Sample records for abundance analysis relative

  1. RELATIVE ABUNDANCE MEASUREMENTS IN PLUMES AND INTERPLUMES

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Guennou, C.; Hahn, M.; Savin, D. W., E-mail: cguennou@iac.es

    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 tomore » 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.« less

  2. Chemical Abundance Analysis of Moving Group W11450 (Latham 1)

    NASA Astrophysics Data System (ADS)

    O'Connell, Julia E.; Martens, Kylee; Frinchaboy, Peter M.

    2016-12-01

    We present elemental abundances for all seven stars in Moving Group W11450 (Latham 1) to determine if they may be chemically related. These stars appear to be both spatially and kinematically related, but no spectroscopic abundance analysis exists in literature. Abundances for eight elements were derived via equivalent width analyses of high-resolution (R ˜ 60,000), high-signal-to-noise ratio (< {{S}}/{{N}}> ˜ 100) spectra obtained with the Otto Struve 2.1 m telescope and the Sandiford Echelle Spectrograph at McDonald Observatory. The large star-to-star scatter in metallicity, -0.55 ≤ [Fe/H] ≤slant 0.06 dex (σ = 0.25), implies these stars were not produced from the same chemically homogeneous molecular cloud, and are therefore not part of a remnant or open cluster as previously proposed. Prior to this analysis, it was suggested that two stars in the group, W11449 and W11450, are possible wide binaries. The candidate wide binary pair show similar chemical abundance patterns with not only iron but with other elements analyzed in this study, suggesting the proposed connection between these two stars may be real.

  3. Histogrammatic Method for Determining Relative Abundance of Input Gas Pulse

    NASA Technical Reports Server (NTRS)

    Mandrake, Lukas; Bornstein, Benjamin J.; Madzunkov, Stojan; MacAskill, John A.

    2012-01-01

    To satisfy the Major Constituents Analysis (MCA) requirements for the Vehicle Cabin Atmosphere Monitor (VCAM), this software analyzes the relative abundance ratios for N2, O2, Ar, and CO2 as a function of time and constructs their best-estimate mean. A histogram is first built of all abundance ratios for each of the species vs time. The abundance peaks corresponding to the intended measurement and any obfuscating background are then separated via standard peak-finding techniques in histogram space. A voting scheme is then used to include/exclude this particular time sample in the final average based on its membership to the intended measurement or the background population. This results in a robust and reasonable estimate of the abundance of trace components such as CO2 and Ar even in the presence of obfuscating backgrounds internal to the VCAM device. VCAM can provide a means for monitoring the air within the enclosed environments, such as the ISS (International Space Station), Crew Exploration Vehicle (CEV), a Lunar Habitat, or another vehicle traveling to Mars. Its miniature pre-concentrator, gas chromatograph (GC), and mass spectrometer can provide unbiased detection of a large number of organic species as well as MCA analysis. VCAM s software can identify the concentration of trace chemicals and whether the chemicals are on a targeted list of hazardous compounds. This innovation s performance and reliability on orbit, along with the ground team s assessment of its raw data and analysis results, will validate its technology for future use and development.

  4. 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.

  5. Multidirectional abundance shifts among North American birds and the relative influence of multifaceted climate factors.

    PubMed

    Huang, Qiongyu; Sauer, John R; Dubayah, Ralph O

    2017-09-01

    Shifts in species distributions are major fingerprint of climate change. Examining changes in species abundance structures at a continental scale enables robust evaluation of climate change influences, but few studies have conducted these evaluations due to limited data and methodological constraints. In this study, we estimate temporal changes in abundance from North American Breeding Bird Survey data at the scale of physiographic strata to examine the relative influence of different components of climatic factors and evaluate the hypothesis that shifting species distributions are multidirectional in resident bird species in North America. We quantify the direction and velocity of the abundance shifts of 57 permanent resident birds over 44 years using a centroid analysis. For species with significant abundance shifts in the centroid analysis, we conduct a more intensive correlative analysis to identify climate components most strongly associated with composite change of abundance within strata. Our analysis focus on two contrasts: the relative importance of climate extremes vs. averages, and of temperature vs. precipitation in strength of association with abundance change. Our study shows that 36 species had significant abundance shifts over the study period. The average velocity of the centroid is 5.89 km·yr -1 . The shifted distance on average covers 259 km, 9% of range extent. Our results strongly suggest that the climate change fingerprint in studied avian distributions is multidirectional. Among 6 directions with significant abundance shifts, the northwestward shift was observed in the largest number of species (n = 13). The temperature/average climate model consistently has greater predictive ability than the precipitation/extreme climate model in explaining strata-level abundance change. Our study shows heterogeneous avian responses to recent environmental changes. It highlights needs for more species-specific approaches to examine contributing

  6. 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...

  7. The relative abundance of neon and magnesium in the solar corona

    NASA Technical Reports Server (NTRS)

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

    1976-01-01

    A technique is proposed for specifically determining the relative solar coronal abundance of neon and magnesium. The relative abundance is calculated directly from the relative intensity of the resonance lines of Ne X (12.134A) and Mg XI (9.169A) without the need for the development of a detailed model of the thermal structure of the corona. Moderate resolution Bragg crystal spectrometer results from the OVI-10 satellite were used to determine a coronal neon to magnesium relative abundance of 1.47 + or - 0.38. The application of this technique to a recent higher resolution rocket observation gave an abundance ratio of approximately 0.93 + or - 0.15.

  8. 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...

  9. 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

  10. Temperature relations and abundance determinations in H II regions

    NASA Astrophysics Data System (ADS)

    Arellano-Córdova, K. Z.; Rodríguez, M.; Delgado-Inglada, G.

    2017-11-01

    Most abundance determinations in H II regions, especially for extragalactic regions, are based on the use of temperature relations, usually between Te[N II] and Te[O III]. The calibration of strong-line methods also generally rely on the use of these relations. We explore here the reliability of old and new Te[N II]-Te[O III] relations, their dispersions, and their effects on the calculation of chemical abundances. In order to do so, we have compiled and analyzed in a homogeneous way a sample of 155 H II regions that have measurements of both temperatures. We find that some of the largest departures from the temperature relation are probably due to shocks affecting Te[N II]. We consider the effects of recombination in Te[N II] and of line blending in Te[O III], and find a residual dependence of the temperature relation on the degree of ionization. We provide new robust fits of the relation and show that our fits lead to better abundance determinations. Our fits are very similar to the most used temperature relation, based on a grid of photoionization models by Stasińska (1982), and variously cited as Campbell et al. (1986) or Garnett (1992).

  11. 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

  12. 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.

  13. A Differential Abundance Analysis of Very Metal-poor Stars

    NASA Astrophysics Data System (ADS)

    O'Malley, Erin M.; McWilliam, Andrew; Chaboyer, Brian; Thompson, Ian

    2017-04-01

    We have performed a differential line-by-line chemical abundance analysis, ultimately relative to the Sun, of nine very metal-poor main-sequence (MS) halo stars, near [Fe/H] = -2 dex. Our abundances range from -2.66≤slant [{Fe}/{{H}}]≤slant -1.40 dex with conservative uncertainties of 0.07 dex. We find an average [α/Fe] = 0.34 ± 0.09 dex, typical of the Milky Way. While our spectroscopic atmosphere parameters provide good agreement with Hubble Space Telescope parallaxes, there is significant disagreement with temperature and gravity parameters indicated by observed colors and theoretical isochrones. Although a systematic underestimate of the stellar temperature by a few hundred degrees could explain this difference, it is not supported by current effective temperature studies and would create large uncertainties in the abundance determinations. Both 1D and < 3{{D}}> hydrodynamical models combined with separate 1D non-LTE effects do not yet account for the atmospheres of real metal-poor MS stars, but a fully 3D non-LTE treatment may be able to explain the ionization imbalance found in this work.

  14. 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.

  15. Abundance Analysis of 17 Planetary Nebulae from High-Resolution Optical Spectroscopy

    NASA Astrophysics Data System (ADS)

    Sherrard, Cameroun G.; Sterling, Nicholas C.; Dinerstein, Harriet L.; Madonna, Simone; Mashburn, Amanda

    2017-06-01

    We present an abundance analysis of 17 planetary nebulae (PNe) observed with the 2D-coudé echelle spectrograph on the 2.7-m Harlan J. Smith telescope at McDonald Observatory. The spectra cover the wavelength range 3600--10,400 Å at a resolution R = 36,700, and are the first high-resolution optical spectra for many objects in our sample. The number of emission lines detected in individual nebulae range from ~125 to over 600. We derive temperatures, densities, and abundances from collisionally-excited lines using the PyNeb package (Luridiana et al. 2015, A&A, 573, A42) and the ionization correction factor scheme of Delgado-Inglada et al. (2014, MNRAS, 440, 536). The abundances of light elements agree with previous estimates for most of the PNe. Several objects exhibit emission lines of refractory elements such as K and Fe, and neutron-capture elements that can be enriched by the s-process. We find that K and Fe are depleted relative to solar by ~0.3--0.7~dex and 1-2 dex, respectively, and find evidence for s-process enrichments in 10 objects. Several objects in our sample exhibit C, N, and O recombination lines that are useful for abundance determinations. These transitions are used to compute abundance discrepancy factors (ADFs), the ratio of ionic abundances derived from permitted lines to those from collisionally-excited transitions. We explore relations among depletion factors, ADFs, s-process enrichment factors, and other nebular stellar and nebular properties. We acknowledge support from NSF awards AST-901432 and AST-0708429.

  16. Absolute quantification of microbial taxon abundances.

    PubMed

    Props, Ruben; Kerckhof, Frederiek-Maarten; Rubbens, Peter; De Vrieze, Jo; Hernandez Sanabria, Emma; Waegeman, Willem; Monsieurs, Pieter; Hammes, Frederik; Boon, Nico

    2017-02-01

    High-throughput amplicon sequencing has become a well-established approach for microbial community profiling. Correlating shifts in the relative abundances of bacterial taxa with environmental gradients is the goal of many microbiome surveys. As the abundances generated by this technology are semi-quantitative by definition, the observed dynamics may not accurately reflect those of the actual taxon densities. We combined the sequencing approach (16S rRNA gene) with robust single-cell enumeration technologies (flow cytometry) to quantify the absolute taxon abundances. A detailed longitudinal analysis of the absolute abundances resulted in distinct abundance profiles that were less ambiguous and expressed in units that can be directly compared across studies. We further provide evidence that the enrichment of taxa (increase in relative abundance) does not necessarily relate to the outgrowth of taxa (increase in absolute abundance). Our results highlight that both relative and absolute abundances should be considered for a comprehensive biological interpretation of microbiome surveys.

  17. Space-based measurements of elemental abundances and their relation to solar abundances

    NASA Technical Reports Server (NTRS)

    Coplan, M. A.; Ogilvie, K. W.; Bochsler, P.; Geiss, J.

    1990-01-01

    The Ion Composition Instrument (ICI) aboard the ISEE-3/ICE spacecraft was in the solar wind continuously from August 1978 to December 1982. The results made it possible to establish long-term average solar wind abundance values for helium, oxygen, neon, silicon, and iron. The Charge-Energy-Mass instrument aboard the CCE spacecraft of the AMPTE mission has measured the abundance of these elements in the magnetosheath and has also added carbon, nitrogen, magnesium, and sulfur to the list. There is strong evidence that these magnetosheath abundances are representative of the solar wind. Other sources of solar wind abundances are Solar Energetic Particle experiments and Apollo lunar foils. When comparing the abundances from all of these sources with photospheric abundances, it is clear that helium is depleted in the solar wind while silicon and iron are enhanced. Solar wind abundances for carbon, nitrogen, oxygen, and neon correlate well with the photospheric values. The incorporation of minor ions into the solar wind appears to depend upon both the ionization times for the elements and the Coulomb drag exerted by the outflowing proton flux.

  18. 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

  19. [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.

  20. Bacterial 16S rRNA gene analysis revealed that bacteria related to Arcobacter spp. constitute an abundant and common component of the oyster microbiota (Tiostrea chilensis).

    PubMed

    Romero, J; García-Varela, M; Laclette, J P; Espejo, R T

    2002-11-01

    To explore the bacterial microbiota in Chilean oyster (Tiostrea chilensis), a molecular approach that permits detection of different bacteria, independently of their capacity to grow in culture media, was used. Bacterial diversity was assessed by analysis of both the 16S rDNA and the 16S-23S intergenic region, obtained by PCR amplifications of DNA extracted from depurated oysters. RFLP of the PCR amplified 16S rDNA showed a prevailing pattern in most of the individuals analyzed, indicating that a few bacterial species were relatively abundant and common in oysters. Cloning and sequencing of the 16S rDNA with the prevailing RFLP pattern indicated that this rRNA was most closely related to Arcobacter spp. However, analysis by the size of the amplified 16S-23S rRNA intergenic regions revealed not Arcobacter spp. but Staphylococcus spp. related bacteria as a major and common component in oyster. These different results may be caused by the absence of target for one of the primers employed for amplification of the intergenic region. Neither of the two bacteria species found in large abundance was recovered after culturing under aerobic, anaerobic, or microaerophilic conditions. This result, however, is expected because the number of bacteria recovered after cultivation was less than 0.01% of the total. All together, these observations suggest that Arcobacter-related strains are probably abundant and common in the Chilean oyster bacterial microbiota.

  1. Comparison of normalization methods for the analysis of metagenomic gene abundance data.

    PubMed

    Pereira, Mariana Buongermino; Wallroth, Mikael; Jonsson, Viktor; Kristiansson, Erik

    2018-04-20

    In shotgun metagenomics, microbial communities are studied through direct sequencing of DNA without any prior cultivation. By comparing gene abundances estimated from the generated sequencing reads, functional differences between the communities can be identified. However, gene abundance data is affected by high levels of systematic variability, which can greatly reduce the statistical power and introduce false positives. Normalization, which is the process where systematic variability is identified and removed, is therefore a vital part of the data analysis. A wide range of normalization methods for high-dimensional count data has been proposed but their performance on the analysis of shotgun metagenomic data has not been evaluated. Here, we present a systematic evaluation of nine normalization methods for gene abundance data. The methods were evaluated through resampling of three comprehensive datasets, creating a realistic setting that preserved the unique characteristics of metagenomic data. Performance was measured in terms of the methods ability to identify differentially abundant genes (DAGs), correctly calculate unbiased p-values and control the false discovery rate (FDR). Our results showed that the choice of normalization method has a large impact on the end results. When the DAGs were asymmetrically present between the experimental conditions, many normalization methods had a reduced true positive rate (TPR) and a high false positive rate (FPR). The methods trimmed mean of M-values (TMM) and relative log expression (RLE) had the overall highest performance and are therefore recommended for the analysis of gene abundance data. For larger sample sizes, CSS also showed satisfactory performance. This study emphasizes the importance of selecting a suitable normalization methods in the analysis of data from shotgun metagenomics. Our results also demonstrate that improper methods may result in unacceptably high levels of false positives, which in turn may lead

  2. Geo-statistical analysis of Culicoides spp. distribution and abundance in Sicily, Italy.

    PubMed

    Blanda, Valeria; Blanda, Marcellocalogero; La Russa, Francesco; Scimeca, Rossella; Scimeca, Salvatore; D'Agostino, Rosalia; Auteri, Michelangelo; Torina, Alessandra

    2018-02-01

    Biting midges belonging to Culicoides imicola, Culicoides obsoletus complex and Culicoides pulicaris complex (Diptera: Ceratopogonidae) are increasingly implicated as vectors of bluetongue virus in Palaearctic regions. Culicoides obsoletus complex includes C. obsoletus (sensu stricto), C. scoticus, C. dewulfi and C. chiopterus. Culicoides pulicaris and C. lupicaris belong to the Culicoides pulicaris complex. The aim of this study was a geo-statistical analysis of the abundance and spatial distribution of Culicoides spp. involved in bluetongue virus transmission. As part of the national bluetongue surveillance plan 7081 catches were collected in 897 Sicilian farms from 2000 to 2013. Onderstepoort-type blacklight traps were used for sample collection and each catch was analysed for the presence of Culicoides spp. and for the presence and abundance of Culicoides vector species (C. imicola, C. pulicaris / C. obsoletus complexes). A geo-statistical analysis was carried out monthly via the interpolation of measured values based on the Inverse Distance Weighted method, using a GIS tool. Raster maps were reclassified into seven classes according to the presence and abundance of Culicoides, in order to obtain suitable maps for Map Algebra operations. Sicilian provinces showing a very high abundance of Culicoides vector species were Messina (80% of the whole area), Palermo (20%) and Catania (12%). A total of 5654 farms fell within the very high risk area for bluetongue (21% of the 26,676 farms active in Sicily); of these, 3483 farms were in Messina, 1567 in Palermo and 604 in Catania. Culicoides imicola was prevalent in Palermo, C. pulicaris in Messina and C. obsoletus complex was very abundant over the whole island with the highest abundance value in Messina. Our study reports the results of a geo-statistical analysis concerning the abundance and spatial distribution of Culicoides spp. in Sicily throughout the fourteen year study. It provides useful decision support in the

  3. Abundance analysis of roAp stars. IV. HD24712

    NASA Astrophysics Data System (ADS)

    Ryabchikova, T. A.; Landstreet, J. D.; Gelbmann, M. J.; Bolgova, G. T.; Tsymbal, V. V.; Weiss, W. W.

    1997-11-01

    We present the first abundance analysis of the rapidly oscillating chemically peculiar star HD24712, and determine a T_eff,=7250K, log {g},=4.3, and xi_t ,=1kms(-1) . Microturbulence seems to be entirely simulated by a magnetic field with a polar field strength of 4.4kG and of dipolar structure, both of which are supported by our polarimetric observations. Rotation of HD24712 and a spotty surface distribution of the elements result in different mean abundances for different (magnetic) phases. Our results do not support the hypothesis of a monotonic correlation between the amplitude of abundance variations and the atomic number Z, and we present arguments in favour of one of the rotation periods (Prot=12\\fd 4610) discussed in the literature. Rare earth elements are the most overabundant elements relative to the sun, and they have the largest abundance amplitude during a rotation cycle; only Mg has a larger amplitude. For HD24712 we find a clear overabundance of Co while most of the other iron peak elements are underabundant. A comparison of the abundance pattern with the other three roAp stars analyzed so far by us concludes the paper. A systematic difference between surface gravities obtained from spectroscopy and from both asteroseismology and evolutionary tracks is found for the roAp stars HD 24712, alpha Cir, and gamma Equ. Based on observations obtained with the Canada-France-Hawaii telescope, operated by the National Research Council of Canada, the Centre Centre National de la Recherche Scientifique de France, and the University of Hawaii, and on observations obtained at CARSO, Las Campanas, Chile

  4. An abundance analysis of Tau Herculis, B5 IV

    NASA Technical Reports Server (NTRS)

    Adelman, S. J.

    1977-01-01

    An abundance analysis of the sharp-lined star Tau Herculis (B5 IV) has been performed using a fully line-blanketed model atmosphere. The derived abundances are similar to those of the sun and the normal main-sequence B stars Iota Her (B3 V) and Nu Cap (B9 V).

  5. 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.

  6. 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.

  7. Protein relative abundance patterns associated with sucrose-induced dysbiosis are conserved across taxonomically diverse oral microcosm biofilm models of dental caries.

    PubMed

    Rudney, Joel D; Jagtap, Pratik D; Reilly, Cavan S; Chen, Ruoqiong; Markowski, Todd W; Higgins, LeeAnn; Johnson, James E; Griffin, Timothy J

    2015-12-19

    The etiology of dental caries is multifactorial, but frequent consumption of free sugars, notably sucrose, appears to be a major factor driving the supragingival microbiota in the direction of dysbiosis. Recent 16S rRNA-based studies indicated that caries-associated communities were less diverse than healthy supragingival plaque but still displayed considerable taxonomic diversity between individuals. Metagenomic studies likewise have found that healthy oral sites from different people were broadly similar with respect to gene function, even though there was an extensive individual variation in their taxonomic profiles. That pattern may also extend to dysbiotic communities. In that case, shifts in community-wide protein relative abundance might provide better biomarkers of dysbiosis that can be achieved through taxonomy alone. In this study, we used a paired oral microcosm biofilm model of dental caries to investigate differences in community composition and protein relative abundance in the presence and absence of sucrose. This approach provided large quantities of protein, which facilitated deep metaproteomic analysis. Community composition was evaluated using 16S rRNA sequencing and metaproteomic approaches. Although taxonomic diversity was reduced by sucrose pulsing, considerable inter-subject variation in community composition remained. By contrast, functional analysis using the SEED ontology found that sucrose induced changes in protein relative abundance patterns for pathways involving glycolysis, lactate production, aciduricity, and ammonia/glutamate metabolism that were conserved across taxonomically diverse dysbiotic oral microcosm biofilm communities. Our findings support the concept of using function-based changes in protein relative abundance as indicators of dysbiosis. Our microcosm model cannot replicate all aspects of the oral environment, but the deep level of metaproteomic analysis it allows makes it suitable for discovering which proteins are

  8. The abundance properties of nearby late-type galaxies. II. The relation between abundance distributions and surface brightness profiles

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Pilyugin, L. S.; Grebel, E. K.; Zinchenko, I. A.

    2014-12-01

    The relations between oxygen abundance and disk surface brightness (OH–SB relation) in the infrared W1 band are examined for nearby late-type galaxies. The oxygen abundances were presented in Paper I. The photometric characteristics of the disks are inferred here using photometric maps from the literature through bulge-disk decomposition. We find evidence that the OH–SB relation is not unique but depends on the galactocentric distance r (taken as a fraction of the optical radius R{sub 25}) and on the properties of a galaxy: the disk scale length h and the morphological T-type. We suggest a general, four-dimensional OH–SB relation with themore » values r, h, and T as parameters. The parametric OH–SB relation reproduces the observed data better than a simple, one-parameter relation; the deviations resulting when using our parametric relation are smaller by a factor of ∼1.4 than that of the simple relation. The influence of the parameters on the OH–SB relation varies with galactocentric distance. The influence of the T-type on the OH–SB relation is negligible at the centers of galaxies and increases with galactocentric distance. In contrast, the influence of the disk scale length on the OH–SB relation is at a maximum at the centers of galaxies and decreases with galactocentric distance, disappearing at the optical edges of galaxies. Two-dimensional relations can be used to reproduce the observed data at the optical edges of the disks and at the centers of the disks. The disk scale length should be used as a second parameter in the OH–SB relation at the center of the disk while the morphological T-type should be used as a second parameter in the relation at optical edge of the disk. The relations between oxygen abundance and disk surface brightness in the optical B and infrared K bands at the center of the disk and at optical edge of the disk are also considered. The general properties of the abundance–surface brightness relations are similar for

  9. Metal Abundances of KISS Galaxies. VI. New Metallicity Relations for the KISS Sample of Star-forming Galaxies

    NASA Astrophysics Data System (ADS)

    Hirschauer, Alec S.; Salzer, John J.; Janowiecki, Steven; Wegner, Gary A.

    2018-02-01

    We present updated metallicity relations for the spectral database of star-forming galaxies (SFGs) found in the KPNO International Spectroscopic Survey (KISS). New spectral observations of emission-line galaxies obtained from a variety of telescope facilities provide oxygen abundance information. A nearly fourfold increase in the number of KISS objects with robust metallicities relative to our previous analysis provides for an empirical abundance calibration to compute self-consistent metallicity estimates for all SFGs in the sample with adequate spectral data. In addition, a sophisticated spectral energy distribution fitting routine has provided robust calculations of stellar mass. With these new and/or improved galaxy characteristics, we have developed luminosity–metallicity (L–Z) relations, mass–metallicity (M *–Z) relations, and the so-called fundamental metallicity relation (FMR) for over 1450 galaxies from the KISS sample. This KISS M *–Z relation is presented for the first time and demonstrates markedly lower scatter than the KISS L–Z relation. We find that our relations agree reasonably well with previous publications, modulo modest offsets due to differences in the strong emission line metallicity calibrations used. We illustrate an important bias present in previous L–Z and M *–Z studies involving direct-method (T e ) abundances that may result in systematically lower slopes in these relations. Our KISS FMR shows consistency with those found in the literature, albeit with a larger scatter. This is likely a consequence of the KISS sample being biased toward galaxies with high levels of activity.

  10. Depletion of highly abundant proteins in blood plasma by ammonium sulfate precipitation for 2D-PAGE analysis.

    PubMed

    Mahn, Andrea; Ismail, Maritza

    2011-11-15

    Ammonium sulfate precipitation (ASP) was explored as a method for depleting some highly abundant proteins from blood plasma, in order to reduce the dynamic range of protein concentration and to improve the detection of low abundance proteins by 2D-PAGE. 40% ammonium sulfate saturation was chosen since it allowed depleting 39% albumin and 82% α-1-antitrypsin. ASP-depletion showed high reproducibility in 2D-PAGE analysis (4.2% variation in relative abundance of albumin), similar to that offered by commercial affinity-depletion columns. Besides, it allowed detecting 59 spots per gel, very close to the number of spots detected in immuno-affinity-depleted plasma. Thus, ASP at 40% saturation is a reliable depletion method that may help in proteomic analysis of blood plasma. Finally, ASP-depletion seems to be complementary to hydrophobic interaction chromatography (HIC)-depletion, and therefore an ASP-step followed by a HIC-step could probably deplete the most highly abundant plasma proteins, thus improving the detection of low abundance proteins by 2D-PAGE. Copyright © 2011 Elsevier B.V. All rights reserved.

  11. 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.

  12. 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.

  13. 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

  14. Oxygen abundances in halo stars

    NASA Astrophysics Data System (ADS)

    Bessell, Michael S.; Sutherland, Ralph S.; Ruan, Kui

    1991-12-01

    The present study determines the oxygen abundance for a sample of metal-poor G dwarfs by analysis of OH lines between 3080 and 3200 A and the permitted high-excitation far-red O I triple. The oxygen abundances determined from the low-excitation OH lines are up to 0.55 dex lower than those measured from the high-excitation O I lines. The abundances for the far-red O I triplet lines agree with those rederived from Abia and Rebolo (1989), and the abundances from the OH lines in dwarfs and giants are in agreement with the rederived O abundances of Barbuy (1988) and others from the forbidden resonance O I line. Because the chi = 0.1.7 eV OH lines are formed in the same layers as the majority of Fe, Ti, and other neutral metal lines used for abundance analyses, it is argued that the OH lines and the forbidden O I line yield the true oxygen abundances relative to the metals.

  15. Abundance Analysis of the Helium Weak Star 20-TAURI

    NASA Astrophysics Data System (ADS)

    Mon, M.; Hirata, R.; Sadakane, K.

    An abundance analysis of the helium-weak star 20 Tauri is performed with a fully line-blanketed model atmosphere. The adopted atmospheric parameters are Teff =12600 K and log g=3.2. These values are lower by about 1000 K in Teff and 0.3 in log g than those used in previous investigations, and 20 Tau is the coolest star among the group of helium-weak star. A value of log N(He)/N(H)=-1.7 is found from the average of six He I lines. Mg, Si, Ca, and Ni are underabundant, while P and Mn are overabundant. The abundances of C, Ti, Cr, and Fe coincide with the solar values within ±0.3 dex. Upper limits of the abundances of S, Sc, and Sr are estimated and these elements are not overabundant. The observed abundance pattern in 20 Tau is quite different from those in other helium-weak stars, while it shows a mild characteristic of Mn-Hg stars.

  16. 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

  17. Stellar Oxygen Abundances

    NASA Astrophysics Data System (ADS)

    King, Jeremy

    1994-04-01

    This dissertation addresses several issues concerning stellar oxygen abundances. The 7774 {\\AA} O I triplet equivalent widths of Abia & Rebolo [1989, AJ, 347, 186] for metal-poor dwarfs are found to be systematically too high. I also argue that current effective temperatures used in halo star abundance studies may be ~150 K too low. New color-Teff relations are derived for metal-poor stars. Using the revised Teff values and improved equivalent widths for the 7774A O I triplet, the mean [O/Fe] ratio for a handful of halo stars is found to be +0.52 with no dependence on Teff or [Fe/H]. Possible cosmological implications of the hotter Teff scale are discussed along with additional evidence supporting the need for a higher temperature scale for metal-poor stars. Our Teff scale leads to a Spite Li plateau value of N(Li)=2.28 +/- 0.09. A conservative minimal primordial value of N(Li)=2.35 is inferred. If errors in the observations and models are considered, consistency with standard models of Big Bang nucleosynthesis is still achieved with this larger Li abundance. The revised Teff scale raises the observed B/Be ratio of HD 140283 from 10 to 12, making its value more comfortably consistent with the production of the observed B and Be by ordinary spallation. Our Teff values are found to be in good agreement with values predicted from both the Victoria and Yale isochrone color-Teff relations. Thus, it appears likely that no changes in globular cluster ages would result. Next, we examine the location of the break in the [O/Fe] versus [Fe/H] plane in a quantitative fashion. Analysis of a relatively homogeneous data set does not favor any unique break point in the range -1.7 analysis also indicates that [O/Fe] is constant in the halo (at least for [Fe/H] >/= -3), in agreement with the new results for halo dwarfs. We find that the gap in the observed [O/H] distribution, noted by Wheeler et al

  18. 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

  19. Clustering in the stellar abundance space

    NASA Astrophysics Data System (ADS)

    Boesso, R.; Rocha-Pinto, H. J.

    2018-03-01

    We have studied the chemical enrichment history of the interstellar medium through an analysis of the n-dimensional stellar abundance space. This work is a non-parametric analysis of the stellar chemical abundance space. The main goal is to study the stars from their organization within this abundance space. Within this space, we seek to find clusters (in a statistical sense), that is, stars likely to share similar chemo-evolutionary history, using two methods: the hierarchical clustering and the principal component analysis. We analysed some selected abundance surveys available in the literature. For each sample, we labelled the group of stars according to its average abundance curve. In all samples, we identify the existence of a main enrichment pattern of the stars, which we call chemical enrichment flow. This flow is set by the structured and well-defined mean rate at which the abundances of the interstellar medium increase, resulting from the mixture of the material ejected from the stars and stellar mass-loss and interstellar medium gas. One of the main results of our analysis is the identification of subgroups of stars with peculiar chemistry. These stars are situated in regions outside of the enrichment flow in the abundance space. These peculiar stars show a mismatch in the enrichment rate of a few elements, such as Mg, Si, Sc and V, when compared to the mean enrichment rate of the other elements of the same stars. We believe that the existence of these groups of stars with peculiar chemistry may be related to the accretion of planetary material on to stellar surfaces or may be due to production of the same chemical element by different nucleosynthetic sites.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    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 abundancemore » 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.« less

  1. 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.

  2. Archaeal and bacterial H-GDGTs are abundant in peat and their relative abundance is positively correlated with temperature

    NASA Astrophysics Data System (ADS)

    Naafs, B. D. A.; McCormick, D.; Inglis, G. N.; Pancost, R. D.; T-GRES Peat Database Collaborators

    2018-04-01

    Glycerol monoalkyl glycerol tetraether lipids (GMGTs; also called 'H-GDGTs') differ from the more commonly studied glycerol dialkyl glycerol tetraether (GDGTs) in that they have an additional covalent bond that links the two alkyl chains. Six different archaeal isoprenoidal H-GDGTs (H-isoGDGTs) and one branched H-GDGT (H-brGDGT), presumably produced by bacteria, have previously been found. However, the function of H-GDGTs in both domains of life is unknown. It is thought that the formation of this additional covalent bond results in enhanced membrane stability, accounting for the high abundance of H-GDGTs in extreme environments such as geothermal settings, but so far there has been little evidence to support this hypothesis. Here we report the distribution of H-GDGTs in a global peat database (n = 471) with a broad range in mean annual air temperature (MAAT) and pH. This is the first finding of H-GDGTs in soils (specifically, peat), highlighting that H-GDGTs are widespread in mesophilic settings. In addition, we report the presence of two new H-brGDGTs with one (H-1034) and two (H-1048) additional methyl groups, respectively. Our results suggest that the relative abundance of both bacterial and archaeal H-GDGTs compared to regular GDGTs is related to temperature with the highest relative abundance of H-GDGTs in tropical peats. Although other factors besides temperature likely also play a role, these results do support the hypothesis that H-GDGTs are an adaptation to temperature to maintain membrane stability. The observation that both bacterial and archaeal membrane lipids respond to temperature indicates the same adaption across the lipid divide between these two domains of life, suggesting parallel or convergent evolution (potentially facilitated by lateral gene transfer).

  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. 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.

  5. 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.

  6. 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

  7. 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

  8. Distribution and relative abundance of fishes in littoral areas of Chief Joseph Reservoir, Columbia River

    USGS Publications Warehouse

    Gadomski, Dena M.; Venditti, David A.; Robinson, T. Craig; Beeman, John W.; Maule, Alec G.

    2004-01-01

    We surveyed fish assemblages in littoral areas of Chief Joseph Reservoir of the upper Columbia River to aid in understanding this ecosystem. Fish distributions and abundances were examined during April-July 1999 in relation to environmental conditions in the reservoir. We also compared the fish assemblages in Chief Joseph reservoir in 1999 to a past study conducted during 1974-1975, and to assemblages in other areas of the Columbia River. During 67 hr of electrofishing and 78 beach seine hauls in Chief Joseph Reservoir, 7460 fishes representing 8 families were collected. The majority of the catch was native – northern pikeminnow; redside shiners; longnose, bridgelip, and largescale suckers; and sculpins. The most abundant introduced species was walleye, and one species, rainbow trout, was mostly of net-pen origin. Larger sizes of suckers and northern pikeminnow were most abundant in the upper reservoir, likely due to upstream spawning migrations. The lower reservoir contained greater abundances of smaller fishes, and this area had lower flows, smaller substrates, and more complex shorelines that offered these fishes refugia. Only adult suckers displayed significant differences in abundances related to substrate. The relative abundances of species appeared to have changed since the 1970s, when the dominant fishes were northern pikeminnow, peamouth, largescale suckers, and walleye. Fish assemblage differences between Chief Joseph Reservoir and lower Columbia River reservoirs were also evident due to the morphology of the reservoir, its more northerly location, and the lack of fish passage facilities at Chief Joseph Dam. Our study is one of the few descriptions of fishes in the upper Columbia Rivers.

  9. Distribution and abundance of juvenile demersal fishes in relation to summer hypoxia and other environmental variables in coastal Oregon, USA

    NASA Astrophysics Data System (ADS)

    Sobocinski, Kathryn L.; Ciannelli, Lorenzo; Wakefield, W. Waldo; Yergey, Matthew E.; Johnson-Colegrove, Angela

    2018-05-01

    The juvenile demersal fish assemblage along the Pacific Northwest coast has received little attention relative to adult life history stages since pioneering work in the 1970s. Increasing severity of hypoxia along the Oregon coast in recent years has prompted investigations into the response of biota in this region. We used summer data (2008-2013) from a beam trawl survey targeting juvenile demersal fishes in soft-bottom habitats along the Oregon coast to describe patterns of distribution and abundance at fixed sampling stations (from 30 m to 100 m depth). We relate the assemblage and abundance of the common species to environmental variables and analyze condition of recently settled fish (<50 mm SL). Most of the captured fishes were young-of-the-year flatfishes, dominated by Butter Sole (Isopsetta isolepis), English Sole (Parophrys vetulus), Speckled Sanddab (Citharichthys stigmaeus), and Pacific Sanddab (Citharichthys sordidus). Community analysis of the full dataset showed some variation in species richness among years and high evenness across all sampling sites and years. Depth was a structuring variable for the community, indicated by multivariate nonmetric multidimensional scaling analysis. Generalized additive models for common flatfish species abundances during the summer months indicated depth preferences, with Butter Sole, English Sole, and Speckled Sanddab at shallower locations and Pacific Sanddab occurring at deeper locations farther offshore. Additionally, while most common species were collected in high abundances in hypoxic conditions, dissolved oxygen was a significant factor in determining flatfish abundance. Condition factor was weakly negatively impacted by low dissolved oxygen for the species assessed, but the strength of the relationship varied by species. Increased sampling frequency and spatial coverage would improve our understanding of this community, especially in light of changing environmental drivers such as decreasing pH, warming water

  10. 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.

  11. Prevalence of avian haemosporidian parasites is positively related to the abundance of host species at multiple sites within a region.

    PubMed

    Ellis, Vincenzo A; Medeiros, Matthew C I; Collins, Michael D; Sari, Eloisa H R; Coffey, Elyse D; Dickerson, Rebecca C; Lugarini, Camile; Stratford, Jeffrey A; Henry, Donata R; Merrill, Loren; Matthews, Alix E; Hanson, Alison A; Roberts, Jackson R; Joyce, Michael; Kunkel, Melanie R; Ricklefs, Robert E

    2017-01-01

    Parasite prevalence is thought to be positively related to host population density owing to enhanced contagion. However, the relationship between prevalence and local abundance of multiple host species is underexplored. We surveyed birds and their haemosporidian parasites (genera Plasmodium and Haemoproteus) at multiple sites across eastern North America to test whether the prevalence of these parasites in a host species at a particular site is related to that host's local abundance. Prevalence was positively related to host abundance within most sites, although the effect was stronger and more consistent for Plasmodium than for Haemoproteus. In contrast, prevalence was not related to variation in the abundance of most individual host species among sites across the region. These results suggest that parasite prevalence partly reflects the relative abundances of host species in local assemblages. However, three nonnative host species had low prevalence despite being relatively abundant at one site, as predicted by the enemy release hypothesis.

  12. 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.

  13. Fear or food - abundance of red fox in relation to occurrence of lynx and wolf.

    PubMed

    Wikenros, Camilla; Aronsson, Malin; Liberg, Olof; Jarnemo, Anders; Hansson, Jessica; Wallgren, Märtha; Sand, Håkan; Bergström, Roger

    2017-08-22

    Apex predators may affect mesopredators through intraguild predation and/or supply of carrion from their prey, causing a trade-off between avoidance and attractiveness. We used wildlife triangle snow-tracking data to investigate the abundance of red fox (Vulpes vulpes) in relation to lynx (Lynx lynx) and wolf (Canis lupus) occurrence as well as land composition and vole (Microtus spp.) density. Data from the Swedish wolf-monitoring system and VHF/GPS-collared wolves were used to study the effect of wolf pack size and time since wolf territory establishment on fox abundance. Bottom-up processes were more influential than top-down effects as the proportion of arable land was the key indicator of fox abundance at the landscape level. At this spatial scale, there was no effect of wolf abundance on fox abundance, whereas lynx abundance had a positive effect. In contrast, at the wolf territory level there was a negative effect of wolves on fox abundance when including detailed information of pack size and time since territory establishment, whereas there was no effect of lynx abundance. This study shows that different apex predator species may affect mesopredator abundance in different ways and that the results may be dependent on the spatiotemporal scale and resolution of the data.

  14. Variation of tsetse fly abundance in relation to habitat and host presence in the Maasai Steppe, Tanzania.

    PubMed

    Ngonyoka, Anibariki; Gwakisa, Paul S; Estes, Anna B; Nnko, Happiness J; Hudson, Peter J; Cattadori, Isabella M

    2017-06-01

    Human activities modify ecosystem structure and function and can also alter the vital rates of vectors and thus the risk of infection with vector-borne diseases. In the Maasai Steppe ecosystem of northern Tanzania, local communities depend on livestock and suitable pasture that is shared with wildlife, which can increase tsetse abundance and the risk of trypanosomiasis. We monitored the monthly tsetse fly abundance adjacent to Tarangire National Park in 2014-2015 using geo-referenced, baited epsilon traps. We examined the effect of habitat types and vegetation greenness (NDVI) on the relative abundance of tsetse fly species. Host availability (livestock and wildlife) was also recorded within 100×100 m of each trap site. The highest tsetse abundance was found in the ecotone between Acacia-Commiphora woodland and grassland, and the lowest in riverine woodland. Glossina swynnertoni was the most abundant species (68%) trapped throughout the entire study, while G. pallidipes was the least common (4%). Relative species abundance was negatively associated with NDVI, with greatest abundance observed in the dry season. The relationship with the abundance of wildlife and livestock was more complex, as we found positive and negative associations depending on the host and fly species. While habitat is important for tsetse distribution, hosts also play a critical role in affecting fly abundance and, potentially, trypanosomiasis risk. © 2017 The Society for Vector Ecology.

  15. Negative plant-soil feedback predicts tree-species relative abundance in a tropical forest.

    PubMed

    Mangan, Scott A; Schnitzer, Stefan A; Herre, Edward A; Mack, Keenan M L; Valencia, Mariana C; Sanchez, Evelyn I; Bever, James D

    2010-08-05

    The accumulation of species-specific enemies around adults is hypothesized to maintain plant diversity by limiting the recruitment of conspecific seedlings relative to heterospecific seedlings. Although previous studies in forested ecosystems have documented patterns consistent with the process of negative feedback, these studies are unable to address which classes of enemies (for example, pathogens, invertebrates, mammals) exhibit species-specific effects strong enough to generate negative feedback, and whether negative feedback at the level of the individual tree is sufficient to influence community-wide forest composition. Here we use fully reciprocal shade-house and field experiments to test whether the performance of conspecific tree seedlings (relative to heterospecific seedlings) is reduced when grown in the presence of enemies associated with adult trees. Both experiments provide strong evidence for negative plant-soil feedback mediated by soil biota. In contrast, above-ground enemies (mammals, foliar herbivores and foliar pathogens) contributed little to negative feedback observed in the field. In both experiments, we found that tree species that showed stronger negative feedback were less common as adults in the forest community, indicating that susceptibility to soil biota may determine species relative abundance in these tropical forests. Finally, our simulation models confirm that the strength of local negative feedback that we measured is sufficient to produce the observed community-wide patterns in tree-species relative abundance. Our findings indicate that plant-soil feedback is an important mechanism that can maintain species diversity and explain patterns of tree-species relative abundance in tropical forests.

  16. 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.

  17. 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.

  18. 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.

  19. 454 Pyrosequencing to Describe Microbial Eukaryotic Community Composition, Diversity and Relative Abundance: A Test for Marine Haptophytes

    PubMed Central

    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

  20. GLOBULAR CLUSTER ABUNDANCES FROM HIGH-RESOLUTION, INTEGRATED-LIGHT SPECTROSCOPY. II. EXPANDING THE METALLICITY RANGE FOR OLD CLUSTERS AND UPDATED ANALYSIS TECHNIQUES

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Colucci, Janet E.; Bernstein, Rebecca A.; McWilliam, Andrew

    2017-01-10

    We present abundances of globular clusters (GCs) in the Milky Way and Fornax from integrated-light (IL) spectra. Our goal is to evaluate the consistency of the IL analysis relative to standard abundance analysis for individual stars in those same clusters. This sample includes an updated analysis of seven clusters from our previous publications and results for five new clusters that expand the metallicity range over which our technique has been tested. We find that the [Fe/H] measured from IL spectra agrees to ∼0.1 dex for GCs with metallicities as high as [Fe/H] = −0.3, but the abundances measured for more metal-rich clustersmore » may be underestimated. In addition we systematically evaluate the accuracy of abundance ratios, [X/Fe], for Na i, Mg i, Al i, Si i, Ca i, Ti i, Ti ii, Sc ii, V i, Cr i, Mn i, Co i, Ni i, Cu i, Y ii, Zr i, Ba ii, La ii, Nd ii, and Eu ii. The elements for which the IL analysis gives results that are most similar to analysis of individual stellar spectra are Fe i, Ca i, Si i, Ni i, and Ba ii. The elements that show the greatest differences include Mg i and Zr i. Some elements show good agreement only over a limited range in metallicity. More stellar abundance data in these clusters would enable more complete evaluation of the IL results for other important elements.« less

  1. Globular Cluster Abundances from High-resolution, Integrated-light Spectroscopy. II. Expanding the Metallicity Range for Old Clusters and Updated Analysis Techniques

    NASA Astrophysics Data System (ADS)

    Colucci, Janet E.; Bernstein, Rebecca A.; McWilliam, Andrew

    2017-01-01

    We present abundances of globular clusters (GCs) in the Milky Way and Fornax from integrated-light (IL) spectra. Our goal is to evaluate the consistency of the IL analysis relative to standard abundance analysis for individual stars in those same clusters. This sample includes an updated analysis of seven clusters from our previous publications and results for five new clusters that expand the metallicity range over which our technique has been tested. We find that the [Fe/H] measured from IL spectra agrees to ˜0.1 dex for GCs with metallicities as high as [Fe/H] = -0.3, but the abundances measured for more metal-rich clusters may be underestimated. In addition we systematically evaluate the accuracy of abundance ratios, [X/Fe], for Na I, Mg I, Al I, Si I, Ca I, Ti I, Ti II, Sc II, V I, Cr I, Mn I, Co I, Ni I, Cu I, Y II, Zr I, Ba II, La II, Nd II, and Eu II. The elements for which the IL analysis gives results that are most similar to analysis of individual stellar spectra are Fe I, Ca I, Si I, Ni I, and Ba II. The elements that show the greatest differences include Mg I and Zr I. Some elements show good agreement only over a limited range in metallicity. More stellar abundance data in these clusters would enable more complete evaluation of the IL results for other important elements. This paper includes data gathered with the 6.5 m Magellan Telescopes located at Las Campanas Observatory, Chile.

  2. Estimating abundance

    USGS Publications Warehouse

    Sutherland, Chris; Royle, Andy

    2016-01-01

    This chapter provides a non-technical overview of ‘closed population capture–recapture’ models, a class of well-established models that are widely applied in ecology, such as removal sampling, covariate models, and distance sampling. These methods are regularly adopted for studies of reptiles, in order to estimate abundance from counts of marked individuals while accounting for imperfect detection. Thus, the chapter describes some classic closed population models for estimating abundance, with considerations for some recent extensions that provide a spatial context for the estimation of abundance, and therefore density. Finally, the chapter suggests some software for use in data analysis, such as the Windows-based program MARK, and provides an example of estimating abundance and density of reptiles using an artificial cover object survey of Slow Worms (Anguis fragilis).

  3. The Faber–Jackson relation and Fundamental Plane from halo abundance matching

    DOE PAGES

    Desmond, Harry; Wechsler, Risa H.

    2016-11-02

    The Fundamental Plane (FP) describes the relation between the stellar mass, size, and velocity dispersion of elliptical galaxies; the Faber–Jackson relation (FJR) is its projection on to {mass, velocity} space. In this work, we re-deploy and expand the framework of Desmond & Wechsler to ask whether abundance matching-based Λ-cold dark matter models which have shown success in matching the spatial distribution of galaxies are also capable of explaining key properties of the FJR and FP, including their scatter. Within our framework, agreement with the normalization of the FJR requires haloes to expand in response to disc formation. We find thatmore » the tilt of the FP may be explained by a combination of the observed non-homology in galaxy structure and the variation in mass-to-light ratio produced by abundance matching with a universal initial mass function, provided that the anisotropy of stellar motions is taken into account. However, the predicted scatter around the FP is considerably increased by situating galaxies in cosmologically motivated haloes due to the variations in halo properties at fixed stellar mass and appears to exceed that of the data. Finally, this implies that additional correlations between galaxy and halo variables may be required to fully reconcile these models with elliptical galaxy scaling relations.« less

  4. The relation of sediment texture to macro- and microplastic abundance in intertidal zone

    NASA Astrophysics Data System (ADS)

    Wahyuningsih, H.; Bangun, A. P.; Muhtadi, A.

    2018-02-01

    The intertidal zone is a waters area directly affected by the contamination of plastic debris from land and sea. The aim of this research were to analyze the relation of sediment texture to macro- and micro plastic abundance and also to determine appropriate management strategy. This research was conducted in intertidal zone Jaring Halus Village Langkat Regency North Sumatera Province on February-April 2017. Plastic debris was collected using quadrat transect. Sediment was collected with correct, up to a depth of least 30 cm. Abundance of micro plastic in Station 1 were positively tolerated with clay (0.509), and silt (0.787) and negatively correlations with sand (0.709) Station 2 were positively correlations with sand (0.645) and negatively correlations with clay (0.575), and silt (0.626) Station 3 were positively correlations with clay (0.435), and silt (0.466) and negatively correlations with sand (0.599). The abundance of microplastic was positively correlations with the abundance of microplastic (0.765). Microplastic density is directly proportional to the content of clay and dust. The higher the clay and dust content the higher the micro plastic density.

  5. The relative importance of water temperature and residence time in predicting cyanobacteria abundance in regulated rivers.

    PubMed

    Cha, YoonKyung; Cho, Kyung Hwa; Lee, Hyuk; Kang, Taegu; Kim, Joon Ha

    2017-11-01

    Despite a growing awareness of the problems associated with cyanobacterial blooms in rivers, and particularly in regulated rivers, the drivers of bloom formation and abundance in rivers are not well understood. We developed a Bayesian hierarchical model to assess the relative importance of predictors of summer cyanobacteria abundance, and to test whether the relative importance of each predictor varies by site, using monitoring data from 16 sites in the four major rivers of South Korea. The results suggested that temperature and residence time, but not nutrient levels, are important predictors of summer cyanobacteria abundance in rivers. Although the two predictors were of similar significance across the sites, the residence time was marginally better in accounting for the variation in cyanobacteria abundance. The model with spatial hierarchy demonstrated that temperature played a consistently significant role at all sites, and showed no effect from site-specific factors. In contrast, the importance of residence time varied significantly from site to site. This variation was shown to depend on the trophic state, indicated by the chlorophyll-a and total phosphorus levels. Our results also suggested that the magnitude of weir inflow is a key factor determining the cyanobacteria abundance under baseline conditions. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. 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. Published 2012. This article is a U.S. Government work and is in the public domain in the USA.

  7. Rapid Determination of Mineral Abundance by X-ray Microfluorescence Mapping and Multispectral Image Analysis

    NASA Astrophysics Data System (ADS)

    Moscati, R. J.; Marshall, B. D.

    2005-12-01

    X-ray microfluorescence (XRMF) spectrometry is a rapid, accurate technique to map element abundances of rock surfaces (such as thin-section billets, the block remaining when a thin section is prepared). Scanning a specimen with a collimated primary X-ray beam (100 μm diameter) generates characteristic secondary X-rays that yield the relative chemical abundances for the major rock-/mineral-forming analytes (such as Si, Al, K, Ca, and Fe). When Cu-rich epoxy is used to impregnate billets, XRMF also can determine porosity from the Cu abundance. Common billet scan size is 30 x 15 mm and the typical mapping time rarely exceeds 2.5 hrs (much faster than traditional point-counting). No polishing or coating is required for the billets, although removing coarse striations or gross irregularities on billet surfaces should improve the spatial accuracy of the maps. Background counts, spectral artifacts, and diffraction peaks typically are inconsequential for maps of major elements. An operational check is performed after every 10 analyses on a standard that contains precisely measured areas of Mn and Mo. Reproducibility of the calculated area ratio of Mn:Mo is consistently within 5% of the known value. For each billet, the single element maps (TIFF files) generated by XRMF are imported into MultiSpec© (a program developed at Purdue University for analysis of multispectral image data, available from http://dynamo.ecn.purdue.edu/~biehl/MultiSpec/) where mineral phases can be spectrally identified and their relative abundances quantified. The element maps for each billet are layered to produce a multi-element file for mineral classification and statistical processing, including modal estimates of mineral abundance. Although mineral identification is possible even if the mineralogy is unknown, prior petrographic examination of the corresponding thin section yields more accurate maps because the software can be set to identify all similar pixels. Caution is needed when using

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

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

    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 Nemore » 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.« less

  9. Normalization and microbial differential abundance strategies depend upon data characteristics.

    PubMed

    Weiss, Sophie; Xu, Zhenjiang Zech; Peddada, Shyamal; Amir, Amnon; Bittinger, Kyle; Gonzalez, Antonio; Lozupone, Catherine; Zaneveld, Jesse R; Vázquez-Baeza, Yoshiki; Birmingham, Amanda; Hyde, Embriette R; Knight, Rob

    2017-03-03

    Data from 16S ribosomal RNA (rRNA) amplicon sequencing present challenges to ecological and statistical interpretation. In particular, library sizes often vary over several ranges of magnitude, and the data contains many zeros. Although we are typically interested in comparing relative abundance of taxa in the ecosystem of two or more groups, we can only measure the taxon relative abundance in specimens obtained from the ecosystems. Because the comparison of taxon relative abundance in the specimen is not equivalent to the comparison of taxon relative abundance in the ecosystems, this presents a special challenge. Second, because the relative abundance of taxa in the specimen (as well as in the ecosystem) sum to 1, these are compositional data. Because the compositional data are constrained by the simplex (sum to 1) and are not unconstrained in the Euclidean space, many standard methods of analysis are not applicable. Here, we evaluate how these challenges impact the performance of existing normalization methods and differential abundance analyses. Effects on normalization: Most normalization methods enable successful clustering of samples according to biological origin when the groups differ substantially in their overall microbial composition. Rarefying more clearly clusters samples according to biological origin than other normalization techniques do for ordination metrics based on presence or absence. Alternate normalization measures are potentially vulnerable to artifacts due to library size. Effects on differential abundance testing: We build on a previous work to evaluate seven proposed statistical methods using rarefied as well as raw data. Our simulation studies suggest that the false discovery rates of many differential abundance-testing methods are not increased by rarefying itself, although of course rarefying results in a loss of sensitivity due to elimination of a portion of available data. For groups with large (~10×) differences in the average

  10. OXYGEN ABUNDANCES IN CEPHEIDS

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Luck, R. E.; Andrievsky, S. M.; Korotin, S. N.

    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 NLTEmore » 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.« less

  11. Project VeSElkA: results of abundance analysis for HD 53929 and HD 63975

    NASA Astrophysics Data System (ADS)

    Ndiaye, M. L.; LeBlanc, F.; Khalack, V.

    2018-03-01

    Project VeSElkA (Vertical Stratification of Element Abundances) has been initiated with the aim to detect and study the vertical stratification of element abundances in the atmosphere of chemically peculiar stars. Abundance stratification occurs in hydrodynamically stable stellar atmospheres due to the migration of the elements caused by atomic diffusion. Two HgMn stars, HD 53929 and HD 63975 were selected from the VeSElkA sample and analysed with the aim to detect some abundance peculiarities employing the ZEEMAN2 code. We present the results of abundance analysis of HD 53929 and HD 63975 observed recently with the spectropolarimeter ESPaDOnS at Canada-France-Hawaii Telescope. Evidence of phosphorus vertical stratification was detected in the atmosphere of these two stars. In both cases, phosphorus abundance increases strongly towards the superficial layers. The strong overabundance of Mn found in stellar atmosphere of both stars confirms that they are HgMn type stars.

  12. Relative and contextual contribution of different sources to the composition and abundance of indoor air bacteria in residences.

    PubMed

    Miletto, Marzia; Lindow, Steven E

    2015-12-10

    The study of the microbial communities in the built environment is of critical importance as humans spend the majority of their time indoors. While the microorganisms in living spaces, especially those in the air, can impact health and well-being, little is known of their identity and the processes that determine their assembly. We investigated the source-sink relationships of airborne bacteria in 29 homes in the San Francisco Bay Area. Samples taken in the sites expected to be source habitats for indoor air microbes were analyzed by 16S rRNA-based pyrosequencing and quantitative PCR. The community composition was related to the characteristics of the household collected at the time of sampling, including the number of residents and pets, activity levels, frequency of cooking and vacuum cleaning, extent of natural ventilation, and abundance and type of vegetation surrounding the building. Indoor air harbored a diverse bacterial community dominated by Diaphorobacter sp., Propionibacterium sp., Sphingomonas sp., and Alicyclobacillus sp. Source-sink analysis suggested that outdoor air was the primary source of indoor air microbes in most homes. Bacterial phylogenetic diversity and relative abundance in indoor air did not differ statistically from that in outdoor air. Moreover, the abundance of bacteria in outdoor air was positively correlated with that in indoor air, as would be expected if outdoor air was the main contributor to the bacterial community in indoor bioaerosols. The number of residents, presence of pets, and local tap water also influenced the diversity and size of indoor air microbes. The bacterial load in air increased with the number of residents, activity, and frequency of natural ventilation, and the proportion of bacteria putatively derived from skin increased with the number of residents. Vacuum cleaning increased the signature of pet- and floor-derived bacteria in indoor air, while the frequency of natural ventilation decreased the relative

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

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

    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 andmore » 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.« less

  14. High-resolution abundance analysis of the metallic-line star HR 7250

    NASA Astrophysics Data System (ADS)

    Elmaslı, Aslı; Ünal, Kübraözge; Çalışkan, Şeyma

    2018-07-01

    We estimated the stellar parameters and chemical abundances of the highly neglected A-type star HR 7250. The star's high resolution spectrum, spanning a wavelength range from 3900 to 7900 Å, was obtained at the TÜBİTAK National Observatory. We derived the abundances of 14 elements (O, Na, Mg, Si, S, Ca, Sc, Ti, Cr, Fe, Ni, Sr, Y, and Ba) for HR 7250 from the unblended lines of the star's spectrum. Our analysis shows that HR 7250 is a chemically peculiar Am star. We also estimated its age and mass as 400 ± 70 Myr and 3.25 ± 0.17 M⊙ from evolutionary tracks and isochrones.

  15. 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.

  16. Doppler Imaging and Chemical Abundance Analysis of EK Dra: Capabilities of Small Telescopes

    NASA Astrophysics Data System (ADS)

    Kilicoglu, Tolgahan; Senavci, H. V.; Bahar, E.; Isik, E.; Montes, D.; Hussain, G. A. J.

    2018-04-01

    We investigate the chromospheric and spot activity behaviour of the young Solar-like star EK Dra via Doppler imaging and spectral synthesis methods, using mid-resolution time series spectra of the system. We also present the atmospheric parameters and detailed elemental photospheric abundances of the star. The chemical abundance pattern of EK Dra do not suggest any remarkable peculiarities except few elements. The Titanium Oxide (TiO) bandheads at 7000 - 7100 A region also give clues about the spot temperature that may be cooler than 4000 K. In addition, we also discuss the capabilities of small telescopes (40 cm in our case) and medium resolution spectrographs in terms of Doppler imaging and chemical abundance analysis.

  17. Landbird species composition and relative abundance during migration along the Rio Grande

    Treesearch

    Wang Yong; Deborah M. Finch

    1996-01-01

    In this paper, we report species composition and relative abundances of stopover migrants during spring and fall migration along the middle Rio Grande in 1994. We recorded 157 landbird species using mist-netting and survey methods at two sites on the Rio Grande, the Bosque del Apache and the Rio Grande Nature Center. A total of 6,509 birds was captured during spring...

  18. 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

  19. Leaf Selection by Two Bornean Colobine Monkeys in Relation to Plant Chemistry and Abundance

    PubMed Central

    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

  20. Weather-related indices of autumn–winter Dabbling Duck abundance in Middle North America

    Treesearch

    Michael L. Schummer; Richard Kaminski; Andrew H. Raedeke; David A. Graber

    2010-01-01

    Research on effects of key weather stimuli influencing waterfowl migration during autumn and winter is limited. We investigated relationships between changes in relative abundances of mallard (Anas platyrhynchos) and other dabbling ducks (Anas spp.) and weather variables at midlatitude locations in North America. We used waterfowl survey data from Missouri Conservation...

  1. Plasma proteomic analysis reveals altered protein abundances in cardiovascular disease.

    PubMed

    Lygirou, Vasiliki; Latosinska, Agnieszka; Makridakis, Manousos; Mullen, William; Delles, Christian; Schanstra, Joost P; Zoidakis, Jerome; Pieske, Burkert; Mischak, Harald; Vlahou, Antonia

    2018-04-17

    Cardiovascular disease (CVD) describes the pathological conditions of the heart and blood vessels. Despite the large number of studies on CVD and its etiology, its key modulators remain largely unknown. To this end, we performed a comprehensive proteomic analysis of blood plasma, with the scope to identify disease-associated changes after placing them in the context of existing knowledge, and generate a well characterized dataset for further use in CVD multi-omics integrative analysis. LC-MS/MS was employed to analyze plasma from 32 subjects (19 cases of various CVD phenotypes and 13 controls) in two steps: discovery (13 cases and 8 controls) and test (6 cases and 5 controls) set analysis. Following label-free quantification, the detected proteins were correlated to existing plasma proteomics datasets (plasma proteome database; PPD) and functionally annotated (Cytoscape, Ingenuity Pathway Analysis). Differential expression was defined based on identification confidence (≥ 2 peptides per protein), statistical significance (Mann-Whitney p value ≤ 0.05) and a minimum of twofold change. Peptides detected in at least 50% of samples per group were considered, resulting in a total of 3796 identified proteins (838 proteins based on ≥ 2 peptides). Pathway annotation confirmed the functional relevance of the findings (representation of complement cascade, fibrin clot formation, platelet degranulation, etc.). Correlation of the relative abundance of the proteins identified in the discovery set with their reported concentrations in the PPD was significant, confirming the validity of the quantification method. The discovery set analysis revealed 100 differentially expressed proteins between cases and controls, 39 of which were verified (≥ twofold change) in the test set. These included proteins already studied in the context of CVD (such as apolipoprotein B, alpha-2-macroglobulin), as well as novel findings (such as low density lipoprotein receptor related

  2. Microbial abundance on the eggs of a passerine bird and related fitness consequences between urban and rural habitats

    PubMed Central

    Lee, Sang-im; Lee, Hyunna; Jablonski, Piotr G.; Choe, Jae Chun

    2017-01-01

    Urban environments present novel and challenging habitats to wildlife. In addition to well-known difference in abiotic factors between rural and urban environments, the biotic environment, including microbial fauna, may also differ significantly. In this study, we aimed to compare the change in microbial abundance on eggshells during incubation between urban and rural populations of a passerine bird, the Eurasian Magpie (Pica pica), and examine the consequences of any differences in microbial abundances in terms of hatching success and nestling survival. Using real-time PCR, we quantified the abundances of total bacteria, Escherichia coli/Shigella spp., surfactin-producing Bacillus spp. and Candida albicans on the eggshells of magpies. We found that urban magpie eggs harboured greater abundances of E. coli/Shigella spp. and C. albicans before incubation than rural magpie eggs. During incubation, there was an increase in the total bacterial load, but a decrease in C. albicans on urban eggs relative to rural eggs. Rural eggs showed a greater increase in E. coli/Shigella spp. relative to their urban counterpart. Hatching success of the brood was generally lower in urban than rural population. Nestling survival was differentially related with the eggshell microbial abundance between urban and rural populations, which was speculated to be the result of the difference in the strength of the interaction among the microbes. This is the first demonstration that avian clutches in urban and rural populations differ in eggshell microbial abundance, which can be further related to the difference in hatching success and nestling survival in these two types of environments. We suggest that future studies on the eggshell microbes should investigate the interaction among the microbes, because the incubation and/or environmental factors such as urbanization or climate condition can influence the dynamic interactions among the microbes on the eggshells which can further determine the

  3. Microbial abundance on the eggs of a passerine bird and related fitness consequences between urban and rural habitats.

    PubMed

    Lee, Sang-Im; Lee, Hyunna; Jablonski, Piotr G; Choe, Jae Chun; Husby, Magne

    2017-01-01

    Urban environments present novel and challenging habitats to wildlife. In addition to well-known difference in abiotic factors between rural and urban environments, the biotic environment, including microbial fauna, may also differ significantly. In this study, we aimed to compare the change in microbial abundance on eggshells during incubation between urban and rural populations of a passerine bird, the Eurasian Magpie (Pica pica), and examine the consequences of any differences in microbial abundances in terms of hatching success and nestling survival. Using real-time PCR, we quantified the abundances of total bacteria, Escherichia coli/Shigella spp., surfactin-producing Bacillus spp. and Candida albicans on the eggshells of magpies. We found that urban magpie eggs harboured greater abundances of E. coli/Shigella spp. and C. albicans before incubation than rural magpie eggs. During incubation, there was an increase in the total bacterial load, but a decrease in C. albicans on urban eggs relative to rural eggs. Rural eggs showed a greater increase in E. coli/Shigella spp. relative to their urban counterpart. Hatching success of the brood was generally lower in urban than rural population. Nestling survival was differentially related with the eggshell microbial abundance between urban and rural populations, which was speculated to be the result of the difference in the strength of the interaction among the microbes. This is the first demonstration that avian clutches in urban and rural populations differ in eggshell microbial abundance, which can be further related to the difference in hatching success and nestling survival in these two types of environments. We suggest that future studies on the eggshell microbes should investigate the interaction among the microbes, because the incubation and/or environmental factors such as urbanization or climate condition can influence the dynamic interactions among the microbes on the eggshells which can further determine the

  4. Stellar oxygen abundances. I - A resolution to the 7774 A O I abundance discrepancy

    NASA Astrophysics Data System (ADS)

    King, Jeremy R.

    1993-09-01

    We investigate the discrepancy between O/Fe abundance ratios of metal-poor stars derived from the 7774 A O I triplet and O/Fe ratios determined from other oxygen lines. We propose a possible resolution to this discrepancy which also eliminates the correlation of O/Fe and T(eff) found in a recent 7774 A O I analysis. The equivalent widths of Abia & Rebolo (1989) are found to be systematically too high by 25 percent. Arguments are presented that current temperature estimates for halo stars are 150-200 K too low. Using the guidance of both model atmospheres and other empirical color-T(eff) relations, we construct new color temperature relations for metal-poor stars. These relations are tied to the temperature scale of Saxner & Hammarback (1985) for metal-rich stars. We use (b-y) and (V-K) indices to redetermine values of T(eff) for a handful of halo stars. (B-V)-T(eff) relations which do not take into account the effects of metallicity are found to be inadequate. Revised O/Fe ratios are determined using the new temperature scale. The mean abundance ratio of the reanalyzed halo dwarfs is about +0.52. There is no trend of O/Fe with Fe/H or T(eff).

  5. Bacterial community structure and abundances of antibiotic resistance genes in heavy metals contaminated agricultural soil.

    PubMed

    Zhang, Fengli; Zhao, Xiaoxue; Li, Qingbo; Liu, Jia; Ding, Jizhe; Wu, Huiying; Zhao, Zongsheng; Ba, Yue; Cheng, Xuemin; Cui, Liuxin; Li, Hongping; Zhu, Jingyuan

    2018-04-01

    Soil contamination with heavy metals is a worldwide problem especially in China. The interrelation of soil bacterial community structure, antibiotic resistance genes, and heavy metal contamination in soil is still unclear. Here, seven agricultural areas (G1-G7) with heavy metal contamination were sampled with different distances (741 to 2556 m) to the factory. Denaturing gradient gel electrophoresis (DGGE) and Shannon index were used to analyze bacterial community diversity. Real-time fluorescence quantitative PCR was used to detect the relative abundance of ARGs sul1, sul2, tetA, tetM, tetW, one mobile genetic elements (MGE) inti1. Results showed that all samples were polluted by Cadmium (Cd), and some of them were polluted by lead (Pb), mercury (Hg), arsenic (As), copper (Cu), and zinc (Zn). DGGE showed that the most abundant bacterial species were found in G7 with the lightest heavy metal contamination. The results of the principal component analysis and clustering analysis both showed that G7 could not be classified with other samples. The relative abundance of sul1 was correlated with Cu, Zn concentration. Gene sul2 are positively related with total phosphorus, and tetM was associated with organic matter. Total gene abundances and relative abundance of inti1 both correlated with organic matter. Redundancy analysis showed that Zn and sul2 were significantly related with bacterial community structure. Together, our results indicate a complex linkage between soil heavy metal concentration, bacterial community composition, and some global disseminated ARG abundance.

  6. Caffeine Bitterness is Related to Daily Caffeine Intake and Bitter Receptor mRNA Abundance in Human Taste Tissue

    PubMed Central

    Lipchock, Sarah V.; Spielman, Andrew I.; Mennella, Julie A.; Mansfield, Corrine J.; Hwang, Liang-Dar; Douglas, Jennifer E.; Reed, Danielle R.

    2018-01-01

    We investigated whether the abundance of bitter receptor mRNA expression from human taste papillae is related to an individual’s perceptual ratings of bitter intensity and habitual intake of bitter drinks. Ratings of the bitterness of caffeine and quinine and three other bitter stimuli (urea, propylthiouracil, and denatonium benzoate) were compared with relative taste papilla mRNA abundance of bitter receptors that respond to the corresponding bitter stimuli in cell-based assays (TAS2R4, TAS2R10, TAS2R38, TAS2R43, and TAS2R46). We calculated caffeine and quinine intake from a food frequency questionnaire. The bitterness of caffeine was related to the abundance of the combined mRNA expression of these known receptors, r = 0.47, p = .05, and self-reported daily caffeine intake, t(18) = 2.78, p = .012. The results of linear modeling indicated that 47% of the variance among subjects in the rating of caffeine bitterness was accounted for by these two factors (habitual caffeine intake and taste receptor mRNA abundance). We observed no such relationships for quinine but consumption of its primary dietary form (tonic water) was uncommon. Overall, diet and TAS2R gene expression in taste papillae are related to individual differences in caffeine perception. PMID:28118781

  7. Microplitis demolitor bracovirus genome segments vary in abundance and are individually packaged in virions

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Beck, Markus H.; Inman, Ross B.; Strand, Michael R.

