the classes S8, S9, M4, M6, M48, and U32 were identified in NW4327, many of which can degrade collagen. Collagenase activity in NW4327 and its absence in the nonpathogenic P. agarivorans KMM 255(T) reinforced the invasiveness of NW4327. This is the first report unambiguously identifying a sponge pathogen and providing the first insights into the virulence genes present in any pathogenic Pseudoalteromonas genome. The investigation supports a theoretical study predicting high abundance of terrestrial virulence gene homologues in marine bacteria.

  20. Phylogenetic Analysis of Nonthermophilic Members of the Kingdom Crenarchaeota and Their Diversity and Abundance in Soils

    PubMed Central

    Buckley, Daniel H.; Graber, Joseph R.; Schmidt, Thomas M.

    1998-01-01

    Within the last several years, molecular techniques have uncovered numerous 16S rRNA gene (rDNA) sequences which represent a unique and globally distributed lineage of the kingdom Crenarchaeota that is phylogenetically distinct from currently characterized crenarchaeotal species. rDNA sequences of members of this novel crenarchaeotal group have been recovered from low- to moderate-temperature environments (−1.5 to 32°C), in contrast to the high-temperature environments (temperature, >80°C) required for growth of the currently recognized crenarchaeotal species. We determined the diversity and abundance of the nonthermophilic members of the Crenarchaeota in soil samples taken from cultivated and uncultivated fields located at the Kellogg Biological Station’s Long-Term Ecological Research site (Hickory Corners, Mich.). Clones were generated from 16S rDNA that was amplified by using broad-specificity archaeal PCR primers. Twelve crenarchaeotal sequences were identified, and the phylogenetic relationships between these sequences and previously described crenarchaeotal 16S rDNA sequences were determined. Phylogenetic analyses included nonthermophilic crenarchaeotal sequences found in public databases and revealed that the nonthermophilic Crenarchaeota group is composed of at least four distinct phylogenetic clusters. A 16S rRNA-targeted oligonucleotide probe specific for all known nonthermophilic crenarchaeotal sequences was designed and used to determine their abundance in soil samples. The nonthermophilic Crenarchaeota accounted for as much as 1.42% ± 0.42% of the 16S rRNA in the soils analyzed. PMID:9797286

  1. Dimensional Analysis and General Relativity

    NASA Astrophysics Data System (ADS)

    Lovatt, Ian

    2009-02-01

    Newton's law of gravitation is a central topic in the first-year physics curriculum. A lecturer can go beyond the physical details and use the history of gravitation to discuss the development of scientific ideas; unfortunately, the most recent chapter in this history, general relativity, is not covered in first-year courses. This paper discusses some topics that can be introduced with the judicious use of the dimensionless quantity GM/Rc2: deflection of light by a massive object, perihelion precession, gravitational redshifts, and the Global Positioning System (GPS).

  2. Elemental abundance analysis of the early-type members of the open cluster M6: Preliminary results

    NASA Astrophysics Data System (ADS)

    Kııçoǧlu, T.; Monier, R.; Fossati, L.

    2014-11-01

    Differences in chemical composition among main sequence stars within a given cluster are probably due to differences in their masses and other effects such as radiative diffusion, magnetic field, rotation, mixing mechanisms, mass loss, accretion and multiplicity. The early type main-sequence members of open clusters of different ages support studies of the competition between radiative diffusion and mixing mechanisms. We have analysed low- and high-resolution spectra covering the spectral range λ 4500-5840 Å of late B-, A- and F-type members of the open cluster M6 (age ˜100 Myr). The spectra were obtained with the FLAMES/GIRAFFE spectrograph mounted at UT2, the 8-m VLT telescope. The effective temperatures, surface gravities and microturbulent velocities of the stars were derived from both photometric and spectral methods. We have also performed a chemical abundance analysis using synthetic spectra. Abundances were determined for the elements C, O, Mg, Si, Ca, Sc, Ti, Cr, Mn, Fe, Ni, Y and Ba. The star-to-star variations in element abundances among the members of M6 are discussed.

  3. Estimating stellar atmospheric parameters, absolute magnitudes and elemental abundances from the LAMOST spectra with Kernel-based Principal Component Analysis

    NASA Astrophysics Data System (ADS)

    Xiang, M.-S.; Liu, X.-W.; Shi, J.-R.; Yuan, H.-B.; Huang, Y.; Luo, A.-L.; Zhang, H.-W.; Zhao, Y.-H.; Zhang, J.-N.; Ren, J.-J.; Chen, B.-Q.; Wang, C.; Li, J.; Huo, Z.-Y.; Zhang, W.; Wang, J.-L.; Zhang, Y.; Hou, Y.-H.; Wang, Y.-F.

    2016-10-01

    Accurate determination of stellar atmospheric parameters and elemental abundances is crucial for Galactic archeology via large-scale spectroscopic surveys. In this paper, we estimate stellar atmospheric parameters - effective temperature Teff, surface gravity log g and metallicity [Fe/H], absolute magnitudes MV and MKs, α-element to metal (and iron) abundance ratio [α/M] (and [α/Fe]), as well as carbon and nitrogen abundances [C/H] and [N/H] from the LAMOST spectra with a multivariate regression method based on kernel-based principal component analysis, using stars in common with other surveys (Hipparcos, Kepler, APOGEE) as training data sets. Both internal and external examinations indicate that given a spectral signal-to-noise ratio (SNR) better than 50, our method is capable of delivering stellar parameters with a precision of ˜100 K for Teff, ˜0.1 dex for log g, 0.3 - 0.4 mag for MV and MKs, 0.1 dex for [Fe/H], [C/H] and [N/H], and better than 0.05 dex for [α/M] ([α/Fe]). The results are satisfactory even for a spectral SNR of 20. The work presents first determinations of [C/H] and [N/H] abundances from a vast data set of LAMOST, and, to our knowledge, the first reported implementation of absolute magnitude estimation directly based on the observed spectra. The derived stellar parameters for millions of stars from the LAMOST surveys will be publicly available in the form of value-added catalogues.

  4. Phylogenetic analysis of microalgae based on highly abundant proteins using mass spectrometry.

    PubMed

    Lee, Hae-Won; Roh, Seong Woon; Cho, Kichul; Kim, Kil-Nam; Cha, In-Tae; Yim, Kyung June; Song, Hye Seon; Nam, Young-Do; Oda, Tatsuya; Chung, Young-Ho; Kim, Soo Jung; Choi, Jong-Soon; Kim, Daekyung

    2015-01-01

    The blooms of toxic phototrophic microorganisms, such as microalgae and cyanobacteria, which are typically found in freshwater and marine environments, are becoming more frequent and problematic in aquatic systems. Due to accumulation of toxic algae, harmful algal blooms (HABs) exert negative effects on aquatic systems. Therefore, rapid detection of harmful microalgae is important for monitoring the occurrence of HABs. Mass spectrometry-based methods have become sensitive, specific techniques for the identification and characterization of microorganisms. Matrix-assisted laser desorption/ionization (MALDI) with time-of-flight (TOF) mass spectrometry (MS) allows us to measure a unique molecular fingerprint of highly abundant proteins in a microorganism and has been used for the rapid, accurate identification of bacteria and fungi in clinical microbiology. Here, we tested the specificity of MALDI-TOF MS using microalgal strains (Heterocapsa, Alexandrium, Nannochloropsis, Chaetoceros, Chlorella, and Dunaliella spp.). Our research suggested that this method was comparable in terms of the rapid identification of microalgea to conventional methods based on genetic information and morphology. Thus, this efficient mass spectrometry-based technique may have applications in the rapid identification of harmful microorganisms from aquatic environmental samples.

  5. Proteome analysis of abundant proteins extracted from the leaf of Gynura procumbens (Lour.) Merr.

    PubMed

    Hew, Chaw-Sen; Gam, Lay-Harn

    2011-12-01

    Gynura procumbens (Lour.) Merr. is a traditionally used medicinal plant to decrease cholesterol level, reduce high blood pressure, control diabetics, and for treatment of cancer. In our present study, a proteomic approach was applied to study the proteome of the plant that had never analyzed before. We have identified 92 abundantly expressed proteins from the leaves of G. procumbens (Lour.) Merr. Amongst the identified proteins was miraculin, a taste-masking agent with high commercial value. Miraculin made up ∼0.1% of the total protein extracted; the finding of miraculin gave a great commercial value to G. procumbens (Lour.) Merr. as miraculin's natural source is limited while the production of recombinant miraculin faced challenges of not being able to exhibit the taste-masking effect as in the natural miraculin. We believe the discovery of miraculin in G. procumbens (Lour.) Merr., provides commercial feasibility of miraculin in view of the availability of G. procumbens (Lour.) Merr. that grow wildly and easily in tropical climate. PMID:21938418

  6. Phylogenetic analysis of microalgae based on highly abundant proteins using mass spectrometry.

    PubMed

    Lee, Hae-Won; Roh, Seong Woon; Cho, Kichul; Kim, Kil-Nam; Cha, In-Tae; Yim, Kyung June; Song, Hye Seon; Nam, Young-Do; Oda, Tatsuya; Chung, Young-Ho; Kim, Soo Jung; Choi, Jong-Soon; Kim, Daekyung

    2015-01-01

    The blooms of toxic phototrophic microorganisms, such as microalgae and cyanobacteria, which are typically found in freshwater and marine environments, are becoming more frequent and problematic in aquatic systems. Due to accumulation of toxic algae, harmful algal blooms (HABs) exert negative effects on aquatic systems. Therefore, rapid detection of harmful microalgae is important for monitoring the occurrence of HABs. Mass spectrometry-based methods have become sensitive, specific techniques for the identification and characterization of microorganisms. Matrix-assisted laser desorption/ionization (MALDI) with time-of-flight (TOF) mass spectrometry (MS) allows us to measure a unique molecular fingerprint of highly abundant proteins in a microorganism and has been used for the rapid, accurate identification of bacteria and fungi in clinical microbiology. Here, we tested the specificity of MALDI-TOF MS using microalgal strains (Heterocapsa, Alexandrium, Nannochloropsis, Chaetoceros, Chlorella, and Dunaliella spp.). Our research suggested that this method was comparable in terms of the rapid identification of microalgea to conventional methods based on genetic information and morphology. Thus, this efficient mass spectrometry-based technique may have applications in the rapid identification of harmful microorganisms from aquatic environmental samples. PMID:25476355

  7. Relative abundances of methane- and sulfur-oxidizing symbionts in gills of the deep-sea hydrothermal vent mussel Bathymodiolus azoricus under pressure

    NASA Astrophysics Data System (ADS)

    Szafranski, Kamil M.; Piquet, Bérénice; Shillito, Bruce; Lallier, François H.; Duperron, Sébastien

    2015-07-01

    The deep-sea mussel Bathymodiolus azoricus dominates hydrothermal vent fauna in the Azores region. The gills of this species house methane- and sulfur-oxidizing bacteria that fulfill most of the mussel's nutritional requirements. Previous studies suggested that the ratio between methane- and sulfur-oxidizers could vary in response to the availability of electron donors in their environment, and this flexibility is considered a key factor in explaining the ecological success of the species. However, previous studies were based on non-isobaric recovery of specimens, with experiments at atmospheric pressure which may have induced artifacts. This study investigates the effect of pressure-related stress during recovery and experimentation on the relative abundances of bacterial symbionts. Mussel specimens were recovered for the first time using the pressure-maintaining device PERISCOP. Specimens were subsequently transferred into pressurized vessels and exposed to various chemical conditions. Using optimized fluorescence in situ hybridization-based approaches, relative abundance of symbionts were measured. Our results show that the recovery method (isobaric versus non-isobaric) does not influence the abundances of bacterial symbionts. Significant differences occur among specimens sampled from two contrasting sites. Exposure of mussels from the deeper site to sulfide and bicarbonate, and to bicarbonate alone, both resulted in a rapid and significant increase in the relative abundance of sulfur-oxidizers. Results reported herein are congruent with those from previous reports investigating mussels originating from shallow sites and kept at ambient pressure. Isobaric recovery and maintenance allowed us to perform in vivo experiments in specimens from a deeper site that could not be maintained alive at ambient pressure, and will greatly improve the chances of identifying the molecular mechanisms underlying the dialogue between bathymodioline hosts and symbionts.

  8. Mapping the ranges and relative abundance of the two principal African malaria vectors, Anopheles gambiae sensu stricto and An. arabiensis, using climate data.

    PubMed Central

    Lindsay, S W; Parson, L; Thomas, C J

    1998-01-01

    Members of the Anopheles gambiae complex are major malaria vectors in Africa. We tested the hypothesis that the range and relative abundance of the two major vectors in the complex, An. gambiae sensu stricto and An. arabiensis, could be defined by climate. Climate was characterized at mosquito survey sites by extracting data for each location from climate surfaces using a Geographical Information System. Annual precipitation, together with annual and wet season temperature, defined the ranges of both vectors and were used to map suitable climate zones. Using data from West Africa, we found that where the species were sympatric, An. gambiae s.s. predominated in saturated environments, and An. arabiensis was more common in sites subject to desiccation (r2 = 0.875, p < 0.001). We used the nonlinear equation that best described this relationship to map habitat suitability across Africa. This simple model predicted accurately the relative abundance of both vectors in Tanzania (rs = 0.745, p = 0.002), where species composition is highly variable. The combined maps of species' range and relative abundance showed very good agreement with published maps. This technique represents a new approach to mapping the distribution of malaria vectors over large areas and may facilitate species-specific vector control activities. PMID:9633110

  9. Direct Distances to Cepheids in the Large Magellanic Cloud: Evidence for a Universal Slope of the Period-Luminosity Relation up to Solar Abundance

    NASA Astrophysics Data System (ADS)

    Gieren, Wolfgang; Storm, Jesper; Barnes, Thomas G., III; Fouqué, Pascal; Pietrzyński, Grzegorz; Kienzle, Francesco

    2005-07-01

    by OGLE-II and Persson and coworkers. From our 13 Cepheids, we determine the LMC distance modulus to be 18.56+/-0.04 mag, with an additional estimated systematic uncertainty of ~0.1 mag. Using the same corrected p-factor law to redetermine the distances of the Galactic Cepheids, the new Galactic PL relations are also found consistent with the observed optical and near-infrared PL relations in the LMC. Our main conclusion from the ISB analysis of the LMC Cepheid sample is that, within current uncertainties, there seems to be no significant difference between the slopes of the PL relations in the Milky Way and LMC. With literature data on more metal-poor systems, it seems now possible to conclude that the slope of the Cepheid PL relation is independent of metallicity in the broad range in [Fe/H] from -1.0 dex to solar abundance, within a small uncertainty. The new evidence from the first ISB analysis of a sizable sample of LMC Cepheids suggests that the previous, steeper Galactic PL relations obtained from this technique were caused by an underestimation of the period dependence in the model-based p-factor law used in the previous work. We emphasize, however, that our current results must be substantiated by new theoretical models capable of explaining the steeper period dependence of the p-factor law, and we will also need data on more LMC field Cepheids to rule out remaining concerns about the validity of our current interpretation.

  10. Annual cycle in abundance, distribution, and size in relation to hydrography of important copepod species in the western Arctic Ocean

    NASA Astrophysics Data System (ADS)

    Ashjian, Carin J.; Campbell, Robert G.; Welch, Harold E.; Butler, Mari; Van Keuren, Donna

    2003-10-01

    A yearlong study of the zooplankton biomass and the abundance, vertical distribution, life stage proportions, and body size and condition for five target copepod species ( Calanus glacialis, C. hyperboreus, Metridia longa, Microcalanus pygmaeus, Oithona similis) was conducted from October 1997 to October 1998 in the Western Arctic Ocean. The research was staged from Ice Station SHEBA that drifted from Canadian Basin over the Northwind Ridge and Chukchi Plateau and back over the Basin during this period. Four hydrographic regimes were surveyed during the period of the study. Zooplankton biomass was least over the basin during the fall and winter and greatest over the Chukchi Plateau during summer, with most biomass in the 200-1500 m depth interval except during summer when greatest biomass was present in the upper 200 m. The five copepod species followed two general life history strategies: (1) sustained reproduction with all life stages present throughout the year and constant depth distribution ( M. longa, M. pygmaeus, O. similis) and (2) pulsed reproduction with overlapping cohorts present and ontogenetic redistribution of preferred depths through the year ( C. glacialis, C. hyperboreus). Body size and condition did not demonstrate consistent temporal or regional patterns. Based on population age structure, both C. hyperboreus and C. glacialis were reproducing in the Arctic Ocean. However, extremely low abundances of C. glacialis suggested that this species may not be self-sustaining in the Arctic Ocean. Plankton biomass was consistent with that observed in recent studies and supported an emerging paradigm of a more productive Arctic Ocean than traditionally believed.

  11. Sims Analysis of Water Abundance and Hydrogen Isotope in Lunar Highland Plagioclase

    NASA Technical Reports Server (NTRS)

    Hui, Hejiu; Guan, Yunbin; Chen, Yang; Peslier, Anne H.; Zhang, Youxue; Liu, Yang; Rossman, George R.; Eiler, John M.; Neal, Clive R.

    2015-01-01

    The detection of indigenous water in mare basaltic glass beads has challenged the view established since the Apollo era of a "dry" Moon. Since this discovery, measurements of water in lunar apatite, olivine-hosted melt inclusions, agglutinates, and nominally anhydrous minerals have confirmed that lunar igneous materials contain water, implying that some parts of lunar mantle may have as much water as Earth's upper mantle. The interpretation of hydrogen (H) isotopes in lunar samples, however, is controversial. The large variation of H isotope ratios in lunar apatite (delta Deuterium = -202 to +1010 per mille) has been taken as evidence that water in the lunar interior comes from the lunar mantle, solar wind protons, and/or comets. The very low deuterium/H ratios in lunar agglutinates indicate that solar wind protons have contributed to their hydrogen content. Conversely, H isotopes in lunar volcanic glass beads and olivine-hosted melt inclusions being similar to those of common terrestrial igneous rocks, suggest a common origin for water in both Earth and Moon. Lunar water could be inherited from carbonaceous chondrites, consistent with the model of late accretion of chondrite-type materials to the Moon as proposed by. One complication about the sources of lunar water, is that geologic processes (e.g., late accretion and magmatic degassing) may have modified the H isotope signatures of lunar materials. Recent FTIR analyses have shown that plagioclases in lunar ferroan anorthosite contain approximately 6 ppm H2O. So far, ferroan anorthosite is the only available lithology that is believed to be a primary product of the lunar magma ocean (LMO). A possible consequence is that the LMO could have contained up to approximately 320 ppm H2O. Here we examine the possible sources of water in the LMO through measurements of water abundances and H isotopes in plagioclase of two ferroan anorthosites and one troctolite from lunar highlands.

  12. Abundance and diversity of resistance genes in the sugarcane transcriptome revealed by in silico analysis.

    PubMed

    Wanderley-Nogueira, A C; Soares-Cavalcanti, N M; Morais, D A L; Belarmino, L C; Barbosa-Silva, A; Benko-Iseppon, A M

    2007-10-05

    Resistance genes (R-genes) are responsible for the first interaction of the plant with pathogens being responsible for the activation (or not) of the defense response. Despite their importance and abundance, no tools for their automatic annotation are available yet. The present study analyzed R-genes in the sugarcane expressed sequence tags database which includes 26 libraries of different tissues and development stages comprising 237,954 expressed sequence tags. A new annotation routine was used in order to avoid redundancies and overestimation of R-gene number, common mistakes in previous evaluations. After in silico screening, 280 R-genes were identified, with 196 bearing the complete domains expected. Regarding the alignments, most of the sugarcane's clusters yielded best matches with proteins from Oryza sativa, probably due to the prevalence of sequences of this monocot in data banks. All R-gene classes were found except the subclass LRR-NBS-TIR (leucine-rich repeats, nucleotide-binding site, including Toll interleukin-1 receptors), with prevalence of the kinase (Pto-like) class. R-genes were expressed in all libraries, but flowers, transition root to shoot, and roots were the most representative, suggesting that in sugarcane the expression of R-genes in non-induced conditions prevails in these tissues. In leaves, only low level of expression was found for some gene classes, while others were completely absent. A high allelic diversity was found in all classes of R-genes, sometimes showing best alignments with dicotyledons, despite the great number of genes from rice, maize and other grasses deposited in data banks. The results and future possibilities regarding R-genes in sugarcane research and breeding are further discussed.

  13. Abundances and implications of volatile-bearing species from evolved gas analysis of the Rocknest aeolian deposit, Gale Crater, Mars

    NASA Astrophysics Data System (ADS)

    Archer, Paul Douglas; Franz, Heather B.; Sutter, Brad; Arevalo, Ricardo D.; Coll, Patrice; Eigenbrode, Jennifer L.; Glavin, Daniel P.; Jones, John J.; Leshin, Laurie A.; Mahaffy, Paul R.; McAdam, Amy C.; McKay, Christopher P.; Ming, Douglas W.; Morris, Richard V.; Navarro-González, Rafael; Niles, Paul B.; Pavlov, Alex; Squyres, Steven W.; Stern, Jennifer C.; Steele, Andrew; Wray, James J.

    2014-01-01

    The Sample Analysis at Mars (SAM) instrument on the Mars Science Laboratory (MSL) rover Curiosity detected evolved gases during thermal analysis of soil samples from the Rocknest aeolian deposit in Gale Crater. Major species detected (in order of decreasing molar abundance) were H2O, SO2, CO2, and O2, all at the µmol level, with HCl, H2S, NH3, NO, and HCN present at the tens to hundreds of nmol level. We compute weight % numbers for the major gases evolved by assuming a likely source and calculate abundances between 0.5 and 3 wt.%. The evolution of these gases implies the presence of both oxidized (perchlorates) and reduced (sulfides or H-bearing) species as well as minerals formed under alkaline (carbonates) and possibly acidic (sulfates) conditions. Possible source phases in the Rocknest material are hydrated amorphous material, minor clay minerals, and hydrated perchlorate salts (all potential H2O sources), carbonates (CO2), perchlorates (O2 and HCl), and potential N-bearing materials (e.g., Martian nitrates, terrestrial or Martian nitrogenated organics, ammonium salts) that evolve NH3, NO, and/or HCN. We conclude that Rocknest materials are a physical mixture in chemical disequilibrium, consistent with aeolian mixing, and that although weathering is not extensive, it may be ongoing even under current Martian surface conditions.

  14. Relativity Concept Inventory: Development, Analysis, and Results

    ERIC Educational Resources Information Center

    Aslanides, J. S.; Savage, C. M.

    2013-01-01

    We report on a concept inventory for special relativity: the development process, data analysis methods, and results from an introductory relativity class. The Relativity Concept Inventory tests understanding of relativistic concepts. An unusual feature is confidence testing for each question. This can provide additional information; for example,…

  15. Relative Abundance of Carsonella ruddii (Gamma Proteobacterium) in Females and Males of Cacopsylla pyricola (Hemiptera: Psyllidae) and Bactericera cockerelli (Hemiptera: Triozidae)

    PubMed Central

    Cooper, W. Rodney; Garczynski, Stephen F.; Horton, David R.

