Science.gov

Sample records for abundance analysis relative

  1. RELATIVE ABUNDANCE MEASUREMENTS IN PLUMES AND INTERPLUMES

    SciTech Connect

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

    2015-07-10

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

  2. 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

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

    USGS Publications Warehouse

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

    2002-01-01

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

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

    SciTech Connect

    Nie, Lei; Wu, Gang; Zhang, Weiwen

    2006-12-01

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

  5. Accurate genome relative abundance estimation based on shotgun metagenomic reads.

    PubMed

    Xia, Li C; Cram, Jacob A; Chen, Ting; Fuhrman, Jed A; Sun, Fengzhu

    2011-01-01

    Accurate estimation of microbial community composition based on metagenomic sequencing data is fundamental for subsequent metagenomics analysis. Prevalent estimation methods are mainly based on directly summarizing alignment results or its variants; often result in biased and/or unstable estimates. We have developed a unified probabilistic framework (named GRAMMy) by explicitly modeling read assignment ambiguities, genome size biases and read distributions along the genomes. Maximum likelihood method is employed to compute Genome Relative Abundance of microbial communities using the Mixture Model theory (GRAMMy). GRAMMy has been demonstrated to give estimates that are accurate and robust across both simulated and real read benchmark datasets. We applied GRAMMy to a collection of 34 metagenomic read sets from four metagenomics projects and identified 99 frequent species (minimally 0.5% abundant in at least 50% of the data-sets) in the human gut samples. Our results show substantial improvements over previous studies, such as adjusting the over-estimated abundance for Bacteroides species for human gut samples, by providing a new reference-based strategy for metagenomic sample comparisons. GRAMMy can be used flexibly with many read assignment tools (mapping, alignment or composition-based) even with low-sensitivity mapping results from huge short-read datasets. It will be increasingly useful as an accurate and robust tool for abundance estimation with the growing size of read sets and the expanding database of reference genomes.

  6. Principal component analysis on chemical abundances spaces

    NASA Astrophysics Data System (ADS)

    Ting, Yuan-Sen; Freeman, Kenneth C.; Kobayashi, Chiaki; De Silva, Gayandhi M.; Bland-Hawthorn, Joss

    2012-04-01

    In preparation for the High Efficiency and Resolution Multi-Element Spectrograph (HERMES) chemical tagging survey of about a million Galactic FGK stars, we estimate the number of independent dimensions of the space defined by the stellar chemical element abundances [X/Fe]. This leads to a way to study the origin of elements from observed chemical abundances using principal component analysis. We explore abundances in several environments, including solar neighbourhood thin/thick disc stars, halo metal-poor stars, globular clusters, open clusters, the Large Magellanic Cloud and the Fornax dwarf spheroidal galaxy. By studying solar-neighbourhood stars, we confirm the universality of the r-process that tends to produce [neutron-capture elements/Fe] in a constant ratio. We find that, especially at low metallicity, the production of r-process elements is likely to be associated with the production of α-elements. This may support the core-collapse supernovae as the r-process site. We also verify the overabundances of light s-process elements at low metallicity, and find that the relative contribution decreases at higher metallicity, which suggests that this lighter elements primary process may be associated with massive stars. We also verify the contribution from the s-process in low-mass asymptotic giant branch (AGB) stars at high metallicity. Our analysis reveals two types of core-collapse supernovae: one produces mainly α-elements, the other produces both α-elements and Fe-peak elements with a large enhancement of heavy Fe-peak elements which may be the contribution from hypernovae. Excluding light elements that may be subject to internal mixing, K and Cu, we find that the [X/Fe] chemical abundance space in the solar neighbourhood has about six independent dimensions both at low metallicity (-3.5 ≲ [Fe/H] ≲-2) and high metallicity ([Fe/H] ≳-1). However the dimensions come from very different origins in these two cases. The extra contribution from low-mass AGB

  7. 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...

  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. 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.

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

    PubMed

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

    2014-01-01

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

  11. Relative resource abundance explains butterfly biodiversity in island communities.

    PubMed

    Yamamoto, Naoaki; Yokoyama, Jun; Kawata, Masakado

    2007-06-19

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

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

    SciTech Connect

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

    1993-12-31

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

  13. 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.

  14. Changes in protein abundance between tender and tough meat from bovine longissimus thoracis muscle assessed by isobaric Tag for Relative and Absolute Quantitation (iTRAQ) and 2-dimensional gel electrophoresis analysis.