    2007-03-01

    Polydnaviruses (PDVs) are distinguished by their unique association with parasitoid wasps and their segmented, double-stranded (ds) DNA genomes that are non-equimolar in abundance. Relatively little is actually known, however, about genome packaging or segment abundance of these viruses. Here, we conducted electron microscopy (EM) and real-time polymerase chain reaction (PCR) studies to characterize packaging and segment abundance of Microplitis demolitor bracovirus (MdBV). Like other PDVs, MdBV replicates in the ovaries of females where virions accumulate to form a suspension called calyx fluid. Wasps then inject a quantity of calyx fluid when ovipositing into hosts. The MdBV genome consists of 15more » segments that range from 3.6 (segment A) to 34.3 kb (segment O). EM analysis indicated that MdBV virions contain a single nucleocapsid that encapsidates one circular DNA of variable size. We developed a semi-quantitative real-time PCR assay using SYBR Green I. This assay indicated that five (J, O, H, N and B) segments of the MdBV genome accounted for more than 60% of the viral DNAs in calyx fluid. Estimates of relative segment abundance using our real-time PCR assay were also very similar to DNA size distributions determined from micrographs. Analysis of parasitized Pseudoplusia includens larvae indicated that copy number of MdBV segments C, B and J varied between hosts but their relative abundance within a host was virtually identical to their abundance in calyx fluid. Among-tissue assays indicated that each viral segment was most abundant in hemocytes and least abundant in salivary glands. However, the relative abundance of each segment to one another was similar in all tissues. We also found no clear relationship between MdBV segment and transcript abundance in hemocytes and fat body.« less

  8. 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.

  9. Gray whale distribution relative to benthic invertebrate biomass and abundance: Northeastern Chukchi Sea 2009-2012

    NASA Astrophysics Data System (ADS)

    Brower, Amelia A.; Ferguson, Megan C.; Schonberg, Susan V.; Jewett, Stephen C.; Clarke, Janet T.

    2017-10-01

    The shallow continental shelf waters of the Bering and Chukchi seas are the northernmost foraging grounds of North Pacific gray whales (Eschrichtius robustus). Benthic amphipods are considered the primary prey of gray whales in these waters, although no comprehensive quantitative analysis has been performed to support this assumption. Gray whale relative abundance, distribution, and behavior in the northeastern Chukchi Sea (69°-72°N, 155-169°W) were documented during aerial surveys in June-October 2009-2012. Concurrently, vessel-based benthic infaunal sampling was conducted in the area in July-August 2009-10, September 2011, and August 2012. Gray whales were seen in the study area each month that surveys were conducted, with the majority of whales feeding. Statistical analyses confirm that the highest densities of feeding gray whales were associated with high benthic amphipod abundance, primarily within 70 km of shore from Point Barrow to Icy Cape, in water <50 m deep. Conversely, gray whales were not seen in 40-km×40-km cells containing benthic sampling stations with 85 m-2 or fewer amphipods. Continuing broad-scale aerial surveys in the Chukchi Sea and prey sampling near feeding gray whales will be an important means to monitor and document ongoing and predicted ecosystem changes.

  10. Environmental and habitat drivers of relative abundance for a suite of azteca-attacking Pseudacteon phorid flies.

    PubMed

    Reese, Katlynd M; Philpott, Stacy M

    2012-10-01

    Phoridae (Diptera) have widespread impacts on insect communities by limiting host ant behavior. However, phorid-ant interactions may vary with habitat or environmental conditions. Three Pseudacteon species parasitize Azteca instabilis Fr. Smith, a common ant in coffee agroecosystems, and limit A. instabilis foraging, indirectly benefiting other insects. However, little is known about how phorid abundance, behavior, and effects change with environmental conditions. In shaded coffee systems, coffee (Coffea arabica L.) grows under a range of shade conditions and management changes affect species interactions. For example, Pseudacteon spp. more strongly limit A. instabilis foraging in low-shade coffee habitats. We sampled relative abundance of three phorid species around A. instabilis nests in three coffee habitats varying in shade management during dry and wet seasons. We measured canopy cover, tree richness, tree density, leaf litter depth, and number of nearby trees with A. instabilis to determine whether these habitat factors correlate with phorid abundance. P. laciniosus Brown was the most abundant phorid in both seasons. Phorid relative abundance did not differ by habitat, but did differ by season. P. laciniosus accounted for a higher proportion of phorids in the wet season (91.4%) than in the dry season (78.9%), and P. planidorsalis Brown accounted for a larger percent in the dry season (21.1%) than in the wet season (7.3%). Phorid composition did not differ with habitat type, and none of the measured environmental variables correlated with changes in phorid composition. Thus, phorids in coffee agroecosystems respond to large seasonal differences, but not differences between coffee habitats.

  11. 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

  12. 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

  13. Coexistence and relative abundance in plant communities are determined by feedbacks when the scale of feedback and dispersal is local.

    PubMed

    Mack, Keenan M L; Bever, James D

    2014-09-01

    1. Negative plant-soil feedback occurs when the presence of an individual of a particular species at a particular site decreases the relative success of individuals of the same species compared to those other species at that site. This effect favors heterospecifics thereby facilitating coexistence and maintaining diversity. Empirical work has demonstrated that the average strengths of these feedbacks correlate with the relative abundance of species within a community, suggesting that feedbacks are an important driver of plant community composition. Understanding what factors contribute to the generation of this relationship is necessary for diagnosing the dynamic forces that maintain diversity in plant communities. 2. We used a spatially explicit, individual-based computer simulation to test the effects of dispersal distance, the size of feedback neighbourhoods, the strength of pairwise feedbacks and community wide variation of feedbacks, community richness, as well as life-history differences on the dependence of relative abundance on strength of feedback. 3. We found a positive dependence of relative abundance of a species on its average feedback for local scale dispersal and feedback. However, we found that the strength of this dependence decreased as either the spatial scale of dispersal and/or the spatial scale of feedback increased. We also found that for spatially local (i.e. relatively small) scale interaction and dispersal, as the mean strength of feedbacks in the community becomes less negative, the greater the increase in abundance produced by a comparable increase in species-specific average feedback. We found that life-history differences such as mortality rate did not generate a pattern with abundance, nor did they affect the relationship between abundance and average feedback. 4. Synthesis . Our results support the claim that empirical observations of a positive correlation between relative abundance and strength of average feedback serves as

  14. The chemical abundance analysis of normal early A- and late B-type stars

    NASA Astrophysics Data System (ADS)

    Fossati, L.; Ryabchikova, T.; Bagnulo, S.; Alecian, E.; Grunhut, J.; Kochukhov, O.; Wade, G.

    2009-09-01

    Context: Modern spectroscopy of early-type stars often aims at studying complex physical phenomena such as stellar pulsation, the peculiarity of the composition of the photosphere, chemical stratification, the presence of a magnetic field, and its interplay with the stellar atmosphere and the circumstellar environment. Comparatively less attention is paid to identifying and studying the “normal” A- and B-type stars and testing how the basic atomic parameters and standard spectral analysis allow one to fit the observations. By contrast, this kind of study is paramount for eventually allowing one to correctly quantify the impact of the various physical processes that occur inside the atmospheres of A- and B-type stars. Aims: We wish to establish whether the chemical composition of the solar photosphere can be regarded as a reference for early A- and late B-type stars. Methods: We have obtained optical high-resolution, high signal-to-noise ratio spectra of three slowly rotating early-type stars (HD 145788, 21 Peg and π Cet) that show no obvious sign of chemical peculiarity, and performed a very accurate LTE abundance analysis of up to 38 ions of 26 elements (for 21 Peg), using a vast amount of spectral lines visible in the spectral region covered by our spectra. Results: We provide an exhaustive description of the abundance characteristics of the three analysed stars with a critical review of the line parameters used to derive the abundances. We compiled a table of atomic data for more than 1100 measured lines that may be used in the future as a reference. The abundances we obtained for He, C, Al, S, V, Cr, Mn, Fe, Ni, Sr, Y, and Zr are compatible with the solar ones derived with recent 3D radiative-hydrodynamical simulations of the solar photosphere. The abundances of the remaining studied elements show some degree of discrepancy compared to the solar photosphere. Those of N, Na, Mg, Si, Ca, Ti, and Nd may well be ascribed to non-LTE effects; for P, Cl, Sc and

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Colburn, Heather A.; Wunschel, David S.; Kreuzer-Martin, Helen W.

    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 andmore » 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.« less

  16. Exploring the Abundance and Diversity of Bacterial Communities and Quantifying Antibiotic-Related Genes Along an Elevational Gradient in Taibai Mountain, China.

    PubMed

    Peng, Chu; Wang, He; Jiang, Yingying; Yang, Jinhua; Lai, Hangxian; Wei, Xiaomin

    2018-05-10

    Thus far, no studies have investigated the soil microbial diversity over an elevational gradient in Taibai Mountain, the central massif of the Qinling Mountain Range. Here, we used Illumina sequencing and quantitative PCR of the 16S rRNA gene to assess the diversity and abundance of bacterial communities along an elevational gradient in representative vegetation soils in Taibai Mountain. We identified the soil, climate, and vegetation factors driving the variations in soil bacterial community structure by Pearson correlation and redundancy analysis. We also evaluated the potential for antibiotic discovery by quantitative PCR of the PKS-I, PKS-II, and NRPS genes from Actinobacteria. The results showed that soil bacterial alpha diversity increased first and then decreased with an elevational rise in both the northern and southern slopes of Taibai Mountain. The bacterial abundance was significantly correlated with soil organic matter and nitrate nitrogen. The average relative abundance of Actinobacteria in Taibai Mountain was markedly higher than those in other mountain forest soils. The absolute abundance of PKS and NPRS gene was significantly higher in the tested soils compared with the gene copy numbers reported in tropical urban soils. Taibai Mountain is rich in actinomycete resources and has great potential for antibiotic excavation.

  17. 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.

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

    PubMed Central

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

    2009-01-01

    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. PMID:19706391

  19. Size matters: abundance matching, galaxy sizes, and the Tully-Fisher relation in EAGLE

    NASA Astrophysics Data System (ADS)

    Ferrero, Ismael; Navarro, Julio F.; Abadi, Mario G.; Sales, Laura V.; Bower, Richard G.; Crain, Robert A.; Frenk, Carlos S.; Schaller, Matthieu; Schaye, Joop; Theuns, Tom

    2017-02-01

    The Tully-Fisher relation (TFR) links the stellar mass of a disc galaxy, Mstr, to its rotation speed: it is well approximated by a power law, shows little scatter, and evolves weakly with redshift. The relation has been interpreted as reflecting the mass-velocity scaling (M ∝ V3) of dark matter haloes, but this interpretation has been called into question by abundance-matching (AM) models, which predict the galaxy-halo mass relation to deviate substantially from a single power law and to evolve rapidly with redshift. We study the TFR of luminous spirals and its relation to AM using the EAGLE set of Λ cold dark matter (ΛCDM) cosmological simulations. Matching both relations requires disc sizes to satisfy constraints given by the concentration of haloes and their response to galaxy assembly. EAGLE galaxies approximately match these constraints and show a tight mass-velocity scaling that compares favourably with the observed TFR. The TFR is degenerate to changes in galaxy formation efficiency and the mass-size relation; simulations that fail to match the galaxy stellar mass function may fit the observed TFR if galaxies follow a different mass-size relation. The small scatter in the simulated TFR results because, at fixed halo mass, galaxy mass and rotation speed correlate strongly, scattering galaxies along the main relation. EAGLE galaxies evolve with lookback time following approximately the prescriptions of AM models and the observed mass-size relation of bright spirals, leading to a weak TFR evolution consistent with observation out to z = 1. ΛCDM models that match both the abundance and size of galaxies as a function of stellar mass have no difficulty reproducing the observed TFR and its evolution.

  20. Covariation of Peptide Abundances Accurately Reflects Protein Concentration Differences*

    PubMed Central

    Pirmoradian, Mohammad

    2017-01-01

    Most implementations of mass spectrometry-based proteomics involve enzymatic digestion of proteins, expanding the analysis to multiple proteolytic peptides for each protein. Currently, there is no consensus of how to summarize peptides' abundances to protein concentrations, and such efforts are complicated by the fact that error control normally is applied to the identification process, and do not directly control errors linking peptide abundance measures to protein concentration. Peptides resulting from suboptimal digestion or being partially modified are not representative of the protein concentration. Without a mechanism to remove such unrepresentative peptides, their abundance adversely impacts the estimation of their protein's concentration. Here, we present a relative quantification approach, Diffacto, that applies factor analysis to extract the covariation of peptides' abundances. The method enables a weighted geometrical average summarization and automatic elimination of incoherent peptides. We demonstrate, based on a set of controlled label-free experiments using standard mixtures of proteins, that the covariation structure extracted by the factor analysis accurately reflects protein concentrations. In the 1% peptide-spectrum match-level FDR data set, as many as 11% of the peptides have abundance differences incoherent with the other peptides attributed to the same protein. If not controlled, such contradicting peptide abundance have a severe impact on protein quantifications. When adding the quantities of each protein's three most abundant peptides, we note as many as 14% of the proteins being estimated as having a negative correlation with their actual concentration differences between samples. Diffacto reduced the amount of such obviously incorrectly quantified proteins to 1.6%. Furthermore, by analyzing clinical data sets from two breast cancer studies, our method revealed the persistent proteomic signatures linked to three subtypes of breast cancer

  1. 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.

  2. Intestinal parasites of the Arctic fox in relation to the abundance and distribution of intermediate hosts.

    PubMed

    Stien, A; Voutilainen, L; Haukisalmi, V; Fuglei, E; Mørk, T; Yoccoz, N G; Ims, R A; Henttonen, H

    2010-01-01

    The intestinal parasite community of Arctic foxes (Vulpes lagopus) on the Svalbard archipelago in the High Arctic was investigated in relation to the abundance and distribution of intermediate hosts. Five species of cestodes (Echinococcus multilocularis, Taenia crassiceps, Taenia polyacantha, Taenia krabbei and Diphyllobothrium sp.), ascaridoid nematodes and one unidentified acanthocephalan species were found. The cestodes E. multilocularis, T. crassiceps and T. polyacantha all showed a decreasing prevalence in the fox population with increasing distance from their spatially restricted intermediate host population of sibling voles (Microtus levis). In addition, the prevalence of E. multilocularis in a sample from the vole population was directly related to the local vole abundance. The cestode T. krabbei uses reindeer as intermediate host, and its prevalence in female foxes was positively related to the density of reindeer (Rangifer tarandus platyrhyncus). Finally, the prevalence of the ascaridoid nematodes also decreased with increasing distance from the vole population, a finding that is consistent with the idea that voles are involved in transmission, most likely as paratenic hosts. The prevalence of the remaining species (Diphyllobothrium sp. and an unidentified acanthocephalan) was very low. We conclude that the distribution and abundance of intermediate host structure the gastrointestinal parasite community of the Arctic fox on the Svalbard archipelago.

  3. Relative abundance of total subgingival plaque-specific bacteria in salivary microbiota reflects the overall periodontal condition in patients with periodontitis.

    PubMed

    Kageyama, Shinya; Takeshita, Toru; Asakawa, Mikari; Shibata, Yukie; Takeuchi, Kenji; Yamanaka, Wataru; Yamashita, Yoshihisa

    2017-01-01

    Increasing attention is being focused on evaluating the salivary microbiota as a promising method for monitoring oral health; however, its bacterial composition greatly differs from that of dental plaque microbiota, which is a dominant etiologic factor of oral diseases. This study evaluated the relative abundance of subgingival plaque-specific bacteria in the salivary microbiota and examined a relationship between the abundance and severity of periodontal condition in patients with periodontitis. Four samples (subgingival and supragingival plaques, saliva, and tongue coating) per each subject were collected from 14 patients with a broad range of severity of periodontitis before periodontal therapy. The bacterial composition was analyzed by 16S rRNA gene amplicon sequencing using Ion PGM. Of the 66 species-level operational taxonomic units (OTUs) representing the mean relative abundance of ≥ 1% in any of the four niches, 12 OTUs corresponding to known periodontal pathogens, including Porphyromonas gingivalis, were characteristically predominant in the subgingival plaque and constituted 37.3 ± 22.9% of the microbiota. The total relative abundance of these OTUs occupied only 1.6 ± 1.2% of the salivary microbiota, but significantly correlated with the percentage of diseased sites (periodontal pocket depth ≥ 4 mm; r = 0.78, P < 0.001), in addition to the abundance of subgingival plaque microbiota (r = 0.61, P = 0.02). After periodontal therapy, the total relative abundance of these 12 OTUs was evaluated as well as before periodontal therapy and reductions of the abundance through periodontal therapy were strongly correlated in saliva and subgingival plaque (r = 0.81, P < 0.001). Based on these results, salivary microbiota might be a promising target for the evaluation of subgingival plaque-derived bacteria representing the present condition of periodontal health.

  4. Relative abundance of total subgingival plaque-specific bacteria in salivary microbiota reflects the overall periodontal condition in patients with periodontitis

    PubMed Central

    Kageyama, Shinya; Takeshita, Toru; Asakawa, Mikari; Shibata, Yukie; Takeuchi, Kenji; Yamanaka, Wataru

    2017-01-01

    Increasing attention is being focused on evaluating the salivary microbiota as a promising method for monitoring oral health; however, its bacterial composition greatly differs from that of dental plaque microbiota, which is a dominant etiologic factor of oral diseases. This study evaluated the relative abundance of subgingival plaque-specific bacteria in the salivary microbiota and examined a relationship between the abundance and severity of periodontal condition in patients with periodontitis. Four samples (subgingival and supragingival plaques, saliva, and tongue coating) per each subject were collected from 14 patients with a broad range of severity of periodontitis before periodontal therapy. The bacterial composition was analyzed by 16S rRNA gene amplicon sequencing using Ion PGM. Of the 66 species-level operational taxonomic units (OTUs) representing the mean relative abundance of ≥ 1% in any of the four niches, 12 OTUs corresponding to known periodontal pathogens, including Porphyromonas gingivalis, were characteristically predominant in the subgingival plaque and constituted 37.3 ± 22.9% of the microbiota. The total relative abundance of these OTUs occupied only 1.6 ± 1.2% of the salivary microbiota, but significantly correlated with the percentage of diseased sites (periodontal pocket depth ≥ 4 mm; r = 0.78, P < 0.001), in addition to the abundance of subgingival plaque microbiota (r = 0.61, P = 0.02). After periodontal therapy, the total relative abundance of these 12 OTUs was evaluated as well as before periodontal therapy and reductions of the abundance through periodontal therapy were strongly correlated in saliva and subgingival plaque (r = 0.81, P < 0.001). Based on these results, salivary microbiota might be a promising target for the evaluation of subgingival plaque-derived bacteria representing the present condition of periodontal health. PMID:28369125

  5. Seasonal and annual variation in the diet of Atlantic cod (Gadus morhua) in relation to the abundance of capelin (Mallotus villosus) off eastern Newfoundland, Canada

    USGS Publications Warehouse

    Methven, David A.; Piatt, John F.

    1989-01-01

    The importance of capelin as prey for cod has long been known (Thompson, 1943; and see Lilly (1987) for a review); however, no studies have been conducted on how the highly dynamic seasonal and yearly variations in capelin abundance affect cod diet. We studied the occurrence of capelin in cod stomachs in relation to the relative abundance of capelin at Witless Bay, Newfoundland (47°15’N 52°46’W), during June, July and August, 1982-1984. The mean number of capelin per stomach and the per cent occurrence of stomachs containing capelin were determined for each collection of stomachs. A total of 680 stomachs were examined. Cod were sampled from those caught in gillnets by fishermen and averaged 66 cm ± 8 (s.d.) in 1983 and 62 cm ± 8 (s.d.) in 1984. Relative abundance of capelin in the local habitat was determined by conducting hydroacoustic surveys around Gull Island in Witless Bay, the same area where cod were collected for stomach content analysis. Only hydroacoustic surveys conducted within three days of cod stomach collections were analyzed. Further details of hydroacoustic surveys including quantifications of acoustic echograms are described in Piatt (1989).

  6. 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, Allen 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

  7. Experimental and theoretical oscillator strengths of Mg I for accurate abundance analysis

    NASA Astrophysics Data System (ADS)

    Pehlivan Rhodin, A.; Hartman, H.; Nilsson, H.; Jönsson, P.

    2017-02-01

    Context. With the aid of stellar abundance analysis, it is possible to study the galactic formation and evolution. Magnesium is an important element to trace the α-element evolution in our Galaxy. For chemical abundance analysis, such as magnesium abundance, accurate and complete atomic data are essential. Inaccurate atomic data lead to uncertain abundances and prevent discrimination between different evolution models. Aims: We study the spectrum of neutral magnesium from laboratory measurements and theoretical calculations. Our aim is to improve the oscillator strengths (f-values) of Mg I lines and to create a complete set of accurate atomic data, particularly for the near-IR region. Methods: We derived oscillator strengths by combining the experimental branching fractions with radiative lifetimes reported in the literature and computed in this work. A hollow cathode discharge lamp was used to produce free atoms in the plasma and a Fourier transform spectrometer recorded the intensity-calibrated high-resolution spectra. In addition, we performed theoretical calculations using the multiconfiguration Hartree-Fock program ATSP2K. Results: This project provides a set of experimental and theoretical oscillator strengths. We derived 34 experimental oscillator strengths. Except from the Mg I optical triplet lines (3p 3P°0,1,2-4s 3S1), these oscillator strengths are measured for the first time. The theoretical oscillator strengths are in very good agreement with the experimental data and complement the missing transitions of the experimental data up to n = 7 from even and odd parity terms. We present an evaluated set of oscillator strengths, gf, with uncertainties as small as 5%. The new values of the Mg I optical triplet line (3p 3P°0,1,2-4s 3S1) oscillator strength values are 0.08 dex larger than the previous measurements.

  8. Predicting network modules of cell cycle regulators using relative protein abundance statistics.

    PubMed

    Oguz, Cihan; Watson, Layne T; Baumann, William T; Tyson, John J

    2017-02-28

    Parameter estimation in systems biology is typically done by enforcing experimental observations through an objective function as the parameter space of a model is explored by numerical simulations. Past studies have shown that one usually finds a set of "feasible" parameter vectors that fit the available experimental data equally well, and that these alternative vectors can make different predictions under novel experimental conditions. In this study, we characterize the feasible region of a complex model of the budding yeast cell cycle under a large set of discrete experimental constraints in order to test whether the statistical features of relative protein abundance predictions are influenced by the topology of the cell cycle regulatory network. Using differential evolution, we generate an ensemble of feasible parameter vectors that reproduce the phenotypes (viable or inviable) of wild-type yeast cells and 110 mutant strains. We use this ensemble to predict the phenotypes of 129 mutant strains for which experimental data is not available. We identify 86 novel mutants that are predicted to be viable and then rank the cell cycle proteins in terms of their contributions to cumulative variability of relative protein abundance predictions. Proteins involved in "regulation of cell size" and "regulation of G1/S transition" contribute most to predictive variability, whereas proteins involved in "positive regulation of transcription involved in exit from mitosis," "mitotic spindle assembly checkpoint" and "negative regulation of cyclin-dependent protein kinase by cyclin degradation" contribute the least. These results suggest that the statistics of these predictions may be generating patterns specific to individual network modules (START, S/G2/M, and EXIT). To test this hypothesis, we develop random forest models for predicting the network modules of cell cycle regulators using relative abundance statistics as model inputs. Predictive performance is assessed by the

  9. Relative Abundance in Bacterial and Fungal Gut Microbes in Obese Children: A Case Control Study.

    PubMed

    Borgo, Francesca; Verduci, Elvira; Riva, Alessandra; Lassandro, Carlotta; Riva, Enrica; Morace, Giulia; Borghi, Elisa

    2017-02-01

    Differences in relative proportions of gut microbial communities in adults have been correlated with intestinal diseases and obesity. In this study we evaluated the gut microbiota biodiversity, both bacterial and fungal, in obese and normal-weight school-aged children. We studied 28 obese (mean age 10.03 ± 0.68) and 33 age- and sex-matched normal-weight children. BMI z-scores were calculated, and the obesity condition was defined according to the WHO criteria. Fecal samples were analyzed by 16S rRNA amplification followed by denaturing gradient gel electrophoresis (DGGE) analysis and sequencing. Real-time polymerase chain reaction (PCR) was performed to quantify the most representative microbial species and genera. DGGE profiles showed high bacterial biodiversity without significant correlations with BMI z-score groups. Compared to bacterial profiles, we observed lower richness in yeast species. Sequence of the most representative bands gave back Eubacterium rectale, Saccharomyces cerevisiae, Candida albicans, and C. glabrata as present in all samples. Debaryomyces hansenii was present only in two obese children. Obese children revealed a significantly lower abundance in Akkermansia muciniphyla, Faecalibacterium prausnitzii, Bacteroides/Prevotella group, Candida spp., and Saccharomyces spp. (P = 0.031, P = 0.044, P = 0.003, P = 0.047, and P = 0.034, respectively). Taking into account the complexity of obesity, our data suggest that differences in relative abundance of some core microbial species, preexisting or diet driven, could actively be part of its etiology. This study improved our knowledge about the fungal population in the pediatric school-age population and highlighted the need to consider the influence of cross-kingdom relationships.

  10. 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.

  11. 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.

  12. 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.

  13. PPAK wide-field Integral Field Spectroscopy of NGC 628 - II. Emission line abundance analysis

    NASA Astrophysics Data System (ADS)

    Rosales-Ortega, F. F.; Díaz, A. I.; Kennicutt, R. C.; Sánchez, S. F.

    2011-08-01

    In this second paper of the series, we present the two-dimensional (2D) emission line abundance analysis of NGC 628, the largest object within the PPAK Integral Field Spectroscopy (IFS) Nearby Galaxies Survey, PINGS. We introduce the methodology applied to the 2D IFS data in order to extract and deal with large spectral samples, from which a 2D abundance analysis can be later performed. We obtain the most complete and reliable abundance gradient of the galaxy up to date, by using the largest number of spectroscopic points sampled in the galaxy, and by comparing the statistical significance of different strong-line metallicity indicators. We find features not previously reported for this galaxy that imply a multimodality of the abundance gradient consistent with a nearly flat distribution in the innermost regions of the galaxy, a steep negative gradient along the disc and a shallow gradient or nearly constant metallicity beyond the optical edge of the galaxy. The N/O ratio seems to follow the same radial behaviour. We demonstrate that the observed dispersion in metallicity shows no systematic dependence with the spatial position, signal-to-noise ratio or ionization conditions, implying that the scatter in abundance for a given radius is reflecting a true spatial physical variation of the oxygen content. Furthermore, by exploiting the 2D IFS data, we were able to construct the 2D metallicity structure of the galaxy, detecting regions of metal enhancement and showing that they vary depending on the choice of the metallicity estimator. The analysis of axisymmetric variations in the disc of NGC 628 suggest that the physical conditions and the star formation history of different symmetric regions of the galaxy have evolved in a different manner. Based on observations made at the Centro Astronómico Hispano Alemán (CAHA) at Calar Alto, operated jointly by the Max-Planck Institut für Astronomie and the Instituto de Astrofísica de Andalucía (CSIC).

  14. 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

  15. 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).

  16. 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.

  17. 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.

  18. 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.

  19. Abundances in metal-rich stars. Detailed abundance analysis of 47 G and K dwarf stars with [Me/H] > 0.10 dex

    NASA Astrophysics Data System (ADS)

    Feltzing, S.; Gustafsson, B.

    1998-04-01

    We have derived elemental abundances of O, Na, Mg, Al, Si, Ca, Ti, Cr, Mn, Fe, Co, Ni as well as for a number of s-elements for 47 G and K dwarf, with [Me/H]>0.1 dex. The selection of stars was based on their kinematics as well as on their uvby-beta photometry. One sample of stars on rather eccentric orbits traces the chemical evolution interior to the solar orbit and another, on circular orbits, the evolution around the solar orbit. A few Extreme Population I stars were included in the latter sample. The stars have -0.1 dex < [Fe/H] < 0.42 dex. The spectroscopic [Fe/H] correlate well with the [Me/H] derived from uvby-beta photometry. We find that the elemental abundances of Mg, Al, Si, Ca, Ti, Cr and Ni all follow [Fe/H]. Our data put further constraints on models of galactic chemical evolution, in particular of Cr, Mn and Co which have not previously been studied for dwarf stars with [Me/H] >0.1 dex. The increase in [Na/Fe] and [Al/Fe] as a function of [Fe/H] found previously by \\cite[Edvardsson et al. (1993a)]{Edv93} has been confirmed for [Na/Fe]. This upturning relation, and the scatter around it, are shown not to be due to a mixture of populations with different mean distances to the galactic centre. We do not confirm the same trend for aluminium, which is somewhat surprising since both these elements are thought to be produced in the same environments in the pre-supernova stars. Nor have we been able to trace any tendency for relative abundances of O, Si, and Ti relative to Fe to vary with the stellar velocities, i.e. the stars present mean distance to the galactic centre. These results imply that there is no significant difference in the chemical evolution of the different stellar populations for stars with [Me/H]>0.1 dex. We find that [O/Fe] continue to decline with increasing [Fe/H] and that oxygen and europium correlate well. However [Si/Fe] and [Ca/Fe] seem to stay constant. A real (``cosmic'') scatter in [Ti/Fe] at given [Fe/H] is suggested as well as

  20. Chemical abundance analysis of 13 southern symbiotic giants from high-resolution spectra at ˜1.56 μm

    NASA Astrophysics Data System (ADS)

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

    2017-04-01

    Symbiotic stars (SySt) are binaries composed of a star in the later stages of evolution and a stellar remnant. The enhanced mass-loss from the giant drives interacting mass exchange and makes these systems laboratories for understanding binary evolution. Studies of the chemical compositions are particularly useful since this parameter has strong impact on the evolutionary path. The previous paper in this series presented photospheric abundances for 24 giants in S-type SySt enabling a first statistical analysis. Here, we present results for an additional sample of 13 giants. The aims are to improve statistics of chemical composition involved in the evolution of SySt, to study evolutionary status, mass transfer and to interpret this in terms of Galactic populations. High-resolution, near-IR spectra are used, employing the spectrum synthesis method in a classical approach, to obtain abundances of CNO and elements around the iron peak (Fe, Ti, Ni). Low-resolution spectra in the region around the Ca II triplet were used for spectral classification. The metallicities obtained cover a wide range with a maximum around ˜- 0.2 dex. The enrichment in the 14N isotope indicates that these giants have experienced the first dredge-up. Relative O and Fe abundances indicate that most SySt belong to the Galactic disc; however, in a few cases, the extended thick-disc/halo is suggested. Difficult to explain, relatively high Ti abundances can indicate that adopted microturbulent velocities were too small by ˜0.2-0.3 km s-1. The revised spectral types for V2905 Sgr, and WRAY 17-89 are M3 and M6.5, respectively.

  1. Project VeSElkA: abundance analysis of chemical species in HD 41076 and HD 148330

    NASA Astrophysics Data System (ADS)

    Khalack, V.; Gallant, G.; Thibeault, C.

    2017-10-01

    A new semi-automatic approach is employed to carry out the abundance analysis of high-resolution spectra of HD 41076 and HD 148330 obtained recently with the spectropolarimetre Echelle SpectroPolarimetric Device for Observations of Stars at the Canada-France-Hawaii Telescope. This approach allows to prepare in a semi-automatic mode the input data for the modified zeeman2 code and to analyse several hundreds of line profiles in sequence during a single run. It also provides more information on abundance distribution for each chemical element at the deeper atmospheric layers. Our analysis of the Balmer profiles observed in the spectra of HD 41076 and HD 148330 has resulted in the estimates of their effective temperature, gravity, metallicity and radial velocity. The respective models of stellar atmosphere have been calculated with the code phoenix and used to carry out abundance analysis employing the modified zeeman2 code. The analysis shows a deficit of the C, N, F, Mg, Ca, Ti, V, Cu, Y, Mo, Sm and Gd, and overabundance of Cr, Mn, Fe, Co, Ni, Sr, Zr, Ba, Ce, Nd and Dy in the stellar atmosphere of HD 41076. In the atmosphere of HD 148330, the C, N and Mo appear to be underabundant, while the Ne, Na, Al, Si, P, Ca, Ti, V, Cr, Mn, Fe, Co, Ni, Zn, Sr, Y, Zr, Ba, Ce, Pr, Nd, Sm, Eu, Gd and Dy are overabundant. We also have found signatures of vertical abundance stratification of Fe, Ti, Cr and Mn in HD 41076, and of Fe, Ti, V, Cr, Mn, Y, Zr, Ce, Nd, Sm and Gd in HD 148330.

  2. 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.

  3. Diversity and relative abundance of the bacterial pathogen, Flavobacterium spp., infecting reproductive ecotypes of kokanee salmon.

    PubMed

    Lemay, Matthew A; Russello, Michael A

    2014-11-04

    Understanding the distribution and abundance of pathogens can provide insight into the evolution and ecology of their host species. Previous research in kokanee, the freshwater form of sockeye salmon (Oncorhynchus nerka), found evidence that populations spawning in streams may experience a greater pathogen load compared with populations that spawn on beaches. In this study we tested for differences in the abundance and diversity of the gram-negative bacteria, Flavobacterium spp., infecting tissues of kokanee in both of these spawning habitats (streams and beaches). Molecular assays were carried out using primers designed to amplify a ~200 nucleotide region of the gene encoding the ATP synthase alpha subunit (AtpA) within the genus Flavobacterium. Using a combination of DNA sequencing and quantitative PCR (qPCR) we compared the diversity and relative abundance of Flavobacterium AtpA amplicons present in DNA extracted from tissue samples of kokanee collected from each spawning habitat. We identified 10 Flavobacterium AtpA haplotypes among the tissues of stream-spawning kokanee and seven haplotypes among the tissues of beach-spawning kokanee, with only two haplotypes shared between spawning habitats. Haplotypes occurring in the same clade as F. psychrophilum were the most prevalent (92% of all reads, 60% of all haplotypes), and occurred in kokanee from both spawning habitats (streams and beaches). Subsequent qPCR assays did not find any significant difference in the relative abundance of Flavobacterium AtpA amplicons between samples from the different spawning habitats. We confirmed the presence of Flavobacterium spp. in both spawning habitats and found weak evidence for increased Flavobacterium diversity in kokanee sampled from stream-spawning sites. However, the quantity of Flavobacterium DNA did not differ between spawning habitats. We recommend further study aimed at quantifying pathogen diversity and abundance in population-level samples of kokanee combined with

  4. Solar abundance of silicon

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Holweger, H.

    1973-07-01

    An analysis of 19 photospheric Si I lines whose oscillator strengths have recently been detertmined by Garz (1973) leads to a solar abundance of silicon, log epsilon /sub Si/ = 7.65 plus or minus 0.07, on the scale where log epsilon /sub H/ = 12. Together with the sodium abundance determained earlier by the same method, a solar abundance ratio /sup epsilon /Na//sup epsilon /Si = 0.045 ( plus or minus 10%) results. Within the error limits this a grees wtth the meteoritic ratio found in carbonaceous chondrites. Results concerning line-broadening by hydrogen are discussed. (auth)

  5. 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.

  6. Differential Ablation of Cosmic Dust and Implications for the Relative Abundances of Atmospheric Metals

    NASA Astrophysics Data System (ADS)

    McNeil, W. J.

    1997-09-01

    Metals in the Earth's atmosphere are of interest and importance for several reasons. Emission lines from the sodium layer are used for wave front corrections in imaging space objects. The ionospheric metals present background contamination for remote sensing and tracking of space- born objects. Ionization during meteor showers may also interfere with communications. Although it is generally accepted that extraterrestrial material is the source of metals in the atmospheric, the relative abundances of mesospheric metals and ions present us with a conundrum. Lidar observations have consistently shown that the abundances of neutral metals in the atmospheric and the abundances of these metals in the meteoric material that falls to earth are significantly disproportionate. For example, the column density of neutral sodium is perhaps two orders of magnitude larger than that of calcium, while the abundances in meteorites are approximately equal. To complicate matters further, ion mass spectroscopy has shown that the abundances of the meteoric ions match reasonably well those in the meteorites. We present here a model that attempts to address these discrepancies. At the heart of the model is the concept of differential ablation, which suggests that more volatile metals sublimate earlier in the descent of a cosmic dust particle than do the less volatile components. The modeling is carried out comprehensively, beginning with the heating and vaporization of the dust particles. The vaporization rate is computed as a function of altitude from an ensemble of particles to give a deposition function which is then injected into a fully time-dependent kinetic code which allows for vertical diffusion and includes diurnal dependence through both the models of the major atmospheric components and through transport of the ions due to electric fields.

  7. Estimating abundance: Chapter 27

    USGS Publications Warehouse

    Royle, J. Andrew

    2016-01-01

    This chapter provides a non-technical overview of ‘closed population capture–recapture’ models, a class of well-established models that are widely applied in ecology, such as removal sampling, covariate models, and distance sampling. These methods are regularly adopted for studies of reptiles, in order to estimate abundance from counts of marked individuals while accounting for imperfect detection. Thus, the chapter describes some classic closed population models for estimating abundance, with considerations for some recent extensions that provide a spatial context for the estimation of abundance, and therefore density. Finally, the chapter suggests some software for use in data analysis, such as the Windows-based program MARK, and provides an example of estimating abundance and density of reptiles using an artificial cover object survey of Slow Worms (Anguis fragilis).

  8. 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.

  9. LDL receptor-related protein 1 regulates the abundance of diverse cell-signaling proteins in the plasma membrane proteome.

    PubMed

    Gaultier, Alban; Simon, Gabriel; Niessen, Sherry; Dix, Melissa; Takimoto, Shinako; Cravatt, Benjamin F; Gonias, Steven L

    2010-12-03

    LDL receptor-related protein 1 (LRP1) is an endocytic receptor, reported to regulate the abundance of other receptors in the plasma membrane, including uPAR and tissue factor. The goal of this study was to identify novel plasma membrane proteins, involved in cell-signaling, that are regulated by LRP1. Membrane protein ectodomains were prepared from RAW 264.7 cells in which LRP1 was silenced and control cells using protease K. Peptides were identified by LC-MS/MS. By analysis of spectral counts, 31 transmembrane and secreted proteins were regulated in abundance at least 2-fold when LRP1 was silenced. Validation studies confirmed that semaphorin4D (Sema4D), plexin domain-containing protein-1 (Plxdc1), and neuropilin-1 were more abundant in the membranes of LRP1 gene-silenced cells. Regulation of Plxdc1 by LRP1 was confirmed in CHO cells, as a second model system. Plxdc1 coimmunoprecipitated with LRP1 from extracts of RAW 264.7 cells and mouse liver. Although Sema4D did not coimmunoprecipitate with LRP1, the cell-surface level of Sema4D was increased by RAP, which binds to LRP1 and inhibits binding of other ligands. These studies identify Plxdc1, Sema4D, and neuropilin-1 as novel LRP1-regulated cell-signaling proteins. Overall, LRP1 emerges as a generalized regulator of the plasma membrane proteome.

  10. Abundance analysis of a CEMP-no star in the Carina dwarf spheroidal galaxy

    NASA Astrophysics Data System (ADS)

    Susmitha, A.; Koch, A.; Sivarani, T.

    2017-10-01

    Carbon-enhanced metal-poor (CEMP) stars bear important imprints of the early chemical enrichment of any stellar system. While these stars are known to exist in copious amounts in the Milky Way halo, detailed chemical abundance data from the faint dwarf spheroidal (dSph) satellites are still sparse, although the relative fraction of these stars increases with decreasing metallicity. Here, we report the abundance analysis of a metal-poor ([ Fe / H ] = - 2.5 dex), carbon-rich ([C/Fe] = 1.4 dex) star, ALW-8, in the Carina dSph using high-resolution spectroscopy obtained with the ESO/UVES instrument. Its spectrum does not indicate any over-enhancements of neutron capture elements. Thus classified as a CEMP-no star, this is the first detection of this kind of star in Carina. Another of our sample stars, ALW-1, is shown to be a CEMP-s star, but its immediate binarity prompted us to discard it from a detailed analysis. The majority of the 18 chemical elements we measured are typical of Carina's field star population and also agree with CEMP stars in other dSph galaxies. Similar to the only known CEMP-no star in the Sculptor dSph and the weak-r-process star HD 122563, the lack of any strong barium-enhancement is accompanied by a moderate overabundance in yttrium, indicating a weak r-process activity. The overall abundance pattern confirms that, also in Carina, the formation site for CEMP-no stars has been affected by both faint supernovae and by standard core collapse supernovae. Whichever process was responsible for the heavy element production in ALW-8 must be a ubiquitous source to pollute the CEMP-no stars, acting independently of the environment such as in the Galactic halo or in dSphs. Based on observations collected at the European Southern Observatory at Paranal, Chile; Large Programme proposal 171.B- 0520.Table A.1 is also available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http

  11. 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.

  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 Chemical Elements in RR Lyrae Variables and their Kinematic Parameters

    NASA Astrophysics Data System (ADS)

    Gozha, M. L.; Marsakov, V. A.; Koval', V. V.

    2018-03-01

    A catalog of the chemical and spatial-kinematic parameters of 415 RR Lyrae variables (Lyrids) in the galactic field is compiled. Spectroscopic determinations of the relative abundances of 13 chemical elements in 101 of the RR Lyrae variables are collected from 25 papers published between 1995 and 2017. The data from different sources are reduced to a single solar abundance scale. The mean weighted chemical abundances are calculated with coefficients inversely proportional to the reported errors. An analysis of the deviations in the published relative abundances in each star from the mean square values calculated from them reveals an absence of systematic biases among the results from the various articles. The rectangular coordinates of 407 of the RR Lyrae variables and the components of the three-dimensional (3D) velocities of 401 of the stars are calculated using data from several sources. The collected data on the abundances of chemical elements produced by various nuclear fusion processes for the RR Lyrae variables of the field, as well as the calculated 3D velocities, can be used for studying the evolution of the Galaxy.

  14. Climatic effects on mosquito abundance in Mediterranean wetlands

    PubMed Central

    2014-01-01

    Background The impact of climate change on vector-borne diseases is highly controversial. One of the principal points of debate is whether or not climate influences mosquito abundance, a key factor in disease transmission. Methods To test this hypothesis, we analysed ten years of data (2003–2012) from biweekly surveys to assess inter-annual and seasonal relationships between the abundance of seven mosquito species known to be pathogen vectors (West Nile virus, Usutu virus, dirofilariasis and Plasmodium sp.) and several climatic variables in two wetlands in SW Spain. Results Within-season abundance patterns were related to climatic variables (i.e. temperature, rainfall, tide heights, relative humidity and photoperiod) that varied according to the mosquito species in question. Rainfall during winter months was positively related to Culex pipiens and Ochlerotatus detritus annual abundances. Annual maximum temperatures were non-linearly related to annual Cx. pipiens abundance, while annual mean temperatures were positively related to annual Ochlerotatus caspius abundance. Finally, we modelled shifts in mosquito abundances using the A2 and B2 temperature and rainfall climate change scenarios for the period 2011–2100. While Oc. caspius, an important anthropophilic species, may increase in abundance, no changes are expected for Cx. pipiens or the salt-marsh mosquito Oc. detritus. Conclusions Our results highlight that the effects of climate are species-specific, place-specific and non-linear and that linear approaches will therefore overestimate the effect of climate change on mosquito abundances at high temperatures. Climate warming does not necessarily lead to an increase in mosquito abundance in natural Mediterranean wetlands and will affect, above all, species such as Oc. caspius whose numbers are not closely linked to rainfall and are influenced, rather, by local tidal patterns and temperatures. The final impact of changes in vector abundance on disease frequency

  15. Differentially abundant proteins associated with heterosis in the primary roots of popcorn.

    PubMed

    Rockenbach, Mathias F; Corrêa, Caio C G; Heringer, Angelo S; Freitas, Ismael L J; Santa-Catarina, Claudete; do Amaral-Júnior, Antônio T; Silveira, Vanildo

    2018-01-01

    Although heterosis has significantly contributed to increases in worldwide crop production, the molecular mechanisms regulating this phenomenon are still unknown. In the present study, we used a comparative proteomic approach to explore hybrid vigor via the proteome of both the popcorn L54 ♀ and P8 ♂ genotypes and the resultant UENF/UEM01 hybrid cross. To analyze the differentially abundant proteins involved in heterosis, we used the primary roots of these genotypes to analyze growth parameters and extract proteins. The results of the growth parameter analysis showed that the mid- and best-parent heterosis were positive for root length and root dry matter but negative for root fresh matter, seedling fresh matter, and protein content. The comparative proteomic analysis identified 1343 proteins in the primary roots of hybrid UENF/UEM01 and its parental lines; 220 proteins were differentially regulated in terms of protein abundance. The mass spectrometry proteomic data are available via ProteomeXchange with identifier "PXD009436". A total of 62 regulated proteins were classified as nonadditive, of which 53.2% were classified as high parent abundance (+), 17.8% as above-high parent abundance (+ +), 16.1% as below-low parent abundance (- -), and 12.9% as low parent abundance (-). A total of 22 biological processes were associated with nonadditive proteins; processes involving translation, ribosome biogenesis, and energy-related metabolism represented 45.2% of the nonadditive proteins. Our results suggest that heterosis in the popcorn hybrid UENF/UEM01 at an early stage of plant development is associated with an up-regulation of proteins related to synthesis and energy metabolism.

  16. 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 H.

    2016-01-01

    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.

  17. An abundance analysis from the STIS-HST UV spectrum of the non-magnetic Bp star HR 6000

    NASA Astrophysics Data System (ADS)

    Castelli, F.; Cowley, C. R.; Ayres, T. R.; Catanzaro, G.; Leone, F.

    2017-05-01

    Context. The sharp-line spectrum of the non-magnetic, main-sequence Bp star HR 6000 has peculiarities that distinguish it from those of the HgMn stars with which it is sometimes associated. The position of the star close to the center of the Lupus 3 molecular cloud, whose estimated age is on the order of 9.1 ± 2.1 Myr, has lead to the hypothesis that the anomalous peculiarities of HR 6000 can be explained by the young age of the star. Aims: Observational material from the Hubble Space Telescope (HST) provides the opportunity to extend the abundance analysis previously performed for the optical region and clarify the properties of this remarkable peculiar star. Our aim was to obtain the atmospheric abundances for all the elements observed in a broad region from 1250 to 10 000 Å. Methods: An LTE synthetic spectrum was compared with a high-resolution spectrum observed with the Space Telescope Imaging Spectrograph (STIS) equipment in the 1250-3040 Å interval. Abundances were changed until the synthetic spectrum fit the observed spectrum. The assumed model is an LTE, plane-parallel, line-blanketed ATLAS12 model already used for the abundance analysis of a high-resolution optical spectrum observed at ESO with the Ultraviolet and Visual Echelle Spectrograph (UVES). The stellar parameters are Teff = 13450 K, log g = 4.3, and zero microturbulent velocity. Results: Abundances for 28 elements and 7 upper limits were derived from the ultraviolet spectrum. Adding results from previous work, we have now quantitative results for 37 elements, some of which show striking contrasts with those of a broad sample of HgMn stars. The analysis has pointed out numerous abundance anomalies, such as ionization anomalies and line-to-line variation in the derived abundances, in particular for silicon. The inferred discrepancies could be explained by non-LTE effects and with the occurrence of diffusion and vertical abundance stratification. In the framework of the last hypothesis, we

  18. The Absolute Abundance of Iron in the Solar Corona.

    PubMed

    White; Thomas; Brosius; Kundu

    2000-05-10

    We present a measurement of the abundance of Fe relative to H in the solar corona using a technique that differs from previous spectroscopic and solar wind measurements. Our method combines EUV line data from the Coronal Diagnostic Spectrometer (CDS) on the Solar and Heliospheric Observatory with thermal bremsstrahlung radio data from the VLA. The coronal Fe abundance is derived by equating the thermal bremsstrahlung radio emission calculated from the EUV Fe line data to that observed with the VLA, treating the Fe/H abundance as the sole unknown. We apply this technique to a compact cool active region and find Fe&solm0;H=1.56x10-4, or about 4 times its value in the solar photosphere. Uncertainties in the CDS radiometric calibration, the VLA intensity measurements, the atomic parameters, and the assumptions made in the spectral analysis yield net uncertainties of approximately 20%. This result implies that low first ionization potential elements such as Fe are enhanced in the solar corona relative to photospheric values.

  19. A Comparative Analysis of Chemical Abundances in Andromeda's Stellar Halo and Dwarf Galaxies

    NASA Astrophysics Data System (ADS)

    Gilbert, Karoline; Kirby, Evan N.; Escala, Ivanna; Wojno, Jennifer

    2018-06-01

    Stellar halos provide a record of the earliest stages of a galaxy’s formation as well as the mass growth of later epochs. All stages of accretion are represented in the halo: (1) fully phase-mixed stars accreted at early times, (2) stars in distinct tidal streams, and (3) stars in satellite galaxies that will eventually be tidally incorporated into the halo. Chemical abundances encode information about the environment in which a star formed: specifically, the relative abundances of [Fe/H] and [α/Fe] provide an indication of the amount and duration of star formation. While these abundances have been measured for statistically significant samples of halo and dwarf galaxy stars in the Milky Way, they remain largely unknown in Andromeda. We have undertaken a systematic survey to measure [Fe/H] and [α/Fe] in fields throughout the M31 system, including the halo, tidal streams, satellite galaxies, and the disk. I will provide an overview of the survey and its goals and present first results, including the abundance distributions for five M31 dSphs, measurements of [Fe/H] and [α/Fe] of stars in M31's halo, and comparisons to existing measurements of Milky Way dSph and halo stars.

  20. Multiple marker abundance profiling: combining selected reaction monitoring and data-dependent acquisition for rapid estimation of organelle abundance in subcellular samples

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Hooper, Cornelia M.; Stevens, Tim J.; Saukkonen, Anna

    Measuring changes in protein or organelle abundance in the cell is an essential, but challenging aspect of cell biology. Frequently-used methods for determining organelle abundance typically rely on detection of a very few marker proteins, so are unsatisfactory. In silico estimates of protein abundances from publicly available protein spectra can provide useful standard abundance values but contain only data from tissue proteomes, and are not coupled to organelle localization data. A new protein abundance score, the normalized protein abundance scale (NPAS), expands on the number of scored proteins and the scoring accuracy of lower-abundance proteins in Arabidopsis. NPAS was combinedmore » with subcellular protein localization data, facilitating quantitative estimations of organelle abundance during routine experimental procedures. A suite of targeted proteomics markers for subcellular compartment markers was developed, enabling independent verification of in silico estimates for relative organelle abundance. Estimation of relative organelle abundance was found to be reproducible and consistent over a range of tissues and growth conditions. In silico abundance estimations and localization data have been combined into an online tool, multiple marker abundance profiling, available in the SUBA4 toolbox (http://suba.live).« less

  1. Multiple marker abundance profiling: combining selected reaction monitoring and data-dependent acquisition for rapid estimation of organelle abundance in subcellular samples

    DOE PAGES

    Hooper, Cornelia M.; Stevens, Tim J.; Saukkonen, Anna; ...

    2017-10-12

    Measuring changes in protein or organelle abundance in the cell is an essential, but challenging aspect of cell biology. Frequently-used methods for determining organelle abundance typically rely on detection of a very few marker proteins, so are unsatisfactory. In silico estimates of protein abundances from publicly available protein spectra can provide useful standard abundance values but contain only data from tissue proteomes, and are not coupled to organelle localization data. A new protein abundance score, the normalized protein abundance scale (NPAS), expands on the number of scored proteins and the scoring accuracy of lower-abundance proteins in Arabidopsis. NPAS was combinedmore » with subcellular protein localization data, facilitating quantitative estimations of organelle abundance during routine experimental procedures. A suite of targeted proteomics markers for subcellular compartment markers was developed, enabling independent verification of in silico estimates for relative organelle abundance. Estimation of relative organelle abundance was found to be reproducible and consistent over a range of tissues and growth conditions. In silico abundance estimations and localization data have been combined into an online tool, multiple marker abundance profiling, available in the SUBA4 toolbox (http://suba.live).« less

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Wunschel, David S.; Kreuzer-Martin, Helen W.; Antolick, Kathryn C.

    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 componentsmore » 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

  3. 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

  4. Detailed abundance analysis of globular clusters in the Local Group. NGC 147, NGC 6822, and Messier 33

    NASA Astrophysics Data System (ADS)

    Larsen, S. S.; Brodie, J. P.; Wasserman, A.; Strader, J.

    2018-06-01

    Context. Globular clusters (GCs) are emerging as powerful tracers of the chemical composition of extragalactic stellar populations. Aims: We present new abundance measurements for 11 GCs in the Local Group galaxies NGC 147, NGC 6822, and Messier 33. These are combined with previously published observations of four GCs in the Fornax and Wolf-Lundmark-Melotte (WLM) galaxies. Methods: The abundances were determined from analyses of integrated-light spectra obtained with the HIRES spectrograph on the Keck I telescope and with UVES on the Very Large Telescope (VLT). We used our analysis technique that was developed for this purpose and tested on Milky Way GCs. Results: We find that the clusters with [Fe/H] < -1.5 are all α-enhanced at about the same level as Milky Way GCs. Their Na abundances are also generally enhanced relative to Milky Way halo stars, suggesting that these extragalactic GCs resemble their Milky Way counterparts in containing large numbers of Na-rich stars. For [Fe/H] > -1.5, the GCs in M33 are also α-enhanced, while the GCs that belong to dwarfs (NGC 6822 SC7 and Fornax 4) have closer to solar-scaled α-element abundances. The abundance patterns in SC7 are remarkably similar to those in the Galactic GC Ruprecht 106, including significantly subsolar [Na/Fe] and [Ni/Fe] ratios. In NGC 147, the GCs with [Fe/H] < -2.0 account for about 6% of the total luminosity of stars in the same metallicity range, a lower fraction than those previously found in the Fornax and WLM galaxies, but substantially higher than in the Milky Way halo. Conclusions: At low metallicities, the abundance patterns suggest that GCs in the Milky Way, dwarf galaxies, and M33 experienced similar enrichment histories and/or processes. At higher metallicities, the lower levels of α-enhancement in the GCs found in dwarf galaxies resemble the abundance patterns observed in field stars in nearby dwarfs. Constraining the presence of multiple populations in these GCs is complicated by lack

  5. A Comparison of Observed Abundances in Five Well-Studied Planetary Nebulae

    NASA Astrophysics Data System (ADS)

    Tanner, Jolene; Balick, B.; Kwitter, K. B.

    2013-01-01

    We have assembled data and derived abundances in several recent careful studies for five bright planetary nebulae (PNe) of low, moderate, and high ionization and relatively simple morphology. Each of the studies employ different apertures, aperture placement, and facilities for the observations. Various methods were used to derive total abundances. All used spectral windows that included [OII]3727 in the UV through Argon lines in the red. Our ultimate goal is to determine the extent to which the derived abundances are consistent. We show that the reddening-corrected line ratios are surprisingly similar despite the different modes of observation and that the various abundance analysis methods yield generally consistent results for He/H, N/H, O/H, and Ne/H (within 50% with a few larger deviations). In addition we processed the line ratios from the different sources using a common abundance derivation method (ELSA) to search for clues of systematic methodological inconsistencies. None were uncovered.

  6. Winter Avian Distribution and Relative Abundance in Six Terrestrial Habitats on Southern Eleuthera, The Bahamas

    Treesearch

    DAVE CURRIE; JOSEPH M. WUNDERLE JR.; DAVID N. EWERT; ANCILLENO DAVIS; ZEKO MCKENZIE

    2005-01-01

    We studied winter avian distribution and relative abundance in six common terrestrial broadleaf habitats, selected on a continuum of disturbance from recently disturbed (abandoned plantation) to mature vegetation (tall coppice), on the island of Eleuthera, The Bahamas. During 158-point counts conducted 22 January—10 March 2003, 1357 individuals were detected,...

  7. APOGEE Chemical Abundances of the Sagittarius Dwarf Galaxy

    NASA Astrophysics Data System (ADS)

    Hasselquist, Sten; Shetrone, Matthew; Smith, Verne; Holtzman, Jon; McWilliam, Andrew; Fernández-Trincado, J. G.; Beers, Timothy C.; Majewski, Steven R.; Nidever, David L.; Tang, Baitian; Tissera, Patricia B.; Fernández Alvar, Emma; Allende Prieto, Carlos; Almeida, Andres; Anguiano, Borja; Battaglia, Giuseppina; Carigi, Leticia; Delgado Inglada, Gloria; Frinchaboy, Peter; García-Hernández, D. A.; Geisler, Doug; Minniti, Dante; Placco, Vinicius M.; Schultheis, Mathias; Sobeck, Jennifer; Villanova, Sandro

    2017-08-01

    The Apache Point Observatory Galactic Evolution Experiment provides the opportunity of measuring elemental abundances for C, N, O, Na, Mg, Al, Si, P, K, Ca, V, Cr, Mn, Fe, Co, and Ni in vast numbers of stars. We analyze thechemical-abundance patterns of these elements for 158 red giant stars belonging to the Sagittarius dwarf galaxy (Sgr). This is the largest sample of Sgr stars with detailed chemical abundances, and it is the first time that C, N, P, K, V, Cr, Co, and Ni have been studied at high resolution in this galaxy. We find that the Sgr stars with [Fe/H] ≳ -0.8 are deficient in all elemental abundance ratios (expressed as [X/Fe]) relative to the Milky Way, suggesting that the Sgr stars observed today were formed from gas that was less enriched by Type II SNe than stars formed in the Milky Way. By examining the relative deficiencies of the hydrostatic (O, Na, Mg, and Al) and explosive (Si, P, K, and Mn) elements, our analysis supports the argument that previous generations of Sgr stars were formed with a top-light initial mass function, one lacking the most massive stars that would normally pollute the interstellar medium with the hydrostatic elements. We use a simple chemical-evolution model, flexCE, to further support our claim and conclude that recent stellar generations of Fornax and the Large Magellanic Cloud could also have formed according to a top-light initial mass function.

  8. Differentially abundant proteins associated with heterosis in the primary roots of popcorn

    PubMed Central

    Heringer, Angelo S.; Freitas, Ismael L. J.; Santa-Catarina, Claudete; do Amaral-Júnior, Antônio T.

    2018-01-01

    Although heterosis has significantly contributed to increases in worldwide crop production, the molecular mechanisms regulating this phenomenon are still unknown. In the present study, we used a comparative proteomic approach to explore hybrid vigor via the proteome of both the popcorn L54 ♀ and P8 ♂ genotypes and the resultant UENF/UEM01 hybrid cross. To analyze the differentially abundant proteins involved in heterosis, we used the primary roots of these genotypes to analyze growth parameters and extract proteins. The results of the growth parameter analysis showed that the mid- and best-parent heterosis were positive for root length and root dry matter but negative for root fresh matter, seedling fresh matter, and protein content. The comparative proteomic analysis identified 1343 proteins in the primary roots of hybrid UENF/UEM01 and its parental lines; 220 proteins were differentially regulated in terms of protein abundance. The mass spectrometry proteomic data are available via ProteomeXchange with identifier “PXD009436”. A total of 62 regulated proteins were classified as nonadditive, of which 53.2% were classified as high parent abundance (+), 17.8% as above-high parent abundance (+ +), 16.1% as below-low parent abundance (− −), and 12.9% as low parent abundance (-). A total of 22 biological processes were associated with nonadditive proteins; processes involving translation, ribosome biogenesis, and energy-related metabolism represented 45.2% of the nonadditive proteins. Our results suggest that heterosis in the popcorn hybrid UENF/UEM01 at an early stage of plant development is associated with an up-regulation of proteins related to synthesis and energy metabolism. PMID:29758068

  9. Monitoring Butterfly Abundance: Beyond Pollard Walks

    PubMed Central

    Pellet, Jérôme; Bried, Jason T.; Parietti, David; Gander, Antoine; Heer, Patrick O.; Cherix, Daniel; Arlettaz, Raphaël

    2012-01-01

    Most butterfly monitoring protocols rely on counts along transects (Pollard walks) to generate species abundance indices and track population trends. It is still too often ignored that a population count results from two processes: the biological process (true abundance) and the statistical process (our ability to properly quantify abundance). Because individual detectability tends to vary in space (e.g., among sites) and time (e.g., among years), it remains unclear whether index counts truly reflect population sizes and trends. This study compares capture-mark-recapture (absolute abundance) and count-index (relative abundance) monitoring methods in three species (Maculinea nausithous and Iolana iolas: Lycaenidae; Minois dryas: Satyridae) in contrasted habitat types. We demonstrate that intraspecific variability in individual detectability under standard monitoring conditions is probably the rule rather than the exception, which questions the reliability of count-based indices to estimate and compare specific population abundance. Our results suggest that the accuracy of count-based methods depends heavily on the ecology and behavior of the target species, as well as on the type of habitat in which surveys take place. Monitoring programs designed to assess the abundance and trends in butterfly populations should incorporate a measure of detectability. We discuss the relative advantages and inconveniences of current monitoring methods and analytical approaches with respect to the characteristics of the species under scrutiny and resources availability. PMID:22859980

  10. Abundance analysis of neodymium in the solar atmosphere

    NASA Astrophysics Data System (ADS)

    Abdelkawy, Ali G. A.; Shaltout, Abdelrazek M. K.; Beheary, M. M.; Bakry, A.

    2017-10-01

    Based on non-local thermodynamical equilibrium (NLTE) calculations, the solar neodymium (Nd) content was found based on a model atom of singly ionized neodymium (Nd II) containing 153 energy levels and 42 line transitions plus the ground state of Nd III. Here, we re-derive the solar Nd abundance using the model of the solar photosphere of Holweger & Müller.We succeed in selecting a good sample line list, relying on 20 Nd II solar lines together with the most accurate transition probabilities measured experimentally and available observational data. With damping parameters obtained from the literature, we find a mean NLTE solar photospheric Nd abundance of log ɛNd(1D) = 1.43 ± 0.16, which is in excellent agreement with the meteoritic value (log ɛNd = 1.45 ± 0.02). For a set of selected Nd II lines, the NLTE abundance correction is found to be +0.01 dex compared with the standard LTE effect. The influence of collisional interactions with electrons and neutral hydrogen atoms is investigated in detail.

  11. Bulk and rare earth abundances in the Luna 16 soil levels A and D.

    NASA Technical Reports Server (NTRS)

    Gillum, D. E.; Ehmann, W. D.; Wakita, H.; Schmitt, R. A.

    1972-01-01

    Determination of the abundances of major, minor, and trace elements by means of sequential INAA (instrumental neutron activation analysis) in two Luna 16 soils, at levels A (about 7 cm depth) and D (about 30 cm depth). Abundances of the bulk elements in Luna 16 soils generally agree with the values reported by Vinogradov (1971). Elemental abundances of both bulk and trace elements are nearly the same for the two A and D soil levels. Overall, the chemical compositions of the two Luna 16 soils are more closely related to Apollo 11 soil 10084 than to Apollo 12 and 14 soils, with the exception of TiO2 abundances.-

  12. A Comparison of Relative Abundance and Biomass of Ground-Dwelling Arthropods Under Different Forest Management Practices

    Treesearch

    Cathryn H. Greenberg; Arlene McGrane

    1996-01-01

    Habitat structural characteristics and relative abundance and biomass of ground-dwelling arthropods were compared among four replicated stand treatments: intense burning and salvage logging; clearcutting followed by roller-chopping (100% soil surface disturbance): clearcutting followed by bracke seeding (30% soil surface disturbance); and naturally regenerated mature...

  13. Continuously Monocropped Jerusalem Artichoke Changed Soil Bacterial Community Composition and Ammonia-Oxidizing and Denitrifying Bacteria Abundances.

    PubMed

    Zhou, Xingang; Wang, Zhilin; Jia, Huiting; Li, Li; Wu, Fengzhi

    2018-01-01

    Soil microbial communities have profound effects on the growth, nutrition and health of plants in agroecosystems. Understanding soil microbial dynamics in cropping systems can assist in determining how agricultural practices influence soil processes mediated by microorganisms. In this study, soil bacterial communities were monitored in a continuously monocropped Jerusalem artichoke (JA) system, in which JA was successively monocropped for 3 years in a wheat field. Soil bacterial community compositions were estimated by amplicon sequencing of the 16S rRNA gene. Abundances of ammonia-oxidizing and denitrifying bacteria were estimated by quantitative PCR analysis of the amoA , nirS , and nirK genes. Results showed that 1-2 years of monocropping of JA did not significantly impact the microbial alpha diversity, and the third cropping of JA decreased the microbial alpha diversity ( P < 0.05). Principal coordinates analysis and permutational multivariate analysis of variance analyses revealed that continuous monocropping of JA changed soil bacterial community structure and function profile ( P < 0.001). At the phylum level, the wheat field was characterized with higher relative abundances of Latescibacteria , Planctomycetes , and Cyanobacteria , the first cropping of JA with Actinobacteria , the second cropping of JA with Acidobacteria , Armatimonadetes , Gemmatimonadetes , and Proteobacteria . At the genus level, the first cropping of JA was enriched with bacterial species with pathogen-antagonistic and/or plant growth promoting potentials, while members of genera that included potential denitrifiers increased in the second and third cropping of JA. The first cropping of JA had higher relative abundances of KO terms related to lignocellulose degradation and phosphorus cycling, the second cropping of JA had higher relative abundances of KO terms nitrous-oxide reductase and nitric-oxide reductase, and the third cropping of JA had higher relative abundances of KO terms

  14. Seasonal abundance of Lutzomyia longipalpis (Diptera: Psychodidae) at an endemic focus of visceral leishmaniasis in Colombia.

    PubMed

    Morrison, A C; Ferro, C; Pardo, R; Torres, M; Devlin, B; Wilson, M L; Tesh, R B

    1995-07-01

    Ecological studies on the sand fly Lutzomyia longipalpis (Lutz & Neiva) were conducted during 1990-1993 in a small rural community in Colombia where American visceral leishmaniasis is endemic. Standardized weekly sand fly collections made from pigpens and natural resting sites displayed a bimodal annual abundance cycle, with a small peak occurring in October-November and a larger one in April-May. Time series analysis was employed to quantify the associations between sand fly abundance and weather factors (temperature, relative humidity, and rainfall). In addition to a prominent 6-mo cycle. Fourier analysis of the collection data demonstrated that the L. longipalpis population also exhibited a 5- to 8-wk cycle that may represent the length of larval development. Autoregressive moving average models were fit to weekly collection data and their residuals were regressed against rainfall, temperature, and relative humidity. A significant positive association between female L. longipalpis abundance and the relative humidity and rainfall recorded 3 wk earlier was found, indicating that these factors may be of value in predicting sand fly abundance. Additionally, these data indicated that L. longipalpis larvae may become quiescent during adverse conditions.

  15. A search for stars of very low metal abundance. VI. Detailed abundances of 313 metal-poor stars

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Roederer, Ian U.; Preston, George W.; Thompson, Ian B.

    2014-06-01

    We present radial velocities, equivalent widths, model atmosphere parameters, and abundances or upper limits for 53 species of 48 elements derived from high resolution optical spectroscopy of 313 metal-poor stars. A majority of these stars were selected from the metal-poor candidates of the HK Survey of Beers, Preston, and Shectman. We derive detailed abundances for 61% of these stars for the first time. Spectra were obtained during a 10 yr observing campaign using the Magellan Inamori Kyocera Echelle spectrograph on the Magellan Telescopes at Las Campanas Observatory, the Robert G. Tull Coudé Spectrograph on the Harlan J. Smith Telescope atmore » McDonald Observatory, and the High Resolution Spectrograph on the Hobby-Eberly Telescope at McDonald Observatory. We perform a standard LTE abundance analysis using MARCS model atmospheres, and we apply line-by-line statistical corrections to minimize systematic abundance differences arising when different sets of lines are available for analysis. We identify several abundance correlations with effective temperature. A comparison with previous abundance analyses reveals significant differences in stellar parameters, which we investigate in detail. Our metallicities are, on average, lower by ≈0.25 dex for red giants and ≈0.04 dex for subgiants. Our sample contains 19 stars with [Fe/H] ≤–3.5, 84 stars with [Fe/H] ≤–3.0, and 210 stars with [Fe/H] ≤–2.5. Detailed abundances are presented here or elsewhere for 91% of the 209 stars with [Fe/H] ≤–2.5 as estimated from medium resolution spectroscopy by Beers, Preston, and Shectman. We will discuss the interpretation of these abundances in subsequent papers.« less

  16. 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.