    2015-01-01

    Carsonella ruddii (Gamma Proteobacterium) is an obligate bacterial endosymbiont of psyllids that produces essential amino acids that are lacking in the insect’s diet. Accurate estimations of Carsonella populations are important to studies of Carsonella-psyllid interactions and to developing ways to target Carsonella for control of psyllid pests including pear psylla, Cacopsylla pyricola (Förster) (Hemiptera: Psyllidae) and potato psyllid, Bactericera cockerelli (Šulc) (Hemiptera: Triozidae). We used two methods, namely fluorescence in situ hybridization and quantitative polymerase chain reaction (qPCR), to estimate relative abundance of Carsonella in bacteriocytes and whole bodies of psyllids, respectively. Using these two methods, we compared Carsonella populations between female and male insects. Estimations using fluorescence in situ hybridization indicated that Carsonella was more abundant in bacteriocytes of female C. pyricola than in those of males, but Carsonella abundance in bacteriocytes did not differ between sexes of B. cockerelli. Analyses by qPCR using whole-body specimens indicated Carsonella was more abundant in females than in males of both psyllids. Neither fluorescence in situ hybridization nor qPCR indicated that Carsonella populations differed in abundance among adults of different ages (0–3 wk after adult eclosion). Using fluorescence in situ hybridization, Carsonella was observed in ovarioles of newly emerged females and formed an aggregation in the posterior end of mature oocytes. Results of our study indicate that female psyllids harbor greater populations of Carsonella than do males and that sex should be controlled for in studies which require estimations of Carsonella populations. PMID:26056318

  16. Relative Abundance of Carsonella ruddii (Gamma Proteobacterium) in Females and Males of Cacopsylla pyricola (Hemiptera: Psyllidae) and Bactericera cockerelli (Hemiptera: Triozidae).

    PubMed

    Cooper, W Rodney; Garczynski, Stephen F; Horton, David R

    2015-01-01

    Carsonella ruddii (Gamma Proteobacterium) is an obligate bacterial endosymbiont of psyllids that produces essential amino acids that are lacking in the insect's diet. Accurate estimations of Carsonella populations are important to studies of Carsonella-psyllid interactions and to developing ways to target Carsonella for control of psyllid pests including pear psylla, Cacopsylla pyricola (Förster) (Hemiptera: Psyllidae) and potato psyllid, Bactericera cockerelli (Šulc) (Hemiptera: Triozidae). We used two methods, namely fluorescence in situ hybridization and quantitative polymerase chain reaction (qPCR), to estimate relative abundance of Carsonella in bacteriocytes and whole bodies of psyllids, respectively. Using these two methods, we compared Carsonella populations between female and male insects. Estimations using fluorescence in situ hybridization indicated that Carsonella was more abundant in bacteriocytes of female C. pyricola than in those of males, but Carsonella abundance in bacteriocytes did not differ between sexes of B. cockerelli. Analyses by qPCR using whole-body specimens indicated Carsonella was more abundant in females than in males of both psyllids. Neither fluorescence in situ hybridization nor qPCR indicated that Carsonella populations differed in abundance among adults of different ages (0-3 wk after adult eclosion). Using fluorescence in situ hybridization, Carsonella was observed in ovarioles of newly emerged females and formed an aggregation in the posterior end of mature oocytes. Results of our study indicate that female psyllids harbor greater populations of Carsonella than do males and that sex should be controlled for in studies which require estimations of Carsonella populations.

  17. Relation between mRNA expression and sequence information in Desulfovibrio vulgaris: Combinatorial contributions of upstream regulatory motifs and coding sequence features to variations in mRNA abundance

    SciTech Connect

    Wu, Gang; Nie, Lei; Zhang, Weiwen

    2006-05-26

    ABSTRACT-The context-dependent expression of genes is the core for biological activities, and significant attention has been given to identification of various factors contributing to gene expression at genomic scale. However, so far this type of analysis has been focused whether on relation between mRNA expression and non-coding sequence features such as upstream regulatory motifs or on correlation between mRN abundance and non-random features in coding sequences (e.g. codon usage and amino acid usage). In this study multiple regression analyses of the mRNA abundance and all sequence information in Desulfovibrio vulgaris were performed, with the goal to investigate how much coding and non-coding sequence features contribute to the variations in mRNA expression, and in what manner they act together...

  18. Analysis of the factors that affect the distribution and abundance of three Neobuxbaumia species (Cactaceae) that differ in their degree of rarity

    NASA Astrophysics Data System (ADS)

    Ruedas, Marcela; Valverde, Teresa; Zavala-Hurtado, José Alejandro

    2006-03-01

    We studied three species of columnar cacti in the genus Neobuxbaumia which differ in their degree of rarity: Neobuxbaumia macrocephala (the rarest), Neobuxbaumia tetetzo (intermediate), and Neobuxbaumia mezcalaensis (the most common). To investigate the ecological factors that limit their distribution and abundance, we surveyed 80 localities within the region of Tehuacan-Cuicatlán, in Central Mexico. At each locality we measured several environmental variables, and the density of the Neobuxbaumia populations present. We used a principal component analysis (PCA) to identify the factors that are associated to the presence/absence of each species. Additionally, we carried out multiple regressions between environmental variables and population density to test whether the variation in these variables was related to changes in abundance. The results show that factors significantly affecting the distribution of these species are mean annual temperature, altitude, rainfall, and soil properties such as texture and organic matter content. N. mezcalaensis reaches maximum population densities of 14,740 plants per ha (average density = 3943 plants per ha) and is associated with localities with relatively abundant rainfall. N. tetetzo shows maximum population densities of 14,060 plants per ha (average = 3070 plants per ha), and is associated with sites located at high latitudes and with high phosphorous content in the soil. The rarest species, N. macrocephala, shows maximum densities of 1180 plants per ha (average = 607 plants per ha) and is associated with localities with high soil calcium content. The distribution of this species is limited to sites with specific values of the environmental variables recorded, conferring it a high habitat specificity which accounts for its rarity.

  19. Seasonal occurrence and relative abundance of aphids on potato plants with classical and transgenic characters of resistance to Colorado potato beetle Leptinotarsa decemlineata (Say).

    PubMed

    Ashouri, A

    2004-01-01

    The seasonal abundance and dynamics of potato-infesting aphids were studied in two seasons, on potato Solanum tuberosum L. with various types of transgenic and classical resistance to primary pests, especially the Colorado potato beetle (CPB), Leptinotarsa decemlineata (Say). The lines tested were the NewLeaf potato, a transgenic expressing the Bacillus thuringiensis CryIIIA toxin (BTT); NYL 235-4 a parental line derived from S. berthaultii (NYL) with a high density of glandular trichomes; and a transgenic line expressing oryzacystatln I (OCI), a proteinase inhibitor gene from rice; potatoes from two commercial cultivars, Superior and Kennebec, served as controls. Over the two seasons, Macrosiphum euphorbiae (Thomas) and, to a lesser extent, Myzus persicae (Sulzer) were by far the most abundant aphids observed in the experimental plots. M. persicae was observed relatively late in the season, and was most abundant on the Kennebec-OCI potato. Macrosiphum euphorbiae was more regular over seasons, and its highest densities were observed on the NYL 235-4 line. The population of M. euphorbiae showed markedly different patterns on the five lines studied, which was clearly related to potato plant phenology. Density of M. euphorbiae was observed on the NYL 235-4 line, in late July and early August.

  20. Unexpected abundance and long-term relative stability of the brown alga Cystoseira amentacea, hitherto regarded as a threatened species, in the north-western Mediterranean Sea.

    PubMed

    Thibaut, Thierry; Blanfuné, Aurélie; Markovic, Laurent; Verlaque, Marc; Boudouresque, Charles F; Perret-Boudouresque, Michèle; Maćic, Vesna; Bottin, Lorraine

    2014-12-15

    Cystoseira amentacea is a Mediterranean endemic alga thriving on very shallow rocky substrates. It has been considered as a threatened species, having experienced a steady decline and is therefore protected by international conventions. The historical distribution of the species has been assessed along the French Mediterranean coast, on the basis of 467 articles and herbarium vouchers. We have produced an accurate map of its current distribution and abundance along 1832 km of coastline, through in situ surveys. C. amentacea was observed along 1125 km of shoreline, including 33% of almost continuous or continuous belt. In most of its range, there is no evidence of loss, except in 4 areas of Provence, French Riviera and Corsica. A significant relation was found between the absence or low abundance of C. amentacea and the vicinity of ports and large sewage outfalls. The status of conservation of the species should therefore be reassessed. PMID:25440190

  1. Unexpected abundance and long-term relative stability of the brown alga Cystoseira amentacea, hitherto regarded as a threatened species, in the north-western Mediterranean Sea.

    PubMed

    Thibaut, Thierry; Blanfuné, Aurélie; Markovic, Laurent; Verlaque, Marc; Boudouresque, Charles F; Perret-Boudouresque, Michèle; Maćic, Vesna; Bottin, Lorraine

    2014-12-15

    Cystoseira amentacea is a Mediterranean endemic alga thriving on very shallow rocky substrates. It has been considered as a threatened species, having experienced a steady decline and is therefore protected by international conventions. The historical distribution of the species has been assessed along the French Mediterranean coast, on the basis of 467 articles and herbarium vouchers. We have produced an accurate map of its current distribution and abundance along 1832 km of coastline, through in situ surveys. C. amentacea was observed along 1125 km of shoreline, including 33% of almost continuous or continuous belt. In most of its range, there is no evidence of loss, except in 4 areas of Provence, French Riviera and Corsica. A significant relation was found between the absence or low abundance of C. amentacea and the vicinity of ports and large sewage outfalls. The status of conservation of the species should therefore be reassessed.

  2. Abundance of ticks (Acari: Ixodidae) infesting the western fence lizard, Sceloporus occidentalis, in relation to environmental factors.

    PubMed

    Tälleklint-Eisen, L; Eisen, R J

    1999-09-01

    We examined the impact of environmental characteristics, such as habitat type, topographic exposure and presence of leaf litter, on the abundance of Ixodes pacificus ticks infesting the western fence lizard (Sceloporus occidentalis) at the University of California Hopland Research and Extension Center (HREC), Mendocino County, California. A total of 383 adult lizards were slip-noosed and examined for tick infestation in April and May 1998. At least 94% of the lizards were infested by ticks and at least 20% of the females and 33% of the males carried > 15 ticks. This intensive utilization of western fence lizards (which do not serve as natural reservoirs for Lyme disease spirochetes) by subadult ticks, is probably the primary reason for the low prevalence of infection with Borrelia burgdorferi in I. pacificus nymphs and adults previously recorded at the HREC. Tick loads were higher on male than female lizards. Also, male lizards were generally more heavily infested in late April than in late May. The prevalence of tick infestation exceeded 88% in all habitat types but males collected in woodland and grass/woodland edges had higher tick loads than those collected in open grassland. Male lizards captured in open, exposed grassland tended to carry heavier tick loads in northern/eastern, as compared to southern/western, exposures, and when leaf litter was present. PMID:10581712

  3. Species richness, relative abundance, and habitat associations of nocturnal birds along the rio grande in Southern texas

    USGS Publications Warehouse

    Skoruppa, M.K.; Woodin, M.C.; Blacklock, G.

    2009-01-01

    The segment of the Rio Grande between International Falcon Reservoir and Del Rio, Texas (distance ca. 350 km), remains largely unexplored ornithologically. We surveyed nocturnal birds monthly during February-June 1998 at 19 stations along the Rio Grande (n = 6) and at upland stock ponds (n = 13) in Webb County, Texas. We conducted 10-min point counts (n = 89) after sunset and before moonset. Four species of owls and five species of nightjars were detected. Nightjars, as a group, were nearly five limes more abundant (mean number/count = 2.63) than owls (mean number = 0.55). The most, common owl, the great horned owl (Bubo virginianus), had a mean number of 0.25/point count. The mean for elf owls (Micrathene whitneyi) was 0.16/point count. The most common nightjars were the common poorwill (Phalaenoptilus nuttallii; 1.21/point count) and lesser nighthawk (Chordeiles acutipennir, 1.16/point count). Survey sites on the river supported more species (mean = 2.2) than did upland stock ponds (mean = 1.4). However, only one species (common pauraque, Nyctidromus albicollis) showed a preference for the river sites. Our results establish this segment of the Rio Grande in southern Texas as an area of high diversity of nightjars in the United States, matched (in numbers of species) only by southeastern Arizona and southwestern New Mexico.

  4. Variability of invertebrate abundance in drinking water distribution systems in the Netherlands in relation to biostability and sediment volumes.

    PubMed

    van Lieverloo, J Hein M; Hoogenboezem, Wim; Veenendaal, Gerrit; van der Kooij, Dick

    2012-10-15

    A survey of invertebrates in drinking water from treatment works, internal taps and hydrants on mains was carried out by almost all water companies in the Netherlands from September 1993 to August 1995. Aquatic sow bugs (Asellidae, 1-12 mm) and oligochaeta worms (Oligochaeta, 1-100 mm), both known to have caused rare though embarrassing consumer complaints, were found to form 98% of the mean biomass in water flushed from mains. Their numbers in the mains water ranged up to 1500 (mean 37) Asellidae m(-3) and up to 9900 (mean 135) Oligochaeta m(-3). Smaller crustaceans (0.5-2 mm) dominated the numbers in water from mains. e.g. water fleas (Cladocera and Copepoda up to 14,000 m(-3)). Common invertebrates in treated water and in tap water were Rotifera (<1 mm) and nematode worms (Nematoda, <2 mm). No Asellidae, large Oligochaeta (>5 mm) or other large invertebrates were found in 1560 samples of 200 l treated water or tap water. Large variations in invertebrate abundance were found within and between distribution systems. Of the variability of mean biomass in mains per system, 55%, 60% and 63% could statistically be explained by differences in the Biofilm Formation Rate, non-particulate organic matter and the permanganate index of the treated water of the treatment works respectively. A similar correlation was found between mean invertebrate biomass and mean sediment volumes in the distribution systems (R(2) = 52%).

  5. The 20Ne(d,p)21Ne transfer reaction in relation to the s-process abundances

    NASA Astrophysics Data System (ADS)

    Nsangu, C. T.; Laird, A. M.; Parikh, A.; Adsley, P.; Birch, M. D.; Chen, A. A.; Faestermann, T.; Fox, S. P.; Fulton, B. R.; Hertenberger, R.; Irvine, D.; Kay, B. P.; Longland, R.; Manwell, S.; Murphy, A. St. J.; Schmitt, K.; de Séréville, N.; Tomlinson, J. R.; Wirth, H.-F.

    2016-01-01

    A study of the 20Ne(d,p)21Ne transfer reaction was performed using the Quadrupole Dipole Dipole Dipole (Q3D) magnetic spectrograph in Garching, Germany. The experiment probed excitation energies in 21Ne ranging from 6.9 MeV to 8.5 MeV. The aim was to investigate the spectroscopic information of 21Ne within the Gamow window of core helium burning in massive stars. Further information in this region will help reduce the uncertainties on the extrapolation down to Gamow window cross sections of the 17O(α,γ)21Ne reaction. In low metallicity stars, this reaction has a direct impact on s-process abundances by determining the fate of 16O as either a neutron poison or a neutron absorber. The experiment used a 22-MeV deuteron beam, with intensities varying from 0.5-1 μA, and an implanted target of 20Ne of 7 μg/cm2 in 40 μg/cm2 carbon foils. Sixteen 21Ne peaks have been identified in the Ex = 6.9-8.5 MeV range, of which only thirteen peaks correspond to known states. Only the previously-known Ex = 7.960 MeV state was observed within the Gamow window.

  6. Variability of invertebrate abundance in drinking water distribution systems in the Netherlands in relation to biostability and sediment volumes.

    PubMed

    van Lieverloo, J Hein M; Hoogenboezem, Wim; Veenendaal, Gerrit; van der Kooij, Dick

    2012-10-15

    A survey of invertebrates in drinking water from treatment works, internal taps and hydrants on mains was carried out by almost all water companies in the Netherlands from September 1993 to August 1995. Aquatic sow bugs (Asellidae, 1-12 mm) and oligochaeta worms (Oligochaeta, 1-100 mm), both known to have caused rare though embarrassing consumer complaints, were found to form 98% of the mean biomass in water flushed from mains. Their numbers in the mains water ranged up to 1500 (mean 37) Asellidae m(-3) and up to 9900 (mean 135) Oligochaeta m(-3). Smaller crustaceans (0.5-2 mm) dominated the numbers in water from mains. e.g. water fleas (Cladocera and Copepoda up to 14,000 m(-3)). Common invertebrates in treated water and in tap water were Rotifera (<1 mm) and nematode worms (Nematoda, <2 mm). No Asellidae, large Oligochaeta (>5 mm) or other large invertebrates were found in 1560 samples of 200 l treated water or tap water. Large variations in invertebrate abundance were found within and between distribution systems. Of the variability of mean biomass in mains per system, 55%, 60% and 63% could statistically be explained by differences in the Biofilm Formation Rate, non-particulate organic matter and the permanganate index of the treated water of the treatment works respectively. A similar correlation was found between mean invertebrate biomass and mean sediment volumes in the distribution systems (R(2) = 52%). PMID:22840474

  7. OXYGEN ABUNDANCES IN CEPHEIDS

    SciTech Connect

    Luck, R. E.; Andrievsky, S. M.; Korotin, S. N.; Kovtyukh, V. V. E-mail: serkor@skyline.od.ua E-mail: scan@deneb1.odessa.ua

    2013-07-01

    Oxygen abundances in later-type stars, and intermediate-mass stars in particular, are usually determined from the [O I] line at 630.0 nm, and to a lesser extent, from the O I triplet at 615.7 nm. The near-IR triplets at 777.4 nm and 844.6 nm are strong in these stars and generally do not suffer from severe blending with other species. However, these latter two triplets suffer from strong non-local thermodynamic equilibrium (NLTE) effects and thus see limited use in abundance analyses. In this paper, we derive oxygen abundances in a large sample of Cepheids using the near-IR triplets from an NLTE analysis, and compare those abundances to values derived from a local thermodynamic equilibrium (LTE) analysis of the [O I] 630.0 nm line and the O I 615.7 nm triplet as well as LTE abundances for the 777.4 nm triplet. All of these lines suffer from line strength problems making them sensitive to either measurement complications (weak lines) or to line saturation difficulties (strong lines). Upon this realization, the LTE results for the [O I] lines and the O I 615.7 nm triplet are in adequate agreement with the abundance from the NLTE analysis of the near-IR triplets.

  8. Seasonal changes in the relative abundance of uncultivated sulfate-reducing bacteria in a salt marsh sediment and in the rhizosphere of Spartina alterniflora.

    PubMed

    Rooney-Varga, J N; Devereux, R; Evans, R S; Hines, M E

    1997-10-01

    Phylogenetic diversity and community composition of sulfate-reducing bacteria in a salt marsh sediment and in the rhizosphere of Spartina alterniflora were investigated. Uncultivated Desulfobacteriaceae family-related phylotypes were studied by selectively amplifying 16S rRNA gene fragments from DNA extracted from salt marsh rhizosphere samples. Two novel phylotypes were retrieved from rhizosphere samples, with A01 having 89.1% sequence similarity with Desulfococcus multivorans and 4D19 having 96.3% sequence similarity with Desulfosarcina variabilis. Additionally, six sequences that were extremely closely related to Desulfococcus multivorans (99% sequence similarity) were found. Reference RNAs containing sequences identical to corresponding cloned regions of A01 or 4D19 16S rRNA were synthesized via in vitro transcription and were used in subsequent quantitative membrane hybridization experiments. Oligonucleotide probes A01-183 and 4D19-189 were designed to specifically target these two novel phylotypes and were tested for target specificity against synthesized RNA and reference RNAs extracted from pure cultures. The newly designed probes were then used, together with eubacterial probes, to determine the relative abundances of the novel phylotypes in the salt marsh sediment and the rhizosphere. Mean relative abundances of A01-183 and 4D19-189 targets were 7.5 and 3.4%, respectively, suggesting that the target organisms of A01-183 and, to a lesser extent, of 4D19-189 play an important role in the salt marsh sediment and the Spartina rhizosphere. A seasonal trend of increased A01 relative abundance during the period of vegetative plant growth was evident, suggesting a close interaction between A01 and S. alterniflora.

  9. Coronal abundances and their variation

    NASA Technical Reports Server (NTRS)

    Saba, Julia L. R.

    1994-01-01

    This contract supports the investigation of elemental abundances in the solar corona, principally through analysis of high-resolution software X-ray spectra from the Flat Crystal Spectrometer on NASA's Solar Maximum Mission. The goals of the study are a characterization of the mean values of relative abundances of elements accessible in the FCS data, and information on the extent and circumstances of their variability. This report is a summation of the data analysis and reporting activities which occurred since the last report, submitted two months early, in April 1994, to facilitate evaluation of the first year's progress for contract renewal. Hence this report covers the period 15 April 1994 - 15 December 1994. A list of publications resulting from this research is included.

  10. Distribution and Abundance of Phlebotominae, Vectors of Leishmaniasis, in Argentina: Spatial and Temporal Analysis at Different Scales

    PubMed Central

    Quintana, María Gabriela; Fernández, María Soledad; Salomón, Oscar Daniel

    2012-01-01

    The spatial-temporal analysis of the abundance of insects, vectors of tegumentary leishmaniasis (TL) and visceral leishmaniasis (VL), was performed in Argentina using spatial-temporal increasing scales. In the microscale (microfocal), the effect of the primary vegetation-crop interface in vector abundance was observed, and also how the shelters, food sources, and other environmental characteristics contribute to habitat microheterogeneity and so to a microheterogeneous vector distribution. In the mesoscale (locality or epidemic focus), the results from different foci of TL (rural and periurban) and VL (urban) suggested a metapopulation structure determined partially by quantifiable habitat variables that could explain the increase of risk associated to an increase of vector-human contact due to climatic or anthropogenic changes. In the macroscale (regional), captures of vectors and records of human cases allowed the construction of risk maps and predictive models of vector distribution. In conclusion, in order to obtain valid results transferrable to control programs from spatial studies, special attention should be paid in order to assure the consistency between the spatial scales of the hypotheses, data, and analytical tools of each experimental or descriptive design. PMID:22315620

  11. Do attacks by jaguars Panthera onca and pumas Puma concolor (Carnivora: Felidae) on livestock correlate with species richness and relative abundance of wild prey?

    PubMed

    Burgas, Albert; Amit, Ronit; Lopez, Bernat C

    2014-12-01

    Abstract: Attacks by big cats on livestock are one of the major causes of human-felid conflicts and, therefore, an important factor in the conservation of these species. It has been argued that a reduction in natural prey abundance promotes attacks on domestic species, but few studies have tested this statement, and some have delivered contradictory results. We investigated whether the occurrence of attacks to livestock by jaguar and puma relates to the abundance and richness of their natural prey. In the rainy season 2009, we tracked potential prey species counting signs of presence along linear transects in 14 non-attacked cattle farms (control) and in 14 attacked cattle farms in NW Costa Rica. There was a negative relationship between the occurrence of attacks and both species richness (p = 0.0014) and abundance (p = 0.0012) of natural prey. Our results support the establishment of actions to promote support and recovery of natural prey, in order to diminish attacks on livestock, while maintaining jaguar and puma populations.

  12. Variation in large-bodied fish-community structure and abundance in relation to water-management regime in a large regulated river.