    PubMed

    Bjarnadóttir, S G; Hollung, K; Høy, M; Bendixen, E; Codrea, M C; Veiseth-Kent, E

    2012-06-01

    The aim of this study was to find potential biomarkers for meat tenderness in bovine Longissimus thoracis muscle and to compare results from isobaric Tag for Relative and Absolute Quantitation (iTRAQ) and 2-dimensional gel electrophoresis (2-DE) analysis. The experiment included 4 tender and 4 tough samples, based on shear force measurements at 7 d postmortem, from young Norwegian red (NRF) bulls, taken at 1 h postmortem. A number of the proteins which have previously been related to tenderness were found to change in abundance between tender and tough samples, both in iTRAQ (P < 0.1) and 2-DE analysis (P < 0.05). Furthermore, 3 proteins that have not previously been related to tenderness were found to change significantly in abundance between tender and tough meat samples in the present study. These include proteins related to control of flux through the tricarboxylate cycle [2-oxoglutarate dehydrogenase complex component E2 (OGDC-E2)], apoptosis (galectin-1) and regulatory role in the release of Ca(2+) from intracellular stores (annexin A6). Even though the overlap in significantly changing proteins was relatively low between iTRAQ and 2-DE analysis, certain proteins predicted to have the same function were found in both analyses and showed similar changes between the groups, such as structural proteins and proteins related to apoptosis and energy metabolism.

  15. Relative species abundance of replicator dynamics with sparse interactions

    NASA Astrophysics Data System (ADS)

    Obuchi, Tomoyuki; Kabashima, Yoshiyuki; Tokita, Kei

    2016-11-01

    A theory of relative species abundance on sparsely-connected networks is presented by investigating the replicator dynamics with symmetric interactions. Sparseness of a network involves difficulty in analyzing the fixed points of the equation, and we avoid this problem by treating large self interaction u, which allows us to construct a perturbative expansion. Based on this perturbation, we find that the nature of the interactions is directly connected to the abundance distribution, and some characteristic behaviors, such as multiple peaks in the abundance distribution and all species coexistence at moderate values of u, are discovered in a wide class of the distribution of the interactions. The all species coexistence collapses at a critical value of u, u c , and this collapsing is regarded as a phase transition. To get more quantitative information, we also construct a non-perturbative theory on random graphs based on techniques of statistical mechanics. The result shows those characteristic behaviors are sustained well even for not large u. For even smaller values of u, extinct species start to appear and the abundance distribution becomes rounded and closer to a standard functional form. Another interesting finding is the non-monotonic behavior of diversity, which quantifies the number of coexisting species, when changing the ratio of mutualistic relations Δ . These results are examined by numerical simulations, which show that our theory is exact for the case without extinct species, but becomes less and less precise as the proportion of extinct species grows.

  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.

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

    SciTech Connect

    Skillman, E.D. )

    1989-12-01

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

  18. 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.

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

    PubMed Central

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

    2016-01-01

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

  20. 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.

  1. 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.

  2. 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

  3. Abundance analysis of barium and mild barium stars

    NASA Astrophysics Data System (ADS)

    Smiljanic, R.; Porto de Mello, G. F.; da Silva, L.

    2007-06-01

    Aims:We compare and discuss abundances and trends in normal giants, mild barium, and barium stars, searching for differences and similarities between barium and mild barium stars that could help shed some light on the origin of these similar objects. Also, we search for nucleosynthetic effects possibly related to the s-process that were observed in the literature for elements like Cu in other types of s-process enriched stars. Methods: High signal to noise, high resolution spectra were obtained for a sample of normal, mild barium, and barium giants. Atmospheric parameters were determined from the Fe i and Fe ii lines. Abundances for Na, Mg, Al, Si, Ca, Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Sr, Y, Zr, Ba, La, Ce, Nd, Sm, Eu, and Gd, were determined from equivalent widths and model atmospheres in a differential analysis, with the red giant ɛ Vir as the standard star. Results: The different levels of s-process overabundances of barium and mild barium stars were earlier suggested to be related to the stellar metallicity. Contrary to this suggestion, we found in this work no evidence of barium and mild barium having a different range in metallicity. However, comparing the ratio of abundances of heavy to light s-process elements, we found some evidence that they do not share the same neutron exposure parameter. The exact mechanism controlling this difference is still not clear. As a by-product of this analysis we identify two normal red giants misclassified as mild barium stars. The relevance of this finding is discussed. Concerning the suggested nucleosynthetic effects possibly related to the s-process, for elements like Cu, Mn, V and Sc, we found no evidence for an anomalous behavior in any of the s-process enriched stars analyzed here. However, further work is still needed since a clear [Cu/Fe] vs. [Ba/Fe] anticorrelation exists for other s-process enriched objects. Observations collected at ESO, La Silla, Chile, within the ON/ESO agreements. Tables 8-10 are only