  17. 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.

  18. The Influence of Herbivory on the net rate of Increase of Gypsy Moth Abundance: A Modeling Analysis

    Treesearch

     Harry T.  Valentine

    1983-01-01

    A differential equation model of gypsy moth abundance, average larval dry weight, and food abundance was used to analyze the effects of changes in foliar chemistry on the net per capita rate of increase in a gypsy moth population. If relative consumption rate per larva is unaffected by herbivory, a reduction in the nutritional value of foliage reduces the net rate of...

  19. Relative abundance of heavy ions in the inner zone of the radiation belts of the earth

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Panasyuk, M.I.

    1986-03-01

    The energy dependences of the relative abundances of energetic (E > 1 MeV/nucleon) H, He, and O ions in the radiation belts are analyzed on the basis of experimental results obtained from measurement of their spectral characteristics on several satellites: Molniya-2, Kosmos-900, Prognoz-5, Explorer-45, ISEE-1, and OV1-19. It is shown that the formation of the energy dependence of He/H and O/H can be explained with a model providing for ion diffusion into the interior of the radiation belts with Coulomb losses taken into account under thecondition that the total-energy spectra at the boundary are more rigid for the heavy ionsmore » and are determined by such parameters of the quiet solar wind as the relative concentrations of the individual ion components and their charge states. It is shown that the fluxes of O and Fe ions with E > 1 MeV/nucleon measured on the orbital stations Salyut-6 and Skylab have an energy dependence of the relative abundances not inconsistent with above-noted mechanism for the formation of energetic ions of the inner radiation belt.« less

  20. 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

  1. 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.

  2. 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

  3. Change in avian abundance predicted from regional forest inventory data

    USGS Publications Warehouse

    Twedt, Daniel J.; Tirpak, John M.; Jones-Farrand, D. Todd; Thompson, Frank R.; Uihlein, William B.; Fitzgerald, Jane A.

    2010-01-01

    An inability to predict population response to future habitat projections is a shortcoming in bird conservation planning. We sought to predict avian response to projections of future forest conditions that were developed from nationwide forest surveys within the Forest Inventory and Analysis (FIA) program. To accomplish this, we evaluated the historical relationship between silvicolous bird populations and FIA-derived forest conditions within 25 ecoregions that comprise the southeastern United States. We aggregated forest area by forest ownership, forest type, and tree size-class categories in county-based ecoregions for 5 time periods spanning 1963-2008. We assessed the relationship of forest data with contemporaneous indices of abundance for 24 silvicolous bird species that were obtained from Breeding Bird Surveys. Relationships between bird abundance and forest inventory data for 18 species were deemed sufficient as predictive models. We used these empirically derived relationships between regional forest conditions and bird populations to predict relative changes in abundance of these species within ecoregions that are anticipated to coincide with projected changes in forest variables through 2040. Predicted abundances of these 18 species are expected to remain relatively stable in over a quarter (27%) of the ecoregions. However, change in forest area and redistribution of forest types will likely result in changed abundance of some species within many ecosystems. For example, abundances of 11 species, including pine warbler (Dendroica pinus), brown-headed nuthatch (Sitta pusilla), and chuckwills- widow (Caprimulgus carolinensis), are projected to increase within more ecoregions than ecoregions where they will decrease. For 6 other species, such as blue-winged warbler (Vermivora pinus), Carolina wren (Thryothorus ludovicianus), and indigo bunting (Passerina cyanea), we projected abundances will decrease within more ecoregions than ecoregions where they will

  4. APOGEE Chemical Abundances of the Sagittarius Dwarf Galaxy

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Hasselquist, Sten; Holtzman, Jon; Shetrone, Matthew

    The Apache Point Observatory Galactic Evolution Experiment provides the opportunity of measuring elemental abundances for C, N, O, Na, Mg, Al, Si, P, K, Ca, V, Cr, Mn, Fe, Co, and Ni in vast numbers of stars. We analyze thechemical-abundance patterns of these elements for 158 red giant stars belonging to the Sagittarius dwarf galaxy (Sgr). This is the largest sample of Sgr stars with detailed chemical abundances, and it is the first time that C, N, P, K, V, Cr, Co, and Ni have been studied at high resolution in this galaxy. We find that the Sgr stars withmore » [Fe/H] ≳ −0.8 are deficient in all elemental abundance ratios (expressed as [X/Fe]) relative to the Milky Way, suggesting that the Sgr stars observed today were formed from gas that was less enriched by Type II SNe than stars formed in the Milky Way. By examining the relative deficiencies of the hydrostatic (O, Na, Mg, and Al) and explosive (Si, P, K, and Mn) elements, our analysis supports the argument that previous generations of Sgr stars were formed with a top-light initial mass function, one lacking the most massive stars that would normally pollute the interstellar medium with the hydrostatic elements. We use a simple chemical-evolution model, flexCE, to further support our claim and conclude that recent stellar generations of Fornax and the Large Magellanic Cloud could also have formed according to a top-light initial mass function.« less

  5. 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.

  6. APOGEE Chemical Abundances of the Sagittarius Dwarf Galaxy System

    NASA Astrophysics Data System (ADS)

    Hasselquist, Sten; Shetrone, Matthew D.; Smith, Verne V.; Holtzman, Jon A.; McWilliam, Andrew; APOGEE Team

    2018-06-01

    The Apache Point Observatory Galactic Evolution Experiment provides the opportunity of measuring elemental abundances for C, N, O, Na, Mg, Al, Si, P, K, Ca, V, Cr, Mn, Fe, Co, and Ni in vast numbers of stars. We analyze the chemical-abundance patterns of these elements for 158 red giant stars belonging to the Sagittarius dwarf galaxy (Sgr). This is the largest sample of Sgr stars with detailed chemical abundances, and it is the first time that C, N, P, K, V, Cr, Co, and Ni have been studied at high resolution in this galaxy. We find that the Sgr stars with [Fe/H] > -0.8 are deficient in all elemental abundance ratios (expressed as [X/Fe]) relative to the Milky Way, suggesting that the Sgr stars observed today were formed from gas that was less enriched by Type II SNe than stars formed in the Milky Way. By examining the relative deficiencies of the hydrostatic (O, Na, Mg, and Al) and explosive (Si, P, K, and Mn) elements, our analysis supports the argument that previous generations of Sgr stars were formed with a top-light initial mass function, one lacking the most massive stars that would normally pollute the interstellar medium with the hydrostatic elements. We use a simple chemical-evolution model, flexCE, to further support our claim and conclude that recent stellar generations of Fornax and the Large Magellanic Cloud could also have formed according to a top-light initial mass function. We then exploit the unique chemical abundance patters of the Sgr core to trace stars belonging to the Sgr tidal streams elsewhere in the Milky Way.

  7. Financial development and oil resource abundance-growth relations: evidence from panel data.

    PubMed

    Law, Siong Hook; Moradbeigi, Maryam

    2017-10-01

    This study investigates whether financial development dampens the negative impact of oil resource abundance on economic growth. Because of substantial cross-sectional dependence in our data, which contain a core sample of 63 oil-producing countries from 1980 through 2010, we use the common correlated effect mean group (CCEMG) estimator to account for the high degree of heterogeneity and drop the outlier countries. The empirical results reveal that oil resource abundance affects the growth rate in output contingent on the degree of development in financial markets. More developed financial markets can channel the revenues from oil into more productive activities and thus offset the negative effects of oil resource abundance on economic growth. Thus, better financial development can reverse resource curse or enhance resource blessing in oil-rich economies.

  8. Factors affecting the abundance of selected fishes near oil and gas platforms in the northern Gulf of Mexico

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Stanley, D.R.; Wilson, C.A.

    1991-01-01

    A logbook program was initiated to determine the relative abundance of selected fish species around oil and gas platforms off the Louisiana coast. Logbooks were maintained by 55 anglers and 10 charterboat operators from March 1987 to March 1988. A total of 36,839 fish were caught representing over 46 different species. Principal component analysis (PCA) grouped the seventeen most abundant species into reef fish, pelagic fish, bluefish-red drum, Atlantic croaker-silver/sand seatrout, and cobia-shark-blue runner associations. Multiple regression analyses were used to compare PCA groupings to physical platform, temporal, geological, and angler characteristic variables and their interactions. Reef fish, Atlantic croaker,more » and silver/sand seatrout abundances were highest near large, structurally complex platforms in relatively deep water. High spotted seatrout abundances were correlated with small, unmanned oil and gas platforms in shallow water. Pelagic fish, bluefish, red drum, cobia, and shark abundances were not related to the physical parameters of the platforms.« less

  9. Determination of lunar ilmenite abundances from remotely sensed data

    NASA Technical Reports Server (NTRS)

    Larson, Stephen M.; Johnson, Jeffrey R.; Singer, Robert B.

    1991-01-01

    The mineral ilmenite (FeTiO3) was found in abundance in lunar mare soils returned during the Apollo project. Lunar ilmenite often contains greater than 50 weight-percent titanium dioxide (TiO2), and is a primary potential resource for oxygen and other raw materials to supply future lunar bases. Chemical and spectroscopic analysis of the returned lunar soils produced an empirical function that relates the spectral reflectance ratio at 400 and 560 nm to the weight percent abundance of TiO2. This allowed mapping of the lunar TiO2 distribution using telescopic vidicon multispectral imaging from the ground; however, the time variant photometric response of the vidicon detectors produced abundance uncertainties of at least 2 to 5 percent. Since that time, solid-state charge-coupled device (CCD) detector technology capable of much improved photometric response has become available. An investigation of the lunar TiO2 distribution was carried out utilizing groundbased telescopic CCD multispectral imagery and spectroscopy. The work was approached in phases to develop optimum technique based upon initial results. The goal is to achieve the best possible TiO2 abundance maps from the ground as a precursor to lunar orbiter and robotic sample return missions, and to produce a better idea of the peak abundances of TiO2 for benefaction studies. These phases and the results are summarized.

  10. A Gestational High Protein Diet Affects the Abundance of Muscle Transcripts Related to Cell Cycle Regulation throughout Development in Porcine Progeny

    PubMed Central

    Oster, Michael; Murani, Eduard; Metges, Cornelia C.; Ponsuksili, Siriluck; Wimmers, Klaus

    2012-01-01

    Background In various animal models pregnancy diets have been shown to affect offspring phenotype. Indeed, the underlying programming of development is associated with modulations in birth weight, body composition, and continual diet-dependent modifications of offspring metabolism until adulthood, producing the hypothesis that the offspring's transcriptome is permanently altered depending on maternal diet. Methodology/Principal Findings To assess alterations of the offspring's transcriptome due to gestational protein supply, German Landrace sows were fed isoenergetic diets containing protein levels of either 30% (high protein - HP) or 12% (adequate protein - AP) throughout their pregnancy. Offspring muscle tissue (M. longissimus dorsi) was collected at 94 days post conception (dpc), and 1, 28, and 188 days post natum (dpn) for use with Affymetrix GeneChip Porcine Genome Arrays and subsequent statistical and Ingenuity pathway analyses. Numerous transcripts were found to have altered abundance at 94 dpc and 1 dpn; at 28 dpn no transcripts were altered, and at 188 dpn only a few transcripts showed a different abundance between diet groups. However, when assessing transcriptional changes across developmental time points, marked differences were obvious among the dietary groups. Depending on the gestational dietary exposure, short- and long-term effects were observed for mRNA expression of genes related to cell cycle regulation, energy metabolism, growth factor signaling pathways, and nucleic acid metabolism. In particular, the abundance of transcripts related to cell cycle remained divergent among the groups during development. Conclusion Expression analysis indicates that maternal protein supply induced programming of the offspring's genome; early postnatal compensation of the slight growth retardation obvious at birth in HP piglets resulted, as did a permanently different developmental alteration and responsiveness to the common environment of the transcriptome. The

  11. Carbon and nitrogen abundances determined from transition layer lines

    NASA Technical Reports Server (NTRS)

    Boehm-Vitense, Erika; Mena-Werth, Jose

    1992-01-01

    The possibility of determining relative carbon, nitrogen, and silicon abundances from the emission-line fluxes in the lower transition layers between stellar chromospheres and coronae is explored. Observations for main-sequence and luminosity class IV stars with presumably solar element abundances show that for the lower transition layers Em = BT sup -gamma. For a given carbon abundance the constants gamma and B in this relation can be determined from the C II and C IV emission-line fluxes. From the N V and S IV lines, the abundances of these elements relative to carbon can be determined from their surface emission-line fluxes. Ratios of N/C abundances determined in this way for some giants and supergiants agree within the limits of errors with those determined from molecular bands. For giants, an increase in the ratio of N/C at B-V of about 0.8 is found, as expected theoretically.

  12. Thermal affinity as the dominant factor changing Mediterranean fish abundances.

    PubMed

    Givan, Or; Edelist, Dor; Sonin, Oren; Belmaker, Jonathan

    2018-01-01

    Recent decades have seen profound changes in species abundance and community composition. In the marine environment, the major anthropogenic drivers of change comprise exploitation, invasion by nonindigenous species, and climate change. However, the magnitude of these stressors has been widely debated and we lack empirical estimates of their relative importance. In this study, we focused on Eastern Mediterranean, a region exposed to an invasion of species of Red Sea origin, extreme climate change, and high fishing pressure. We estimated changes in fish abundance using two fish trawl surveys spanning a 20-year period, and correlated these changes with estimated sensitivity of species to the different stressors. We estimated sensitivity to invasion using the trait similarity between indigenous and nonindigenous species; sensitivity to fishing using a published composite index based on the species' life-history; and sensitivity to climate change using species climatic affinity based on occurrence data. Using both a meta-analytical method and random forest analysis, we found that for shallow-water species the most important driver of population size changes is sensitivity to climate change. Species with an affinity to warm climates increased in relative abundance and species with an affinity to cold climates decreased suggesting a strong response to warming local sea temperatures over recent decades. This decrease in the abundance of cold-water-associated species at the trailing "warm" end of their distribution has been rarely documented. Despite the immense biomass of nonindigenous species and the presumed high fishing pressure, these two latter factors seem to have only a minor role in explaining abundance changes. The decline in abundance of indigenous species of cold-water origin indicates a future major restructuring of fish communities in the Mediterranean in response to the ongoing warming, with unknown impacts on ecosystem function. © 2017 John Wiley & Sons

  13. Solar abundances as derived from solar energetic particles

    NASA Technical Reports Server (NTRS)

    Stone, E. C.

    1989-01-01

    Recent studies have shown that there are well defined average abundances of heavy (Z above 2) solar energetic particles (SEPs), with variations in the acceleration and propagation producing a systematic flare-to-flare fractionation that depends on the charge per unit mass of the ion. Correcting the average SEP abundances for this fractionation yields SEP-derived coronal abundances for 20 elements. High-resolution SEP studies have also provided isotopic abundances for five elements. SEP-derived abundances indicate that elements with high first ionization potentials (greater than 10 eV) are depleted in the corona relative to the photosphere and provide new information on the solar abundance of C and Ne-22.

  14. 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.

  15. 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.

  16. Identity and abundance of active sulfate-reducing bacteria in deep tidal flat sediments determined by directed cultivation and CARD-FISH analysis.

    PubMed

    Gittel, Antje; Mussmann, Marc; Sass, Henrik; Cypionka, Heribert; Könneke, Martin

    2008-10-01

    The identity and abundance of potentially active sulfate-reducing bacteria (SRB) in several metre deep sediments of a tidal sand flat in the German Wadden Sea were assessed by directed cultivation and cultivation-independent CARD-FISH analysis (catalysed reporter deposition fluorescence in situ hybridization). Presumably abundant SRB from different sediment layers between 0.5 and 4 m depth were selectively enriched in up to million-fold diluted cultures supplemented with lactate, acetate or hydrogen. Partial 16S rRNA gene sequences obtained from highest dilution steps showing sulfide formation indicated growth of deltaproteobacterial SRB belonging to the Desulfobulbaceae and the Desulfobacteraceae as well as of members of the Firmicutes. Subsequent isolation resulted in 10 novel phylotypes of both litho- and organotrophic sulfate-reducing Deltaproteobacteria. Molecular pre-screening identified six isolates as members of the Desulfobulbaceae, sharing highest identities with either candidatus 'Desulfobacterium corrodens' (95-97%) or Desulfobacterium catecholicum (98%), and four isolates as members of Desulfobacteraceae, being related to either Desulfobacter psychrotolerans (98%) or Desulfobacula phenolica (95-97%). Relatives of D. phenolica were exlusively isolated from 50 and 100 cm deep sediments with 10 and 2 mM of pore water sulfate respectively. In contrast, relatives of D. corrodens, D. psychrotolerans and D. catecholicum were also obtained from layers deeper than 100 cm and with less than 2 mM sulfate. The high in situ abundance of members of both families in sediment layers beneath 50 cm could be confirmed via CARD-FISH analysis performed with a set of six SRB-specific oligonucleotide probes. Moreover, SRB represented a numerically significant fraction of the microbial community throughout the sediment (up to 7%) and reached even higher cell numbers in deep, sulfate-poor layers than in the sulfate-rich surface sediment. This relatively large community size of

  17. A Simple Method for Rapid Depletion of Rubisco from Soybean (Glycine max) Leaf for Proteomic Analysis of Lower Abundance Proteins

    USDA-ARS?s Scientific Manuscript database

    2-DE analysis of complex plant proteomes has limited dynamic resolution because only abundant proteins can be detected. Proteomic assessment of the low abundance proteins within leaf tissue is difficult when it is comprised of 30 – 50% of the CO2 fixation enzyme Rubisco. Resolution can be improved t...

  18. The abundance of ultra-diffuse galaxies from groups to clusters. UDGs are relatively more common in more massive haloes

    NASA Astrophysics Data System (ADS)

    van der Burg, Remco F. J.; Hoekstra, Henk; Muzzin, Adam; Sifón, Cristóbal; Viola, Massimo; Bremer, Malcolm N.; Brough, Sarah; Driver, Simon P.; Erben, Thomas; Heymans, Catherine; Hildebrandt, Hendrik; Holwerda, Benne W.; Klaes, Dominik; Kuijken, Konrad; McGee, Sean; Nakajima, Reiko; Napolitano, Nicola; Norberg, Peder; Taylor, Edward N.; Valentijn, Edwin

    2017-11-01

    In recent years, many studies have reported substantial populations of large galaxies with low surface brightness in local galaxy clusters. Various theories that aim to explain the presence of such ultra-diffuse galaxies (UDGs) have since been proposed. A key question that will help to distinguish between models is whether UDGs have counterparts in host haloes with lower masses, and if so, what their abundance as a function of halo mass is. We here extend our previous study of UDGs in galaxy clusters to galaxy groups. We measure the abundance of UDGs in 325 spectroscopically selected groups from the Galaxy And Mass Assembly (GAMA) survey. We make use of the overlapping imaging from the ESO Kilo-Degree Survey (KiDS), from which we can identify galaxies with mean surface brightnesses within their effective radii down to 25.5 mag arcsec-2 in the r band. We are able to measure a significant overdensity of UDGs (with sizes reff ≥ 1.5 kpc) in galaxy groups down to M200 = 1012 M⊙, a regime where approximately only one in ten groups contains a UDG that we can detect. We combine measurements of the abundance of UDGs in haloes that cover three orders of magnitude in halo mass, finding that their numbers scale quite steeply with halo mass: NUDG(R < R200) ∝ M2001.11±0.07. To better interpret this, we also measure the mass-richness relation for brighter galaxies down to Mr* + 2.5 in the same GAMA groups, and find a much shallower relation of NBright(R < R200) ∝ M2000.78±0.05. This shows that compared to bright galaxies, UDGs are relatively more abundant in massive clusters than in groups. We discuss the implications, but it is still unclear whether this difference is related to a higher destruction rate of UDGs in groups or if massive haloes have a positive effect on UDG formation.

  19. 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

  20. Coyote abundance in relation to habitat characteristics in Sierra San Luis, Sonora, Mexico

    Treesearch

    Eduardo Ponce Guevara; Karla Pelz Serrano; Carlos A. Lopez Gonzalez

    2005-01-01

    Coyotes have expanded their historical distribution range because of anthropogenic activities and habitat transformation, where forests have been considered marginal habitat. We tested the relationship between vegetation structure and coyote abundance in different habitat types. We expected to find a higher abundance in open lands than in thicker areas. We used scent...

  1. Composition and abundance of tree regeneration

    Treesearch

    Todd F. Hutchinson; Elaine Kennedy Sutherland; Charles T. Scott

    2003-01-01

    The composition and abundance of tree seedlings and saplings in the four study areas in southern Ohio were related to soil moisture via a GIS-derived integrated moisture index and to soil texture and fertility. For seedlings, the total abundance of small stems (less than 30 cm tall) was significantly greater on xeric plots (81,987/ha) than on intermediate (54,531/ha)...

  2. Seasonal abundance and vertical distribution of capelin (Mallotus villosus) in relation to water temperature at a coastal site off eastern Newfoundland

    USGS Publications Warehouse

    Methven, David A.; Piatt, John F.

    1991-01-01

    The seasonal abundance and vertical distribution of capelin in relation to water temperature have been investigated by conducting repeated hydroacoustic surveys at a coastal site off eastern Newfoundland. Water temperatures were warmer in 1983 than in 1984 as indicated by the earlier appearance and greater depth of the seasonal thermocline. Correspondingly, schools of capelin appeared earlier, were more abundant, and extended deeper in the water column in 1983 than in 1984. Most capelin were found between the surface and the 5°C isotherm. In both years, initial peaks of capelin abundance occurred when nearshore water temperatures increased from about 0-1°C to above 6°C and, at or near, periods of maximum tidal oscillation. Short-term variations in the depth of the 5°C isotherm were related to nearshore wind-induced upwelling events. Annual variations corresponded to the volume of cold (>0°C) water and sea-ice transported south by the Labrador Current.

  3. 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.

  4. Thresholds in the response of free-floating plant abundance to variation in hydraulic connectivity, nutrients, and macrophyte abundance in a large floodplain river

    USGS Publications Warehouse

    Giblin, Shawn M.; Houser, Jeffrey N.; Sullivan, John F.; Langrehr, H.A.; Rogala, James T.; Campbell, Benjamin D.

    2014-01-01

    Duckweed and other free-floating plants (FFP) can form dense surface mats that affect ecosystem condition and processes, and can impair public use of aquatic resources. FFP obtain their nutrients from the water column, and the formation of dense FFP mats can be a consequence and indicator of river eutrophication. We conducted two complementary surveys of diverse aquatic areas of the Upper Mississippi River as an in situ approach for estimating thresholds in the response of FFP abundance to nutrient concentration and physical conditions in a large, floodplain river. Local regression analysis was used to estimate thresholds in the relations between FFP abundance and phosphorus (P) concentration (0.167 mg l−1L), nitrogen (N) concentration (0.808 mg l−1), water velocity (0.095 m s−1), and aquatic macrophyte abundance (65 % cover). FFP tissue concentrations suggested P limitation was more likely in spring, N limitation was more likely in late summer, and N limitation was most likely in backwaters with minimal hydraulic connection to the channel. The thresholds estimated here, along with observed patterns in nutrient limitation, provide river scientists and managers with criteria to consider when attempting to modify FFP abundance in off-channel areas of large river systems.

  5. Abundance models improve spatial and temporal prioritization of conservation resources.

    PubMed

    Johnston, Alison; Fink, Daniel; Reynolds, Mark D; Hochachka, Wesley M; Sullivan, Brian L; Bruns, Nicholas E; Hallstein, Eric; Merrifield, Matt S; Matsumoto, Sandi; Kelling, Steve

    2015-10-01

    Conservation prioritization requires knowledge about organism distribution and density. This information is often inferred from models that estimate the probability of species occurrence rather than from models that estimate species abundance, because abundance data are harder to obtain and model. However, occurrence and abundance may not display similar patterns and therefore development of robust, scalable, abundance models is critical to ensuring that scarce conservation resources are applied where they can have the greatest benefits. Motivated by a dynamic land conservation program, we develop and assess a general method for modeling relative abundance using citizen science monitoring data. Weekly estimates of relative abundance and occurrence were compared for prioritizing times and locations of conservation actions for migratory waterbird species in California, USA. We found that abundance estimates consistently provided better rankings of observed counts than occurrence estimates. Additionally, the relationship between abundance and occurrence was nonlinear and varied by species and season. Across species, locations prioritized by occurrence models had only 10-58% overlap with locations prioritized by abundance models, highlighting that occurrence models will not typically identify the locations of highest abundance that are vital for conservation of populations.

  6. Oxygen abundance distributions in six late-type galaxies based on SALT spectra of H II regions

    NASA Astrophysics Data System (ADS)

    Zinchenko, I. A.; Kniazev, A. Y.; Grebel, E. K.; Pilyugin, L. S.

    2015-10-01

    Spectra of 34 H ii regions in the late-type galaxies NGC 1087, NGC 2967, NGC 3023, NGC 4030, NGC 4123, and NGC 4517A were observed with the South African Large Telescope (SALT). In all 34 H ii regions, oxygen abundances were determined through the "counterpart" method (C method). Additionally, in two H ii regions in which we detected auroral lines, we measured oxygen abundances with the classic Te method. We also estimated the abundances in our H ii regions using the O3N2 and N2 calibrations and compared those with the C-based abundances. With these data, we examined the radial abundance distributions in the disks of our target galaxies. We derived surface-brightness profiles and other characteristics of the disks (the surface brightness at the disk center and the disk scale length) in three photometric bands for each galaxy using publicly available photometric imaging data. The radial distributions of the oxygen abundances predicted by the relation between abundance and disk surface brightness in the W1 band obtained for spiral galaxies in our previous study are close to the radial distributions of the oxygen abundances determined from the analysis of the emission line spectra for four galaxies where this relation is applicable. Hence, when the surface-brightness profile of a late-type galaxy is known, this parametric relation can be used to estimate the likely present-day oxygen abundance in the disk of the galaxy. Based on observations made with the Southern African Large Telescope, programs 2012-1-RSA_OTH-001, 2012-2-RSA_OTH-003 and 2013-1-RSA_OTH-005.

  7. Diel, Seasonal, and Interannual Variability in Abundance of Major Mesozooplankton Taxa in the Sargasso Sea as Related to Changing Environmental Parameters

    NASA Astrophysics Data System (ADS)

    Ivory, J.; Steinberg, D. K.; Latour, R. J.

    2016-02-01

    Temporal changes in mesozooplankton community structure affect planktonic food web interactions and biogeochemical cycling. Epipelagic mesozooplankton biomass in the Sargasso Sea has increased over the last two decades, with a related increase in zooplankton-mediated carbon export. Unknown, however, is what are the patterns and variability at different temporal scales (diel, seasonal, and interannual) in abundance of each major zooplankton taxon, and how do these patterns relate to physical and other environmental changes? We enumerated major taxa of mesozooplankton collected from monthly day and night net tows in the epipelagic zone at the Bermuda Atlantic Time-series Study (BATS) site in the Sargasso Sea from 1999 to 2010. Abundances of each taxon were determined using a ZooScan optical imaging system and microscopy. Generalized Linear Models (GLMs) were used to determine what environmental parameters best explain abundance of major taxa. We used annual averages to consider broader patterns. Zooplankton taxa with the most pronounced diel vertical migration (i.e., night:day ratio, N:D, >>1) included Limacina spp. pteropods (N:D=2.02), euphausiids (1.93), calanoid copepods (1.34), and heteropods (1.34). Taxa with a pronounced spring abundance peak included chaetognaths, larvaceans, and Limacina spp. pteropods, while harpacticoid copepods peaked in late summer, and calanoid copepods in both spring and summer. Environmental variables affecting abundance differed amongst taxa. For example, calanoid copepod density was highly influenced by the abundance of a major predator- chaetognaths. Multi-year densities of calanoid copepods and ostracods both increased with increasing Water Column Stratification Index and the Atlantic Multidecadal Oscillation (AMO) index, indicating warmer sea surface temperatures are favorable for these taxa. We discuss how these temporal patterns at different scales help predict effects of global climate change on the zooplankton community.

  8. Consistency of mist netting and point counts in assessing landbird species richness and relative abundance during migration

    Treesearch

    Yong Wang; Deborah M. Finch

    2002-01-01

    We compared consistency of species richness and relative abundance data collected concurrently using mist netting and point counts during migration in riparian habitats along the middle Rio Grande of central New Mexico. Mist netting detected 74% and point counts detected 82% of the 197 species encountered during the study. Species that mist netting failed to capture...

  9. 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.

  10. Meta-analysis reveals that seed-applied neonicotinoids and pyrethroids have similar negative effects on abundance of arthropod natural enemies

    PubMed Central

    Tooker, John F.

    2016-01-01

    crop species, neonicotinoid active ingredients, or methodological choices. Discussion Our meta-analysis of nearly 1,000 observations from North American and European field studies revealed that seed-applied neonicotinoids reduced the abundance of arthropod natural enemies similarly to broadcast applications of pyrethroid insecticides. These findings suggest that substituting pyrethroids for seed-applied neonicotinoids, or vice versa, will have little net affect on natural enemy abundance. Consistent with previous lab work, our results also suggest that seed-applied neonicotinoids are less toxic to spiders and mites, which can contribute substantially to biological control in many agricultural systems. Finally, our ability to interpret the negative effect of neonicotinoids on natural enemies is constrained by difficulty relating natural-enemy abundance to biological control function; this is an important area for future study. PMID:27957400

  11. Meta-analysis reveals that seed-applied neonicotinoids and pyrethroids have similar negative effects on abundance of arthropod natural enemies.

    PubMed

    Douglas, Margaret R; Tooker, John F

    2016-01-01

    , neonicotinoid active ingredients, or methodological choices. Our meta-analysis of nearly 1,000 observations from North American and European field studies revealed that seed-applied neonicotinoids reduced the abundance of arthropod natural enemies similarly to broadcast applications of pyrethroid insecticides. These findings suggest that substituting pyrethroids for seed-applied neonicotinoids, or vice versa, will have little net affect on natural enemy abundance. Consistent with previous lab work, our results also suggest that seed-applied neonicotinoids are less toxic to spiders and mites, which can contribute substantially to biological control in many agricultural systems. Finally, our ability to interpret the negative effect of neonicotinoids on natural enemies is constrained by difficulty relating natural-enemy abundance to biological control function; this is an important area for future study.

  12. Long-term temporal and spatial changes in the richness and relative abundance of the inshore fish community of the British North Sea Coast

    NASA Astrophysics Data System (ADS)

    Henderson, Peter A.

    2017-09-01

    Changes in temporal and spatial composition of the British inshore North Sea fish community are reviewed. Sampling from the cooling water filter screens of power stations bordering the North Sea commenced in the early 1960s. To date, a total of 112 marine fish species have been recorded, a high proportion of the total inshore fish species complement of shallow North Sea British waters. The unrecorded top predators, such as large sharks, swordfish and tuna are not regularly observed in waters < 20 m deep. The greatest species number (92) is reported from fully marine waters in East Anglia. A group of 18 ubiquitous, high abundance, taxa form a core inshore community throughout the region in both estuarine and marine waters. They show a high level of concordance in relative abundance along the British east coast from the 1970s to the present. A second group of 20 species are abundant, but more restricted in habitat. Where they do occur, this group are usually always present and form together with the ubiquitous taxa the local core community. The third group of 67 species, are never abundant and are restricted in occurrence both spatially and temporally. Total species richness declines between 50 and 56°N, probably because high summer temperatures allow the southern North Sea to support summer migrants entering via the English Channel. Since the 1960s there has been a notable recovery in fish diversity and abundance in large industrialised estuaries such as the Thames and the Firth of Forth. Linked to spawning and nursery habitat gain, smelt, Osmerus eperlangus, and bass, Dicentrarchus labrax, have greatly increased in abundance. There is no evidence for a decline in species richness since the 1970s. However, elasmobranch species number has declined while two species Raja clavata and Scyliorhinus canicula have remained abundant and one, Mustelus asterias, has increased in abundance. It is argued that overexploitation and habitat destruction remain, as they have been

  13. 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. © The Authors 2016. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  14. Iron abundance in the hot DA white dwarfs Feige 24 and G191 B2B

    NASA Technical Reports Server (NTRS)

    Vennes, Stephane; Chayer, Pierre; Thorstensen, John R.; Bowyer, Stuart; Shipman, Harry L.

    1992-01-01

    Attention is given to model calculations of the far- and extreme-UV line spectra of highly ionized Fe species (Fe IV, Fe V, and Fe VI) for hot high-gravity H-rich stars. A spectral analysis of 31 hr of exposure of the DA white dwarf Feige 24 with IUE in the echelle mode reveals the presence of Fe with an abundance relative to H by number of (5-10) x 10 exp -6 with an uncertainty dominated by the determination of stellar parameters. An analysis of IUE data from the white dwarf G191 B2B results in a similar Fe abundance if this star shares similar atmospheric parameters (Teff, g) with Feige 24. Fe is thus the second most abundant photospheric element in hot DA white dwarfs.

  15. 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.

  16. Rare earth element abundances in presolar SiC

    NASA Astrophysics Data System (ADS)

    Ireland, T. R.; Ávila, J. N.; Lugaro, M.; Cristallo, S.; Holden, P.; Lanc, P.; Nittler, L.; Alexander, C. M. O'D.; Gyngard, F.; Amari, S.

    2018-01-01

    Individual isotope abundances of Ba, lanthanides of the rare earth element (REE) group, and Hf have been determined in bulk samples of fine-grained silicon carbide (SiC) from the Murchison CM2 chondrite. The analytical protocol involved secondary ion mass spectrometry with combined high mass resolution and energy filtering to exclude REE oxide isobars and Si-C-O clusters from the peaks of interest. Relative sensitivity factors were determined through analysis of NIST SRM reference glasses (610 and 612) as well as a trace-element enriched SiC ceramic. When normalised to chondrite abundances, the presolar SiC REE pattern shows significant deficits at Eu and Yb, which are the most volatile of the REE. The pattern is very similar to that observed for Group III refractory inclusions. The SiC abundances were also normalised to s-process model predictions for the envelope compositions of low-mass (1.5-3 M⊙) AGB stars with close-to-solar metallicities (Z = 0.014 and 0.02). The overall trace element abundances (excluding Eu and Yb) appear consistent with the predicted s-process patterns. The depletions of Eu and Yb suggest that these elements remained in the gas phase during the condensation of SiC. The lack of depletion in some other moderately refractory elements (like Ba), and the presence of volatile elements (e.g. Xe) indicates that these elements were incorporated into SiC by other mechanisms, most likely ion implantation.

  17. Interstellar abundances - Gas and dust

    NASA Technical Reports Server (NTRS)

    Field, G. B.

    1974-01-01

    Data on abundances of interstellar atoms, ions and molecules in front of zeta Oph are assembled and analyzed. The gas-phase abundances of at least 11 heavy elements are significantly lower, relative to hydrogen, than in the solar system. The abundance deficiencies of certain elements correlate with the temperatures derived theoretically for particle condensation in stellar atmospheres or nebulae, suggesting that these elements have condensed into dust grains near stars. There is evidence that other elements have accreted onto such grains after their arrival in interstellar space. The extinction spectrum of zeta Oph can be explained qualitatively and, to a degree, quantitatively by dust grains composed of silicates, graphite, silicon carbide, and iron, with mantles composed of complex molecules of H, C, N, and O. This composition is consistent with the observed gas-phase deficiencies.

  18. 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

  19. Lithium abundance patterns of late-F stars: an in-depth analysis of the lithium desert

    NASA Astrophysics Data System (ADS)

    Aguilera-Gómez, Claudia; Ramírez, Iván; Chanamé, Julio

    2018-06-01

    Aims: We address the existence and origin of the lithium (Li) desert, a region in the Li-Teff plane sparsely populated by stars. Here we analyze some of the explanations that have been suggested for this region, including mixing in the late main sequence, a Li dip origin for stars with low Li abundances in the region, and a possible relation with the presence of planets. Methods: To study the Li desert, we measured the atmospheric parameters and Li abundance of 227 late-F dwarfs and subgiants, chosen to be in the Teff range of the desert and without previous Li abundance measurements. Subsequently, we complemented those with literature data to obtain a homogeneous catalog of 2318 stars, for which we compute masses and ages. We characterize stars surrounding the region of the Li desert. Results: We conclude that stars with low Li abundances below the desert are more massive and more evolved than stars above the desert. Given the unexpected presence of low Li abundance stars in this effective temperature range, we concentrate on finding their origin. We conclude that these stars with low Li abundance do not evolve from stars above the desert: at a given mass, stars with low Li (i.e., below the desert) are more metal-poor. Conclusions: Instead, we suggest that stars below the Li desert are consistent with having evolved from the Li dip, discarding the need to invoke additional mixing to explain this feature. Thus, stars below the Li desert are not peculiar and are only distinguished from other subgiants evolved from the Li dip in that their combination of atmospheric parameters locates them in a range of effective temperatures where otherwise only high Li abundance stars would be found (i.e., stars above the desert). Full Tables 1 and 3 are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/614/A55This paper includes observations collected at The McDonald Observatory and

  20. 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

  1. 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.

  2. 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.

  3. Actinide abundances in ordinary chondrites

    USGS Publications Warehouse

    Hagee, B.; Bernatowicz, T.J.; Podosek, F.A.; Johnson, M.L.; Burnett, D.S.; Tatsumoto, M.

    1990-01-01

    Measurements of 244Pu fission Xe, U, Th, and light REE (LREE) abundances, along with modal petrographic determinations of phosphate abundances, were carried out on equilibrated ordinary chondrites in order to define better the solar system Pu abundance and to determine the degree of variation of actinide and LREE abundances. Our data permit comparison of the directly measured Pu/ U ratio with that determined indirectly as (Pu/Nd) ?? (Nd/U) assuming that Pu behaves chemically as a LREE. Except for Guaren??a, and perhaps H chondrites in general, Pu concentrations are similar to that determined previously for St. Se??verin, although less precise because of higher trapped Xe contents. Trapped 130Xe 136Xe ratios appear to vary from meteorite to meteorite, but, relative to AVCC, all are similar in the sense of having less of the interstellar heavy Xe found in carbonaceous chondrite acid residues. The Pu/U and Pu/Nd ratios are consistent with previous data for St. Se??verin, but both tend to be slightly higher than those inferred from previous data on Angra dos Reis. Although significant variations exist, the distribution of our Th/U ratios, along with other precise isotope dilution data for ordinary chondrites, is rather symmetric about the CI chondrite value; however, actinide/(LREE) ratios are systematically lower than the CI value. Variations in actinide or LREE absolute and relative abundances are interpreted as reflecting differences in the proportions and/or compositions of more primitive components (chondrules and CAI materials?) incorporated into different regions of the ordinary chondrite parent bodies. The observed variations of Th/U, Nd/U, or Ce/U suggest that measurements of Pu/U on any single equilibrated ordinary chondrite specimen, such as St. Se??verin, should statistically be within ??20-30% of the average solar system value, although it is also clear that anomalous samples exist. ?? 1990.

  4. Environmental drivers of denitrification rates and denitrifying gene abundances in channels and riparian areas

    NASA Astrophysics Data System (ADS)

    Tomasek, Abigail; Kozarek, Jessica L.; Hondzo, Miki; Lurndahl, Nicole; Sadowsky, Michael J.; Wang, Ping; Staley, Christopher

    2017-08-01

    Intensive agriculture in the Midwestern United States contributes to excess nitrogen in surface water and groundwater, negatively affecting human health and aquatic ecosystems. Complete denitrification removes reactive nitrogen from aquatic environments and releases inert dinitrogen gas. We examined denitrification rates and the abundances of denitrifying genes and total bacteria at three sites in an agricultural watershed and in an experimental stream in Minnesota. Sampling was conducted along transects with a gradient from always inundated (in-channel), to periodically inundated, to noninundated conditions to determine how denitrification rates and gene abundances varied from channels to riparian areas with different inundation histories. Results indicate a coupling between environmental parameters, gene abundances, and denitrification rates at the in-channel locations, and limited to no coupling at the periodically inundated and noninundated locations, respectively. Nutrient-amended potential denitrification rates for the in-channel locations were significantly correlated (α = 0.05) with five of six measured denitrifying gene abundances, whereas the periodically inundated and noninundated locations were each only significantly correlated with the abundance of one denitrifying gene. These results suggest that DNA-based analysis of denitrifying gene abundances alone cannot predict functional responses (denitrification potential), especially in studies with varying hydrologic regimes. A scaling analysis was performed to develop a predictive functional relationship relating environmental parameters to denitrification rates for in-channel locations. This method could be applied to other geographic and climatic regions to predict the occurrence of denitrification hot spots.

  5. The metal-rich abundance pattern - spectroscopic properties and abundances for 107 main-sequence stars

    NASA Astrophysics Data System (ADS)

    Ivanyuk, O. M.; Jenkins, J. S.; Pavlenko, Ya. V.; Jones, H. R. A.; Pinfield, D. J.

    2017-07-01

    We report results from the high-resolution spectral analysis of the 107 metal-rich (mostly [Fe/H] ≥ 7.67 dex) target stars from the Calan-Hertfordshire Extrasolar Planet Search programme observed with HARPS. Using our procedure of finding the best fit to the absorption line profiles in the observed spectra, we measure the abundances of Na, Mg, Al, Si, Ca, Ti, Cr, Mn, Fe, Ni, Cu and Zn, and then compare them with known results from different authors. Most of our abundances agree with these works at the level of ±0.05 dex or better for the stars we have in common. However, we do find systematic differences that make direct inferences difficult. Our analysis suggests that the selection of line lists and atomic line data along with the adopted continuum level influence these differences the most. At the same time, we confirm the positive trends of abundances versus metallicity for Na, Mn, Ni and, to a lesser degree, Al. A slight negative trend is observed for Ca, whereas Si and Cr tend to follow iron. Our analysis allows us to determine the positively skewed normal distribution of projected rotational velocities with a maximum peaking at 3 km s-1. Finally, we obtained a Gaussian distribution of microturbulent velocities that has a maximum at 1.2 km s-1 and a full width at half-maximum Δv1/2 = 0.35 km s-1, indicating that metal-rich dwarfs and subgiants in our sample have a very restricted range in microturbulent velocity.

  6. A Differential Chemical Abundance Scale for the Globular Cluster M5

    NASA Astrophysics Data System (ADS)

    Koch, Andreas; McWilliam, Andrew

    2010-06-01

    We present LTE chemical abundances for five red giants and one AGB star in the Galactic globular cluster (GC) M5 based on high-resolution spectroscopy using the Magellan Inamori Kyocera Echelle spectrograph on the Magellan 6.5 m Clay telescope. Our results are based on a line-by-line differential abundance analysis relative to the well-studied red giant Arcturus. The stars in our sample that overlap with existing studies in the literature are consistent with published values for [Fe/H] and agree to within typically 0.04 dex for the α-elements. Most deviations can be assigned to varying analysis techniques in the literature. This strengthens our newly established differential GC abundance scale and advocates future use of this method. In particular, we confirm a mean [Fe I/H] of -1.33 ± 0.03 (stat.) ±0.03 (sys.) dex and also reproduce M5's enhancement in the α-elements (O, Mg, Si, Ca, Ti) at +0.4 dex, rendering M5 a typical representative of the Galactic halo. Over-ionization of Fe I in the atmospheres of these stars by non-LTE effects is found to be less than 0.07 dex. Five of our six stars show O-Na-Al-Mg abundance patterns consistent with pollution by proton-capture nucleosynthesis products. This paper includes data gathered with the 6.5 m Magellan Telescopes located at Las Campanas Observatory, Chile.

  7. Conventional oil and natural gas infrastructure increases brown-headed cowbird (Molothrus ater) relative abundance and parasitism in mixed-grass prairie.

    PubMed

    Bernath-Plaisted, Jacy; Nenninger, Heather; Koper, Nicola

    2017-07-01

    The rapid expansion of oil and natural gas development across the Northern Great Plains has contributed to habitat fragmentation, which may facilitate brood parasitism of ground-nesting grassland songbird nests by brown-headed cowbirds ( Molothrus ater ), an obligate brood parasite, through the introduction of perches and anthropogenic edges. We tested this hypothesis by measuring brown-headed cowbird relative abundance and brood parasitism rates of Savannah sparrow ( Passerculus sandwichensis ) nests in relation to the presence of infrastructure features and proximity to potential perches and edge habitat. The presence of oil and natural gas infrastructure increased brown-headed cowbird relative abundance by a magnitude of four times, which resulted in four times greater brood parasitism rates at infrastructure sites. While the presence of infrastructure and the proximity to roads were influential in predicting brood parasitism rates, the proximity of perch sites was not. This suggests that brood parasitism associated with oil and natural gas infrastructure may result in additional pressures that reduce productivity of this declining grassland songbird.

  8. Relative Abundance and Diversity of Bacterial Methanotrophs at the Oxic–Anoxic Interface of the Congo Deep-Sea Fan

    PubMed Central

    Bessette, Sandrine; Moalic, Yann; Gautey, Sébastien; Lesongeur, Françoise; Godfroy, Anne; Toffin, Laurent

    2017-01-01

    Sitting at ∼5,000 m water depth on the Congo-Angola margin and ∼760 km offshore of the West African coast, the recent lobe complex of the Congo deep-sea fan receives large amounts of fluvial sediments (3–5% organic carbon). This organic-rich sedimentation area harbors habitats with chemosynthetic communities similar to those of cold seeps. In this study, we investigated relative abundance, diversity and distribution of aerobic methane-oxidizing bacteria (MOB) communities at the oxic–anoxic interface of sedimentary habitats by using fluorescence in situ hybridization and comparative sequence analysis of particulate mono-oxygenase (pmoA) genes. Our findings revealed that sedimentary habitats of the recent lobe complex hosted type I and type II MOB cells and comparisons of pmoA community compositions showed variations among the different organic-rich habitats. Furthermore, the pmoA lineages were taxonomically more diverse compared to methane seep environments and were related to those found at cold seeps. Surprisingly, MOB phylogenetic lineages typical of terrestrial environments were observed at such water depth. In contrast, MOB cells or pmoA sequences were not detected at the previous lobe complex that is disconnected from the Congo River inputs. PMID:28487684

  9. Relative Abundance and Diversity of Bacterial Methanotrophs at the Oxic-Anoxic Interface of the Congo Deep-Sea Fan.

    PubMed

    Bessette, Sandrine; Moalic, Yann; Gautey, Sébastien; Lesongeur, Françoise; Godfroy, Anne; Toffin, Laurent

    2017-01-01

    Sitting at ∼5,000 m water depth on the Congo-Angola margin and ∼760 km offshore of the West African coast, the recent lobe complex of the Congo deep-sea fan receives large amounts of fluvial sediments (3-5% organic carbon). This organic-rich sedimentation area harbors habitats with chemosynthetic communities similar to those of cold seeps. In this study, we investigated relative abundance, diversity and distribution of aerobic methane-oxidizing bacteria (MOB) communities at the oxic-anoxic interface of sedimentary habitats by using fluorescence in situ hybridization and comparative sequence analysis of particulate mono-oxygenase ( pmoA ) genes. Our findings revealed that sedimentary habitats of the recent lobe complex hosted type I and type II MOB cells and comparisons of pmoA community compositions showed variations among the different organic-rich habitats. Furthermore, the pmoA lineages were taxonomically more diverse compared to methane seep environments and were related to those found at cold seeps. Surprisingly, MOB phylogenetic lineages typical of terrestrial environments were observed at such water depth. In contrast, MOB cells or pmoA sequences were not detected at the previous lobe complex that is disconnected from the Congo River inputs.

  10. Associations of hypoosmotic swelling test, relative sperm volume shift, aquaporin7 mRNA abundance and bull fertility estimates.

    PubMed

    Kasimanickam, R K; Kasimanickam, V R; Arangasamy, A; Kastelic, J P

    2017-02-01

    Mammalian sperm are exposed to a natural hypoosmotic environment during male-to-female reproductive tract transition; although this activates sperm motility in vivo, excessive swelling can harm sperm structure and function. Aquaporins (AQPs) is a family of membrane-channel proteins implicated in sperm osmoregulation. The objective was to determine associations among relative sperm volume shift, hypoosmotic swelling test (HOST), sperm aquaporin (AQP) 7 mRNA abundances, and sire conception rate (SCR; fertility estimate) in Holstein bulls at a commercial artificial insemination center. Three or four sires for each full point SCR score from -4 to +4 were included. Each SCR estimate for study bulls (N = 30) was based on > 500 services (mean ± SEM) of 725 ± 13 services/sire). Sperm from a single collection day (two ejaculates) from these commercial Holstein bulls were used. Relative mRNA expression of AQP7 in sperm was determined by polymerase chain reaction. Mean relative sperm volume shift and percentage of sperm reacted in a HOST (% HOST) were determined (400 sperm per bull) after incubating in isoosmotic (300 mOsm/kg) and hypoosmotic (100 mOsm/kg) solutions for 30 min. There was no correlation between %HOST and SCR (r = 0.28 P > 0.1). However, there was a positive correlation between relative sperm volume shift and SCR (r = 0.65, P < 0.05). Furthermore, AQP7 mRNA abundance was positively correlated to both relative volume shift (r = 0.73; P < 0.05) and to SCR (r = 0.67; P < 0.05). The mRNA expressions of AQP7 and relative sperm volume shift differed (P < 0.05) among low- (<2 SCR), average- (-2 to +2) and high- (>2) fertility sire groups. In conclusion, bulls with higher SCR had significantly greater AQP7 mRNA abundance in frozen-thawed sperm. This plausibly contributed to greater regulation of sperm volume shift, which apparently conferred protection from detrimental swelling and impaired functions. Copyright © 2016 Elsevier Inc. All

  11. Utilizing individual fish biomass and relative abundance models to map environmental niche associations of adult and juvenile targeted fishes.

    PubMed

    Galaiduk, Ronen; Radford, Ben T; Harvey, Euan S

    2018-06-21

    Many fishes undergo ontogenetic habitat shifts to meet their energy and resource needs as they grow. Habitat resource partitioning and patterns of habitat connectivity between conspecific fishes at different life-history stages is a significant knowledge gap. Species distribution models were used to examine patterns in the relative abundance, individual biomass estimates and environmental niche associations of different life stages of three iconic West Australian fishes. Continuous predictive maps describing the spatial distribution of abundance and individual biomass of the study species were created as well predictive hotspot maps that identify possible areas for aggregation of individuals of similar life stages of multiple species (i.e. spawning grounds, fisheries refugia or nursery areas). The models and maps indicate that processes driving the abundance patterns could be different from the body size associated demographic processes throughout an individual's life cycle. Incorporating life-history in the spatially explicit management plans can ensure that critical habitat of the vulnerable stages (e.g. juvenile fish, spawning stock) is included within proposed protected areas and can enhance connectivity between various functional areas (e.g. nursery areas and adult populations) which, in turn, can improve the abundance of targeted species as well as other fish species relying on healthy ecosystem functioning.

  12. Influence of temporal variation and host condition on helminth abundance in the lizard Tropidurus hispidus from north-eastern Brazil.

    PubMed

    Filho, J A Araujo; Brito, S V; Lima, V F; Pereira, A M A; Mesquita, D O; Albuquerque, R L; Almeida, W O

    2017-05-01

    Ecological characteristics and environmental variation influence both host species composition and parasite abundance. Abiotic factors such as rainfall and temperature can improve parasite development and increase its reproduction rate. The comparison of these assemblages between different environments may give us a more refined analysis of how environment affects the variation of helminth parasite abundance. The aim of the present study was to evaluate how temporal variation, host size, sex and reproduction affect helminth abundance in the Tropidurus hispidus lizard in Caatinga, Restinga and Atlantic Forest environments. Overall, larger-sized lizards showed higher helminth abundance. We found a monthly variation in the helminth species abundance in all studied areas. In the Caatinga area, monoxenic and heteroxenic parasites were related to the rainy season and to the reproductive period of lizards. In Restinga, monoxenic and heteroxenic helminth species were more abundant during the driest months. In the Atlantic Forest, the rainy and host reproductive season occurred continuously throughout the year, so parasite abundance was relatively constant. Nevertheless, heteroxenic species were more abundant in this area. The present results showed that the temporal variation, body size, sex, reproductive period and habitat type influence the abundance and composition of helminth species in T. hispidus.

  13. Inventory of high-abundance mRNAs in skeletal muscle of normal men.

    PubMed

    Welle, S; Bhatt, K; Thornton, C A

    1999-05-01

    G42875rial analysis of gene expression (SAGE) method was used to generate a catalog of 53,875 short (14 base) expressed sequence tags from polyadenylated RNA obtained from vastus lateralis muscle of healthy young men. Over 12,000 unique tags were detected. The frequency of occurrence of each tag reflects the relative abundance of the corresponding mRNA. The mRNA species that were detected 10 or more times, each comprising >/=0.02% of the mRNA population, accounted for 64% of the mRNA mass but <10% of the total number of mRNA species detected. Almost all of the abundant tags matched mRNA or EST sequences cataloged in GenBank. Mitochondrial transcripts accounted for approximately 20% of the polyadenylated RNA. Transcripts encoding proteins of the myofibrils were the most abundant nuclear-encoded mRNAs. Transcripts encoding ribosomal proteins, and those encoding proteins involved in energy metabolism, also were very abundant. The database can be used as a reference for investigations of alterations in gene expression associated with conditions that influence muscle function, such as muscular dystrophies, aging, and exercise.

  14. Nucleosynthesis: Stellar and Solar Abundances and Atomic Data

    NASA Technical Reports Server (NTRS)

    Cowan, John J.; Lawler, James E.; Sneden, Christopher; DenHartog, E. A.; Collier, Jason; Dodge, Homer L.

    2006-01-01

    Abundance observations indicate the presence of often surprisingly large amounts of neutron capture (i.e., s- and r-process) elements in old Galactic halo and globular cluster stars. These observations provide insight into the nature of the earliest generations of stars in the Galaxy the progenitors of the halo stars responsible for neutron-capture synthesis. Comparisons of abundance trends can be used to understand the chemical evolution of the Galaxy and the nature of heavy element nucleosynthesis. In addition age determinations, based upon long-lived radioactive nuclei abundances, can now be obtained. These stellar abundance determinations depend critically upon atomic data. Improved laboratory transition probabilities have been recently obtained for a number of elements. These new gf values have been used to greatly refine the abundances of neutron-capture elemental abundances in the solar photosphere and in very metal-poor Galactic halo stars. The newly determined stellar abundances are surprisingly consistent with a (relative) Solar System r-process pattern, and are also consistent with abundance predictions expected from such neutron-capture nucleosynthesis.

  15. 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

  16. BOND: A quantum of solace for nebular abundance determinations

    NASA Astrophysics Data System (ADS)

    Vale Asari, N.; Stasińska, G.; Morisset, C.; Cid Fernandes, R.

    2017-11-01

    The abundances of chemical elements other than hydrogen and helium in a galaxy are the fossil record of its star formation history. Empirical relations such as mass-metallicity relation are thus seen as guides for studies on the history and chemical evolution of galaxies. Those relations usually rely on nebular metallicities measured with strong-line methods, which assume that H II regions are a one- (or at most two-) parameter family where the oxygen abundance is the driving quantity. Nature is however much more complex than that, and metallicities from strong lines may be strongly biased. We have developed the method BOND (Bayesian Oxygen and Nitrogen abundance Determinations) to simultaneously derive oxygen and nitrogen abundances in giant H II regions by comparing strong and semi-strong observed emission lines to a carefully-defined, finely-meshed grid of photoionization models. Our code and results are public and available at http://bond.ufsc.br.

  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. A TiO2 abundance map for the northern maria

    NASA Technical Reports Server (NTRS)

    Johnson, T. V.; Saunders, R. S.; Matson, D. L.; Mosher, J. A.

    1977-01-01

    A map of TiO2 abundance for most of the northern maria is presented. The telescopic data base used is the 0.38/0.56-micron ratio mosaic from Johnson et at. (1977). The titanium content has been estimated using the correlation established by Charette et al. (1974). The combination of observational, processing, and calibration errors indicates that the TiO2 map is accurate to + or - 2% (wt% TiO2) for high TiO2 content (more than 5%) and + or - 1% for low values of TiO2. Analysis of the lunar sample and telescopic data suggests strongly that the spectral parameter mapped is sensitive primarily to TiO2 abundance in the range 3-9% and does not correlate directly with iron content. It is suggested, however, that for the low TiO2 mare regions (less than 2-3% TiO2) there may be a relation between the spectral ratio and iron content and that some of the reddest mare areas in the Imbrium region may have low iron contents as well as low titanium abundances.

  19. Identification of stress responsive genes by studying specific relationships between mRNA and protein abundance.

    PubMed

    Morimoto, Shimpei; Yahara, Koji

    2018-03-01

    Protein expression is regulated by the production and degradation of mRNAs and proteins but the specifics of their relationship are controversial. Although technological advances have enabled genome-wide and time-series surveys of mRNA and protein abundance, recent studies have shown paradoxical results, with most statistical analyses being limited to linear correlation, or analysis of variance applied separately to mRNA and protein datasets. Here, using recently analyzed genome-wide time-series data, we have developed a statistical analysis framework for identifying which types of genes or biological gene groups have significant correlation between mRNA and protein abundance after accounting for potential time delays. Our framework stratifies all genes in terms of the extent of time delay, conducts gene clustering in each stratum, and performs a non-parametric statistical test of the correlation between mRNA and protein abundance in a gene cluster. Consequently, we revealed stronger correlations than previously reported between mRNA and protein abundance in two metabolic pathways. Moreover, we identified a pair of stress responsive genes ( ADC17 and KIN1 ) that showed a highly similar time series of mRNA and protein abundance. Furthermore, we confirmed robustness of the analysis framework by applying it to another genome-wide time-series data and identifying a cytoskeleton-related gene cluster (keratin 18, keratin 17, and mitotic spindle positioning) that shows similar correlation. The significant correlation and highly similar changes of mRNA and protein abundance suggests a concerted role of these genes in cellular stress response, which we consider provides an answer to the question of the specific relationships between mRNA and protein in a cell. In addition, our framework for studying the relationship between mRNAs and proteins in a cell will provide a basis for studying specific relationships between mRNA and protein abundance after accounting for potential

  20. Genome-wide analysis of coordinated transcript abundance during seed development in different Brassica rapa morphotypes.

    PubMed

    Basnet, Ram Kumar; Moreno-Pachon, Natalia; Lin, Ke; Bucher, Johan; Visser, Richard G F; Maliepaard, Chris; Bonnema, Guusje

    2013-12-01

    Brassica seeds are important as basic units of plant growth and sources of vegetable oil. Seed development is regulated by many dynamic metabolic processes controlled by complex networks of spatially and temporally expressed genes. We conducted a global microarray gene co-expression analysis by measuring transcript abundance of developing seeds from two diverse B. rapa morphotypes: a pak choi (leafy-type) and a yellow sarson (oil-type), and two of their doubled haploid (DH) progenies, (1) to study the timing of metabolic processes in developing seeds, (2) to explore the major transcriptional differences in developing seeds of the two morphotypes, and (3) to identify the optimum stage for a genetical genomics study in B. rapa seed. Seed developmental stages were similar in developing seeds of pak choi and yellow sarson of B. rapa; however, the colour of embryo and seed coat differed among these two morphotypes. In this study, most transcriptional changes occurred between 25 and 35 DAP, which shows that the timing of seed developmental processes in B. rapa is at later developmental stages than in the related species B. napus. Using a Weighted Gene Co-expression Network Analysis (WGCNA), we identified 47 "gene modules", of which 27 showed a significant association with temporal and/or genotypic variation. An additional hierarchical cluster analysis identified broad spectra of gene expression patterns during seed development. The predominant variation in gene expression was according to developmental stages rather than morphotype differences. Since lipids are the major storage compounds of Brassica seeds, we investigated in more detail the regulation of lipid metabolism. Four co-regulated gene clusters were identified with 17 putative cis-regulatory elements predicted in their 1000 bp upstream region, either specific or common to different lipid metabolic pathways. This is the first study of genome-wide profiling of transcript abundance during seed development in B

  1. Ar39 Detection at the 10-16 Isotopic Abundance Level with Atom Trap Trace Analysis

    NASA Astrophysics Data System (ADS)

    Jiang, W.; Williams, W.; Bailey, K.; Davis, A. M.; Hu, S.-M.; Lu, Z.-T.; O'Connor, T. P.; Purtschert, R.; Sturchio, N. C.; Sun, Y. R.; Mueller, P.

    2011-03-01

    Atom trap trace analysis, a laser-based atom counting method, has been applied to analyze atmospheric Ar39 (half-life=269yr), a cosmogenic isotope with an isotopic abundance of 8×10-16. 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.

  2. Terrestrial salamander abundance on reclaimed mountaintop removal mines

    USGS Publications Warehouse

    Wood, Petra Bohall; Williams, Jennifer M.

    2013-01-01

    Mountaintop removal mining, a large-scale disturbance affecting vegetation, soil structure, and topography, converts landscapes from mature forests to extensive grassland and shrubland habitats. We sampled salamanders using drift-fence arrays and coverboard transects on and near mountaintop removal mines in southern West Virginia, USA, during 2000–2002. We compared terrestrial salamander relative abundance and species richness of un-mined, intact forest with habitats on reclaimed mountaintop removal mines (reclaimed grassland, reclaimed shrubland, and fragmented forest). Salamanders within forests increased in relative abundance with increasing distance from reclaimed mine edge. Reclaimed grassland and shrubland habitats had lower relative abundance and species richness than forests. Characteristics of reclaimed habitats that likely contributed to lower salamander abundance included poor soils (dry, compacted, little organic matter, high rock content), reduced vertical structure of vegetation and little tree cover, and low litter and woody debris cover. Past research has shown that salamander populations reduced by clearcutting may rebound in 15–24 years. Time since disturbance was 7–28 years in reclaimed habitats on our study areas and salamander populations had not reached levels found in adjacent mature forests.

  3. 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.

  4. 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. © 2012 Blackwell Verlag GmbH.

  5. Carbon abundances, major element chemistry, and mineralogy of hydrated interplanetary dust particles

    NASA Technical Reports Server (NTRS)

    Keller, L. P.; Thomas, K. L.; Mckay, D. S.

    1993-01-01

    Hydrated interplanetary dust particles (IDP's) comprise a major fraction of the interplanetary dust particles collected in the stratosphere. While much is known about the mineralogy and chemistry of hydrated IDP's, little is known about the C abundance in this class of IDP's, the nature of the C-bearing phases, and how the C abundance is related to other physical properties of hydrated IDP's. Bulk compositional data (including C and O) for 11 hydrated IDP's that were subsequently examined by the transition electron microscopy (TEM) to determine their mineralogy and mineral chemistry are reported. Our analysis indicates that these hydrated IDP's are strongly enriched in C relative to the most C-rich meteorites. The average abundance of C in these hydrated IDP's is 4X CI chondrite values. The bulk compositions (including C and O) of 11 hydrated IDP's were determined by thin-window, energy-dispersive x ray (EDX) spectroscopy of the uncoated IDP's on Be substrates in the scanning electron microscopy (SEM). As a check on our C measurements, one of the IDP's (L2006H5) was embedded in glassy S, and microtome thin sections were prepared and placed onto Be substrates. Thin-film EDX analyses of multiple thin sections of L2006H5 show good agreement with the bulk value determined in the SEM. Following EDX analysis, the mineralogy and mineral chemistry of each IDP was determined by analyzing ultramicrotome thin sections in a TEM equipped with an EDX spectrometer.

  6. Abundance of introduced species at home predicts abundance away in herbaceous communities

    USGS Publications Warehouse

    Firn, Jennifer; Moore, Joslin L.; MacDougall, Andrew S.; Borer, Elizabeth T.; Seabloom, Eric W.; HilleRisLambers, Janneke; Harpole, W. Stanley; Cleland, Elsa E.; Brown, Cynthia S.; Knops, Johannes M.H.; Prober, Suzanne M.; Pyke, David A.; Farrell, Kelly A.; Bakker, John D.; O'Halloran, Lydia R.; Adler, Peter B.; Collins, Scott L.; D'Antonio, Carla M.; Crawley, Michael J.; Wolkovich, Elizabeth M.; La Pierre, Kimberly J.; Melbourne, Brett A.; Hautier, Yann; Morgan, John W.; Leakey, Andrew D.B.; Kay, Adam; McCulley, Rebecca; Davies, Kendi F.; Stevens, Carly J.; Chu, Cheng-Jin; Holl, Karen D.; Klein, Julia A.; Fay, Phillip A.; Hagenah, Nicole; Kirkman, Kevin P.; Buckley, Yvonne M.

    2011-01-01

    Many ecosystems worldwide are dominated by introduced plant species, leading to loss of biodiversity and ecosystem function. A common but rarely tested assumption is that these plants are more abundant in introduced vs. native communities, because ecological or evolutionary-based shifts in populations underlie invasion success. Here, data for 26 herbaceous species at 39 sites, within eight countries, revealed that species abundances were similar at native (home) and introduced (away) sites - grass species were generally abundant home and away, while forbs were low in abundance, but more abundant at home. Sites with six or more of these species had similar community abundance hierarchies, suggesting that suites of introduced species are assembling similarly on different continents. Overall, we found that substantial changes to populations are not necessarily a pre-condition for invasion success and that increases in species abundance are unusual. Instead, abundance at home predicts abundance away, a potentially useful additional criterion for biosecurity programmes.

  7. 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 ...

  8. Relative abundance of the southern pine beetle associates in East Texas

    Treesearch

    John C. Moser; R. C. Thatcher; L. S. Pickard

    1971-01-01

    More than 90 species of insects were identified in bolts taken from east Texas loblolly pines infested by the southern pine beetle, Dendroctonus frontalis Zimmermann and by Ips engraver beetles (Coleoptera: scolytidae). Seasonal abundance of the associates generally paralleled that of the southern pine beetle.

  9. Hierarchical models of animal abundance and occurrence

    USGS Publications Warehouse

    Royle, J. Andrew; Dorazio, R.M.

    2006-01-01

    Much of animal ecology is devoted to studies of abundance and occurrence of species, based on surveys of spatially referenced sample units. These surveys frequently yield sparse counts that are contaminated by imperfect detection, making direct inference about abundance or occurrence based on observational data infeasible. This article describes a flexible hierarchical modeling framework for estimation and inference about animal abundance and occurrence from survey data that are subject to imperfect detection. Within this framework, we specify models of abundance and detectability of animals at the level of the local populations defined by the sample units. Information at the level of the local population is aggregated by specifying models that describe variation in abundance and detection among sites. We describe likelihood-based and Bayesian methods for estimation and inference under the resulting hierarchical model. We provide two examples of the application of hierarchical models to animal survey data, the first based on removal counts of stream fish and the second based on avian quadrat counts. For both examples, we provide a Bayesian analysis of the models using the software WinBUGS.

  10. Predicting the Dynamics of Protein Abundance

    PubMed Central

    Mehdi, Ahmed M.; Patrick, Ralph; Bailey, Timothy L.; Bodén, Mikael

    2014-01-01

    Protein synthesis is finely regulated across all organisms, from bacteria to humans, and its integrity underpins many important processes. Emerging evidence suggests that the dynamic range of protein abundance is greater than that observed at the transcript level. Technological breakthroughs now mean that sequencing-based measurement of mRNA levels is routine, but protocols for measuring protein abundance remain both complex and expensive. This paper introduces a Bayesian network that integrates transcriptomic and proteomic data to predict protein abundance and to model the effects of its determinants. We aim to use this model to follow a molecular response over time, from condition-specific data, in order to understand adaptation during processes such as the cell cycle. With microarray data now available for many conditions, the general utility of a protein abundance predictor is broad. Whereas most quantitative proteomics studies have focused on higher organisms, we developed a predictive model of protein abundance for both Saccharomyces cerevisiae and Schizosaccharomyces pombe to explore the latitude at the protein level. Our predictor primarily relies on mRNA level, mRNA–protein interaction, mRNA folding energy and half-life, and tRNA adaptation. The combination of key features, allowing for the low certainty and uneven coverage of experimental observations, gives comparatively minor but robust prediction accuracy. The model substantially improved the analysis of protein regulation during the cell cycle: predicted protein abundance identified twice as many cell-cycle-associated proteins as experimental mRNA levels. Predicted protein abundance was more dynamic than observed mRNA expression, agreeing with experimental protein abundance from a human cell line. We illustrate how the same model can be used to predict the folding energy of mRNA when protein abundance is available, lending credence to the emerging view that mRNA folding affects translation

  11. Predicting the dynamics of protein abundance.

    PubMed

    Mehdi, Ahmed M; Patrick, Ralph; Bailey, Timothy L; Bodén, Mikael

    2014-05-01

    Protein synthesis is finely regulated across all organisms, from bacteria to humans, and its integrity underpins many important processes. Emerging evidence suggests that the dynamic range of protein abundance is greater than that observed at the transcript level. Technological breakthroughs now mean that sequencing-based measurement of mRNA levels is routine, but protocols for measuring protein abundance remain both complex and expensive. This paper introduces a Bayesian network that integrates transcriptomic and proteomic data to predict protein abundance and to model the effects of its determinants. We aim to use this model to follow a molecular response over time, from condition-specific data, in order to understand adaptation during processes such as the cell cycle. With microarray data now available for many conditions, the general utility of a protein abundance predictor is broad. Whereas most quantitative proteomics studies have focused on higher organisms, we developed a predictive model of protein abundance for both Saccharomyces cerevisiae and Schizosaccharomyces pombe to explore the latitude at the protein level. Our predictor primarily relies on mRNA level, mRNA-protein interaction, mRNA folding energy and half-life, and tRNA adaptation. The combination of key features, allowing for the low certainty and uneven coverage of experimental observations, gives comparatively minor but robust prediction accuracy. The model substantially improved the analysis of protein regulation during the cell cycle: predicted protein abundance identified twice as many cell-cycle-associated proteins as experimental mRNA levels. Predicted protein abundance was more dynamic than observed mRNA expression, agreeing with experimental protein abundance from a human cell line. We illustrate how the same model can be used to predict the folding energy of mRNA when protein abundance is available, lending credence to the emerging view that mRNA folding affects translation efficiency

  12. EMBATTLED BIVALVES: BIOGEOGRAPHIC DISTRIBUTIONS AND ABUNDANCES FROM THE BEAUFORT SEA TO THE GULF OF CALIFORNIA

    EPA Science Inventory

    As part of an EPA/USGS project to predict the relative vulnerability of near-coastal species to climate change, we have synthesized in a web-based tool, the Coastal Biogeographic Risk Analysis Tool (CBRAT), the biogeographic distributions and abundances of bivalves, found in dept...