    PubMed

    Haxton, T J; Findlay, C S

    2009-07-01

    Variation in life-history traits (growth, condition, mortality and recruitment) and relative abundance of 11 large-bodied fish species was investigated among three water-management regimes (unimpounded, run-of-the-river and winter reservoirs) in the large regulated Ottawa River, Canada. If waterpower management had an effect on fishes, then (1) would be expected community structuring among water-management regimes and (2) species with similar life-history traits should be affected in a similar manner. Large-bodied fish communities were assessed using two different standard index-netting techniques, one using trap nets and the other gillnets. Community structure could be discriminated based on species caught in nets using holographic neural networks (78.8% correct overall classification rate using trap nets and 76.0% using gillnets); therefore, water-management regimes affected community structure in the Ottawa River. Littoral zone benthivores were significantly lower in abundance (P < 0.001) or absent in winter reservoirs, whereas the abundance of planktivores or species that were planktivorous at young ages were significantly greater than in unimpounded river reaches. Growth, condition and mortality did not vary among reach types except smallmouth bass Micropterus dolomieu were in better condition in winter reservoirs than unimpounded reaches. Lake sturgeon Acipenser fulvescens recruitment was impaired in run-of-the-river reaches, whereas recruitment for other species that spawn in fast water was not affected.

  13. Do attacks by jaguars Panthera onca and pumas Puma concolor (Carnivora: Felidae) on livestock correlate with species richness and relative abundance of wild prey?

    PubMed

    Burgas, Albert; Amit, Ronit; Lopez, Bernat C

    2014-12-01

    Abstract: Attacks by big cats on livestock are one of the major causes of human-felid conflicts and, therefore, an important factor in the conservation of these species. It has been argued that a reduction in natural prey abundance promotes attacks on domestic species, but few studies have tested this statement, and some have delivered contradictory results. We investigated whether the occurrence of attacks to livestock by jaguar and puma relates to the abundance and richness of their natural prey. In the rainy season 2009, we tracked potential prey species counting signs of presence along linear transects in 14 non-attacked cattle farms (control) and in 14 attacked cattle farms in NW Costa Rica. There was a negative relationship between the occurrence of attacks and both species richness (p = 0.0014) and abundance (p = 0.0012) of natural prey. Our results support the establishment of actions to promote support and recovery of natural prey, in order to diminish attacks on livestock, while maintaining jaguar and puma populations. PMID:25720180

  14. Relative error covariance analysis techniques and application

    NASA Technical Reports Server (NTRS)

    Wolff, Peter, J.; Williams, Bobby G.

    1988-01-01

    A technique for computing the error covariance of the difference between two estimators derived from different (possibly overlapping) data arcs is presented. The relative error covariance is useful for predicting the achievable consistency between Kalman-Bucy filtered estimates generated from two (not necessarily disjoint) data sets. The relative error covariance analysis technique is then applied to a Venus Orbiter simulation.

  15. Spatial, temporal, and habitat-related variation in abundance of pelagic fishes in the Gulf of Mexico: potential implications of the deepwater horizon oil spill.

    PubMed

    Rooker, Jay R; Kitchens, Larissa L; Dance, Michael A; Wells, R J David; Falterman, Brett; Cornic, Maëlle

    2013-01-01

    Time-series data collected over a four-year period were used to characterize patterns of abundance for pelagic fishes in the northern Gulf of Mexico (GoM) before (2007-2009) and after (2010) the Deepwater Horizon oil spill. Four numerically dominant pelagic species (blackfin tuna, blue marlin, dolphinfish, and sailfish) were included in our assessment, and larval density of each species was lower in 2010 than any of the three years prior to the oil spill, although larval abundance in 2010 was often statistically similar to other years surveyed. To assess potential overlap between suitable habitat of pelagic fish larvae and surface oil, generalized additive models (GAMs) were developed to evaluate the influence of ocean conditions on the abundance of larvae from 2007-2009. Explanatory variables from GAMs were then linked to environmental data from 2010 to predict the probability of occurrence for each species. The spatial extent of surface oil overlapped with early life habitat of each species, possibly indicating that the availability of high quality habitat was affected by the DH oil spill. Shifts in the distribution of spawning adults is another factor known to influence the abundance of larvae, and the spatial occurrence of a model pelagic predator (blue marlin) was characterized over the same four-year period using electronic tags. The spatial extent of oil coincided with areas used by adult blue marlin from 2007-2009, and the occurrence of blue marlin in areas impacted by the DH oil spill was lower in 2010 relative to pre-spill years.

  16. Spatial, Temporal, and Habitat-Related Variation in Abundance of Pelagic Fishes in the Gulf of Mexico: Potential Implications of the Deepwater Horizon Oil Spill

    PubMed Central

    Rooker, Jay R.; Kitchens, Larissa L.; Dance, Michael A.; Wells, R. J. David; Falterman, Brett; Cornic, Maëlle

    2013-01-01

    Time-series data collected over a four-year period were used to characterize patterns of abundance for pelagic fishes in the northern Gulf of Mexico (GoM) before (2007–2009) and after (2010) the Deepwater Horizon oil spill. Four numerically dominant pelagic species (blackfin tuna, blue marlin, dolphinfish, and sailfish) were included in our assessment, and larval density of each species was lower in 2010 than any of the three years prior to the oil spill, although larval abundance in 2010 was often statistically similar to other years surveyed. To assess potential overlap between suitable habitat of pelagic fish larvae and surface oil, generalized additive models (GAMs) were developed to evaluate the influence of ocean conditions on the abundance of larvae from 2007–2009. Explanatory variables from GAMs were then linked to environmental data from 2010 to predict the probability of occurrence for each species. The spatial extent of surface oil overlapped with early life habitat of each species, possibly indicating that the availability of high quality habitat was affected by the DH oil spill. Shifts in the distribution of spawning adults is another factor known to influence the abundance of larvae, and the spatial occurrence of a model pelagic predator (blue marlin) was characterized over the same four-year period using electronic tags. The spatial extent of oil coincided with areas used by adult blue marlin from 2007–2009, and the occurrence of blue marlin in areas impacted by the DH oil spill was lower in 2010 relative to pre-spill years. PMID:24130759

  17. Estimating wetland vegetation abundance from Landsat-8 operational land imager imagery: a comparison between linear spectral mixture analysis and multinomial logit modeling methods

    NASA Astrophysics Data System (ADS)

    Zhang, Min; Gong, Zhaoning; Zhao, Wenji; Pu, Ruiliang; Liu, Ke

    2016-01-01

    Mapping vegetation abundance by using remote sensing data is an efficient means for detecting changes of an eco-environment. With Landsat-8 operational land imager (OLI) imagery acquired on July 31, 2013, both linear spectral mixture analysis (LSMA) and multinomial logit model (MNLM) methods were applied to estimate and assess the vegetation abundance in the Wild Duck Lake Wetland in Beijing, China. To improve mapping vegetation abundance and increase the number of endmembers in spectral mixture analysis, normalized difference vegetation index was extracted from OLI imagery along with the seven reflective bands of OLI data for estimating the vegetation abundance. Five endmembers were selected, which include terrestrial plants, aquatic plants, bare soil, high albedo, and low albedo. The vegetation abundance mapping results from Landsat OLI data were finally evaluated by utilizing a WorldView-2 multispectral imagery. Similar spatial patterns of vegetation abundance produced by both fully constrained LSMA algorithm and MNLM methods were observed: higher vegetation abundance levels were distributed in agricultural and riparian areas while lower levels in urban/built-up areas. The experimental results also indicate that the MNLM model outperformed the LSMA algorithm with smaller root mean square error (0.0152 versus 0.0252) and higher coefficient of determination (0.7856 versus 0.7214) as the MNLM model could handle the nonlinear reflection phenomenon better than the LSMA with mixed pixels.

  18. Relativity concept inventory: Development, analysis, and results

    NASA Astrophysics Data System (ADS)

    Aslanides, J. S.; Savage, C. M.

    2013-06-01

    We report on a concept inventory for special relativity: the development process, data analysis methods, and results from an introductory relativity class. The Relativity Concept Inventory tests understanding of relativistic concepts. An unusual feature is confidence testing for each question. This can provide additional information; for example, high confidence correlated with incorrect answers suggests a misconception. A novel aspect of our data analysis is the use of Monte Carlo simulations to determine the significance of correlations. This approach is particularly useful for small sample sizes, such as ours. Our results show a gender bias that was not present in course assessment, similar to that reported for the Force Concept Inventory.

  19. Abundance and Temperature Dependency of Protein-Protein Interaction Revealed by Interface Structure Analysis and Stability Evolution.

    PubMed

    He, Yi-Ming; Ma, Bin-Guang

    2016-01-01

    Protein complexes are major forms of protein-protein interactions and implement essential biological functions. The subunit interface in a protein complex is related to its thermostability. Though the roles of interface properties in thermal adaptation have been investigated for protein complexes, the relationship between the interface size and the expression level of the subunits remains unknown. In the present work, we studied this relationship and found a positive correlation in thermophiles rather than mesophiles. Moreover, we found that the protein interaction strength in complexes is not only temperature-dependent but also abundance-dependent. The underlying mechanism for the observed correlation was explored by simulating the evolution of protein interface stability, which highlights the avoidance of misinteraction. Our findings make more complete the picture of the mechanisms for protein complex thermal adaptation and provide new insights into the principles of protein-protein interactions. PMID:27220911

  20. Abundance and Temperature Dependency of Protein-Protein Interaction Revealed by Interface Structure Analysis and Stability Evolution

    NASA Astrophysics Data System (ADS)

    He, Yi-Ming; Ma, Bin-Guang

    2016-05-01

    Protein complexes are major forms of protein-protein interactions and implement essential biological functions. The subunit interface in a protein complex is related to its thermostability. Though the roles of interface properties in thermal adaptation have been investigated for protein complexes, the relationship between the interface size and the expression level of the subunits remains unknown. In the present work, we studied this relationship and found a positive correlation in thermophiles rather than mesophiles. Moreover, we found that the protein interaction strength in complexes is not only temperature-dependent but also abundance-dependent. The underlying mechanism for the observed correlation was explored by simulating the evolution of protein interface stability, which highlights the avoidance of misinteraction. Our findings make more complete the picture of the mechanisms for protein complex thermal adaptation and provide new insights into the principles of protein-protein interactions.

  1. Source apportionment of atmospheric PAHs in the Western Balkans by natural abundance radiocarbon analysis

    SciTech Connect

    Zdenek Zencak; Jana Klanova; Ivan Holoubek; Oerjan Gustafsson

    2007-06-01

    Progress in source apportionment of priority combustion-derived atmospheric pollutants can be made by an inverse approach to inventory emissions, namely, receptor-based compound class-specific radiocarbon analysis (CCSRA) of target pollutants. In the present study, CCSRA of the combustion-derived polycyclic aromatic hydrocarbons (PAHs) present in the atmosphere of the countries of the former republic of Yugoslavia was performed. The carbon stable isotope composition ({delta}{sup 13}C) of PAHs varied between -27.68 and -27.19{per_thousand}, whereas {Delta}{sup 14}C values ranged from -568{per_thousand} for PAHs sampled in Kosovo to -288{per_thousand} for PAHs sampled in the Sarajevo area. The application of an isotopic mass balance model to these {Delta}{sup 14}C data revealed a significant contribution (35-65%) from the combustion of non-fossil material to the atmospheric PAH pollution, even in urban and industrialized areas. Furthermore, consistency was observed between the isotopic composition of PAHs obtained by high-volume sampling and those collected by passive sampling. This encourages the use of passive samplers for CCSRA applications. This marks the first time that a CCSRA investigation could be executed on a geographically wide scale, providing a quantitative field-based source apportionment, which points out that also non-fossil combustion processes should be targeted for remedial action. 36 refs., 1 fig., 3 tabs.

  2. Changes in the concentration and relative abundance of alkanes and PAHs from the Deepwater Horizon oiling of coastal marshes.

    PubMed

    Turner, R E; Overton, E B; Meyer, B M; Miles, M S; Hooper-Bui, L

    2014-09-15

    We determined changes of 28 alkanes and 43 different PAHs in 418 wetland soil samples collected on ten sampling trips to three Louisiana estuaries before and after they were oiled from the 2010 Deepwater Horizon disaster. There was a significant decline in 22 of the 28 alkane analytes (0.42% day(-1)), no change in 6, over 2.5 years. The concentration of five aromatic petroleum hydrocarbons (PAHs) increased (range 0.25-0.70% day(-1)), whereas the total PAH pool did not change. Of these five, naphthalene and C-1-naphthalenes are suggested to be of higher toxicity than the other three because of their relatively higher volatility or solubility. The relative proportions of alkane analytes, but not PAHs, does not yet resemble that in the pre-oiled marshes after 3 years, The trajectories of nine indicators for degradation/weathering were either inconclusive or misleading (alkanes) or confirmed the relatively meager degradation of PAHs. PMID:25127500

  3. [Relative abundance and microhabitat use by the frog Geobatrachus walkeri (Anura: Strabomantidae) in two habitats of Sierra Nevada de Santa Marta, Colombia].

    PubMed

    Martínez Baños, Vera; Pacheco Florez, Vanesa; Ramírez-Pinilla, Martha P

    2011-06-01

    Geobatrachus walkeri belongs to a monotypic frog genus endemic to the San Lorenzo area, Sierra Nevada de Santa Marta, Colombia. This species has been categorized as endangered because of its small distribution area and the decline in the extent and quality of its habitat. It inhabits two forest types with different composition and structure, the native secondary forest and a pine plantation (dominated by Pinus patula). To compare the relative abundance and microhabitat use of this species in these habitat types, 30 quadrants/environment were distributed randomly. The individual number, microhabitat use and other aspects of its natural history were registered using visual encounter surveys in both sites, including non-sampled areas in the quadrants. The relative abundance of frogs was significantly different between habitats and among seasons. The highest abundance of G. walkeri relative to the total area was found in the pine plantation, being 2.3 times higher than in the natural forest. More frogs were significantly found during the rainy season; nevertheless, active individuals were also found during the dry season. Significant differences were found in the microhabitat use with respect to the forest type and season. The most frequently microhabitat used in the two forest types was the pine leaf-litter; besides, in the native forest, the microhabitat occupied more frequently presented medium and large size stones. Geobatrachus walkeri is a successful species in pine plantations, associated permanently to its leaf-litter environment where it seems to develop its entire life cycle. The clear modifications in the soils and water, derived from the introduction of the pine plantation in this area, seem not to have negatively affected the conservation and successful maintenance of this species.

  4. Improved Statistical Analysis of Low Abundance Phenomena in Bimodal Bacterial Populations

    PubMed Central

    Reinhard, Friedrich; van der Meer, Jan Roelof

    2013-01-01

    Accurate detection of subpopulation size determinations in bimodal populations remains problematic yet it represents a powerful way by which cellular heterogeneity under different environmental conditions can be compared. So far, most studies have relied on qualitative descriptions of population distribution patterns, on population-independent descriptors, or on arbitrary placement of thresholds distinguishing biological ON from OFF states. We found that all these methods fall short of accurately describing small population sizes in bimodal populations. Here we propose a simple, statistics-based method for the analysis of small subpopulation sizes for use in the free software environment R and test this method on real as well as simulated data. Four so-called population splitting methods were designed with different algorithms that can estimate subpopulation sizes from bimodal populations. All four methods proved more precise than previously used methods when analyzing subpopulation sizes of transfer competent cells arising in populations of the bacterium Pseudomonas knackmussii B13. The methods’ resolving powers were further explored by bootstrapping and simulations. Two of the methods were not severely limited by the proportions of subpopulations they could estimate correctly, but the two others only allowed accurate subpopulation quantification when this amounted to less than 25% of the total population. In contrast, only one method was still sufficiently accurate with subpopulations smaller than 1% of the total population. This study proposes a number of rational approximations to quantifying small subpopulations and offers an easy-to-use protocol for their implementation in the open source statistical software environment R. PMID:24205184

  5. Systematic analysis of intron size and abundance parameters in diverse lineages.

    PubMed

    Wu, Jiayan; Xiao, Jingfa; Wang, Lingping; Zhong, Jun; Yin, Hongyan; Wu, Shuangxiu; Zhang, Zhang; Yu, Jun

    2013-10-01

    All eukaryotic genomes have genes with introns in variable sizes. As far as spliceosomal introns are concerned, there are at least three basic parameters to stratify introns across diverse eukaryotic taxa: size, number, and sequence context. The number parameter is highly variable in lower eukaryotes, especially among protozoan and fungal species, which ranges from less than 4% to 78% of the genes. Over greater evolutionary time scales, the number parameter undoubtedly increases as observed in higher plants and higher vertebrates, reaching greater than 12.5 exons per gene in average among mammalian genomes. The size parameter is more complex, where multiple modes appear at work. Aside from intronless genes, there are three other types of intron-containing genes: half-sized, minimal, and size-expandable introns. The half-sized introns have only been found in a limited number of genomes among protozoan and fungal lineages and the other two types are prevalent in all animal and plant genomes. Among the size-expandable introns, the sizes of plant introns are expansion-limited in that the large introns exceeding 1000 bp are fewer in numbers and transposon-free as compared to the large introns among animals, where the larger introns are filled with transposable elements and appear expansion-flexible, reaching several kilobasepairs (kbp) and even thousands of kbp in size. Most of the intron parameters can be studied as signatures of the specific splicing machineries of different eukaryotic lineages and are highly relevant to the regulation of gene expression and functionality. In particular, the transcription-splicing-export coupling of eukaryotic intron dispensing leads to a working hypothesis that all intron parameters are evolved to be efficient and function-related in processing and routing the spliced transcripts.

  6. Plant and soil natural abundance delta (15)N: indicators of relative rates of nitrogen cycling in temperate forest ecosystems.

    PubMed

    Templer, Pamela H; Arthur, Mary A; Lovett, Gary M; Weathers, Kathleen C

    2007-08-01

    Watersheds within the Catskill Mountains, New York, receive among the highest rates of nitrogen (N) deposition in the northeastern United States and are beginning to show signs of N saturation. Despite similar amounts of N deposition across watersheds within the Catskill Mountains, rates of soil N cycling and N retention vary significantly among stands of different tree species. We examined the potential use of delta (15)N of plants and soils as an indicator of relative forest soil N cycling rates. We analyzed the delta (15)N of foliage, litterfall, bole wood, surface litter layer, fine roots and organic soil from single-species stands of American beech (Fagus grandifolia), eastern hemlock (Tsuga canadensis), red oak (Quercus rubra), and sugar maple (Acer saccharum). Fine root and organic soil delta (15)N values were highest within sugar maple stands, which correlated significantly with higher rates of net mineralization and nitrification. Results from this study suggest that fine root and organic soil delta (15)N can be used as an indicator of relative rates of soil N cycling. Although not statistically significant, delta (15)N was highest within foliage, wood and litterfall of beech stands, a tree species associated with intermediate levels of soil N cycling rates and forest N retention. Our results show that belowground delta (15)N values are a better indicator of relative rates of soil N cycling than are aboveground delta (15)N values.

  7. Sodium abundances of AGB and RGB stars in Galactic globular clusters. I. Analysis and results of NGC 2808

    NASA Astrophysics Data System (ADS)

    Wang, Y.; Primas, F.; Charbonnel, C.; Van der Swaelmen, M.; Bono, G.; Chantereau, W.; Zhao, G.

    2016-07-01

    Context. Galactic globular clusters (GC) are known to have multiple stellar populations and be characterised by similar chemical features, e.g. O-Na anti-correlation. While second-population stars, identified by their Na overabundance, have been found from the main sequence turn-off up to the tip of the red giant branch (RGB) in various Galactic GCs, asymptotic giant branch (AGB) stars have rarely been targeted. The recent finding that NGC 6752 lacks an Na-rich AGB star has thus triggered new studies on AGB stars in GCs, since this result questions our basic understanding of GC formation and stellar evolution theory. Aims: We aim to compare the Na abundance distributions of AGB and RGB stars in Galactic GCs and investigate whether the presence of Na-rich stars on the AGB is metallicity-dependent. Methods: With high-resolution spectra obtained with the multi-object high-resolution spectrograph FLAMES on ESO/VLT, we derived accurate Na abundances for 31 AGB and 40 RGB stars in the Galactic GC NGC 2808. Results: We find that NGC 2808 has a mean metallicity of -1.11 ± 0.08 dex, in good agreement with earlier analyses. Comparable Na abundance dispersions are derived for our AGB and RGB samples, with the AGB stars being slightly more concentrated than the RGB stars. The ratios of Na-poor first-population to Na-rich second-population stars are 45:55 in the AGB sample and 48:52 in the RGB sample. Conclusions: NGC 2808 has Na-rich second-population AGB stars, which turn out to be even more numerous - in relative terms - than their Na-poor AGB counterparts and the Na-rich stars on the RGB. Our findings are well reproduced by the fast rotating massive stars scenario and they do not contradict the recent results that there is not an Na-rich AGB star in NGC 6752. NGC 2808 thus joins the larger group of Galactic GCs for which Na-rich second-population stars on the AGB have recently been found. Based on observations made with ESO telescopes at the La Silla Paranal Observatory

  8. Distribution and abundance of human-specific Bacteroides and relation to traditional indicators in an urban tropical catchment

    PubMed Central

    Nshimyimana, J P; Ekklesia, E; Shanahan, P; Chua, L H C; Thompson, J R

    2014-01-01

    Aims The study goals were to determine the relationship between faecal indicator bacteria (FIB), the HF183 marker and land use, and the phylogenetic diversity of HF183 marker sequences in a tropical urban watershed. Methods and Results Total coliforms, Escherichia coli, and HF183 were quantified in 81 samples categorized as undeveloped, residential and horticultural from the Kranji Reservoir and Catchment in Singapore. Quantitative-PCR for HF183 followed by analysis of variance indicated that horticultural areas had significantly higher geometric means for marker levels (4·3 × 104 HF183-GE 100 ml−1) than nonhorticultural areas (3·07 × 103 HF183-GE 100 ml−1). E. coli and HF183 were moderately correlated in horticultural areas (R = 0·59, P = 0·0077), but not elsewhere in the catchment. Initial upstream surveys of candidate sources revealed elevated HF183 in a wastewater treatment effluent but not in aquaculture ponds. The HF183 marker was cloned, sequenced and determined by phylogenetic analysis to match the original marker description. Conclusion We show that quantification of the HF183 marker is a useful tool for mapping the spatial distribution and potential sources of human sewage contamination in tropical environments such as Singapore. Significance and Impact A major challenge for assessment of water quality in tropical environments is the natural occurrence and nonconservative behaviour of FIB. The HF183 marker has been employed in temperate environments as an alternative indicator for human sewage contamination. Our study supports the use of the HF183 marker as an indicator for human sewage in Singapore and motivates further work to determine HF183 marker levels that correspond to public health risk in tropical environments. PMID:24460587

  9. Constrained Maximum Likelihood Estimation of Relative Abundances of Protein Conformation in a Heterogeneous Mixture from Small Angle X-Ray Scattering Intensity Measurements

    PubMed Central

    Onuk, A. Emre; Akcakaya, Murat; Bardhan, Jaydeep P.; Erdogmus, Deniz; Brooks, Dana H.; Makowski, Lee

    2015-01-01

    In this paper, we describe a model for maximum likelihood estimation (MLE) of the relative abundances of different conformations of a protein in a heterogeneous mixture from small angle X-ray scattering (SAXS) intensities. To consider cases where the solution includes intermediate or unknown conformations, we develop a subset selection method based on k-means clustering and the Cramér-Rao bound on the mixture coefficient estimation error to find a sparse basis set that represents the space spanned by the measured SAXS intensities of the known conformations of a protein. Then, using the selected basis set and the assumptions on the model for the intensity measurements, we show that the MLE model can be expressed as a constrained convex optimization problem. Employing the adenylate kinase (ADK) protein and its known conformations as an example, and using Monte Carlo simulations, we demonstrate the performance of the proposed estimation scheme. Here, although we use 45 crystallographically determined experimental structures and we could generate many more using, for instance, molecular dynamics calculations, the clustering technique indicates that the data cannot support the determination of relative abundances for more than 5 conformations. The estimation of this maximum number of conformations is intrinsic to the methodology we have used here. PMID:26924916

  10. Changes in the relative abundance and movement of insect pollinators during the flowering cycle of Brassica rapa crops: implications for gene flow.