  4. The Impact of Enhanced He and CNONa Abundances on Globular Cluster Relative Age-Dating Methods

    NASA Astrophysics Data System (ADS)

    Marín-Franch, Antonio; Cassisi, Santi; Aparicio, Antonio; Pietrinferni, Adriano

    2010-05-01

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

  5. Abundance analysis of the outer halo globular cluster Palomar 14

    NASA Astrophysics Data System (ADS)

    Çalışkan, Ş.; Christlieb, N.; Grebel, E. K.

    2012-01-01

    We determine the elemental abundances of nine red giant stars belonging to Palomar 14 (Pal 14). Pal 14 is an outer halo globular cluster (GC) at a distance of ~70 kpc. Our abundance analysis is based on high-resolution spectra and one-dimensional stellar model atmospheres. We derived the abundances for the iron peak elements Sc, V, Cr, Mn, Co, Ni, the α-elements O, Mg, Si, Ca, Ti, the light odd element Na, and the neutron-capture elements Y, Zr, Ba, La, Ce, Nd, Eu, Dy, and Cu. Our data do not permit us to investigate light element (i.e., O to Mg) abundance variations. The neutron-capture elements show an r-process signature. We compare our measurements with the abundance ratios of inner and other outer halo GCs, halo field stars, GCs of recognized extragalactic origin, and stars in dwarf spheroidal galaxies (dSphs). The abundance pattern of Pal 14 is almost identical to those of Pal 3 and Pal 4, the next distant members of the outer halo GC population after Pal 14. The abundance pattern of Pal 14 is also similar to those of the inner halo GCs, halo field stars, and GCs of recognized extragalactic origin, but differs from what is customarily found in dSphs field stars. The abundance properties of Pal 14, as well as those of the other outer halo GCs, are thus compatible with an accretion origin from dSphs. Whether or not GC accretion played a role, it seems that the formation conditions of outer halo GCs and GCs in dSphs were similar. Based on observations collected at the European Southern Observatory, Chile (Program IDs 077.B-0769).Tables A.1 and A.2 are only available at the CDS via anonymous ftp to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/537/A83

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

    PubMed Central

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

    2016-01-01

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

  7. 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

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

    SciTech Connect

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

    2010-05-10

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

  9. Chemical Abundance Analysis of the Symbiotic Red Giants

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

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

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

    SciTech Connect

    Pilyugin, L. S.; Grebel, E. K.; Zinchenko, I. A.; Kniazev, A. Y. E-mail: grebel@ari.uni-heidelberg.de E-mail: akniazev@saao.ac.za

    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 the 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 the

  11. Postnatal changes in the relative abundance of intestinal Lactobacillus spp. in newborn calves

    PubMed Central

    TAKINO, Tadashi; KATO-MORI, Yuko; MOTOOKA, Daisuke; NAKAMURA, Shota; IIDA, Tetsuya; HAGIWARA, Katsuro

    2017-01-01

    The intestinal microbiota of newborn calves changes during the early postnatal period and influences their health and immune function. We studied the compositional changes in the intestinal microbiome of newborn calves during the first week after birth by metagenomic analysis. In feces from newborn calves, we identified 4 bacterial phyla, namely, Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. The relative abundance of Lactobacillaceae significantly increased from day 1 to day 7. We evaluated Lactobacillus spp. colony numbers using selective agar plates and confirmed that the abundance of Lactobacillus spp. significantly increased during the first 7 days after birth. In conclusion, Lactobacillus spp. colonized the intestinal tract of calves during the first 7 days after birth. PMID:28070087

  12. Chemical abundance analysis of π Dra and HR 7545

    NASA Astrophysics Data System (ADS)

    Elmaslı, Aslı; Nasolo, Yahya

    2017-02-01

    We carried out detailed abundance analysis of two A-type stars; π Dra and HR 7545. High resolution echelle spectra of these stars were obtained at the TÜBİTAK National Observatory. We determined the fundamental parameters of each target star using traditional methods. We also plotted the stars on the H-R diagram and calculated the masses from evolutionary tracks and ages from isochrones.