  13. Conventional oil and natural gas infrastructure increases brown-headed cowbird (Molothrus ater) relative abundance and parasitism in mixed-grass prairie

    PubMed Central

    Nenninger, Heather; Koper, Nicola

    2017-01-01

    The rapid expansion of oil and natural gas development across the Northern Great Plains has contributed to habitat fragmentation, which may facilitate brood parasitism of ground-nesting grassland songbird nests by brown-headed cowbirds (Molothrus ater), an obligate brood parasite, through the introduction of perches and anthropogenic edges. We tested this hypothesis by measuring brown-headed cowbird relative abundance and brood parasitism rates of Savannah sparrow (Passerculus sandwichensis) nests in relation to the presence of infrastructure features and proximity to potential perches and edge habitat. The presence of oil and natural gas infrastructure increased brown-headed cowbird relative abundance by a magnitude of four times, which resulted in four times greater brood parasitism rates at infrastructure sites. While the presence of infrastructure and the proximity to roads were influential in predicting brood parasitism rates, the proximity of perch sites was not. This suggests that brood parasitism associated with oil and natural gas infrastructure may result in additional pressures that reduce productivity of this declining grassland songbird. PMID:28791134

  14. Chemical Abundance Analysis of Three α-poor, Metal-poor Stars in the Ultrafaint Dwarf Galaxy Horologium I

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Nagasawa, D. Q.; Marshall, J. L.; Li, T. S.

    We present chemical abundance measurements of three stars in the ultrafaint dwarf galaxy Horologium I, a Milky Way satellite discovered by the Dark Energy Survey. Using high-resolution spectroscopic observations, we measure the metallicity of the three stars, as well as abundance ratios of several α-elements, iron-peak elements, and neutron-capture elements. The abundance pattern is relatively consistent among all three stars, which have a low average metallicity of [Fe/H] ~ –2.6 and are not α-enhanced ([α/Fe] ~ 0.0). This result is unexpected when compared to other low-metallicity stars in the Galactic halo and other ultrafaint dwarfs and suggests the possibility ofmore » a different mechanism for the enrichment of Hor I compared to other satellites. Here, we discuss possible scenarios that could lead to this observed nucleosynthetic signature, including extended star formation, enrichment by a Population III supernova, and or an association with the Large Magellanic Cloud.« less

  15. Chemical Abundance Analysis of Three α-poor, Metal-poor Stars in the Ultrafaint Dwarf Galaxy Horologium I

    DOE PAGES

    Nagasawa, D. Q.; Marshall, J. L.; Li, T. S.; ...

    2018-01-11

    We present chemical abundance measurements of three stars in the ultrafaint dwarf galaxy Horologium I, a Milky Way satellite discovered by the Dark Energy Survey. Using high-resolution spectroscopic observations, we measure the metallicity of the three stars, as well as abundance ratios of several α-elements, iron-peak elements, and neutron-capture elements. The abundance pattern is relatively consistent among all three stars, which have a low average metallicity of [Fe/H] ~ –2.6 and are not α-enhanced ([α/Fe] ~ 0.0). This result is unexpected when compared to other low-metallicity stars in the Galactic halo and other ultrafaint dwarfs and suggests the possibility ofmore » a different mechanism for the enrichment of Hor I compared to other satellites. Here, we discuss possible scenarios that could lead to this observed nucleosynthetic signature, including extended star formation, enrichment by a Population III supernova, and or an association with the Large Magellanic Cloud.« less

  16. A nondestructive technique to monitor the relative abundance of terrestrial salamanders

    Treesearch

    Richard M. DeGraaf; Mariko Yamasaki

    1992-01-01

    Salamanders are abundant vertebrates in many forest ecosystems, and their annual biomass production can be important in forest food webs (Pough et al. 1987). Population densities of eastern redback salamanders (Plethodon cinereus) can exceed 2 individuals/m2 in deciduous forests of the United States (Heatwole 1962, Jaeger 1980...

  17. Rare-earth abundances in chondritic meteorites

    NASA Technical Reports Server (NTRS)

    Evensen, N. M.; Hamilton, P. J.; Onions, R. K.

    1978-01-01

    Fifteen chondrites, including eight carbonaceous chondrites, were analyzed for rare earth element abundances by isotope dilution. Examination of REE for a large number of individual chondrites shows that only a small proportion of the analyses have flat unfractionated REE patterns within experimental error. While some of the remaining analyses are consistent with magmatic fractionation, many patterns, in particular those with positive Ce anomalies, can not be explained by known magmatic processes. Elemental abundance anomalies are found in all major chondrite classes. The persistence of anomalies in chondritic materials relatively removed from direct condensational processes implies that anomalous components are resistant to equilibrium or were introduced at a late stage of chondrite formation. Large-scale segregation of gas and condensate is implied, and bulk variations in REE abundances between planetary bodies is possible.

  18. Elemental Abundances of Ultra-Heavy Galactic Cosmic Rays from the SuperTIGER Instrument

    NASA Astrophysics Data System (ADS)

    Murphy, Ryan

    2016-07-01

    The SuperTIGER (Trans-Iron Galactic Element Recorder) experiment was launched on a long-duration balloon flight from Williams Field, Antarctica, on December 8, 2012. The instrument measured the relative elemental abundances of Galactic Cosmic Rays (GCR) for charge (Z) Z>10 with excellent charge resolution, displaying well resolved individual element peaks for 10 ≤ Z ≤ 40. During its record-breaking 55-day flight, SuperTIGER collected ˜4.73 x10^{6} Iron nuclei, ˜8 times as many as detected by its predecessor, TIGER, with charge resolution at iron of 0.17 cu. SuperTIGER measures charge (Z) and energy (E) using a combination of three scintillator and two Cherenkov detectors, and employs a scintillating fiber hodoscope for event trajectory determination. The SuperTIGER data have been analyzed to correct for instrument effects and remove events that underwent nuclear interactions within the instrument. The data include more than 600 events in the charge range 30 < Z ≤ 40. SuperTIGER is the first experiment to resolve elemental abundances of every element in this charge range with high statistics and single-element resolution. The relative abundances of the galactic cosmic ray source have been derived from the measured relative elemental abundances using atmospheric and interstellar propagations. The SuperTIGER measured abundances are generally consistent with previous experimental results from TIGER and ACE-CRIS, with improved statistical precision. The SuperTIGER results confirm the earlier results from TIGER, supporting a model of cosmic-ray origin in OB associations, with preferential acceleration of refractory elements over volatile elements ordered by atomic mass (A). A second SuperTIGER Antarctic flight is planned for December 2017. Details of the instrument, flight, data analysis, and ongoing preparations will be presented.

  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. A high deuterium abundance at redshift z = 0.7.

    PubMed

    Webb, J K; Carswell, R F; Lanzetta, K M; Ferlet, R; Lemoine, M; Vidal-Madjar, A; Bowen, D V

    1997-07-17

    Of the light elements, the primordial abundance of deuterium relative to hydrogen, (D/H)p, provides the most sensitive diagnostic for the cosmological mass density parameter, omegaB. Recent high-redshift D/H measurements are highly discrepant, although this may reflect observational uncertainties. The larger primordial D/H values imply a low omegaB (requiring the Universe to be dominated by non-baryonic matter), and cause problems for galactic chemical evolution models, which have difficulty in reproducing the steep decline in D/H to the present-day values. Conversely, the lower D/H values measured at high redshift imply an omegaB greater than that derived from 7Li and 4He abundance measurements, and may require a deuterium-abundance evolution that is too low to easily explain. Here we report the first measurement of D/H at intermediate redshift (z = 0.7010), in a gas cloud selected to minimize observational uncertainties. Our analysis yields a value of D/H ((2.0 +/- 0.5) x 10[-4]) which is at the upper end of the range of values measured at high redshifts. This finding, together with other independent observations, suggests that there may be inhomogeneity in (D/H)p of at least a factor of ten.

  1. Relative abundance and species richness of terrestrial salamanders on hardwood ecosystem experiment sites before harvesting

    Treesearch

    Jami E. MacNeil; Rod N. Williams

    2013-01-01

    Terrestrial salamanders are ideal indicators of forest ecosystem integrity due to their abundance, their role in nutrient cycling, and their sensitivity to environmental change. To understand better how terrestrial salamanders are affected by forest management practices, we monitored species diversity and abundance before implementation of timber harvests within the...

  2. Traffic-Related Air Pollution, Blood Pressure, and Adaptive Response of Mitochondrial Abundance.

    PubMed

    Zhong, Jia; Cayir, Akin; Trevisi, Letizia; Sanchez-Guerra, Marco; Lin, Xinyi; Peng, Cheng; Bind, Marie-Abèle; Prada, Diddier; Laue, Hannah; Brennan, Kasey J M; Dereix, Alexandra; Sparrow, David; Vokonas, Pantel; Schwartz, Joel; Baccarelli, Andrea A

    2016-01-26

    Exposure to black carbon (BC), a tracer of vehicular-traffic pollution, is associated with increased blood pressure (BP). Identifying biological factors that attenuate BC effects on BP can inform prevention. We evaluated the role of mitochondrial abundance, an adaptive mechanism compensating for cellular-redox imbalance, in the BC-BP relationship. At ≥ 1 visits among 675 older men from the Normative Aging Study (observations=1252), we assessed daily BP and ambient BC levels from a stationary monitor. To determine blood mitochondrial abundance, we used whole blood to analyze mitochondrial-to-nuclear DNA ratio (mtDNA/nDNA) using quantitative polymerase chain reaction. Every standard deviation increase in the 28-day BC moving average was associated with 1.97 mm Hg (95% confidence interval [CI], 1.23-2.72; P<0.0001) and 3.46 mm Hg (95% CI, 2.06-4.87; P<0.0001) higher diastolic and systolic BP, respectively. Positive BC-BP associations existed throughout all time windows. BC moving averages (5-day to 28-day) were associated with increased mtDNA/nDNA; every standard deviation increase in 28-day BC moving average was associated with 0.12 standard deviation (95% CI, 0.03-0.20; P=0.007) higher mtDNA/nDNA. High mtDNA/nDNA significantly attenuated the BC-systolic BP association throughout all time windows. The estimated effect of 28-day BC moving average on systolic BP was 1.95-fold larger for individuals at the lowest mtDNA/nDNA quartile midpoint (4.68 mm Hg; 95% CI, 3.03-6.33; P<0.0001), in comparison with the top quartile midpoint (2.40 mm Hg; 95% CI, 0.81-3.99; P=0.003). In older adults, short-term to moderate-term ambient BC levels were associated with increased BP and blood mitochondrial abundance. Our findings indicate that increased blood mitochondrial abundance is a compensatory response and attenuates the cardiac effects of BC. © 2015 American Heart Association, Inc.

  3. Discrete False-Discovery Rate Improves Identification of Differentially Abundant Microbes.

    PubMed

    Jiang, Lingjing; Amir, Amnon; Morton, James T; Heller, Ruth; Arias-Castro, Ery; Knight, Rob

    2017-01-01

    Differential abundance testing is a critical task in microbiome studies that is complicated by the sparsity of data matrices. Here we adapt for microbiome studies a solution from the field of gene expression analysis to produce a new method, discrete false-discovery rate (DS-FDR), that greatly improves the power to detect differential taxa by exploiting the discreteness of the data. Additionally, DS-FDR is relatively robust to the number of noninformative features, and thus removes the problem of filtering taxonomy tables by an arbitrary abundance threshold. We show by using a combination of simulations and reanalysis of nine real-world microbiome data sets that this new method outperforms existing methods at the differential abundance testing task, producing a false-discovery rate that is up to threefold more accurate, and halves the number of samples required to find a given difference (thus increasing the efficiency of microbiome experiments considerably). We therefore expect DS-FDR to be widely applied in microbiome studies. IMPORTANCE DS-FDR can achieve higher statistical power to detect significant findings in sparse and noisy microbiome data compared to the commonly used Benjamini-Hochberg procedure and other FDR-controlling procedures.

  4. The Mean Life Squared Relationship for Abundances of Extinct Radioactivities

    NASA Technical Reports Server (NTRS)

    Lodders, K.; Cameron, A. G. W.

    2004-01-01

    We discovered that the abundances of now extinct radioactivities (relative to stable reference isotopes) in meteorites vary as a function of their mean lifetimes squared. This relationship applies to chondrites, achondrites, and irons but to calcium-aluminum inclusions (CAIs). Certain meteorites contain excesses in isotopic abundances from the decay of radioactive isotopes with half-lives much less than the age of the solar system. These short-lived radioactivities are now extinct, but they were alive when meteorites assembled in the early solar system. The origin of these radioactivities and the processes which control their abundances in the solar nebula are still not well understood. Some clues may come from our finding that the meteoritic abundances of now extinct radioactivities (relative to stable reference isotopes) vary as a function of their mean lifetimes squared. This relationship applies to chondrites, achondrites, and irons, but not to CAIs. This points to at least two different processes establishing the abundances of short-lived isotopes found in the meteoritic record.

  5. Silicon to iron abundances in solar cosmic rays and in the sun

    NASA Technical Reports Server (NTRS)

    Vahia, M. N.; Biswas, S.; Durgaprasad, N.

    1985-01-01

    Differential spectra of even charged nuclei between Si and Fe in the August 4, 1972 event were made in the energy region of 10 to 40 MeV/n-1 using rocket borne plastic detectors. The resulting relative abundances of elements and low energy enhancements are obtained and compared with spectroscopically determined photospheric abundances. The implications of the relative abundances on the acceleration mechanisms is discussed.

  6. Spectroscopic Observation and Analysis of H II Regions in M33 with MMT: Temperatures and Oxygen Abundances

    NASA Astrophysics Data System (ADS)

    Lin, Zesen; Hu, Ning; Kong, Xu; Gao, Yulong; Zou, Hu; Wang, Enci; Cheng, Fuzhen; Fang, Guanwen; Lin, Lin; Wang, Jing

    2017-06-01

    The spectra of 413 star-forming (or H II) regions in M33 (NGC 598) were observed using the multifiber spectrograph of Hectospec at the 6.5 m Multiple Mirror Telescope. Using this homogeneous spectra sample, we measured the intensities of emission lines and some physical parameters, such as electron temperatures, electron densities, and metallicities. Oxygen abundances were derived via the direct method (when available) and two empirical strong-line methods, namely, O3N2 and N2. At the high-metallicity end, oxygen abundances derived from the O3N2 calibration were higher than those derived from the N2 index, indicating an inconsistency between O3N2 and N2 calibrations. We present a detailed analysis of the spatial distribution of gas-phase oxygen abundances in M33 and confirm the existence of the axisymmetric global metallicity distribution that is widely assumed in the literature. Local variations were also observed and subsequently associated with spiral structures to provide evidence of radial migration driven by arms. Our O/H gradient fitted out to 1.1 R 25 resulted in slopes of -0.17 ± 0.03, -0.19 ± 0.01, and -0.16 ± 0.17 dex {R}25-1, utilizing abundances from O3N2, N2 diagnostics, and a direct method, respectively.

  7. Spatial patterns in the abundance of the coastal horned lizard

    USGS Publications Warehouse

    Fisher, Robert N.; Suarez, Andrew V.; Case, Ted J.

    2002-01-01

    Coastal horned lizards (   Phrynosoma coronatum) have undergone severe declines in southern California and are a candidate species for state and federal listing under the Endangered Species Act. Quantitative data on their habitat use, abundance, and distribution are lacking, however. We investigated the determinants of abundance for coastal horned lizards at multiple spatial scales throughout southern California. Specifically, we estimated lizard distribution and abundance by establishing 256 pitfall trap arrays clustered within 21 sites across four counties. These arrays were sampled bimonthly for 2–3 years. At each array we measured 26 “local” site descriptors and averaged these values with other “regional” measures to determine site characteristics. Our analyses were successful at identifying factors within and among sites correlated with the presence and abundance of coastal horned lizards. These factors included the absence of the invasive Argentine ant (  Linepithema humile) (and presence of native ant species eaten by the lizards), the presence of chaparral community plants, and the presence of sandy substrates. At a regional scale the relative abundance of Argentine ants was correlated with the relative amount of developed edge around a site. There was no evidence for spatial autocorrelation, even at the scale of the arrays within sites, suggesting that the determinants of the presence or absence and abundance of horned lizard can vary over relatively small spatial scales ( hundreds of meters). Our results suggest that a gap-type approach may miss some of the fine-scale determinants of species abundance in fragmented habitats.

  8. Colonial, more widely distributed and less abundant bird species undergo wider population fluctuations independent of their population trend

    PubMed Central

    Møller, Anders P.

    2017-01-01

    Understanding temporal variability in population size is important for conservation biology because wide population fluctuations increase the risk of extinction. Previous studies suggested that certain ecological, demographic, life-history and genetic characteristics of species might be related to the degree of their population fluctuations. We checked whether that was the case in a large sample of 231 European breeding bird species while taking a number of potentially confounding factors such as population trends or similarities among species due to common descent into account. When species-specific characteristics were analysed one by one, the magnitude of population fluctuations was positively related to coloniality, habitat, total breeding range, heterogeneity of breeding distribution and natal dispersal, and negatively related to urbanisation, abundance, relative number of subspecies, parasitism and proportion of polymorphic loci. However, when abundance (population size) was included in the analyses of the other parameters, only coloniality, habitat, total breeding range and abundance remained significantly related to population fluctuations. The analysis including all these predictors simultaneously showed that population size fluctuated more in colonial, less abundant species with larger breeding ranges. Other parameters seemed to be related to population fluctuations only because of their association with abundance or coloniality. The unexpected positive relationship between population fluctuations and total breeding range did not seem to be mediated by abundance. The link between population fluctuations and coloniality suggests a previously unrecognized cost of coloniality. The negative relationship between population size and population fluctuations might be explained by at least three types of non-mutually exclusive stochastic processes: demographic, environmental and genetic stochasticity. Measurement error in population indices, which was unknown, may

  9. Effect of Game Management on Wild Red-Legged Partridge Abundance

    PubMed Central

    Díaz-Fernández, Silvia; Arroyo, Beatriz; Casas, Fabián; Martinez-Haro, Monica; Viñuela, Javier

    2013-01-01

    The reduction of game and fish populations has increased investment in management practices. Hunting and fishing managers use several tools to maximize harvest. Managers need to know the impact their management has on wild populations. This issue is especially important to improve management efficacy and biodiversity conservation. We used questionnaires and field bird surveys in 48 hunting estates to assess whether red-legged partridge Alectoris rufa young/adult ratio and summer abundance were related to the intensity of management (provision of supplementary food and water, predator control and releases of farm-bred partridges), harvest intensity or habitat in Central Spain. We hypothesized that partridge abundance would be higher where management practices were applied more intensively. Variation in young/adult ratio among estates was best explained by habitat, year and some management practices. Density of feeders and water points had a positive relationship with this ratio, while the density of partridges released and magpies controlled were negatively related to it. The variables with greatest relative importance were feeders, releases and year. Variations in post-breeding red-legged partridge abundance among estates were best explained by habitat, year, the same management variables that influenced young/adult ratio, and harvest intensity. Harvest intensity was negatively related to partridge abundance. The other management variables had the same type of relationship with abundance as with young/adult ratio, except magpie control. Variables with greatest relative importance were habitat, feeders, water points, releases and harvest intensity. Our study suggests that management had an overall important effect on post-breeding partridge abundance. However, this effect varied among tools, as some had the desired effect (increase in partridge abundance), whereas others did not or even had a negative relationship (such as release of farm-reared birds) and can be

  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. 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 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.

  12. Infrastructure features outperform environmental variables explaining rabbit abundance around motorways.

    PubMed

    Planillo, Aimara; Malo, Juan E

    2018-01-01

    Human disturbance is widespread across landscapes in the form of roads that alter wildlife populations. Knowing which road features are responsible for the species response and their relevance in comparison with environmental variables will provide useful information for effective conservation measures. We sampled relative abundance of European rabbits, a very widespread species, in motorway verges at regional scale, in an area with large variability in environmental and infrastructure conditions. Environmental variables included vegetation structure, plant productivity, distance to water sources, and altitude. Infrastructure characteristics were the type of vegetation in verges, verge width, traffic volume, and the presence of embankments. We performed a variance partitioning analysis to determine the relative importance of two sets of variables on rabbit abundance. Additionally, we identified the most important variables and their effects model averaging after model selection by AICc on hypothesis-based models. As a group, infrastructure features explained four times more variability in rabbit abundance than environmental variables, being the effects of the former critical in motorway stretches located in altered landscapes with no available habitat for rabbits, such as agricultural fields. Model selection and Akaike weights showed that verge width and traffic volume are the most important variables explaining rabbit abundance index, with positive and negative effects, respectively. In the light of these results, the response of species to the infrastructure can be modulated through the modification of motorway features, being some of them manageable in the design phase. The identification of such features leads to suggestions for improvement through low-cost corrective measures and conservation plans. As a general indication, keeping motorway verges less than 10 m wide will prevent high densities of rabbits and avoid the unwanted effects that rabbit populations

  13. 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 ( 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 the

  14. Long-term and widespread changes in agricultural practices influence ring-necked pheasant abundance in California

    USGS Publications Warehouse

    Coates, Peter S.; Brussee, Brianne E.; Howe, Kristy B.; Fleskes, Joseph P.; Dwight, Ian; Connelly, Daniel P.; Meshriy, Matt G.; Gardner, Scott C.

    2017-01-01

    Declines in bird populations in agricultural regions of North America and Europe have been attributed to agricultural industrialization, increases in use of agrochemical application, and increased predation related to habitat modification. Based on count data compiled from Breeding Bird Survey (BBS) from 1974 to 2012, Christmas Bird Count (CBC) collected from 1914 to 2013, and hunter data from Annual Game Take Survey (AGTS) for years 1948–2010, ring-necked pheasants (Phasianus colchicus) in California have experienced substantial declines in agricultural environments. Using a modeling approach that integrates all three forms of survey data into a joint response abundance index, we found pheasant abundance was related to the amount of harvested and unharvested crop land, types of crops produced, amount of total pesticide applied, minimum temperature, precipitation, and numbers of avian competitors and predators. Specifically, major changes in agricultural practices over the last three decades were associated with declines in pheasant numbers and likely reflected widespread loss of habitat. For example, increases in cropland were associated with increased pheasant abundance during early years of study but this effect decreased through time, such that no association in recent years was evidenced. A post hoc analysis revealed that crops beneficial to pheasant abundance (e.g., barley) have declined substantially in recent decades and were replaced by less advantageous crops (e.g., nut trees). An additional analysis using a restricted data set (1990–2013) indicated recent negative impacts on pheasant numbers associated with land use practices were also associated with relatively high levels of pesticide application. Our results may provide valuable information for management policies aimed at reducing widespread declines in pheasant populations in California and may be applicable to other avian species within agricultural settings. Furthermore, this general

  15. 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.

  16. Probabilisitc Geobiological Classification Using Elemental Abundance Distributions and Lossless Image Compression in Recent and Modern Organisms

    NASA Technical Reports Server (NTRS)

    Storrie-Lombardi, Michael C.; Hoover, Richard B.

    2005-01-01

    Last year we presented techniques for the detection of fossils during robotic missions to Mars using both structural and chemical signatures[Storrie-Lombardi and Hoover, 2004]. Analyses included lossless compression of photographic images to estimate the relative complexity of a putative fossil compared to the rock matrix [Corsetti and Storrie-Lombardi, 2003] and elemental abundance distributions to provide mineralogical classification of the rock matrix [Storrie-Lombardi and Fisk, 2004]. We presented a classification strategy employing two exploratory classification algorithms (Principal Component Analysis and Hierarchical Cluster Analysis) and non-linear stochastic neural network to produce a Bayesian estimate of classification accuracy. We now present an extension of our previous experiments exploring putative fossil forms morphologically resembling cyanobacteria discovered in the Orgueil meteorite. Elemental abundances (C6, N7, O8, Na11, Mg12, Ai13, Si14, P15, S16, Cl17, K19, Ca20, Fe26) obtained for both extant cyanobacteria and fossil trilobites produce signatures readily distinguishing them from meteorite targets. When compared to elemental abundance signatures for extant cyanobacteria Orgueil structures exhibit decreased abundances for C6, N7, Na11, All3, P15, Cl17, K19, Ca20 and increases in Mg12, S16, Fe26. Diatoms and silicified portions of cyanobacterial sheaths exhibiting high levels of silicon and correspondingly low levels of carbon cluster more closely with terrestrial fossils than with extant cyanobacteria. Compression indices verify that variations in random and redundant textural patterns between perceived forms and the background matrix contribute significantly to morphological visual identification. The results provide a quantitative probabilistic methodology for discriminating putatitive fossils from the surrounding rock matrix and &om extant organisms using both structural and chemical information. The techniques described appear applicable

  17. Herpetofaunal species composition and relative abundance among three New England forest types

    Treesearch

    Richard M. DeGraaf; Deborah D. Rudis

    1990-01-01

    Drift fences and pitfall traps captured > 2000 reptiles and amphibians during 2 years; the most common species were wood frog (Rana sylvatica), American toad (Bufo americanus), and redback salamander (Plethodon cinereus). There were differences in species abundances among streamside and upland...

  18. Vertical distribution and relative abundance of gelatinous zooplankton, in situ observations near the Mid-Atlantic Ridge

    NASA Astrophysics Data System (ADS)

    Youngbluth, M.; Sørnes, T.; Hosia, A.; Stemmann, L.

    2008-01-01

    Fourteen dives were conducted with the ROVs Aglantha and Bathysaurus to depths of 2335 m along the Mid-Atlantic Ridge (42∘52'- 53∘17'N). The most frequently observed gelatinous fauna in order of overall abundance included medusae, ctenophores, siphonophores, appendicularians, and tunicates. All of these animals, except the tunicates, occurred throughout the water column. Their relative abundances differed with depth and location. Identification to species was limited to easily recognized fauna because relatively few gelatinous animals were collected. Each group of gelatinous zooplankton tended to be most numerous in a region just south of the Charlie-Gibbs Fracture Zone. Medusae (mainly Aeginura grimaldii) were the most frequently encountered animals (up to 25 individuals per 100m3). On a vertical scale their abundance peaked from 550 to 800 m and these maxima were consistently within the SAIW and NACWe. In the NACW their densities were notably lower (up 2 individuals per 100m3) and the majority of the population was deeper, ranging from 800 to 1050 m. Ctenophores (mainly Bathocyroe fosteri) were most prominent (as many as 27 individuals per 100m3) in a zone from 300 to 600 m in the NACWe. Appendicularians (primarily oikopleurids) had a broader vertical distribution in all water masses, mainly from 450 to 1000 m. Up to 12 houses per 100m3 were noted in the NACWe, and these estimates are considered to be very conservative. Sorties near the sea floor (as deep as 2100 m) indicated these detritivores were a prominent component (up to 5 houses per 100m3) of the epibenthic macrozooplankton. Siphonophores (mostly calycophorans) reached densities of about 14 colonies per 100m3 in the NACWe and occurred mainly from 300 to 600 m, at most locations. Tunicates (salps and doliolids) were patchy in their distribution and infrequently observed. Salps were numerous (up to 3 solitary individuals per 100m3) at only one location (sta. 50) near the surface. Deep-living doliolids

  19. Predictive modelling of habitat use by marine predators with respect to the abundance and depth distribution of pelagic prey

    USGS Publications Warehouse

    Boyd, Charlotte; Castillo, Ramiro; Hunt, George L.; Punt, André E..; VanBlaricom, Glenn R.; Weimerskirch, Henri; Bertrand, Sophie

    2015-01-01

    Analysis of the relative importance of abundance and accessibility is essential for the design and evaluation of effective management responses to reduced prey availability for seabirds and other top predators in marine systems.

  20. Tree hole mosquito species composition and relative abundances differ between urban and adjacent forest habitats in northwestern Argentina.

    PubMed

    Mangudo, C; Aparicio, J P; Rossi, G C; Gleiser, R M

    2018-04-01

    Water-holding tree holes are main larval habitats for many pathogen vectors, especially mosquitoes (Diptera: Culicidae). Along 3 years, the diversity and composition of mosquito species in tree holes of two neighbouring but completely different environments, a city and its adjacent forest, were compared using generalized linear mixed models, PERMANOVA, SIMPER and species association indexes. The city area (Northwest Argentina) is highly relevant epidemiologically due to the presence of Aedes aegypti L. (main dengue vector) and occurrence of dengue outbreaks; the Yungas rainforests are highly biologically diverse. In total seven mosquito species were recorded, in descending order of abundance: Ae. aegypti, Haemagogus spegazzinii Brèthes, Sabethes purpureus (Theobald), Toxorhynchites guadeloupensis Dyar and Knab, Aedes terrens Walker, Haemagogus leucocelaenus Dyar & Shannon and Sabethes petrocchiae (Shannon and Del Ponte). The seven mosquito species were recorded in both city sites and forested areas; however, their mosquito communities significantly diverged because of marked differences in the frequency and relative abundance of some species: Tx. guadeloupensis and Ae. aegypti were significantly more abundant in forest and urban areas, respectively. Positive significant associations were detected between Ae. aegypti, Hg. spegazzinii and Hg. leucocelaenus. The combined presence of Ae. aegypti, Haemagogus and Sabethes in the area also highlight a potential risk of yellow fever epidemics. Overall results show an impoverished tree hole mosquito fauna in urban environments, reflecting negative effects of urbanization on mosquito diversity.

  1. When should we expect microbial phenotypic traits to predict microbial abundances?

    PubMed

    Fox, Jeremy W

    2012-01-01

    Species' phenotypic traits may predict their relative abundances. Intuitively, this is because locally abundant species have traits making them well-adapted to local abiotic and biotic conditions, while locally rare species are not as well-adapted. But this intuition may not be valid. If competing species vary in how well-adapted they are to local conditions, why doesn't the best-adapted species simply exclude the others entirely? But conversely, if species exhibit niche differences that allow them to coexist, then by definition there is no single best adapted species. Rather, demographic rates depend on species' relative abundances, so that phenotypic traits conferring high adaptedness do not necessarily confer high abundance. I illustrate these points using a simple theoretical model incorporating adjustable levels of "adaptedness" and "niche differences." Even very small niche differences can weaken or even reverse the expected correlation between adaptive traits and abundance. Conversely, adaptive traits confer high abundance when niche differences are very strong. Future work should be directed toward understanding the link between phenotypic traits and frequency-dependence of demographic rates.

  2. Cross-correlation map analyses show weather variation influences on mosquito abundance patterns in Saginaw County, Michigan, 1989-2005.

    PubMed

    Chuang, Ting-Wu; Ionides, Edward L; Knepper, Randall G; Stanuszek, William W; Walker, Edward D; Wilson, Mark L

    2012-07-01

    Weather is important determinant of mosquito abundance that, in turn, influences vectorborne disease dynamics. In temperate regions, transmission generally is seasonal as mosquito abundance and behavior varies with temperature, precipitation, and other meteorological factors. We investigated how such factors affected species-specific mosquito abundance patterns in Saginaw County, MI, during a 17-yr period. Systematic sampling was undertaken at 22 trapping sites from May to September, during 1989-2005, for 19,228 trap-nights and 300,770 mosquitoes in total. Aedes vexans (Meigen), Culex pipiens L. and Culex restuans Theobald, the most abundant species, were analyzed. Weather data included local daily maximum temperature, minimum temperature, total precipitation, and average relative humidity. In addition to standard statistical methods, cross-correlation mapping was used to evaluate temporal associations with various lag periods between weather variables and species-specific mosquito abundances. Overall, the average number of mosquitoes was 4.90 per trap-night for Ae. vexans, 2.12 for Cx. pipiens, and 1.23 for Cx. restuans. Statistical analysis of the considerable temporal variability in species-specific abundances indicated that precipitation and relative humidity 1 wk prior were significantly positively associated with Ae. vexans, whereas elevated maximum temperature had a negative effect during summer. Cx. pipiens abundance was positively influenced by the preceding minimum temperature in the early season but negatively associated with precipitation during summer and with maximum temperature in July and August. Cx. restuans showed the least weather association, with only relative humidity 2-24 d prior being linked positively during late spring-early summer. The recently developed analytical method applied in this study could enhance our understanding of the influences of weather variability on mosquito population dynamics.

  3. Climatic Variables Do Not Directly Predict Spider Richness and Abundance in Semiarid Caatinga Vegetation, Brazil.

    PubMed

    Carvalho, Leonardo S; Sebastian, Nicholas; Araújo, Helder F P; Dias, Sidclay C; Venticinque, Eduardo; Brescovit, Antonio D; Vasconcellos, Alexandre

    2015-02-01

    Spiders are abundant in tropical ecosystems and exert predatory pressure on a wide variety of invertebrate populations and also serve as prey for many others organisms, being part of complex interrelationships influenced directly and indirectly by a myriad of factors. We examined the influence of biotic (i.e., prey availability) and abiotic (i.e., temperature, precipitation, relative humidity, real evapotranspiration) factors on species richness and abundance during a two-year period in the semiarid Caatinga vegetation in northeastern Brazil. Data were analyzed through partial autocorrelation functions, cross correlations, and a path analysis. A total of 2522 spiders were collected with beating tray, pit-fall traps, and malaise traps, comprising 91 species and 34 families. Spider abundance peaked in the rainy season. Our results suggest that total invertebrate abundance has a direct influence on spider richness and abundance, whereas the effects of precipitation were mainly indirectly related to most spider assemblage parameters. The increase in vegetation cover with the rainy season in the Caatinga provides more breeding and foraging sites for spiders and stimulates their activities. Additionally, rainfall in arid and semiarid ecosystems stimulated the activity and reproduction of many herbivore and detritivore invertebrates dependent on plant biomass and necromass consumption, leading to an increase in spider prey availability. © The Author 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  4. Abundance, biting behaviour and parous rate of anopheline mosquito species in relation to malaria incidence in gold-mining areas of southern Venezuela.

    PubMed

    Moreno, J E; Rubio-Palis, Y; Páez, E; Pérez, E; Sánchez, V

    2007-12-01

    A longitudinal entomological and epidemiological study was conducted in five localities of southern Venezuela between January 1999 and April 2000 to determine the abundance, biting behaviour and parity of anopheline mosquitoes (Diptera: Culicidae) in relation to climate variables and malaria incidence. A total of 3685 female anopheline mosquitoes, representing six species, were collected. The most abundant species were Anopheles marajoara Galvão & Damasceno (60.7%) and Anopheles darlingi Root (35.1%), which together represented 95.8% of the total anophelines collected. Abundance and species distribution varied by locality. Malaria prevalence varied from 12.5 to 21.4 cases per 1000 population. Transmission occurred throughout the year; the annual parasite index (API) for the study period was 813.0 cases per 1000 population, with a range of 71.6-2492 per 1000 population, depending on locality. Plasmodium vivax (Grassi & Feletti) (Coccidia: Plasmodiidae) accounted for 78.6% of cases, Plasmodium falciparum (Welch) for 21.4% and mixed infections (Pv+Pf) for < 0.1%. Anopheles marajoara and An. darlingi were more abundant during the rainy season (April-September). There was no significant correlation (P > 0.05) between mosquito abundance and rainfall. Correlations between malaria incidence by parasite species and mosquito abundance were not significant (P > 0.05). Monthly parous rates were similar for An. marajoara and An. darlingi throughout the year, with two peaks that coincided with the dry-rainy transition period and the period of less rain. Peaks in the incidence of malaria cases were observed 1 month after major peaks in biting rates of parous anophelines. Anopheles darlingi engages in biting activity throughout the night, with two minor peaks at 23.00-00.00 hours and 03.00-04.00 hours. Anopheles marajoara has a different pattern, with a biting peak at 19.00-21.00 hours and 76.6% of biting occurring before midnight. Although both vectors bite indoors and outdoors

  5. 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.

  6. [Brant goose colonies near snowy owls: internest distances in relation to lemming and arctic fox abundance].

    PubMed

    Kharitonov, S P; Volkov, A E; Willems, F; van Kleef, H; Klaassen, R H G; Nowak, D J; Nowak, A I; Bublichenko, A G

    2008-01-01

    Brant goose colonies around snowy owl nests have been studied near Meduza Bay (73 degrees 21' N, 80 degrees 32' E) and in the lower reaches of the Uboinaya River (73 degrees 37' N, 82 degrees 10' E), the northwestern Taimyr Peninsula, from 1999 to 2006. All brant nests within 680 m from an owl nest have been regarded as an individual colony. The results show that the area of the colony is always larger than the guarded area around the owl nest. In years of high abundance of lemmings, brant geese nest generally closer to the owl nest than in years of high abundance. When arctic foxes are abundant, however, brant geese nest significantly closer to owls than when the foxes are scarce, irrespective of lemming abundance. The mechanism of brant colony formation around owl nests is based on a number of stimuli.

  7. Pathogenic Streptomyces spp. abundance affected by potato cultivars.

    PubMed

    Nahar, Kamrun; Goyer, Claudia; Zebarth, Bernie J; Burton, David L; Whitney, Sean

    2018-04-16

    Potato cultivars vary in their tolerance to common scab (CS), however how they affect CS-causing Streptomyces spp. populations over time is poorly understood. This study investigated the effects of potato cultivar on pathogenic Streptomyces spp. abundance, measured using quantitative PCR, in three spatial locations in a CS-infested field: 1) soil close to the plant (SCP); 2) rhizosphere (RS); and 3) geocaulosphere (GS) soils. Two tolerant (Gold Rush, Hindenburg) and two susceptible cultivars (Green Mountain, Agria) were tested. The abundance of pathogenic Streptomyces spp. significantly increased in late August compared with other dates in RS of susceptible cultivars in both years. Abundance of pathogenic Streptomyces spp., when averaged over locations and time, was significantly greater in susceptible cultivars compared with tolerant cultivars in 2014. Principal coordinates analysis showed that SCP and RS soil properties (pH, organic carbon and nitrogen concentrations) explained 68% and 76% of total variation in Streptomyces spp. abundance among cultivars in 2013, respectively, suggesting that cultivars influenced CS pathogen growth conditions. The results suggested that the genetic background of potato cultivars influenced the abundance of pathogenic Streptomyces spp., with 5 to 6 times more abundant Streptomyces spp. in RS of susceptible cultivars compared with tolerant cultivars, which would result in substantially more inoculum left in the field after harvest.  .

  8. Abundance and productivity of birds over an elevational gradient

    Treesearch

    Kathryn L. Purcell

    2002-01-01

    This study is investigating the abundance and productivity of birds breeding in four forest types over an elevational gradient in conifer forests of the southern Sierra Nevada of California to identify the most productive habitats for each species, and to examine elevational shifts in abundance, especially as they relate to temperature and precipitation. Species...

  9. 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

  10. Stellar Oxygen Abundances.V.Abundances of Two Hyades Dwarfs Derived from the 6300 Angstroms [OI] Line

    NASA Astrophysics Data System (ADS)

    King, Jeremy R.; Hiltgen, Daniel D.

    1996-12-01

    We present observations of the 6300 Å [O I] spectral region in two cool Hyades dwarfs, vB 79 and vB 25. We derive a mean iron abundance, [Fe/H]˜+0.11, in good agreement with recent analyses of F and G Hyades dwarfs. The O abundance derived from spectrum synthesis, [O/H]˜+0.15, is between the values deduced by Garcia Lopez et al. (1993, ApJ, 412, 173; [O/H]=-0.05 to -0.10) and King (1993, Ph. D. Dissertation, University of Hawaii; [O/H]=+0.26), who employed the 7774 Å O I triplet in hotter Hyades dwarfs. An accounting of differences between these two 7774 Å analyses is given. Our [O I]-based determination suggests the Hyades O abundance itself is super-solar, though [O/Fe]˜0.0; however, systematic errors as large as 0.10-0.15 dex cannot be ruled out. The Hyades giants show an unexpected ˜0.23 dex O deficit relative to our dwarf value. While some suggestive evidence for non-standard nuclear processing and mixing in the Hyades giants may exist, we find it unconvincing. Rather, model atmosphere deficiencies or [O I] -region blending features that are still unrecognized by laboratory and theoretical efforts may contribute to the giant-dwarf O discrepancy. Finally, our high O abundance is marginally consistent with values claimed to provide a solution to the Hyades Li problem from standard stellar models. However, it is not clear that these models do in fact reproduce the extant Li data. Our Li abundance upper limit for vB 25 is at least 0.5 dex lower than the abundances of two tidally locked binaries of similar Teff. Standard stellar models of uniform composition and age are not able to reproduce such scatter in Li.

  11. Sunspots, Starspots, and Elemental Abundances

    NASA Astrophysics Data System (ADS)

    Doschek, George A.; Warren, Harry P.

    2017-08-01

    The composition of plasma in solar and stellar atmospheres is not fixed, but varies from feature to feature. These variations are organized by the First Ionization Potential (FIP) of the element. Solar measurements often indicate that low FIP elements (< 10eV, such as Fe, Si, Mg) are enriched by factors of 3-4 in the corona relative to high FIP elements (>10 eV, such as C, N, O, Ar, He) compared to abundances in the photosphere. Stellar observations have also shown similar enrichments. An inverse FIP effect, where the low FIP elements are depleted, has been observed in stellar coronae of stars believed to have large starspots in their photospheres. The abundances are important for determining radiative loss rates in models, tracing the origin of the slow solar wind, and for understanding wave propagation in the chromosphere and corona. Recently, inverse FIP effects have been discovered in the Sun (Doschek, Warren, & Feldman 2015, ApJ, 808, L7) from spectra obtained by the Extreme-ultraviolet Imaging Spectrometer (EIS) on the Hinode spacecraft. The inverse FIP regions seem always to be near sunspots and cover only a very small area (characteristic length = a few arcseconds). However, in pursuing the search for inverse FIP regions, we have found that in some sunspot groups the coronal abundance at a temperature of 3-4 MK can be near photospheric over much larger areas of the sun near the sunspots (e.g., 6,000 arcsec2). Also, sometimes the abundances at 3-4 MK are in between coronal and photospheric values. This can occur in small areas of an active region. It is predicted (Laming 2015, Sol. Phys., 12, 2) that the FIP effect should be highly variable in the corona. Several examples of coronal abundance variations are presented. Our work indicates that a comprehensive re-investigation of solar abundances is highly desirable. This work is supported by a NASA Hinode grant.

  12. Changes in Abundance of Oral Microbiota Associated with Oral Cancer

    PubMed Central

    Schmidt, Brian L.; Kuczynski, Justin; Bhattacharya, Aditi; Huey, Bing; Corby, Patricia M.; Queiroz, Erica L. S.; Nightingale, Kira; Kerr, A. Ross; DeLacure, Mark D.; Veeramachaneni, Ratna; Olshen, Adam B.; Albertson, Donna G.

    2014-01-01

    Individual bacteria and shifts in the composition of the microbiome have been associated with human diseases including cancer. To investigate changes in the microbiome associated with oral cancers, we profiled cancers and anatomically matched contralateral normal tissue from the same patient by sequencing 16S rDNA hypervariable region amplicons. In cancer samples from both a discovery and a subsequent confirmation cohort, abundance of Firmicutes (especially Streptococcus) and Actinobacteria (especially Rothia) was significantly decreased relative to contralateral normal samples from the same patient. Significant decreases in abundance of these phyla were observed for pre-cancers, but not when comparing samples from contralateral sites (tongue and floor of mouth) from healthy individuals. Weighted UniFrac principal coordinates analysis based on 12 taxa separated most cancers from other samples with greatest separation of node positive cases. These studies begin to develop a framework for exploiting the oral microbiome for monitoring oral cancer development, progression and recurrence. PMID:24887397

  13. A new solar carbon abundance based on non-LTE CN molecular spectra

    NASA Technical Reports Server (NTRS)

    Mount, G. H.; Linsky, J. L.

    1975-01-01

    A detailed non-LTE analysis of solar CN spectra strongly suggest a revised carbon abundance for the sun. We recommend a value of log carbon abundance = 8.35 plus or minus 0.15 which is significantly lower than the presently accepted value of log carbon abundance = 8.55. This revision may have important consequences in astrophysics.

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

    USGS Publications Warehouse

    Campbell Grant, Evan H.; Jung, Robin E.; Rice, Karen 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.

  15. Understanding Phlebotomus perniciosus abundance in south-east Spain: assessing the role of environmental and anthropic factors.

    PubMed

    Risueño, José; Muñoz, Clara; Pérez-Cutillas, Pedro; Goyena, Elena; Gonzálvez, Moisés; Ortuño, María; Bernal, Luis Jesús; Ortiz, Juana; Alten, Bulent; Berriatua, Eduardo

    2017-04-19

    Leishmaniosis is associated with Phlebotomus sand fly vector density, but our knowledge of the environmental framework that regulates highly overdispersed vector abundance distributions is limited. We used a standardized sampling procedure in the bioclimatically diverse Murcia Region in Spain and multilevel regression models for count data to estimate P. perniciosus abundance in relation to environmental and anthropic factors. Twenty-five dog and sheep premises were sampled for sand flies using adhesive and light-attraction traps, from late May to early October 2015. Temperature, relative humidity and other animal- and premise-related data recorded on site and other environmental data were extracted from digital databases using a geographical information system. The relationship between sand fly abundance and explanatory variables was analysed using binomial regression models. The total number of sand flies captured, mostly with light-attraction traps, was 3,644 specimens, including 80% P. perniciosus, the main L. infantum vector in Spain. Abundance varied between and within zones and was positively associated with increasing altitude from 0 to 900 m above sea level, except from 500 to 700 m where it was low. Populations peaked in July and especially during a 3-day heat wave when relative humidity and wind speed plummeted. Regression models indicated that climate and not land use or soil characteristics have the greatest impact on this species density on a large geographical scale. In contrast, micro-environmental factors such as animal building characteristics and husbandry practices affect sand fly population size on a smaller scale. A standardised sampling procedure and statistical analysis for highly overdispersed distributions allow reliable estimation of P. perniciosus abundance and identification of environmental drivers. While climatic variables have the greatest impact at macro-environmental scale, anthropic factors may be determinant at a micro

  16. Report on carbon and nitrogen abundance studies

    NASA Technical Reports Server (NTRS)

    Boehm-Vitense, Erika

    1991-01-01

    The aim of the proposal was to determine the nitrogen to carbon abundance ratios from transition layer lines in stars with different T(sub eff) and luminosities. The equations which give the surface emission line fluxes and the measured ratio of the NV to CIV emission line fluxes are presented and explained. The abundance results are compared with those of photospheric abundance studies for stars in common with the photospheric investigations. The results show that the analyses are at least as accurate as the photospheric determinations. These studies can be extended to F and early G stars for which photospheric abundance determinations for giants are hard to do because molecular bands become too weak. The abundance determination in the context of stellar evolution is addressed. The N/C abundance ratio increases steeply at the point of evolution for which the convection zone reaches deepest. Looking at the evolution of the rotation velocities v sin i, a steep decrease in v sin i is related to the increasing depth of the convection zone. It is concluded that the decrease in v sin i for T(sub eff) less than or approximately = 5800 K is most probably due to the rearrangement of the angular momentum in the stars due to deep convective mixing. It appears that the convection zone is rotating with nearly depth independent angular momentum. Other research results and ongoing projects are discussed.

  17. Environmental DNA (eDNA) detects the invasive rusty crayfish Orconectes rusticus at low abundances.

    PubMed

    Dougherty, Matthew M; Larson, Eric R; Renshaw, Mark A; Gantz, Crysta A; Egan, Scott P; Erickson, Daniel M; Lodge, David M

    2016-06-01

    Early detection is invaluable for the cost-effective control and eradication of invasive species, yet many traditional sampling techniques are ineffective at the low population abundances found at the onset of the invasion process. Environmental DNA (eDNA) is a promising and sensitive tool for early detection of some invasive species, but its efficacy has not yet been evaluated for many taxonomic groups and habitat types.We evaluated the ability of eDNA to detect the invasive rusty crayfish Orconectes rusticus and to reflect patterns of its relative abundance, in upper Midwest, USA, inland lakes. We paired conventional baited trapping as a measure of crayfish relative abundance with water samples for eDNA, which were analysed in the laboratory with a qPCR assay. We modelled detection probability for O. rusticus eDNA using relative abundance and site characteristics as covariates and also tested the relationship between eDNA copy number and O. rusticus relative abundance.We detected O. rusticus eDNA in all lakes where this species was collected by trapping, down to low relative abundances, as well as in two lakes where trap catch was zero. Detection probability of O. rusticus eDNA was well predicted by relative abundance of this species and lake water clarity. However, there was poor correspondence between eDNA copy number and O. rusticus relative abundance estimated by trap catches. Synthesis and applications . Our study demonstrates a field and laboratory protocol for eDNA monitoring of crayfish invasions, with results of statistical models that provide guidance of sampling effort and detection probabilities for researchers in other regions and systems. We propose eDNA be included as a tool in surveillance for invasive or imperilled crayfishes and other benthic arthropods.

  18. Observationally Constraining Gas Giant Composition via Their Host Star Abundances

    NASA Astrophysics Data System (ADS)

    Teske, Johanna; Thorngren, Daniel; Fortney, Jonathan

    2018-01-01

    While the photospheric abundances of the Sun match many rock-forming elemental abundances in the Earth to within 10 mol%, as well as in Mars, the Moon, and meteorites, the Solar System giant planets are of distinctly non-stellar composition — Jupiter's bulk metallicity (inferred from its bulk density, measured from spacecraft data) is ∼ x5-10 solar, and Saturn is ∼ x10-20 solar. This knowledge has led to dramatic advances in understanding models of core accretion, which now match the heavy element enrichment of each of the Solar System's giant planets. However, we have thus far lacked similar data for exoplanets to use as a check for formation and composition models over a much larger parameter space. Here we present a study of the host stars of a sample of cool transiting gas giants with measured bulk metal fractions (as in Thorngren et al. 2016) to better constrain the relation Zplanet/Zstar — giant exoplanet metal enrichment relative to the host star. We add a new dimension of chemical variation, measuring C, O, Mg, Si, Ni, and well as Fe (on which previous Zplanet/Zstar calculations were based). Our analysis provides the best constraints to date on giant exoplanet interior composition and how this relates to formation environment, and make testable predictions for JWST observations of exoplanet atmospheres.

  19. Using long-term data to predict fish abundance: the case of Prochilodus lineatus (Characiformes, Prochilodontidae) in the intensely regulated upper Paraná River

    USGS Publications Warehouse

    Piana, Pitágoras A.; Cardoso, Bárbara F.; Dias, Joilson; Gomes, Luiz C.; Agostinho, Angelo A.; Miranda, Leandro E.

    2017-01-01

    Populations show spatial-temporal fluctuations in abundance, partly due to random processes and partly due to self-regulatory processes. We evaluated the effects of various external factors on the population numerical abundance of curimba Prochilodus lineatus in the upper Paraná River floodplain, Brazil, over a 19-year period. Panel data analysis was applied to examine the structure of temporal and spatial abundance while controlling auto-regressive processes and spatial non-homogeneity variances that often obscure relationships. As sources of population variation, we considered predation, competition, selected abiotic variables, construction of a dam upstream of the study area, water level and flood intensity during the spawning period. We found that biological interactions (predation and competition) were not significantly related to variations in curimba abundance; specific conductance was a space indicator of abundance, apparently linked to the biology of the species; intensity of floods determined inter-annual variation in abundances; Porto Primavera Dam negatively impacted the abundances at sites in the floodplain directly affected by discharges from the dam. Panel data analysis was a powerful tool that identified the need for intense flooding to maintain high abundances of curimba in the upper Paraná River. We believe our results apply to other species with similar life strategy.

  20. Explaining variation in adult Anopheles indoor resting abundance: the relative effects of larval habitat proximity and insecticide-treated bed net use.

    PubMed

    McCann, Robert S; Messina, Joseph P; MacFarlane, David W; Bayoh, M Nabie; Gimnig, John E; Giorgi, Emanuele; Walker, Edward D

    2017-07-17

    Spatial determinants of malaria risk within communities are associated with heterogeneity of exposure to vector mosquitoes. The abundance of adult malaria vectors inside people's houses, where most transmission takes place, should be associated with several factors: proximity of houses to larval habitats, structural characteristics of houses, indoor use of vector control tools containing insecticides, and human behavioural and environmental factors in and near houses. While most previous studies have assessed the association of larval habitat proximity in landscapes with relatively low densities of larval habitats, in this study these relationships were analysed in a region of rural, lowland western Kenya with high larval habitat density. 525 houses were sampled for indoor-resting mosquitoes across an 8 by 8 km study area using the pyrethrum spray catch method. A predictive model of larval habitat location in this landscape, previously verified, provided derivations of indices of larval habitat proximity to houses. Using geostatistical regression models, the association of larval habitat proximity, long-lasting insecticidal nets (LLIN) use, house structural characteristics (wall type, roof type), and peridomestic variables (cooking in the house, cattle near the house, number of people sleeping in the house) with mosquito abundance in houses was quantified. Vector abundance was low (mean, 1.1 adult Anopheles per house). Proximity of larval habitats was a strong predictor of Anopheles abundance. Houses without an LLIN had more female Anopheles gambiae s.s., Anopheles arabiensis and Anopheles funestus than houses where some people used an LLIN (rate ratios, 95% CI 0.87, 0.85-0.89; 0.84, 0.82-0.86; 0.38, 0.37-0.40) and houses where everyone used an LLIN (RR, 95% CI 0.49, 0.48-0.50; 0.39, 0.39-0.40; 0.60, 0.58-0.61). Cooking in the house also reduced Anopheles abundance across all species. The number of people sleeping in the house, presence of cattle near the house

  1. 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

  2. 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) were analyzed to compute their elemental abundances using ATLAS9 (Kurucz, 1993; 2005; Sbordone et al., 2004). In our analysis we assumed local thermodynamic equilibrium. The atmospheric parameters of HD 80057 used in this study are from Firnstein and Przybilla (2012), and that of HD 80404 are derived from spectral energy distribution, ionization equilibria of Cr I/II and Fe I/II, the fits to the wings of Balmer and Paschen lines as Teff = 7700 ± 150 K and log g = 1.60 ± 0.15 (in cgs). The microturbulent velocities of HD 80057 and HD 80404 have been determined as 4.3 ± 0.1 and 2.2 ± 0.0 km s^-1, respectively. The rotational velocities are 15 ± 1 and 7 ± 2 km s^-1 and their macroturbulence velocities are 24 ± 2 and 2 ± 1 km s^1. We have given the abundances of 25 ions of 19 elements for HD 80057 and 36 ions of 25 elements for HD 80404. The abundances are close to solar values, except for some elements (Na, Sc, Ti, V, Ba, and Sr). We have found the metallicities [M/H] for HD 80057 and HD 80404 as -0.16 ± 0.24 and -0.04 ± 0.16 dex, respectively. The evolutionary status of these stars are discussed and their nitrogen-to-carbon (N/C) and nitrogen-to-oxygen (N/O) ratios show that they are in their blue supergiant phase before the red supergiant region.

  3. Stronger warming effects on microbial abundances in colder regions

    PubMed Central

    Chen, Ji; Luo, Yiqi; Xia, Jianyang; Jiang, Lifen; Zhou, Xuhui; Lu, Meng; Liang, Junyi; Shi, Zheng; Shelton, Shelby; Cao, Junji

    2015-01-01

    Soil microbes play critical roles in regulating terrestrial carbon (C) cycle and its feedback to climate change. However, it is still unclear how the soil microbial community and abundance respond to future climate change scenarios. In this meta-analysis, we synthesized the responses of microbial community and abundance to experimental warming from 64 published field studies. Our results showed that warming significantly increased soil microbial abundance by 7.6% on average. When grouped by vegetation or soil types, tundras and histosols had the strongest microbial responses to warming with increased microbial, fungal, and bacterial abundances by 15.0%, 9.5% and 37.0% in tundra, and 16.5%, 13.2% and 13.3% in histosols, respectively. We found significant negative relationships of the response ratios of microbial, fungal and bacterial abundances with the mean annual temperature, indicating that warming had stronger effects in colder than warmer regions. Moreover, the response ratios of microbial abundance to warming were positively correlated with those of soil respiration. Our findings therefore indicate that the large quantities of C stored in colder regions are likely to be more vulnerable to climate warming than the soil C stored in other warmer regions. PMID:26658882

  4. Element abundances at high redshift

    NASA Technical Reports Server (NTRS)

    Meyer, David M.; Welty, D. E.; York, D. G.

    1989-01-01

    Abundances of Si(+), S(+), Cr(+), Mn(+), Fe(_), and Zn(+) are considered for two absorption-line systems in the spectrum of the QSO PKS 0528 - 250. Zinc and sulfur are underabundant, relative to H, by a factor of 10 compared to their solar and Galactic interstellar abundances. The silicon-, chromium-, iron-, and nickel-to-hydrogen ratios are less than the solar values and comparable to the local interstellar ratios. A straightforward interpretation is that nucleosynthesis in these high-redshift systems has led to only about one-tenth as much heavy production as in the gas clouds around the sun, and that the amount of the observed underabundances attributable to grain depletion is small. The dust-to-gas ratio in these clouds is less than 8 percent of the Galactic value.

  5. Chemical Abundance Measurements of Ultra-Faint Dwarf Galaxies Discovered by the Dark Energy Survey

    NASA Astrophysics Data System (ADS)

    Nagasawa, Daniel; Marshall, Jennifer L.; Simon, Joshua D.; Hansen, Terese; Li, Ting; Bernstein, Rebecca; Balbinot, Eduardo; Drlica-Wagner, Alex; Pace, Andrew; Strigari, Louis; Pellegrino, Craig; DePoy, Darren L.; Suntzeff, Nicholas; Bechtol, Keith; Dark Energy Suvey

    2018-01-01

    We present chemical abundance analysis results derived from high-resolution spectroscopy of ultra-faint dwarfs discovered by the Dark Energy Survey. Ultra-faint dwarf galaxies preserve a fossil record of the chemical abundance patterns imprinted by the first stars in the Universe. High-resolution spectroscopic observations of member stars in several recently discovered Milky Way satellites reveal a range of abundance patterns among ultra-faint dwarfs suggesting that star formation processes in the early Universe were quite diverse. The chemical content provides a glimpse not only of the varied nucleosynthetic processes and chemical history of the dwarfs themselves, but also the environment in which they were formed. We present the chemical abundance analysis of these objects and discuss possible explanations for the observed abundance patterns.

  6. 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.

  7. Abundance and persistence of antibiotic resistance genes in livestock farms: a comprehensive investigation in eastern China.

    PubMed

    Cheng, Weixiao; Chen, Hong; Su, Chao; Yan, Shuhai

    2013-11-01

    Increases of antibiotic resistance genes in the environment may pose a threat to public health. The purpose of this study was to investigate the abundance and diversity of tetracycline (tet) and sulfonamide (sul) resistance genes in eight livestock farms in Hangzhou, eastern China. Ten tet genes (tetA, tetB, tetC, tetG, tetL, tetM, tetO, tetQ, tetW, and tetX), two sul genes (sulI and sulII), and one genetic element associated with mobile antibiotic resistance genes [class 1 integron (intI1)] were quantified by real-time polymerase chain reaction. No significant difference was found in the abundance of the tet and sul genes in various scales of pig, chicken, and duck farms (P>0.05). The average abundance of ribosomal protection protein genes (tetQ, tetM, tetW, and tetO) in the manure and wastewater samples was higher than most of the efflux pump genes (tetA, tetB, tetC, and tetL) and enzymatic modification gene (tetX) (P<0.05), except for efflux pump gene tetG, which was abundant and showed no difference from tetM. Most ARGs had higher relative abundance in the wastewater lagoon than in manures even after treatment. Although the three ribosomal protection protein genes (tetQ, tetW, and tetO) had higher relative abundance, numbers were reduced during the complete wastewater treatment process in pig farms (P<0.05). The relative abundance of tetG, sulI, and sulII increased after the wastewater treatment and the removal of these three genes exhibited significant positive correlations with the intI1 gene (tetG: R(2)=0.60, P<0.05; sulI: R(2)=0.72, P<0.05; sulII: R(2)=0.62, P<0.05), suggesting that intI1 may be involved in their proliferation. As for tetM and sulII genes, a highly significant difference was found in manure samples between pig farms and duck farms (P<0.001). Phylogenetic analysis showed that tetM was more diverse in duck farms than in pig farms. Additionally, sulII sequence was conserved both in pig and duck farms. This is the first comprehensive study to

  8. Analysis of low abundant trehalose-6-phosphate and related metabolites in Medicago truncatula by hydrophilic interaction liquid chromatography-triple quadrupole mass spectrometry.

    PubMed

    Mata, Ana Teresa; Jorge, Tiago Filipe; Ferreira, João; do Rosário Bronze, Maria; Branco, Diana; Fevereiro, Pedro; Araújo, Susana; António, Carla

    2016-12-16

    Trehalose-6-phosphate (T6P) is an important signaling metabolite involved in plant growth control that inhibits the sucrose nonfermenting-1-related protein kinase 1 (SnRK1), a key regulator of energy and carbon metabolism in plants. The quantification of T6P in plant tissues is fundamental to improve our understanding of sugar signaling and the links between plant growth and development in response to stress conditions. However, the almost undetectable levels of T6P together with the complex plant matrix and the presence of T6P isomers such as sucrose-6-phosphate (S6P), makes the detection of this metabolite challenging. This work describes the development and validation of a hydrophilic interaction chromatography (HILIC) method for the on-line coupling with negative ion electrospray (ESI) triple quadrupole tandem mass spectrometry (MS/MS) in the highly sensitive and selective multiple reaction monitoring (MRM) mode for the target analysis of metabolic intermediates of the biosynthesis of trehalose, including glucose-6-phosphate (G6P), uridine 5-diphospho-glucose (UDPG), T6P (and its isomer S6P). Enhanced signal in the MRM mode and improved chromatographic separation for each compound were obtained using piperidine and methylphosphonic acid as additives in the HILIC mobile phase. The optimized HILIC-ESI-QqQ-MS/MS method increases the range of sensitive analytical methodologies for the quantification of key low-abundant metabolites, and was applied to quantify the fluctuations of S6P, T6P and G6P in Medicago truncatula plants in response to environmental stress. The levels of S6P, T6P, and G6P in M. truncatula plant tissues (roots and leaves) exposed to a water deficit and recovery treatment, ranged from 30 to 150pmolg -1 FW, 16-120pmolg -1 FW, and 330-1690pmolg -1 FW, respectively. Copyright © 2016 Elsevier B.V. All rights reserved.

  9. Observations on abundance of bluntnose sixgill sharks, Hexanchus griseus, in an urban waterway in Puget Sound, 2003-2005.

    PubMed

    Griffing, Denise; Larson, Shawn; Hollander, Joel; Carpenter, Tim; Christiansen, Jeff; Doss, Charles

    2014-01-01

    The bluntnose sixgill shark, Hexanchus griseus, is a widely distributed but poorly understood large, apex predator. Anecdotal reports of diver-shark encounters in the late 1990's and early 2000's in the Pacific Northwest stimulated interest in the normally deep-dwelling shark and its presence in the shallow waters of Puget Sound. Analysis of underwater video documenting sharks at the Seattle Aquarium's sixgill research site in Elliott Bay and mark-resight techniques were used to answer research questions about abundance and seasonality. Seasonal changes in relative abundance in Puget Sound from 2003-2005 are reported here. At the Seattle Aquarium study site, 45 sixgills were tagged with modified Floy visual marker tags, along with an estimated 197 observations of untagged sharks plus 31 returning tagged sharks, for a total of 273 sixgill observations recorded. A mark-resight statistical model based on analysis of underwater video estimated a range of abundance from a high of 98 sharks seen in July of 2004 to a low of 32 sharks seen in March of 2004. Both analyses found sixgills significantly more abundant in the summer months at the Seattle Aquarium's research station.

  10. Observations on Abundance of Bluntnose Sixgill Sharks, Hexanchus griseus, in an Urban Waterway in Puget Sound, 2003-2005

    PubMed Central

    Griffing, Denise; Larson, Shawn; Hollander, Joel; Carpenter, Tim; Christiansen, Jeff; Doss, Charles

    2014-01-01

    The bluntnose sixgill shark, Hexanchus griseus, is a widely distributed but poorly understood large, apex predator. Anecdotal reports of diver-shark encounters in the late 1990’s and early 2000’s in the Pacific Northwest stimulated interest in the normally deep-dwelling shark and its presence in the shallow waters of Puget Sound. Analysis of underwater video documenting sharks at the Seattle Aquarium’s sixgill research site in Elliott Bay and mark-resight techniques were used to answer research questions about abundance and seasonality. Seasonal changes in relative abundance in Puget Sound from 2003–2005 are reported here. At the Seattle Aquarium study site, 45 sixgills were tagged with modified Floy visual marker tags, along with an estimated 197 observations of untagged sharks plus 31 returning tagged sharks, for a total of 273 sixgill observations recorded. A mark-resight statistical model based on analysis of underwater video estimated a range of abundance from a high of 98 sharks seen in July of 2004 to a low of 32 sharks seen in March of 2004. Both analyses found sixgills significantly more abundant in the summer months at the Seattle Aquarium’s research station. PMID:24475229

  11. Can Occupancy–Abundance Models Be Used to Monitor Wolf Abundance?

    PubMed Central

    Latham, M. Cecilia; Latham, A. David M.; Webb, Nathan F.; Mccutchen, Nicole A.; Boutin, Stan

    2014-01-01

    Estimating the abundance of wild carnivores is of foremost importance for conservation and management. However, given their elusive habits, direct observations of these animals are difficult to obtain, so abundance is more commonly estimated from sign surveys or radio-marked individuals. These methods can be costly and difficult, particularly in large areas with heavy forest cover. As an alternative, recent research has suggested that wolf abundance can be estimated from occupancy–abundance curves derived from “virtual” surveys of simulated wolf track networks. Although potentially more cost-effective, the utility of this approach hinges on its robustness to violations of its assumptions. We assessed the sensitivity of the occupancy–abundance approach to four assumptions: variation in wolf movement rates, changes in pack cohesion, presence of lone wolves, and size of survey units. Our simulations showed that occupancy rates and wolf pack abundances were biased high if track surveys were conducted when wolves made long compared to short movements, wolf packs were moving as multiple hunting units as opposed to a cohesive pack, and lone wolves were moving throughout the surveyed landscape. We also found that larger survey units (400 and 576 km2) were more robust to changes in these factors than smaller survey units (36 and 144 km2). However, occupancy rates derived from large survey units rapidly reached an asymptote at 100% occupancy, suggesting that these large units are inappropriate for areas with moderate to high wolf densities (>15 wolves/1,000 km2). Virtually-derived occupancy–abundance relationships can be a useful method for monitoring wolves and other elusive wildlife if applied within certain constraints, in particular biological knowledge of the surveyed species needs to be incorporated into the design of the occupancy surveys. Further, we suggest that the applicability of this method could be extended by directly incorporating some of its

  12. The formation of the Milky Way halo and its dwarf satellites; a NLTE-1D abundance analysis. I. Homogeneous set of atmospheric parameters

    NASA Astrophysics Data System (ADS)

    Mashonkina, L.; Jablonka, P.; Pakhomov, Yu.; Sitnova, T.; North, P.