    PubMed

    Mesa, Laura A; Howlett, Bradley G; Grant, Jan E; Didham, Raphael K

    2013-01-01

    The potential movement of transgenes from genetically modified crops to non-genetically modified crops via insect-mediated pollen dispersal has been highlighted as one of the areas of greatest concern in regards to genetically modified crops. Pollen movement depends sensitively on spatial and temporal variation in the movement of insect pollinators between crop fields. This study tested the degree of variation in the diversity and relative abundance of flower-visiting insects entering versus leaving pak choi, Brassica rapa var. chinensis L. (Brassicales: Brassicaceae), crops throughout different stages of the flowering cycle. The relative abundance of flower-visiting insects varied significantly with Brassica crop phenology. Greater numbers of flower-visiting insects were captured inside rather than outside the crop fields, with the highest capture rates of flower-visitors coinciding with the peak of flowering in both spring-flowering and summer-flowering crops. Moreover, the ratio of flower-visiting insects entering versus leaving crop fields also varied considerably with changing crop phenology. Despite high variation in relative capture rates, the data strongly indicate non-random patterns of variation in insect movement in relation to crop phenology, with early-season aggregation of flower-visiting insects entering and remaining in the crop, and then mass emigration of flower-visiting insects leaving the crop late in the flowering season. Although pollen movement late in the flowering cycle might contribute relatively little to total seed set (and hence crop production), the findings here suggest that extensive late-season pollinator redistribution in the landscape could contribute disproportionately to long-distance gene movement between crops.

  11. Changes in the relative abundance and movement of insect pollinators during the flowering cycle of Brassica rapa crops: implications for gene flow.

    PubMed

    Mesa, Laura A; Howlett, Bradley G; Grant, Jan E; Didham, Raphael K

    2013-01-01

    The potential movement of transgenes from genetically modified crops to non-genetically modified crops via insect-mediated pollen dispersal has been highlighted as one of the areas of greatest concern in regards to genetically modified crops. Pollen movement depends sensitively on spatial and temporal variation in the movement of insect pollinators between crop fields. This study tested the degree of variation in the diversity and relative abundance of flower-visiting insects entering versus leaving pak choi, Brassica rapa var. chinensis L. (Brassicales: Brassicaceae), crops throughout different stages of the flowering cycle. The relative abundance of flower-visiting insects varied significantly with Brassica crop phenology. Greater numbers of flower-visiting insects were captured inside rather than outside the crop fields, with the highest capture rates of flower-visitors coinciding with the peak of flowering in both spring-flowering and summer-flowering crops. Moreover, the ratio of flower-visiting insects entering versus leaving crop fields also varied considerably with changing crop phenology. Despite high variation in relative capture rates, the data strongly indicate non-random patterns of variation in insect movement in relation to crop phenology, with early-season aggregation of flower-visiting insects entering and remaining in the crop, and then mass emigration of flower-visiting insects leaving the crop late in the flowering season. Although pollen movement late in the flowering cycle might contribute relatively little to total seed set (and hence crop production), the findings here suggest that extensive late-season pollinator redistribution in the landscape could contribute disproportionately to long-distance gene movement between crops. PMID:23937538

  12. Changes in the Relative Abundance and Movement of Insect Pollinators During the Flowering Cycle of Brassica rapa Crops: Implications for Gene Flow

    PubMed Central

    Mesa, Laura A.; Howlett, Bradley G.; Grant, Jan E.; Didham, Raphael K.

    2013-01-01

    The potential movement of transgenes from genetically modified crops to non-genetically modified crops via insect-mediated pollen dispersal has been highlighted as one of the areas of greatest concern in regards to genetically modified crops. Pollen movement depends sensitively on spatial and temporal variation in the movement of insect pollinators between crop fields. This study tested the degree of variation in the diversity and relative abundance of flower-visiting insects entering versus leaving pak choi, Brassica rapa var. chinensis L. (Brassicales: Brassicaceae), crops throughout different stages of the flowering cycle. The relative abundance of flower-visiting insects varied significantly with Brassica crop phenology. Greater numbers of flower-visiting insects were captured inside rather than outside the crop fields, with the highest capture rates of flower-visitors coinciding with the peak of flowering in both spring-flowering and summer-flowering crops. Moreover, the ratio of flower-visiting insects entering versus leaving crop fields also varied considerably with changing crop phenology. Despite high variation in relative capture rates, the data strongly indicate non-random patterns of variation in insect movement in relation to crop phenology, with early-season aggregation of flower-visiting insects entering and remaining in the crop, and then mass emigration of flower-visiting insects leaving the crop late in the flowering season. Although pollen movement late in the flowering cycle might contribute relatively little to total seed set (and hence crop production), the findings here suggest that extensive late-season pollinator redistribution in the landscape could contribute disproportionately to long-distance gene movement between crops. PMID:23937538

  13. Sulfuric acid vapor and other cloud-related gases in the Venus atmosphere - Abundances inferred from observed radio opacity

    NASA Technical Reports Server (NTRS)

    Steffes, P. G.; Eshleman, V. R.

    1982-01-01

    It is suggested that the absorbing characteristics of sulfuric acid vapor appear to reconcile what had been thought to be an inconsistency among measurements and deductions regarding the constituents of the Venus atmosphere and radio occultation, radar reflection, and radio emission measurements of its opacity. Laboratory measurements of sulfuric acid, sulfur dioxide, water vapor, and carbon dioxide are used to model relative contributions to opacity as a function of height in a way that is consistent with observations of the constituents and absorbing properties of the atmosphere. It is concluded that sulfuric acid vapor is likely to be the principal microwave absorber in the 30-50 km altitude range of the middle atmosphere of Venus.

  14. Mitosomes of Entamoeba histolytica are abundant mitochondrion-related remnant organelles that lack a detectable organellar genome.

    PubMed

    León-Avila, Gloria; Tovar, Jorge

    2004-05-01

    The existence of mitochondrion-related relict organelles (mitosomes) in the amitochondrial human pathogen Entamoeba histolytica and the detection of extranuclear DNA-containing cytoplasmic structures (EhKOs) has led to the suggestion that a remnant genome from the original mitochondrial endosymbiont might have been retained in this organism. This study reports on the mutually exclusive distribution of Cpn60 and extranuclear DNA in E. histolytica and on the distribution of Cpn60-containing mitosomes in this parasite. In situ nick-translation coupled to immunofluorescence microscopy failed to detect the presence of DNA in mitosomes, either in fixed parasite trophozoites or in partially purified organellar fractions. These results indicate that a remnant organellar genome has not been retained in E. histolytica mitosomes and demonstrate unequivocally that EhKOs and mitosomes are distinct and unrelated cellular structures. PMID:15133087

  15. A Bayesian hierarchical model of Antarctic fur seal foraging and pup growth related to sea ice and prey abundance.

    PubMed

    Hiruki-Raring, Lisa M; Ver Hoef, Jay M; Boveng, Peter L; Bengtson, John L

    2012-03-01

    We created a Bayesian hierarchical model (BHM) to investigate ecosystem relationships between the physical ecosystem (sea ice extent), a prey measure (krill density), predator behaviors (diving and foraging effort of female Antarctic fur seals, Arctocephalus gazella, with pups) and predator characteristics (mass of maternal fur seals and pups). We collected data on Antarctic fur seals from 1987/1988 to 1994/1995 at Seal Island, Antarctica. The BHM allowed us to link together predators and prey into a model that uses all the data efficiently and accounts for major sources of uncertainty. Based on the literature, we made hypotheses about the relationships in the model, which we compared with the model outcome after fitting the BHM. For each BHM parameter, we calculated the mean of the posterior density and the 95% credible interval. Our model confirmed others' findings that increased sea ice was related to increased krill density. Higher krill density led to reduced dive intensity of maternal fur seals, as measured by dive depth and duration, and to less time spent foraging by maternal fur seals. Heavier maternal fur seals and lower maternal foraging effort resulted in heavier pups at 22 d. No relationship was found between krill density and maternal mass, or between maternal mass and foraging effort on pup growth rates between 22 and 85 days of age. Maternal mass may have reflected environmental conditions prior to the pup provisioning season, rather than summer prey densities. Maternal mass and foraging effort were not related to pup growth rates between 22 and 85 d, possibly indicating that food was not limiting, food sources other than krill were being used, or differences occurred before pups reached age 22 d.

  16. Genome analysis of Excretory/Secretory proteins in Taenia solium reveals their Abundance of Antigenic Regions (AAR)

    PubMed Central

    Gomez, Sandra; Adalid-Peralta, Laura; Palafox-Fonseca, Hector; Cantu-Robles, Vito Adrian; Soberón, Xavier; Sciutto, Edda; Fragoso, Gladis; Bobes, Raúl J.; Laclette, Juan P.; Yauner, Luis del Pozo; Ochoa-Leyva, Adrián

    2015-01-01

    Excretory/Secretory (ES) proteins play an important role in the host-parasite interactions. Experimental identification of ES proteins is time-consuming and expensive. Alternative bioinformatics approaches are cost-effective and can be used to prioritize the experimental analysis of therapeutic targets for parasitic diseases. Here we predicted and functionally annotated the ES proteins in T. solium genome using an integration of bioinformatics tools. Additionally, we developed a novel measurement to evaluate the potential antigenicity of T. solium secretome using sequence length and number of antigenic regions of ES proteins. This measurement was formalized as the Abundance of Antigenic Regions (AAR) value. AAR value for secretome showed a similar value to that obtained for a set of experimentally determined antigenic proteins and was different to the calculated value for the non-ES proteins of T. solium genome. Furthermore, we calculated the AAR values for known helminth secretomes and they were similar to that obtained for T. solium. The results reveal the utility of AAR value as a novel genomic measurement to evaluate the potential antigenicity of secretomes. This comprehensive analysis of T. solium secretome provides functional information for future experimental studies, including the identification of novel ES proteins of therapeutic, diagnosis and immunological interest. PMID:25989346

  17. Genome analysis of Excretory/Secretory proteins in Taenia solium reveals their Abundance of Antigenic Regions (AAR).

    PubMed

    Gomez, Sandra; Adalid-Peralta, Laura; Palafox-Fonseca, Hector; Cantu-Robles, Vito Adrian; Soberón, Xavier; Sciutto, Edda; Fragoso, Gladis; Bobes, Raúl J; Laclette, Juan P; Yauner, Luis del Pozo; Ochoa-Leyva, Adrián

    2015-05-19

    Excretory/Secretory (ES) proteins play an important role in the host-parasite interactions. Experimental identification of ES proteins is time-consuming and expensive. Alternative bioinformatics approaches are cost-effective and can be used to prioritize the experimental analysis of therapeutic targets for parasitic diseases. Here we predicted and functionally annotated the ES proteins in T. solium genome using an integration of bioinformatics tools. Additionally, we developed a novel measurement to evaluate the potential antigenicity of T. solium secretome using sequence length and number of antigenic regions of ES proteins. This measurement was formalized as the Abundance of Antigenic Regions (AAR) value. AAR value for secretome showed a similar value to that obtained for a set of experimentally determined antigenic proteins and was different to the calculated value for the non-ES proteins of T. solium genome. Furthermore, we calculated the AAR values for known helminth secretomes and they were similar to that obtained for T. solium. The results reveal the utility of AAR value as a novel genomic measurement to evaluate the potential antigenicity of secretomes. This comprehensive analysis of T. solium secretome provides functional information for future experimental studies, including the identification of novel ES proteins of therapeutic, diagnosis and immunological interest.

  18. Oxygen abundance maps of CALIFA galaxies

    NASA Astrophysics Data System (ADS)

    Zinchenko, I. A.; Pilyugin, L. S.; Grebel, E. K.; Sánchez, S. F.; Vílchez, J. M.

    2016-11-01

    We construct maps of the oxygen abundance distribution across the discs of 88 galaxies using Calar Alto Legacy Integral Field Area survey (CALIFA) Data Release 2 (DR2) spectra. The position of the centre of a galaxy (coordinates on the plate) was also taken from the CALIFA DR2. The galaxy inclination, the position angle of the major axis, and the optical radius were determined from the analysis of the surface brightnesses in the Sloan Digital Sky Survey (SDSS) g and r bands of the photometric maps of SDSS Data Release 9. We explore the global azimuthal abundance asymmetry in the discs of the CALIFA galaxies and the presence of a break in the radial oxygen abundance distribution. We found that there is no significant global azimuthal asymmetry for our sample of galaxies, i.e. the asymmetry is small, usually lower than 0.05 dex. The scatter in oxygen abundances around the abundance gradient has a comparable value, ≲0.05 dex. A significant (possibly dominant) fraction of the asymmetry can be attributed to the uncertainties in the geometrical parameters of these galaxies. There is evidence for a flattening of the radial abundance gradient in the central part of 18 galaxies. We also estimated the geometric parameters (coordinates of the centre, the galaxy inclination and the position angle of the major axis) of our galaxies from the analysis of the abundance map. The photometry-map-based and the abundance-map-based geometrical parameters are relatively close to each other for the majority of the galaxies but the discrepancy is large for a few galaxies with a flat radial abundance gradient.

  19. Abundance of BER-related proteins depends on cell proliferation status and the presence of DNA polymerase β

    PubMed Central

    Yamamoto, Mizuki; Yamamoto, Ryohei; Takenaka, Shigeo; Matsuyama, Satoshi; Kubo, Kihei

    2015-01-01

    In mammalian cells, murine N-methylpurine DNA glycosylase (MPG) removes bases damaged spontaneously or by chemical agents through the process called base excision repair (BER). In this study, we investigated the influence of POL β deficiency on MPG-initiated BER efficiency and the expression levels of BER-related proteins in log-phase and growth-arrested (G0) mouse embryonic fibroblasts (MEFs). G0 wild-type (WT) or POL β–deficient (Pol β–KO) cells showed greater resistance to methyl methanesulfonate than did log-phase cells, and repair of methylated bases was less efficient in the G0 cells. Apex1 mRNA expression was significantly lower in Pol β–KO or G0 WT MEFs than in log-phase WT MEFs. Moreover, although Mpg mRNA levels did not differ significantly among cell types, MPG protein levels were significantly higher in log-phase WT cells than in log-phase Pol β–KO cells or either type of G0 cells. Additionally, proliferating cell nuclear antigen protein levels were also reduced in log-phase Pol β–KO cells or either type of G0 cells. These results indicated that MPG-initiated BER functions mainly in proliferating cells, but less so in G0 cells, and that POL β may be involved in regulation of the amount of intracellular repair proteins. PMID:25829532

  20. Relative abundance and distribution of fishes within an established Area of Critical Environmental Concern, of the Amargosa River Canyon and Willow Creek, Inyo and San Bernardino Counties, California

    USGS Publications Warehouse

    Scoppettone, G. Gary; Hereford, Mark E.; Rissler, Peter H.; Johnson, Danielle M.; Salgado, Antonio

    2011-01-01

    The Amargosa River Canyon of San Bernardino and Inyo County, California, has been designated by the Bureau of Land Management as an Area of Critical Environmental Concern, due in part to its unique flora and fauna. As a task of the Area of Critical Environmental Concern implementation plan, a survey of native fishes was conducted from June 21 to August 12, 2010. Geographic Information System tools were used to map sampling locations, which were spaced at 50-meter intervals. Global Positioning Systems were used to locate sampling stations, and stations with adequate water for successful trapping were sampled with baited minnow traps. Amargosa River pupfish (Cyprinodon nevadensis amargosae) and speckled dace (Rhinichthys osculus spp.) were widespread throughout Armargosa River Canyon. Throughout the study area 8,558 pupfish were captured at 194 stations; 3,472 speckled dace were captured at 210 stations; 238 red-swamp crayfish (Procambarus clarkia) were captured at 83 stations; and 1,095 western mosquitofish (Gambusia affinus) were captured at 110 stations. Pupfish were most abundant in open water habitat with native riparian vegetation, and they were significantly less abundant where the stream was completely covered by cattails or where saltcedar (Tamarix sp.) dominated the riparian corridor. There was no relationship between stream cover and speckled dace distribution. Non-native western mosquitofish and red-swamp crayfish densities were significantly higher in stream reaches dominated by saltcedar. The continued spread of saltcedar threatens to negatively affect pupfish and potentially reduce speckled dace abundance throughout the Amargosa River Canyon. This study can serve as baseline information for observing native fish populations in the future, as related to potential changes to the Amargosa River Canyon ecosystem.

  1. Abundance and activity of soil microorganisms in Cedrus atlantica forests are more related to land use than to altitude or latitude

    NASA Astrophysics Data System (ADS)

    Ramírez Rojas, Irene; Perez Fernandez, María; Moreno Gallardo, Laura; Lechuga Ordoñez, Victor; Linares, Juan Carlos

    2016-04-01

    Several environmental traits might change the abundance and the function of soil microorganisms in forest soils by plant-mediated reactions. Few studies have related the landscape-scale forest structural diversity with the micro-scale distribution of microorganism and their activities. High mountain environments harbor ecosystems that are very sensitive to global change and hence highly vulnerable, as those of Atlantic cedar. Altitudinal gradients in mountains are orrelated with changes in vegetation. We propose that altitudinal gradients drive shifts in microbial communities and are correlated with land uses. Thus, the latitudinal and longitudinal pattern of abundance and activity of soil micro-organisms was studied in an intercontinental comparison. We investigate soil extractable organic carbon (EOC) and nitrogen and carbon, microbial biomass and microbial metabolic activities at eight different sites along the latitudinal range of Cedrus atlantica, covering different altitudes and soils characteristics both in Southern Spain and Northern Morocco. Analyses of the abundances of total bacteria, (16S rRNA gene), was conducted using the Ilumina metagenomics technique. Results show that the stands at the highest altitudes had distinct microbial and biochemical characteristics compared with other areas. Overall, microbial activity, as measured by soil respiration, is higher in forests subjected to lower human pressure than in stands highly degraded, probably reflecting the quality of litter input that results of the influence of local assemblage of different tree, shrub and annual species, though changes in the soil N and C contents. Indeed, total soil C and N contents explained the microbial properties at every scale. Our results suggest that in contrast to the observed pronounced altitudinal changes, the kind of human-mediate land management has a stronger role in defining changes in microbial composition and activities in the investigated forest systems.

  2. Meta-Analysis of Quantification Methods Shows that Archaea and Bacteria Have Similar Abundances in the Subseafloor

    PubMed Central

    May, Megan K.; Kevorkian, Richard T.; Steen, Andrew D.

    2013-01-01

    There is no universally accepted method to quantify bacteria and archaea in seawater and marine sediments, and different methods have produced conflicting results with the same samples. To identify best practices, we compiled data from 65 studies, plus our own measurements, in which bacteria and archaea were quantified with fluorescent in situ hybridization (FISH), catalyzed reporter deposition FISH (CARD-FISH), polyribonucleotide FISH, or quantitative PCR (qPCR). To estimate efficiency, we defined “yield” to be the sum of bacteria and archaea counted by these techniques divided by the total number of cells. In seawater, the yield was high (median, 71%) and was similar for FISH, CARD-FISH, and polyribonucleotide FISH. In sediments, only measurements by CARD-FISH in which archaeal cells were permeabilized with proteinase K showed high yields (median, 84%). Therefore, the majority of cells in both environments appear to be alive, since they contain intact ribosomes. In sediments, the sum of bacterial and archaeal 16S rRNA gene qPCR counts was not closely related to cell counts, even after accounting for variations in copy numbers per genome. However, qPCR measurements were precise relative to other qPCR measurements made on the same samples. qPCR is therefore a reliable relative quantification method. Inconsistent results for the relative abundance of bacteria versus archaea in deep subsurface sediments were resolved by the removal of CARD-FISH measurements in which lysozyme was used to permeabilize archaeal cells and qPCR measurements which used ARCH516 as an archaeal primer or TaqMan probe. Data from best-practice methods showed that archaea and bacteria decreased as the depth in seawater and marine sediments increased, although archaea decreased more slowly. PMID:24096423

  3. Meta-analysis of quantification methods shows that archaea and bacteria have similar abundances in the subseafloor.

    PubMed

    Lloyd, Karen G; May, Megan K; Kevorkian, Richard T; Steen, Andrew D

    2013-12-01

    There is no universally accepted method to quantify bacteria and archaea in seawater and marine sediments, and different methods have produced conflicting results with the same samples. To identify best practices, we compiled data from 65 studies, plus our own measurements, in which bacteria and archaea were quantified with fluorescent in situ hybridization (FISH), catalyzed reporter deposition FISH (CARD-FISH), polyribonucleotide FISH, or quantitative PCR (qPCR). To estimate efficiency, we defined "yield" to be the sum of bacteria and archaea counted by these techniques divided by the total number of cells. In seawater, the yield was high (median, 71%) and was similar for FISH, CARD-FISH, and polyribonucleotide FISH. In sediments, only measurements by CARD-FISH in which archaeal cells were permeabilized with proteinase K showed high yields (median, 84%). Therefore, the majority of cells in both environments appear to be alive, since they contain intact ribosomes. In sediments, the sum of bacterial and archaeal 16S rRNA gene qPCR counts was not closely related to cell counts, even after accounting for variations in copy numbers per genome. However, qPCR measurements were precise relative to other qPCR measurements made on the same samples. qPCR is therefore a reliable relative quantification method. Inconsistent results for the relative abundance of bacteria versus archaea in deep subsurface sediments were resolved by the removal of CARD-FISH measurements in which lysozyme was used to permeabilize archaeal cells and qPCR measurements which used ARCH516 as an archaeal primer or TaqMan probe. Data from best-practice methods showed that archaea and bacteria decreased as the depth in seawater and marine sediments increased, although archaea decreased more slowly.

  4. Pain related inflammation analysis using infrared images

    NASA Astrophysics Data System (ADS)

    Bhowmik, Mrinal Kanti; Bardhan, Shawli; Das, Kakali; Bhattacharjee, Debotosh; Nath, Satyabrata

    2016-05-01

    Medical Infrared Thermography (MIT) offers a potential non-invasive, non-contact and radiation free imaging modality for assessment of abnormal inflammation having pain in the human body. The assessment of inflammation mainly depends on the emission of heat from the skin surface. Arthritis is a disease of joint damage that generates inflammation in one or more anatomical joints of the body. Osteoarthritis (OA) is the most frequent appearing form of arthritis, and rheumatoid arthritis (RA) is the most threatening form of them. In this study, the inflammatory analysis has been performed on the infrared images of patients suffering from RA and OA. For the analysis, a dataset of 30 bilateral knee thermograms has been captured from the patient of RA and OA by following a thermogram acquisition standard. The thermograms are pre-processed, and areas of interest are extracted for further processing. The investigation of the spread of inflammation is performed along with the statistical analysis of the pre-processed thermograms. The objectives of the study include: i) Generation of a novel thermogram acquisition standard for inflammatory pain disease ii) Analysis of the spread of the inflammation related to RA and OA using K-means clustering. iii) First and second order statistical analysis of pre-processed thermograms. The conclusion reflects that, in most of the cases, RA oriented inflammation affects bilateral knees whereas inflammation related to OA present in the unilateral knee. Also due to the spread of inflammation in OA, contralateral asymmetries are detected through the statistical analysis.