  13. Abundance analysis of s-process enhanced barium stars

    NASA Astrophysics Data System (ADS)

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

    2016-12-01

    Detailed chemical composition studies of stars with enhanced abundances of neutron-capture elements can provide observational constraints for neutron-capture nucleosynthesis studies and clues for understanding their contribution to the Galactic chemical enrichment. We present abundance results from high-resolution spectral analyses of a sample of four chemically peculiar stars characterized by s-process enhancement. High-resolution spectra (R ˜ 42 000) of these objects spanning a wavelength range from 4000 to 6800 Å are taken from the ELODIE archive. We have estimated the stellar atmospheric parameters, the effective temperature Teff, the surface gravity log g and metallicity [Fe/H] from local thermodynamic equilibrium analysis using model atmospheres. We report estimates of elemental abundances for several neutron-capture elements, Sr, Y, Zr, Ba, La, Ce, Pr, Nd, Sm, Eu and Dy. While HD 49641 and HD 58368 show [Ba/Fe] ≥ 1.16, the other two objects HD 119650 and HD 191010 are found to be mild barium stars with [Ba/Fe] ˜ 0.4. The derived abundances of the elements are interpreted on the basis of existing theories for understanding their origin and evolution.

  14. Rock type identification and abundance estimation from hyperspectral analysis

    NASA Astrophysics Data System (ADS)

    Feng, Jilu

    This study explores the usefulness of hyperspectral data to discriminate rock units and estimate the abundance of sulfides in rocks. Airborne visible-near infrared (VIS-NIR) hyperspectral data collected from northern Cape Smith, Quebec and laboratory thermal infrared reflectance (TIR) data measured on rock samples from eight different mines in the Sudbury Basin, Ontario are involved in the analysis. The study addressed four different geological application scenarios with the aim of retrieving useful lithological information from rock spectra while minimizing the influence of varying environmental factors. The research first examines the effects of topography on the selection of rock endmembers from airborne VIS_NIR spectra and demonstrates how a topographic correction process can improve the discrimination of rock units. It demonstrates that traditional ways of selecting spectral endmembers from hyperspectral data for areas of rugged terrain cannot provide representative rock unit signatures. The second part of the research targeted the mapping of wall rock in an underground environment using TIR spectra. Rock samples from mines of the Sudbury Basin in Ontario were measured using naturally broken surfaces both dry and wet to address environmental conditions encountered underground. An innovative method applying a spectral angle mapper on the 2nd derivative of rock spectra from 700--1300 cm-1 was proved to be robust to remove the effect of liquid water, local geometry and disseminated sulfide ores while preserving diagnostic rock signatures for mapping. The study then focuses on retrieving sulfide information from TIR to estimate ore (total sulfide abundance) grade on naturally broken rock faces and separate ore-bearing rocks from their host rocks in an underground environment regardless of rock types. An important finding is that reflectance at 1319 cm -1, where most silicate rocks demonstrate low reflectance, is related to total sulfide concentration in rocks

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

    PubMed

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

    2006-02-01

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

  16. Fluorescent peptide biosensor for probing the relative abundance of cyclin-dependent kinases in living cells.

    PubMed

    Kurzawa, Laetitia; Pellerano, Morgan; Coppolani, J B; Morris, May C

    2011-01-01

    Cyclin-dependant kinases play a central role in coordinating cell growth and division, and in sustaining proliferation of cancer cells, thereby constituting attractive pharmacological targets. However, there are no direct means of assessing their relative abundance in living cells, current approaches being limited to antigenic and proteomic analysis of fixed cells. In order to probe the relative abundance of these kinases directly in living cells, we have developed a fluorescent peptide biosensor with biligand affinity for CDKs and cyclins in vitro, that retains endogenous CDK/cyclin complexes from cell extracts, and that bears an environmentally-sensitive probe, whose fluorescence increases in a sensitive fashion upon recognition of its targets. CDKSENS was introduced into living cells, through complexation with the cell-penetrating carrier CADY2 and applied to assess the relative abundance of CDK/Cyclins through fluorescence imaging and ratiometric quantification. This peptide biosensor technology affords direct and sensitive readout of CDK/cyclin complex levels, and reports on differences in complex formation when tampering with a single CDK or cyclin. CDKSENS further allows for detection of differences between different healthy and cancer cell lines, thereby enabling to distinguish cells that express high levels of these heterodimeric kinases, from cells that present decreased or defective assemblies. This fluorescent biosensor technology provides information on the overall status of CDK/Cyclin complexes which cannot be obtained through antigenic detection of individual subunits, in a non-invasive fashion which does not require cell fixation or extraction procedures. As such it provides promising perspectives for monitoring the response to therapeutics that affect CDK/Cyclin abundance, for cell-based drug discovery strategies and fluorescence-based cancer diagnostics.