    2017-08-01

    We present a homogeneous set of accurate atmospheric parameters for a complete sample of very and extremely metal-poor stars in the dwarf spheroidal galaxies (dSphs) Sculptor, Ursa Minor, Sextans, Fornax, Boötes I, Ursa Major II, and Leo IV. We also deliver a Milky Way (MW) comparison sample of giant stars covering the - 4 < [Fe/H] < - 1.7 metallicity range. We show that, in the [Fe/H] ≿ - 3.7 regime, the non-local thermodynamic equilibrium (NLTE) calculations with non-spectroscopic effective temperature (Teff) and surface gravity (log g) based on the photometric methods and known distance provide consistent abundances of the Fe I and Fe II lines. This justifies the Fe I/Fe II ionisation equilibrium method to determine log g for the MW halo giants with unknown distance. The atmospheric parameters of the dSphs and MW stars were checked with independent methods. In the [Fe/H] > - 3.5 regime, the Ti I/Ti II ionisation equilibrium is fulfilled in the NLTE calculations. In the log g - Teff plane, all the stars sit on the giant branch of the evolutionary tracks corresponding to [Fe/H] = - 2 to - 4, in line with their metallicities. For some of the most metal-poor stars of our sample, we achieve relatively inconsistent NLTE abundances from the two ionisation stages for both iron and titanium. We suggest that this is a consequence of the uncertainty in the Teff-colour relation at those metallicities. The results of this work provide the basis for a detailed abundance analysis presented in a companion paper. Tables A.1 and A.2 are also available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/604/A129

  13. The Relative Abundance and Transcriptional Activity of Marine Sponge-Associated Microorganisms Emphasizing Groups Involved in Sulfur Cycle.

    PubMed

    Jensen, Sigmund; Fortunato, Sofia A V; Hoffmann, Friederike; Hoem, Solveig; Rapp, Hans Tore; Øvreås, Lise; Torsvik, Vigdis L

    2017-04-01

    During the last decades, our knowledge about the activity of sponge-associated microorganisms and their contribution to biogeochemical cycling has gradually increased. Functional groups involved in carbon and nitrogen metabolism are well documented, whereas knowledge about microorganisms involved in the sulfur cycle is still limited. Both sulfate reduction and sulfide oxidation has been detected in the cold water sponge Geodia barretti from Korsfjord in Norway, and with specimens from this site, the present study aims to identify extant versus active sponge-associated microbiota with focus on sulfur metabolism. Comparative analysis of small subunit ribosomal RNA (16S rRNA) gene (DNA) and transcript (complementary DNA (cDNA)) libraries revealed profound differences. The transcript library was predominated by Chloroflexi despite their low abundance in the gene library. An opposite result was found for Acidobacteria. Proteobacteria were detected in both libraries with representatives of the Alpha- and Gammaproteobacteria related to clades with presumably thiotrophic bacteria from sponges and other marine invertebrates. Sequences that clustered with sponge-associated Deltaproteobacteria were remotely related to cultivated sulfate-reducing bacteria. The microbes involved in sulfur cycling were identified by the functional gene aprA (adenosine-5'-phosphosulfate reductase) and its transcript. Of the aprA sequences (DNA and cDNA), 87 % affiliated with sulfur-oxidizing bacteria. They clustered with Alphaproteobacteria and with clades of deep-branching Gammaproteobacteria. The remaining sequences clustered with sulfate-reducing Archaea of the phylum Euryarchaeota. These results indicate an active role of yet uncharacterized Bacteria and Archaea in the sponge's sulfur cycle.

  14. Multi-scale models of grassland passerine abundance in a fragmented system in Wisconsin

    USGS Publications Warehouse

    Renfrew, R.B.; Ribic, C.A.

    2008-01-01

    Fragmentation of grasslands has been implicated in grassland bird population declines. Multi-scale models are being increasingly used to assess potential factors that influence grassland bird presence, abundance, and productivity. However, studies rarely assess fragmentation metrics, and seldom evaluate more than two scales or interactions among scales. We evaluated the relative importance of characteristics at multiple scales to patterns in relative abundance of Savannah Sparrow (Passerculus sandwichensis), Grasshopper Sparrow (Ammodramus savannarum), Eastern Meadowlark (Sturnella magna), and Bobolink (Dolichonyx oryzivorus). We surveyed birds in 74 southwestern Wisconsin pastures from 1997 to 1999 and compared models with explanatory variables from multiple scales: within-patch vegetation structure (microhabitat), patch (macrohabitat), and three landscape extents. We also examined interactions between macrohabitat and landscape factors. Core area of pastures was an important predictor of relative abundance, and composition of the landscape was more important than configuration. Relative abundance was frequently higher in pastures with more core area and in landscapes with more grassland and less wooded area. The direction and strength of the effect of core pasture size on relative abundance changed depending on amount of wooded area in the landscape. Relative abundance of grassland birds was associated with landscape variables more frequently at the 1200-m scale than at smaller scales. To develop better predictive models, parameters at multiple scales and their interactive effects should be included, and results should be evaluated in the context of microhabitat variability, landscape composition, and fragmentation in the study area. ?? 2007 Springer Science+Business Media B.V.

  15. Cyanide and isocyanide abundances in the cold, dark cloud TMC-1

    NASA Technical Reports Server (NTRS)

    Irvine, W. M.; Schloerb, F. P.

    1984-01-01

    Cold, dark molecular clouds are particularly useful for the study of interstellar chemistry because their physical parameters are better understood than those of heterogeneous, complex giant molecular clouds. Another advantage is their relatively small distance from the solar system. The present investigaation has the objective to provide accurate abundance ratios for several cyanides and isocyanides in order to constrain models of dark cloud chemistry. The relative abundances of such related species can be particularly useful for the study of chemical processes. The cloud TMC-1 considered in the current study has a remarkably high abundance of acetylene and polyacetylene derivatives. Data at 3 mm, corresponding to the J = 1 to 0 transitions of HCN, H(C-13)N, HN(C-13), HC(N-15), and H(N-15)C were obtained.

  16. Implications of Abundant Gas and Oil for Climate Forcing

    NASA Astrophysics Data System (ADS)

    Edmonds, J.

    2015-12-01

    Perhaps the most important development in the field of energy over the past decade has been the advent of technologies that enable the production of larger volumes of natural gas and oil at lower cost. The availability of more abundant gas and oil is reshaping the global energy system, with implications for both evolving emissions of CO2 and other climate forcers. More abundant gas and oil will also transform the character of greenhouse gas emissions mitigation. We review recent findings regarding the impact of abundant gas and oil for climate forcing and the challenge of emissions mitigation. We find strong evidence that, absent policies to limits its penetration against renewable energy, abundant gas has little observable impact on CO2 emissions, and tends to increase overall climate forcing, though the latter finding is subject to substantial uncertainty. The presence of abundant gas also affects emissions mitigation. There is relatively little literature exploring the implication of expanded gas availability on the difficulty in meeting emissions mitigation goals. However, preliminary results indicate that on global scales abundant gas does not substantially affect the cost of emissions mitigation, even though natural gas could have an expanded role in emissions mitigation scenarios as compared with scenarios in which natural gas is less abundant.

  17. The Abundances of the Fe Group Elements in AV 304, an Abundance Standard in the Small Magellanic Cloud

    NASA Astrophysics Data System (ADS)

    Peters, Geraldine J.; Lanz, Thierry; Bouret, Jean-Claude; Proffitt, Charles R.; Adelman, Saul J.; Hubeny, Ivan

    2018-06-01

    AV 304 is a B0.5 IV field star in the Small Magellanic Cloud with ultra-sharp spectral lines that has emerged as an abundance standard. We have combined recent spectroscopic observations from the Cosmic Origins Spectrograph (COS) on the Hubble Space Telescope with archival data from the Far Ultraviolet Spectroscopic Explorer (FUSE) and ESO’s VLT/UVES to determine the abundances of the Fe group elements (Ti, V, Cr, Mn, Fe, Co, & Ni). The analysis was carried through using the Hubeny/Lanz NLTE programs TLUSTY/SYNSPEC. The COS observations were secured with the G130M, G160M, G185M, and G225M gratings. Combined with the FUSE data, we have achieved spectral coverage in the UV from 950 to 2400 A. Measurable lines from the Fe group, except for a very few multiplets of Fe II, III are not observed in optical spectra. The following stellar parameters were found: Teff = 27500±500 K, log g = 3.7±0.1 cm/s2, Vturb= 1±1 km/s, and v sin i = 8 ±2 km/s. The Fe abundance appears to be only slightly lower than the mean depletion in the SMC, but the other Fe group elements are underabundant by 0.3 dex or more. This study confirmed the low abundance of nitrogen (-1.25 dex relative to the solar value) that was reported by Peters & Adelman (ASP Conf. Series, 348, p. 136, 2006). Whereas the light elements are delivered to the ISM by core-collapse supernovae (CCSNe), the Fe group elements are believed to come mostly from low/intermediate mass binaries containing white dwarfs that undergo SNe Ia explosions. A single SNe Ia can deliver 0.5 solar masses of pure Fe (and maybe Mn) to the ISM compared with about 0.07 solar masses from a CCSNe. It appears that there is very little processed material from its interior in the atmosphere of AV 304 and that the star did not form from an interstellar cloud that was enriched by material from earlier supernova activity. Support from STScI grants HST-GO-14081.002 and HST-GO-13346.022, and USC’s Women in Science and Engineering (WiSE) program is

  18. Predictive modelling of habitat selection by marine predators with respect to the abundance and depth distribution of pelagic prey.

    PubMed

    Boyd, Charlotte; Castillo, Ramiro; Hunt, George L; Punt, André E; VanBlaricom, Glenn R; Weimerskirch, Henri; Bertrand, Sophie

    2015-11-01

    Understanding the ecological processes that underpin species distribution patterns is a fundamental goal in spatial ecology. However, developing predictive models of habitat use is challenging for species that forage in marine environments, as both predators and prey are often highly mobile and difficult to monitor. Consequently, few studies have developed resource selection functions for marine predators based directly on the abundance and distribution of their prey. We analysed contemporaneous data on the diving locations of two seabird species, the shallow-diving Peruvian Booby (Sula variegata) and deeper diving Guanay Cormorant (Phalacrocorax bougainvilliorum), and the abundance and depth distribution of their main prey, Peruvian anchoveta (Engraulis ringens). Based on this unique data set, we developed resource selection functions to test the hypothesis that the probability of seabird diving behaviour at a given location is a function of the relative abundance of prey in the upper water column. For both species, we show that the probability of diving behaviour is mostly explained by the distribution of prey at shallow depths. While the probability of diving behaviour increases sharply with prey abundance at relatively low levels of abundance, support for including abundance in addition to the depth distribution of prey is weak, suggesting that prey abundance was not a major factor determining the location of diving behaviour during the study period. The study thus highlights the importance of the depth distribution of prey for two species of seabird with different diving capabilities. The results complement previous research that points towards the importance of oceanographic processes that enhance the accessibility of prey to seabirds. The implications are that locations where prey is predictably found at accessible depths may be more important for surface foragers, such as seabirds, than locations where prey is predictably abundant. Analysis of the relative

  19. Screening molecular associations with lipid membranes using natural abundance 13C cross-polarization magic-angle spinning NMR and principal component analysis.

    PubMed

    Middleton, David A; Hughes, Eleri; Madine, Jillian

    2004-08-11

    We describe an NMR approach for detecting the interactions between phospholipid membranes and proteins, peptides, or small molecules. First, 1H-13C dipolar coupling profiles are obtained from hydrated lipid samples at natural isotope abundance using cross-polarization magic-angle spinning NMR methods. Principal component analysis of dipolar coupling profiles for synthetic lipid membranes in the presence of a range of biologically active additives reveals clusters that relate to different modes of interaction of the additives with the lipid bilayer. Finally, by representing profiles from multiple samples in the form of contour plots, it is possible to reveal statistically significant changes in dipolar couplings, which reflect perturbations in the lipid molecules at the membrane surface or within the hydrophobic interior.

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

    USGS Publications Warehouse

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

    2014-01-01

    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 log10E. 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.

  1. Taxon abundance, diversity, co-occurrence and network analysis of the ruminal microbiota in response to dietary changes in dairy cows.

    PubMed

    Tapio, Ilma; Fischer, Daniel; Blasco, Lucia; Tapio, Miika; Wallace, R John; Bayat, Ali R; Ventto, Laura; Kahala, Minna; Negussie, Enyew; Shingfield, Kevin J; Vilkki, Johanna

    2017-01-01

    The ruminal microbiome, comprising large numbers of bacteria, ciliate protozoa, archaea and fungi, responds to diet and dietary additives in a complex way. The aim of this study was to investigate the benefits of increasing the depth of the community analysis in describing and explaining responses to dietary changes. Quantitative PCR, ssu rRNA amplicon based taxa composition, diversity and co-occurrence network analyses were applied to ruminal digesta samples obtained from four multiparous Nordic Red dairy cows fitted with rumen cannulae. The cows received diets with forage:concentrate ratio either 35:65 (diet H) or 65:35 (L), supplemented or not with sunflower oil (SO) (0 or 50 g/kg diet dry matter), supplied in a 4 × 4 Latin square design with a 2 × 2 factorial arrangement of treatments and four 35-day periods. Digesta samples were collected on days 22 and 24 and combined. QPCR provided a broad picture in which a large fall in the abundance of fungi was seen with SO in the H but not the L diet. Amplicon sequencing showed higher community diversity indices in L as compared to H diets and revealed diet specific taxa abundance changes, highlighting large differences in protozoal and fungal composition. Methanobrevibacter ruminantium and Mbb. gottschalkii dominated archaeal communities, and their abundance correlated negatively with each other. Co-occurrence network analysis provided evidence that no microbial domain played a more central role in network formation, that some minor-abundance taxa were at nodes of highest centrality, and that microbial interactions were diet specific. Networks added new dimensions to our understanding of the diet effect on rumen microbial community interactions.

  2. Taxon abundance, diversity, co-occurrence and network analysis of the ruminal microbiota in response to dietary changes in dairy cows

    PubMed Central

    Fischer, Daniel; Blasco, Lucia; Tapio, Miika; Wallace, R. John; Bayat, Ali R.; Ventto, Laura; Kahala, Minna; Negussie, Enyew; Vilkki, Johanna

    2017-01-01

    The ruminal microbiome, comprising large numbers of bacteria, ciliate protozoa, archaea and fungi, responds to diet and dietary additives in a complex way. The aim of this study was to investigate the benefits of increasing the depth of the community analysis in describing and explaining responses to dietary changes. Quantitative PCR, ssu rRNA amplicon based taxa composition, diversity and co-occurrence network analyses were applied to ruminal digesta samples obtained from four multiparous Nordic Red dairy cows fitted with rumen cannulae. The cows received diets with forage:concentrate ratio either 35:65 (diet H) or 65:35 (L), supplemented or not with sunflower oil (SO) (0 or 50 g/kg diet dry matter), supplied in a 4 × 4 Latin square design with a 2 × 2 factorial arrangement of treatments and four 35-day periods. Digesta samples were collected on days 22 and 24 and combined. QPCR provided a broad picture in which a large fall in the abundance of fungi was seen with SO in the H but not the L diet. Amplicon sequencing showed higher community diversity indices in L as compared to H diets and revealed diet specific taxa abundance changes, highlighting large differences in protozoal and fungal composition. Methanobrevibacter ruminantium and Mbb. gottschalkii dominated archaeal communities, and their abundance correlated negatively with each other. Co-occurrence network analysis provided evidence that no microbial domain played a more central role in network formation, that some minor-abundance taxa were at nodes of highest centrality, and that microbial interactions were diet specific. Networks added new dimensions to our understanding of the diet effect on rumen microbial community interactions. PMID:28704445

  3. The UCSD HIRES/Keck I Damped Lyα Abundance Database. II. The Implications

    NASA Astrophysics Data System (ADS)

    Prochaska, Jason X.; Wolfe, Arthur M.

    2002-02-01

    We present a comprehensive analysis of the damped Lyα (DLA) abundance database presented in the first paper of this series. This database provides a homogeneous set of abundance measurements for many elements including Si, Cr, Ni, Zn, Fe, Al, S, Co, O, and Ar from 38 DLA systems with zabs>1.5. With little exception, these DLA systems exhibit very similar relative abundances. There is no significant correlation in X/Fe with [Fe/H] metallicity, and the dispersion in X/Fe is small at all metallicity. We search the database for trends indicative of dust depletion and in a few cases find strong evidence. Specifically, we identify a correlation between [Si/Ti] and [Zn/Fe] which is unambiguous evidence for depletion. Following Hou and colleagues, we present [X/Si] abundances against [Si/H]+logN(HI) and note trends of decreasing X/Si with increasing [Si/H]+logN(HI) which argue for dust depletion. Similarly, comparisons of [Si/Fe] and [Si/Cr] against [Si/H] indicate significant depletion at [Si/H]>-1 but suggest essentially dust-free damped systems at [Si/H]<-1.5 dex. We present a discussion on the nucleosynthetic history of the DLA systems by focusing on abundance patterns which are minimally affected by dust depletion. We find [Si/Fe]-->0.25 dex as [Zn/Fe]-->0 and that the [Si/Fe] values exhibit a plateau of ~0.3 dex at [Si/H]<-1.5 dex. Together these trends indicate significant α-enrichment in the DLA systems at low metallicity, an interpretation further supported by the observed O/Fe, S/Fe, and Ar/Fe ratios. Comparing the relative abundances of the Fe peak elements, we identify important offsets from solar relative abundances for Cr, Ni, and Fe which suggest variations in nucleosynthesis along the Fe peak. Finally, the DLA systems exhibit a modest odd-even effect revealed by Si/Al, [Si/Al]~0.4 dex, which is significantly smaller than values observed in Galactic halo stars of comparable metallicity. These observations present strong evidence that the DLA systems and

  4. Nanoplankton and picoplankton in the Western English Channel: abundance and seasonality from 2007-2013

    NASA Astrophysics Data System (ADS)

    Tarran, Glen A.; Bruun, John T.

    2015-09-01

    The nano- and picoplankton community at Station L4 in the Western English Channel was studied between 2007 and 2013 by flow cytometry to quantify abundance and investigate seasonal cycles within these communities. Nanoplankton included both photosynthetic and heterotrophic eukaryotic single-celled organisms while the picoplankton included picoeukaryote phytoplankton, Synechococcus sp. cyanobacteria and heterotrophic bacteria. A Box-Jenkins Transfer Function climatology analysis of surface data revealed that Synechococcus sp., cryptophytes, and heterotrophic flagellates had bimodal annual cycles. Nanoeukaryotes and both high and low nucleic acid-containing bacteria (HNA and LNA, respectively) groups exhibited unimodal annual cycles. Phaeocystis sp., whilst having clearly defined abundance maxima in spring was not detectable the rest of the year. Coccolithophores exhibited a weak seasonal cycle, with abundance peaks in spring and autumn. Picoeukaryotes did not exhibit a discernable seasonal cycle at the surface. Timings of maximum group abundance varied through the year. Phaeocystis sp. and heterotrophic flagellates peaked in April/May. Nanoeukaryotes and HNA bacteria peaked in June/July and had relatively high abundance throughout the summer. Synechococcus sp., cryptophytes and LNA bacteria all peaked from mid to late September. The transfer function model techniques used represent a useful means of identifying repeating annual cycles in time series data with the added ability to detect trends and harmonic terms at different time scales from months to decades.

  5. Organic farming enhances soil microbial abundance and activity—A meta-analysis and meta-regression

    PubMed Central

    Symnaczik, Sarah; Mäder, Paul; De Deyn, Gerlinde; Gattinger, Andreas

    2017-01-01

    Population growth and climate change challenge our food and farming systems and provide arguments for an increased intensification of agriculture. A promising option is eco-functional intensification through organic farming, an approach based on using and enhancing internal natural resources and processes to secure and improve agricultural productivity, while minimizing negative environmental impacts. In this concept an active soil microbiota plays an important role for various soil based ecosystem services such as nutrient cycling, erosion control and pest and disease regulation. Several studies have reported a positive effect of organic farming on soil health and quality including microbial community traits. However, so far no systematic quantification of whether organic farming systems comprise larger and more active soil microbial communities compared to conventional farming systems was performed on a global scale. Therefore, we conducted a meta-analysis on current literature to quantify possible differences in key indicators for soil microbial abundance and activity in organic and conventional cropping systems. All together we integrated data from 56 mainly peer-reviewed papers into our analysis, including 149 pairwise comparisons originating from different climatic zones and experimental duration ranging from 3 to more than 100 years. Overall, we found that organic systems had 32% to 84% greater microbial biomass carbon, microbial biomass nitrogen, total phospholipid fatty-acids, and dehydrogenase, urease and protease activities than conventional systems. Exclusively the metabolic quotient as an indicator for stresses on microbial communities remained unaffected by the farming systems. Categorical subgroup analysis revealed that crop rotation, the inclusion of legumes in the crop rotation and organic inputs are important farming practices affecting soil microbial community size and activity. Furthermore, we show that differences in microbial size and activity

  6. Estimating abundances of interacting species using morphological traits, foraging guilds, and habitat

    USGS Publications Warehouse

    Dorazio, Robert M.; Connor, Edward F.

    2014-01-01

    We developed a statistical model to estimate the abundances of potentially interacting species encountered while conducting point-count surveys at a set of ecologically relevant locations - as in a metacommunity of species. In the model we assume that abundances of species with similar traits (e.g., body size) are potentially correlated and that these correlations, when present, may exist among all species or only among functionally related species (such as members of the same foraging guild). We also assume that species-specific abundances vary among locations owing to systematic and stochastic sources of heterogeneity. For example, if abundances differ among locations due to differences in habitat, then measures of habitat may be included in the model as covariates. Naturally, the quantitative effects of these covariates are assumed to differ among species. Our model also accounts for the effects of detectability on the observed counts of each species. This aspect of the model is especially important for rare or uncommon species that may be difficult to detect in community-level surveys. Estimating the detectability of each species requires sampling locations to be surveyed repeatedly using different observers or different visits of a single observer. As an illustration, we fitted models to species-specific counts of birds obtained while sampling an avian community during the breeding season. In the analysis we examined whether species abundances appeared to be correlated due to similarities in morphological measures (body mass, beak length, tarsus length, wing length, tail length) and whether these correlations existed among all species or only among species of the same foraging guild. We also used the model to estimate the effects of forested area on species abundances and the effects of sound power output (as measured by body size) on species detection probabilities.

  7. 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.

  8. Chemical Abundance Analysis of Three α-poor, Metal-poor Stars in the Ultrafaint Dwarf Galaxy Horologium I

    NASA Astrophysics Data System (ADS)

    Nagasawa, D. Q.; Marshall, J. L.; Li, T. S.; Hansen, T. T.; Simon, J. D.; Bernstein, R. A.; Balbinot, E.; Drlica-Wagner, A.; Pace, A. B.; Strigari, L. E.; Pellegrino, C. M.; DePoy, D. L.; Suntzeff, N. B.; Bechtol, K.; Walker, A. R.; Abbott, T. M. C.; Abdalla, F. B.; Allam, S.; Annis, J.; Benoit-Lévy, A.; Bertin, E.; Brooks, D.; Carnero Rosell, A.; Carrasco Kind, M.; Carretero, J.; Cunha, C. E.; D’Andrea, C. B.; da Costa, L. N.; Davis, C.; Desai, S.; Doel, P.; Eifler, T. F.; Flaugher, B.; Fosalba, P.; Frieman, J.; García-Bellido, J.; Gaztanaga, E.; Gerdes, D. W.; Gruen, D.; Gruendl, R. A.; Gschwend, J.; Gutierrez, G.; Hartley, W. G.; Honscheid, K.; James, D. J.; Jeltema, T.; Krause, E.; Kuehn, K.; Kuhlmann, S.; Kuropatkin, N.; March, M.; Miquel, R.; Nord, B.; Roodman, A.; Sanchez, E.; Santiago, B.; Scarpine, V.; Schindler, R.; Schubnell, M.; Sevilla-Noarbe, I.; Smith, M.; Smith, R. C.; Soares-Santos, M.; Sobreira, F.; Suchyta, E.; Tarle, G.; Thomas, D.; Tucker, D. L.; Wechsler, R. H.; Wolf, R. C.; Yanny, B.

    2018-01-01

    We present chemical abundance measurements of three stars in the ultrafaint dwarf galaxy Horologium I, a Milky Way satellite discovered by the Dark Energy Survey. Using high-resolution spectroscopic observations, we measure the metallicity of the three stars, as well as abundance ratios of several α-elements, iron-peak elements, and neutron-capture elements. The abundance pattern is relatively consistent among all three stars, which have a low average metallicity of [Fe/H] ∼ ‑2.6 and are not α-enhanced ([α/Fe] ∼ 0.0). This result is unexpected when compared to other low-metallicity stars in the Galactic halo and other ultrafaint dwarfs and suggests the possibility of a different mechanism for the enrichment of Hor I compared to other satellites. We discuss possible scenarios that could lead to this observed nucleosynthetic signature, including extended star formation, enrichment by a Population III supernova, and or an association with the Large Magellanic Cloud. This paper includes data gathered with the 6.5 m Magellan Telescopes located at Las Campanas Observatory, Chile. This paper also includes data based on observations made with the ESO Very Large Telescope at Paranal Observatory, Chile (ID 096.D-0967(B); PI: E. Balbinot).

  9. Constraints on the Mass–Richness Relation from the Abundance and Weak Lensing of SDSS Clusters

    NASA Astrophysics Data System (ADS)

    Murata, Ryoma; Nishimichi, Takahiro; Takada, Masahiro; Miyatake, Hironao; Shirasaki, Masato; More, Surhud; Takahashi, Ryuichi; Osato, Ken

    2018-02-01

    We constrain the scaling relation between optical richness (λ) and halo mass (M) for a sample of Sloan Digital Sky Survey (SDSS) red-sequence Matched-filter Probabilistic Percolation (redMaPPer) galaxy clusters within the context of the Planck cosmological model. We use a forward modeling approach where we model the probability distribution of optical richness for a given mass, P({ln}λ | M). To model the abundance and the stacked lensing profiles, we use an emulator specifically built to interpolate the halo mass function and the stacked lensing profile for an arbitrary set of halo mass and redshift, which is calibrated based on a suite of high-resolution N-body simulations. We apply our method to 8312 SDSS redMaPPer clusters with 20 ≤ λ ≤ 100 and 0.10 ≤ z λ ≤ 0.33 and show that the lognormal distribution model for P(λ | M), with four free parameters, well reproduces the measured abundances and lensing profiles simultaneously. The constraints are characterized by the mean relation, < {ln}λ > (M)=A+B{ln}(M/{M}pivot}), with A={3.207}-0.046+0.044 and B={0.993}-0.055+0.041 (68% CL), where the pivot mass scale M pivot = 3 × 1014 h ‑1 M ⊙, and the scatter {σ }lnλ | M}={σ }0+q{ln}(M/{M}pivot}) with {σ }0={0.456}-0.039+0.047 and q=-{0.169}-0.026+0.035. We find that a large scatter in halo masses is required at the lowest-richness bins (20 ≤ λ ≲ 30) in order to reproduce the measurements. Without such a large scatter, the model prediction for the lensing profiles tends to overestimate the measured amplitudes. This might imply a possible contamination of intrinsically low-richness clusters due to the projection effects. Such a low-mass halo contribution is significantly reduced when applying our method to the sample of 30 ≤ λ ≤ 100.

  10. Composition of fungal soil communities varies with plant abundance and geographic origin

    PubMed Central

    Reininger, Vanessa; Martinez-Garcia, Laura B.; Sanderson, Laura; Antunes, Pedro M.

    2015-01-01

    Interactions of belowground fungal communities with exotic and native plant species may be important drivers of plant community structure in invaded grasslands. However, field surveys linking plant community structure with belowground fungal communities are missing. We investigated whether a selected number of abundant and relatively rare plants, either native or exotic, from an old-field site associate with different fungal communities. We also assessed whether these plants showed different symbiotic relationships with soil biota through their roots. We characterized the plant community and collected roots to investigate fungal communities using 454 pyrosequencing and assessed arbuscular mycorrhizal colonization and enemy-induced lesions. Differences in fungal communities were considered based on the assessment of α- and β diversity depending on plant ‘abundance’ and ‘origin’. Plant abundance and origin determined the fungal community. Fungal richness was higher for native abundant as opposed to relatively rare native plant species. However, this was not observed for exotics of contrasting abundance. Regardless of their origin, β diversity was higher for rare than for abundant species. Abundant exotics in the community, which happen to be grasses, were the least mycorrhizal whereas rare natives were most susceptible to enemy attack. Our results suggest that compared with exotics, the relative abundance of remnant native plant species in our old-field site is still linked to the structure of belowground fungal communities. In contrast, exotic species may act as a disturbing agent contributing towards the homogenization of soil fungal communities, potentially changing feedback interactions. PMID:26371291

  11. Geographical factors of the abundance of flora in Russian cities

    NASA Astrophysics Data System (ADS)

    Veselkin, D. V.; Tretyakova, A. S.; Senator, S. A.; Saksonov, S. V.; Mukhin, V. A.; Rozenberg, G. S.

    2017-09-01

    An analysis of data on the species abundance of flora in 89 cities (urban flora) of the Russian Federation facilitated determination of its main factors. It has been revealed that the factors determining the abundance of native and alien components of urban flora vary. The city area and population number are the main factors of the total number of species and of the abundance of native species in urban flora. The diversity and participation of alien species increase in parallel with. the urbanization rate, anthropogenic transformation of the regions, and the age of cities and are in adverse correlation with the climate severity.

  12. Stronger warming effects on microbial abundances in colder regions

    DOE PAGES

    Chen, Ji; Luo, Yiqi; Xia, Jianyang; ...

    2015-12-10

    Soil microbes play critical roles in regulating terrestrial carbon (C) cycle and its feedback to climate change. However, it is still unclear how the soil microbial community and abundance respond to future climate change scenarios. In this meta-analysis, we synthesized the responses of microbial community and abundance to experimental warming from 64 published field studies. Our results showed that warming significantly increased soil microbial abundance by 7.6% on average. When grouped by vegetation or soil types, tundras and histosols had the strongest microbial responses to warming with increased microbial, fungal, and bacterial abundances by 15.0%, 9.5% and 37.0% in tundra,more » and 16.5%, 13.2% and 13.3% in histosols, respectively. We found significant negative relationships of the response ratios of microbial, fungal and bacterial abundances with the mean annual temperature, indicating that warming had stronger effects in colder than warmer regions. Moreover, the response ratios of microbial abundance to warming were positively correlated with those of soil respiration. Our results therefore indicate that the large quantities of C stored in colder regions are likely to be more vulnerable to climate warming than the soil C stored in other warmer regions.« less

  13. In Abundance: Networked Participatory Practices as Scholarship

    ERIC Educational Resources Information Center

    Stewart, Bonnie E.

    2015-01-01

    In an era of knowledge abundance, scholars have the capacity to distribute and share ideas and artifacts via digital networks, yet networked scholarship often remains unrecognized within institutional spheres of influence. Using ethnographic methods including participant observation, interviews, and document analysis, this study investigates…

  14. Rhenium-osmium isotope and highly-siderophile-element abundance systematics of angrite meteorites

    NASA Astrophysics Data System (ADS)

    Riches, Amy J. V.; Day, James M. D.; Walker, Richard J.; Simonetti, Antonio; Liu, Yang; Neal, Clive R.; Taylor, Lawrence A.

    2012-11-01

    Coupled 187Os/188Os compositions and highly-siderophile-element (HSE: Os, Ir, Ru, Pt, Pd, and Re) abundance data are reported for eight angrite achondrite meteorites that include quenched- and slowly-cooled textural types. These data are combined with new major- and trace-element concentrations determined for bulk-rock powder fractions and constituent mineral phases, to assess angrite petrogenesis. Angrite meteorites span a wide-range of HSE abundances from <0.005 ppb Os (e.g., Northwest Africa [NWA] 1296; Angra dos Reis) to >100 ppb Os (NWA 4931). Chondritic to supra-chondritic 187Os/188Os (0.1201-0.2127) measured for Angra dos Reis and quenched-angrites correspond to inter- and intra-sample heterogeneities in Re/Os and HSE abundances. Quenched-angrites have chondritic-relative rare-earth-element (REE) abundances at 10-15×CI-chondrite, and their Os-isotope and HSE abundance variations represent mixtures of pristine uncontaminated crustal materials that experienced addition (<0.8%) of exogenous chondritic materials during or after crystallization. Slowly-cooled angrites (NWA 4590 and NWA 4801) have fractionated REE-patterns, chondritic to sub-chondritic 187Os/188Os (0.1056-0.1195), as well as low-Re/Os (0.03-0.13), Pd/Os (0.071-0.946), and relatively low-Pt/Os (0.792-2.640). Sub-chondritic 187Os/188Os compositions in NWA 4590 and NWA 4801 are unusual amongst planetary basalts, and their HSE and REE characteristics may be linked to melting of mantle sources that witnessed prior basaltic melt depletion. Angrite HSE-Yb systematics suggest that the HSE behaved moderately-incompatibly during angrite magma crystallization, implying the presence of metal in the crystallizing assemblage. The new HSE abundance and 187Os/188Os compositions indicate that the silicate mantle of the angrite parent body(ies) (APB) had HSE abundances in chondritic-relative proportions but at variable abundances at the time of angrite crystallization. The HSE systematics of angrites are

  15. Globular Cluster Abundances from High-Resolution Integrated-Light Spectra. I. 47 Tuc

    NASA Astrophysics Data System (ADS)

    McWilliam, Andrew; Bernstein, Rebecca A.

    2008-09-01

    We describe the detailed chemical abundance analysis of a high-resolution (R ~ 35,000), integrated-light (IL), spectrum of the core of the Galactic globular cluster 47 Tuc, obtained using the du Pont echelle at Las Campanas. We develop an abundance analysis strategy that can be applied to spatial unresolved extragalactic clusters. We have computed abundances for Na, Mg, Al, Si, Ca, Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Y, Zr, Ba, La, Nd, and Eu. For an analysis with the known color-magnitude diagram (CMD) for 47 Tuc we obtain a mean [Fe/H] value of -0.75 +/- 0.026 +/- 0.045 dex (random and systematic error), in good agreement with the mean of five recent high-resolution abundance studies, at -0.70 dex. Typical random errors on our mean [X/Fe] ratios are 0.07-0.10 dex, similar to studies of individual stars in 47 Tuc. Na and Al appear enhanced, perhaps due to proton burning in the most luminous cluster stars. Our IL abundance analysis with an unknown CMD employed theoretical Teramo isochrones; however, we apply zero-point abundance corrections to account for the factor of 3 underprediction of stars at the AGB bump luminosity. While line diagnostics alone provide only mild constraints on the cluster age (ruling out ages younger than ~2 Gyr), when theoretical IL B - V colors are combined with metallicity derived from the Fe I lines, the age is constrained to 10-15 Gyr and we obtain [ Fe/H ] = - 0.70 +/- 0.021 +/- 0.052 dex. We find that Fe I line diagnostics may also be used to constrain the horizontal-branch morphology of an unresolved cluster. Lastly, our spectrum synthesis of 5.4 million TiO lines indicates that the 7300-7600 Å TiO window should be useful for estimating the effect of M giants on the IL abundances, and important for clusters more metal-rich than 47 Tuc.

  16. Monitoring waterbird abundance in wetlands: The importance of controlling results for variation in water depth

    USGS Publications Warehouse

    Bolduc, F.; Afton, A.D.

    2008-01-01

    Wetland use by waterbirds is highly dependent on water depth, and depth requirements generally vary among species. Furthermore, water depth within wetlands often varies greatly over time due to unpredictable hydrological events, making comparisons of waterbird abundance among wetlands difficult as effects of habitat variables and water depth are confounded. Species-specific relationships between bird abundance and water depth necessarily are non-linear; thus, we developed a methodology to correct waterbird abundance for variation in water depth, based on the non-parametric regression of these two variables. Accordingly, we used the difference between observed and predicted abundances from non-parametric regression (analogous to parametric residuals) as an estimate of bird abundance at equivalent water depths. We scaled this difference to levels of observed and predicted abundances using the formula: ((observed - predicted abundance)/(observed + predicted abundance)) ?? 100. This estimate also corresponds to the observed:predicted abundance ratio, which allows easy interpretation of results. We illustrated this methodology using two hypothetical species that differed in water depth and wetland preferences. Comparisons of wetlands, using both observed and relative corrected abundances, indicated that relative corrected abundance adequately separates the effect of water depth from the effect of wetlands. ?? 2008 Elsevier B.V.

  17. [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.

  18. Links between Ammonia Oxidizer Community Structure, Abundance, and Nitrification Potential in Acidic Soils ▿ †

    PubMed Central

    Yao, Huaiying; Gao, Yangmei; Nicol, Graeme W.; Campbell, Colin D.; Prosser, James I.; Zhang, Limei; Han, Wenyan; Singh, Brajesh K.

    2011-01-01

    Ammonia oxidation is the first and rate-limiting step of nitrification and is performed by both ammonia-oxidizing archaea (AOA) and bacteria (AOB). However, the environmental drivers controlling the abundance, composition, and activity of AOA and AOB communities are not well characterized, and the relative importance of these two groups in soil nitrification is still debated. Chinese tea orchard soils provide an excellent system for investigating the long-term effects of low pH and nitrogen fertilization strategies. AOA and AOB abundance and community composition were therefore investigated in tea soils and adjacent pine forest soils, using quantitative PCR (qPCR), terminal restriction fragment length polymorphism (T-RFLP) and sequence analysis of respective ammonia monooxygenase (amoA) genes. There was strong evidence that soil pH was an important factor controlling AOB but not AOA abundance, and the ratio of AOA to AOB amoA gene abundance increased with decreasing soil pH in the tea orchard soils. In contrast, T-RFLP analysis suggested that soil pH was a key explanatory variable for both AOA and AOB community structure, but a significant relationship between community abundance and nitrification potential was observed only for AOA. High potential nitrification rates indicated that nitrification was mainly driven by AOA in these acidic soils. Dominant AOA amoA sequences in the highly acidic tea soils were all placed within a specific clade, and one AOA genotype appears to be well adapted to growth in highly acidic soils. Specific AOA and AOB populations dominated in soils at particular pH values and N content, suggesting adaptation to specific niches. PMID:21571885

  19. 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.

  20. Seasonality and relative abundance of Tabanidae (Diptera) captured on horses in the Pantanal, Brazil.

    PubMed

    Barros, A T

    2001-10-01

    Once a month, from June 1992 to May 1993, collections of tabanids on horse were conducted in the Nhecolândia, Pantanal State of Mato Grosso do Sul, Brazil. Tabanid catches using hand nets were conducted from sunrise to sunset at grassland and cerradão (dense savanna) habitats. A total of 3,442 tabanids from 21 species,12 genera, and 3 subfamilies were collected. Although species abundance varied seasonally depending on habitat, no habitat specificity was observed for the most abundant species. In the grassland, 1,625 (47.2%) tabanids belonging to 19 species were collected, while 1,817 (52.8%) tabanids from 17 species were caught in the cerradão. The number of tabanid species varied from 7 during winter (July/August) to 15 in the spring (October). Tabanus importunus (56%) was the most abundant species, followed by T. occidentalis (8.2%), and T. claripennis (8.1%). The tabanid peak, in October, coincided with the beginning of the rainy season. The population peak of most species, including those with higher vector potential, suggests that the rainy season can be considered as the period of potentially higher risk of mechanical transmission of pathogens by tabanids to horses in the region.

  1. Collision-Induced Dissociation of Deprotonated Peptides. Relative Abundance of Side-Chain Neutral Losses, Residue-Specific Product Ions, and Comparison with Protonated Peptides

    NASA Astrophysics Data System (ADS)

    Liang, Yuxue; Neta, Pedatsur; Yang, Xiaoyu; Stein, Stephen E.

    2018-03-01

    High-accuracy MS/MS spectra of deprotonated ions of 390 dipeptides and 137 peptides with three to six residues are studied. Many amino acid residues undergo neutral losses from their side chains. The most abundant is the loss of acetaldehyde from threonine. The abundance of losses from the side chains of other amino acids is estimated relative to that of threonine. While some amino acids lose the whole side chain, others lose only part of it, and some exhibit two or more different losses. Side-chain neutral losses are less abundant in the spectra of protonated peptides, being significant mainly for methionine and arginine. In addition to the neutral losses, many amino acid residues in deprotonated peptides produce specific negative ions after peptide bond cleavage. An expanded list of fragment ions from protonated peptides is also presented and compared with those of deprotonated peptides. Fragment ions are mostly different for these two cases. These lists of fragments are used to annotate peptide mass spectral libraries and to aid in the confirmation of specific amino acids in peptides. [Figure not available: see fulltext.

  2. Collision-Induced Dissociation of Deprotonated Peptides. Relative Abundance of Side-Chain Neutral Losses, Residue-Specific Product Ions, and Comparison with Protonated Peptides.

    PubMed

    Liang, Yuxue; Neta, Pedatsur; Yang, Xiaoyu; Stein, Stephen E

    2018-03-01

    High-accuracy MS/MS spectra of deprotonated ions of 390 dipeptides and 137 peptides with three to six residues are studied. Many amino acid residues undergo neutral losses from their side chains. The most abundant is the loss of acetaldehyde from threonine. The abundance of losses from the side chains of other amino acids is estimated relative to that of threonine. While some amino acids lose the whole side chain, others lose only part of it, and some exhibit two or more different losses. Side-chain neutral losses are less abundant in the spectra of protonated peptides, being significant mainly for methionine and arginine. In addition to the neutral losses, many amino acid residues in deprotonated peptides produce specific negative ions after peptide bond cleavage. An expanded list of fragment ions from protonated peptides is also presented and compared with those of deprotonated peptides. Fragment ions are mostly different for these two cases. These lists of fragments are used to annotate peptide mass spectral libraries and to aid in the confirmation of specific amino acids in peptides. Graphical Abstract ᅟ.

  3. Calcium ionization balance and argon/calcium abundance in solar flares

    NASA Astrophysics Data System (ADS)

    Antonucci, E.; Marocchi, D.; Gabriel, A. H.; Doschek, G. A.

    1987-12-01

    An earlier analysis of solar flare calcium spectra from XRP and P78-1 aimed at measuring the calcium ionization balance resulted in an ambiguity due to a line blend between the calcium q line and an Ar XVII line. In the present work the calcium line 'r' is included in the analysis in order to resolve this problem. It is shown that the correct calcium ionization balance is that indicated in the earlier paper as corresponding to an argon/calcium abundance ratio of 0.2. The argon/calcium abundance ratio in the group of solar flares studied is shown to be 0.2 + or - 0.2. It is further argued that while the abundance of heavy elements may be enhanced in energetic flare events, this enhancement is less for argon than for calcium, leading to an argon/calcium ratio smaller than that present in the quiet sun.

  4. NEON AND OXYGEN ABUNDANCES AND ABUNDANCE RATIO IN THE SOLAR CORONA

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Landi, E.; Testa, P., E-mail: elandi@umich.edu

    2015-02-20

    In this work we determine the Ne/O abundance ratio from Solar and Heliospheric Observatory (SOHO)/Solar Ultraviolet Measurement of Emitted Radiation (SUMER) off-disk observations of quiescent streamers over the 1996-2008 period. We find that the Ne/O ratio is approximately constant over solar cycle 23 from 1996 to 2005, at a value of 0.099 ± 0.017; this value is lower than the transition region determinations from the quiet Sun used to infer the neon photospheric abundance from the oxygen photospheric abundance. Also, the Ne/O ratio we determined from SUMER is in excellent agreement with in situ determinations from ACE/SWICS. In 2005-2008, the Ne/O abundancemore » ratio increased with time and reached 0.25 ± 0.05, following the same trend found in the slowest wind analyzed by ACE/SWICS. Further, we measure the absolute abundance in the corona for both oxygen and neon from the data set of 1996 November 22, obtaining A {sub o} = 8.99 ± 0.04 and A {sub Ne} = 7.92 ± 0.03, and we find that both elements are affected by the first ionization potential (FIP) effect, with oxygen being enhanced by a factor of 1.4-2.1 over its photospheric abundance, and neon being changed by a factor of 0.75-1.20. We conclude that the Ne/O ratio is not constant in the solar atmosphere, both in time and at different heights, and that it cannot be reliably used to infer the neon abundance in the photosphere. Also, we argue that the FIP effect was less effective during the minimum of solar cycle 24, and that the Ne/O = 0.25 ± 0.05 value measured at that time is closer to the true photospheric value, leading to a neon photospheric abundance larger than assumed by ≈40%. We discuss the implications of these results for the solar abundance problem, for the FIP effect, and for the identification of the source regions of the solar wind.« less

  5. Diet and condition of mesopredators on coral reefs in relation to shark abundance

    PubMed Central

    Meekan, Mark G.; Meeuwig, Jessica J.

    2017-01-01

    Reef sharks may influence the foraging behaviour of mesopredatory teleosts on coral reefs via both risk effects and competitive exclusion. We used a “natural experiment” to test the hypothesis that the loss of sharks on coral reefs can influence the diet and body condition of mesopredatory fishes by comparing two remote, atoll-like reef systems, the Rowley Shoals and the Scott Reefs, in northwestern Australia. The Rowley Shoals are a marine reserve where sharks are abundant, whereas at the Scott Reefs numbers of sharks have been reduced by centuries of targeted fishing. On reefs where sharks were rare, the gut contents of five species of mesopredatory teleosts largely contained fish while on reefs with abundant sharks, the same mesopredatory species consumed a larger proportion of benthic invertebrates. These measures of diet were correlated with changes in body condition, such that the condition of mesopredatory teleosts was significantly poorer on reefs with higher shark abundance. Condition was defined as body weight, height and width for a given length and also estimated via several indices of condition. Due to the nature of natural experiments, alternative explanations cannot be discounted. However, the results were consistent with the hypothesis that loss of sharks may influence the diet and condition of mesopredators and by association, their fecundity and trophic role. Regardless of the mechanism (risk effects, competitive release, or other), our findings suggest that overfishing of sharks has the potential to trigger trophic cascades on coral reefs and that further declines in shark populations globally should be prevented to protect ecosystem health. PMID:28422965

  6. Diet and condition of mesopredators on coral reefs in relation to shark abundance.

    PubMed

    Barley, Shanta C; Meekan, Mark G; Meeuwig, Jessica J

    2017-01-01

    Reef sharks may influence the foraging behaviour of mesopredatory teleosts on coral reefs via both risk effects and competitive exclusion. We used a "natural experiment" to test the hypothesis that the loss of sharks on coral reefs can influence the diet and body condition of mesopredatory fishes by comparing two remote, atoll-like reef systems, the Rowley Shoals and the Scott Reefs, in northwestern Australia. The Rowley Shoals are a marine reserve where sharks are abundant, whereas at the Scott Reefs numbers of sharks have been reduced by centuries of targeted fishing. On reefs where sharks were rare, the gut contents of five species of mesopredatory teleosts largely contained fish while on reefs with abundant sharks, the same mesopredatory species consumed a larger proportion of benthic invertebrates. These measures of diet were correlated with changes in body condition, such that the condition of mesopredatory teleosts was significantly poorer on reefs with higher shark abundance. Condition was defined as body weight, height and width for a given length and also estimated via several indices of condition. Due to the nature of natural experiments, alternative explanations cannot be discounted. However, the results were consistent with the hypothesis that loss of sharks may influence the diet and condition of mesopredators and by association, their fecundity and trophic role. Regardless of the mechanism (risk effects, competitive release, or other), our findings suggest that overfishing of sharks has the potential to trigger trophic cascades on coral reefs and that further declines in shark populations globally should be prevented to protect ecosystem health.

  7. Aquifer water abundance evaluation using a fuzzy- comprehensive weighting method

    NASA Astrophysics Data System (ADS)

    Wei, Z.

    2016-08-01

    Aquifer water abundance evaluation is a highly relevant issue that has been researched for many years. Despite prior research, problems with the conventional evaluation method remain. This paper establishes an aquifer water abundance evaluation method that combines fuzzy evaluation with a comprehensive weighting method to overcome both the subjectivity and lack of conformity in determining weight by pure data analysis alone. First, this paper introduces the principle of a fuzzy-comprehensive weighting method. Second, the example of well field no. 3 (of a coalfield) is used to illustrate the method's process. The evaluation results show that this method is can more suitably meet the real requirements of aquifer water abundance assessment, leading to more precise and accurate evaluations. Ultimately, this paper provides a new method for aquifer water abundance evaluation.

  8. Electroconvulsive shock increases preproenkephalin messenger RNA abundance in rat hypothalamus.

    PubMed Central

    Yoshikawa, K; Hong, J S; Sabol, S L

    1985-01-01

    Daily administration of electroconvulsive shock (ECS) to rats for 10 days increased the content of [Met5]enkephalin in the hypothalamus and the striatum by 64% and 45%, respectively. The effect of ECS on the relative abundance of mRNA coding for the enkephalin precursor preproenkephalin was investigated. Analysis by cell-free translation of polyadenylylated RNA and immunoprecipitation of preproenkephalin revealed ECS-elicited increases of 79% and 14% in preproenkephalin mRNA activity in the hypothalamus and striatum, respectively. ECS treatment did not affect the general translational activity of total polyadenylylated RNA from these brain regions. A 32P-labeled probe prepared from a rat preproenkephalin cDNA clone hybridized with an apparently single species of polyadenylylated RNA of approximately equal to 1450 nucleotides from both hypothalamus and striatum. Dot-blot hybridization of polyadenylylated RNA with the rat probe indicated that ECS elicits a 76% increase in the preproenkephalin mRNA abundance in the hypothalamus and no significant change in the striatum. These results suggest that ECS treatment leads to enhanced biosynthesis of the enkephalin precursor in hypothalamic neurons. Images PMID:2578669

  9. Moist-soil seed abundance in managed wetlands in the Mississippi Alluvial Valley

    USGS Publications Warehouse

    Kross, J.; Kaminski, R.M.; Reinecke, K.J.; Penny, E.J.; Pearse, A.T.

    2008-01-01

    Managed moist-soil units support early succession herbaceous vegetation that produces seeds, tubers, and other plant parts used by waterfowl in the Mississippi Alluvial Valley (MAV), USA. We conducted a stratified multi-stage sample survey on state and federal lands in the MAV of Arkansas, Louisiana, Mississippi, and Missouri during autumns 2002?2004 to generate a contemporary estimate of combined dry mass of seeds and tubers (herein seed abundance) in managed moist-soil units for use by the Lower Mississippi Valley Joint Venture (LMVJV) of the North American Waterfowl Management Plan. We also examined variation in mean seed abundance among moist-soil units in 2003 and 2004 in relation to management intensity (active or passive), soil pH and nutrient levels, proportional occurrence of plant life-forms (e.g., grass, flatsedge, and forb; vine; woody plants), and unit area. Estimates of mean seed abundance were similar in 2002 (X over bar = 537.1 kg/ha, SE = 100.1) and 2004 (X over bar = 555.2 kg/ha, SE = 105.2) but 35?40% less in 2003 (X over bar = 396.8 kg/ha, SE = 116.1). Averaged over years, seed abundance was 496.3 kg/ha (SE = 62.0; CV = 12.5%). Multiple regression analysis indicated seed abundance varied among moist-soil units inversely with proportional occurrence of woody vegetation and unit area and was greater in actively than passively managed units (R2adj = 0.37). Species of early succession grasses occurred more frequently in actively than passively managed units (P < 0.09), whereas mid- and late-succession plants occurred more often in passively managed units (P < 0.02). We recommend the LMVJV consider 556 kg/ha as a measure of seed abundance for use in estimating carrying capacity in managed moist-soil units on public lands in the MAV. We recommend active management of moist-soil units to achieve maximum potential seed production and further research to determine recovery rates of seeds of various sizes from core samples and the relationship between

  10. 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.

  11. Peculiar Abundances Observed in the Hot Subdwarf OB Star LB 3241

    NASA Astrophysics Data System (ADS)

    Chayer, Pierre; Dupuis, J.; Dixon, W. V.; Giguere, E.

    2010-01-01

    We present a spectral synthesis analysis of the hot subdwarf OB star LB 3241. The analysis is based on spectra obtained by the Far Ultraviolet Spectroscopic Explorer (FUSE). With an effective temperature of 41,000 K and a gravity of log g = 5.7, the position of LB 3241 in a Teff-log g diagram suggests that it has evolved from the extreme horizontal branch. Such stars evolve into white dwarfs without ascending the asymptotic giant branch after the helium core exhaustion. Arsenic (Z = 33), selenium (34), and tellurium (52) are observed in the atmosphere of LB 3241, and are a first for a hot subdwarf star. LB 3241 shows peculiar chemical abundances that exhibit trends observed in cooler sdB stars. The content of its atmosphere in light elements is about a factor ten lower than that of the Sun, except for nitrogen which has a solar abundance. The Fe abundance is consistent with a solar abundance, but abundances of elements beyond the iron peak (As, Se, Te, Pb) show enrichments over the solar values by factors ranging from 10 to 300. These observations suggest that competing mechanisms must counterbalance the effects of the downward diffusion. The FUSE observations also suggest that LB 3241 is a radial velocity variable.

  12. Long-term change in benthopelagic fish abundance in the abyssal northeast Pacific Ocean.

    PubMed

    Bailey, D M; Ruhl, H A; Smith, K L

    2006-03-01

    Food web structure, particularly the relative importance of bottom-up and top-down control of animal abundances, is poorly known for the Earth's largest habitats: the abyssal plains. A unique 15-yr time series of climate, productivity, particulate flux, and abundance of primary consumers (primarily echinoderms) and secondary consumers (fish) was examined to elucidate the response of trophic levels to temporal variation in one another. Towed camera sled deployments in the abyssal northeast Pacific (4100 m water depth) showed that annual mean numbers of the dominant fish genus (Coryphaenoides spp.) more than doubled over the period 1989-2004. Coryphaenoides spp. abundance was significantly correlated with total abundance of mobile epibenthic megafauna (echinoderms), with changes in fish abundance lagging behind changes in the echinoderms. Direct correlations between surface climate and fish abundances, and particulate organic carbon (POC) flux and fish abundances, were insignificant, which may be related to the varied response of the potential prey taxa to climate and POC flux. This study provides a rare opportunity to study the long-term dynamics of an unexploited marine fish population and suggests a dominant role for bottom-up control in this system.

  13. Multi-year assessment of coastal planktonic fungi reveals environmental drivers of diversity and abundance

    PubMed Central

    Taylor, Joe D; Cunliffe, Michael

    2016-01-01

    Mycoplankton have so far been a neglected component of pelagic marine ecosystems, having been poorly studied relative to other plankton groups. Currently, there is a lack of understanding of how mycoplankton diversity changes through time, and the identity of controlling environmental drivers. Using Fungi-specific high-throughput sequencing and quantitative PCR analysis of plankton DNA samples collected over 6 years from the coastal biodiversity time series site Station L4 situated off Plymouth (UK), we have assessed changes in the temporal variability of mycoplankton diversity and abundance in relation to co-occurring environmental variables. Mycoplankton diversity at Station L4 was dominated by Ascomycota, Basidiomycota and Chytridiomycota, with several orders within these phyla frequently abundant and dominant in multiple years. Repeating interannual mycoplankton blooms were linked to potential controlling environmental drivers, including nitrogen availability and temperature. Specific relationships between mycoplankton and other plankton groups were also identified, with seasonal chytrid blooms matching diatom blooms in consecutive years. Mycoplankton α-diversity was greatest during periods of reduced salinity at Station L4, indicative of riverine input to the ecosystem. Mycoplankton abundance also increased during periods of reduced salinity, and when potential substrate availability was increased, including particulate organic matter. This study has identified possible controlling environmental drivers of mycoplankton diversity and abundance in a coastal sea ecosystem, and therefore sheds new light on the biology and ecology of an enigmatic marine plankton group. Mycoplankton have several potential functional roles, including saprotrophs and parasites, that should now be considered within the consensus view of pelagic ecosystem functioning and services. PMID:26943623

  14. How Ants Drop Out: Ant Abundance on Tropical Mountains

    PubMed Central

    Longino, John T.; Branstetter, Michael G.; Colwell, Robert K.

    2014-01-01

    In tropical wet forests, ants are a large proportion of the animal biomass, but the factors determining abundance are not well understood. We characterized ant abundance in the litter layer of 41 mature wet forest sites spread throughout Central America (Chiapas, Guatemala, Honduras, Nicaragua, and Costa Rica) and examined the impact of elevation (as a proxy for temperature) and community species richness. Sites were intentionally chosen to minimize variation in precipitation and seasonality. From sea level to 1500 m ant abundance very gradually declined, community richness declined more rapidly than abundance, and the local frequency of the locally most common species increased. These results suggest that within this elevational zone, density compensation is acting, maintaining high ant abundance as richness declines. In contrast, in sites above 1500 m, ant abundance dropped abruptly to much lower levels. Among these high montane sites, community richness explained much more of the variation in abundance than elevation, and there was no evidence of density compensation. The relative stability of abundance below 1500 m may be caused by opposing effects of temperature on productivity and metabolism. Lower temperatures may decrease productivity and thus the amount of food available for consumers, but slower metabolisms of consumers may allow maintenance of higher biomass at lower resource supply rates. Ant communities at these lower elevations may be highly interactive, the result of continuous habitat presence over geological time. High montane sites may be ephemeral in geological time, resulting in non-interactive communities dominated by historical and stochastic processes. Abundance in these sites may be determined by the number of species that manage to colonize and/or avoid extinction on mountaintops. PMID:25098722

  15. How ants drop out: ant abundance on tropical mountains.

    PubMed

    Longino, John T; Branstetter, Michael G; Colwell, Robert K

    2014-01-01

    In tropical wet forests, ants are a large proportion of the animal biomass, but the factors determining abundance are not well understood. We characterized ant abundance in the litter layer of 41 mature wet forest sites spread throughout Central America (Chiapas, Guatemala, Honduras, Nicaragua, and Costa Rica) and examined the impact of elevation (as a proxy for temperature) and community species richness. Sites were intentionally chosen to minimize variation in precipitation and seasonality. From sea level to 1500 m ant abundance very gradually declined, community richness declined more rapidly than abundance, and the local frequency of the locally most common species increased. These results suggest that within this elevational zone, density compensation is acting, maintaining high ant abundance as richness declines. In contrast, in sites above 1500 m, ant abundance dropped abruptly to much lower levels. Among these high montane sites, community richness explained much more of the variation in abundance than elevation, and there was no evidence of density compensation. The relative stability of abundance below 1500 m may be caused by opposing effects of temperature on productivity and metabolism. Lower temperatures may decrease productivity and thus the amount of food available for consumers, but slower metabolisms of consumers may allow maintenance of higher biomass at lower resource supply rates. Ant communities at these lower elevations may be highly interactive, the result of continuous habitat presence over geological time. High montane sites may be ephemeral in geological time, resulting in non-interactive communities dominated by historical and stochastic processes. Abundance in these sites may be determined by the number of species that manage to colonize and/or avoid extinction on mountaintops.

  16. Abundances in Eight M31 Planetary Nebulae

    NASA Astrophysics Data System (ADS)

    Hensley, Kerry G.; Kwitter, Karen B.; Corradi, Romano; Galera-Rosillo, R.; Balick, Bruce; Henry, Richard B. C.

    2014-06-01

    As part of a continuing project using planetary nebulae (PNe) to study the chemical evolution and formation history of M31 (see accompanying poster by Balick et al.), we obtained spectra of eight PNe in the fall of 2013 with the OSIRIS spectrograph on the GTC. All of these PNe are located outside M31’s inner disk and bulge. Spectral coverage extended from 3700-7800Å with a resolution of ~6 Å. Especially important in abundance determinations is the detection of the weak, temperature-sensitive auroral line of [O III], at 4363Å, which is often contaminated by Hg I 4358Å from streetlights; the remoteness of the GTC eliminated this difficulty. We reduced and measured the spectra using IRAF, and derived nebular diagnostics and abundances with ELSA, our in-house five-level-atom program. Here we report the chemical abundances determined from these spectra. The bottom line is that the oxygen abundances in these PNe are all within a factor of 2-3 of the solar value, (as are all the other M31 PNe our team has previously measured) despite the significant range of galactocentric distance. Future work will use these abundances to constrain models of the central star to estimate progenitor masses and ages. In particular we will use the results to investigate the hypothesis that these PNe might represent a population related to the encounter between M31 and M33 ~3 Gy ago. We gratefully acknowledge support from Williams College.

  17. Modeling unobserved sources of heterogeneity in animal abundance using a Dirichlet process prior

    USGS Publications Warehouse

    Dorazio, R.M.; Mukherjee, B.; Zhang, L.; Ghosh, M.; Jelks, H.L.; Jordan, F.

    2008-01-01

    In surveys of natural populations of animals, a sampling protocol is often spatially replicated to collect a representative sample of the population. In these surveys, differences in abundance of animals among sample locations may induce spatial heterogeneity in the counts associated with a particular sampling protocol. For some species, the sources of heterogeneity in abundance may be unknown or unmeasurable, leading one to specify the variation in abundance among sample locations stochastically. However, choosing a parametric model for the distribution of unmeasured heterogeneity is potentially subject to error and can have profound effects on predictions of abundance at unsampled locations. In this article, we develop an alternative approach wherein a Dirichlet process prior is assumed for the distribution of latent abundances. This approach allows for uncertainty in model specification and for natural clustering in the distribution of abundances in a data-adaptive way. We apply this approach in an analysis of counts based on removal samples of an endangered fish species, the Okaloosa darter. Results of our data analysis and simulation studies suggest that our implementation of the Dirichlet process prior has several attractive features not shared by conventional, fully parametric alternatives. ?? 2008, The International Biometric Society.

  18. An Empirical Relation Between the Lunar Prospector Gamma-Ray and Soil Sample Th Abundances

    NASA Technical Reports Server (NTRS)

    Gillis, Jeffrey J.; Jolliff, Brad L.; Korotev, Randy L.; Lawrence, David J.

    2000-01-01

    This abstract compares Th abundances for soils from Apollo 12, 14, 16, and the lunar feldspathic meteorites with Th concentrations using a theoretical calibration of the Lunar Prospector gamma-ray data.

  19. The dependence of oxygen and nitrogen abundances on stellar mass from the CALIFA survey

    NASA Astrophysics Data System (ADS)

    Pérez-Montero, E.; García-Benito, R.; Vílchez, J. M.; Sánchez, S. F.; Kehrig, C.; Husemann, B.; Duarte Puertas, S.; Iglesias-Páramo, J.; Galbany, L.; Mollá, M.; Walcher, C. J.; Ascasíbar, Y.; González Delgado, R. M.; Marino, R. A.; Masegosa, J.; Pérez, E.; Rosales-Ortega, F. F.; Sánchez-Blázquez, P.; Bland-Hawthorn, J.; Bomans, D.; López-Sánchez, Á. R.; Ziegler, B.; Califa Collaboration

    2016-10-01

    Context. The study of the integrated properties of star-forming galaxies is central to understand their formation and evolution. Some of these properties are extensive and therefore their analysis require totally covering and spatially resolved observations. Among these properties, metallicity can be defined in spiral discs by means of integral field spectroscopy (IFS) of individual H II regions. The simultaneous analysis of the abundances of primary elements, as oxygen, and secondary, as nitrogen, also provides clues about the star formation history and the processes that shape the build-up of spiral discs. Aims: Our main aim is to analyse simultaneously O/H and N/O abundance ratios in H II regions in different radial positions of the discs in a large sample of spiral galaxies to obtain the slopes and the characteristic abundance ratios that can be related to their integrated properties. Methods: We analysed the optical spectra of individual selected H II regions extracted from a sample of 350 spiral galaxies of the CALIFA survey. We calculated total O/H abundances and, for the first time, N/O ratios using the semi-empirical routine Hii-Chi-mistry, which, according to Pérez-Montero (2014, MNRAS, 441, 2663), is consistent with the direct method and reduces the uncertainty in the O/H derivation using [N II] lines owing to the dispersion in the O/H-N/O relation. Then we performed linear fittings to the abundances as a function of the de-projected galactocentric distances. Results: The analysis of the radial distribution both for O/H and N/O in the non-interacting galaxies reveals that both average slopes are negative, but a non-negligible fraction of objects have a flat or even a positive gradient (at least 10% for O/H and 4% for N/O). The slopes normalised to the effective radius appear to have a slight dependence on the total stellar mass and the morphological type, as late low-mass objects tend to have flatter slopes. No clear relation is found, however, to

  20. A Comprehensive Analysis of Uncertainties Affecting the Stellar Mass-Halo Mass Relation for 0

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Behroozi, Peter S.; Conroy, Charlie; Wechsler, Risa H.

    2010-06-07

    We conduct a comprehensive analysis of the relationship between central galaxies and their host dark matter halos, as characterized by the stellar mass - halo mass (SM-HM) relation, with rigorous consideration of uncertainties. Our analysis focuses on results from the abundance matching technique, which assumes that every dark matter halo or subhalo above a specific mass threshold hosts one galaxy. We provide a robust estimate of the SM-HM relation for 0 < z < 1 and discuss the quantitative effects of uncertainties in observed galaxy stellar mass functions (GSMFs) (including stellar mass estimates and counting uncertainties), halo mass functions (includingmore » cosmology and uncertainties from substructure), and the abundance matching technique used to link galaxies to halos (including scatter in this connection). Our analysis results in a robust estimate of the SM-HM relation and its evolution from z=0 to z=4. The shape and evolution are well constrained for z < 1. The largest uncertainties at these redshifts are due to stellar mass estimates (0.25 dex uncertainty in normalization); however, failure to account for scatter in stellar masses at fixed halo mass can lead to errors of similar magnitude in the SM-HM relation for central galaxies in massive halos. We also investigate the SM-HM relation to z = 4, although the shape of the relation at higher redshifts remains fairly unconstrained when uncertainties are taken into account. We find that the integrated star formation at a given halo mass peaks at 10-20% of available baryons for all redshifts from 0 to 4. This peak occurs at a halo mass of 7 x 10{sup 11} M{sub {circle_dot}} at z = 0 and this mass increases by a factor of 5 to z = 4. At lower and higher masses, star formation is substantially less efficient, with stellar mass scaling as M{sub *} {approx} M{sub h}{sup 2.3} at low masses and M{sub *} {approx} M{sub h}{sup 0.29} at high masses. The typical stellar mass for halos with mass less than 10{sup 12} M

  1. Improved Yttrium and Zirconium Abundances in Metal-Poor Stars

    NASA Astrophysics Data System (ADS)

    Violante, Renata; Biemont, E.; Cowan, J. J.; Sneden, C.

    2012-01-01

    Abstract We present new abundances of the lighter n-capture elements, Yttrium (Z=39) and Zirconium (Z=40) in the very metal poor, r-process rich stars BD+17 3248 and HD 221170. Very accurate abundances were obtained by use of the new transition probabilities for Y II published by Biémont et al. 2011, and Zr II by Malcheva et al. 2006, and by expanding the number of transitions employed for each element. For example, in BD+17 3248, we find log ɛπσιλον=-0.03 +/- 0.03 (σιγμα=0.15, from 23 lines) for Y II. As for Zr II, log ɛπσιλον = 0.65 +/- 0.03 (σɛγμα = 0.1, from 13 lines). The resulting abundance ratio is log ɛπσιλον [Y/Zr] = -0.68 +/- 0.05. The results for HD 221170 are in accord with those of BD+17 3248. The quantity of lines used to form the abundance means has increased significantly since the original studies of these stars, resulting in more trustworthy abundances. These observed abundance ratios are in agreement with an r-process-only value predicted from stellar models, but is under-abundant compared to an empirical model derived from direct analyses of meteoritic material. This ambiguity should stimulate further nucleosynthetic analysis to explain this abundance ratio. We would like to extend our gratitude to NSF grant AST-0908978 and the University of Texas Astronomy Department Rex G. Baker, Jr. Endowment for their financial support in this project.

  2. 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.