  5. The relative accuracy of standard estimators for macrofaunal abundance and species richness derived from selected intertidal transect designs used to sample exposed sandy beaches

    NASA Astrophysics Data System (ADS)

    Schoeman, transect designs used to sample exposed sandy beaches D. S.; Wheeler, M.; Wait, M.

    2003-10-01

    In order to ensure that patterns detected in field samples reflect real ecological processes rather than methodological idiosyncrasies, it is important that researchers attempt to understand the consequences of the sampling and analytical designs that they select. This is especially true for sandy beach ecology, which has lagged somewhat behind ecological studies of other intertidal habitats. This paper investigates the performance of routine estimators of macrofaunal abundance and species richness, which are variables that have been widely used to infer predictable patterns of biodiversity across a gradient of beach types. To do this, a total of six shore-normal strip transects were sampled on three exposed, oceanic sandy beaches in the Eastern Cape, South Africa. These transects comprised contiguous quadrats arranged linearly between the spring high and low water marks. Using simple Monte Carlo simulation techniques, data collected from the strip transects were used to assess the accuracy of parameter estimates from different sampling strategies relative to their true values (macrofaunal abundance ranged 595-1369 individuals transect -1; species richness ranged 12-21 species transect -1). Results indicated that estimates from the various transect methods performed in a similar manner both within beaches and among beaches. Estimates for macrofaunal abundance tended to be negatively biased, especially at levels of sampling effort most commonly reported in the literature, and accuracy decreased with decreasing sampling effort. By the same token, estimates for species richness were always negatively biased and were also characterised by low precision. Furthermore, triplicate transects comprising a sampled area in the region of 4 m 2 (as has been previously recommended) are expected to miss more than 30% of the species that occur on the transect. Surprisingly, for both macrofaunal abundance and species richness, estimates based on data from transects sampling quadrats

  6. The relative abundance and seasonal distribution correspond with the sources of polycyclic aromatic hydrocarbons (PAHs) in the surface sediments of Chenab River, Pakistan.

    PubMed

    Hussain, Imran; Syed, Jabir Hussain; Kamal, Atif; Iqbal, Mehreen; Eqani, Syed-Ali-Mustjab-Akbar-Shah; Bong, Chui Wei; Taqi, Malik Mumtaz; Reichenauer, Thomas G; Zhang, Gan; Malik, Riffat Naseem

    2016-06-01

    Chenab River is one of the most important rivers of Punjab Province (Pakistan) that receives huge input of industrial effluents and municipal sewage from major cities in the Central Punjab, Pakistan. The current study was designed to evaluate the concentration levels and associated ecological risks of USEPA priority polycyclic aromatic hydrocarbons (PAHs) in the surface sediments of Chenab River. Sampling was performed from eight (n = 24) sampling stations of Chenab River and its tributaries. We observed a relatively high abundance of ∑16PAHs during the summer season (i.e. 554 ng g(-1)) versus that in the winter season (i.e. 361 ng g(-1)), with an overall abundance of two-, five- and six-ring PAH congeners. Results also revealed that the nitrate and phosphate contents in the sediments were closely associated with low molecular weight (LMW) and high molecular weight (HMW) PAHs, respectively. Source apportionment results showed that the combustion of fossil fuels appears to be the key source of PAHs in the study area. The risk quotient (RQ) values indicated that seven PAH congeners (i.e. phenanthrene, anthracene, fluoranthene, pyrene, benzo(a)pyrene, chrysene and benzo(a)anthracene) could pose serious threats to the aquatic life of the riverine ecosystem in Pakistan. PMID:27234513

  7. Variation in the impact of climate change on flowering phenology and abundance: An examination of two pairs of closely related wildflower species.

    PubMed

    Miller-Rushing, Abraham J; Inouye, David W

    2009-10-01

    Variability in plant phenological responses to climate change is likely to lead to changes in many ecological relationships as the climate continues to change. We used a 34-yr record of flowering times and flower abundance for four species (two Delphinium [Ranunculaceae] species and two Mertensia [Boraginaceae] species) from a subalpine plant community near the Rocky Mountain Biological Laboratory to test the hypothesis that the phenologies of early-flowering species change more rapidly in response to climatological and other abiotic cues than do late-flowering species, a pattern previously found in plant communities in North America and Europe. We also explored a related hypothesis, that flower abundance of late-flowering species is more responsive to changes in climate than that of early-flowering species. The Delphinium species did not support these hypotheses, but the Mertensia species did. The difference between the peak flowering times of the early and late Mertensia species is expanding, leading to a period of diminished resources for pollinators that specialize on this genus. Mertensia ciliata populations are already severely declining in our study area, possibly as a result of earlier snowmelt. Together, these results show that the reported differences between early- and late-flowering species may be widespread, but they are not ubiquitous.

  8. Depth-related distribution and abundance of seastars (Echinodermata: Asteroidea) in the Porcupine Seabight and Porcupine Abyssal Plain, N.E. Atlantic

    NASA Astrophysics Data System (ADS)

    Howell, Kerry L.; Billett, David S. M.; Tyler, Paul A.

    2002-10-01

    The depth-related distribution of seastar (Echinodermata: Asteroidea) species between 150 and 4950 m in the Porcupine Seabight and Porcupine Abyssal Plain is described. 47 species of asteroid were identified from ˜14,000 individuals collected. The bathymetric range of each species is recorded. What are considered quantitative data, from an acoustically monitored epibenthic sledge and supplementary data from otter trawls, are used to display the relative abundance of individuals within their bathymetric range. Asteroid species are found to have very narrow centres of distribution in which they are abundant, despite much wider total adult depth ranges. Centres of distribution may be skewed. This might result from competition for resources or be related to the occurrence of favourable habitats at particular depths. The bathymetric distributions of the juveniles of some species extend outside the adult depth ranges. There is a distinct pattern of zonation with two major regions of faunal change and six distinct zones. An upper slope zone ranges from 150 to ˜700 m depth, an upper bathyal zone between 700 and 1100 m, a mid-bathyal zone from 1100 to1700 m and a lower bathyal zone between 1700 and 2500 m. Below 2500 m the lower continental slope and continental rise have a characteristic asteroid fauna. The abyssal zone starts at about 2800 m. Regions of major faunal change are identified at the boundaries of both upper and mid-bathyal zones and at the transition of bathyal to abyssal fauna. Diversity is greatest at ˜1800 m, decreasing with depth to ˜2600 m before increasing again to high levels at ˜4700 m.

  9. The Metal Abundances across Cosmic Time (MACT) Survey. II. Evolution of the Mass–metallicity Relation over 8 Billion Years, Using [OIII]4363AA-based Metallicities

    NASA Astrophysics Data System (ADS)

    Ly, Chun; Malkan, Matthew A.; Rigby, Jane R.; Nagao, Tohru

    2016-09-01

    We present the first results from MMT and Keck spectroscopy for a large sample of 0.1≤slant z≤slant 1 emission-line galaxies selected from our narrowband imaging in the Subaru Deep Field. We measured the weak [O iii] λ4363 emission line for 164 galaxies (66 with at least 3σ detections, and 98 with significant upper limits). The strength of this line is set by the electron temperature for the ionized gas. Because the gas temperature is regulated by the metal content, the gas-phase oxygen abundance is inversely correlated with [O iii] λ4363 line strength. Our temperature-based metallicity study is the first to span ≈ 8 Gyr of cosmic time and ≈ 3 dex in stellar mass for low-mass galaxies, {log}({M}\\star /{M}ȯ )≈ 6.0–9.0. Using extensive multi-wavelength photometry, we measure the evolution of the stellar mass–gas metallicity relation and its dependence on dust-corrected star formation rate (SFR). The latter is obtained from high signal-to-noise Balmer emission-line measurements. Our mass–metallicity relation is consistent with Andrews & Martini at z≤slant 0.3, and evolves toward lower abundances at a given stellar mass, {log}{({{O/H}})\\propto (1+z)}-{2.32-0.26+0.52}. We find that galaxies with lower metallicities have higher SFRs at a given stellar mass and redshift, although the scatter is large (≈ 0.3 dex) and the trend is weaker than seen in local studies. We also compare our mass–metallicity relation against predictions from high-resolution galaxy formation simulations, and find good agreement with models that adopt energy- and momentum-driven stellar feedback. We identified 16 extremely metal-poor galaxies with abundances of less than a tenth of solar; our most metal-poor galaxy at z≈ 0.84 is similar to I Zw 18.

  10. Influence of pregnancy in mid-to-late gestation on circulating metabolites, visceral organ mass, and abundance of proteins relating to energy metabolism in mature beef cows.

    PubMed

    Wood, K M; Awda, B J; Fitzsimmons, C; Miller, S P; McBride, B W; Swanson, K C

    2013-12-01

    In mid-to-late gestation, nutrient demand increases to meet the growth requirements of the conceptus and cows may alter metabolism in response to energy demands of pregnancy. By better understanding the metabolic role of pregnancy, there may be opportunities to better understand maintenance energy costs and improve overall feed efficiency. Eighteen mature Simmental/Angus crossbred cows, pregnant (PREG; n = 9) and nonpregnant (OPEN; n = 9), were used to investigate the effect of pregnancy on BW change, carcass traits, visceral organ mass, and circulating serum metabolites. Cows were blocked by day of expected parturition such that each block was slaughtered 4 to 5 wk before parturition. Cows were individually fed for ad libitum intake using Calan gates for 89 to 105 d. Cows were weighed, ultrasounded for rib (over the 12th and 13th rib) and rump fat, and a serum sample obtained at d 1, 56, and 3 to 5 d before slaughter. At slaughter, organs were removed, trimmed of fat, and weighed. Serum was analyzed for β-hydroxybutyrate (BHBA), NEFA, glucose, urea, total cholesterol, and triiodothyronine (T3). Tissue samples from liver, kidney, sternomandibularis muscle, ruminal papillae, pancreas, and small intestinal mucosa were collected at slaughter and snap frozen in liquid N. Western blots were conducted to quantify abundance of: proliferating cell nuclear antigen (PCNA), ATP synthase, ubiquitin, and Na(+)/K+ ATPase for all tissues; PPARγ, PPARγ coactivator 1α (PGC1-α), 5'-adenosine monophosphate-activated protein kinase (AMPK) and phosphorylated-AMPK (pAMPK) for liver, muscle, and rumen; phosphoenolpyruvate carboxykinase (PEPCK) for liver and kidney; and uncoupling protein 2 (UCP2) for liver. Data were analyzed using PROC MIXED in SAS as a replicated randomized complete block. Liver weights (actual, relative to BW, relative to HCW) were heavier (P ≤ 0.02) in OPEN. Rumen mass and kidney fat weight, both relative to BW, were also greater (P ≤ 0.04) in OPEN. On d 56

  11. The Metal Abundances across Cosmic Time (MACT) Survey. II. Evolution of the Mass-metallicity Relation over 8 Billion Years, Using [OIII]4363AA-based Metallicities

    NASA Astrophysics Data System (ADS)

    Ly, Chun; Malkan, Matthew A.; Rigby, Jane R.; Nagao, Tohru

    2016-09-01

    We present the first results from MMT and Keck spectroscopy for a large sample of 0.1≤slant z≤slant 1 emission-line galaxies selected from our narrowband imaging in the Subaru Deep Field. We measured the weak [O iii] λ4363 emission line for 164 galaxies (66 with at least 3σ detections, and 98 with significant upper limits). The strength of this line is set by the electron temperature for the ionized gas. Because the gas temperature is regulated by the metal content, the gas-phase oxygen abundance is inversely correlated with [O iii] λ4363 line strength. Our temperature-based metallicity study is the first to span ≈ 8 Gyr of cosmic time and ≈ 3 dex in stellar mass for low-mass galaxies, {log}({M}\\star /{M}⊙ )≈ 6.0-9.0. Using extensive multi-wavelength photometry, we measure the evolution of the stellar mass-gas metallicity relation and its dependence on dust-corrected star formation rate (SFR). The latter is obtained from high signal-to-noise Balmer emission-line measurements. Our mass-metallicity relation is consistent with Andrews & Martini at z≤slant 0.3, and evolves toward lower abundances at a given stellar mass, {log}{({{O/H}})\\propto (1+z)}-{2.32-0.26+0.52}. We find that galaxies with lower metallicities have higher SFRs at a given stellar mass and redshift, although the scatter is large (≈ 0.3 dex) and the trend is weaker than seen in local studies. We also compare our mass-metallicity relation against predictions from high-resolution galaxy formation simulations, and find good agreement with models that adopt energy- and momentum-driven stellar feedback. We identified 16 extremely metal-poor galaxies with abundances of less than a tenth of solar; our most metal-poor galaxy at z≈ 0.84 is similar to I Zw 18.

  12. [Variability in the relative abundance, size structure and sex ratio of the dolphinfish Coryphaena hippurus (Pisces: Coryphaenidae) in the Gulf of Tehuantepec, México].

    PubMed

    Alejo-Plata, Carmen; Gómez, José Luis; Serrano-Guzmán, Saúl J

    2014-06-01

    Variability in the relative abundance, size structure and sex ratio of the dolphinfish Coryphaena hippurus (Pisces: Coryphaenidae) in the Gulf of Tehuantepec, México. The dolphinfish (Coryphaena hippurus), is an oceanic epipelagic fish found worldwide in tropical and subtropical waters, with a high dispersal capability via large-scale migrations. This fast-swimming top-level predator is abundant in the Gulf of Tehuantepec, where it is caught incidentally by artisanal fisheries, and represents a target species for both recreational and commercial fisheries in Mexico, Ecuador, Peru and Central America. Nowadays, local fishery information on this species is scarce, thus our objective was to analyze the size structure by sex and the catch-per-unit-effort (CPUE) tendency of dolphinfish caught in the Gulf of Tehuantepec, from 2000 to 2007. For this, fishery catches information was obtained from the artisanal fleet, at six landing sites in the Gulf, and the sex ratio, fork length (FL) and the catch per unit effort (CPUE) were estimated. From all sampling sites, a total of 3 494 females, and 3 877 males were obtained, and dolphinfish size as fork length (FL) ranged from 20.5 to 152cm. Fish size ranged from 25.5 to 148cm furcal length (FL) in males, and 20.5 to 129cm FL in females. The sex ratio (males:females) was 1:1, except in April-May (1:1.5, p < 0.05) and November (1:0.5, p < 0.05). The sex ratio at different size classes showed a significant bias towards females at smaller sizes (< 75cm FL), whereas the males were predominant in larger size classes (> 100cm FL). The size structure was bimodal, with a variation in the size average; the modes were defined as the small group (FL = 50-55cm) and the large size group (FL = 100-110cm). The CPUE showed seasonal changes: values were high for the November-December period, and values were lower for July-August. The seasonal and inter annual variation in the abundance of dolphinfish is probably related to a pre

  13. Glycan Degradation (GlyDeR) Analysis Predicts Mammalian Gut Microbiota Abundance and Host Diet-Specific Adaptations

    PubMed Central

    Zarecki, Raphy; Oberhardt, Matthew; Ursell, Luke K.; Kupiec, Martin; Knight, Rob; Gophna, Uri; Ruppin, Eytan

    2014-01-01

    ABSTRACT Glycans form the primary nutritional source for microbes in the human gut, and understanding their metabolism is a critical yet understudied aspect of microbiome research. Here, we present a novel computational pipeline for modeling glycan degradation (GlyDeR) which predicts the glycan degradation potency of 10,000 reference glycans based on either genomic or metagenomic data. We first validated GlyDeR by comparing degradation profiles for genomes in the Human Microbiome Project against KEGG reaction annotations. Next, we applied GlyDeR to the analysis of human and mammalian gut microbial communities, which revealed that the glycan degradation potential of a community is strongly linked to host diet and can be used to predict diet with higher accuracy than sequence data alone. Finally, we show that a microbe’s glycan degradation potential is significantly correlated (R = 0.46) with its abundance, with even higher correlations for potential pathogens such as the class Clostridia (R = 0.76). GlyDeR therefore represents an important tool for advancing our understanding of bacterial metabolism in the gut and for the future development of more effective prebiotics for microbial community manipulation. PMID:25118239

  14. Abundances of Volatile - Bearing Species from Evolved Gas Analysis of Samples from the Rocknest Aeolian Bedform in Gale Crater

    NASA Technical Reports Server (NTRS)

    Archer, P. D., Jr.; Franc, H. B.; Sutter, B.; McAdam, A.; Ming, D. W.; Morris, R. V.; Mahaffy, P. R.

    2013-01-01

    The Sample Analysis at Mars (SAM) instrument suite on board the Mars Science Laboratory (MSL) recently ran four samples from an aeolian bedform named Rocknest. SAM detected the evolution of H2O, CO2, O2, and SO2, indicative of the presence of multiple volatile bearing species (Fig 1). The Rocknest bedform is a windblown deposit selected as representative of both the windblown material in Gale crater as well as the globally-distributed martian dust. Four samples of Rocknest material were analyzed by SAM, all from the fifth scoop taken at this location. The material delivered to SAM passed through a 150 m sieve and is assumed to have been well mixed during the sample acquisition/preparation/handoff process. SAM heated the Rocknest samples to approx.835 C at a ramp rate of 35 C/min with a He carrier gas flow rate of apprx.1.5 standard cubic centimeters per minute and at an oven pressure of 30 mbar [1]. Evolved gases were detected by a quadrupole mass spectrometer (QMS). This abstract presents the molar abundances of H2O, CO2, O2, and SO2 as well as their concentration in rocknest samples using an estimated sample mass.

  15. Actinide abundances in ordinary chondrites

    NASA Technical Reports Server (NTRS)

    Hagee, B.; Bernatowicz, T. J.; Podosek, F. A.; Johnson, M. L.; Burnett, D. S.

    1990-01-01

    Measurements of actinide and light REE (LREE) abundances and of phosphate abundances in equilibrated ordinary chondrites were obtained and were used to define the Pu abundance in the solar system and to determine the degree of variation of actinide and LREE abundances. The results were also used to compare directly the Pu/U ratio with the earlier obtained ratio determined indirectly, as (Pu/Nd)x(Nd/U), assuming that Pu behaves chemically as a LREE. The data, combined with high-accuracy isotope-dilution data from the literature, show that the degree of gram-scale variability of the Th, U, and LREE abundances for equilibrated ordinary chondrites is a factor of 2-3 for absolute abundances and up to 50 percent for relative abundances. The observed variations are interpreted as reflecting the differences in the compositions and/or proportions of solar nebula components accreted to ordinary chondrite parent bodies.

  16. Method optimization for proteomic analysis of soybean leaf: Improvements in identification of new and low-abundance proteins

    PubMed Central

    Mesquita, Rosilene Oliveira; de Almeida Soares, Eduardo; de Barros, Everaldo Gonçalves; Loureiro, Marcelo Ehlers

    2012-01-01

    The most critical step in any proteomic study is protein extraction and sample preparation. Better solubilization increases the separation and resolution of gels, allowing identification of a higher number of proteins and more accurate quantitation of differences in gene expression. Despite the existence of published results for the optimization of proteomic analyses of soybean seeds, no comparable data are available for proteomic studies of soybean leaf tissue. In this work we have tested the effects of modification of a TCA-acetone method on the resolution of 2-DE gels of leaves and roots of soybean. Better focusing was obtained when both mercaptoethanol and dithiothreitol were used in the extraction buffer simultaneously. Increasing the number of washes of TCA precipitated protein with acetone, using a final wash with 80% ethanol and using sonication to ressuspend the pellet increased the number of detected proteins as well the resolution of the 2-DE gels. Using this approach we have constructed a soybean protein map. The major group of identified proteins corresponded to genes of unknown function. The second and third most abundant groups of proteins were composed of photosynthesis and metabolism related genes. The resulting protocol improved protein solubility and gel resolution allowing the identification of 122 soybean leaf proteins, 72 of which were not detected in other published soybean leaf 2-DE gel datasets, including a transcription factor and several signaling proteins. PMID:22802721

  17. 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 analysis. Results showed that the total amount of ammonium oxidation, nitrite oxidation, denitrification, and anammox increased with the elevated dissolved oxygen levels, but the amount of ammonium release decreased inversely. The increasing DO level also raised the total amount of nitrogen loss (from 6.12 mg N to 35.44 mg N) and its proportion to ammonium liberated (from 12.96% to 99.84%), but the contributions of anammox to nitrogen loss in each incubation showed no significant difference (83.36% to 89.19%). The dissolved oxygen facilitated an exponential increasing of the anammox oxidizing archaea (AOA) and bacteria (AOB), and raised the denitrifiers (nirK and nirS gene) 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.

  18. Influence of observers and stream flow on northern two-lined salamander (Eurycea bislineata bislineata) relative abundance estimates in Acadia and Shenandoah National Parks, USA

    USGS Publications Warehouse

    Crocker, J.B.; Bank, M.S.; Loftin, C.S.; Jung Brown, R.E.

    2007-01-01

    We investigated effects of observers and stream flow on Northern Two-Lined Salamander (Eurycea bislineata bislineata) counts in streams in Acadia (ANP) and Shenandoah National Parks (SNP). We counted salamanders in 22 ANP streams during high flow (May to June 2002) and during low flow (July 2002). We also counted salamanders in SNP in nine streams during high flow (summer 2003) and 11 streams during low flow (summers 2001?02, 2004). In 2002, we used a modified cover-controlled active search method with a first and second observer. In succession, observers turned over 100 rocks along five 1-m belt transects across the streambed. The difference between observers in total salamander counts was not significant. We counted fewer E. b. bislineata during high flow conditions, confirming that detection of this species is reduced during high flow periods and that assessment of stream salamander relative abundance is likely more reliable during low or base flow conditions.

  19. Species composition and relative abundance of sand flies of the genus Lutzomyia (Diptera: Psychodidae) at an endemic focus of visceral leishmaniasis in Colombia.

    PubMed

    Ferro, C; Morrison, A C; Torres, M; Pardo, R; Wilson, M L; Tesh, R B

    1995-07-01

    Ecological studies on the sand fly Lutzomyia longipalpis (Lutz & Neiva) were conducted during 1990-1993 at a small rural community in Colombia where American visceral leishmaniasis is endemic. Weekly sand fly collections were made from pigpens, houses, and natural resting sites, using hand-held aspirators, sticky (oiled) paper traps, and opossum-baited Disney traps. In total, 263,094 sand flies were collected; L. longipalpis predominated (86.1%), followed by L. trinidadensis (11.0%), L. cayennensis (2.7%), and 8 other Lutzomyia species. The species composition and sex ratio of these sand flies varied among sites and by collection method. L. longipalpis were captured most efficiently by direct aspiration from animal bait. Conversely, sticky paper traps, especially inside houses and at rock resting sites, collected a greater diversity of species, but a lower relative abundance of L. longipalpis.

  20. Spatial variation in abundance, size and orientation of juvenile corals related to the biomass of parrotfishes on the Great Barrier Reef, Australia.