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

    PubMed

    Serra, François; Becher, Verónica; Dopazo, Hernán

    2013-01-01

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

  18. Null model analysis of species associations using abundance data.

    PubMed

    Ulrich, Werner; Gotelli, Nicholas J

    2010-11-01

    reinforces a previous meta-analysis of presence/absence matrices. However, using two of the metrics we detected a significant pattern of aggregation for plants and for the interaction matrices (which include plant-pollinator data sets). These results suggest that abundance matrices, analyzed with an appropriate null model, may be a powerful tool for quantifying patterns of species segregation and aggregation.

  19. 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.

  20. Multi-directional Abundance Shifts Among North American Birds and the Relative Influence of Multi-Faceted Climate Factors.

    PubMed

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

    2017-03-12

    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 multi-directional 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 hypotheses focus on two contrasts: the relative importance of climate extremes versus averages, and of temperature versus 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

  1. 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

  2. Relative Abundance of Oligosaccharides in Candida Species as Determined by Fluorophore-Assisted Carbohydrate Electrophoresis

    PubMed Central

    Goins, Tresa L.; Cutler, Jim E.

    2000-01-01

    Fluorophore-assisted carbohydrate electrophoresis (FACE) is a straightforward, sensitive method for determining the presence and relative abundance of individual oligomannosyl residues in Candida mannoprotein, the major antigenic determinant located on the outer surface of the yeast cell wall. The single terminal aldehydes of oligomannosyl residues released by hydrolysis were tagged with the charged fluorophore 8-aminonaphthalene-1,3,6-trisulfonate (ANTS) and separated with high resolution on the basis of size by polyacrylamide gel electrophoresis. ANTS fluorescence labeling was not biased by oligomannoside length; therefore, band fluorescence intensity was directly related to the relative abundance of individual oligomannoside moieties in heterogeneous samples. FACE analysis revealed the major oligomannosides released by acid hydrolysis and β-elimination of Fehling-precipitated mannan from Candida albicans, which were the same as those previously reported in studies based on mass and nuclear magnetic spectroscopic analysis. FACE was also amenable to the analysis of samples obtained by direct hydrolysis of whole yeast cells. Whole-cell acid hydrolysis and whole-cell β-elimination of two isolates each of C. albicans, C. glabrata, C. krusei, C. lusitaniae, C. parapsilosis, C. rugosa, C. stellatoidea, and C. tropicalis resulted in oligomannoside gel banding patterns that were species and strain specific for the 16 isolates surveyed. Whereas some bands were specific for an individual isolate or species, other bands were shared by two or three species in various groupings. Differences in the mannoprotein composition of C. albicans A9 and four spontaneous cell surface mutants were also detected. Mannan “fingerprints,” or banding pattern profiles, derived from the electrophoretic mobilities of individual bands relative to the migration of acid-hydrolyzed dextran (relative migration index) yielded profiles characteristic of individual isolates not revealed by

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

    PubMed

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

    2014-12-01

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

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

    SciTech Connect

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

    1998-09-01

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

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

    SciTech Connect

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

    1998-09-01

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

  6. 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

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

    PubMed

    Shakir, Muhammad Mussadiq; Ahmed, Sohail

    2015-05-01

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

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

    NASA Technical Reports Server (NTRS)

    Webster, Christopher R.; Mahaffy, Paul R.

    2011-01-01

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

  9. 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.

  10. Low relative abundances of the mucolytic bacterium Akkermansia muciniphila and Bifidobacterium spp. in feces of children with autism.

    PubMed

    Wang, Lv; Christophersen, Claus T; Sorich, Michael J; Gerber, Jacobus P; Angley, Manya T; Conlon, Michael A

    2011-09-01

    Gastrointestinal disturbance is frequently reported for individuals with autism. We used quantitative real-time PCR analysis to quantify fecal bacteria that could influence gastrointestinal health in children with and without autism. Lower relative abundances of Bifidobacteria species and the mucolytic bacterium Akkermansia muciniphila were found in children with autism, the latter suggesting mucus barrier changes.

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

    PubMed

    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

    2014-10-01

    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.

  12. 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.

  13. Hexapeptide libraries for enhanced protein PTM identification and relative abundance profiling in whole human saliva.