  3. Seasonal Variation in Abundance and Diversity of Bacterial Methanotrophs in Five Temperate Lakes

    PubMed Central

    Samad, Md Sainur; Bertilsson, Stefan

    2017-01-01

    Lakes are significant sources of methane (CH4) to the atmosphere. Within these systems, methanotrophs consume CH4 and act as a potential biofilter mitigating the emission of this potent greenhouse gas. However, it is still not well understood how spatial and temporal variation in environmental parameters influence the abundance, diversity, and community structure of methanotrophs in lakes. To address this gap in knowledge, we collected water samples from three depths (surface, middle, and bottom) representing oxic to suboxic or anoxic zones of five different Swedish lakes in winter (ice-covered) and summer. Methanotroph abundance was determined by quantitative real time polymerase chain reaction and a comparison to environmental variables showed that temperature, season as well as depth, phosphate concentration, dissolved oxygen, and CH4 explained the observed variation in methanotroph abundance. Due to minimal differences in methane concentrations (0.19 and 0.29 μM for summer and winter, respectively), only a weak and even negative correlation was observed between CH4 and methanotrophs, which was possibly due to usage of CH4. Methanotrophs were present at concentrations ranging from 105 to 106 copies/l throughout the oxic (surface) and suboxic/anoxic (bottom) water mass of the lakes, but always contributed less than 1.3% to the total microbial community. Relative methanotroph abundance was significantly higher in winter than in summer and consistently increased with depth in the lakes. Phylogenetic analysis of pmoA genes in two clone libraries from two of the ice-covered lakes (Ekoln and Ramsen) separated the methanotrophs into five distinct clusters of Methylobacter sp. (Type I). Terminal restriction fragment length polymorphism analysis of the pmoA gene further revealed significant differences in methanotrophic communities between lakes as well as between winter and summer while there were no significant differences between water layers. The study provides new

  4. The abundance and relative volatility of refractory trace elements in Allende Ca,Al-rich inclusions - Implications for chemical and physical processes in the solar nebula

    NASA Technical Reports Server (NTRS)

    Kornacki, Alan S.; Fegley, Bruce, Jr.

    1986-01-01

    The relative volatilities of lithophile refractory trace elements (LRTE) were determined using calculated 50-percent condensation temperatures. Then, the refractory trace-element abundances were measured in about 100 Allende inclusions. The abundance patterns found in Allende Ca,Al-rich inclusions (CAIs) and ultrarefractory inclusions were used to empirically modify the calculated LRTE volatility sequence. In addition, the importance of crystal-chemical effects, diffusion constraints, and grain transport for the origin of the trace-element chemistry of Allende CAIs (which have important implications for chemical and physical processes in the solar nebula) is discussed.

  5. Cetacean distribution and abundance in relation to oceanographic domains on the eastern Bering Sea shelf: 1999-2004

    NASA Astrophysics Data System (ADS)

    Friday, Nancy A.; Waite, Janice M.; Zerbini, Alexandre N.; Moore, Sue E.

    2012-06-01

    Visual line transect surveys for cetaceans were conducted on the eastern Bering Sea shelf in association with pollock stock assessment surveys aboard the NOAA ship Miller Freeman in June and July of 1999, 2000, 2002, and 2004. Transect survey effort ranged from 1188 km in 1999 to 3761 km in 2002. Fin whales (Balaenoptera physalus) were the most common large whale in all years except 2004 when humpback whales (Megaptera novaeangliae) were more abundant. Dall's porpoise (Phocoenoides dalli) were the most common small cetacean in all years. Abundance estimates were calculated by year for each oceanographic domain: coastal, middle, and outer/slope. The middle and outer/slope domains were divided into two strata ("north" and "south") because of variable survey effort. The distribution and abundance of baleen whales changed between the earlier (colder) and later (warmer) survey years. Fin whales consistently occupied the outer shelf and secondarily the middle shelf, and their abundance was an order of magnitude greater in cold compared to warm years. Humpback whales "lived on the margin" of the northern Alaska Peninsula, eastern Aleutian Islands and Bristol Bay; their preferred habitat is possibly associated with areas of high prey availability due to nutrient upwelling and aggregation mechanisms. Minke whales (Balaenoptera acutorostrata) occur shoreward of fin whales in the outer and middle shelf and in coastal habitats along the Alaska Peninsula. The highest abundance for this species was observed in a cold (1999) year. No clear relationship emerged for odontocetes with regard to warm and cold years. Dall's porpoise occupied both outer and middle domains and harbor porpoise (Phocoena phocoena) were more common in middle and coastal domains. This study provided a unique, broad-scale assessment of cetacean distribution and abundance on the eastern Bering Sea shelf and a baseline for future comparisons.

  6. Carbon and nitrogen abundances in metal-poor dwarfs of the solar neighborhood

    NASA Technical Reports Server (NTRS)

    Carbon, Duane F.; Barbuy, Beatrice; Kraft, Robert P.; Friel, Eileen D.; Suntzeff, Nicholas B.

    1987-01-01

    Intermediate-resolution C, N, and Fe abundance spectra for 83 subdwarfs in the lowest metallicity range (-1.5 to -3.2), obtained with the Lick Observatory 3.1-m Shane telescope, are analyzed. The effects of subgiants and binaries on the sample are examined. The relation between (B-V) and (V-K) and effective temperature is studied. C/Fe, N/Fe, and Fe/H abundances were determined using the model-atmosphere technique of spectrum synthesis. The derived abundance values are compared with data from previous investigations. It is observed that there is good correlation between the Fe/H abundance values derived from the intermediate-resolution spectra and those based on high-resolution spectra; C/Fe abundance values are constant; and there is an upturn in the C/Fe abundance values at the very lowest metallicities.

  7. Temporal Variability of Stream Macroinvertebrate Abundance and Biomass Following Pesticide Disturbance

    Treesearch

    John J. Hutchens; Keun Chung; J. Bruce Wallace

    1998-01-01

    We determined the extent of macroinvertebrate recovery in a former pesticide-treated stream (FTS) relative to a reference stream (RS) by examining macroinvertebrate colonizing red maple (Acer rubrum L.) litter bags between 5 to 10 y following pesticide treatment. Mean abundance and biomass, varibility in abundance and biomass (using the coefficient...

  8. The role of geography and host abundance in the distribution of parasitoids of an alien pest

    PubMed Central

    Nováková, Petra; Holuša, Jaroslav

    2016-01-01

    Chalcid wasps (Hymenoptera: Chalcidoidea) are probably the most effective and abundant parasitoids of the horse chestnut leaf miner (Cameraria ohridella), an alien pest in Europe that lacks specialized enemies. We studied how the species richness and abundance of chalcids are influenced by altitude, direction of an alien spread and host abundance of C. ohridella. We quantified the numbers and species richness of chalcid wasps and the numbers of C. ohridella that emerged from horse chestnut (Aesculus hippocastanum) leaf litter samples collected from 35 sites in the Czech Republic. Species richness of chalcids, which was considered an indicator of the possible adaptation of parasitoids to this alien host, was unrelated to C. ohridella abundance, direction of spread, or altitude. Chalcid abundance, which was considered an indicator of parasitism of the alien host, was strongly and positively related to C. ohridella abundance. Chalcid abundance was negatively related to direction of spread and positively related, although in a non-linear manner, to altitude. The relationship of chalcid abundance with direction of spread and altitude was weaker than that with C. ohridella abundance. The results provide evidence that biological control of the alien pest C. ohridella by natural enemies might develop in the future. PMID:26819849

  9. Cosmological evolution of the nitrogen abundance

    NASA Astrophysics Data System (ADS)

    Vangioni, Elisabeth; Dvorkin, Irina; Olive, Keith A.; Dubois, Yohan; Molaro, Paolo; Petitjean, Patrick; Silk, Joe; Kimm, Taysun

    2018-06-01

    The abundance of nitrogen in the interstellar medium is a powerful probe of star formation processes over cosmological time-scales. Since nitrogen can be produced both in massive and intermediate-mass stars with metallicity-dependent yields, its evolution is challenging to model, as evidenced by the differences between theoretical predictions and observations. In this work, we attempt to identify the sources of these discrepancies using a cosmic evolution model. To further complicate matters, there is considerable dispersion in the abundances from observations of damped Lyα absorbers (DLAs) at z ˜ 2-3. We study the evolution of nitrogen with a detailed cosmic chemical evolution model and find good agreement with these observations, including the relative abundances of (N/O) and (N/Si). We find that the principal contribution of nitrogen comes from intermediate-mass stars, with the exception of systems with the lowest N/H, where nitrogen production might possibly be dominated by massive stars. This last result could be strengthened if stellar rotation which is important at low metallicity can produce significant amounts of nitrogen. Moreover, these systems likely reside in host galaxies with stellar masses below 108.5 M⊙. We also study the origin of the observed dispersion in nitrogen abundances using the cosmological hydrodynamical simulations Horizon-AGN. We conclude that this dispersion can originate from two effects: difference in the masses of the DLA host galaxies, and difference in their position inside the galaxy.

  10. Spectroscopic abundance analyses of the 3He stars HD 185330 and 3 Cen A

    NASA Astrophysics Data System (ADS)

    Sadakane, Kozo; Nishimura, Masayoshi

    2018-04-01

    Abundances of 21 elements in two 3He stars, HD 185330 and 3 Cen A, have been analysed relative to the well-studied sharp-lined B3 V star ι Her. Six elements (P, Ti, Mn, Fe, Ni, and Br) are over-abundant in these two peculiar stars, while six elements (C, O, Mg, Al, S, and Cl) are under-abundant. Absorption lines of the two rarely observed heavy elements Br II and Kr II are detected in both stars and these elements are both over-abundant. The centroid wavelengths of the Ca II infrared triplet lines in these stars are redshifted relative to those lines in ι Her and the presence of heavy isotopes of Ca (mass number 44-46) in these two stars is confirmed. In spite of these similarities, there are several remarkable differences in abundance pattern between these two stars. N is under-abundant in HD 185330, as in many Hg-Mn stars, while it is significantly over-abundant in 3 Cen A. P and Ga are both over-abundant in 3 Cen A, while only P is over-abundant and no trace of absorption line of Ga II can be found in HD 185330. Large over-abundances of Kr and Xe are found in both stars, while the abundance ratio Kr/Xe is significantly different between them (-1.4 dex in HD 185330 and +1.2 dex in 3 Cen A). Some physical explanations are needed to account for these qualitative differences.

  11. Spectroscopic abundance analyses of the 3He stars HD 185330 and 3 Cen A

    NASA Astrophysics Data System (ADS)

    Sadakane, Kozo; Nishimura, Masayoshi

    2018-06-01

    Abundances of 21 elements in two 3He stars, HD 185330 and 3 Cen A, have been analysed relative to the well-studied sharp-lined B3 V star ι Her. Six elements (P, Ti, Mn, Fe, Ni, and Br) are over-abundant in these two peculiar stars, while six elements (C, O, Mg, Al, S, and Cl) are under-abundant. Absorption lines of the two rarely observed heavy elements Br II and Kr II are detected in both stars and these elements are both over-abundant. The centroid wavelengths of the Ca II infrared triplet lines in these stars are redshifted relative to those lines in ι Her and the presence of heavy isotopes of Ca (mass number 44-46) in these two stars is confirmed. In spite of these similarities, there are several remarkable differences in abundance pattern between these two stars. N is under-abundant in HD 185330, as in many Hg-Mn stars, while it is significantly over-abundant in 3 Cen A. P and Ga are both over-abundant in 3 Cen A, while only P is over-abundant and no trace of absorption line of Ga II can be found in HD 185330. Large over-abundances of Kr and Xe are found in both stars, while the abundance ratio Kr/Xe is significantly different between them (-1.4 dex in HD 185330 and +1.2 dex in 3 Cen A). Some physical explanations are needed to account for these qualitative differences.

  12. Interstellar abundances and depletions inferred from observations of neutral atoms

    NASA Technical Reports Server (NTRS)

    Snow, T. P.

    1984-01-01

    Data on neutral atomic species are analyzed for the purpose of inferring relative elemental abundances and depletions in diffuse cloud cores, where it is assumed that densities are enhanced in comparison with mean densities over integrated lines of sight. Column densities of neutral atoms are compared to yield relative column densities of singly ionized species, which are assumed dominant in cloud cores. This paper incorporates a survey of literature data on neutral atomic abundances with the result that no systematic enhancement in the depletions of calcium or iron in cloud cores is found, except for zeta Ophiuchi. This may imply that depletions are not influenced by density, but other data argue against this interpretation. It is concluded either that in general all elements are depleted together in dense regions so that their relative abundances remain constant, or that typical diffuse clouds do not have significant cores, but instead are reasonably homogeneous. The data show a probable correlation between cloud-core depletion and hydrogen-molecular fraction, supporting the assumption that overall depletions are a function of density.

  13. Differential abundance analysis of mesocarp protein from high- and low-yielding oil palms associates non-oil biosynthetic enzymes to lipid biosynthesis.

    PubMed

    Ooi, Tony Eng Keong; Yeap, Wan Chin; Daim, Leona Daniela Jeffery; Ng, Boon Zean; Lee, Fong Chin; Othman, Ainul Masni; Appleton, David Ross; Chew, Fook Tim; Kulaveerasingam, Harikrishna

    2015-01-01

    The oil palm Elaeis guineensis Jacq. which produces the highest yield per unit land area of the oil crops is the most important commercial oil crop in South East Asia. The fleshy mesocarp of oil palm fruit, where oil is mostly derived from, contains up to 90 % dry weight of oil (one of the most concentrated in plant tissues). Hence, there is attention given to gain insights into the processes of oil deposition in this oil rich tissue. For that purpose, two-dimensional differential gel electrophoresis (DIGE) coupled with western assays, were used here to analyze differential protein levels in genetically-related high-and low-yielding oil palm mesocarps. From the DIGE comparative analysis in combination with western analysis, 41 unique differentially accumulated proteins were discovered. Functional categorization of these proteins placed them in the metabolisms of lipid, carbohydrate, amino acids, energy, structural proteins, as well as in other functions. In particular, higher abundance of fructose-1,6-biphosphate aldolase combined with reduced level of triosephosphate isomerase and glyceraldehyde-3-phosphate dehydrogenase may be indicative of important flux balance changes in glycolysis, while amino acid metabolism also appeared to be closely linked with oil yield. Forty-one proteins in several important biological pathways were identified as exhibiting differential in abundance at critical oil production stages. These confirm that oil yield is a complex trait involving the regulation of genes in multiple biological pathways. The results also provide insights into key control points of lipid biosynthesis in oil palm and can assist in the development of genetic markers for use in oil palm breeding programmes.

  14. Sighting frequency and relative abundance of bottlenose dolphins (Tursiops truncatus) along the northeast coast of Margarita Island and Los Frailes Archipelago, Venezuela.

    PubMed

    Oviedo, Lenin; Silva, Noemi

    2005-01-01

    The study of local cetaceans in Venezuela has a very recent history, and few efforts have been made in the assessment of coastal populations based on field research. The occurrence of whales and dolphins along the northeast coast of Venezuela has been documented through sightings and stranding records. Given the underwater topographical features and the influence of upwelling processes, this area is considered a very productive coastal ecosystem. Our objective was to establish the sighting frequency and relative abundance of bottlenose dolphins in the area. Sighting records were gathered on bottlenose dolphins and other cetacean species occurring along the northeast coast of Margarita Island and Los Frailes Archipelago through direct observation during land-based (6 surveys, 48 hours of observation) and boat-based surveys (24 surveys, 121 hours of observation, 1295 km covered). A sighting frequency was calculated using two methodologies and then compared, considering: 1) a mean effective observation time (4.27 hours), and 2) distance covered with cetacean sightings (1108 kin). A third method is proposed relating a mean effective distance covered with cetacean sightings and expressed as a percentage. The abundance index was calculated using the mean effective observation time. The sighting frequency of Tursiops truncattus in the study area was 3 - 4 sightings per day of 4.27 observation hours, or by 185 kilometers covered. The relative abundance was calculated as 35 dolphins in the study area, so a total population of less than 60 dolphins could inhabit the proposed range. Tursiops truncatus is the dominant species in the northeast coast of Margarita Island and Los Frailes Archipelago with 70% of all the sightings, so this locality could be termed as the distribution range of a possible local population of bottlenose dolphins.

  15. Multidimensional metrics for estimating phage abundance, distribution, gene density, and sequence coverage in metagenomes

    PubMed Central

    Aziz, Ramy K.; Dwivedi, Bhakti; Akhter, Sajia; Breitbart, Mya; Edwards, Robert A.

    2015-01-01

    Phages are the most abundant biological entities on Earth and play major ecological roles, yet the current sequenced phage genomes do not adequately represent their diversity, and little is known about the abundance and distribution of these sequenced genomes in nature. Although the study of phage ecology has benefited tremendously from the emergence of metagenomic sequencing, a systematic survey of phage genes and genomes in various ecosystems is still lacking, and fundamental questions about phage biology, lifestyle, and ecology remain unanswered. To address these questions and improve comparative analysis of phages in different metagenomes, we screened a core set of publicly available metagenomic samples for sequences related to completely sequenced phages using the web tool, Phage Eco-Locator. We then adopted and deployed an array of mathematical and statistical metrics for a multidimensional estimation of the abundance and distribution of phage genes and genomes in various ecosystems. Experiments using those metrics individually showed their usefulness in emphasizing the pervasive, yet uneven, distribution of known phage sequences in environmental metagenomes. Using these metrics in combination allowed us to resolve phage genomes into clusters that correlated with their genotypes and taxonomic classes as well as their ecological properties. We propose adding this set of metrics to current metaviromic analysis pipelines, where they can provide insight regarding phage mosaicism, habitat specificity, and evolution. PMID:26005436

  16. Multidimensional metrics for estimating phage abundance, distribution, gene density, and sequence coverage in metagenomes

    DOE PAGES

    Aziz, Ramy K.; Dwivedi, Bhakti; Akhter, Sajia; ...

    2015-05-08

    Phages are the most abundant biological entities on Earth and play major ecological roles, yet the current sequenced phage genomes do not adequately represent their diversity, and little is known about the abundance and distribution of these sequenced genomes in nature. Although the study of phage ecology has benefited tremendously from the emergence of metagenomic sequencing, a systematic survey of phage genes and genomes in various ecosystems is still lacking, and fundamental questions about phage biology, lifestyle, and ecology remain unanswered. To address these questions and improve comparative analysis of phages in different metagenomes, we screened a core set ofmore » publicly available metagenomic samples for sequences related to completely sequenced phages using the web tool, Phage Eco-Locator. We then adopted and deployed an array of mathematical and statistical metrics for a multidimensional estimation of the abundance and distribution of phage genes and genomes in various ecosystems. Experiments using those metrics individually showed their usefulness in emphasizing the pervasive, yet uneven, distribution of known phage sequences in environmental metagenomes. Using these metrics in combination allowed us to resolve phage genomes into clusters that correlated with their genotypes and taxonomic classes as well as their ecological properties. By adding this set of metrics to current metaviromic analysis pipelines, where they can provide insight regarding phage mosaicism, habitat specificity, and evolution.« less

  17. Multidimensional metrics for estimating phage abundance, distribution, gene density, and sequence coverage in metagenomes

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Aziz, Ramy K.; Dwivedi, Bhakti; Akhter, Sajia

    Phages are the most abundant biological entities on Earth and play major ecological roles, yet the current sequenced phage genomes do not adequately represent their diversity, and little is known about the abundance and distribution of these sequenced genomes in nature. Although the study of phage ecology has benefited tremendously from the emergence of metagenomic sequencing, a systematic survey of phage genes and genomes in various ecosystems is still lacking, and fundamental questions about phage biology, lifestyle, and ecology remain unanswered. To address these questions and improve comparative analysis of phages in different metagenomes, we screened a core set ofmore » publicly available metagenomic samples for sequences related to completely sequenced phages using the web tool, Phage Eco-Locator. We then adopted and deployed an array of mathematical and statistical metrics for a multidimensional estimation of the abundance and distribution of phage genes and genomes in various ecosystems. Experiments using those metrics individually showed their usefulness in emphasizing the pervasive, yet uneven, distribution of known phage sequences in environmental metagenomes. Using these metrics in combination allowed us to resolve phage genomes into clusters that correlated with their genotypes and taxonomic classes as well as their ecological properties. By adding this set of metrics to current metaviromic analysis pipelines, where they can provide insight regarding phage mosaicism, habitat specificity, and evolution.« less

  18. Nematode diversity, abundance and community structure 50 years after the formation of the volcanic island of Surtsey

    NASA Astrophysics Data System (ADS)

    Ilieva-Makulec, K.; Bjarnadottir, B.; Sigurdsson, B. D.

    2014-10-01

    The soil nematode fauna can give important insights into soil development and other habitat changes that occur during primary succession. We investigated the generic composition, density, distribution and community structure of nematodes 50 years after the formation of a pristine volcanic island, Surtsey, Iceland. Part of the island has received additional nutrient inputs from seagulls breeding there since 1985, while the reminder has been much less affected and is at present found at a different successional sere. In total, 25 genera of nematodes were identified, of which 14 were reported on Surtsey for the first time. Nematode communities were more diverse in the more infertile area outside the gull colony, where 24 genera were found, compared to 18 inside. The trophic structure of the nematode communities showed relatively higher abundance of fungal feeders in the infertile areas, but relatively more bacterial- and plant-feeders inside the colony. Nematode abundance in surface soil was, however, significantly higher within the gull colony, with 16.7 ind. cm-2 compared to 3.6 ind. cm-2 outside. A multivariate analysis indicated that the nematode abundance and distribution on Surtsey were most strongly related to the soil C : N ratio, soil acidity, plant cover and biomass, soil temperature and soil depth.

  19. An Abundance Analysis of Two Carbon-Rich Proto-Planetary Nebulae: IRAS Z02229+6208 And IRAS 07430+1115

    NASA Technical Reports Server (NTRS)

    Reddy, Bacham E.; Bakker, Eric J.; Hrivnak, Bruce J.

    1999-01-01

    In this paper, we present an LTE abundance analysis of two new proto-planetary nebulae, IRAS Z02229 + 6208 and IRAS 07430 + 1115, based on high-resolution (R approximately equal 55,000) optical echelle spectra. Results show that both stars are metal-poor ([Fe/H] = -0.5) and overabundant in C, N, and s-process elements. The average elemental abundances are [C/Fe] = +0.8, [N/Fe] = +1.2, and [s-process/Fe] = +1.4 for IRAS Z02229 + 6208, and [C/Fe] = +0.6, [N/Fe] = +0.4, and [s-process/Fe] = +1.6 for IRAS 07430+ 1115. These abundances suggest that the stars have experienced nucleo-synthesis on the asymptotic giant branch (AGB), and the resultant products of CNO, 3alpha, and s-process reactions were brought to the photosphere during shell flashes and deep mixing episodes during the AGB phase of their evolution. Of major significance is the measurement of a high Li abundance in both stars, log epsilon(Li) approximately equal 2.3 and 2.4 for IRAS Z02229 + 6208 and IRAS 07430 + 1115, respectively. This may be the result of hot bottom burning, below the deep convective zone. We also present an analysis of the circumstellar molecular (C2 and CN) and atomic (Na I and K I) absorption spectra of both stars. We derive rotational temperatures, column densities, and envelope expansion velocities using molecular C2 Phillips and CN Red system bands. The values derived for expansion velocities, 8-14 km/s, are typical of the values found for post-AGB stars. IRAS 07430+ 1115 is unusual in that it shows P Cygni-shaped C2 emission profiles in the spectra of the circumstellar envelope. A minimum distance for IRAS Z02229+6208, determined from interstellar Na I lines, suggests that it is evolved from an intermediate-mass star. Including these two stars, the number of post-AGB stars for which clear C, N, and s-process elemental overabundances are found rises to eight. IRAS Z02229 + 6208 is known to possess the 21 micron emission feature in its mid-infrared spectrum; these results support the

  20. Rényi entropy, abundance distribution, and the equivalence of ensembles.

    PubMed

    Mora, Thierry; Walczak, Aleksandra M

    2016-05-01

    Distributions of abundances or frequencies play an important role in many fields of science, from biology to sociology, as does the Rényi entropy, which measures the diversity of a statistical ensemble. We derive a mathematical relation between the abundance distribution and the Rényi entropy, by analogy with the equivalence of ensembles in thermodynamics. The abundance distribution is mapped onto the density of states, and the Rényi entropy to the free energy. The two quantities are related in the thermodynamic limit by a Legendre transform, by virtue of the equivalence between the micro-canonical and canonical ensembles. In this limit, we show how the Rényi entropy can be constructed geometrically from rank-frequency plots. This mapping predicts that non-concave regions of the rank-frequency curve should result in kinks in the Rényi entropy as a function of its order. We illustrate our results on simple examples, and emphasize the limitations of the equivalence of ensembles when a thermodynamic limit is not well defined. Our results help choose reliable diversity measures based on the experimental accuracy of the abundance distributions in particular frequency ranges.

  1. 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, Michael 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

  2. Pressure shifts and abundance gradients in the atmosphere of the DAZ white dwarf GALEX J193156.8+011745

    NASA Astrophysics Data System (ADS)

    Vennes, S.; Kawka, A.; Németh, P.

    2011-06-01

    We present a detailed model atmosphere analysis of high-dispersion and high signal-to-noise ratio spectra of the heavily polluted DAZ white dwarf GALEX J1931+0117. The spectra obtained with the Very Large Telescope (VLT)-Kueyen/UV-Visual Echelle Spectrograph show several well-resolved Si II spectral lines enabling a study of pressure effects on line profiles. We observed large Stark shifts in silicon lines in agreement with theoretical predictions and laboratory measurements. Taking into account Stark shifts in the calculation of synthetic spectra, we reduced the scatter in individual line radial velocity measurements from ˜3 to ≲1 km s-1. We present revised abundances of O, Mg, Si, Ca and Fe based on a critical review of line-broadening parameters and oscillator strengths. The new measurements are generally in agreement with our previous analysis with the exception of magnesium with a revised abundance of a factor of 2 lower than previously estimated. The magnesium, silicon and iron abundances exceed solar abundances, but the oxygen and calcium abundances are below solar. Also, we compared the observed line profiles to synthetic spectra computed with variable accretion rates and vertical abundance distributions assuming diffusive steady state. The inferred accretion rates vary from ? for calcium to 2 × 109 g s-1 for oxygen. We find that the accretion flow must be oxygen rich while being deficient in calcium relative to solar abundances. The lack of radial velocity variations between two measurement epochs suggests that GALEX J1931+0117 is probably not in a close binary and that the source of the accreted material resides in a debris disc. Based on observations made with European Southern Observatory (ESO) telescopes at the La Silla Paranal Observatory under programme 283.D-5060.

  3. Oxygen Abundances in the Rings of Polar-Ring Galaxies

    NASA Astrophysics Data System (ADS)

    Radtke, I. R.; Eskridge, P. B.; Pogge, R. W.

    2003-05-01

    Polar ring galaxies (PRGs) are typically early-type (S0 or E) galaxies surrounded by rings of gas, dust, and stars orbiting nearly perpendicular to the principle plane of the host galaxy (Whitmore et al. 1990 AJ 100 1489). Given that PRGs have two separate, perpendicular axes of rotation, it is clear on dynamical grounds that PRGs are the products of merger events between two galaxies, but are observed in a state where two distinct kinematic and morphological structures are still apparent. As such, they present a unique opportunity to study merger events in systems where the debris is not confused with material from the host. Our understanding of the relative importance of polar ring systems in the overall process of galaxy evolution is confounded by our lack of knowledge regarding the typical lifetimes and evolutionary histories of polar rings. A crucial factor for understanding the formation and evolution of PRGs is information regarding the elemental abundances of the ring material. Polar rings are typically rich in {\\protectH 2} regions. Optical spectroscopy of these {\\protectH 2} regions can tell us their density, temperature, and oxygen abundance. Our earlier work (Eskridge & Pogge 1997 ApJ 486 259) revealed roughly Solar oxygen abundances for {\\protectH 2} regions in the polar ring of NGC 2685. We have extended this project, and now have spectra for six PRGs. Analysis of the data for II Zw 73 and UGC 7576 reveal the polar rings of these galaxies to have {\\protectH 2} region oxygen abundances in the range 0.3 to 0.6 Solar, substantially less than found for NGC 2685. Abundances in this range are much easier to explain with conventional models of chemical enrichment and polar ring formation. We shall present results for our full sample. Taken as a whole, this sample will provide a clear foundation for the typical chemical enrichment patterns in polar rings, and thus provide a clearer understanding of the formation and evolution of these curious objects. We

  4. Invasive lionfish reduce native fish abundance on a regional scale

    NASA Astrophysics Data System (ADS)

    Ballew, Nicholas G.; Bacheler, Nathan M.; Kellison, G. Todd; Schueller, Amy M.

    2016-08-01

    Invasive lionfish pose an unprecedented threat to biodiversity and fisheries throughout Atlantic waters off of the southeastern United States, the Caribbean, and the Gulf of Mexico. Here, we employ a spatially replicated Before-After-Control-Impact analysis with temporal pairing to quantify for the first time the impact of the lionfish invasion on native fish abundance across a broad regional scale and over the entire duration of the lionfish invasion (1990-2014). Our results suggest that 1) lionfish-impacted areas off of the southeastern United States are most prevalent off-shore near the continental shelf-break but are also common near-shore and 2) in impacted areas, lionfish have reduced tomtate (a native forage fish) abundance by 45% since the invasion began. Tomtate served as a model native fish species in our analysis, and as such, it is likely that the lionfish invasion has had similar impacts on other species, some of which may be of economic importance. Barring the development of a control strategy that reverses the lionfish invasion, the abundance of lionfish in the Atlantic, Caribbean, and Gulf of Mexico will likely remain at or above current levels. Consequently, the effect of lionfish on native fish abundance will likely continue for the foreseeable future.

  5. Invasive lionfish reduce native fish abundance on a regional scale.

    PubMed

    Ballew, Nicholas G; Bacheler, Nathan M; Kellison, G Todd; Schueller, Amy M

    2016-08-31

    Invasive lionfish pose an unprecedented threat to biodiversity and fisheries throughout Atlantic waters off of the southeastern United States, the Caribbean, and the Gulf of Mexico. Here, we employ a spatially replicated Before-After-Control-Impact analysis with temporal pairing to quantify for the first time the impact of the lionfish invasion on native fish abundance across a broad regional scale and over the entire duration of the lionfish invasion (1990-2014). Our results suggest that 1) lionfish-impacted areas off of the southeastern United States are most prevalent off-shore near the continental shelf-break but are also common near-shore and 2) in impacted areas, lionfish have reduced tomtate (a native forage fish) abundance by 45% since the invasion began. Tomtate served as a model native fish species in our analysis, and as such, it is likely that the lionfish invasion has had similar impacts on other species, some of which may be of economic importance. Barring the development of a control strategy that reverses the lionfish invasion, the abundance of lionfish in the Atlantic, Caribbean, and Gulf of Mexico will likely remain at or above current levels. Consequently, the effect of lionfish on native fish abundance will likely continue for the foreseeable future.

  6. Invasive lionfish reduce native fish abundance on a regional scale

    PubMed Central

    Ballew, Nicholas G.; Bacheler, Nathan M.; Kellison, G. Todd; Schueller, Amy M.

    2016-01-01

    Invasive lionfish pose an unprecedented threat to biodiversity and fisheries throughout Atlantic waters off of the southeastern United States, the Caribbean, and the Gulf of Mexico. Here, we employ a spatially replicated Before-After-Control-Impact analysis with temporal pairing to quantify for the first time the impact of the lionfish invasion on native fish abundance across a broad regional scale and over the entire duration of the lionfish invasion (1990–2014). Our results suggest that 1) lionfish-impacted areas off of the southeastern United States are most prevalent off-shore near the continental shelf-break but are also common near-shore and 2) in impacted areas, lionfish have reduced tomtate (a native forage fish) abundance by 45% since the invasion began. Tomtate served as a model native fish species in our analysis, and as such, it is likely that the lionfish invasion has had similar impacts on other species, some of which may be of economic importance. Barring the development of a control strategy that reverses the lionfish invasion, the abundance of lionfish in the Atlantic, Caribbean, and Gulf of Mexico will likely remain at or above current levels. Consequently, the effect of lionfish on native fish abundance will likely continue for the foreseeable future. PMID:27578096

  7. Relative abundance of deformed wing virus, Varroa destructor virus 1, and their recombinants in honey bees (Apis mellifera) assessed by kmer analysis of public RNA-Seq data

    USGS Publications Warehouse

    Cornman, Robert S.

    2017-01-01

    Deformed wing virus (DWV) is a major pathogen of concern to apiculture, and recent reports have indicated the local predominance and potential virulence of recombinants between DWV and a related virus, Varroa destructor virus 1 (VDV). However, little is known about the frequency and titer of VDV and recombinants relative to DWV generally. In this study, I assessed the relative occurrence and titer of DWV and VDV in public RNA-seq accessions of honey bee using a rapid, kmer-based approach. Three recombinant types were detectable graphically and corroborated by de novo assembly. Recombination breakpoints did not disrupt the capsid-encoding region, consistent with previous reports, and both VDV- and DWV-derived capsids were observed in recombinant backgrounds. High abundance of VDV kmers was largely restricted to recombinant forms. Non-metric multidimensional scaling identified genotypic clusters among DWV isolates, which was corroborated by read mapping and consensus generation. The recently described DWV-C lineage was not detected in the searched accessions. The data further highlight the utility of high-throughput sequencing to monitor viral polymorphisms and statistically test biological predictors of titer, and point to the need for consistent methodologies and sampling schemes.

  8. Study of biological communities subject to imperfect detection: Bias and precision of community N-mixture abundance models in small-sample situations

    USGS Publications Warehouse

    Yamaura, Yuichi; Kery, Marc; Royle, Andy

    2016-01-01

    Community N-mixture abundance models for replicated counts provide a powerful and novel framework for drawing inferences related to species abundance within communities subject to imperfect detection. To assess the performance of these models, and to compare them to related community occupancy models in situations with marginal information, we used simulation to examine the effects of mean abundance (λ¯: 0.1, 0.5, 1, 5), detection probability (p¯: 0.1, 0.2, 0.5), and number of sampling sites (n site : 10, 20, 40) and visits (n visit : 2, 3, 4) on the bias and precision of species-level parameters (mean abundance and covariate effect) and a community-level parameter (species richness). Bias and imprecision of estimates decreased when any of the four variables (λ¯, p¯, n site , n visit ) increased. Detection probability p¯ was most important for the estimates of mean abundance, while λ¯ was most influential for covariate effect and species richness estimates. For all parameters, increasing n site was more beneficial than increasing n visit . Minimal conditions for obtaining adequate performance of community abundance models were n site  ≥ 20, p¯ ≥ 0.2, and λ¯ ≥ 0.5. At lower abundance, the performance of community abundance and community occupancy models as species richness estimators were comparable. We then used additive partitioning analysis to reveal that raw species counts can overestimate β diversity both of species richness and the Shannon index, while community abundance models yielded better estimates. Community N-mixture abundance models thus have great potential for use with community ecology or conservation applications provided that replicated counts are available.

  9. Host trait combinations drive abundance and canopy distribution of atmospheric bromeliad assemblages.

    PubMed

    Chaves, Cleber Juliano Neves; Dyonisio, Júlio César; Rossatto, Davi Rodrigo

    2016-01-01

    Epiphytes are strongly dependent on the conditions created by their host's traits and a certain degree of specificity is expected between them, even if these species are largely abundant in a series of tree hosts of a given environment, as in the case of atmospheric bromeliads. Despite their considerable abundance in these environments, we hypothesize that stochasticity alone cannot explain the presence and abundance of atmospheric bromeliads on host trees, since host traits could have a greater influence on the establishment of these bromeliads. We used secondary and reforested seasonal forests and three distinct silvicultures to test whether species richness, phylogenetic diversity and functional diversity of trees can predict the differential presence, abundance and distribution of atmospheric bromeliads on hosts. We compared the observed parameters of their assemblage with null models and performed successive variance hierarchic partitions of abundance and distribution of the assemblage to detect the influence of multiple traits of the tree hosts. Our results do not indicate direct relationships between the abundance of atmospheric bromeliads and phylogenetic or functional diversity of trees, but instead indicate that bromeliads occurred on fewer tree species than expected by chance. We distinguished functional tree patterns that can improve or reduce the abundance of atmospheric bromeliads, and change their distribution on branches and trunk. While individual tree traits are related to increased abundance, species traits are related to the canopy distribution of atmospheric bromeliad assemblages. A balance among these tree functional patterns drives the atmospheric bromeliad assemblage of the forest patches. Published by Oxford University Press on behalf of the Annals of Botany Company.

  10. Host trait combinations drive abundance and canopy distribution of atmospheric bromeliad assemblages

    PubMed Central

    Chaves, Cleber Juliano Neves; Dyonisio, Júlio César; Rossatto, Davi Rodrigo

    2016-01-01

    Epiphytes are strongly dependent on the conditions created by their host's traits and a certain degree of specificity is expected between them, even if these species are largely abundant in a series of tree hosts of a given environment, as in the case of atmospheric bromeliads. Despite their considerable abundance in these environments, we hypothesize that stochasticity alone cannot explain the presence and abundance of atmospheric bromeliads on host trees, since host traits could have a greater influence on the establishment of these bromeliads. We used secondary and reforested seasonal forests and three distinct silvicultures to test whether species richness, phylogenetic diversity and functional diversity of trees can predict the differential presence, abundance and distribution of atmospheric bromeliads on hosts. We compared the observed parameters of their assemblage with null models and performed successive variance hierarchic partitions of abundance and distribution of the assemblage to detect the influence of multiple traits of the tree hosts. Our results do not indicate direct relationships between the abundance of atmospheric bromeliads and phylogenetic or functional diversity of trees, but instead indicate that bromeliads occurred on fewer tree species than expected by chance. We distinguished functional tree patterns that can improve or reduce the abundance of atmospheric bromeliads, and change their distribution on branches and trunk. While individual tree traits are related to increased abundance, species traits are related to the canopy distribution of atmospheric bromeliad assemblages. A balance among these tree functional patterns drives the atmospheric bromeliad assemblage of the forest patches. PMID:26888951

  11. Bumble bee nest abundance, foraging distance, and host-plant reproduction: implications for management and conservation.

    PubMed

    Geib, Jennifer C; Strange, James P; Galenj, Candace

    2015-04-01

    Recent reports of global declines in pollinator species imply an urgent need to assess the abundance of native pollinators and density-dependent benefits for linked plants. In this study, we investigated (1) pollinator nest distributions and estimated colony abundances, (2) the relationship between abundances of foraging workers and the number of nests they represent, (3) pollinator foraging ranges, and (4) the relationship between pollinator abundance and plant reproduction. We examined these questions in an alpine ecosystem in the Colorado Rocky Mountains, focusing on four alpine bumble bee species (Bombus balteatus, B. flavifrons, B. bifarius, and B. sylvicola), and two host plants that differ in their degrees of pollinator specialization (Trifolium dasyphyllum and T. parryi). Using microsatellites, we found that estimated colony abundances among Bombus species ranged from ~18 to 78 colonies/0.01 km2. The long-tongued species B. balteatus was most common, especially high above treeline, but the subalpine species B. bifarius was unexpectedly abundant for this elevation range. Nests detected among sampled foragers of each species were correlated with the number of foragers caught. Foraging ranges were smaller than expected for all Bombus species, ranging from 25 to 110 m. Fruit set for the specialized plant, Trifolium parryi, was positively related to the abundance of its Bombus pollinator. In contrast, fruit set for the generalized plant, T. dasyphyllum, was related to abundance of all Bombus species. Because forager abundance was related to nest abundance of each Bombus species and was an equally effective predictor of plant fecundity, forager inventories are probably suitable for assessing the health of outcrossing plant populations. However, nest abundance, rather than forager abundance, better reflects demographic and genetic health in populations of eusocial pollinators such as bumble bees. Development of models incorporating the parameters we have measured

  12. Direct evidence that density-dependent regulation underpins the temporal stability of abundant species in a diverse animal community

    PubMed Central

    Henderson, Peter A.; Magurran, Anne E.

    2014-01-01

    To understand how ecosystems are structured and stabilized, and to identify when communities are at risk of damage or collapse, we need to know how the abundances of the taxa in the entire assemblage vary over ecologically meaningful timescales. Here, we present an analysis of species temporal variability within a single large vertebrate community. Using an exceptionally complete 33-year monthly time series following the dynamics of 81 species of fishes, we show that the most abundant species are least variable in terms of temporal biomass, because they are under density-dependent (negative feedback) regulation. At the other extreme, a relatively large number of low abundance transient species exhibit the greatest population variability. The high stability of the consistently common high abundance species—a result of density-dependence—is reflected in the observation that they consistently represent over 98% of total fish biomass. This leads to steady ecosystem nutrient and energy flux irrespective of the changes in species number and abundance among the large number of low abundance transient species. While the density-dependence of the core species ensures stability under the existing environmental regime, the pool of transient species may support long-term stability by replacing core species should environmental conditions change. PMID:25100702

  13. Occurrence and abundance of antibiotic resistance genes in agricultural soil receiving dairy manure.

    PubMed

    McKinney, Chad W; Dungan, Robert S; Moore, Amber; Leytem, April B

    2018-03-01

    Animal manures are commonly used to enhance soil fertility, but there are growing concerns over the impact of this practice on the development and dissemination of antibiotic resistance. The aim of this field study was to determine the effect of annual dairy manure applications on the occurrence and abundance of antibiotic resistance genes (ARGs) in an agricultural soil during four years of crop production. Treatments included (i) control (no fertilizer or manure), (ii) inorganic fertilizer and (iii) dairy manure at three application rates. Quantitative PCR was used to determine absolute (per g dry soil) and relative (per 16S rRNA gene) abundances of ARGs in DNA extracted from soils. Six ARGs and one class 1 integron were targeted. This study found that (i) manure application increases ARG abundances above background soil levels; (ii) the higher the manure application rate, the higher the ARG abundance in soil; (iii) the amount of manure applied is more important than reoccurring annual applications of the same amount of manure; (iv) absolute abundance and occurrence of ARGs decreases with increasing soil depth, but relative abundances remained constant. This study demonstrated that dairy manure applications to soil significantly increase the abundance of clinically relevant ARGs when compared to control and inorganic fertilized plots.

  14. Landscape capability predicts upland game bird abundance and occurrence

    USGS Publications Warehouse

    Loman, Zachary G.; Blomberg, Erik J.; DeLuca, William; Harrison, Daniel J.; Loftin, Cyndy; Wood, Petra B.

    2017-01-01

    Landscape capability (LC) models are a spatial tool with potential applications in conservation planning. We used survey data to validate LC models as predictors of occurrence and abundance at broad and fine scales for American woodcock (Scolopax minor) and ruffed grouse (Bonasa umbellus). Landscape capability models were reliable predictors of occurrence but were less indicative of relative abundance at route (11.5–14.6 km) and point scales (0.5–1 km). As predictors of occurrence, LC models had high sensitivity (0.71–0.93) and were accurate (0.71–0.88) and precise (0.88 and 0.92 for woodcock and grouse, respectively). Models did not predict point-scale abundance independent of the ability to predict occurrence of either species. The LC models are useful predictors of patterns of occurrences in the northeastern United States, but they have limited utility as predictors of fine-scale or route-specific abundances

  15. Factors responsible for Ixodes ricinus nymph abundance: Are soil features indicators of tick abundance in a French region where Lyme borreliosis is endemic?

    PubMed

    Goldstein, Valérie; Boulanger, Nathalie; Schwartz, Dominique; George, Jean-Claude; Ertlen, Damien; Zilliox, Laurence; Schaeffer, Mickaël; Jaulhac, Benoît

    2018-05-01

    In Europe, the hard tick Ixodes ricinus (Acari: Ixodidae) is the main vector of Lyme borreliosis spirochetes (Borrelia burgdorferi sensu lato group). A field study was conducted to evaluate the abundance of Ixodes nymphs in the French region of Alsace, where Lyme borreliosis is endemic, and to determine whether environmental factors such as soil moisture and composition may be associated with nymph abundance. In the ten sites studied, ticks were collected by drag sampling from March to October in 2013 and 2014. Temperature, relative humidity, saturation deficit, soil pH, humus composition and type of vegetation were recorded at each site. The abundance of I. ricinus was highly variable from one site to another. Inter-annual variations were also observed, since the nymph abundance were higher in 2013 than in 2014. This study shows that humus type can be indicative of nymph abundance. Three types of humus were observed: (1) moder, (2) mull, and (3) mull-moder humus. One of them, moder humus, which is characterized by a thick layer of fragmented leaves, was found in multivariate analyses to be strongly associated with the nymph abundance. This study demonstrates that factors such as saturation deficit do not suffice to explain the differences in nymph abundance among sites. The composition of the soil and especially the type of humus should also be taken into consideration when assessing acarological risk. Copyright © 2018 Elsevier GmbH. All rights reserved.

  16. 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.

  17. Effects of Reservoir Characteristics on Malaria and its vector Abundance: A Case Study of the Bongo District of Ghana

    NASA Astrophysics Data System (ADS)

    Ofosu, E.; Awuah, E.; Annor, F. O.

    2009-04-01

    In the seven (7) administrative zones of the Bongo District of the Upper East Region of Ghana, the occurrences of malaria and relative abundance of the principal malaria vector, Anopheles species, were studied as a function of the presence and characteristics of reservoirs during the rainy season. Case studies in the sub-Sahara Africa indicate that malaria transmission may increase decrease or remain largely unchanged as a consequence of reservoir presence. Analysis made, shows that the distance from reservoir to settlement and surface area of reservoirs significantly affected adult Anopheles mosquito abundance. Percentage of inhabitants using insecticide treated nets, livestock population density, human population density and Anopheles mosquito abundance significantly affected the occurrence of malaria. The results suggest that vector control targeted at reservoir characteristics and larval control, and supplemented by high patronage of insecticide treated nets may be an effective approach for epidemic malaria control in the Bongo District. Key Words: Bongo District, Reservoir, Anopheles species, Malaria, Vector abundance.

  18. CORRELATION OF RED-SHOULDERED HAWK ABUNDANCE AND MACROHABITAT CHARACTERISTICS IN SOUTHERN OHIO

    EPA Science Inventory

    We measured an index of Red-shouldered Hawk (Buteo lineatus) abundance along streams in southern Ohio and related differences in abundance index to landscape scale habitat characteristics within the surveyed areas. Fifteen study sites, each a 5.8-km reach of permanent stream, we...

  19. Comparative composition, diversity, and abundance of oligosaccharides in early lactation milk from commercial dairy and beef cows

    PubMed Central

    Sischo, William M.; Short, Diana M.; Geissler, Mareen; Bunyatratchata, Apichaya; Barile, Daniela

    2017-01-01

    Prebiotics are nondigestible dietary ingredients, usually oligosaccharides (OS), that provide a health benefit to the host by directly modulating the gut microbiota. Although there is some information describing OS content in dairy-source milk, no information is available to describe the OS content of beef-source milk. Given the different trait emphasis between dairy and beef for milk production and calf survivability, it is plausible that OS composition, diversity, and abundance differ between production types. The goal of this study was to compare OS in milk from commercial dairy and beef cows in early lactation. Early-lactation multiparous cows (5–12 d in milk) from 5 commercial Holstein dairy herds and 5 Angus or Angus hybrid beef herds were sampled once. Milk was obtained from each enrolled cow and frozen on the farm. Subsequently, each milk sample was assessed for total solids, pH, and OS content and relative abundance. Oligosaccharide diversity and abundance within and between samples was transformed through principal component analysis to reduce data complexity. Factors from principal component analysis were used to create similarity clusters, which were subsequently used in a multivariate logistic regression. In total, 30 OS were identified in early-lactation cow milk, including 21 distinct OS and 9 isomers with unique retention times. The majority of OS detected in the milk samples were present in all individual samples regardless of production type. Two clusters described distribution patterns of OS for the study sample; when median OS abundance was compared between the 2 clusters, we found that overall OS relative abundance was consistently greater in the cluster dominated by beef cows. For several of the structures, including those with known prebiotic effect, the difference in abundance was 2- to 4-fold greater in the beef-dominated cluster. Assuming that beef OS content in milk is the gold standard for cattle, it is likely that preweaning dairy

  20. DETAILED ABUNDANCES OF THE SOLAR TWINS 16 CYGNI A AND B: CONSTRAINING PLANET FORMATION MODELS

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Schuler, Simon C.; Cunha, Katia; Smith, Verne V.

    2011-08-20

    Results of a detailed abundance analysis of the solar twins 16 Cyg A and 16 Cyg B based on high-resolution, high signal-to-noise ratio echelle spectroscopy are presented. 16 Cyg B is known to host a giant planet while no planets have yet been detected around 16 Cyg A. Stellar parameters are derived directly from our high-quality spectra, and the stars are found to be physically similar, with {Delta}T{sub eff} = +43 K, {Delta}log g = -0.02 dex, and {Delta}{xi} = +0.10 km s{sup -1} (in the sense of A - B), consistent with previous findings. Abundances of 15 elements aremore » derived and are found to be indistinguishable between the two stars. The abundances of each element differ by {<=}0.026 dex, and the mean difference is +0.003 {+-} 0.015 ({sigma}) dex. Aside from Li, which has been previously shown to be depleted by a factor of at least 4.5 in 16 Cyg B relative to 16 Cyg A, the two stars appear to be chemically identical. The abundances of each star demonstrate a positive correlation with the condensation temperature of the elements (T{sub c}); the slopes of the trends are also indistinguishable. In accordance with recent suggestions, the positive slopes of the [m/H]-T{sub c} relations may imply that terrestrial planets have not formed around either 16 Cyg A or 16 Cyg B. The physical characteristics of the 16 Cyg system are discussed in terms of planet formation models, and plausible mechanisms that can account for the lack of detected planets around 16 Cyg A, the disparate Li abundances of 16 Cyg A and B, and the eccentricity of the planet 16 Cyg B b are suggested.« less

  1. [Influences of long-term application of organic and inorganic fertilizers on the composition and abundance of nirS-type denitrifiers in black soil].

    PubMed

    Yin, Chang; Fan, Fen-Liang; Li, Zhao-Jun; Song, A-Lin; Zhu, Ping; Peng, Chang; Liang, Yong-Chao

    2012-11-01

    The objectives of this study were to explore the effects of long-term organic and inorganic fertilizations on the composition and abundance of nirS-type denitrifiers in black soil. Soil samples were collected from 4 treatments (i. e. no fertilizer treatment, CK; organic manure treatment, OM; chemical fertilizer treatment (NPK) and combination of organic and chemical fertilizers treatment (MNPK)) in Gongzhuling Long-term Fertilization Experiment Station. Composition and abundance of nirS-type denitrifiers were analyzed with terminal restriction fragment length polymorphism (T-RFLP) and real-time quantitative PCR (Q-PCR), respectively. Denitrification enzyme activity (DEA) and soil properties were also measured. Application of organic fertilizers (OM and MNPK) significantly increased the DEAs of black soil, with the DEAs in OM and MNPK being 5.92 and 6.03 times higher than that in CK treatment, respectively, whereas there was no significant difference between NPK and CK. OM and MNPK treatments increased the abundances of nirS-type denitrifiers by 2.73 and 3.83 times relative to that of CK treatment, respectively. The abundance of nirS-type denitrifiers in NPK treatment was not significantly different from that of CK. The T-RFLP analysis of nirS genes showed significant differences in community composition between organic and inorganic treatments, with the emergence of a 79 bp T-RF, a significant decrease in relative abundance of the 84 bp T-RF and a loss of the 99 bp T-RF in all organic treatments. Phylogenetic analysis indicated that the airS-type denitrifiers in the black soil were mainly composed of alpha, beta and gamma-Proteobacteria. The 79 bp-type denitrifiers inhabiting exclusively in organic treatments (OM and MNPK) were affiliated to Pseudomonadaceae in gamma-Proteobacteria and Burkholderiales in beta-Proteobacteria. The 84 bp-types were related to Burkholderiales and Rhodocyclales. Correlation analysis indicated that pH, concentrations of total nitrogen

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

    Treesearch

    Paul Stephen Corn; Erin Muths; Amanda M. Kissel; Rick D. Scherer

    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...

  3. Using spatiotemporal statistical models to estimate animal abundance and infer ecological dynamics from survey counts

    USGS Publications Warehouse

    Conn, Paul B.; Johnson, Devin S.; Ver Hoef, Jay M.; Hooten, Mevin B.; London, Joshua M.; Boveng, Peter L.

    2015-01-01

    Ecologists often fit models to survey data to estimate and explain variation in animal abundance. Such models typically require that animal density remains constant across the landscape where sampling is being conducted, a potentially problematic assumption for animals inhabiting dynamic landscapes or otherwise exhibiting considerable spatiotemporal variation in density. We review several concepts from the burgeoning literature on spatiotemporal statistical models, including the nature of the temporal structure (i.e., descriptive or dynamical) and strategies for dimension reduction to promote computational tractability. We also review several features as they specifically relate to abundance estimation, including boundary conditions, population closure, choice of link function, and extrapolation of predicted relationships to unsampled areas. We then compare a suite of novel and existing spatiotemporal hierarchical models for animal count data that permit animal density to vary over space and time, including formulations motivated by resource selection and allowing for closed populations. We gauge the relative performance (bias, precision, computational demands) of alternative spatiotemporal models when confronted with simulated and real data sets from dynamic animal populations. For the latter, we analyze spotted seal (Phoca largha) counts from an aerial survey of the Bering Sea where the quantity and quality of suitable habitat (sea ice) changed dramatically while surveys were being conducted. Simulation analyses suggested that multiple types of spatiotemporal models provide reasonable inference (low positive bias, high precision) about animal abundance, but have potential for overestimating precision. Analysis of spotted seal data indicated that several model formulations, including those based on a log-Gaussian Cox process, had a tendency to overestimate abundance. By contrast, a model that included a population closure assumption and a scale prior on total

  4. Fossil Signatures Using Elemental Abundance Distributions and Bayesian Probabilistic Classification

    NASA Technical Reports Server (NTRS)

    Hoover, Richard B.; Storrie-Lombardi, Michael C.

    2004-01-01

    Elemental abundances (C6, N7, O8, Na11, Mg12, Al3, P15, S16, Cl17, K19, Ca20, Ti22, Mn25, Fe26, and Ni28) were obtained for a set of terrestrial fossils and the rock matrix surrounding them. Principal Component Analysis extracted five factors accounting for the 92.5% of the data variance, i.e. information content, of the elemental abundance data. Hierarchical Cluster Analysis provided unsupervised sample classification distinguishing fossil from matrix samples on the basis of either raw abundances or PCA input that agreed strongly with visual classification. A stochastic, non-linear Artificial Neural Network produced a Bayesian probability of correct sample classification. The results provide a quantitative probabilistic methodology for discriminating terrestrial fossils from the surrounding rock matrix using chemical information. To demonstrate the applicability of these techniques to the assessment of meteoritic samples or in situ extraterrestrial exploration, we present preliminary data on samples of the Orgueil meteorite. In both systems an elemental signature produces target classification decisions remarkably consistent with morphological classification by a human expert using only structural (visual) information. We discuss the possibility of implementing a complexity analysis metric capable of automating certain image analysis and pattern recognition abilities of the human eye using low magnification optical microscopy images and discuss the extension of this technique across multiple scales.

  5. Deuterium Abundance in the Local Interstellar Medium

    NASA Technical Reports Server (NTRS)

    Ferlet, R.; Gry, C.; Vidal-Madjar, A.

    1984-01-01

    The present situation of deuterium abundance evaluation in interstellar space is discussed, and it is shown that it should be or = .00001 by studying in more detail lambda the Sco line of sight and by observing two NaI interstellar components toward that star, it can be shown that the D/H evaluation made toward lambda Sco is in fact related to the local interstellar medium (less than 10 pc from the Sun). Because this evaluation is also or = .00001 it is in striking contrast with the one made toward alpha Aur (D/H or = .000018 confirming the fact that the deuterium abundance in the local interstellar medium varies by at least a factor of two over few parsecs.

  6. The Open Cluster Chemical Abundances and Mapping (OCCAM) Survey: Current Status

    NASA Astrophysics Data System (ADS)

    Frinchaboy, Peter; O'Connell, Julia; Donor, John; Cunha, Katia; Thompson, Benjamin; Melendez, Matthew; Shetrone, Matthew; Zasowski, Gail; Majewski, Steven R.; APOGEE TEAM

    2018-01-01

    The Open Cluster Chemical Analysis and Mapping (OCCAM) survey aims to produce a comprehensive, uniform, infrared-based data set forhundreds of open clusters, and constrain key Galactic dynamical and chemical parameters using the SDSS/APOGEE survey and follow-up from the McDonald Observatory Otto Struve 2.1-m telescope and Sandiford Cass Echelle Spectrograph (R ~ 60,000). We report on multi-element radial abundance gradients obtained from a sample of over 30 disk open clusters. The APOGEE chemical abundances were derived automatically by the ASPCAP pipeline and these are part of the SDSS IV Data Release 14, optical follow-up were analyzed using equivalent width analysis and spectral synthesis. We present the current open cluster sample that spans a significant range in age allowing exploration of the evolution of the Galactic abundance gradients. This work is supported by an NSF AAG grants AST-1311835 & AST-1715662.

  7. Chemical abundances and kinematics of TYC 5619-109-1

    NASA Astrophysics Data System (ADS)

    Pereira, C. B.; Smith, V. V.; Drake, N. A.; Roig, F.; Hasselquist, S.; Cunha, K.; Jilinski, E.

    2017-07-01

    Previous determinations of chemical abundances of the metal-poor red giant TYC 5619-109-1, derived via high-resolution near-infrared spectra from the Apache Point Observatory Galactic Evolution Experiment survey, indicate that this star is strongly enriched in the elements N and Al. Here, we obtain and analyse high-resolution optical spectra of TYC 5619-109-1 to verify these large N and Al overabundances and to measure abundances of a wider range of chemical elements. Our analysis confirms the N- and Al-rich nature of this star, and shows that the abundances of the s-process elements are also strongly enhanced, particularly in the heavy second s-process peak elements (Ba, La, Ce, Nd). Lighter s-process elements (Y, Zr) show smaller overabundances, and the ratio of the light-to-heavy s-process elements is consistent with the 13C(α, n)16O neutron source operating in a low-metallicity environment. The lack of Tc I lines and the abundance of Nb compared to Zr indicate that this red giant is probably not a thermally pulsing asymptotic giant branch (TP-AGB) star. Mass transfer from a former s-process-rich TP-AGB companion may produce the observed overabundances, but our radial velocity analysis provides no evidence that TYC 5619-109-1 is a binary with a white dwarf companion. We suggest that TYC 5619-109-1 formed from gas already strongly enriched in s-process elements, as found in many dwarf galaxies and globular clusters. A dynamical analysis reveals that there is only a small probability that TYC 5619-109-1 is an escaped member of a globular cluster, and in this case the most likely candidate would be ω Cen.

  8. [Comparison of acetonitrile, ethanol and chromatographic column to eliminate high-abundance proteins in human serum].

    PubMed

    Li, Yin; Liao, Ming; He, Xiao; Zhou, Yi; Luo, Rong; Li, Hongtao; Wang, Yun; He, Min

    2012-11-01

    To compare the effects of acetonitrile precipitation, ethanol precipitation and multiple affinity chromatography column Human 14 removal to eliminate high-abundance proteins in human serum. Elimination of serum high-abundance proteins performed with acetonitrile precipitation, ethanol precipitation and multiple affinity chromatography column Human 14 removal. Bis-Tris Mini Gels electrophoresis and two-dimensional gel electrophoresis to detect the effect. Grey value analysis from 1-DE figure showed that after serum processed by acetonitrile method, multiple affinity chromatography column Human 14 removal method and ethanol method, the grey value of albumin changed into 157.2, 40.8 and 8.2 respectively from the original value of 19. 2-DE analysis results indicated that using multiple affinity chromatography column Human 14 method, the protein points noticeable increased by 137 compared to the original serum. After processed by acetonitrile method and ethanol method, the protein point reduced, but the low abundance protein point emerged. The acetonitrile precipitation could eliminate the vast majority of high abundance proteins in serum and gain more proteins of low molecular weight, ethanol precipitation could eliminate part of high abundance proteins in serum, but low abundance proteins less harvested, and multiple affinity chromatography column Human 14 method could effectively removed the high abundance proteins, and keep a large number of low abundance proteins.

  9. Late-Quaternary variation in C3 and C4 grass abundance in southeastern Australia as inferred from δ13C analysis: Assessing the roles of climate, pCO2, and fire

    NASA Astrophysics Data System (ADS)

    Nelson, David M.; Urban, Michael A.; Kershaw, A. Peter; Hu, Feng Sheng

    2016-05-01

    Climate, atmospheric pCO2, and fire all may exert major influences on the relative abundance of C3 and C4 grasses in the present-day vegetation. However, the relative role of these factors in driving variation in C3 and C4 grass abundances in the paleorecord is uncertain, and C4 abundance is often interpreted narrowly as a proxy indicator of aridity or pCO2. We measured δ13C values of individual grains of grass (Poaceae) pollen in the sediments of two sites in southeastern Australia to assess changes in the proportions of C3 and C4 grasses during the past 25,000 years. These data were compared with shifts in pCO2, temperature, moisture balance, and fire to assess how these factors were related to long-term variation of C4 grass abundance during the late Quaternary. At Caledonia Fen, a high-elevation site in the Snowy Mountains, C4 grass abundance decreased from an average of 66% during the glacial period to 11% during the Holocene, primarily in response to increased pCO2 and temperature. In contrast, this pattern did not exist in low-elevation savannah woodlands around Tower Hill Northwest Crater, where C4 grass abundance instead varied in response to shifts in regional aridity. Fire did not appear to have strongly influenced the proportions of C3 and C4 grasses on the landscape at millennial timescales at either site. These patterns are similar to those of a recent study in East Africa, suggesting that elevation-related climatic differences influence how the abundance of C3 and C4 grasses responds to shifts in climate and pCO2. These results caution against using C4 plant abundance as a proxy indicator of either climate or pCO2 without an adequate understanding of key controlling factors.

  10. Effects of landscape anthropization on mosquito community composition and abundance

    NASA Astrophysics Data System (ADS)

    Ferraguti, Martina; Martínez-de La Puente, Josué; Roiz, David; Ruiz, Santiago; Soriguer, Ramón; Figuerola, Jordi

    2016-07-01

    Anthropogenic landscape transformation has an important effect on vector-borne pathogen transmission. However, the effects of urbanization on mosquito communities are still only poorly known. Here, we evaluate how land-use characteristics are related to the abundance and community composition of mosquitoes in an area with endemic circulation of numerous mosquito-borne pathogens. We collected 340 829 female mosquitoes belonging to 13 species at 45 localities spatially grouped in 15 trios formed by 1 urban, 1 rural and 1 natural area. Mosquito abundance and species richness were greater in natural and rural areas than in urban areas. Environmental factors including land use, vegetation and hydrological characteristics were related to mosquito abundance and community composition. Given the differing competences of each species in pathogen transmission, these results provide valuable information on the transmission potential of mosquito-borne pathogens that will be of great use in public and animal health management by allowing, for instance, the identification of the priority areas for pathogen surveillance and vector control.

  11. Effects of landscape anthropization on mosquito community composition and abundance

    PubMed Central

    Ferraguti, Martina; Martínez-de la Puente, Josué; Roiz, David; Ruiz, Santiago; Soriguer, Ramón; Figuerola, Jordi

    2016-01-01

    Anthropogenic landscape transformation has an important effect on vector-borne pathogen transmission. However, the effects of urbanization on mosquito communities are still only poorly known. Here, we evaluate how land-use characteristics are related to the abundance and community composition of mosquitoes in an area with endemic circulation of numerous mosquito-borne pathogens. We collected 340 829 female mosquitoes belonging to 13 species at 45 localities spatially grouped in 15 trios formed by 1 urban, 1 rural and 1 natural area. Mosquito abundance and species richness were greater in natural and rural areas than in urban areas. Environmental factors including land use, vegetation and hydrological characteristics were related to mosquito abundance and community composition. Given the differing competences of each species in pathogen transmission, these results provide valuable information on the transmission potential of mosquito-borne pathogens that will be of great use in public and animal health management by allowing, for instance, the identification of the priority areas for pathogen surveillance and vector control. PMID:27373794

  12. Project VeSElkA: a search for the vertical stratification of element abundances in HD 157087

    NASA Astrophysics Data System (ADS)

    Khalack, V.

    2018-06-01

    The new spectropolarimetric spectra of HD 157087 obtained recently with ESPaDOnS (Echelle SpectroPolarimetric Device for Observations of Stars) at the Canada-France-Hawaii Telescope are analysed to verify the nature of this object. The fundamental stellar parameters Teff = 8882 K, log g = 3.57 were obtained for HD 157087 from the analysis of nine Balmer line profiles in two available spectra. A comparison of the results of our abundance analysis with previously published data shows a variability of the average abundance with time for some chemical species, while the abundances of other elements remain almost constant. The abundance analysis also reveals evidence of a significant abundance increase towards the deeper atmospheric layers for C, S, Ca, Sc, V, Cr, Mn, Co, Ni and Zr. Together with the discovered enhanced abundance of Ca and Sc, this finding contradicts the classification of HD 157087 as a marginal Am star. An analysis of the available measurements of radial velocity revealed long- and short-period variations. The long-period variation supports the idea that HD 157087 is an astrometric binary system with a period longer than 6 yr. The presence of the short-period variation of Vr, as well as the detection of the temporal variation of the average abundance, suggests that HD 157087 may be a triple system, in which a short-period binary rotates around a third star. In this case, the short-period binary may consist of slowly rotating Am and A (or Ap with a weak magnetic field) stars that have similar effective temperatures and surface gravities, but different abundance peculiarities.

  13. Abundance patterns of the light neutron-capture elements in very and extremely metal-poor stars

    NASA Astrophysics Data System (ADS)

    Spite, F.; Spite, M.; Barbuy, B.; Bonifacio, P.; Caffau, E.; François, P.

    2018-03-01

    Aims: The abundance patterns of the neutron-capture elements in metal-poor stars provide a unique record of the nucleosynthesis products of the earlier massive primitive objects. Methods: We measured new abundances of so-called light neutron-capture of first peak elements using local thermodynamic equilibrium (LTE) 1D analysis; this analysis resulted in a sample of 11 very metal-poor stars, from [Fe/H] = -2.5 to [Fe/H] = -3.4, and one carbon-rich star, CS 22949-037 with [Fe/H] = -4.0. The abundances were compared to those observed in two classical metal-poor stars: the typical r-rich star CS 31082-001 ([Eu/Fe] > +1.0) and the r-poor star HD 122563 ([Eu/Fe] < 0.0), which are known to present a strong enrichment of the first peak neutron-capture elements relative to the second peak. Results: Within the first peak, the abundances are well correlated in analogy to the well-known correlation inside the abundances of the second-peak elements. In contrast, there is no correlation between any first peak element with any second peak element. We show that the scatter of the ratio of the first peak abundance over second peak abundance increases when the mean abundance of the second peak elements decreases from r-rich to r-poor stars. We found two new r-poor stars that are very similar to HD 122563. A third r-poor star, CS 22897-008, is even more extreme; this star shows the most extreme example of first peak elements enrichment to date. On the contrary, another r-poor star (BD-18 5550) has a pattern of first peak elements that is similar to the typical r-rich stars CS 31082-001, however this star has some Mo enrichment. Conclusions: The distribution of the neutron-capture elements in our very metal-poor stars can be understood as the combination of at least two mechanisms: one that enriches the forming stars cloud homogeneously through the main r-process and leads to an element pattern similar to the r-rich stars, such as CS 31082-001; and another that forms mainly lighter

  14. 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.

  15. The Abundance of Large Arcs From CLASH

    NASA Astrophysics Data System (ADS)

    Xu, Bingxiao; Postman, Marc; Meneghetti, Massimo; Coe, Dan A.; Clash Team

    2015-01-01

    We have developed an automated arc-finding algorithm to perform a rigorous comparison of the observed and simulated abundance of large lensed background galaxies (a.k.a arcs). We use images from the CLASH program to derive our observed arc abundance. Simulated CLASH images are created by performing ray tracing through mock clusters generated by the N-body simulation calibrated tool -- MOKA, and N-body/hydrodynamic simulations -- MUSIC, over the same mass and redshift range as the CLASH X-ray selected sample. We derive a lensing efficiency of 15 ± 3 arcs per cluster for the X-ray selected CLASH sample and 4 ± 2 arcs per cluster for the simulated sample. The marginally significant difference (3.0 σ) between the results for the observations and the simulations can be explained by the systematically smaller area with magnification larger than 3 (by a factor of ˜4) in both MOKA and MUSIC mass models relative to those derived from the CLASH data. Accounting for this difference brings the observed and simulated arc statistics into full agreement. We find that the source redshift distribution does not have big impact on the arc abundance but the arc abundance is very sensitive to the concentration of the dark matter halos. Our results suggest that the solution to the "arc statistics problem" lies primarily in matching the cluster dark matter distribution.