    PubMed

    Trapon, Melanie L; Pratchett, Morgan S; Hoey, Andrew S

    2013-01-01

    For species with complex life histories such as scleractinian corals, processes occurring early in life can greatly influence the number of individuals entering the adult population. A plethora of studies have examined settlement patterns of coral larvae, mostly on artificial substrata, and the composition of adult corals across multiple spatial and temporal scales. However, relatively few studies have examined the spatial distribution of small (≤50 mm diameter) sexually immature corals on natural reef substrata. We, therefore, quantified the variation in the abundance, composition and size of juvenile corals (≤50 mm diameter) among 27 sites, nine reefs, and three latitudes spanning over 1000 km on Australia's Great Barrier Reef. Overall, 2801 juveniles were recorded with a mean density of 6.9 (±0.3 SE) ind.m(-2), with Acropora, Pocillopora, and Porites accounting for 84.1% of all juvenile corals surveyed. Size-class structure, orientation on the substrate and taxonomic composition of juvenile corals varied significantly among latitudinal sectors. The abundance of juvenile corals varied both within (6-13 ind.m(-2)) and among reefs (2.8-11.1 ind.m(-2)) but was fairly similar among latitudes (6.1-8.2 ind.m(-2)), despite marked latitudinal variation in larval supply and settlement rates previously found at this scale. Furthermore, the density of juvenile corals was negatively correlated with the biomass of scraping and excavating parrotfishes across all sites, revealing a potentially important role of parrotfishes in determining distribution patterns of juvenile corals on the Great Barrier Reef. While numerous studies have advocated the importance of parrotfishes for clearing space on the substrate to facilitate coral settlement, our results suggest that at high biomass they may have a detrimental effect on juvenile coral assemblages. There is, however, a clear need to directly quantify rates of mortality and growth of juvenile corals to understand the relative

  1. Stink bug species composition and relative abundance of the redbanded stink bug (Hemiptera: Pentatomidae) in soybean in the upper gulf coast Texas.

    PubMed

    Vyavhare, Suhas S; Way, Michael O; Medina, Raul F

    2014-12-01

    Stink bugs are the primary arthropod soybean pests in the southern United States. Historically, important stink bug species damaging soybeans in the southern United States included the southern green stink bug Nezara viridula (L.), the green stink bug Chinavia hilaris (Say), and the brown stink bug Euschistus servus (Say) (Hemiptera: Pentatomidae). The redbanded stink bug, Piezodorus guildinii (Westwood), has recently become an economic pest of soybean in the southern region of the United States, especially in Louisiana and Texas. Little is known about current stink bug species composition and relative abundance in Texan soybean agro-ecosystems. To fill this gap, commercial soybean fields in the Upper Gulf Coast of Texas were sampled weekly during the growing season using a sweep net throughout R2 (full flowering) to R7 (beginning maturity) from 2011 to 2013. Adults and nymphs (third, fourth, and fifth instars) of redbanded stink bug, southern green stink bug, green stink bug, and brown stink bug were counted per 25 sweeps. The relative abundance of redbanded stink bug was significantly higher than any other stink bug species throughout 2011-2013. Over 65% of the total population of major stink bugs collected during this period were redbanded stink bugs and ≍19% were southern green stink bugs. The highest redbanded stink bug densities and the highest ratio of redbanded stink bug nymphs to adults were recorded at R7. Results from this study show that redbanded stink bug has become the predominant stink bug species in soybean in the Upper Gulf Coast of Texas. PMID:25290375

  2. Stink bug species composition and relative abundance of the redbanded stink bug (Hemiptera: Pentatomidae) in soybean in the upper gulf coast Texas.

    PubMed

    Vyavhare, Suhas S; Way, Michael O; Medina, Raul F

    2014-12-01

    Stink bugs are the primary arthropod soybean pests in the southern United States. Historically, important stink bug species damaging soybeans in the southern United States included the southern green stink bug Nezara viridula (L.), the green stink bug Chinavia hilaris (Say), and the brown stink bug Euschistus servus (Say) (Hemiptera: Pentatomidae). The redbanded stink bug, Piezodorus guildinii (Westwood), has recently become an economic pest of soybean in the southern region of the United States, especially in Louisiana and Texas. Little is known about current stink bug species composition and relative abundance in Texan soybean agro-ecosystems. To fill this gap, commercial soybean fields in the Upper Gulf Coast of Texas were sampled weekly during the growing season using a sweep net throughout R2 (full flowering) to R7 (beginning maturity) from 2011 to 2013. Adults and nymphs (third, fourth, and fifth instars) of redbanded stink bug, southern green stink bug, green stink bug, and brown stink bug were counted per 25 sweeps. The relative abundance of redbanded stink bug was significantly higher than any other stink bug species throughout 2011-2013. Over 65% of the total population of major stink bugs collected during this period were redbanded stink bugs and ≍19% were southern green stink bugs. The highest redbanded stink bug densities and the highest ratio of redbanded stink bug nymphs to adults were recorded at R7. Results from this study show that redbanded stink bug has become the predominant stink bug species in soybean in the Upper Gulf Coast of Texas.

  3. Relative abundance, site fidelity, and survival of adult lake trout in Lake Michigan from 1999 to 2001: Implications for future restoration strategies

    USGS Publications Warehouse

    Bronte, C.R.; Holey, M.E.; Madenjian, C.P.; Jonas, J.L.; Claramunt, R.M.; McKee, P.C.; Toneys, M.L.; Ebener, M.P.; Breidert, B.; Fleischer, G.W.; Hess, R.; Martell, A.W.; Olsen, E.J.

    2007-01-01

    We compared the relative abundance of lake trout Salvelinus namaycush spawners in gill nets during fall 1999–2001 in Lake Michigan at 19 stocked spawning sites with that at 25 unstocked sites to evaluate how effective site-specific stocking was in recolonizing historically important spawning reefs. The abundance of adult fish was higher at stocked onshore and offshore sites than at unstocked sites. This suggests that site-specific stocking is more effective at establishing spawning aggregations than relying on the ability of hatchery-reared lake trout to find spawning reefs, especially those offshore. Spawner densities were generally too low and too young at most sites to expect significant natural reproduction. However, densities were sufficiently high at some sites for reproduction to occur and therefore the lack of recruitment was attributable to other factors. Less than 3% of all spawners could have been wild fish, which indicates that little natural reproduction occurred in past years. Wounding by sea lamprey Petromyzon marinus was generally lower for Seneca Lake strain fish and highest for strains from Lake Superior. Fish captured at offshore sites in southern Lake Michigan had the lowest probability of wounding, while fish at onshore sites in northern Lake Michigan had the highest probability. The relative survival of the Seneca Lake strain was higher than that of the Lewis Lake or the Marquette strains for the older year-classes examined. Survival differences among strains were less evident for younger year-classes. Recaptures of coded-wire-tagged fish of five strains indicated that most fish returned to their stocking site or to a nearby site and that dispersal from stocking sites during spawning was about 100 km. Restoration strategies should rely on site-specific stocking of lake trout strains with good survival at selected historically important offshore spawning sites to increase egg deposition and the probability of natural reproduction in Lake

  4. Applications of gray relational analysis in gastroenterology

    PubMed Central

    Tan, Xue-Rui; Li, Yu-Guang; Chen, Ming-Zhe

    2005-01-01

    AIM: To introduce the basic methods of gray relational analysis (GRA) and to illustrate its applications in gastroenterology. METHODS: With the essential formulae of GRA and several typically practical examples, the procedure of GRA was introduced. Examples were drawn from the gastroenterological studies. Thus the trait of GRA could be demonstrated. RESULTS: The superiority of GRA in gastroenterological study was proved by the examples. CONCLUSION: GRA can be applied mechanically or flexibly in gastroenterology. PMID:15948254

  5. Dietary sunflower oil modulates milk fatty acid composition without major changes in adipose and mammary tissue fatty acid profile or related gene mRNA abundance in sheep.

    PubMed

    Castro-Carrera, T; Frutos, P; Leroux, C; Chilliard, Y; Hervás, G; Belenguer, A; Bernard, L; Toral, P G

    2015-04-01

    There are very few studies in ruminants characterizing mammary and adipose tissue (AT) expression of genes and gene networks for diets causing variations in milk fatty acid (FA) composition without altering milk fat secretion, and even less complementing this information with data on tissue FA profiles. This work was conducted in sheep in order to investigate the response of the mammary gland and the subcutaneous and perirenal AT, in terms of FA profile and mRNA abundance of genes involved in lipid metabolism, to a diet known to modify milk FA composition. Ten lactating Assaf ewes were randomly assigned to two treatments consisting of a total mixed ration based on alfalfa hay and a concentrate (60 : 40) supplemented with 0 (control diet) or 25 (SO diet) g of sunflower oil/kg of diet dry matter for 7 weeks. Milk composition, including FA profile, was analysed after 48 days on treatments. On day 49, the animals were euthanized and tissue samples were collected to analyse FA and mRNA abundance of 16 candidate genes. Feeding SO did not affect animal performance but modified milk FA composition. Major changes included decreases in the concentration of FA derived from de novo synthesis (e.g. 12:0, 14:0 and 16:0) and increases in that of long-chain FA (e.g. 18:0, c9-18:1, trans-18:1 isomers and c9,t11-CLA); however, they were not accompanied by significant variations in the mRNA abundance of the studied lipogenic genes (i.e. ACACA, FASN, LPL, CD36, FABP3, SCD1 and SCD5) and transcription factors (SREBF1 and PPARG), or in the constituent FA of mammary tissue. Regarding the FA composition of AT, the little influence of SO did not appear to be linked to changes in gene mRNA abundance (decreases of GPAM and SREBF1 in both tissues, and of PPARG in the subcutaneous depot). Similarly, the great variation between AT (higher contents of saturated FA and trans-18:1 isomers in the perirenal, and of cis-18:1, c9,t11-CLA and n-3 PUFA in the subcutaneous AT) could not be related to

  6. Multiscale Abundance and Size Distribution of Inclusions in the Allende CV3 Meteorite by X-Ray Image Analysis of Slabs

    NASA Astrophysics Data System (ADS)

    Ebel, D. S.; Brunner, C. E.; Weisberg, M. K.

    2008-03-01

    Analysis of combined X-ray (CMAS + Fe) and BSE maps of Allende slabs (13 µm/pxl) and sections (4-5 µm/pxl) (>19 mm2) yield higher matrix and AOA, lower CAI abundances than McSween (1977). Size distributions of chondrules and CAIs are similar.

  7. [Diversity, relative abundance and activity patterns of medium and large mammals in a tropical deciduous forest in the Isthmus of Tehuantepec, Oaxaca, Mexico].

    PubMed

    Cortés-Marcial, Malinalli; Briones-Salas, Miguel

    2014-12-01

    The use of camera traps and mammal track search are complementary methods to monitoring species of which is not well documented their natural history, as in the case of medium and large mammals. To ensure its conservation and good management, it is necessary to generate information about the structure of the community and their populations. The objective of the present study was to estimate the diversity, relative abundance and activity patterns of medium and large mammals in a tropical deciduous forest located in the Isthmus of Tehuantepec, Oaxaca, Mexico. Samplings were conducted in three month intervals, from September 2011 to May 2013. We used photographic-sampling and track search, two complementary sampling methods. For photographic-sampling, 12 camera traps were placed covering an area of 60 km2, while for the tracks search a monthly tour of four line-transect surveys of three kilometers length each was undertaken. We obtained a total of 344 pictures with 5292 trap-days total sampling effort; in addition, 187 track records in a total of 144 km. With both methods we registered 21 species of mammals, in 13 families and seven orders, and five species resulted in new records to the area. The diversity index of Shannon-Wiener obtained with the method of tracks was H' = 2.41, while the most abundant species were Urocyon cinereoargen- teus (IAR = 0.23) and Pecari tajacu (IAR = 0.20). By the method of trap the most abundant species were P. tajacu (IAR = 2.62) and Nasua narica (IAR = 1.28). In terms of patterns of activity P. tajacu, N. narica and Odocoileus virginianus were primarily diurnal species; Canis latrans and Leopardus pardalis did not show preference for any schedule in particular, and Didelphis virginiana and Dasypus novemcinctus preferred to have nocturnal activity. This information can be of help to the creation of programs of management and conservation of mam- mals of medium and large in the Isthmus of Tehuantepec, Oaxaca, México.

  8. Abundance estimation and conservation biology

    USGS Publications Warehouse

    Nichols, J.D.; MacKenzie, D.I.

    2004-01-01

    should be focused on relationships between demographic processes such as survival and recruitment, the two quantities responsible for changes in abundance, rather than simply on the magnitudes of these quantities. They describe a type of Jolly–Seber capture–recapture model that permits inference about the underlying relationship between per capita recruitment rates and survival rates (Link & Barker, this volume). Implementation used Bayesian Markov Chain Monte Carlo methods and appeared to work well, yielding inferences about the relationship between recruitment and survival that were robust to selection of prior distribution. We believe that readers will find their arguments compelling, and we expect to see increased use of hierarchical modeling approaches in capture–recapture and related fields. Otto (presentation without paper) also recommended use of hierarchical models in analysis of multiple data sources dealing with population dynamics of North American mallards. He integrated survival inferences from ringing data, abundance information from aerial survey data, and recruitment information based on age ratios from a harvest survey. He used a Leslie matrix population projection model as an integrating framework and obtained estimates of breeding population size using all data.Otto’s approach also permitted inference about biases in estimated quantities. As with the work of Link & Barker (2004), we find Otto’s recommendation to use hierarchical models to integrate data from multiple sources to be very compelling. Alisauskas et al. (2004) report results of an analysis of capture–recapture data for a askatchewan population of white–winged scoters. They used the approach of Pradel (1996) to estimate population growth rate (See the PDF) directly. Estimates for 1975–1985 were quite low, but estimates for the recent period, 2000–2003,increased to values > 1. Parameter estimates for seniority, survival and per capita recruitment (Pradel, 1996) led to the

  9. Diet of juvenile lake trout in southern Lake Ontario in relation to abundance and size of prey fishes, 1979-1987

    USGS Publications Warehouse

    Elrod, Joseph H.; O'Gorman, Robert

    1991-01-01

    We examined the diet of juvenile lake trout Salvelinus namaycush (<450 mm, total length) in Lake Ontario during four sampling periods (April–May, June, July–August, and October 1979–1987) in relation to changes in prey fish abundance in the depth zone where we caught the lake trout. Over all years combined, slimy sculpins Cottus cognatus contributed the most (39–52%) by wet weight to the diet, followed by alewives Alosa pseudoharengus(3–38%), rainbow smelt Osmerus mordax (17–43%), and johnny darters Etheostoma nigrum(2–10%). Over 90% of alewives eaten during April–May and June were age 1, and 98% of those eaten during October were age 0 (few alewives were eaten in July–August). Mean lengths of rainbow smelt and slimy sculpins in stomachs increased with size of lake trout. Juvenile lake trout generally fed opportunistically—seasonal and annual changes in diet usually reflected seasonal and annual changes in abundance of prey fishes near bottom where we captured the lake trout. Furthermore, diet within a given season varied with depth of capture of lake trout, and changes with depth in proportions of prey species in lake trout stomachs mirrored changes in proportions of the prey species in trawl catches at the same depth. Alewives (ages 0 and 1) were the only prey fish eaten in substantial quantities by both juvenile lake trout and other salmonines, and thus are a potential focus of competition between these predators.

  10. Douglas-fir forests in the Cascade Mountains of Oregon and Washington: is the abundance of small mammals related to stand age and moisture?

    USGS Publications Warehouse

    Coen, P.S.; Bury, R.B.; Spies, T.A.

    1988-01-01

    Red tree voles (Arborimus longicaudus) were the only small mammal strongly associated with old-growth forests, whereas vagrant shrews (Sorex vagrans) were most abundant in young forests. Pacific marsh shrews (S. bendirii) were most abundant in wet old-growth forests, but abundance of this species in young (wet) forests needs further study. Clearcuts had a mammalian fauna distinct from young forest stands. Abundance of several species was correlated to habitat features unique to naturally regenerated forests, indicated an urgent need to study the long-term effects of forest management to nongame wildlife.

  11. Abundance, behavior, and movement patterns of western gray whales in relation to a 3-D seismic survey, Northeast Sakhalin Island, Russia.

    PubMed

    Gailey, Glenn; Würsig, Bernd; McDonald, Trent L

    2007-11-01

    A geophysical seismic survey was conducted in the summer of 2001 off the northeastern coast of Sakhalin Island, Russia. The area of seismic exploration was immediately adjacent to the Piltun feeding grounds of the endangered western gray whale (Eschrichtius robustus). This study investigates relative abundance, behavior, and movement patterns of gray whales in relation to occurrence and proximity to the seismic survey by employing scan sampling, focal follow, and theodolite tracking methodologies. These data were analyzed in relation to temporal, environmental, and seismic related variables to evaluate potential disturbance reactions of gray whales to the seismic survey. The relative numbers of whales and pods recorded from five shore-based stations were not significantly different during periods when seismic surveys were occurring compared to periods when no seismic surveys were occurring and to the post-seismic period. Univariate analyses indicated no significant statistical correlation between seismic survey variables and any of the eleven movement and behavior variables. Multiple regression analyses indicated that, after accounting for temporal and environmental variables, 6 of 11 movement and behavior variables (linearity, acceleration, mean direction, blows per surfacing, and surface-dive blow rate) were not significantly associated with seismic survey variables, and 5 of 11 variables (leg speed, reorientation rate, distance-from-shore, blow interval, and dive time) were significantly associated with seismic survey variables. In summary, after accounting for environmental variables, no correlation was found between seismic survey variables and the linearity of whale movements, changes in whale swimming speed between theodolite fixes, mean direction of whale movement, mean number of whale exhalations per minute at the surface, mean time at the surface, and mean number of exhalations per minute during a whales surface-to-dive cycle. In contrast, at higher

  12. Identifying related journals through log analysis

    PubMed Central

    Lu, Zhiyong; Xie, Natalie; Wilbur, W. John

    2009-01-01

    Motivation: With the explosion of biomedical literature and the evolution of online and open access, scientists are reading more articles from a wider variety of journals. Thus, the list of core journals relevant to their research may be less obvious and may often change over time. To help researchers quickly identify appropriate journals to read and publish in, we developed a web application for finding related journals based on the analysis of PubMed log data. Availability: http://www.ncbi.nlm.nih.gov/IRET/Journals Contact: luzh@ncbi.nlm.nih.gov Supplementary information: Supplementary data are available at Bioinformatics online. PMID:19734155

  13. ABUNDANCE OF SEAGRASS (ZOSTERA MARINA L.) AND MACROALGAE IN RELATION TO THE SALINITY-TEMPERATURE GRADIENT IN YAQUINA BAY, OREGON, USA

    EPA Science Inventory

    The distribution and abundance of the seagrass, Zostera marina, and the associated macroalgae are described for Yaquina Bay, Oregon, U.S.A. Possible relationships between plant abundance and physical-chemical characteristics of the water column were also explored. Study sites w...

  14. Species richness and relative species abundance of Nymphalidae (Lepidoptera) in three forests with different perturbations in the North-Central Caribbean of Costa Rica.

    PubMed

    Stephen, Carolyn; Sánchez, Ragde

    2014-09-01

    Measurements of species richness and species abundance can have important implications for regulations and conservation. This study investigated species richness and abundance of butterflies in the family Nymphalidae at undisturbed, and disturbed habitats in Tirimbina Biological Reserve and Nogal Private Reserve, Sarapiquí, Costa Rica. Traps baited with rotten banana were placed in the canopy and the understory of three habitats: within mature forest, at a river/forest border, and at a banana plantation/forest border. In total, 71 species and 487 individuals were caught and identified during May and June 2011 and May 2013. Species richness and species abundance were found to increase significantly at perturbed habitats (p < 0.0001, p < 0.0001, respectively). The edge effect, in which species richness and abundance increase due to greater complementary resources from different habitats, could be one possible explanation for increased species richness and abundance. PMID:25412524

  15. Evaluation of strontium isotope abundance ratios in combination with multi-elemental analysis as a possible tool to study the geographical origin of ciders.

    PubMed

    García-Ruiz, Silvia; Moldovan, Mariella; Fortunato, Giuseppino; Wunderli, Samuel; García Alonso, J Ignacio

    2007-05-01

    In order to evaluate alternative analytical methodologies to study the geographical origin of ciders, both multi-elemental analysis and Sr isotope abundance ratios in combination with multivariate statistical analysis were estimated in 67 samples from England, Switzerland, France and two Spanish regions (Asturias and the Basque Country). A methodology for the precise and accurate determination of the (87)Sr/(86)Sr isotope abundance ratio in ciders by multicollector inductively coupled plasma mass spectrometry (MC-ICP-MS) was developed. Major elements (Na, K, Ca and Mg) were measured by ICP-AES and minor and trace elements (Li, Be, B, Al, Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Ga, As, Se, Rb, Sr, Y, Mo, Cd, Sn, Sb, Cs, Ba, La, Ce, W, Tl, Pb, Bi, Th and U) were measured by ICP-MS using a collision cell instrument operated in multitune mode. An analysis of variance (ANOVA test) indicated that group means for B, Cr, Fe, Ni, Cu, Se, Cd, Cs, Ce, W, Pb, Bi and U did not show any significant differences at the 95% confidence level, so these elements were rejected for further statistical analysis. Another group of elements (Li, Be, Sc, Co, Ga, Y, Sn, Sb, La, Tl, Th) was removed from the data set because concentrations were close to the limits of detection for many samples. Therefore, the remaining elements (Na, Mg, Al, K, Ca, Ti, V, Mn, Zn, As, Rb, Sr, Mo, Ba) together with (87)Sr/(86)Sr isotope abundance ratio were considered for principal component analysis (PCA) and linear discriminant analysis (LDA). Finally, LDA was able to classify correctly 100% of cider samples coming from different Spanish regions, France, England and Switzerland when considering Na, Mg, Al, K, Ca, Ti, V, Mn, Zn, As, Rb, Sr, Mo, Ba and (87)Sr/(86)Sr isotope abundance ratio as original variables. PMID:17416223

  16. ANALYSIS OF TWO SMALL MAGELLANIC CLOUD H II REGIONS CONSIDERING THERMAL INHOMOGENEITIES: IMPLICATIONS FOR THE DETERMINATIONS OF EXTRAGALACTIC CHEMICAL ABUNDANCES

    SciTech Connect

    Pena-Guerrero, Maria A.; Peimbert, Antonio; Peimbert, Manuel; Ruiz, Maria Teresa E-mail: antonio@astroscu.unam.mx E-mail: mtruiz@das.uchile.cl

    2012-02-20

    We present long-slit spectrophotometry considering the presence of thermal inhomogeneities (t{sup 2}) of two H II regions in the Small Magellanic Cloud (SMC): NGC 456 and NGC 460. Physical conditions and chemical abundances were determined for three positions in NGC 456 and one position in NGC 460, first under the assumption of uniform temperature and then allowing for the possibility of thermal inhomogeneities. We determined t{sup 2} values based on three different methods: (1) by comparing the temperature derived using oxygen forbidden lines with the temperature derived using helium recombination lines (RLs), (2) by comparing the abundances derived from oxygen forbidden lines with those derived from oxygen RLs, and (3) by comparing the abundances derived from ultraviolet carbon forbidden lines with those derived from optical carbon RLs. The first two methods averaged t{sup 2} = 0.067 {+-} 0.013 for NGC 456 and t{sup 2} = 0.036 {+-} 0.027 for NGC 460. These values of t{sup 2} imply that when gaseous abundances are determined with collisionally excited lines they are underestimated by a factor of nearly two. From these objects and others in the literature, we find that in order to account for thermal inhomogeneities and dust depletion, the O/H ratio in low-metallicity H II regions should be corrected by 0.25-0.45 dex depending on the thermal structure of the nebula or by 0.35 dex if such information is not available.