    PubMed

    Bandhakavi, Sricharan; Van Riper, Susan K; Tawfik, Pierre N; Stone, Matthew D; Haddad, Tufia; Rhodus, Nelson L; Carlis, John V; Griffin, Timothy J

    2011-03-04

    Dynamic range compression (DRC) by hexapeptide libraries increases MS/MS-based identification of lower-abundance proteins in complex mixtures. However, two unanswered questions impede fully realizing DRC's potential in shotgun proteomics. First, does DRC enhance identification of post-translationally modified proteins? Second, can DRC be incorporated into a workflow enabling relative protein abundance profiling? We sought to answer both questions analyzing human whole saliva. Addressing question one, we coupled DRC with covalent glycopeptide enrichment and MS/MS. With DRC we identified ∼2 times more N-linked glycoproteins and their glycosylation sites than without DRC, dramatically increasing the known salivary glycoprotein catalog. Addressing question two, we compared differentially stable isotope-labeled saliva samples pooled from healthy and metastatic breast cancer women using a multidimensional peptide fractionation-based workflow, analyzing in parallel one sample portion with DRC and one portion without. Our workflow categorizes proteins with higher absolute abundance, whose relative abundance ratios are altered by DRC, from proteins of lower absolute abundance detected only after DRC. Within each of these salivary protein categories, we identified novel abundance changes putatively associated with breast cancer, demonstrating feasibility and benefits of DRC for relative abundance profiling. Collectively, our results bring us closer to realizing the full potential of DRC for proteomic studies.

  14. 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.

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

    NASA Astrophysics Data System (ADS)

    Stout, Jane C.; Casey, Leanne M.

    2014-02-01

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

  16. Abundance of West Nile virus mosquito vectors in relation to climate and landscape variables.

    PubMed

    Deichmeister, Jayne M; Telang, Aparna

    2011-06-01

    It is currently unclear if the potential for West Nile virus transmission by mosquito vectors in the eastern United States is related to landscape or climate factors or both. We compared abundance of vector species between urban and suburban neighborhoods of Henrico County, VA, in relation to the following factors: temperature, precipitation, canopy cover, building footprint, and proximity to drainage infrastructure. Mosquitoes were collected throughout the 2005, 2006, and 2007 seasons and tested for West Nile virus (WNV) in pools of 10-50. Test results of mosquito pools were compared to average site abundance from 37 sites in Henrico County, VA; abundance was then examined in relation to ecological variables. Urban infrastructure was positively correlated with the abundance of Culex pipiens L./Cx. restuans, and our findings implicate combined sewer overflow systems as large contributors to Culex vector populations. No measure of urbanization examined in our study was correlated with Aedes albopictus abundance. Our study showed that certain landscape variables identified using Geographic Information Systems are valuable for predicting primary WNV vector abundance in Virginia, and that temperature along with low precipitation are strong predictors of population growth. Our results support other regional studies that found WNV proliferates under drought conditions.

  17. 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.

  18. Environmental Sequencing Provides Reasonable Estimates of the Relative Abundance of Specific Picoeukaryotes

    PubMed Central

    Forn, Irene; Romac, Sarah; Logares, Ramiro; de Vargas, Colomban

    2016-01-01

    ABSTRACT High-throughput sequencing (HTS) is revolutionizing environmental surveys of microbial diversity in the three domains of life by providing detailed information on which taxa are present in microbial assemblages. However, it is still unclear how the relative abundance of specific taxa gathered by HTS correlates with cell abundances. Here, we quantified the relative cell abundance of 6 picoeukaryotic taxa in 13 planktonic samples from 6 European coastal sites using epifluorescence microscopy on tyramide signal amplification-fluorescence in situ hybridization preparations. These relative abundance values were then compared with HTS data obtained in three separate molecular surveys: 454 sequencing of the V4 region of the 18S ribosomal DNA (rDNA) using DNA and RNA extracts (DNA-V4 and cDNA-V4) and Illumina sequencing of the V9 region (cDNA-V9). The microscopic and molecular signals were generally correlated, indicating that a relative increase in specific 18S rDNA was the result of a large proportion of cells in the given taxa. Despite these positive correlations, the slopes often deviated from 1, precluding a direct translation of sequences to cells. Our data highlighted clear differences depending on the nucleic acid template or the 18S rDNA region targeted. Thus, the molecular signal obtained using cDNA templates was always closer to relative cell abundances, while the V4 and V9 regions gave better results depending on the taxa. Our data support the quantitative use of HTS data but warn about considering it as a direct proxy of cell abundances. IMPORTANCE Direct studies on marine picoeukaryotes by epifluorescence microscopy are problematic due to the lack of morphological features and due to the limited number and poor resolution of specific phylogenetic probes used in fluorescence in situ hybridization (FISH) routines. As a consequence, there is an increasing use of molecular methods, including high-throughput sequencing (HTS), to study marine microbial

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

    PubMed

    Lind, Eric M; Barbosa, Pedro

    2010-11-01

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

  20. [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.