  16. Chemical abundances of globular clusters in NGC 5128 (Centaurus A)

    NASA Astrophysics Data System (ADS)

    Hernandez, Svea; Larsen, Søren; Trager, Scott; Kaper, Lex; Groot, Paul

    2018-06-01

    We perform a detailed abundance analysis on integrated-light spectra of 20 globular clusters (GCs) in the early-type galaxy NGC 5128 (Centaurus A). The GCs were observed with X-Shooter on the Very Large Telescope (VLT). The cluster sample spans a metallicity range of -1.92 < [Fe/H] < -0.13 dex. Using theoretical isochrones, we compute synthetic integrated-light spectra and iterate the individual abundances until the best fit to the observations is obtained. We measured abundances of Mg, Ca, and Ti, and find a slightly higher enhancement in NGC 5128 GCs with metallicities [Fe/H] < -0.75 dex, of the order of ˜0.1 dex, than in the average values observed in the Milky Way (MW) for GCs of the same metallicity. If this α-enhancement in the metal-poor GCs in NGC 5128 is genuine, it could hint at a chemical enrichment history different than that experienced by the MW. We also measure Na abundances in 9 out of 20 GCs. We find evidence for intracluster abundance variations in six of these clusters where we see enhanced [Na/Fe] > +0.25 dex. We obtain the first abundance measurements of Cr, Mn, and Ni for a sample of the GC population in NGC 5128 and find consistency with the overall trends observed in the MW, with a slight enhancement (<0.1 dex) in the Fe-peak abundances measured in the NGC 5128.

  17. 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

  18. The distribution, relative abundance, and seasonal phenology of Ceratitis capitata, Ceratitis rosa, and Ceratitis cosyra (Diptera: Tephritidae) in South Africa.

    PubMed

    De Villiers, Marelize; Manrakhan, Aruna; Addison, Pia; Hattingh, Vaughan

    2013-10-01

    Ceratitis capitata (Wiedemann), Ceratitis rosa Karsch, and Ceratitis cosyra (Walker) are fruit fly species (Diptera: Tephritidae) of economic importance in South Africa. These pests cause direct damage to a number of commercially produced fruit and are of phytosanitary concern. A study was conducted to determine the distribution, relative abundance, and seasonal occurrence of the three species in different climatic regions of South Africa. The relative abundance and seasonal phenology of C. capitata and C. rosa were also compared between production areas and home gardens in Stellenbosch, Western Cape. Yellow bucket traps baited with Biolure were used to trap the flies over a 2-yr period in the different sampling areas. Different fruit types were sampled in Stellenbosch to determine fruit fly infestation. C. capitata was found to have a widespread distribution in South Africa, whereas C. rosa were absent from or only present in low numbers in the drier regions. C. cosyra was restricted to the North East and East coast, following a similar pattern to the distribution of marula, Sclerocarrya birrea, an important wild host. Fruit in home gardens provided a breeding ground for C. capitata and C. rosa and a source for infestation of orchards when fruit started to mature, highlighting the need for an area-wide strategy for the control of fruit flies.

  19. Technical Report on Modeling for Quasispecies Abundance Inference with Confidence Intervals from Metagenomic Sequence Data

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    McLoughlin, K.

    2016-01-11

    The overall aim of this project is to develop a software package, called MetaQuant, that can determine the constituents of a complex microbial sample and estimate their relative abundances by analysis of metagenomic sequencing data. The goal for Task 1 is to create a generative model describing the stochastic process underlying the creation of sequence read pairs in the data set. The stages in this generative process include the selection of a source genome sequence for each read pair, with probability dependent on its abundance in the sample. The other stages describe the evolution of the source genome from itsmore » nearest common ancestor with a reference genome, breakage of the source DNA into short fragments, and the errors in sequencing the ends of the fragments to produce read pairs.« less

  20. Like will to like: abundances of closely related species can predict susceptibility to intestinal colonization by pathogenic and commensal bacteria.

    PubMed

    Stecher, Bärbel; Chaffron, Samuel; Käppeli, Rina; Hapfelmeier, Siegfried; Freedrich, Susanne; Weber, Thomas C; Kirundi, Jorum; Suar, Mrutyunjay; McCoy, Kathy D; von Mering, Christian; Macpherson, Andrew J; Hardt, Wolf-Dietrich

    2010-01-01

    The intestinal ecosystem is formed by a complex, yet highly characteristic microbial community. The parameters defining whether this community permits invasion of a new bacterial species are unclear. In particular, inhibition of enteropathogen infection by the gut microbiota ( = colonization resistance) is poorly understood. To analyze the mechanisms of microbiota-mediated protection from Salmonella enterica induced enterocolitis, we used a mouse infection model and large scale high-throughput pyrosequencing. In contrast to conventional mice (CON), mice with a gut microbiota of low complexity (LCM) were highly susceptible to S. enterica induced colonization and enterocolitis. Colonization resistance was partially restored in LCM-animals by co-housing with conventional mice for 21 days (LCM(con21)). 16S rRNA sequence analysis comparing LCM, LCM(con21) and CON gut microbiota revealed that gut microbiota complexity increased upon conventionalization and correlated with increased resistance to S. enterica infection. Comparative microbiota analysis of mice with varying degrees of colonization resistance allowed us to identify intestinal ecosystem characteristics associated with susceptibility to S. enterica infection. Moreover, this system enabled us to gain further insights into the general principles of gut ecosystem invasion by non-pathogenic, commensal bacteria. Mice harboring high commensal E. coli densities were more susceptible to S. enterica induced gut inflammation. Similarly, mice with high titers of Lactobacilli were more efficiently colonized by a commensal Lactobacillus reuteri(RR) strain after oral inoculation. Upon examination of 16S rRNA sequence data from 9 CON mice we found that closely related phylotypes generally display significantly correlated abundances (co-occurrence), more so than distantly related phylotypes. Thus, in essence, the presence of closely related species can increase the chance of invasion of newly incoming species into the gut

  1. Abundance of red spruce regeneration across spruce-hardwood ecotones at Gaudineer Knob, West Virginia

    Treesearch

    Albert E. Mayfield; Ray R. Hicks

    2010-01-01

    The abundance of red spruce (Picea rubens Sarg.) in the Central Appalachian Mountains has been drastically reduced over the past 100 to 150 years. The purpose of this study was to examine the potential for increases in the relative abundance of overstory red spruce in a Central Appalachian, high-elevation forest by measuring the abundance of red...

  2. 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

  3. Specific activity and isotope abundances of strontium in purified strontium-82

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Fitzsimmons, J. M.; Medvedev, D. G.; Mausner, L. F.

    2015-11-12

    A linear accelerator was used to irradiate a rubidium chloride target with protons to produce strontium-82 (Sr-82), and the Sr-82 was purified by ion exchange chromatography. The amount of strontium associated with the purified Sr-82 was determined by either: ICP-OES or method B which consisted of a summation of strontium quantified by gamma spectroscopy and ICP-MS. The summation method agreed within 10% to the ICP-OES for the total mass of strontium and the subsequent specific activities were determined to be 0.25–0.52 TBq mg -1. Method B was used to determine the isotope abundances by weight% of the purified Sr-82, andmore » the abundances were: Sr-82 (10–20.7%), Sr-83 (0–0.05%), Sr-84 (35–48.5%), Sr-85 (16–25%), Sr-86 (12.5–23%), Sr-87 (0%), and Sr-88 (0–10%). The purified strontium contained mass amounts of Sr-82, Sr-84, Sr-85, Sr-86, and Sr-88 in abundances not associated with natural abundance, and 90% of the strontium was produced by the proton irradiation. A comparison of ICP-OES and method B for the analysis of Sr-82 indicated analysis by ICP-OES would be easier to determine total mass of strontium and comply with regulatory requirements. An ICP-OES analytical method for Sr-82 analysis was established and validated according to regulatory guidelines.« less

  4. nirS-Encoding denitrifier community composition, distribution, and abundance along the coastal wetlands of China.

    PubMed

    Gao, Juan; Hou, Lijun; Zheng, Yanling; Liu, Min; Yin, Guoyu; Li, Xiaofei; Lin, Xianbiao; Yu, Chendi; Wang, Rong; Jiang, Xiaofen; Sun, Xiuru

    2016-10-01

    For the past few decades, human activities have intensively increased the reactive nitrogen enrichment in China's coastal wetlands. Although denitrification is a critical pathway of nitrogen removal, the understanding of denitrifier community dynamics driving denitrification remains limited in the coastal wetlands. In this study, the diversity, abundance, and community composition of nirS-encoding denitrifiers were analyzed to reveal their variations in China's coastal wetlands. Diverse nirS sequences were obtained and more than 98 % of them shared considerable phylogenetic similarity with sequences obtained from aquatic systems (marine/estuarine/coastal sediments and hypoxia sea water). Clone library analysis revealed that the distribution and composition of nirS-harboring denitrifiers had a significant latitudinal differentiation, but without a seasonal shift. Canonical correspondence analysis showed that the community structure of nirS-encoding denitrifiers was significantly related to temperature and ammonium concentration. The nirS gene abundance ranged from 4.3 × 10(5) to 3.7 × 10(7) copies g(-1) dry sediment, with a significant spatial heterogeneity. Among all detected environmental factors, temperature was a key factor affecting not only the nirS gene abundance but also the community structure of nirS-type denitrifiers. Overall, this study significantly enhances our understanding of the structure and dynamics of denitrifying communities in the coastal wetlands of China.

  5. THE MYSTERIOUS CASE OF THE SOLAR ARGON ABUNDANCE NEAR SUNSPOTS IN FLARES

    DOE Office of Scientific and Technical Information (OSTI.GOV)

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

    Recently we discussed an enhancement of the abundance of Ar xiv relative to Ca xiv near a sunspot during a flare, observed in spectra recorded by the Extreme-ultraviolet Imaging Spectrometer (EIS) on the Hinode spacecraft. The observed Ar xiv/Ca xiv ratio yields an argon/calcium abundance ratio seven times greater than expected from the photospheric abundance. Such a large abundance anomaly is unprecedented in the solar atmosphere. We interpreted this result as being due to an inverse first ionization potential (FIP) effect. In the published work, two lines of Ar xiv were observed, and one line was tentatively identified as anmore » Ar xi line. In this paper, we report observing a similar enhancement in a full-CCD EIS flare spectrum in 13 argon lines that lie within the EIS wavelength ranges. The observed lines include two Ar xi lines, four Ar xiii lines, six Ar xiv lines, and one Ar xv line. The enhancement is far less than reported in Doschek et al. but exhibits similar morphology. The argon abundance is close to a photospheric abundance in the enhanced area, and the abundance could be photospheric. This enhancement occurs in association with a sunspot in a small area only a few arcseconds (1″ = about 700 km) in size. There is no enhancement effect observed in the normally high-FIP sulfur and oxygen line ratios relative to lines of low-FIP elements available to EIS. Calculations of path lengths in the strongest enhanced area in Doschek et al. indicate a depletion of low-FIP elements.« less

  6. Reliable Quantitative Mineral Abundances of the Martian Surface using THEMIS

    NASA Astrophysics Data System (ADS)

    Smith, R. J.; Huang, J.; Ryan, A. J.; Christensen, P. R.

    2013-12-01

    The following presents a proof of concept that given quality data, Thermal Emission Imaging System (THEMIS) data can be used to derive reliable quantitative mineral abundances of the Martian surface using a limited mineral library. The THEMIS instrument aboard the Mars Odyssey spacecraft is a multispectral thermal infrared imager with a spatial resolution of 100 m/pixel. The relatively high spatial resolution along with global coverage makes THEMIS datasets powerful tools for comprehensive fine scale petrologic analyses. However, the spectral resolution of THEMIS is limited to 8 surface sensitive bands between 6.8 and 14.0 μm with an average bandwidth of ~ 1 μm, which complicates atmosphere-surface separation and spectral analysis. This study utilizes the atmospheric correction methods of both Bandfield et al. [2004] and Ryan et al. [2013] joined with the iterative linear deconvolution technique pioneered by Huang et al. [in review] in order to derive fine-scale quantitative mineral abundances of the Martian surface. In general, it can be assumed that surface emissivity combines in a linear fashion in the thermal infrared (TIR) wavelengths such that the emitted energy is proportional to the areal percentage of the minerals present. TIR spectra are unmixed using a set of linear equations involving an endmember library of lab measured mineral spectra. The number of endmembers allowed in a spectral library are restricted to a quantity of n-1 (where n = the number of spectral bands of an instrument), preserving one band for blackbody. Spectral analysis of THEMIS data is thus allowed only seven endmembers. This study attempts to prove that this limitation does not prohibit the derivation of meaningful spectral analyses from THEMIS data. Our study selects THEMIS stamps from a region of Mars that is well characterized in the TIR by the higher spectral resolution, lower spatial resolution Thermal Emission Spectrometer (TES) instrument (143 bands at 10 cm-1 sampling and 3

  7. Distribution and abundance of predators that affect duck production--prairie pothole region

    USGS Publications Warehouse

    Sargeant, A.B.; Greenwood, R.J.; Sovada, M.A.; Shaffer, T.L.

    1993-01-01

    During 1983-88, the relative abundance of 18 species and species-groups of mammalian and avian predators affecting duck production in the prairie pothole region was determined in 33 widely scattered study areas ranging in size from 23-26 km2. Accounts of each studied species and species-group include habitat and history, population structure and reported densities, and information on distribution and abundance from the present study. Index values of undetected, scarce, uncommon, common, or numerous were used to rate abundance of nearly all species in each study area. Principal survey methods were livetrapping of striped skunks (Mephitis mephitis) and Franklin's ground squirrels (Spermophilus franklinii), systematic searches for carnivore tracks in quarter sections (0.65 km2), daily records of sightings of individual predator species, and systematic searches for occupied nests of tree-nesting avian predators. Abundances of predators in individual areas were studied 1-3 years.The distribution and abundance of predator species throughout the prairie pothole region have undergone continual change since settlement of the region by Europeans in the late 1800's. Predator populations in areas we studied differed markedly from those of pristine times. The changes occurred from habitat alterations, human-inflicted mortality of predators, and interspecific relations among predator species. Indices from surveys of tracks revealed a decline in the abundance of red foxes (Vulpes vulpes) and an albeit less consistent decline in the abundance of raccoons (Procyon lotor) with an increase in the abundance of coyotes (Canis latrans). Records of locations of occupied nests revealed great horned owls (Bubo virginianus) and red-tailed hawks (Buteo jamaicensis) tended to nest 0.5 km apart, and American crows (Corvus brachyrhynchos) tended to avoid nesting 0.5 km of nests of red-tailed hawks. Excluding large gulls, for which no measurements of abundance were obtained, the number of

  8. Measuring the expressed abundance of the three phases of water with an imaging spectrometer over melting snow

    NASA Astrophysics Data System (ADS)

    Green, Robert O.; Painter, Thomas H.; Roberts, Dar A.; Dozier, Jeff

    2006-10-01

    From imaging spectrometer data, we simultaneously estimate the abundance of the three phases of water in an environment that includes melting snow, basing the analysis on the spectral shift in the absorption coefficient between water vapor, liquid water, and ice at 940, 980, and 1030 nm respectively. We apply a spectral fitting algorithm that measures the expressed abundance of the three phases of water to a data set acquired by the Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) over Mount Rainier, Washington, on 14 June 1996. Precipitable water vapor varies from 1 mm over the summit of Mount Rainier to 10 mm over the lower valleys to the northwest. Equivalent path absorption of liquid water varies from 0 to 13 mm, with the zero values over rocky areas and high-elevation snow and the high values associated with liquid water held in vegetation canopies and in melting snow. Ice abundance varies from 0 to 30 mm equivalent path absorption in the snow- and glacier-covered portions of Mount Rainier. The water and ice abundances are related to the amount of liquid water and the sizes of the ice grains in the near-surface layer. Precision of the estimates, calculated over locally homogeneous areas, indicates an uncertainty of better than 1.5% for all three phases, except for liquid water in vegetation, where an optimally homogeneous site was not found. The analysis supports new strategies for hydrological research and applications as imaging spectrometers become more available.

  9. The Abundance and Distribution of Presolar Materials in Cluster IDPS

    NASA Technical Reports Server (NTRS)

    Messenger, Scott; Keller, Lindsay; Nakamura-Messenger, Keiko; Ito, Motoo

    2007-01-01

    Presolar grains and remnants of interstellar organic compounds occur in a wide range of primitive solar system materials, including meteorites, interplanetary dust particles (IDPs), and comet Wild-2 samples. Among the most abundant presolar phases are silicate stardust grains and molecular cloud material. However, these materials have also been susceptible to destruction and alteration during parent body and nebular processing. In addition to their importance as direct samples of remote and ancient astrophysical environments, presolar materials thus provide a measure of how well different primitive bodies have preserved the original solar system starting materials. The matrix normalized abundances of presolar silicate grains in meteorites range from 20 ppm in Semarkona and Bishunpur to 170 ppm for Acfer 094. The lower abundances of presolar silicates in Bishunpur and Semarkona has been ascribed to the destruction of presolar silicates during aqueous processes. Presolar silicates appear to be significantly more abundant in anhydrous IDPs, possibly because these materials did not experience parent body hydrothermal alteration. Among IDPs the estimated abundances of presolar silicates vary by more than an order of magnitude, from 480 to 5500 ppm. The wide disparity in the abundances of presolar silicates of IDPs may be a consequence of the relatively small total area analyzed in those studies and the fine grain sizes of the IDPs. Alternatively, there may be a wide range in presolar silicate abundances between different IDPs. This view is supported by the observation that 15N-rich IDPs have higher presolar silicate abundances than those with isotopically normal N.

  10. Analysis of the Plasma Proteome in COPD: Novel Low Abundance Proteins Reflect the Severity of Lung Remodeling

    PubMed Central

    Merali, Salim; Barrero, Carlos A.; Bowler, Russell P.; Chen, Diane Er; Criner, Gerard; Braverman, Alan; Litwin, Samuel; Yeung, Anthony; Kelsen, Steven G.

    2015-01-01

    The search for COPD biomarkers has largely employed a targeted approach that focuses on plasma proteins involved in the systemic inflammatory response and in lung injury and repair. This proof of concept study was designed to test the idea that an open, unbiased, in-depth proteomics approach could identify novel, low abundance plasma proteins i.e., ng/mL concentration, which could serve as potential biomarkers. Differentially expressed proteins were identified in a discovery group with severe COPD (FEV1 <45% predicted; n = 10). Subjects with normal lung function matched for age, sex, ethnicity and smoking history served as controls (n = 10). Pooled plasma from each group was exhaustively immunodepleted of abundant proteins, d separated by 1-D gel electrophoresis and extensively fractionated prior to LC-tandem mass spectroscopy (GeLC-MS). Thirty one differentially expressed proteins were identified in the discovery group including markers of lung defense against oxidant stress, alveolar macrophage activation, and lung tissue injury and repair. Four of the 31 proteins (i.e., GRP78, soluble CD163, IL1AP and MSPT9) were measured in a separate verification group of 80 subjects with varying COPD severity by immunoassay. All 4 were significantly altered in COPD and 2 (GRP78 and soluble CD163) correlated with both FEV1 and the extent of emphysema. In-depth, plasma proteomic analysis identified a group of novel, differentially expressed, low abundance proteins that reflect known pathogenic mechanisms and the severity of lung remodeling in COPD. These proteins may also prove useful as COPD biomarkers. PMID:24111704

  11. Analysis of the plasma proteome in COPD: Novel low abundance proteins reflect the severity of lung remodeling.

    PubMed

    Merali, Salim; Barrero, Carlos A; Bowler, Russell P; Chen, Diane Er; Criner, Gerard; Braverman, Alan; Litwin, Samuel; Yeung, Anthony; Kelsen, Steven G

    2014-04-01

    The search for COPD biomarkers has largely employed a targeted approach that focuses on plasma proteins involved in the systemic inflammatory response and in lung injury and repair. This proof of concept study was designed to test the idea that an open, unbiased, in-depth proteomics approach could identify novel, low abundance plasma proteins i.e., ng/mL concentration, which could serve as potential biomarkers. Differentially expressed proteins were identified in a discovery group with severe COPD (FEV1 <45% predicted; n = 10). Subjects with normal lung function matched for age, sex, ethnicity and smoking history served as controls (n = 10). Pooled plasma from each group was exhaustively immunodepleted of abundant proteins, d separated by 1-D gel electrophoresis and extensively fractionated prior to LC-tandem mass spectroscopy (GeLC-MS). Thirty one differentially expressed proteins were identified in the discovery group including markers of lung defense against oxidant stress, alveolar macrophage activation, and lung tissue injury and repair. Four of the 31 proteins (i.e., GRP78, soluble CD163, IL1AP and MSPT9) were measured in a separate verification group of 80 subjects with varying COPD severity by immunoassay. All 4 were significantly altered in COPD and 2 (GRP78 and soluble CD163) correlated with both FEV1 and the extent of emphysema. In-depth, plasma proteomic analysis identified a group of novel, differentially expressed, low abundance proteins that reflect known pathogenic mechanisms and the severity of lung remodeling in COPD. These proteins may also prove useful as COPD biomarkers.

  12. One Percent Determination of the Primordial Deuterium Abundance

    NASA Astrophysics Data System (ADS)

    Cooke, Ryan J.; Pettini, Max; Steidel, Charles C.

    2018-03-01

    We report a reanalysis of a near-pristine absorption system, located at a redshift {z}abs}=2.52564 toward the quasar Q1243+307, based on the combination of archival and new data obtained with the HIRES echelle spectrograph on the Keck telescope. This absorption system, which has an oxygen abundance [O/H] = ‑2.769 ± 0.028 (≃1/600 of the solar abundance), is among the lowest metallicity systems currently known where a precise measurement of the deuterium abundance is afforded. Our detailed analysis of this system concludes, on the basis of eight D I absorption lines, that the deuterium abundance of this gas cloud is {log}}10({{D}}/{{H}})=-4.622+/- 0.015, which is in very good agreement with the results previously reported by Kirkman et al., but with an improvement on the precision of this single measurement by a factor of ∼3.5. Combining this new estimate with our previous sample of six high precision and homogeneously analyzed D/H measurements, we deduce that the primordial deuterium abundance is {log}}10{({{D}}/{{H}})}{{P}}=-4.5974+/- 0.0052 or, expressed as a linear quantity, {10}5{({{D}}/{{H}})}{{P}}=2.527+/- 0.030; this value corresponds to a one percent determination of the primordial deuterium abundance. Combining our result with a big bang nucleosynthesis (BBN) calculation that uses the latest nuclear physics input, we find that the baryon density derived from BBN agrees to within 2σ of the latest results from the Planck cosmic microwave background data. Based on observations collected at the W.M. Keck Observatory which is operated as a scientific partnership among the California Institute of Technology, the University of California, and the National Aeronautics and Space Administration. The Observatory was made possible by the generous financial support of the W.M. Keck Foundation.

  13. Abundance and Source Population of Suprathermal Heavy Ions in Corotating Interaction Regions

    NASA Astrophysics Data System (ADS)

    Jensema, R. J.; Desai, M. I.; Broiles, T. W.; Dayeh, M. A.

    2015-12-01

    In this study we analyze the abundances of suprathermal heavy ions in 75 Corotating Interaction Region (CIR) events between January 1st 1995 and December 31st 2008. We correlate the heavy ion abundances in these CIRs with those measured in the solar wind and suprathermal populations upstream of these events. Our analysis reveals that the CIR suprathermal heavy ion abundances vary by nearly two orders of magnitude over the solar activity cycle, with higher abundances (e.g., Fe/O) occurring during solar maximum and depleted values occurring during solar minimum. The abundances are also energy dependent, with larger abundances at higher energies, particularly during solar maximum. Following the method used by Mason et al. 2008, we correlate the CIR abundances with the corresponding solar wind and suprathermal values measured during 6-hour intervals for upstream periods spanning 10 days prior to the start of each CIR event. This correlation reveals that suprathermal heavy ions are better correlated with upstream suprathermal abundances measured at the same energy compared with the solar wind heavy ion abundances. Using the 6-hour averaging method, we also identified timeframes of maximum correlation between the CIR and the upstream suprathermal abundances, and find that the time of maximum correlation depends on the energy of the suprathermal ions. We discuss the implications of these results in terms of previous studies of CIR and suprathermal particles, and CIR seed populations and acceleration mechanisms.

  14. Comparative bacterial community analysis in relatively pristine and anthropogenically influenced mangrove ecosystems on the Red Sea.

    PubMed

    Ullah, Riaz; Yasir, Muhammad; Khan, Imran; Bibi, Fehmida; Sohrab, Sayed Sartaj; Al-Ansari, Ahmed; Al-Abbasi, Fahad; Al-Sofyani, Abdulmohsin A; Daur, Ihsanullah; Lee, Seon-Woo; Azhar, Esam I

    2017-08-01

    Mangrove habitats are ecologically important ecosystems that are under severe pressure worldwide because of environmental changes and human activities. In this study, 16S rRNA gene amplicon deep-sequencing was used to compare bacterial communities in Red Sea mangrove ecosystems at anthropogenically influenced coastal sites with those at a relatively pristine island site. In total, 32 phyla were identified from the mangrove rhizospheres, with Proteobacteria predominating at each of the studied sites; however, the relative abundance was significantly decreased at the coastal sites (Mastorah, MG-MS; Ar-Rayis, MG-AR) compared with the pristine island site near Dhahban (MG-DBI). The phyla Actinobacteria, Firmicutes, Acidobacteria, Chloroflexi, Spirochetes, and Planctomycetes were present at a relative abundance of >1% at the MG-MS and MG-AR sites, but their concentration was <1% at the MG-DBI site. A total of 1659 operational taxonomic units (OTUs) were identified at the species level, and approximately 945 OTUs were shared across the different sampling sites. Multivariate principal coordinate data analysis separated the MG-DBI site from the MG-AR and MG-MS cluster. Specific bacterial taxa were enriched at each location, and in particular, the genera Pseudoalteromonas and Cobetia were predominantly identified in the MG-DBI site compared with the anthropogenically influenced coastal sites.

  15. Nitrifier Gene Abundance and Diversity in Sediments Impacted by Acid Mine Drainage

    PubMed Central

    Ramanathan, Bhargavi; Boddicker, Andrew M.; Roane, Timberley M.; Mosier, Annika C.

    2017-01-01

    Extremely acidic and metal-rich acid mine drainage (AMD) waters can have severe toxicological effects on aquatic ecosystems. AMD has been shown to completely halt nitrification, which plays an important role in transferring nitrogen to higher organisms and in mitigating nitrogen pollution. We evaluated the gene abundance and diversity of nitrifying microbes in AMD-impacted sediments: ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and nitrite-oxidizing bacteria (NOB). Samples were collected from the Iron Springs Mining District (Ophir, CO, United States) during early and late summer in 2013 and 2014. Many of the sites were characterized by low pH (<5) and high metal concentrations. Sequence analyses revealed AOA genes related to Nitrososphaera, Nitrosotalea, and Nitrosoarchaeum; AOB genes related to Nitrosomonas and Nitrosospira; and NOB genes related to Nitrospira. The overall abundance of AOA, AOB and NOB was examined using quantitative PCR (qPCR) amplification of the amoA and nxrB functional genes and 16S rRNA genes. Gene copy numbers ranged from 3.2 × 104 – 4.9 × 107 archaeal amoA copies ∗ μg DNA-1, 1.5 × 103 – 5.3 × 105 AOB 16S rRNA copies ∗ μg DNA-1, and 1.3 × 106 – 7.7 × 107 Nitrospira nxrB copies ∗ μg DNA-1. Overall, Nitrospira nxrB genes were found to be more abundant than AOB 16S rRNA and archaeal amoA genes in most of the sample sites across 2013 and 2014. AOB 16S rRNA and Nitrospira nxrB genes were quantified in sediments with pH as low as 3.2, and AOA amoA genes were quantified in sediments as low as 3.5. Though pH varied across all sites (pH 3.2–8.3), pH was not strongly correlated to the overall community structure or relative abundance of individual OTUs for any gene (based on CCA and Spearman correlations). pH was positivity correlated to the total abundance (qPCR) of AOB 16S rRNA genes, but not for any other genes. Metals were not correlated to the overall nitrifier community composition or abundance, but

  16. Variations in iron and calcium abundances during solar flares

    NASA Astrophysics Data System (ADS)

    Antonucci, E.; Martin, R.

    1995-07-01

    Evidence for variations in iron and calcium abundances during the impulsive phase of solar flares has been obtained by analyzing the Ca XIX and Fe XXV spectra, detected with the Bent Crystal Spectrometer of the Solar Maximum Mission. The plasma thermal conditions have been investigated by considering different temperature indicators: namely, the temperatures TCa and TFe, derived from the intensity ratios of the dielectronic recombination satellites to the resonance line, and the temperature TCaFe, calculated from the ratio of the resonance lines of Ca XIX and Fe XXV, which is also depending on the Fe/Ca abundance ratio. The observed values of TCa and TFe can be ascribed to the specific characteristics of the plasma therma distribution, the corresponding values of TCaFe can be explained by allowing also for variations in the Fe/Ca abundance ratio relative to the photospheric ratio by a factor within 0.2 and 2.4. According to the observed abundance variations, the events analyzed can be divided in Ca-rich and Fe-rich flares.

  17. Massive star formation in Wolf-Rayet galaxies. IV. Colours, chemical-composition analysis and metallicity-luminosity relations

    NASA Astrophysics Data System (ADS)

    López-Sánchez, Á. R.; Esteban, C.

    2010-07-01

    Aims: We have performed a comprehensive multiwavelength analysis of a sample of 20 starburst galaxies that show a substantial population of very young massive stars, most of them classified as Wolf-Rayet (WR) galaxies. In this paper, the forth of the series, we present the global analysis of the derived photometric and chemical properties. Methods: We compare optical/NIR colours and the physical properties (reddening coefficient, equivalent widths of the emission and underlying absorption lines, ionization degree, electron density, and electron temperature) and chemical properties (oxygen abundances and N/O, S/O, Ne/O, Ar/O, and Fe/O ratios) with previous observations and galaxy evolution models. We compile 41 independent star-forming regions - with oxygen abundances between 12 + log(O/H) = 7.58 and 8.75 - , of which 31 have a direct estimate of the electron temperature of the ionized gas. Results: According to their absolute B-magnitude, many of them are not dwarf galaxies, but they should be during their quiescent phase. We found that both c(Hβ) and Wabs increase with increasing metallicity. The differences in the N/O ratio is explained assuming differences in the star formation histories. We detected a high N/O ratio in objects showing strong WR features (HCG 31 AC, UM 420, IRAS 0828+2816, III Zw 107, ESO 566-8 and NGC 5253). The ejecta of the WR stars may be the origin of the N enrichment in these galaxies. We compared the abundances provided by the direct method with those obtained through empirical calibrations, finding that (i) the Pilyugin method is the best suited empirical calibration for these star-forming galaxies; (ii) the relations provided by Pettini & Pagel (2004, MNRAS, 348, 59) give acceptable results for objects with 12 + log(O/H) > 8.0; and (iii) the results provided by empirical calibrations based on photoionization models are systematically 0.2-0.3 dex higher than the values derived from the direct method. The O and N abundances and the N

  18. CHEMICAL ABUNDANCES IN THE EXTERNALLY POLLUTED WHITE DWARF GD 40: EVIDENCE OF A ROCKY EXTRASOLAR MINOR PLANET

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Klein, B.; Jura, M.; Zuckerman, B.

    2010-02-01

    We present Keck/High Resolution Echelle Spectrometer data with model atmosphere analysis of the helium-dominated polluted white dwarf GD 40, in which we measure atmospheric abundances relative to helium of nine elements: H, O, Mg, Si, Ca, Ti, Cr, Mn, and Fe. Apart from hydrogen, whose association with the other contaminants is uncertain, this material most likely accreted from GD 40's circumstellar dust disk whose existence is demonstrated by excess infrared emission. The data are best explained by accretion of rocky planetary material, in which heavy elements are largely contained within oxides, derived from a tidally disrupted minor planet at leastmore » the mass of Juno, and probably as massive as Vesta. The relatively low hydrogen abundance sets an upper limit of 10% water by mass in the inferred parent body, and the relatively high abundances of refractory elements, Ca and Ti, may indicate high-temperature processing. While the overall constitution of the parent body is similar to the bulk Earth being over 85% by mass composed of oxygen, magnesium, silicon, and iron, we find n(Si)/n(Mg) = 0.30 +- 0.11, significantly smaller than the ratio near unity for the bulk Earth, chondrites, the Sun, and nearby stars. This result suggests that differentiation occurred within the parent body.« less

  19. Lithium Abundance in M3 Red Giant

    NASA Astrophysics Data System (ADS)

    Givens, Rashad; Pilachowski, Catherine A.

    2015-01-01

    We present the abundance of lithium in the red giant star vZ 1050 (SK 291) in the globular cluster M3. A previous survey of giants in the cluster showed that like IV-101, vZ 1050 displays a prominent Li I 6707 Å feature. vZ 1050 lies on the blue side of the red giant branch about 1.3 magnitudes above the level of the horizontal branch, and may be an asymptotic giant branch star. A high resolution spectrum of M3 vZ1050 was obtained with the ARC 3.5m telescope and the ARC Echelle Spectrograph (ARCES). Atmospheric parameters were determined using Fe I and Fe II lines from the spectrum using the MOOG spectral analysis program, and the lithium abundance was determined using spectrum synthesis.

  20. Horvitz-Thompson survey sample methods for estimating large-scale animal abundance

    USGS Publications Warehouse

    Samuel, M.D.; Garton, E.O.

    1994-01-01

    Large-scale surveys to estimate animal abundance can be useful for monitoring population status and trends, for measuring responses to management or environmental alterations, and for testing ecological hypotheses about abundance. However, large-scale surveys may be expensive and logistically complex. To ensure resources are not wasted on unattainable targets, the goals and uses of each survey should be specified carefully and alternative methods for addressing these objectives always should be considered. During survey design, the impoflance of each survey error component (spatial design, propofiion of detected animals, precision in detection) should be considered carefully to produce a complete statistically based survey. Failure to address these three survey components may produce population estimates that are inaccurate (biased low), have unrealistic precision (too precise) and do not satisfactorily meet the survey objectives. Optimum survey design requires trade-offs in these sources of error relative to the costs of sampling plots and detecting animals on plots, considerations that are specific to the spatial logistics and survey methods. The Horvitz-Thompson estimators provide a comprehensive framework for considering all three survey components during the design and analysis of large-scale wildlife surveys. Problems of spatial and temporal (especially survey to survey) heterogeneity in detection probabilities have received little consideration, but failure to account for heterogeneity produces biased population estimates. The goal of producing unbiased population estimates is in conflict with the increased variation from heterogeneous detection in the population estimate. One solution to this conflict is to use an MSE-based approach to achieve a balance between bias reduction and increased variation. Further research is needed to develop methods that address spatial heterogeneity in detection, evaluate the effects of temporal heterogeneity on survey

  1. Pattern variation of fish fingerling abundance in the Na Thap Tidal river of Southern Thailand: 2005-2015

    NASA Astrophysics Data System (ADS)

    Donroman, T.; Chesoh, S.; Lim, A.

    2018-04-01

    This study aimed to investigate the variation patterns of fish fingerling abundance based on month, year and sampling site. Monthly collecting data set of the Na Thap tidal river of southern Thailand, were obtained from June 2005 to October 2015. The square root transformation was employed for maintaining the fingerling data normality. Factor analysis was applied for clustering number of fingerling species and multiple linear regression was used to examine the association between fingerling density and year, month and site. Results from factor analysis classified fingerling into 3 factors based on saline preference; saline water, freshwater and ubiquitous species. The results showed a statistically high significant relation between fingerling density, month, year and site. Abundance of saline water and ubiquitous fingerling density showed similar pattern. Downstream site presented highest fingerling density whereas almost of freshwater fingerling occurred in upstream. This finding confirmed that factor analysis and the general linear regression method can be used as an effective tool for predicting and monitoring wild fingerling density in order to sustain fish stock management.

  2. Species composition, diversity and relative abundance of amphibians in forests and non-forest habitats on Langkawi Island, Peninsular Malaysia

    NASA Astrophysics Data System (ADS)

    Nur Johana, J.; Muzzneena, A. M.; Grismer, L. L.; Norhayati, A.

    2016-11-01

    Anurans on Langkawi Island, Peninsular Malaysia exhibit variation in their habits and forms, ranging from small (SVL < 25 mm) to large (SVL > 150 mm), and occupy a range of habitats, such as riverine forests, agricultural fields, peat swamps, and lowland and upland dipterocarp forests. These variations provide a platform to explore species diversity, distribution, abundance, microhabitat, and other ecological parameters to understand the distribution patterns and to facilitate conservation and management of sensitive or important species and areas. The objective of this study was to evaluate the diversity and distribution of anuran species in different types of habitat on Langkawi Island. Specimens were collected based on active sampling using the Visual Encounter Survey (VES) method. We surveyed anuran species inhabiting seven types of habitat, namely agriculture (AG), coastal (CL), forest (FT), pond (PD), mangrove (MG), riparian forest (RF) and river (RV). A total of 775 individuals were sampled from all localities, representing 23 species from 12 genera and included all six families of frogs in Malaysia. FT and RF showed high values of Shannon Index, H', 2.60 and 2.38, respectively, followed by the other types of habitat, CL (1.82), RV (1.71), MG (1.56), PD (1.54), and AG (1.53). AG had the highest abundance (156 individuals) compared to other habitat types. Based on Cluster Analysis by using Jaccard coefficient (UPGMA), two groups can be clearly seen and assigned as forested species group (FT and RF) and species associating with human activity (AG, CL, PD, MG and RV). Forest species group is more diverse compared to non-forest group. Nevertheless, non-forest species are found in abundance, highlighting the relevance of these disturbed habitats in supporting the amphibians.

  3. Plant trait-species abundance relationships vary with environmental properties in subtropical forests in eastern china.

    PubMed

    Yan, En-Rong; Yang, Xiao-Dong; Chang, Scott X; Wang, Xi-Hua

    2013-01-01

    Understanding how plant trait-species abundance relationships change with a range of single and multivariate environmental properties is crucial for explaining species abundance and rarity. In this study, the abundance of 94 woody plant species was examined and related to 15 plant leaf and wood traits at both local and landscape scales involving 31 plots in subtropical forests in eastern China. Further, plant trait-species abundance relationships were related to a range of single and multivariate (PCA axes) environmental properties such as air humidity, soil moisture content, soil temperature, soil pH, and soil organic matter, nitrogen (N) and phosphorus (P) contents. At the landscape scale, plant maximum height, and twig and stem wood densities were positively correlated, whereas mean leaf area (MLA), leaf N concentration (LN), and total leaf area per twig size (TLA) were negatively correlated with species abundance. At the plot scale, plant maximum height, leaf and twig dry matter contents, twig and stem wood densities were positively correlated, but MLA, specific leaf area, LN, leaf P concentration and TLA were negatively correlated with species abundance. Plant trait-species abundance relationships shifted over the range of seven single environmental properties and along multivariate environmental axes in a similar way. In conclusion, strong relationships between plant traits and species abundance existed among and within communities. Significant shifts in plant trait-species abundance relationships in a range of environmental properties suggest strong environmental filtering processes that influence species abundance and rarity in the studied subtropical forests.

  4. Patterns in Abundance, Cell Size and Pigment Content of Aerobic Anoxygenic Phototrophic Bacteria along Environmental Gradients in Northern Lakes

    PubMed Central

    Fauteux, Lisa; Cottrell, Matthew T.; Kirchman, David L.; Borrego, Carles M.; Garcia-Chaves, Maria Carolina; del Giorgio, Paul A.

    2015-01-01

    There is now evidence that aerobic anoxygenic phototrophic (AAP) bacteria are widespread across aquatic systems, yet the factors that determine their abundance and activity are still not well understood, particularly in freshwaters. Here we describe the patterns in AAP abundance, cell size and pigment content across wide environmental gradients in 43 temperate and boreal lakes of Québec. AAP bacterial abundance varied from 1.51 to 5.49 x 105 cells mL-1, representing <1 to 37% of total bacterial abundance. AAP bacteria were present year-round, including the ice-cover period, but their abundance relative to total bacterial abundance was significantly lower in winter than in summer (2.6% and 7.7%, respectively). AAP bacterial cells were on average two-fold larger than the average bacterial cell size, thus AAP cells made a greater relative contribution to biomass than to abundance. Bacteriochlorophyll a (BChla) concentration varied widely across lakes, and was not related to AAP bacterial abundance, suggesting a large intrinsic variability in the cellular pigment content. Absolute and relative AAP bacterial abundance increased with dissolved organic carbon (DOC), whereas cell-specific BChla content was negatively related to chlorophyll a (Chla). As a result, both the contribution of AAP bacteria to total prokaryotic abundance, and the cell-specific BChla pigment content were positively correlated with the DOC:Chla ratio, both peaking in highly colored, low-chlorophyll lakes. Our results suggest that photoheterotrophy might represent a significant ecological advantage in highly colored, low-chlorophyll lakes, where DOC pool is chemically and structurally more complex. PMID:25927833

  5. Patterns in Abundance, Cell Size and Pigment Content of Aerobic Anoxygenic Phototrophic Bacteria along Environmental Gradients in Northern Lakes.

    PubMed

    Fauteux, Lisa; Cottrell, Matthew T; Kirchman, David L; Borrego, Carles M; Garcia-Chaves, Maria Carolina; Del Giorgio, Paul A

    2015-01-01

    There is now evidence that aerobic anoxygenic phototrophic (AAP) bacteria are widespread across aquatic systems, yet the factors that determine their abundance and activity are still not well understood, particularly in freshwaters. Here we describe the patterns in AAP abundance, cell size and pigment content across wide environmental gradients in 43 temperate and boreal lakes of Québec. AAP bacterial abundance varied from 1.51 to 5.49 x 105 cells mL-1, representing <1 to 37% of total bacterial abundance. AAP bacteria were present year-round, including the ice-cover period, but their abundance relative to total bacterial abundance was significantly lower in winter than in summer (2.6% and 7.7%, respectively). AAP bacterial cells were on average two-fold larger than the average bacterial cell size, thus AAP cells made a greater relative contribution to biomass than to abundance. Bacteriochlorophyll a (BChla) concentration varied widely across lakes, and was not related to AAP bacterial abundance, suggesting a large intrinsic variability in the cellular pigment content. Absolute and relative AAP bacterial abundance increased with dissolved organic carbon (DOC), whereas cell-specific BChla content was negatively related to chlorophyll a (Chla). As a result, both the contribution of AAP bacteria to total prokaryotic abundance, and the cell-specific BChla pigment content were positively correlated with the DOC:Chla ratio, both peaking in highly colored, low-chlorophyll lakes. Our results suggest that photoheterotrophy might represent a significant ecological advantage in highly colored, low-chlorophyll lakes, where DOC pool is chemically and structurally more complex.

  6. Effect of Fertilizer-P application on the relative abundance of nitrogen cycle genes in a phosphorus limited paddy soil from subtropical region

    NASA Astrophysics Data System (ADS)

    Ge, Tida; Wei, Xiaomeng; Wu, Jinshui

    2017-04-01

    The addition of phosphorus to P-limited soils has been shown to cause a marked increase in the loss of gaseous N. The reasons for this remain unclear but linked nutrient cycling in the rhizosphere (C:N:P) leading to enhanced nitrification and denitrification have been proposed. We investigated the impact of adding P to P-limited soils on the dynamics of soil N-cycle functional genes. Rice seedlings were planted in P poor soils and incubated under different water conditions with or without P application. The abundance of ammonia-oxidizing bacteria and archaea in the rhizosphere and bulk soil were quantified by Real Time PCR (qPCR) using amoA gene abundance. Results showed that P addition resulted in a decrease in soil NH4+ content and a reduction in the the abundance of ammonia-oxidizing bacteria (AOB). There was little measurable effect on ammonia-oxidizing archaea (AOA). As expected from the marked increase in gaseous N loss, the relative abundances of the four functional genes (narG nirK, nirS, nosZ) increased following P application. This is thought to be a consequence of reducing the impact of P limitation on denitrifying bacteria in the bulk soil. The experimental design used allowed us to deteremine whether the gene responses to P addition in the rhizosphere (where the molar ratios of C:N:P were expected to differ) were different from those of the bulk soil. This 'rhizosphere effect' was weakened for ammonia oxidizing functional genes and enhanced for denitrifying funcational genes by P application, resulted in a greater abundance of AOB (amoA gene) and lower amounts of nirK, nirS and nosZ in rhizosphere soil. The work reported here shows the impact of available P in regulating gaseous N loss from soil and demonstrates the importance of stoichiometry and balanced nutrient availability on the fertilization and management of agricultural soils.

  7. THE CURIOUS CASE OF ELEMENTAL ABUNDANCE DIFFERENCES IN THE DUAL HOT JUPITER HOSTS WASP-94A AND B

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Teske, Johanna K.; Khanal, Sandhya; Ramírez, Ivan, E-mail: jteske@carnegiescience.edu

    Binary stars provide an ideal laboratory for investigating the potential effects of planet formation on stellar composition. Assuming that the stars formed in the same environment/from the same material, any compositional anomalies between binary components might indicate differences in how material was sequestered in planets, or accreted by the star in the process of planet formation. We present here a study of the elemental abundance differences between WASP-94A and B, a pair of stars that each host a hot Jupiter exoplanet. The two stars are very similar in spectral type (F8 and F9), and their ∼2700 au separation suggests that their protoplanetarymore » disks were likely not influenced by stellar interactions, but WASP-94Ab’s orbit—misaligned with the host star spin axis and likely retrograde—points toward a dynamically active formation mechanism, perhaps different from that of WASP-94Bb, which is not misaligned and has a nearly circular orbit. Based on our high-quality spectra and strictly relative abundance analysis, we detect a depletion of volatiles (∼−0.02 dex, on average) and enhancement of refractories (∼0.01 dex) in WASP-94A relative to B (standard errors are ∼0.005 dex). This is different from every other published case of binary host star abundances, in which either no significant abundance differences are reported or there is some degree of enhancement in all elements, including volatiles. Several scenarios that may explain the abundance trend are discussed, but none can be definitively accepted or rejected. Additional high-contrast imaging observations to search for companions that may be dynamically affecting the system, as well as a larger sample of binary host star studies, are needed to better understand the curious abundance trends we observe in WASP-94A and B.« less

  8. Primordial helium abundance determination using sulphur as metallicity tracer

    NASA Astrophysics Data System (ADS)

    Fernández, Vital; Terlevich, Elena; Díaz, Angeles I.; Terlevich, Roberto; Rosales-Ortega, F. F.

    2018-05-01

    The primordial helium abundance YP is calculated using sulphur as metallicity tracer in the classical methodology (with YP as an extrapolation of Y to zero metals). The calculated value, YP, S = 0.244 ± 0.006, is in good agreement with the estimate from the Planck experiment, as well as, determinations in the literature using oxygen as the metallicity tracer. The chemical analysis includes the sustraction of the nebular continuum and of the stellar continuum computed from simple stellar population synthesis grids. The S+2 content is measured from the near infrared [SIII]λλ9069Å, 9532Å lines, while an ICF(S3 +) is proposed based on the Ar3 +/Ar2 + fraction. Finally, we apply a multivariable linear regression using simultaneously oxygen, nitrogen and sulphur abundances for the same sample to determine the primordial helium abundance resulting in YP - O, N, S = 0.245 ± 0.007.

  9. Abundance measurements in stellar environments

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Leone, F.

    Most of what we know about stars, and systems of stars, is derived from the analysis of their electromagnetic radiation. This lesson is an attempt to describe to Physicists, without any Astrophysical background, the framework to understand the present status of abundance determination in stellar environments and its limit. These notes are dedicated to the recently passed, November 21, 2013, Prof. Dimitri Mihalas who spent his life confuting the 19th century positivist philosopher Auguste Comte who stated that we shall not at all be able to determine the chemical composition of stars.

  10. Mutation abundance affects the therapeutic efficacy of EGFR-TKI in patients with advanced lung adenocarcinoma: A retrospective analysis.

    PubMed

    Wang, Huijuan; Zhang, Mina; Tang, Wanyu; Ma, Jie; Wei, Bing; Niu, Yuanyuan; Zhang, Guowei; Li, Peng; Yan, Xiangtao; Ma, Zhiyong

    2018-03-22

    To investigate the influence of mutation abundance and sites of epidermal growth factor receptor (EGFR) on therapeutic efficacies of EGFR-tyrosine kinase inhibitor (EGFR-TKIs) treatments of patients with advanced non-small cell lung carcinoma (NSCLC). EGFR mutational sites and mutation abundance were analyzed by amplification refractory mutation system (ARMS) in paraffin-embedded tissue sections taken from primary or metastatic tumors of 194 NSCLC patients. The median progression-free survival (PFS) time of the enrolled patients was 9.3 months (95% CI, 8.2-10.8 months). The PFS was significantly different with EGFR gene mutation abundance after EGFR-TKI therapy (P = 0.014). The median PFS was significantly longer when the cut-off value of EGFR mutation abundance of exon 19 or exon 21, and solely exon 19 was > 26.7% and 61.8%, respectively. For patients who received EGFR-TKI as first-line treatment, the median PFS was significantly longer in the high mutation abundance group than in the low mutation abundance group (12.7 vs 8.7 months, P = 0.002). The PFS benefits were greater in patients with a higher abundance of exon 19 deletion mutations in the EGFR gene after EGFR-TKI treatment and first line EGFR-TKI treatment led to improved PFS in high mutation abundance patients.

  11. Improvement of DGGE analysis by modifications of PCR protocols for analysis of microbial community members with low abundance.

    PubMed

    Wang, Yong-Feng; Zhang, Fang-Qiu; Gu, Ji-Dong

    2014-06-01

    Denaturing gradient gel electrophoresis (DGGE) is a powerful technique to reveal the community structures and composition of microorganisms in complex natural environments and samples. However, positive and reproducible polymerase chain reaction (PCR) products, which are difficult to acquire for some specific samples due to low abundance of the target microorganisms, significantly impair the effective applications of DGGE. Thus, nested PCR is often introduced to generate positive PCR products from the complex samples, but one problem is also introduced: The total number of thermocycling in nested PCR is usually unacceptably high, which results in skewed community structures by generation of random or mismatched PCR products on the DGGE gel, and this was demonstrated in this study. Furthermore, nested PCR could not resolve the uneven representative issue with PCR products of complex samples with unequal richness of microbial population. In order to solve the two problems in nested PCR, the general protocol was modified and improved in this study. Firstly, a general PCR procedure was used to amplify the target genes with the PCR primers without any guanine cytosine (GC) clamp, and then, the resultant PCR products were purified and diluted to 0.01 μg ml(-1). Subsequently, the diluted PCR products were utilized as templates to amplify again with the same PCR primers with the GC clamp for 17 cycles, and the products were finally subjected to DGGE analysis. We demonstrated that this is a much more reliable approach to obtain a high quality DGGE profile with high reproducibility. Thus, we recommend the adoption of this improved protocol in analyzing microorganisms of low abundance in complex samples when applying the DGGE fingerprinting technique to avoid biased results.

  12. Abundance and size changes in the calcareous nannofossil Schizosphaerella - relation to sea-level and palaeoenvironmental change across the Sinemurian to earliest Toarcian of the Paris Basin

    NASA Astrophysics Data System (ADS)

    Peti, Leonie; Thibault, Nicolas

    2017-04-01

    The nannolith Schizosphaerella spp. was predominant in Early Jurassic calcareous nannofossil assemblages. Previous studies have shown a significant drop in abundance and mean size of Schizosphaerella during the early Toarcian Oceanic Anoxic Event which has been interpreted by some authors either as a calcification crisis due to increased pCO2, or as a response to increased nutrient availability, and/or greenhouse warming. Abundance and size changes in Schizosphaerella have here been thoroughly investigated throughout the upper Sinemurian to lowermost Toarcian (Early Jurassic) of the Sancerre-Couy core (Paris Basin) based on 116 samples. Our results show a stepwise rise in abundance of Schizosphaerella in the lower part of the investigated section and a rise in abundance of coccoliths during the major transgression of the Sinemurian, confirming that Schizosphaerella was better adapted to proximal areas than coccoliths. Mixture analysis of the biometric measurements show the existence of three populations of Schizosphaerella, interpreted as different morphotypes with different ecological affinities. Proximal, cool environmental conditions of the upper Sinemurian are associated with a dominance of the large population of Schizosphaerella. A dominance of the medium population, corresponds to cool surface waters and more distal conditions. Warm episodes are systematically linked to a dominance of the small population. Therefore we propose that the size response of Schizosphaerella throughout the Early Jurassic was rather a change in abundance of different ecophenotypes or (sub-) species of Schizosphaerella, with distinct affinities to temperature and proximal/distal environmental conditions.

  13. Variations in abundance, diversity and community composition of airborne fungi in swine houses across seasons

    PubMed Central

    Kumari, Priyanka; Woo, Cheolwoon; Yamamoto, Naomichi; Choi, Hong-Lim

    2016-01-01

    We examined the abundance, diversity and community composition of airborne fungi in swine houses during winter and summer seasons by using quantitative PCR and Illumina HiSeq sequencing of ITS1 region. The abundance of airborne fungi varied significantly only between seasons, while fungal diversity varied significantly both within and between seasons, with both abundance and diversity peaked in winter. The fungal OTU composition was largely structured by the swine house unit and season as well as by their interactions. Of the measured microclimate variables, relative humidity, particulate matters (PMs), ammonia, and stocking density were significantly correlated with fungal OTU composition. The variation in beta diversity was higher within swine houses during summer, which indicates that the airborne fungal community composition was more heterogeneous in summer compared to winter. We also identified several potential allergen/pathogen related fungal genera in swine houses. The total relative abundance of potential allergen/pathogen related fungal genera varied between swine houses in both seasons, and showed positive correlation with PM2.5. Overall, our findings show that the abundance, diversity and composition of airborne fungi are highly variable in swine houses and to a large extent structured by indoor microclimate variables of swine houses. PMID:27892507

  14. Variations in abundance, diversity and community composition of airborne fungi in swine houses across seasons

    NASA Astrophysics Data System (ADS)

    Kumari, Priyanka; Woo, Cheolwoon; Yamamoto, Naomichi; Choi, Hong-Lim

    2016-11-01

    We examined the abundance, diversity and community composition of airborne fungi in swine houses during winter and summer seasons by using quantitative PCR and Illumina HiSeq sequencing of ITS1 region. The abundance of airborne fungi varied significantly only between seasons, while fungal diversity varied significantly both within and between seasons, with both abundance and diversity peaked in winter. The fungal OTU composition was largely structured by the swine house unit and season as well as by their interactions. Of the measured microclimate variables, relative humidity, particulate matters (PMs), ammonia, and stocking density were significantly correlated with fungal OTU composition. The variation in beta diversity was higher within swine houses during summer, which indicates that the airborne fungal community composition was more heterogeneous in summer compared to winter. We also identified several potential allergen/pathogen related fungal genera in swine houses. The total relative abundance of potential allergen/pathogen related fungal genera varied between swine houses in both seasons, and showed positive correlation with PM2.5. Overall, our findings show that the abundance, diversity and composition of airborne fungi are highly variable in swine houses and to a large extent structured by indoor microclimate variables of swine houses.

  15. Preliminary CALET Ultra Heavy Cosmic Ray Abundance Measurements

    NASA Astrophysics Data System (ADS)

    Rauch, Brian; CALET Collaboration

    2017-01-01

    The CALorimetric Electron Telescope (CALET) on the International Space Station (ISS) was launched August 19, 2015 and has been returning excellent data for over a year. The main calorimeter (CAL) on CALET measures the fluxes of high-energy electrons, nuclei and gamma rays. In addition to measuring the energy spectra of the more abundant cosmic-ray nuclei through 26Fe, CAL has the dynamic range to measure the abundances of the ultra-heavy (UH) cosmic-ray nuclei through 40Zr. In an anticipated 5 year mission on the ISS CALET will collect a UH data set with statistics comparable to that achieved with the first flight of the SuperTIGER balloon-borne instrument. The CALET space-based measurement has the advantage of not requiring corrections for atmospheric losses, and unlike other UH measurements the abundances of all nuclei from 1H through 40Zr are observed with the same instrument. We present preliminary CALET UH analysis results from the first year of operation. This research was supported by NASA at Washington University under Grant Number NNX11AE02G.

  16. Interactive effects of wildfire, forest management, and isolation on amphibian and parasite abundance

    USGS Publications Warehouse

    Hossack, Blake R.; Corn, P. Stephen; Winsor H. Lowe,; R. Kenneth Honeycutt,; Sean A. Parks,

    2013-01-01

    Projected increases in wildfire and other climate-driven disturbances will affect populations and communities worldwide, including host–parasite relationships. Research in temperate forests has shown that wildfire can negatively affect amphibians, but this research has occurred primarily outside of managed landscapes where interactions with human disturbances could result in additive or synergistic effects. Furthermore, parasites represent a large component of biodiversity and can affect host fitness and population dynamics, yet they are rarely included in studies of how vertebrate hosts respond to disturbance. To determine how wildfire affects amphibians and their parasites, and whether effects differ between protected and managed landscapes, we compared abundance of two amphibians and two nematodes relative to wildfire extent and severity around wetlands in neighboring protected and managed forests (Montana, USA). Population sizes of adult, male long-toed salamanders (Ambystoma macrodactylum) decreased with increased burn severity, with stronger negative effects on isolated populations and in managed forests. In contrast, breeding population sizes of Columbia spotted frogs (Rana luteiventris) increased with burn extent in both protected and managed protected forests. Path analysis showed that the effects of wildfire on the two species of nematodes were consistent with differences in their life history and transmission strategies and the responses of their hosts. Burn severity indirectly reduced abundance of soil-transmitted Cosmocercoides variabilis through reductions in salamander abundance. Burn severity also directly reduced C. variabilis abundance, possibly though changes in soil conditions. For the aquatically transmitted nematode Gyrinicola batrachiensis, the positive effect of burn extent on density of Columbia spotted frog larvae indirectly increased parasite abundance. Our results show that effects of wildfire on amphibians depend upon burn extent

  17. Comparative composition, diversity, and abundance of oligosaccharides in early lactation milk from commercial dairy and beef cows.

    PubMed

    Sischo, William M; Short, Diana M; Geissler, Mareen; Bunyatratchata, Apichaya; Barile, Daniela

    2017-05-01

    Prebiotics are nondigestible dietary ingredients, usually oligosaccharides (OS), that provide a health benefit to the host by directly modulating the gut microbiota. Although there is some information describing OS content in dairy-source milk, no information is available to describe the OS content of beef-source milk. Given the different trait emphasis between dairy and beef for milk production and calf survivability, it is plausible that OS composition, diversity, and abundance differ between production types. The goal of this study was to compare OS in milk from commercial dairy and beef cows in early lactation. Early-lactation multiparous cows (5-12 d in milk) from 5 commercial Holstein dairy herds and 5 Angus or Angus hybrid beef herds were sampled once. Milk was obtained from each enrolled cow and frozen on the farm. Subsequently, each milk sample was assessed for total solids, pH, and OS content and relative abundance. Oligosaccharide diversity and abundance within and between samples was transformed through principal component analysis to reduce data complexity. Factors from principal component analysis were used to create similarity clusters, which were subsequently used in a multivariate logistic regression. In total, 30 OS were identified in early-lactation cow milk, including 21 distinct OS and 9 isomers with unique retention times. The majority of OS detected in the milk samples were present in all individual samples regardless of production type. Two clusters described distribution patterns of OS for the study sample; when median OS abundance was compared between the 2 clusters, we found that overall OS relative abundance was consistently greater in the cluster dominated by beef cows. For several of the structures, including those with known prebiotic effect, the difference in abundance was 2- to 4-fold greater in the beef-dominated cluster. Assuming that beef OS content in milk is the gold standard for cattle, it is likely that preweaning dairy

  18. Modeling avian abundance from replicated counts using binomial mixture models

    USGS Publications Warehouse

    Kery, Marc; Royle, J. Andrew; Schmid, Hans

    2005-01-01

    Abundance estimation in ecology is usually accomplished by capture–recapture, removal, or distance sampling methods. These may be hard to implement at large spatial scales. In contrast, binomial mixture models enable abundance estimation without individual identification, based simply on temporally and spatially replicated counts. Here, we evaluate mixture models using data from the national breeding bird monitoring program in Switzerland, where some 250 1-km2 quadrats are surveyed using the territory mapping method three times during each breeding season. We chose eight species with contrasting distribution (wide–narrow), abundance (high–low), and detectability (easy–difficult). Abundance was modeled as a random effect with a Poisson or negative binomial distribution, with mean affected by forest cover, elevation, and route length. Detectability was a logit-linear function of survey date, survey date-by-elevation, and sampling effort (time per transect unit). Resulting covariate effects and parameter estimates were consistent with expectations. Detectability per territory (for three surveys) ranged from 0.66 to 0.94 (mean 0.84) for easy species, and from 0.16 to 0.83 (mean 0.53) for difficult species, depended on survey effort for two easy and all four difficult species, and changed seasonally for three easy and three difficult species. Abundance was positively related to route length in three high-abundance and one low-abundance (one easy and three difficult) species, and increased with forest cover in five forest species, decreased for two nonforest species, and was unaffected for a generalist species. Abundance estimates under the most parsimonious mixture models were between 1.1 and 8.9 (median 1.8) times greater than estimates based on territory mapping; hence, three surveys were insufficient to detect all territories for each species. We conclude that binomial mixture models are an important new approach for estimating abundance corrected for

  19. Galactic Abundance Patterns via Peimbert Types I & II Planetary Nebulae

    NASA Astrophysics Data System (ADS)

    Milingo, J. B.; Barnes, K. L.; Kwitter, K. B.; Souza, S. P.; Henry, R. B. C.; Skinner, J. N.

    2005-12-01

    Planetary Nebulae (PNe) are well known fonts of information about both stellar evolution and galactic chemical evolution. Abundance patterns in PNe are used to note signatures and constraints of nuclear processing, and as tracers of the distribution of metals throughout galaxies. In this poster abundance gradients and heavy element ratios are presented based upon newly acquired spectrophotometry of a sample of Galactic Peimbert Type I PNe. This new data set is extracted from spectra that extend from λ 3600 - 9600Å allowing the use of [S III] features at λ 9069 and 9532Å. Since a significant portion of S in PNe resides in S+2 and higher ionization stages, including these features improves the extrapolation from observed ion abundances to total element abundance. An alternate metallicity tracer, Sulfur is precluded from enhancement and depletion across the range of PNe progenitor masses. Its stability in intermediate mass stars makes it a useful tool to probe the natal conditions as well as the evolution of PNe progenitors. This is a continuation of our Type II PNe work, the impetus being to compile a relatively large set of line strengths and abundances with internally consistent observation, reduction, calibration, and abundance determination, minimizing systematic affects that come from compiling various data sets. This research is supported by the AAS Small Research Grants program, the Franklin & Marshall Committee on Grants, and NSF grant AST-0307118.

  20. Principal climatic and edaphic determinants of Culicoides biting midge abundance during the 2007-2008 bluetongue epidemic in the Netherlands, based on OVI light trap data.

    PubMed

    Scolamacchia, F; VAN DEN Broek, J; Meiswinkel, R; Heesterbeek, J A P; Elbers, A R W

    2014-06-01

    Palaearctic Culicoides midges (Diptera: Ceratopogonidae) represent a vital link in the northward advance of certain arboviral pathogens of livestock such as that caused by bluetongue virus. The effects of relevant ecological factors on weekly Culicoides vector abundances during the bluetongue virus serotype 8 epidemics in the Netherlands in 2007 and 2008 were quantified within a hurdle modelling framework. The relative role of meteorological parameters showed a broadly consistent association across species, with larger catches linked to temperature-related variables and lower wind speed. Moreover, vector abundance was found to be influenced by edaphic factors, likely related to species-specific breeding habitat preferences that differed markedly amongst some species. This is the first study on Culicoides vector species in the Netherlands identified during an entomological surveillance programme, in which an attempt is made to pinpoint the factors that influence midge abundance levels. In addition to providing key inputs into risk-mitigating tools for midge-borne pathogens and disease transmission models, the adoption of methods that explicitly address certain features of abundance datasets (frequent zero-count observations and over-dispersion) helped enhance the robustness of the ecological analysis. © 2013 The Royal Entomological Society.

  1. A COMPREHENSIVE ANALYSIS OF UNCERTAINTIES AFFECTING THE STELLAR MASS-HALO MASS RELATION FOR 0 < z < 4

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Behroozi, Peter S.; Wechsler, Risa H.; Conroy, Charlie

    2010-07-01

    We conduct a comprehensive analysis of the relationship between central galaxies and their host dark matter halos, as characterized by the stellar mass-halo mass (SM-HM) relation, with rigorous consideration of uncertainties. Our analysis focuses on results from the abundance matching technique, which assumes that every dark matter halo or subhalo above a specific mass threshold hosts one galaxy. We provide a robust estimate of the SM-HM relation for 0 < z < 1 and discuss the quantitative effects of uncertainties in observed galaxy stellar mass functions (including stellar mass estimates and counting uncertainties), halo mass functions (including cosmology and uncertaintiesmore » from substructure), and the abundance matching technique used to link galaxies to halos (including scatter in this connection). Our analysis results in a robust estimate of the SM-HM relation and its evolution from z = 0 to z = 4. The shape and the evolution are well constrained for z < 1. The largest uncertainties at these redshifts are due to stellar mass estimates (0.25 dex uncertainty in normalization); however, failure to account for scatter in stellar masses at fixed halo mass can lead to errors of similar magnitude in the SM-HM relation for central galaxies in massive halos. We also investigate the SM-HM relation to z = 4, although the shape of the relation at higher redshifts remains fairly unconstrained when uncertainties are taken into account. We find that the integrated star formation at a given halo mass peaks at 10%-20% of available baryons for all redshifts from 0 to 4. This peak occurs at a halo mass of 7 x 10{sup 11} M{sub sun} at z = 0 and this mass increases by a factor of 5 to z = 4. At lower and higher masses, star formation is substantially less efficient, with stellar mass scaling as M{sub *} {approx} M {sup 2.3}{sub h} at low masses and M{sub *} {approx} M {sup 0.29}{sub h} at high masses. The typical stellar mass for halos with mass less than 10{sup 12} M{sub sun

  2. Generalized estimators of avian abundance from count survey data

    USGS Publications Warehouse

    Royle, J. Andrew

    2004-01-01

    I consider modeling avian abundance from spatially referenced bird count data collected according to common protocols such as capture?recapture, multiple observer, removal sampling and simple point counts. Small sample sizes and large numbers of parameters have motivated many analyses that disregard the spatial indexing of the data, and thus do not provide an adequate treatment of spatial structure. I describe a general framework for modeling spatially replicated data that regards local abundance as a random process, motivated by the view that the set of spatially referenced local populations (at the sample locations) constitute a metapopulation. Under this view, attention can be focused on developing a model for the variation in local abundance independent of the sampling protocol being considered. The metapopulation model structure, when combined with the data generating model, define a simple hierarchical model that can be analyzed using conventional methods. The proposed modeling framework is completely general in the sense that broad classes of metapopulation models may be considered, site level covariates on detection and abundance may be considered, and estimates of abundance and related quantities may be obtained for sample locations, groups of locations, unsampled locations. Two brief examples are given, the first involving simple point counts, and the second based on temporary removal counts. Extension of these models to open systems is briefly discussed.

  3. Effect of water irrigation volume on Capsicum frutescens growth and plankton abundance in aquaponics system

    NASA Astrophysics Data System (ADS)

    Andriani, Y.; Dhahiyat, Y.; Zahidah; Subhan, U.; Iskandar; Zidni, I.; Mawardiani, T.

    2018-03-01

    This study aimed to understand Capsicum frutescens growth and plankton abundance in aquaponics culture. A Completely Randomized Design (CRD) with six treatments in triplicates comprising of treatment A (positive control using organic liquid fertilizer), B (negative control without fertilizer), C (drip irrigation aquaponics with a water debit of 100 ml/day/plant), D (drip irrigation aquaponics with a water debit of 150 ml/day/plant), E (drip irrigation with a water debit of 200 ml/day/plant), and F (drip irrigation aquaponics with a water debit of 250 ml/day/plant) was applied. The water used in treatments C, D, E, and F contained comet fish feces as fertilizer. C. frutescens growth and plankton abundance were observed. Analysis was conducted using analysis of variance for plant productivity and descriptive analysis for plankton abundance and water quality. The results of this study showed that the highest plant growth was seen in plants receiving F treatment with 50 ml/day drip irrigation. However, no significant difference was found when compared to the positive control with organic artificial fertilizer. Eleven types of phytoplankton and six types of zooplankton were found, with Stanieria sp. as the most abundant phytoplankton and Brachionus sp. and Epistylis sp. as the most abundant zooplanktons.