  17. Increase of marine juvenile fish abundances in the middle Gironde estuary related to warmer and more saline waters, due to global changes

    NASA Astrophysics Data System (ADS)

    Pasquaud, Stéphanie; Béguer, Mélanie; Larsen, Maja Hjort; Chaalali, Aurélie; Cabral, Henrique; Lobry, Jérémy

    2012-06-01

    Estuaries have an essential ecological function for several marine fish species, that use these systems as nurseries. Previous studies in the Gironde estuary have reported an increase in water temperature and an extended seawater intrusion associated to global changes. In this study, we evaluated whether these changes impact the nursery function in the middle part of the system, based on the analyses of long-term data series (1991-2009) collected in that area. Trend analysis, correlations and generalized additive models (GAM) were computed in order to study the influence of water temperature and salinity changes on marine juveniles occurrence/densities. Results showed that densities of all the studied species (i.e. Engraulis encrasicolus, Sprattus sprattus, Dicentrarchus labrax, Solea solea, Argyrosomus regius, Merlangius merlangus) significantly increased over the period considered. Changes in water temperature and seawater intrusion contributed to explain the variability in presence/absence and in densities of the majority of these species. However, the deviance explained by GAM and the relevance of these two explanatory variables differed considerably according to species. For most species, it was suggested that the interaction of these two factors, and their effects on other variables, may explain the increase in abundance in the middle part of the Gironde. The effects of global changes in this estuarine system may favour its nursery function for marine juveniles, but some evidence of effects at a wider scale (community and ecosystem levels) may alter the structure and functioning of this system.

  18. Relative abundances of sub-iron to iron nuclei in low energy (50-250 MeV/N) cosmic rays as observed in the Skylab experiment

    NASA Technical Reports Server (NTRS)

    Durgaprasad, N.; Yadav, J. S.; Biswas, S.

    1985-01-01

    A Lexan polycarbonate detector exposed on the exterior of Skylab-3 for 73 days during a solar quiet period was used to study the relative abundances of calcium to nickel ions in low energy cosmic rays of 50 to 250 MeV/N. The method of charge identification is based on the measurement of conelength (L) and residual range (R) of these particles in various Lexan sheets. Since more than one cone (sometimes as many as five) is observed and is measured, the charge accuracy becomes precise and accurate. The ratio of (calcium to manganese) to (iron and cobalt) obtained at three energy intervals of 50 to 80, 80 to 150, 150 to 250 and 50 to 250 MeV/N are 7.6 plus or minus 3.8, 2.7 plus or minus 0.8, 1.4 plus or minus 0.6 and 3.3 plus or minus 0.7 respectively. These data thus indicate a large increase of this ratio with decreasing energy. The origin of this strong energy dependence is not understood at present.

  19. Spatio-temporal variation in small mammal species richness, relative abundance and body mass reveal changes in a coastal wetland ecosystem in Ghana.

    PubMed

    Ofori, Benjamin Y; Attuquayefio, Daniel K; Owusu, Erasmus H; Musah, Yahaya; Ntiamoa-Baidu, Yaa

    2016-06-01

    Coastal wetlands in Ghana are under severe threat of anthropogenic drivers of habitat degradation and climate change, thereby increasing the need for assessment and monitoring to inform targeted and effective conservation of these ecosystems. Here, we assess small mammal species richness, relative abundance and body mass in three habitats at the Muni-Pomadze Ramsar site of Ghana, and compare these to baseline data gathered in 1997 to evaluate changes in the wetland ecosystem. Small mammals were live-trapped using Sherman collapsible and pitfall traps. We recorded 84 individuals of 10 species in 1485 trap-nights, whereas the baseline study recorded 45 individuals of seven species in 986 trap-nights. The overall trap-success was therefore greater in the present study (5.66 %) than the baseline study (4.56 %). The species richness increased from one to four in the forest, and from zero to eight in the thicket, but decreased from six to four in the grassland. The total number of individuals increased in all habitats, with the dominant species in the grassland shifting from Lemniscomys striatus to Mastomys erythroleucus. Three species, Malacomys edwardsi, Grammomys poensis and Praomys tullbergi are the first records for the Muni-Pomadze Ramsar site. Generally, the average body mass of individual species in the grassland was lower in the present study. The considerable changes in small mammal community structure suggest changes in the wetland ecosystem. The conservation implications of our findings are discussed. PMID:27154051

  20. Evaluation of relative isotopic abundance measurements in a quadrupole time-of-flight mass spectrometer for elemental composition determination of natural products in traditional Chinese medicine.

    PubMed

    Wu, Zhi-Jun; Huo, Jia-Li; Chen, Jian-Zhong; Li, Na; Fang, Dong-Mei; Chen, Xiao-Zhen; Zhang, Guo-Lin; Wang, Jian-Hua; Xu, Xiao-Ying

    2013-01-01

    The relative isotopic abundance (RIA) measurement errors of a quadrupole time-of-flight (Q-ToF) instrument incorporating analog-to-digital converter detectors were systemically evaluated by stochastically collecting about 200 data in positive ion mass spectrometry (MS) mode. Errors varied with peak intensities at definite spectral acquisition rates but were very close, even if peak intensities changed sharply at different spectral acquisition rates with the same concentration. Intensity thresholds were systematically defined at 1 Hz of spectral acquisition rates. RIA measurement errors were also evaluated using peak area. It seemed that peak area was better adapted for the high-intensity ions while peak intensity was suited for very low-intensity ions. Several known compounds were selected for RIA measurements for product ions in tandem mass spectropmetry (MS/MS) mode. An extract of a representative traditional Chinese medicinal, Paederia scandens was analyzed with high-performance liquid chromatography-electrospray ionization-QToF-MS/MS. The unique elemental compositions of some compounds could not be identified even with exact masses and MS/MS spectra of measured and reference compounds. RIA errors, especially of (M+2)M(-1), provided vital information for determining the elemental composition. PMID:24261081

  1. Evaluation of relative isotopic abundance measurements in a quadrupole time-of-flight mass spectrometer for elemental composition determination of natural products in traditional Chinese medicine.

    PubMed

    Wu, Zhi-Jun; Huo, Jia-Li; Chen, Jian-Zhong; Li, Na; Fang, Dong-Mei; Chen, Xiao-Zhen; Zhang, Guo-Lin; Wang, Jian-Hua; Xu, Xiao-Ying

    2013-01-01

    The relative isotopic abundance (RIA) measurement errors of a quadrupole time-of-flight (Q-ToF) instrument incorporating analog-to-digital converter detectors were systemically evaluated by stochastically collecting about 200 data in positive ion mass spectrometry (MS) mode. Errors varied with peak intensities at definite spectral acquisition rates but were very close, even if peak intensities changed sharply at different spectral acquisition rates with the same concentration. Intensity thresholds were systematically defined at 1 Hz of spectral acquisition rates. RIA measurement errors were also evaluated using peak area. It seemed that peak area was better adapted for the high-intensity ions while peak intensity was suited for very low-intensity ions. Several known compounds were selected for RIA measurements for product ions in tandem mass spectropmetry (MS/MS) mode. An extract of a representative traditional Chinese medicinal, Paederia scandens was analyzed with high-performance liquid chromatography-electrospray ionization-QToF-MS/MS. The unique elemental compositions of some compounds could not be identified even with exact masses and MS/MS spectra of measured and reference compounds. RIA errors, especially of (M+2)M(-1), provided vital information for determining the elemental composition.

  2. Spatio-temporal variation in small mammal species richness, relative abundance and body mass reveal changes in a coastal wetland ecosystem in Ghana.

    PubMed

    Ofori, Benjamin Y; Attuquayefio, Daniel K; Owusu, Erasmus H; Musah, Yahaya; Ntiamoa-Baidu, Yaa

    2016-06-01

    Coastal wetlands in Ghana are under severe threat of anthropogenic drivers of habitat degradation and climate change, thereby increasing the need for assessment and monitoring to inform targeted and effective conservation of these ecosystems. Here, we assess small mammal species richness, relative abundance and body mass in three habitats at the Muni-Pomadze Ramsar site of Ghana, and compare these to baseline data gathered in 1997 to evaluate changes in the wetland ecosystem. Small mammals were live-trapped using Sherman collapsible and pitfall traps. We recorded 84 individuals of 10 species in 1485 trap-nights, whereas the baseline study recorded 45 individuals of seven species in 986 trap-nights. The overall trap-success was therefore greater in the present study (5.66 %) than the baseline study (4.56 %). The species richness increased from one to four in the forest, and from zero to eight in the thicket, but decreased from six to four in the grassland. The total number of individuals increased in all habitats, with the dominant species in the grassland shifting from Lemniscomys striatus to Mastomys erythroleucus. Three species, Malacomys edwardsi, Grammomys poensis and Praomys tullbergi are the first records for the Muni-Pomadze Ramsar site. Generally, the average body mass of individual species in the grassland was lower in the present study. The considerable changes in small mammal community structure suggest changes in the wetland ecosystem. The conservation implications of our findings are discussed.

  3. 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.

  4. AUTOMATED DECONVOLUTION OF COMPOSITE MASS SPECTRA OBTAINED WITH AN OPEN-AIR IONIZATIONS SOURCE BASED ON EXACT MASSES AND RELATIVE ISOTIPIC ABUNDANCES

    EPA Science Inventory

    Chemicals dispersed by accidental, deliberate, or weather-related events must be rapidly identified to assess health risks. Mass spectra from high levels of analytes obtained using rapid, open-air ionization by a Direct Analysis in Real Time (DART®) ion source often contain

  5. The Abundance of Interstellar Fluorine

    NASA Technical Reports Server (NTRS)

    Lauroesch, James T.

    2005-01-01

    The primary objective of this program was to obtain FUSE observations of the interstellar absorption lines of F I at 951 and 954 Angstroms to derive the abundance of fluorine toward the star HD 164816. The nucleosynthetic source(s) of fluorine are still a matter of debate - the present day abundance of fluorine can potentially constrain models for pulsationally driven dredge-up in asymptotic giant branch stars. An accurate measure for the depletion behavior of fluorine will determine whether it may be detectable in QSO absorption line systems - an unambiguous detection of fluorine at suitably high redshifts would provide the best evidence to date for the neutrino process in massive stars. Furthermore, due to its extreme reactivity, measurement of the gas-phase interstellar fluorine abundance is important for models of grain chemistry. Despite the importance of measuring the interstellar fluorine abundance, at the time of our proposal only one previous detection has been made due to the low relative abundance of fluorine, the lack of lines outside the far-UV, and the blending of the available F I transitions with lines of Hz. The star HD 164816 is associated with the Lagoon nebula (M8), and at a distance of approximately 1.5 kpc probes both distant and local gas. Beginning April 8th, 2004 FUSE FP-Split observations of the star HD 164816 were obtained for this program. This data became available in the FUSE data archive May 21, 2004, and these observations were then downloaded and we began our analysis. Our analysis procedure has involved (1) fitting stellar models to the FUSE spectra, (2) using the multiple lines of Hz and N I at other wavelengths in the FUSE bandpass to derive column densities for the lines of H2 and N I which are blended with the F I features at 951 and 954 angstroms (3) the measurement of the column densities of F I and the species O I and C1 I which are important species for the dis-entangling of dust and nucleosynthetic effects. As discussed in

  6. Distribution, abundance, biomass and diversity of benthic infauna in the Northeast Chukchi Sea, Alaska: Relation to environmental variables and marine mammals

    NASA Astrophysics Data System (ADS)

    Schonberg, Susan V.; Clarke, Janet T.; Dunton, Kenneth H.

    2014-04-01

    In summer 2009 and 2010, as part of Chukchi Sea Offshore Monitoring in Drilling Area - Chemical and Benthos (COMIDA CAB) program, we performed a quantitative assessment of the biomass, abundance, and community structure of benthic infaunal populations of the Northeastern Chukchi Sea. This analysis documented a benthic species inventory of 361 taxa collected from 142 individual van Veen grab samples (0.1 m-2) at 52 stations. Infaunal abundance was dominated by Polychaeta, Mollusca, and Crustacea. Large concentrations of bivalves (up to 1235 m-2; 920.2 gww m-2) were collected south of Hanna Shoal where flow from two water masses converge and deposit labile carbon to the seafloor, as indicated by low surface sediment C:N ratios. Amphipods (up to 1640 m-2; 26.0 gww m-2), and polychaetes (up to 4665 m-2; 114.7 gww m-2) were documented from multiple stations west of and within Barrow Canyon. This high productivity was most likely due to the "canyon effect", where marine and coastal detrital carbon supplies are channeled by the canyon structure, enhancing carbon deposition and flux, which supports rich benthic communities within the canyon and surrounding areas. To examine the relationships between infaunal distributions of all collected taxa with the physical environment, we used a Biota and Environment matching (BIO-ENV) routine. A combination of water depth, bottom-water temperature and salinity, surface sediment total organic nitrogen (TON) and sediment C:N molar ratios correlated closest with infaunal abundance distribution (ρ=0.54), indicating that multiple factors influence the success of benthic communities. BIO-ENV routines produced similar correlation results when performed on targeted walrus prey items (bivalves (ρ=0.50), polychaetes (ρ=0.53), but gray whale prey items (amphipods) were not strongly correlated to any combination of physical environmental factors (ρ=0.24). Distributions of primary prey items for gray whales (amphipods) and walruses (bivalves

  7. Quantifying mineral abundances of complex mixtures by coupling spectral deconvolution of SWIR spectra (2.1-2.4 μm) and regression tree analysis

    USGS Publications Warehouse

    Mulder, V.L.; Plotze, Michael; de Bruin, Sytze; Schaepman, Michael E.; Mavris, C.; Kokaly, Raymond F.; Egli, Markus

    2013-01-01

    This paper presents a methodology for assessing mineral abundances of mixtures having more than two constituents using absorption features in the 2.1-2.4 μm wavelength region. In the first step, the absorption behaviour of mineral mixtures is parameterised by exponential Gaussian optimisation. Next, mineral abundances are predicted by regression tree analysis using these parameters as inputs. The approach is demonstrated on a range of prepared samples with known abundances of kaolinite, dioctahedral mica, smectite, calcite and quartz and on a set of field samples from Morocco. The latter contained varying quantities of other minerals, some of which did not have diagnostic absorption features in the 2.1-2.4 μm region. Cross validation showed that the prepared samples of kaolinite, dioctahedral mica, smectite and calcite were predicted with a root mean square error (RMSE) less than 9 wt.%. For the field samples, the RMSE was less than 8 wt.% for calcite, dioctahedral mica and kaolinite abundances. Smectite could not be well predicted, which was attributed to spectral variation of the cations within the dioctahedral layered smectites. Substitution of part of the quartz by chlorite at the prediction phase hardly affected the accuracy of the predicted mineral content; this suggests that the method is robust in handling the omission of minerals during the training phase. The degree of expression of absorption components was different between the field sample and the laboratory mixtures. This demonstrates that the method should be calibrated and trained on local samples. Our method allows the simultaneous quantification of more than two minerals within a complex mixture and thereby enhances the perspectives of spectral analysis for mineral abundances.

  8. Solar abundance of iridium

    PubMed Central

    Drake, Stephen; Aller, Lawrence H.

    1976-01-01

    By a method of spectrum synthesis, which yields log gfA, where g is the statistical weight of the lower level, f is the oscillator strength, and A is the abundance, an attempt is made to deduce the solar iridium abundance from one relatively unblended, but fairly weak IrI line, λ 3220.78 Å. If the Corliss-Bozman f-value for this line is adopted, we find log A(Ir) = 0.82 on the scale log A(H) = 12.00. The discordance with the value found from carbonaceous chondrites may arise from faulty f-values or from difficulties arising from line blending in this far ultraviolet domain of the solar spectrum. PMID:16578735

  9. Bioimpedance analysis and HIV-related fatigue.

    PubMed

    Meynell, Janet; Barroso, Julie

    2005-01-01

    Although various physiological and psychological causes of fatigue in HIV-positive persons have been proposed, it is still not well understood. Bioimpedance analysis has proved to be an easily used, non-invasive measurement of body composition and cellular integrity. This study, looking at whether body composition as measured by bioimpedance analysis is associated with fatigue, is part of a pilot study looking for physiological and psychological biomarkers that could be factors in the fatigue experienced by HIV-positive people. Twenty-nine men and eleven women were measured for height, weight, and bioimpedance analysis. Correlations were examined between fatigue intensity and weight, body mass index, body cell mass, fat-free mass, extracellular mass, and phase angle. Because of the fat redistribution that has occurred with some people taking protease inhibitors, we also examined differences in weight, body mass index, body cell mass, fat-free mass, and fatigue intensity between those taking and those not taking protease inhibitors. There was no association between fatigue intensity and weight, body mass index, body cell mass, fat-free mass, or phase angle, nor were there differences between those taking and those not taking protease inhibitors. However, it was noted that both the phase angle and the ratio of extracellular mass to body cell mass (extracellular mass:body cell mass) were below their respective normal ranges, indicating that the participants were somewhat compromised nutritionally and with regard to cell membrane integrity. Although fatigue was not shown to be related to body composition measurement in this study, further work is needed on the causes of fatigue, because its effects on the lives of HIV-positive people can be devastating.

  10. Integrated analysis of transcriptomic and proteomic data of Desulfovibrio vulgaris: Zero-Inflated Poisson regression models to predict abundance of undetected proteins

    SciTech Connect

    Nie, Lei; Wu, Gang; Brockman, Fred J.; Zhang, Weiwen

    2006-05-04

    Abstract Advances in DNA microarray and proteomics technologies have enabled high-throughput measurement of mRNA expression and protein abundance. Parallel profiling of mRNA and protein on a global scale and integrative analysis of these two data types could provide additional insight into the metabolic mechanisms underlying complex biological systems. However, because protein abundance and mRNA expression are affected by many cellular and physical processes, there have been conflicting results on the correlation of these two measurements. In addition, as current proteomic methods can detect only a small fraction of proteins present in cells, no correlation study of these two data types has been done thus far at the whole-genome level. In this study, we describe a novel data-driven statistical model to integrate whole-genome microarray and proteomic data collected from Desulfovibrio vulgaris grown under three different conditions. Based on the Poisson distribution pattern of proteomic data and the fact that a large number of proteins were undetected (excess zeros), Zero-inflated Poisson models were used to define the correlation pattern of mRNA and protein abundance. The models assumed that there is a probability mass at zero representing some of the undetected proteins because of technical limitations. The models thus use abundance measurements of transcripts and proteins experimentally detected as input to generate predictions of protein abundances as output for all genes in the genome. We demonstrated the statistical models by comparatively analyzing D. vulgaris grown on lactate-based versus formate-based media. The increased expressions of Ech hydrogenase and alcohol dehydrogenase (Adh)-periplasmic Fe-only hydrogenase (Hyd) pathway for ATP synthesis were predicted for D. vulgaris grown on formate.

  11. Surprising abundance of Gallionella-related iron oxidizers in creek sediments at pH 4.4 or at high heavy metal concentrations

    USGS Publications Warehouse

    Fabisch, Maria; Beulig, Felix; Akob, Denise M.; Küsel, Kirsten

    2013-01-01

    We identified and quantified abundant iron-oxidizing bacteria (FeOB) at three iron-rich, metal-contaminated creek sites with increasing sediment pH from extremely acidic (R1, pH 2.7), to moderately acidic (R2, pH 4.4), to slightly acidic (R3, pH 6.3) in a former uranium-mining district. The geochemical parameters showed little variations over the 1.5 year study period. The highest metal concentrations found in creek sediments always coincided with the lowest metal concentrations in creek water at the slightly acidic site R3. Sequential extractions of R3 sediment revealed large portions of heavy metals (Ni, Cu, Zn, Pb, U) bound to the iron oxide fraction. Light microscopy of glass slides exposed in creeks detected twisted stalks characteristic of microaerobic FeOB of the family Gallionellaceae at R3 but also at the acidic site R2. Sequences related to FeOB such as Gallionella ferruginea, Sideroxydans sp. CL21, Ferritrophicum radicicola, and Acidovorax sp. BrG1 were identified in the sediments. The highest fraction of clone sequences similar to the acidophilic “Ferrovum myxofaciens” was detected in R1. Quantitative PCR using primer sets specific for Gallionella spp., Sideroxydans spp., and “Ferrovum myxofaciens” revealed that ~72% (R2 sediment) and 37% (R3 sediment) of total bacterial 16S rRNA gene copies could be assigned to groups of FeOB with dominance of microaerobic Gallionella spp. at both sites. Gallionella spp. had similar and very high absolute and relative gene copy numbers in both sediment communities. Thus, Gallionella-like organisms appear to exhibit a greater acid and metal tolerance than shown before. Microaerobic FeOB from R3 creek sediment enriched in newly developed metal gradient tubes tolerated metal concentrations of 35 mM Co, 24 mM Ni, and 1.3 mM Cd, higher than those in sediments. Our results will extend the limited knowledge of FeOB at contaminated, moderately to slightly acidic environments.

  12. Surprising abundance of Gallionella-related iron oxidizers in creek sediments at pH 4.4 or at high heavy metal concentrations

    PubMed Central

    Fabisch, Maria; Beulig, Felix; Akob, Denise M.; Küsel, Kirsten

    2013-01-01

    We identified and quantified abundant iron-oxidizing bacteria (FeOB) at three iron-rich, metal-contaminated creek sites with increasing sediment pH from extremely acidic (R1, pH 2.7), to moderately acidic (R2, pH 4.4), to slightly acidic (R3, pH 6.3) in a former uranium-mining district. The geochemical parameters showed little variations over the 1.5 year study period. The highest metal concentrations found in creek sediments always coincided with the lowest metal concentrations in creek water at the slightly acidic site R3. Sequential extractions of R3 sediment revealed large portions of heavy metals (Ni, Cu, Zn, Pb, U) bound to the iron oxide fraction. Light microscopy of glass slides exposed in creeks detected twisted stalks characteristic of microaerobic FeOB of the family Gallionellaceae at R3 but also at the acidic site R2. Sequences related to FeOB such as Gallionella ferruginea, Sideroxydans sp. CL21, Ferritrophicum radicicola, and Acidovorax sp. BrG1 were identified in the sediments. The highest fraction of clone sequences similar to the acidophilic “Ferrovum myxofaciens” was detected in R1. Quantitative PCR using primer sets specific for Gallionella spp., Sideroxydans spp., and “Ferrovum myxofaciens” revealed that ~72% (R2 sediment) and 37% (R3 sediment) of total bacterial 16S rRNA gene copies could be assigned to groups of FeOB with dominance of microaerobic Gallionella spp. at both sites. Gallionella spp. had similar and very high absolute and relative gene copy numbers in both sediment communities. Thus, Gallionella-like organisms appear to exhibit a greater acid and metal tolerance than shown before. Microaerobic FeOB from R3 creek sediment enriched in newly developed metal gradient tubes tolerated metal concentrations of 35 mM Co, 24 mM Ni, and 1.3 mM Cd, higher than those in sediments. Our results will extend the limited knowledge of FeOB at contaminated, moderately to slightly acidic environments. PMID:24385973

  13. 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

  14. High-resolution abundance analysis of red giants in the metal-poor bulge globular cluster HP 1

    NASA Astrophysics Data System (ADS)

    Barbuy, B.; Cantelli, E.; Vemado, A.; Ernandes, H.; Ortolani, S.; Saviane, I.; Bica, E.; Minniti, D.; Dias, B.; Momany, Y.; Hill, V.; Zoccali, M.; Siqueira-Mello, C.