  1. Distinctive serum protein profiles involving abundant proteins in lung cancer patients based upon antibody microarray analysis

    PubMed Central

    Gao, Wei-Min; Kuick, Rork; Orchekowski, Randal P; Misek, David E; Qiu, Ji; Greenberg, Alissa K; Rom, William N; Brenner, Dean E; Omenn, Gilbert S; Haab, Brian B; Hanash, Samir M

    2005-01-01

    Background Cancer serum protein profiling by mass spectrometry has uncovered mass profiles that are potentially diagnostic for several common types of cancer. However, direct mass spectrometric profiling has a limited dynamic range and difficulties in providing the identification of the distinctive proteins. We hypothesized that distinctive profiles may result from the differential expression of relatively abundant serum proteins associated with the host response. Methods Eighty-four antibodies, targeting a wide range of serum proteins, were spotted onto nitrocellulose-coated microscope slides. The abundances of the corresponding proteins were measured in 80 serum samples, from 24 newly diagnosed subjects with lung cancer, 24 healthy controls, and 32 subjects with chronic obstructive pulmonary disease (COPD). Two-color rolling-circle amplification was used to measure protein abundance. Results Seven of the 84 antibodies gave a significant difference (p < 0.01) for the lung cancer patients as compared to healthy controls, as well as compared to COPD patients. Proteins that exhibited higher abundances in the lung cancer samples relative to the control samples included C-reactive protein (CRP; a 13.3 fold increase), serum amyloid A (SAA; a 2.0 fold increase), mucin 1 and α-1-antitrypsin (1.4 fold increases). The increased expression levels of CRP and SAA were validated by Western blot analysis. Leave-one-out cross-validation was used to construct Diagonal Linear Discriminant Analysis (DLDA) classifiers. At a cutoff where all 56 of the non-tumor samples were correctly classified, 15/24 lung tumor patient sera were correctly classified. Conclusion Our results suggest that a distinctive serum protein profile involving abundant proteins may be observed in lung cancer patients relative to healthy subjects or patients with chronic disease and may have utility as part of strategies for detecting lung cancer. PMID:16117833

  2. 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.

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

    PubMed

    Hestmark, Geir; Skogesal, Olav; Skullerud, Øystein

    2007-01-01

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

  4. 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

  5. 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.

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

    PubMed

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

    2010-06-01

    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

  7. 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.

  8. 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

  9. Abundance Analysis of the Silicon Star HR 6958

    NASA Astrophysics Data System (ADS)

    Kato, Ken-Ichi

    2003-12-01

    The elemental composition of the chemically peculiar star HR6958 has been studied with emphasis on doubly ionized rare earths. A visual region spectrum taken with the ELODIE spectrograph at the Haute-Provence Observatory was analyzed. A total of 40 elements including Pr III, Nd III, Tb III, Dy III, Ho III, and Er III were identified and their abundances computed. He is deficient by over 1dex with respect to the Sun; the light elements (C-Ca), except for Si, have solar abundances; the iron group elements (Sc-Fe) are overabundant by 1 dex to 2dex, with Ti and Cr highly overabundant; and the lanthanide rare earths are overabundant by 3dex to 4dex. This abundance pattern with He deficient, Si, Ti, Cr, Sr, and Pr overabundant indicates that HR6958 is a member of Si stars.

  10. 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

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

    SciTech Connect

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

    2006-02-15

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

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

    PubMed Central

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

    2010-01-01

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

  13. Genomic analysis of membrane protein families: abundance and conserved motifs

    PubMed Central

    Liu, Yang; Engelman, Donald M; Gerstein, Mark

    2002-01-01

    Background Polytopic membrane proteins can be related to each other on the basis of the number of transmembrane helices and sequence similarities. Building on the Pfam classification of protein domain families, and using transmembrane-helix prediction and sequence-similarity searching, we identified a total of 526 well-characterized membrane protein families in 26 recently sequenced genomes. To this we added a clustering of a number of predicted but unclassified membrane proteins, resulting in a total of 637 membrane protein families. Results Analysis of the occurrence and composition of these families revealed several interesting trends. The number of assigned membrane protein domains has an approximately linear relationship to the total number of open reading frames (ORFs) in 26 genomes studied. Caenorhabditis elegans is an apparent outlier, because of its high representation of seven-span transmembrane (7-TM) chemoreceptor families. In all genomes, including that of C. elegans, the number of distinct membrane protein families has a logarithmic relation to the number of ORFs. Glycine, proline, and tyrosine locations tend to be conserved in transmembrane regions within families, whereas isoleucine, valine, and methionine locations are relatively mutable. Analysis of motifs in putative transmembrane helices reveals that GxxxG and GxxxxxxG (which can be written GG4 and GG7, respectively; see Materials and methods) are among the most prevalent. This was noted in earlier studies; we now find these motifs are particularly well conserved in families, however, especially those corresponding to transporters, symporters, and channels. Conclusions We carried out a genome-wide analysis on patterns of the classified polytopic membrane protein families and analyzed the distribution of conserved amino acids and motifs in the transmembrane helix regions in these families. PMID:12372142