  4. HIGH PRECISION ABUNDANCES OF THE OLD SOLAR TWIN HIP 102152: INSIGHTS ON Li DEPLETION FROM THE OLDEST SUN

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Monroe, TalaWanda R.; Melendez, Jorge; Tucci Maia, Marcelo

    2013-09-10

    We present the first detailed chemical abundance analysis of the old 8.2 Gyr solar twin, HIP 102152. We derive differential abundances of 21 elements relative to the Sun with precisions as high as 0.004 dex ({approx}<1%), using ultra high-resolution (R = 110,000), high S/N UVES spectra obtained on the 8.2 m Very Large Telescope. Our determined metallicity of HIP 102152 is [Fe/H] = -0.013 {+-} 0.004. The atmospheric parameters of the star were determined to be 54 K cooler than the Sun, 0.09 dex lower in surface gravity, and a microturbulence identical to our derived solar value. Elemental abundance ratiosmore » examined versus dust condensation temperature reveal a solar abundance pattern for this star, in contrast to most solar twins. The abundance pattern of HIP 102152 appears to be the most similar to solar of any known solar twin. Abundances of the younger, 2.9 Gyr solar twin, 18 Sco, were also determined from UVES spectra to serve as a comparison for HIP 102152. The solar chemical pattern of HIP 102152 makes it a potential candidate to host terrestrial planets, which is reinforced by the lack of giant planets in its terrestrial planet region. The following non-local thermodynamic equilibrium Li abundances were obtained for HIP 102152, 18 Sco, and the Sun: log {epsilon} (Li) = 0.48 {+-} 0.07, 1.62 {+-} 0.02, and 1.07 {+-} 0.02, respectively. The Li abundance of HIP 102152 is the lowest reported to date for a solar twin, and allows us to consider an emerging, tightly constrained Li-age trend for solar twin stars.« less

  5. The solar photospheric abundance of hafnium and thorium. Results from CO5BOLD 3D hydrodynamic model atmospheres

    NASA Astrophysics Data System (ADS)

    Caffau, E.; Sbordone, L.; Ludwig, H.-G.; Bonifacio, P.; Steffen, M.; Behara, N. T.

    2008-05-01

    Context: The stable element hafnium (Hf) and the radioactive element thorium (Th) were recently suggested as a suitable pair for radioactive dating of stars. The applicability of this elemental pair needs to be established for stellar spectroscopy. Aims: We aim at a spectroscopic determination of the abundance of Hf and Th in the solar photosphere based on a CO5BOLD 3D hydrodynamical model atmosphere. We put this into a wider context by investigating 3D abundance corrections for a set of G- and F-type dwarfs. Methods: High-resolution, high signal-to-noise solar spectra were compared to line synthesis calculations performed on a solar CO5BOLD model. For the other atmospheres, we compared synthetic spectra of CO5BOLD 3D and associated 1D models. Results: For Hf we find a photospheric abundance A(Hf) = 0.87 ± 0.04, in good agreement with a previous analysis, based on 1D model atmospheres. The weak Th II 401.9 nm line constitutes the only Th abundance indicator available in the solar spectrum. It lies in the red wing of a Ni-Fe blend exhibiting a non-negligible convective asymmetry. Accounting for the asymmetry-related additional absorption, we obtain A(Th) = 0.08 ± 0.03, consistent with the meteoritic abundance, and about 0.1 dex lower than obtained in previous photospheric abundance determinations. Conclusions: Only for the second time, to our knowledge, has a non-negligible effect of convective line asymmetries on an abundance derivation been highlighted. Three-dimensional hydrodynamical simulations should be employed to measure Th abundances in dwarfs if similar blending is present, as in the solar case. In contrast, 3D effects on Hf abundances are small in G- to mid F-type dwarfs and sub-giants, and 1D model atmospheres can be conveniently used.

  6. Heavy-Element Abundances in Solar Energetic Particle Events

    NASA Technical Reports Server (NTRS)

    Reames, Donald V.

    2004-01-01

    We survey the relative abundances of elements with 1 less than or = Z less than or = 82 in solar energetic particle (SEP) events observed at 2 - 10 MeV amu" during nearly 9 years aboard the Wind spacecraft, with special emphasis on enhanced abundances of elements with 2Z greater than or = 34. Abundances of Fe/O again show a bimodal distribution with distinct contributions from impulsive and gradual SEP events as seen in earlier solar cycles. Periods with greatly enhanced abundances of (50 less than or = Z less than or = 56)/O, like those with enhanced He-3/He-4, fall prominently in the Fe-rich population of the impulsive SEP events. In a sample of the 39 largest impulsive events, 25 have measurable enhancements in (50 less than or = Z less than or = 56)/O and (76 less than or = Z less than or = 82)/O, relative to coronal values, ranging from approx. 100 to 10,000. By contrast, in a sample of 45 large gradual events the corresponding enhancements vary from approx. 0.2 to 20. However, the magnitude of the heavy-element enhancements in impulsive events is less striking than their strong correlation with the Fe spectral index and flare size, with the largest enhancements occurring in flares with the steepest Fe spectra, the smallest Fe fluence, and the lowest X-ray intensity, as reported here for the first time Thus it seem that small events with low energy input can produce only steep spectra of the dominant species but accelerate rare heavy elements with great efficiency, probably by selective absorption of resonant waves in the flare plasma. With increased energy input, enhancements diminish, as heavy ions are depleted, and spectra of the dominant species harden.

  7. Heavy-Element Abundances in Solar Energetic Particle Events

    NASA Technical Reports Server (NTRS)

    Reames, D. V.; Ng, C. K.

    2004-01-01

    We survey the relative abundances of elements with 1 < or equal to Z < or equal to 82 in solar energetic particle (SEP) events observed at 2-10 MeV/amu during nearly 9 years aboard the Wind spacecraft, with special emphasis on enhanced abundances of elements with Z > or equal to 34. Abundances of Fe/O again show a bimodal distribution with distinct contributions from impulsive and gradual SEP events as seen in earlier solar cycles. Periods with greatly enhanced abundances of (50 < or equal to Z < or equal to 56)/O, like those with enhanced (3)He/(4)He, fall prominently in the Fe-rich population of the impulsive SEP events. In a sample of the 39 largest impulsive events, 25 have measurable enhancements in (50 < or equal to z < or equal to 56)/O and (76 < or equal to Z < or equal to 82)/O, relative to coronal values, ranging from approx. 100 to 10,000. By contrast, in a sample of 45 large gradual events the corresponding enhancements vary from approx. 0.2 to 20. However, the magnitude of the heavy-element enhancements in impulsive events is less striking than their strong correlation with the Fe spectral index and flare size, with the largest enhancements occurring in flares with the steepest Fe spectra, the smallest Fe fluence, and the lowest X-ray intensity, as reported here for the first time. Thus it seems that small events with low energy input can produce only steep spectra of the dominant species but accelerate rare heavy elements with great efficiency, probably by selective absorption of resonant waves in the flare plasma. With increased energy input, enhancements diminish, as heavy ions are depleted, and spectra of the dominant species harden.

  8. Cross-realm assessment of climate change impacts on species' abundance trends.

    PubMed

    Bowler, Diana E; Hof, Christian; Haase, Peter; Kröncke, Ingrid; Schweiger, Oliver; Adrian, Rita; Baert, Léon; Bauer, Hans-Günther; Blick, Theo; Brooker, Rob W; Dekoninck, Wouter; Domisch, Sami; Eckmann, Reiner; Hendrickx, Frederik; Hickler, Thomas; Klotz, Stefan; Kraberg, Alexandra; Kühn, Ingolf; Matesanz, Silvia; Meschede, Angelika; Neumann, Hermann; O'Hara, Robert; Russell, David J; Sell, Anne F; Sonnewald, Moritz; Stoll, Stefan; Sundermann, Andrea; Tackenberg, Oliver; Türkay, Michael; Valladares, Fernando; van Herk, Kok; van Klink, Roel; Vermeulen, Rikjan; Voigtländer, Karin; Wagner, Rüdiger; Welk, Erik; Wiemers, Martin; Wiltshire, Karen H; Böhning-Gaese, Katrin

    2017-02-17

    Climate change, land-use change, pollution and exploitation are among the main drivers of species' population trends; however, their relative importance is much debated. We used a unique collection of over 1,000 local population time series in 22 communities across terrestrial, freshwater and marine realms within central Europe to compare the impacts of long-term temperature change and other environmental drivers from 1980 onwards. To disentangle different drivers, we related species' population trends to species- and driver-specific attributes, such as temperature and habitat preference or pollution tolerance. We found a consistent impact of temperature change on the local abundances of terrestrial species. Populations of warm-dwelling species increased more than those of cold-dwelling species. In contrast, impacts of temperature change on aquatic species' abundances were variable. Effects of temperature preference were more consistent in terrestrial communities than effects of habitat preference, suggesting that the impacts of temperature change have become widespread for recent changes in abundance within many terrestrial communities of central Europe.

  9. Plant Trait-Species Abundance Relationships Vary with Environmental Properties in Subtropical Forests in Eastern China

    PubMed Central

    Yan, En-Rong; Yang, Xiao-Dong; Chang, Scott X.; Wang, Xi-Hua

    2013-01-01

    Understanding how plant trait-species abundance relationships change with a range of single and multivariate environmental properties is crucial for explaining species abundance and rarity. In this study, the abundance of 94 woody plant species was examined and related to 15 plant leaf and wood traits at both local and landscape scales involving 31 plots in subtropical forests in eastern China. Further, plant trait-species abundance relationships were related to a range of single and multivariate (PCA axes) environmental properties such as air humidity, soil moisture content, soil temperature, soil pH, and soil organic matter, nitrogen (N) and phosphorus (P) contents. At the landscape scale, plant maximum height, and twig and stem wood densities were positively correlated, whereas mean leaf area (MLA), leaf N concentration (LN), and total leaf area per twig size (TLA) were negatively correlated with species abundance. At the plot scale, plant maximum height, leaf and twig dry matter contents, twig and stem wood densities were positively correlated, but MLA, specific leaf area, LN, leaf P concentration and TLA were negatively correlated with species abundance. Plant trait-species abundance relationships shifted over the range of seven single environmental properties and along multivariate environmental axes in a similar way. In conclusion, strong relationships between plant traits and species abundance existed among and within communities. Significant shifts in plant trait-species abundance relationships in a range of environmental properties suggest strong environmental filtering processes that influence species abundance and rarity in the studied subtropical forests. PMID:23560114

  10. An integrated analysis based on transcriptome and proteome reveals deastringency-related genes in CPCNA persimmon

    PubMed Central

    Chen, Wenxing; Xiong, Yalou; Xu, Liqing; Zhang, Qinglin; Luo, Zhengrong

    2017-01-01

    Persimmon fruits accumulate a large amount of proanthocyanidins (PAs) during development. PAs cause a dry or puckering sensation due to its astringency. Pollination constant and non-astringent (PCNA) persimmon fruits can lose astringency during fruit ripening. However, little is known about the mechanism of natural de-astringency of Chinese PCNA (CPCNA). To gain insight into the molecular events of CPCNA natural de-astringency, we used mRNA-seq and iTRAQ-based quantitative proteomic analysis to measure changes in genes and proteins expression at two key stages of natural astringency removal (i.e. 10 and 20 weeks after bloom) and water-treated (i.e. 40 °C·12 h) de-astringency fruits. Our analyses show that the three predominantly process in CPCNA de-astringency: (1) water treatment strongly up-regulates glycolysis/acetaldehyde metabolism, (2) expression of genes/proteins involved in PA biosynthetic pathway was remarkably reduced in natural and water-treated de-astringency, (3) sugar metabolism and ethylene related pathway were quite abundant in natural de-astringency. We also found ethylene-related TFs were quite abundant in natural de-astringency, followed by WRKY and NAC transcription factors. These results provide an initial understanding of the predominantly biological processes underlying the natural de-astringency and “coagulation effect” in CPCNA. PMID:28304376

  11. Environmental drivers of Ixodes ricinus abundance in forest fragments of rural European landscapes.

    PubMed

    Ehrmann, Steffen; Liira, Jaan; Gärtner, Stefanie; Hansen, Karin; Brunet, Jörg; Cousins, Sara A O; Deconchat, Marc; Decocq, Guillaume; De Frenne, Pieter; De Smedt, Pallieter; Diekmann, Martin; Gallet-Moron, Emilie; Kolb, Annette; Lenoir, Jonathan; Lindgren, Jessica; Naaf, Tobias; Paal, Taavi; Valdés, Alicia; Verheyen, Kris; Wulf, Monika; Scherer-Lorenzen, Michael

    2017-09-06

    The castor bean tick (Ixodes ricinus) transmits infectious diseases such as Lyme borreliosis, which constitutes an important ecosystem disservice. Despite many local studies, a comprehensive understanding of the key drivers of tick abundance at the continental scale is still lacking. We analyze a large set of environmental factors as potential drivers of I. ricinus abundance. Our multi-scale study was carried out in deciduous forest fragments dispersed within two contrasting rural landscapes of eight regions, along a macroclimatic gradient stretching from southern France to central Sweden and Estonia. We surveyed the abundance of I. ricinus, plant community composition, forest structure and soil properties and compiled data on landscape structure, macroclimate and habitat properties. We used linear mixed models to analyze patterns and derived the relative importance of the significant drivers. Many drivers had, on their own, either a moderate or small explanatory value for the abundance of I. ricinus, but combined they explained a substantial part of variation. This emphasizes the complex ecology of I. ricinus and the relevance of environmental factors for tick abundance. Macroclimate only explained a small fraction of variation, while properties of macro- and microhabitat, which buffer macroclimate, had a considerable impact on tick abundance. The amount of forest and the composition of the surrounding rural landscape were additionally important drivers of tick abundance. Functional (dispersules) and structural (density of tree and shrub layers) properties of the habitat patch played an important role. Various diversity metrics had only a small relative importance. Ontogenetic tick stages showed pronounced differences in their response. The abundance of nymphs and adults is explained by the preceding stage with a positive relationship, indicating a cumulative effect of drivers. Our findings suggest that the ecosystem disservices of tick-borne diseases, via the

  12. High-resolution mapping of elemental abundances of the lunar regolith

    NASA Astrophysics Data System (ADS)

    Wöhler, Christian; Berezhnoy, Alexey; Evans, Richard

    Many attempts have been made to derive elemental abundances of the lunar surface from mul-tispectral images (cf. e.g. [1]). The gamma ray spectrometer on board the Lunar Prospector spacecraft (LP GRS) provided the first "direct" global measurements of lunar elemental abun-dances including Fe, Th (15 km surface resolution), Ti, K, Sm (60 km), Al, O, Si, Mg, Ca, and U (150 km). In this study we rely on the elemental abundance estimation method intro-duced in [2], which is based on spectral features derived from the Clementine UVVIS+NIR data set and estimates the abundances of Ca, Al, Fe, Mg, Ti, and O by applying a second order polynomial regression model with the corresponding LP GRS abundances as "ground truth". The regarded spectral features are the continuum slope, the FWHM of the ferrous absorption trough near 1000 nm after continuum division, and the absorption wavelengths and relative absorption depths (cf. [2,3] for details). A petrographic analysis is performed based on the abundances of the key elements Al, Fe, and Mg [4]. The relative abundances of the endmem-bers mare basalt, Mg-rich rock, and ferroan anorthosite are estimated using Fe-Mg and Al-Mg diagrams, where the endmember compositions are determined based on the three-endmember plane fitted in Al-Fe-Mg space to the elemental abundances at 150 km resolution obtained with the regression model. The root-mean-square deviation from the three-endmember plane is only 0.3 wt percent. Our petrographic map shows Mg-rich rocks in the Mare Frigoris region, on the edges of large maria, in the South Pole Aitken basin, and in some cryptomaria such as the Schiller-Schickard basin. The presence of Mg-rich rocks in Mare Frigoris explains the Fe and Ti depletion discussed in [5]. Furthermore, our analysis confirms that the basalts of eastern mare Frigoris have an atypically high Al content [6]. The region south of Lichtenberg and around Seleucus and Briggs in northwestern Oceanus Procellarum is characterised by

  13. 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

    2016-02-02

    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

  14. Natural variation in stomatal abundance of Arabidopsis thaliana includes cryptic diversity for different developmental processes

    PubMed Central

    Delgado, Dolores; Alonso-Blanco, Carlos; Fenoll, Carmen; Mena, Montaña

    2011-01-01

    Background and Aims Current understanding of stomatal development in Arabidopsis thaliana is based on mutations producing aberrant, often lethal phenotypes. The aim was to discover if naturally occurring viable phenotypes would be useful for studying stomatal development in a species that enables further molecular analysis. Methods Natural variation in stomatal abundance of A. thaliana was explored in two collections comprising 62 wild accessions by surveying adaxial epidermal cell-type proportion (stomatal index) and density (stomatal and pavement cell density) traits in cotyledons and first leaves. Organ size variation was studied in a subset of accessions. For all traits, maternal effects derived from different laboratory environments were evaluated. In four selected accessions, distinct stomatal initiation processes were quantitatively analysed. Key Results and Conclusions Substantial genetic variation was found for all six stomatal abundance-related traits, which were weakly or not affected by laboratory maternal environments. Correlation analyses revealed overall relationships among all traits. Within each organ, stomatal density highly correlated with the other traits, suggesting common genetic bases. Each trait correlated between organs, supporting supra-organ control of stomatal abundance. Clustering analyses identified accessions with uncommon phenotypic patterns, suggesting differences among genetic programmes controlling the various traits. Variation was also found in organ size, which negatively correlated with cell densities in both organs and with stomatal index in the cotyledon. Relative proportions of primary and satellite lineages varied among the accessions analysed, indicating that distinct developmental components contribute to natural diversity in stomatal abundance. Accessions with similar stomatal indices showed different lineage class ratios, revealing hidden developmental phenotypes and showing that genetic determinants of primary and

  15. Big huckleberry abundance as related to environment and associated vegetation near Mount Adams, Washington.

    Treesearch

    Don Minore; Michael E. Dubrasich

    1978-01-01

    Big huckleberry abundance was correlated with associated vegetation and soil pH in a 625-square-kilometer (241-square-mile) area southwest of Mount Adams, Washington. Annual berry production appeared to be influenced by weather more than by site factors in this area. Douglas-fir site index was not correlated with either Vaccinium membranaceum...

  16. Species composition and abundance of mosquito larvae in relation with their habitat characteristics in Mazandaran Province, northern Iran.

    PubMed

    Nikookar, S H; Fazeli-Dinan, M; Azari-Hamidian, S; Mousavinasab, S N; Arabi, M; Ziapour, S P; Shojaee, J; Enayati, A

    2017-10-01

    Mosquitoes transmit a variety of diseases to humans. Their abundance and distribution are related to the characteristics of larval habitats. Mosquito larvae were collected from 120 natural and artificial habitats in 30 villages of 16 counties using standard 350 ml dippers and pipette, on a monthly basis from May-December 2014 in Mazandaran Province, northern Iran. Larval habitat characteristics were recorded separately, based on the conditions of the habitats (permanent or temporary, stagnant or running), type of habitats (natural or artificial), vegetation, exposure to sun, type of bed, water condition (clear or turbid), expanse (m), depth (cm, m) and temperature (°C) of habitats. The relationship between larval density and environmental variables was assessed by Chi-square tests. Totally, 19,840 larvae from three genera and 16 species were collected and identified. Anopheles maculipennis s.l. and Culex pipiens were the dominant species and collected with the highest density in plain areas. The highest number of larvae were collected from natural habitats (60.34%), including; river edge, marsh, pit and wetlands; with temporary and stagnant water, expanse of 0-5 m, depth of 1-25 cm, without plant, shadow-sun, muddy floor, turbid water, temperature 20-25°C and in sunny conditions. River edge and rice fields for An. maculipennis s.l and, wetlands and discarded tires for Cx. pipiens were the main larval habitats in the province. Statistical analysis revealed significant relation between occurrence of An. maculipennis s.l., Cx. pipiens, Culex torrentium, Culex mimeticus and Cs. annulata with each of the environmental variables (P < 0.001). These findings are essential in expanding our knowledge of the vectors ecology specially the type of habitat preference and will be beneficial in larval control programs.

  17. First determination of the tropospheric CO abundance in Saturn

    NASA Astrophysics Data System (ADS)

    Fouchet, Thierry; Lellouch, Emmanuel; Cavalié, Thibault; Bézard, Bruno

    2017-10-01

    In Giant Planets, CO has two potential origins: i) an external source in form of cometary impacts, infalling ring/satellite dust or/and interplanetary particles; ii) an internal origin that involves convective transport from the deep, dense, hot atmosphere where the thermodynamic equilibrium CO abundance is relatively large.In Saturn, submilimeter stratospheric CO emissions have been detected (Cavalié et al. A&A, 510, A88, 2010; Cavalié et al. Icarus, 203, 531, 2009), suggesting a cometary impact 200 years ago. In contrast, no observation was in position to confirm or rule out the presence of CO in Saturn's troposphere (Noll et al. Icarus, 89, 168, 1990).Here, we present CRIRES/ELT 5-μm observations of Saturn that definitely confirm the presence of CO in Saturn's troposphere. We will present the derived CO abundance and its implication for Saturn's tropospheric transport rate and water deep abundance.

  18. Relative and accurate measurement of protein abundance using 15N stable isotope labeling in Arabidopsis (SILIA).

    PubMed

    Guo, Guangyu; Li, Ning

    2011-07-01

    In the quantitative proteomic studies, numerous in vitro and in vivo peptide labeling strategies have been successfully applied to measure differentially regulated protein and peptide abundance. These approaches have been proven to be versatile and repeatable in biological discoveries. (15)N metabolic labeling is one of these widely adopted and economical methods. However, due to the differential incorporation rates of (15)N or (14)N, the labeling results produce imperfectly matched isotopic envelopes between the heavy and light nitrogen-labeled peptides. In the present study, we have modified the solid Arabidopsis growth medium to standardize the (15)N supply, which led to a uniform incorporation of (15)N into the whole plant protein complement. The incorporation rate (97.43±0.11%) of (15)N into (15)N-coded peptides was determined by correlating the intensities of peptide ions with the labeling efficiencies according to Gaussian distribution. The resulting actual incorporation rate (97.44%) and natural abundance of (15)N/(14)N-coded peptides are used to re-calculate the intensities of isotopic envelopes of differentially labeled peptides, respectively. A modified (15)N/(14)N stable isotope labeling strategy, SILIA, is assessed and the results demonstrate that this approach is able to differentiate the fold change in protein abundance down to 10%. The machine dynamic range limitation and purification step will make the precursor ion ratio deriving from the actual ratio fold change. It is suggested that the differentially mixed (15)N-coded and (14)N-coded plant protein samples that are used to establish the protein abundance standard curve should be prepared following a similar protein isolation protocol used to isolate the proteins to be quantitated. Crown Copyright © 2011. Published by Elsevier Ltd. All rights reserved.

  19. 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

  20. 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

  1. 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.

  2. The scaling of urban surface water abundance and impairment with city size

    NASA Astrophysics Data System (ADS)

    Steele, M. K.

    2018-03-01

    Urbanization alters surface water compared to nonurban landscapes, yet little is known regarding how basic aquatic ecosystem characteristics, such as the abundance and impairment of surface water, differ with population size or regional context. This study examined the abundance, scaling, and impairment of surface water by quantifying the stream length, water body area, and impaired stream length for 3520 cities in the United States with populations from 2500 to 18 million. Stream length, water body area, and impaired stream length were quantified using the National Hydrography Dataset and the EPA's 303(d) list. These metrics were scaled with population and city area using single and piecewise power-law models and related to biophysical factors (precipitation, topography) and land cover. Results show that abundance of stream length and water body area in cities actually increases with city area; however, the per person abundance decreases with population size. Relative to population, impaired stream length did not increase until city populations were > 25,000 people, then scaled linearly with population. Some variation in abundance and impairment was explained by biophysical context and land cover. Development intensity correlated with stream density and impairment; however, those relationships depended on the orientation of the land covers. When high intensity development occupied the local elevation highs (+ 15 m) and undeveloped land the elevation lows, the percentage of impaired streams was less than the opposite land cover orientation (- 15 m) or very flat land. These results show that surface water abundance and impairment across contiguous US cities are influenced by city size and by biophysical setting interacting with land cover intensity.

  3. Differential protein abundance of a basolateral MCT1 transporter in the human gastrointestinal tract.

    PubMed

    Al-Mosauwi, Hashemeya; Ryan, Elizabeth; McGrane, Alison; Riveros-Beltran, Stefanie; Walpole, Caragh; Dempsey, Eugene; Courtney, Danielle; Fearon, Naomi; Winter, Desmond; Baird, Alan; Stewart, Gavin

    2016-12-01

    Bacterially derived short chain fatty acids (SCFAs), such as butyrate, are vital in maintaining the symbiotic relationship that exists between humans and their gastrointestinal microbial populations. A key step in this process is the transport of SCFAs across colonic epithelial cells via MCT1 transporters. This study investigated MCT1 protein abundance in various human intestinal tissues. Initial RT-PCR analysis confirmed the expected MCT1 RNA expression pattern of colon > small intestine > stomach. Using surgical resection samples, immunoblot analysis detected higher abundance of a 45 kDa MCT1 protein in colonic tissue compared to ileum tissue (P < 0.001, N = 4, unpaired t-test). Importantly, MCT1 abundance was found to be significantly lower in sigmoid colon compared to ascending colon (P < 0.01, N = 8-11, ANOVA). Finally, immunolocalization studies confirmed MCT1 to be abundant in the basolateral membranes of surface epithelial cells of the ascending, transverse, and descending colon, but significantly less prevalent in the sigmoid colon (P < 0.05, N = 5-21, ANOVA). In conclusion, these data confirm that basolateral MCT1 protein abundance is correlated to levels of bacterially derived SCFAs along the human gastrointestinal tract. These findings highlight the importance of precise tissue location in studies comparing colonic MCT1 abundance between normal and diseased states. © 2016 International Federation for Cell Biology.

  4. Calibration of Gephyrocapsa Coccolith Abundance in Holocene Sediments for Paleo-temperature Assessment

    NASA Astrophysics Data System (ADS)

    Bollmann, J.; Brabec, B.

    2001-12-01

    Abundance and assemblage compositions of microplankton, together with their chemical and stable isotopic composition, have been among the most successful methods in paleoceanography. One of the most frequently applied techniques for reconstruction of paleo-temperature is a transfer function using the relative abundance of planktic foraminifera in sediment samples. Here we present evidence, suggesting that absolute sea surface temperature for a given location can be also calculated from the relative abundance of Gephyrocapsa morphotypes in sediment samples with an accuracy comparable to foraminifera transfer functions. By extrapolating this finding, paleo-enviromental interpretations can be obtained for the Late Pleistocene and discrepancies between the different currently used methods (e.g., foraminifer, alkenone and Ca/Mg derived temperature estimates) might be resolved. Eighty-one Holocene sediment samples were selected from the Pacific, Indian and Atlantic Oceans covering a temperature gradient from 13.4° C to 29.4° C, a salinity gradient from 32.21 to 37.34 and a productivity gradient of 0.045 to 0.492μ g chlorophyll/L. Standard multiple linear regression analyses were applied to this data set, linking the relative abundance of Gephyrocapsa morphotypes to mean sea surface temperature. The best model revealed an r2 of 0.8 with a standard residual error of 1.8° C for calculation of the mean sea surface temperature.

  5. Classifying rarity and abundance at a regional scale: Implementation within a new ecoinformatics tool

    EPA Science Inventory

    One factor that determines a species vulnerability to extinction is its rarity in the environment and a goal of many species analyses is to evaluate geographic patterns of abundance. In an attempt to assess vulnerability to climate change, we evaluated relative species abundance...

  6. [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.

  7. Fear in grasslands: the effect of Eurasian kestrels on skylark abundances

    NASA Astrophysics Data System (ADS)

    Martínez-Padilla, Jesús; Fargallo, Juan A.

    2008-05-01

    Predation has received considerable theoretical and empirical support in population regulation. The effect of predators, however, could be achieved in direct (killing) or indirect effects (such as displacement). In this paper, we explored the relationship between Eurasian kestrels Falco tinnunculus and skylarks Alauda arvensis in Mediterranean grasslands. First, we analysed the presence of skylarks in the kestrel diet over 9 years. We also compared a grassland area of experimentally increased kestrel density and a second grassland as control area to evaluate the direct or indirect effect on skylark abundance. We also considered two different habitats, grazed and ungrazed plots. If skylark abundance decreased as the kestrel breeding season progressed in high-density kestrel area compared with the control area, it would suggest a direct effect (predator hypothesis). If skylark abundance remains constant in both areas of contrasting kestrel density, it would suggest that skylarks avoid kestrels (avoidance hypothesis). We found that skylark abundance decreased in the kestrel area from the beginning of kestrel nest-box installation to recent years. The rate of skylark consumption decreased in a 9-year period as kestrel abundance increased, although the total amount skylark consumption did not show a decreasing trend. In addition, skylarks were more abundant in the kestrel-free area than in the kestrel area. Finally, we found that skylark abundance did not change through the kestrel breeding period in relation to grazing. We suggest that an increased breeding density of kestrels during their breeding period may force the skylarks to breed in other areas, which may explain the decline of their abundance.

  8. Carbon Abundances in Starburst Galaxies of the Local Universe

    NASA Astrophysics Data System (ADS)

    Peña-Guerrero, María A.; Leitherer, Claus; de Mink, Selma; Wofford, Aida; Kewley, Lisa

    2017-10-01

    The cosmological origin of carbon, the fourth most abundant element in the universe, is not well known and a matter of heavy debate. We investigate the behavior of C/O to O/H in order to constrain the production mechanism of carbon. We measured emission-line intensities in the spectral range from 1600 to 10000 Å on Space Telescope Imaging Spectrograph (STIS) long-slit spectra of 18 starburst galaxies in the local universe. We determined chemical abundances through traditional nebular analysis, and we used a Markov Chain Monte Carlo method to determine where our carbon and oxygen abundances lie in the parameter space. We conclude that our C and O abundance measurements are sensible. We analyzed the behavior of our sample in the [C/O] versus [O/H] diagram with respect to other objects such as DLAs, neutral ISM measurements, and disk and halo stars, finding that each type of object seems to be located in a specific region of the diagram. Our sample shows a steeper C/O versus O/H slope with respect to other samples, suggesting that massive stars contribute more to the production of C than N at higher metallicities, only for objects where massive stars are numerous; otherwise, intermediate-mass stars dominate the C and N production.

  9. Changes in abundance and community structure of nematodes from the abyssal polymetallic nodule field, Tropical Northeast Pacific

    NASA Astrophysics Data System (ADS)

    Miljutin, Dmitry; Miljutina, Maria; Messié, Monique

    2015-12-01

    Deep-sea fields of polymetallic nodules in the Clarion-Clipperton Zone (CCFZ, tropical NE Pacific) are currently being investigated to assess their potential for commercial mining. During such mining, benthic communities will be inevitably disturbed or destroyed. Therefore, assessments of their standing stock and composition may be helpful for the future evaluation of possible impacts of commercial nodule exploitation. Analysis of nematode communities (at genus level) inhabiting the French license area of the CCFZ were studied based on data from the cruises NODINAUT (2004) and BIONOD (2012). The total nematode density was ca. 1.5-fold higher in 2012 as compared with 2004. This reflected a 2-2.5 times higher density of non-selective deposit-feeders (i.e. possessing a small buccal cavity without armature) in 2012 compared with 2004, whereas no significant differences between sampling periods were observed in the density of the other feeding groups. Consequently, whilst the list of the most abundant genera was identical, their relative abundances changed significantly. The relative abundance of the genus Thalassomonhystera was two times greater in 2012 than in 2004, whereas the relative abundances of the genera Acantholaimus and Theristus were significantly lower in 2012 (10% and 4%, respectively) than in 2004 (28% and 9%). Nematode diversity (including values of diversity indices and total number of recorded genera) was significantly lower in 2012 in comparison with 2004. Although our data do not take into account seasonal and shorter temporal scales of variability in nematode assemblages, we report here that a certain fraction of variations observed between the two sampling periods could be associated with differences in primary production. Future studies should aim to better characterise temporal variability in nematode communities of the CCFZ at seasonal and interannual scales.

  10. Impact of copper on the diazotroph abundance and community composition during swine manure composting.

    PubMed

    Yin, Yanan; Gu, Jie; Wang, Xiaojuan; Zhang, Kaiyu; Hu, Ting; Ma, Jiyue; Wang, Qianzhi

    2018-05-01

    Biological nitrogen fixation is a major pathway in ecosystems. This study investigated the effects of adding Cu at different levels (0, 200, and 2000 mg kg -1 ) on the diazotroph community during swine manure composting. Quantitative PCR and high-throughput sequencing were used to analyze the abundances of diazotrophs and the community composition based on the nifH gene. The nifH gene copy number was relatively high in the early stage of composting and Cu had a significant inhibitory effect on the nifH copy number. Furthermore, Cu decreased the diversity of nifH and changed the microbial community structure in the early stage. The nifH genes from members of Firmicutes and Clostridium were most abundant. Co-occurrence ecological network analysis showed that the Cu treatments affected the co-occurrence patterns of diazotroph communities and reduced the associations between different diazotrophs. Interestingly, Cu may weaken symbiotic diazotrophic interactions and enhance the roles of free-living diazotrophs. Copyright © 2018 Elsevier Ltd. All rights reserved.

  11. Population Abundance and Ecosystem Service Provision: The Case of Birds

    PubMed Central

    Gaston, Kevin J; Cox, Daniel T C; Canavelli, Sonia B; García, Daniel; Hughes, Baz; Maas, Bea; Martínez, Daniel; Ogada, Darcy; Inger, Richard

    2018-01-01

    Abstract Although there is a diversity of concerns about recent persistent declines in the abundances of many species, the implications for the associated delivery of ecosystem services to people are surprisingly poorly understood. In principle, there are a broad range of potential functional relationships between the abundance of a species or group of species and the magnitude of ecosystem-service provision. Here, we identify the forms these relationships are most likely to take. Focusing on the case of birds, we review the empirical evidence for these functional relationships, with examples of supporting, regulating, and cultural services. Positive relationships between abundance and ecosystem-service provision are the norm (although seldom linear), we found no evidence for hump-shaped relationships, and negative ones were limited to cultural services that value rarity. Given the magnitude of abundance declines among many previously common species, it is likely that there have been substantial losses of ecosystem services, providing important implications for the identification of potential tipping points in relation to defaunation resilience, biodiversity conservation, and human well-being. PMID:29686433

  12. Tungsten Abundances in Hawaiian Picrites: Implications for the Mantle Sources of Hawaiian Volcanoes

    NASA Astrophysics Data System (ADS)

    Ireland, T. J.; Arevalo, R. D.; Walker, R. J.; McDonough, W. F.

    2008-12-01

    Tungsten abundances have been measured in a suite of Hawaiian picrites (MgO >13 wt.%) from nine Hawaiian shield volcanoes (Mauna Kea, Mauna Loa, Hualalai, Loihi, Koolau, Kilauea, Kohala, Lanai and Molokai). Tungsten concentrations in the parental melts for these volcanoes have been estimated via the intersection of linear W-MgO trends with the putative MgO content of the parental melt (~16 wt.%). Tungsten behaves as a highly incompatible trace element in mafic to ultramafic systems; thus, given an independent assessment of the degree of partial melting for each volcanic center, the W abundances in their mantle sources can be determined. The mantle sources for Hualalai, Kilauea, Kohala and Loihi have non- uniform estimated W abundances of 11, 13, 16 and 27 ng/g, respectively, giving an average source abundance of 17±5 ng/g. This average source abundance is nearly six times more enriched than Depleted MORB Mantle (DMM: 3.0±2.3 ng/g) and slightly elevated relative to the Bulk Silicate Earth (BSE: 13±10 ng/g). The relatively high abundances of W in the Hawaiian sources relative to the DMM can potentially be explained as a consequence of crustal recycling. For example, incorporation of 30% oceanic crust (30 ng/g W), including 3% sediment (1500 ng/g W), into a DMM source could create the W enrichment observed in the Loihi source, consistent with estimates from earlier models based on other trace elements and isotope systems. The Hualalai source, however, has also been suggested to contain a substantial recycled component, as implied by similarly radiogenic 187Os/188Os, yet this source has the lowest estimated W abundance among the volcanic centers studied. The conflict between these results may: 1) reflect chemical differences among recycled components, 2) indicate a more complex history for Hualalai samples, e.g. involvement of a melt percolation component, or 3) implicate other sources of W.

  13. PEPA test: fast and powerful differential analysis from relative quantitative proteomics data using shared peptides.

    PubMed

    Jacob, Laurent; Combes, Florence; Burger, Thomas

    2018-06-18

    We propose a new hypothesis test for the differential abundance of proteins in mass-spectrometry based relative quantification. An important feature of this type of high-throughput analyses is that it involves an enzymatic digestion of the sample proteins into peptides prior to identification and quantification. Due to numerous homology sequences, different proteins can lead to peptides with identical amino acid chains, so that their parent protein is ambiguous. These so-called shared peptides make the protein-level statistical analysis a challenge and are often not accounted for. In this article, we use a linear model describing peptide-protein relationships to build a likelihood ratio test of differential abundance for proteins. We show that the likelihood ratio statistic can be computed in linear time with the number of peptides. We also provide the asymptotic null distribution of a regularized version of our statistic. Experiments on both real and simulated datasets show that our procedures outperforms state-of-the-art methods. The procedures are available via the pepa.test function of the DAPAR Bioconductor R package.

  14. Habitat preferences of two sparrow species are modified by abundances of other birds in an urban environment

    PubMed Central

    Skórka, Piotr; Sierpowska, Katarzyna; Haidt, Andżelika; Myczko, Łukasz; Ekner-Grzyb, Anna; Rosin, Zuzanna M.; Kwieciński, Zbigniew; Suchodolska, Joanna; Takacs, Viktoria; Jankowiak, Łukasz; Wasielewski, Oskar; Graclik, Agnieszka; Krawczyk, Agata J.; Kasprzak, Adam; Szwajkowski, Przemysław; Wylegała, Przemysław; Malecha, Anna W.; Mizera, Tadeusz; Tryjanowski, Piotr

    2016-01-01

    Abstract Every species has certain habitat requirements, which may be altered by interactions with other co-occurring species. These interactions are mostly ignored in predictive models trying to identify key habitat variables correlated with species population abundance/occurrence. We investigated how the structure of the urban landscape, food resources, potential competitors, predators, and interaction between these factors influence the abundance of house sparrow Passer domesticus and the tree sparrow P. montanus in sixty 25 ha plots distributed randomly across residential areas of the city of Poznań (Poland). The abundance of the house sparrow was positively correlated with the abundance of pigeons but negatively correlated with human-related food resources. There were significant interaction terms between abundances of other urban species and habitat variables in statistical models. For example, the abundance of house sparrow was negatively correlated with the abundance of corvids and tree sparrows but only when food resources were low. The abundance of tree sparrows positively correlated with density of streets and the distance from the city center. The abundance of this species positively correlated with the abundance of corvids when food resources were low but negatively correlated at low covers of green area. Our study indicates that associations between food resources, habitat covers, and the relative abundance of two sparrow species are altered by the abundance of other urban species. Competition, niche separation and social facilitation may be responsible for these interactive effects. Thus, biotic interactions should be included not only as an additive effect but also as an interaction term between abundance and habitat variables in statistical models predicting species abundance and occurrence. PMID:29491924

  15. Linking species abundance distributions in numerical abundance and biomass through simple assumptions about community structure.

    PubMed

    Henderson, Peter A; Magurran, Anne E

    2010-05-22

    Species abundance distributions (SADs) are widely used as a tool for summarizing ecological communities but may have different shapes, depending on the currency used to measure species importance. We develop a simple plotting method that links SADs in the alternative currencies of numerical abundance and biomass and is underpinned by testable predictions about how organisms occupy physical space. When log numerical abundance is plotted against log biomass, the species lie within an approximately triangular region. Simple energetic and sampling constraints explain the triangular form. The dispersion of species within this triangle is the key to understanding why SADs of numerical abundance and biomass can differ. Given regular or random species dispersion, we can predict the shape of the SAD for both currencies under a variety of sampling regimes. We argue that this dispersion pattern will lie between regular and random for the following reasons. First, regular dispersion patterns will result if communities are comprised groups of organisms that use different components of the physical space (e.g. open water, the sea bed surface or rock crevices in a marine fish assemblage), and if the abundance of species in each of these spatial guilds is linked to the way individuals of varying size use the habitat. Second, temporal variation in abundance and sampling error will tend to randomize this regular pattern. Data from two intensively studied marine ecosystems offer empirical support for these predictions. Our approach also has application in environmental monitoring and the recognition of anthropogenic disturbance, which may change the shape of the triangular region by, for example, the loss of large body size top predators that occur at low abundance.

  16. Linking species abundance distributions in numerical abundance and biomass through simple assumptions about community structure

    PubMed Central

    Henderson, Peter A.; Magurran, Anne E.

    2010-01-01

    Species abundance distributions (SADs) are widely used as a tool for summarizing ecological communities but may have different shapes, depending on the currency used to measure species importance. We develop a simple plotting method that links SADs in the alternative currencies of numerical abundance and biomass and is underpinned by testable predictions about how organisms occupy physical space. When log numerical abundance is plotted against log biomass, the species lie within an approximately triangular region. Simple energetic and sampling constraints explain the triangular form. The dispersion of species within this triangle is the key to understanding why SADs of numerical abundance and biomass can differ. Given regular or random species dispersion, we can predict the shape of the SAD for both currencies under a variety of sampling regimes. We argue that this dispersion pattern will lie between regular and random for the following reasons. First, regular dispersion patterns will result if communities are comprised groups of organisms that use different components of the physical space (e.g. open water, the sea bed surface or rock crevices in a marine fish assemblage), and if the abundance of species in each of these spatial guilds is linked to the way individuals of varying size use the habitat. Second, temporal variation in abundance and sampling error will tend to randomize this regular pattern. Data from two intensively studied marine ecosystems offer empirical support for these predictions. Our approach also has application in environmental monitoring and the recognition of anthropogenic disturbance, which may change the shape of the triangular region by, for example, the loss of large body size top predators that occur at low abundance. PMID:20071388

  17. 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.

  18. Messages from the Reversing Layer: Clues to Planet Formation in Spectral Abundances

    NASA Astrophysics Data System (ADS)

    Brewer, John Michael; Fischer, Debra; Basu, Sarbani

    2017-01-01

    The abundances of elements in the protoplanetary disk evolve over time, but stellar abundances will reflect the initial chemical composition of the disk and this can provide constraints on the range of possible outcomes for planet interiors. Rocky planet habitability depends not just on the availability of liquid water, but also on volcansim and plate tectonics that can stabilize the climate on long timescales. The slow evolution of abundances in stellar photospheres, particularly abundance ratios between elements, makes them ideal laboratories to study primordial disk compositions.In my thesis work, I developed a new spectroscopic analysis procedure that derives gravities consistent with asteroseismology to within 0.05 dex as well as abundances for 15 elements. Using this procedure, we analyzed and published a catalog of accurate stellar parameters and precise abundances for more than 1600 stars and used those to investigate questions of planet formation. The C/O and Mg/Si ratios in the solar neighborhood could affect rocky planet habitability. For lucky cases where planet atmosphereic abundances can be measured, the stellar host C/O and [O/H] ratios carry information about the formation site and migration of hot Jupiters. I will present results on both rocky planet compositions and hot Jupiter migration and discuss how they can help us identify potentially habitable systems and discriminate between different planet formation models.

  19. 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...

  20. Non-CI refractory lithophile abundances in bulk planetary materials

    NASA Astrophysics Data System (ADS)

    Dauphas, N.

    2015-12-01

    Refractory inclusions in meteorites show evidence for fractionation of refractory lithophile elements relative to one another. For bulk planetary materials, it is most often assumed that refractory lithophile elements (e.g., Ca, Al, Ti, REEs) are in proportions similar to CI carbonaceous chondrites, which is taken to be a proxy for solar composition. A diagnostic feature of REE patterns in refractory inclusions in meteorites is the presence of thulium anomalies, arising from the fact that this heavy REE is more volatile than the highly refractory HREEs surrounding it (Tm/Tm* is defined relative to either Er-Yb or Er-Lu). Tm anomalies thus represent an excellent diagnostic tool to test the assumption that refractory lithophile elements have uniform relative abundances at a bulk planetary scale. Prior to this work, high precision Tm measurements were lacking because it is mono-isotopic and as such is not amenable to high-precision single spike measurements. We have developed a multi-collector REE abundance measurement technique to measure all REEs at high precision, including the mono-isotopic ones. This technique was used to revise the abundance of CI and PAAS REE abundances (Pourmand et al. 2012) and the CI composition agrees well with an independent study (Barrat et al. 2012). The same technique was applied to measure REE patterns in 41 chondrites as well as terrestrial rocks (Dauphas and Pourmand, 2015). Our results reveal the presence of Tm anomalies of about -4.5 % in terrestrial rocks, enstatite and ordinary chondrites, relative to carbonaceous chondrites including CIs. This demonstrates that the assumption that refractory lithophile elements are in constant proportions among planetary bodies is unwarranted. It also shows that carbonaceous chondrites cannot be a major constituent of the Earth. The presence of Tm anomalies in meteorites and terrestrial rocks suggests that either (i) the material in the inner part of the solar system was formed from a gas

  1. Baleen whale abundance and distribution in relation to environmental variables and prey density in the Eastern Bering Sea

    NASA Astrophysics Data System (ADS)

    Zerbini, Alexandre N.; Friday, Nancy A.; Palacios, Daniel M.; Waite, Janice M.; Ressler, Patrick H.; Rone, Brenda K.; Moore, Sue E.; Clapham, Phillip J.

    2016-12-01

    The Bering Sea is one of the most productive marine ecosystems in the world and an important habitat for various marine mammal species. Once abundant in this region, most baleen whale species were severely depleted by commercial whaling in the 19th and early 20th centuries. Since their protection in mid-20th century, baleen whale populations have been recovering and reoccupying their historical habitats. These species can consume large amounts of their prey and thus can modify the local structure of ecosystems. Characterizing the extent to which environmental conditions and prey density influence baleen whale abundance in the Eastern Bering Sea is essential to improve our understanding of ecosystem dynamics and to predict how these species might respond to ecosystem variability associated with climate changes. In this study, physiographic, oceanographic, and biological datasets from 2008 to 2010 were combined to model the habitat characteristics of fin whales, humpback whales, and minke whales in the EBS in early summer (June and July) using generalized additive models (GAMs). The explained deviances of the best-supported models were 54.9%, 20.6%, and 68.3% for minke, fin and humpback whales, respectively. Minke and fin whales had similar distribution patterns in the EBS but their abundance was predicted by different explanatory variables. Euphausiid and pollock biomasses, and depth were important predictors of minke whale numbers, while distance to shore, euphausiid biomass, distance to the 200 m isobath, and chlorophyll-a concentration better explained fin whale abundance. Humpback whales showed a preference for shallow, coastal waters north of the Alaska Peninsula. For this species, sea surface temperature, depth, chlorophyll-a concentration and euphausid biomass were important predictors of abundance. This study is the first to provide a habitat baseline for baleen whales in the EBS based on a quantitative assessment of the relationship between whale abundance

  2. The predominantly selfing plant Arabidopsis thaliana experienced a recent reduction in transposable element abundance compared to its outcrossing relative Arabidopsis lyrata

    PubMed Central

    2012-01-01

    Background Transposable elements (TEs) are major contributors to genome evolution. One factor that influences their evolutionary dynamics is whether their host reproduces through selfing or through outcrossing. According to the recombinational spreading hypothesis, for instance, TEs can spread more easily in outcrossing species through recombination, and should thus be less abundant in selfing species. We here studied the distribution and evolutionary dynamics of TE families in the predominantly selfing plant Arabidopsis thaliana and its close outcrossing relative Arabidopsis lyrata on a genome-wide scale. We characterized differences in TE abundance between them and asked which, if any, existing hypotheses about TE abundances may explain these differences. Results We identified 1,819 TE families representing all known classes of TEs in both species, and found three times more copies in the outcrossing A. lyrata than in the predominantly selfing A. thaliana, as well as ten times more TE families unique to A. lyrata. On average, elements in A. lyrata are younger than elements in A. thaliana. In particular, A. thaliana shows a marked decrease in element number that occurred during the most recent 10% of the time interval since A. thaliana split from A. lyrata. This most recent period in the evolution of A. thaliana started approximately 500,000 years ago, assuming a splitting time of 5 million years ago, and coincides with the time at which predominant selfing originated. Conclusions Our results indicate that the mating system may be important for determining TE copy number, and that selfing species are likely to have fewer TEs. PMID:22313744

  3. Abundance of large old trees in wood-pastures of Transylvania (Romania).

    PubMed

    Hartel, Tibor; Hanspach, Jan; Moga, Cosmin I; Holban, Lucian; Szapanyos, Árpád; Tamás, Réka; Hováth, Csaba; Réti, Kinga-Olga

    2018-02-01

    Wood-pastures are special types of agroforestry systems that integrate trees with livestock grazing. Wood pastures can be hotspots for large old tree abundance and have exceptional natural values; but they are declining all over Europe. While presence of large old trees in wood-pastures can provide arguments for their maintenance, actual data on their distribution and abundance are sparse. Our study is the first to survey large old trees in Eastern Europe over such a large area. We surveyed 97 wood-pastures in Transylvania (Romania) in order to (i) provide a descriptive overview of the large old tree abundance; and (ii) to explore the environmental determinants of the abundance and persistence of large old trees in wood-pastures. We identified 2520 large old trees belonging to 16 taxonomic groups. Oak was present in 66% of the wood-pastures, followed by beech (33%), hornbeam (24%) and pear (22%). For each of these four species we constructed a generalized linear model with quasi-Poisson error distribution to explain individual tree abundance. Oak trees were most abundant in large wood-pastures and in wood-pastures from the Saxon cultural region of Transylvania. Beech abundance related positively to elevation and to proximity of human settlements. Abundance of hornbeam was highest in large wood-pastures, in wood-pastures from the Saxon cultural region, and in places with high cover of adjacent forest and a low human population density. Large old pear trees were most abundant in large wood-pastures that were close to paved roads. The maintenance of large old trees in production landscapes is a challenge for science, policy and local people, but it also can serve as an impetus for integrating economic, ecological and social goals within a landscape. Copyright © 2017 Elsevier B.V. All rights reserved.

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

    Treesearch

    Anantha M. Prasad

    2015-01-01

    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...

  5. Abundance ratios in dwarf elliptical galaxies

    NASA Astrophysics Data System (ADS)

    Şen, Ş.; Peletier, R. F.; Boselli, A.; den Brok, M.; Falcón-Barroso, J.; Hensler, G.; Janz, J.; Laurikainen, E.; Lisker, T.; Mentz, J. J.; Paudel, S.; Salo, H.; Sybilska, A.; Toloba, E.; van de Ven, G.; Vazdekis, A.; Yesilyaprak, C.

    2018-04-01

    We determine abundance ratios of 37 dwarf ellipticals (dEs) in the nearby Virgo cluster. This sample is representative of the early-type population of galaxies in the absolute magnitude range -19.0 < Mr < -16.0. We analyse their absorption line-strength indices by means of index-index diagrams and scaling relations and use the stellar population models to interpret them. We present ages, metallicities, and abundance ratios obtained from these dEs within an aperture size of Re/8. We calculate [Na/Fe] from NaD, [Ca/Fe] from Ca4227, and [Mg/Fe] from Mgb. We find that [Na/Fe] is underabundant with respect to solar, whereas [Mg/Fe] is around solar. This is exactly opposite to what is found for giant ellipticals, but follows the trend with metallicity found previously for the Fornax dwarf NGC 1396. We discuss possible formation scenarios that can result in such elemental abundance patterns, and we speculate that dEs have disc-like star formation history (SFH) favouring them to originate from late-type dwarfs or small spirals. Na-yields appear to be very metal-dependent, in agreement with studies of giant ellipticals, probably due to the large dependence on the neutron-excess in stars. We conclude that dEs have undergone a considerable amount of chemical evolution, they are therefore not uniformly old, but have extended SFH, similar to many of the Local Group galaxies.

  6. Seasonal Blowfly Distribution and Abundance in Fragmented Landscapes. Is It Useful in Forensic Inference about Where a Corpse Has Been Decaying?

    PubMed Central

    Zabala, Jabi; Díaz, Beatriz; Saloña-Bordas, Marta I.

    2014-01-01

    Blowflies are insects of forensic interest as they may indicate characteristics of the environment where a body has been laying prior to the discovery. In order to estimate changes in community related to landscape and to assess if blowfly species can be used as indicators of the landscape where a corpse has been decaying, we studied the blowfly community and how it is affected by landscape in a 7,000 km2 region during a whole year. Using baited traps deployed monthly we collected 28,507 individuals of 10 calliphorid species, 7 of them well represented and distributed in the study area. Multiple Analysis of Variance found changes in abundance between seasons in the 7 analyzed species, and changes related to land use in 4 of them (Calliphora vomitoria, Lucilia ampullacea, L. caesar and L. illustris). Generalised Linear Model analyses of abundance of these species compared with landscape descriptors at different scales found only a clear significant relationship between summer abundance of C. vomitoria and distance to urban areas and degree of urbanisation. This relationship explained more deviance when considering the landscape composition at larger geographical scales (up to 2,500 m around sampling site). For the other species, no clear relationship between land uses and abundance was found, and therefore observed changes in their abundance patterns could be the result of other variables, probably small changes in temperature. Our results suggest that blowfly community composition cannot be used to infer in what kind of landscape a corpse has decayed, at least in highly fragmented habitats, the only exception being the summer abundance of C. vomitoria. PMID:24918607

  7. Host-Plant Specialization Mediates the Influence of Plant Abundance on Host Use by Flower Head-Feeding Insects.

    PubMed

    Nobre, Paola A F; Bergamini, Leonardo L; Lewinsohn, Thomas M; Jorge, Leonardo R; Almeida-Neto, Mário

    2016-02-01

    Among-population variation in host use is a common phenomenon in herbivorous insects. The simplest and most trivial explanation for such variation in host use is the among-site variation in plant species composition. Another aspect that can influence spatial variation in host use is the relative abundance of each host-plant species compared to all available hosts. Here, we used endophagous insects that develop in flower heads of Asteraceae species as a study system to investigate how plant abundance influences the pattern of host-plant use by herbivorous insects with distinct levels of host-range specialization. Only herbivores recorded on three or more host species were included in this study. In particular, we tested two related hypotheses: 1) plant abundance has a positive effect on the host-plant preference of herbivorous insects, and 2) the relative importance of plant abundance to host-plant preference is greater for herbivorous species that use a wider range of host-plant species. We analyzed 11 herbivore species in 20 remnants of Cerrado in Southeastern Brazil. For 8 out of 11 herbivore species, plant abundance had a positive influence on host use. In contrast to our expectation, both the most specialized and the most generalist herbivores showed a stronger positive effect of plant species abundance in host use. Thus, we found evidence that although the abundance of plant species is a major factor determining the preferential use of host plants, its relative importance is mediated by the host-range specialization of herbivores.

  8. Woodland pond salamander abundance in relation to forest management and environmental conditions in northern Wisconsin

    Treesearch

    Deahn M. Donner; Christine A. Ribic; Albert J. Beck; Dale Higgins; Dan Eklund; Susan Reinecke

    2015-01-01

    Woodland ponds are important landscape features that help sustain populations of amphibians that require this aquatic habitat for successful reproduction. Species abundance patterns often reflect site-specific differences in hydrology, physical characteristics, and surrounding vegetation. Large-scale processes such as changing land cover and environmental conditions...

  9. 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

  10. Lithium abundance in a sample of solar-like stars

    NASA Astrophysics Data System (ADS)

    López-Valdivia, R.; Hernández-Águila, J. B.; Bertone, E.; Chávez, M.; Cruz-Saenz de Miera, F.; Amazo-Gómez, E. M.

    2015-08-01

    We report on the determination of the lithium abundance [A(Li)] of 52 solar-like stars. For 41 objects the A(Li) here presented corresponds to the first measurement. We have measured the equivalent widths of the 6708 Å lithium feature in high-resolution spectroscopic images (R ˜ 80 000), obtained at the Observatorio Astrofísico Guillermo Haro (Sonora, Mexico), as part of the first scientific observations of the revitalized Lunar and Planetary Laboratory (LPL) Echelle Spectrograph, now known as the Cananea High-resolution Spectrograph (CanHiS). Lithium abundances were derived with the Fortran code MOOG, using as fundamental input a set of atmospheric parameters recently obtained by our group. With the help of an additional small sample with previous A(Li) determinations, we demonstrate that our lithium abundances are in agreement, to within uncertainties, with other works. Two target objects stand out from the rest of the sample. The star BD+47 3218 (Teff = 6050 ± 52 K, A(Li) = 1.86 ± 0.07 dex) lies inside the so-called lithium desert in the A(Li)-Teff plane. The other object, BD+28 4515, has an A(Li) = 3.05 ± 0.07 dex, which is the highest of our sample and compatible with the expected abundances of relatively young stars.

  11. Bringing abundance into environmental politics: Constructing a Zionist network of water abundance, immigration, and colonization.

    PubMed

    Alatout, Samer

    2009-06-01

    For more than five decades, resource scarcity has been the lead story in debates over environmental politics. More importantly, and whenever environmental politics implies conflict, resource scarcity is constructed as the culprit. Abundance of resources, if at all visited in the literature, holds less importance. Resource abundance is seen, at best, as the other side of scarcity--maybe the successful conclusion of multiple interventions that may turn scarcity into abundance. This paper reinstates abundance as a politico-environmental category in its own right. Rather than relegating abundance to a second-order environmental actor that matters only on occasion, this paper foregrounds it as a crucial element in modern environmental politics. On the substantive level, and using insights from science and technology studies, especially a slightly modified actor-network framework, I describe the emergence and consolidation of a Zionist network of abundance, immigration, and colonization in Palestine between 1918 and 1948. The essential argument here is that water abundance was constructed as fact, and became a political rallying point around which a techno-political network emerged that included a great number of elements. To name just a few, the following were enrolled in the service of such a network: geologists, geophysicists, Zionist settlement experts, Zionist organizations, political and technical categories of all sorts, Palestinians as the negated others, Palestinian revolts in search of political rights, the British Mandate authorities, the hydrological system of Palestine, and the absorptive capacity of Palestine, among others. The point was to successfully articulate these disparate elements into a network that seeks opening Palestine for Jewish immigration, redefining Palestinian geography and history through Judeo-Christian Biblical narratives, and, in the process, de-legitimizing political Palestinian presence in historic Palestine.

  12. 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.

  13. Abundances and Depletions of Neutron-capture Elements in the Interstellar Medium

    NASA Astrophysics Data System (ADS)

    Ritchey, A. M.; Federman, S. R.; Lambert, D. L.

    2018-06-01

    We present an extensive analysis of the gas-phase abundances and depletion behaviors of neutron-capture elements in the interstellar medium (ISM). Column densities (or upper limits to the column densities) of Ga II, Ge II, As II, Kr I, Cd II, Sn II, and Pb II are determined for a sample of 69 sight lines with high- and/or medium-resolution archival spectra obtained with the Space Telescope Imaging Spectrograph on board the Hubble Space Telescope. An additional 59 sight lines with column density measurements reported in the literature are included in our analysis. Parameters that characterize the depletion trends of the elements are derived according to the methodology developed by Jenkins. (In an appendix, we present similar depletion results for the light element B.) The depletion patterns exhibited by Ga and Ge comport with expectations based on the depletion results obtained for many other elements. Arsenic exhibits much less depletion than expected, and its abundance in low-depletion sight lines may even be supersolar. We confirm a previous finding by Jenkins that the depletion of Kr increases as the overall depletion level increases from one sight line to another. Cadmium shows no such evidence of increasing depletion. We find a significant amount of scatter in the gas-phase abundances of Sn and Pb. For Sn, at least, the scatter may be evidence of real intrinsic abundance variations due to s-process enrichment combined with inefficient mixing in the ISM.

  14. Carbon and nitrogen biogeochemistry in the ocean: A study using stable isotope natural abundance

    NASA Technical Reports Server (NTRS)

    Rau, G. H.; Desmarais, David J.

    1985-01-01

    Determining the biogeochemical pathways traveled by carbon and nitrogen in the ocean is fundamental to the understanding of how the ocean participates in the cycling of these elements within the biosphere. Because biological production, metabolism, and respiration can significantly alter the natural abundance of C-13 and N-15, these abundances can provide important information about the nature of these biological processes and their variability in the marine environment. The research initially seeks to characterize the spatial and temporal patterns of stable isotope abundances in organic matter, and to relate these abundances to C and N biogeochemical processes within selected areas of the northeastern Pacific Ocean.

  15. Anopheles larval abundance and diversity in three rice agro-village complexes Mwea irrigation scheme, central Kenya.

    PubMed

    Mwangangi, Joseph M; Shililu, Josephat; Muturi, Ephantus J; Muriu, Simon; Jacob, Benjamin; Kabiru, Ephantus W; Mbogo, Charles M; Githure, John; Novak, Robert J

    2010-08-09

    The diversity and abundance of Anopheles larvae has significant influence on the resulting adult mosquito population and hence the dynamics of malaria transmission. Studies were conducted to examine larval habitat dynamics and ecological factors affecting survivorship of aquatic stages of malaria vectors in three agro-ecological settings in Mwea, Kenya. Three villages were selected based on rice husbandry and water management practices. Aquatic habitats in the 3 villages representing planned rice cultivation (Mbui Njeru), unplanned rice cultivation (Kiamachiri) and non-irrigated (Murinduko) agro-ecosystems were sampled every 2 weeks to generate stage-specific estimates of mosquito larval densities, relative abundance and diversity. Records of distance to the nearest homestead, vegetation coverage, surface debris, turbidity, habitat stability, habitat type, rice growth stage, number of rice tillers and percent Azolla cover were taken for each habitat. Captures of early, late instars and pupae accounted for 78.2%, 10.9% and 10.8% of the total Anopheles immatures sampled (n = 29,252), respectively. There were significant differences in larval abundance between 3 agro-ecosystems. The village with 'planned' rice cultivation had relatively lower Anopheles larval densities compared to the villages where 'unplanned' or non-irrigated. Similarly, species composition and richness was higher in the two villages with either 'unplanned' or limited rice cultivation, an indication of the importance of land use patterns on diversity of larval habitat types. Rice fields and associated canals were the most productive habitat types while water pools and puddles were important for short periods during the rainy season. Multiple logistic regression analysis showed that presence of other invertebrates, percentage Azolla cover, distance to nearest homestead, depth and water turbidity were the best predictors for Anopheles mosquito larval abundance. These results suggest that agricultural

  16. RNA-sequencing analysis reveals abundant developmental stage-specific and immunity-related genes in the pollen beetle Meligethes aeneus.

    PubMed

    Vogel, H; Badapanda, C; Knorr, E; Vilcinskas, A

    2014-02-01

    The pollen beetle (Meligethes aeneus) is a major pest of oilseed rape (Brassica napus) and other cruciferous crops in Europe. Pesticide-resistant pollen beetle populations are emerging, increasing the economic impact of this species. We isolated total RNA from the larval and adult stages, the latter either naïve or immunized by injection with bacteria and yeast. High-throughput RNA sequencing (RNA-Seq) was carried out to establish a comprehensive transcriptome catalogue and to screen for developmental stage-specific and immunity-related transcripts. We assembled the transcriptome de novo by combining sequence tags from all developmental stages and treatments. Gene expression data based on normalized read counts revealed several functional gene categories that were differentially expressed between larvae and adults, particularly genes associated with digestion and detoxification that were induced in larvae, and genes associated with reproduction and environmental signalling that were induced in adults. We also identified many genes associated with microbe recognition, immunity-related signalling and defence effectors, such as antimicrobial peptides (AMPs) and lysozymes. Digital gene expression analysis revealed significant differences in the profile of AMPs expressed in larvae, naïve adults and immune-challenged adults, providing insight into the steady-state differences between developmental stages and the complex transcriptional remodelling that occurs following the induction of immunity. Our data provide insight into the adaptive mechanisms used by phytophagous insects and could lead to the development of more effective control strategies for insect pests. © 2013 The Royal Entomological Society.

  17. The boron abundance of Procyon

    NASA Technical Reports Server (NTRS)

    Lemke, Michael; Lambert, David L.; Edvardsson, Bengt

    1993-01-01

    The B I 2496.8 A resonance line and HST/GHRS echelle spectra are used with model atmospheres and synthetic spectra to derive the B abundance of the F dwarfs Procyon (Alpha Canis Minoris), Theta Ursae Majoris, and Iota Pegasi. The B abundance of Theta UMa and Iota Peg is similar to that derived by Boesgaard and Heacox (1978) from the B II resonance line in spectra of A- and B-type stars. These two dwarfs show normal abundances of Li, Be, and B. Procyon, which is highly depleted in Li and Be, is depleted in B by a factor of at least 3. Comparison of the spectra of Procyon and the halo dwarf HD 140283 shows that the B abundance assigned by Duncan et al. (1992) to three halo dwarfs is not greatly overestimated as a result of contamination of the B I line by an unidentified line.

  18. Identifying Type Ia Supernova Mechanisms in Dwarf Spheroidal Galaxies through Analysis of Iron-peak Elemental Abundances

    NASA Astrophysics Data System (ADS)

    Guo, Rachel; Xie, Justin Long; Kirby, Evan N.

    2017-01-01

    Through the fusion of nucleons to produce elements heavier than hydrogen and helium, stellar nucleosynthesis produces most of the elements in the universe. Such is the case in a supernova explosion, which creates most of the elements on the periodic table—including iron-peak elements, atomic numbers 21 through 30—through nucleosynthesis and ejects them into the interstellar medium. In this study, we determine the best theoretical supernova model appropriate for the stars in the dwarf spheroidal galaxies Sculptor, Fornax, Ursa Minor, and Leo II by calculating the abundances of iron-peak elements in these stars. To determine iron-peak elemental abundances, we compare synthesized spectra with observed spectra from medium-resolution spectroscopy and determine the best-fitting spectrum by way of a chi-squared minimization. Through inspecting the relationship between the iron-peak element abundances and the abundance of iron itself and by comparing them to previously hypothesized supernova model theories, we discover that the near-Chandrasekhar mass “n1” model, as predicted by Seitenzahl et al., most accurately represents the trends and patterns within our data, presenting new insight into Type Ia supernovae mechanisms within the Milky Way and beyond.

  19. The use of kDNA minicircle subclass relative abundance to differentiate between Leishmania (L.) infantum and Leishmania (L.) amazonensis.

    PubMed

    Ceccarelli, Marcello; Galluzzi, Luca; Diotallevi, Aurora; Andreoni, Francesca; Fowler, Hailie; Petersen, Christine; Vitale, Fabrizio; Magnani, Mauro

    2017-05-16

    Leishmaniasis is a neglected disease caused by many Leishmania species, belonging to subgenera Leishmania (Leishmania) and Leishmania (Viannia). Several qPCR-based molecular diagnostic approaches have been reported for detection and quantification of Leishmania species. Many of these approaches use the kinetoplast DNA (kDNA) minicircles as the target sequence. These assays had potential cross-species amplification, due to sequence similarity between Leishmania species. Previous works demonstrated discrimination between L. (Leishmania) and L. (Viannia) by SYBR green-based qPCR assays designed on kDNA, followed by melting or high-resolution melt (HRM) analysis. Importantly, these approaches cannot fully distinguish L. (L.) infantum from L. (L.) amazonensis, which can coexist in the same geographical area. DNA from 18 strains/isolates of L. (L.) infantum, L. (L.) amazonensis, L. (V.) braziliensis, L. (V.) panamensis, L. (V.) guyanensis, and 62 clinical samples from L. (L.) infantum-infected dogs were amplified by a previously developed qPCR (qPCR-ML) and subjected to HRM analysis; selected PCR products were sequenced using an ABI PRISM 310 Genetic Analyzer. Based on the obtained sequences, a new SYBR-green qPCR assay (qPCR-ama) intended to amplify a minicircle subclass more abundant in L. (L.) amazonensis was designed. The qPCR-ML followed by HRM analysis did not allow discrimination between L. (L.) amazonensis and L. (L.) infantum in 53.4% of cases. Hence, the novel SYBR green-based qPCR (qPCR-ama) has been tested. This assay achieved a detection limit of 0.1 pg of parasite DNA in samples spiked with host DNA and did not show cross amplification with Trypanosoma cruzi or host DNA. Although the qPCR-ama also amplified L. (L.) infantum strains, the C q values were dramatically increased compared to qPCR-ML. Therefore, the combined analysis of C q values from qPCR-ML and qPCR-ama allowed to distinguish L. (L.) infantum and L. (L.) amazonensis in 100% of tested samples

  20. 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.