    2016-06-01

    Context. The globular cluster HP 1 is projected at only 3.̊33 from the Galactic center. Together with its distance, this makes it one of the most central globular clusters in the Milky Way. It has a blue horizontal branch (BHB) and a metallicity of [Fe/H] ≈ -1.0. This means that it probably is one of the oldest objects in the Galaxy. Abundance ratios can reveal the nucleosynthesis pattern of the first stars as well as the early chemical enrichment and early formation of stellar populations. Aims: High-resolution spectra obtained for six stars were analyzed to derive the abundances of the light elements C, N, O, Na, and Al, the alpha-elements Mg, Si, Ca, and Ti, and the heavy elements Sr, Y, Zr, Ba, La, and Eu. Methods: High-resolution spectra of six red giants that are confirmed members of the bulge globular cluster HP 1 were obtained with the 8 m VLT UT2-Kueyen telescope with the UVES spectrograph in FLAMES-UVES configuration. The spectroscopic parameter derivation was based on the excitation and ionization equilibrium of Fe i and Fe ii. Results: We confirm a mean metallicity of [Fe/H] = -1.06 ± 0.10, by adding the two stars that were previously analyzed in HP 1. The alpha-elements O and Mg are enhanced by about +0.3 ≲ [O,Mg/Fe] ≲ +0.5 dex, Si is moderately enhanced with +0.15 ≲ [Si/Fe] ≲ +0.35 dex, while Ca and Ti show lower values of -0.04 ≲ [Ca,Ti/Fe] ≲ +0.28 dex. The r-element Eu is also enhanced with [Eu/Fe] ≈ +0.4, which together with O and Mg is indicative of early enrichment by type II supernovae. Na and Al are low, but it is unclear if Na-O are anticorrelated. The heavy elements are moderately enhanced, with -0.20 < [La/Fe] < +0.43 dex and 0.0 < [Ba/Fe] < +0.75 dex, which is compatible with r-process formation. The spread in Y, Zr, Ba, and La abundances, on the other hand, appears to be compatible with the spinstar scenario or other additional mechanisms such as the weak r-process. Observations collected at the European Southern

  15. Induction of ketosis in rats fed low-carbohydrate, high-fat diets depends on the relative abundance of dietary fat and protein.

    PubMed

    Bielohuby, Maximilian; Menhofer, Dominik; Kirchner, Henriette; Stoehr, Barbara J M; Müller, Timo D; Stock, Peggy; Hempel, Madlen; Stemmer, Kerstin; Pfluger, Paul T; Kienzle, Ellen; Christ, Bruno; Tschöp, Matthias H; Bidlingmaier, Martin

    2011-01-01

    Low-carbohydrate/high-fat diets (LC-HFDs) in rodent models have been implicated with both weight loss and as a therapeutic approach to treat neurological diseases. LC-HFDs are known to induce ketosis; however, systematic studies analyzing the impact of the macronutrient composition on ketosis induction and weight loss success are lacking. Male Wistar rats were pair-fed for 4 wk either a standard chow diet or one of three different LC-HFDs, which only differed in the relative abundance of fat and protein (percentages of fat/protein in dry matter: LC-75/10; LC-65/20; LC-55/30). We subsequently measured body composition by nuclear magnetic resonance (NMR), analyzed blood chemistry and urine acetone content, evaluated gene expression changes of key ketogenic and gluconeogenic genes, and measured energy expenditure (EE) and locomotor activity (LA) during the first 4 days and after 3 wk on the respective diets. Compared with chow, rats fed with LC-75/10, LC-65/20, and LC-55/30 gained significantly less body weight. Reductions in body weight were mainly due to lower lean body mass and paralleled by significantly increased fat mass. Levels of β-hydroxybutyate were significantly elevated feeding LC-75/10 and LC-65/20 but decreased in parallel to reductions in dietary fat. Acetone was about 16-fold higher with LC-75/10 only (P < 0.001). In contrast, rats fed with LC-55/30 were not ketotic. Serum fibroblast growth factor-21, hepatic mRNA expression of hydroxymethylglutaryl-CoA-lyase, peroxisome proliferator-activated receptor-γ coactivator-1α, and peroxisome proliferator-activated receptor-γ coactivator-1β were increased with LC-75/10 only. Expression of phosphoenolpyruvate carboxykinase and glucose-6-phosphatase was downregulated by 50-70% in LC-HF groups. Furthermore, EE and LA were significantly decreased in all groups fed with LC-HFDs after 3 wk on the diets. In rats, the absence of dietary carbohydrates per se does not induce ketosis. LC-HFDs must be high in fat

  16. Relative Abundance and Plasmodium Infection Rates of Malaria Vectors in and around Jabalpur, a Malaria Endemic Region in Madhya Pradesh State, Central India

    PubMed Central

    Singh, Neeru; Mishra, Ashok K.; Chand, Sunil K.; Bharti, Praveen K.; Singh, Mrigendra P.; Nanda, Nutan; Singh, Om P.; Sodagiri, Kranti; Udhyakumar, Venkatachalam

    2015-01-01

    Background This study was undertaken in two Primary Health Centers (PHCs) of malaria endemic district Jabalpur in Madhya Pradesh (Central India). Methods In this study we had investigated the relative frequencies of the different anopheline species collected within the study areas by using indoor resting catches, CDC light trap and human landing methods. Sibling species of malaria vectors were identified by cytogenetic and molecular techniques. The role of each vector and its sibling species in the transmission of the different Plasmodium species was ascertained by using sporozoite ELISA. Results A total of 52,857 specimens comprising of 17 anopheline species were collected by three different methods (39,964 by indoor resting collections, 1059 by human landing and 11,834 by CDC light trap). Anopheles culicifacies was most predominant species in all collections (55, 71 and 32% in indoor resting, human landing and light trap collections respectively) followed by An. subpictus and An. annularis. All five sibling species of An. culicifacies viz. species A, B, C, D and E were found while only species T and S of An. fluviatilis were collected. The overall sporozoite rate in An. culicifacies and An. fluviatilis were 0.42% (0.25% for P. falciparum and 0.17% for P. vivax) and 0.90% (0.45% for P. falciparum and 0.45% for P. vivax) respectively. An. culicifacies and An. fluviatilis were found harbouring both P. vivax variants VK-210 and VK-247, and P. falciparum. An. culicifacies sibling species C and D were incriminated as vectors during most part of the year while sibling species T of An. fluviatilis was identified as potential vector in monsoon and post monsoon season. Conclusions An. culicifacies species C (59%) was the most abundant species followed by An. culicifacies D (24%), B (8.7%), E (6.7%) and A (1.5%). Among An. fluviatilis sibling species, species T was common (99%) and only few specimens of S were found. Our study provides crucial information on the prevalence

  17. Relative Fecal Abundance of Extended-Spectrum-β-Lactamase-Producing Escherichia coli Strains and Their Occurrence in Urinary Tract Infections in Women

    PubMed Central

    Lixandru, Brandusa; Cojocaru, Radu; Büke, Çağrı; Paramythiotou, Elisabeth; Angebault, Cécile; Visseaux, Claire; Djuikoue, Ingrid; Erdem, Esra; Burduniuc, Olga; El Mniai, Assiya; Marcel, Candice; Perrier, Marion; Kesteman, Thomas; Clermont, Olivier; Denamur, Erick; Armand-Lefèvre, Laurence; Andremont, Antoine

    2013-01-01

    Extended-spectrum-beta-lactamase (ESBL)-producing Escherichia coli (ESBL E. coli) strains are of major concern because few antibiotics remain active against these bacteria. We investigated the association between the fecal relative abundance (RA) of ESBL-producing E. coli (ESBL-RA) and the occurrence of ESBL E. coli urinary tract infections (UTIs). The first stool samples passed after suspicion of UTI from 310 women with subsequently confirmed E. coli UTIs were sampled and tested for ESBL-RA by culture on selective agar. Predictive values of ESBL-RA for ESBL E. coli UTI were analyzed for women who were not exposed to antibiotics when the stool was passed. ESBL E. coli isolates were characterized for ESBL type, phylogroup, relatedness, and virulence factors. The prevalence of ESBL E. coli fecal carriage was 20.3%, with ESBL E. coli UTIs being present in 12.3% of the women. The mean ESBL-RA (95% confidence interval [CI]) was 13-fold higher in women exposed to antibiotics at the time of sampling than in those not exposed (14.3% [range, 5.6% to 36.9%] versus 1.1% [range, 0.32% to 3.6%], respectively; P < 0.001) and 18-fold higher in women with ESBL E. coli UTI than in those with another E. coli UTI (10.0% [range, 0.54% to 100%] versus 0.56% [range, 0.15% to 2.1%[, respectively; P < 0.05). An ESBL-RA of <0.1% was 100% predictive of a non-ESBL E. coli UTI. ESBL type, phylogroup, relatedness, and virulence factors were not found to be associated with ESBL-RA. In conclusion, ESBL-RA was linked to the occurrence of ESBL E. coli UTI in women who were not exposed to antibiotics and who had the same clone of E. coli in urine samples and fecal samples. Especially, a low ESBL-RA appeared to be associated with a low risk of ESBL E. coli infection. PMID:23836184

  18. Chemical abundances and kinematics of barium stars

    NASA Astrophysics Data System (ADS)

    de Castro, D. B.; Pereira, C. B.; Roig, F.; Jilinski, E.; Drake, N. A.; Chavero, C.; Sales Silva, J. V.

    2016-07-01

    In this paper, we present an homogeneous analysis of photospheric abundances based on high-resolution spectroscopy of a sample of 182 barium stars and candidates. We determined atmospheric parameters, spectroscopic distances, stellar masses, ages, luminosities and scaleheight, radial velocities, abundances of the Na, Al, α-elements, iron-peak elements, and s-process elements Y, Zr, La, Ce, and Nd. We employed the local thermodynamic equilibrium model atmospheres of Kurucz and the spectral analysis code MOOG. We found that the metallicities, the temperatures and the surface gravities for barium stars cannot be represented by a single Gaussian distribution. The abundances of α-elements and iron peak elements are similar to those of field giants with the same metallicity. Sodium presents some degree of enrichment in more evolved stars that could be attributed to the NeNa cycle. As expected, the barium stars show overabundance of the elements created by the s-process. By measuring the mean heavy-element abundance pattern as given by the ratio [s/Fe], we found that the barium stars present several degrees of enrichment. We also obtained the [hs/ls] ratio by measuring the photospheric abundances of the Ba-peak and the Zr-peak elements. Our results indicated that the [s/Fe] and the [hs/ls] ratios are strongly anticorrelated with the metallicity. Our kinematical analysis showed that 90 per cent of the barium stars belong to the thin disc population. Based on their luminosities, none of the barium stars are luminous enough to be an asymptotic giant branch star, nor to become self-enriched in the s-process elements. Finally, we determined that the barium stars also follow an age-metallicity relation.

  19. Cetacean distribution and abundance in relation to oceanographic domains on the eastern Bering Sea shelf, June and July of 2002, 2008, and 2010

    NASA Astrophysics Data System (ADS)

    Friday, Nancy A.; Zerbini, Alexandre N.; Waite, Janice M.; Moore, Sue E.; Clapham, Phillip J.

    2013-10-01

    As part of the Bering Sea Project, cetacean surveys were conducted to describe distribution and estimate abundance on the eastern Bering Sea shelf. Three marine mammal observers conducted visual surveys along transect lines sampled during the Alaska Fisheries Science Center walleye pollock assessment survey in June and July of 2008 and 2010. Distribution and abundance in 2008 and 2010 (cold years) are compared with results from a similar survey conducted in 2002 (a warm year), as the only three years that the entire survey area was sampled; patterns largely match those previously observed. Abundance estimates for comparable areas in 2002, 2008 and 2010 were as follows: humpback whales (Megaptera novaeangliae): 231 (CV=0.63), 436 (CV=0.45), and 675 (CV=0.80); fin whales (Balaenoptera physalus): 419 (CV=0.33), 1368 (CV=0.34), and 1061 (CV=0.38); minke whales (Balaenoptera acutorostrata): 389 (CV=0.52), 517 (CV=0.69), and 2020 (CV=0.73); Dall's porpoise (Phocoenoides dalli): 35,303 (CV=0.53), 14,543 (CV=0.32), and 11,143 (CV=0.32); and harbor porpoise (Phocoena phocoena): 1971 (CV=0.46), 4056 (CV=0.40), and 833 (CV=0.66). It should be noted that these abundance estimates are not corrected for biases due to perception, availability, or responsive movement. Estimates for humpback, fin and minke whales increased from 2002 to 2010, while those for harbor and Dall's porpoise decreased; trends were significant for fin whales. It is likely that changes in estimated abundance are due at least in part to shifts in distribution and not just changes in overall population size. Annual abundance estimates were examined by oceanographic domain. Humpback whales were consistently concentrated in coastal waters north of Unimak Pass. Fin whales were broadly distributed in the outer domain and slope in 2008 and 2010, but sightings were sparse in 2002. Minke whales were distributed throughout the study area in 2002 and 2008, but in 2010 they were concentrated in the outer domain and

  20. Relations among Functional Systems in Behavior Analysis

    PubMed Central

    Thompson, Travis

    2007-01-01

    This paper proposes that an organism's integrated repertoire of operant behavior has the status of a biological system, similar to other biological systems, like the nervous, cardiovascular, or immune systems. Evidence from a number of sources indicates that the distinctions between biological and behavioral events is often misleading, engendering counterproductive explanatory controversy. A good deal of what is viewed as biological (often thought to be inaccessible or hypothetical) can become publicly measurable variables using currently available and developing technologies. Moreover, such endogenous variables can serve as establishing operations, discriminative stimuli, conjoint mediating events, and maintaining consequences within a functional analysis of behavior and need not lead to reductionistic explanation. I suggest that explanatory misunderstandings often arise from conflating different levels of analysis and that behavior analysis can extend its reach by identifying variables operating within a functional analysis that also serve functions in other biological systems. PMID:17575907

  1. A Semi-automated Abundance Survey of Ap Stars

    NASA Astrophysics Data System (ADS)

    Hall, Martin P.; Kurtz, Don; Elkin, Vladimir; Bruntt, Hans

    2015-08-01

    We have carried out an abundance analysis on the high-resolution spectra of approximately 350 Ap stars collected between 2007 and 2010 on the FEROS Echelle (Fibre-led, Extended Range, Echelle ) spectrograph housed at the 2.2-m telescope at European Southern Observatory at La Silla, Chile. We employed the VWA package (vsin I, wavelength shift, abundance analysis) for preliminary selection of spectral lines, and a semi-automated set of routines which we developed in the programming language IDL, to calculate the equivalent widths and abundances of ions of Iron and the rare earth elements Neodymium and Praseodymium using the WIDTH program and NEMO model atmospheres. Initial results are presented, which reinforce the correlation between iron abundance and effective temperature, from an over-abundance in the late Bp stars, to under-abundant in the early F stars. Results also suggest that the disequilibrium in abundances of the first and second ionisation stages of these ions in the rapidly oscillating Ap (roAp) stars may a consequence of the relatively cool temperatures of those stars, rather than a signature of pulsation.

  2. Reach-scale distribution dynamics of a grazing stream insect, Micrasema quadriloba Martynov (Brachycentridae, Trichoptera), in relation to current velocity and periphyton abundance.

    PubMed

    Katano, Izumi; Mitsuhashi, Hiromune; Isobe, Yu; Sato, Hiroaki; Oishi, Tadashi

    2005-08-01

    Reach-scale temporal shifts in the distribution of larvae of a grazing caddisfly, Micrasema quadriloba (Brachycentridae), were investigated in a Japanese mountain stream. The larvae showed an aggregated distribution within the reach at the beginning of the immigration, then became randomly dispersed throughout the reach as the immigration progressed. The abundance of periphyton in the reach decreased dramatically with increasing dispersal of the larvae. Simple regression analyses revealed that the stream's flow regime was the most important environmental factor that determined the reach-scale distribution of the larvae and that the relationship between the flow regime and the distribution of the larvae shifted temporally. In addition, our results suggest that only this species of grazing insect, which was dominant in the study reach, controlled the reach-scale abundance of the periphyton.

  3. Anthropogenic soils and land use patterns in relation to small mammal and flea abundance in plague endemic area of Western Usambara Mountains, Tanzania.

    PubMed

    Kimaro, Didas N; Msanya, Balthazar M; Meliyo, Joel; Hieronimo, Proches; Mwango, Sibaway; Kihupi, Nganga I; Gulinck, Hubert; Deckers, Jozef A

    2014-07-01

    Heterogeneity in the landscapes of West Usambara Mountains on land use and human activities has been reported. However, the interface of land use patterns and human modified soils with small mammal and flea abundance for possible explanation of plague has not been explored. This study was carried out to determine the link between anthropogenic soils and land use patterns on small mammal and flea abundance and the occurrence of reported plague in the Western Usambara Mountains in Tanzania. Standard soil survey methods were used to identify and describe soils and land use patterns on lower slopes and valley bottoms on which the surrounding villages are reported to have high and medium plague frequencies. The identified soils were characterised in terms of their morphological and physico-chemical properties and classified according to FAO-World Reference Base for Soil Resources. Small mammals were trapped on the same landscape positions and identified to genus/species level. Fleas were removed from the trapped small mammals, counted and identified to species level. In total 57 small mammals were captured from which 32 fleas were collected. Results show that human settlements and mixed cultivation on lower slopes and continuous vegetable cropping in the valley bottoms are dominant land use types. Intensive use of forest soils, manuring and irrigation on farms in the studied landscapes have contributed to the development of uniquely human modified soils namely Hortic Anthrosols in the lower slopes and Plaggic Irragric Hortic Anthrosols in valley bottoms. The identified anthropogenic soils and land use patterns are associated with high abundance of small mammals (Mastomys natalensis) and flea species (Xenopsylla brasiliensis and Dinopsyllus lypusus). This phenomenon is vividly apparent in the villages with medium to high plague frequencies. The study suggests that plague surveillance programmes should consider the existing relationship between anthropogenic soils, land

  4. Patterns in abundance and size of two deep-water gorgonian octocorals, in relation to depth and substrate features off Nova Scotia

    NASA Astrophysics Data System (ADS)

    Watanabe, Shana; Metaxas, Anna; Sameoto, Jessica; Lawton, Peter

    2009-12-01

    Deep-water corals form unique ecosystems, yet very little is known about factors that regulate their distribution and growth. The abundance and size of two deep-water gorgonian coral species, Paragorgia arborea and Primnoa resedaeformis, and their relationship with depth and substratum cover, were investigated at Northeast Channel, off Nova Scotia, in July 2006. This is the first study to measure abundance and size of these two coral species at depths >500 m in the Canadian Atlantic region. A total of 5 transects between 500 and 1000 m depth were examined using video collected by the remotely operated vehicle ROPOS. Abundance of both species was patchy, but higher at these deeper depths than at <500 m. Abundance generally declined with depth, and was moderately correlated with cover of hard substratum (cobble, boulder, bedrock). These relationships were stronger and less variable for P. resedaeformis than for P. arborea, suggesting that factors such as topographic relief may play an additional role in regulating distributions of P. arborea. Maximum colony height was 125 and 240 cm for P. resedaeformis and P. arborea, respectively, and much greater than recorded for depths <500 m. Overall, colony height and depth relationships were strong for both species, but variable among transects. P. resedaeformis showed a negative relationship with depth, while the opposite was observed for P. arborea, suggesting that the two species are affected differently by factors that vary with depth (e.g. temperature, fishing disturbance). Relationships between colony size and size of attachment stone were stronger for P. arborea, especially for overturned colonies, than for P. resedaeformis, suggesting that availability of suitably coarse substrate may be more important for the long-term persistence of P. arborea colonies.

  5. Partition of the relative contribution of nitrification and denitrification from Amazon forest soils using a model based on bulk 15N of N2O natural abundance determinations.

    NASA Astrophysics Data System (ADS)

    Perez, T. J.; Trumbore, S. E.; Tyler, S. C.; Park, S.; Boering, K.; Decamargo, P.

    2004-12-01

    Most of the available methods for the determination of the relative contribution of nitrification and denitrification to the soil emitted N2O are invasive. Therefore, they could produce biased results due to the change in soil structure, alteration to the microbial community and substrates. However, the soil community bacterial activity has intrinsic properties such as isotopic fractionation factors that are relative constant through different sets of soil conditions. We took advantage of these bacterial properties and devised a mass balance method for partitioning the relative contribution of each process by using: (1) The 15N enrichment factors for N2O production via nitrification and denitrification for soils (determined previously by acetylene addition soil incubation methods) and (2) the δ 15N-N2O soil emission values from the selected studied soils. We selected soils from a forest soil texture gradient from the Tapajos National Forest (TNF), in the Amazon Basin, Pará State, Brazil and Nova Vida Farm (NV), Rondonia State, Brazil where we had determined the 15N enrichment factors for each microbial process and collected N2O soil emissions for bulk stable isotope analysis during the rainy season of 2002. The soils selected were Oxisol (clay) and Ultison (sandy) at TNF and Latosol (sandy loam) at NV. We found that for all studied soils, the relative contribution of nitrification was smaller than 40 %. This corroborates the assumption that the N2O emitted from Amazon forest is mostly denitrification-derived. The advantage of this method is that is non invasive. However, the uncertainties associated with the method increase when δ 15N-N2O values of emitted N2O are smaller than -25 per mil.

  6. Flare Plasma Iron Abundance

    NASA Technical Reports Server (NTRS)

    Dennis, Brian R.; Dan, Chau; Jain, Rajmal; Schwartz, Richard A.; Tolbert, Anne K.

    2008-01-01

    The equivalent width of the iron-line complex at 6.7 keV seen in flare X-ray spectra suggests that the iron abundance of the hottest plasma at temperatures >approx.10 MK may sometimes be significantly lower than the nominal coronal abundance of four times the photospheric value that is commonly assumed. This conclusion is based on X-ray spectral observations of several flares seen in common with the Ramaty High Energy Solar Spectroscopic Imager (RHESSI) and the Solar X-ray Spectrometer (SOXS) on the second Indian geostationary satellite, GSAT-2. The implications of this will be discussed as it relates to the origin of the hot flare plasma - either plasma already in the corona that is directly heated during the flare energy release process or chromospheric plasma that is heated by flare-accelerated particles and driven up into the corona. Other possible explanations of lower-than-expected equivalent widths of the iron-line complex will also be discussed.

  7. Phylogeny, ribosomal RNA gene typing and relative abundance of new Pseudomonas species (sensu stricto) isolated from two pinyon-juniper woodland soils of the arid southwest U.S.

    PubMed

    Kuske, C R; Busch, J D; Adorada, D L; Dunbar, J M; Barns, S M

    1999-05-01

    Rhizosphere-inhabiting Pseudomonas species interact with plant roots and may be important for plant performance under stressful environmental conditions. A comparison was conducted of culturable Pseudomonas isolates associated with pinyon rhizosphere and between-tree interspace areas in a hot, dry, volcanic cinder field and an adjacent sandy loam soil, in order to identify Pseudomonas species which may be involved in pinyon pine survival under stressful conditions. From a collection of 800 isolates, eleven isolates exhibiting different