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. Abundances of TC and related elements in stars of type M, MS, and S

    NASA Astrophysics Data System (ADS)

    Vanture, Andrew D.; Wallerstein, George; Brown, Jeffrey A.; Bazan, Grant

    1991-11-01

    Abundances of Co, Zr, Nb, and Tc relative to V have been derived for a sample of ten M and MS stars from 0.10 A/pixel and 0.04 A/pixel Reticon spectra. On a scale with log N(H) = 12.0 and log N(V) = 4.0, it is found that log N(Tc) is about 1.4 for M stars 1.0 MS stars with Tc. It has been suggested by Dominy and Wallerstein that the presence of Tc in M stars which show no enhancements of other s-process elements can be explained by a 'mini s-process'. Detailed calculations and the observed abundances and Tc and related elements presented in this study put this interpretation in doubt. The observations also fail to support the alternative hypothesis suggested by Malaney and Lattanzio that Tc is produced by the photofission of Th and U.

  20. 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.

  1. Patterns of ant (Hymenoptera: Formicidae) richness and relative abundance along an aridity gradient in Western Venezuela.

    PubMed

    Pérez-Sánchez, A J; Lattke, J E; Viloria, A L

    2013-04-01

    In xeric ecosystems, ant diversity response to aridity varies with rainfall magnitude and gradient extension. At a local scale and with low precipitation regimes, increased aridity leads to a reduction of species richness and an increased relative abundance for some ant species. In order to test this pattern in tropical environments, ant richness and relative abundance variation were evaluated along 35 km of an aridity gradient in the Araya Peninsula, state of Sucre, Venezuela. Three sampling stations comprising five transects each were set up. Pitfall traps and direct collecting from vegetation were assessed per transect. Overall, 52 species, 23 genera, and 7 subfamilies of ants were recorded in the peninsula. The total number of species and genera recorded by both sampling stations and transects decreased linearly with increasing aridity. Total relative abundance was highest in the most arid portion of the peninsula, with Crematogaster rochai (Forel) and Camponotus conspicuus zonatus (Emery) (Hymenoptera: Formicidae) being the numerically dominant species. Spatial and multivariate analyses revealed significant changes in ant composition every 11 km of distance, and showed a decrease of ant diversity with the increase of harsh conditions in the gradient. Here, we discuss how local geographic and topographic features of Araya originate the aridity gradient and so affect the microhabitat conditions for the ant fauna.

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

    SciTech Connect

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

    2014-03-10

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

  3. 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.

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

    PubMed

    Fleming, Genie M; Diffendorfer, James E; Zedler, Paul H

    2009-12-01

    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.

  5. 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

  6. Chemical analysis of CH stars - II. Atmospheric parameters and elemental abundances

    NASA Astrophysics Data System (ADS)

    Karinkuzhi, Drisya; Goswami, Aruna

    2015-01-01

    We present detailed chemical analyses for a sample of 12 stars selected from the CH star catalogue of Bartkevicius. The sample includes two confirmed binaries, four objects that are known to show radial velocity variations and the rest with no information on the binary status. A primary objective is to examine if all these objects exhibit chemical abundances characteristics of CH stars, based on detailed chemical composition study using high-resolution spectra. We have used high-resolution (R ˜ 42 000) spectra from the ELODIE archive. These spectra cover 3900 to 6800 Å in the wavelength range. We have estimated the stellar atmospheric parameters, the effective temperature Teff, the surface gravity log g, and metallicity [Fe/H] from local thermodynamic equilibrium analysis using model atmospheres. Estimated temperatures of these objects cover a wide range from 4200 to 6640 K, the surface gravity from 0.6 to 4.3 and metallicity from -0.13 to -1.5. We report updates on elemental abundances for several heavy elements, Sr, Y, Zr, Ba, La, Ce, Pr, Nd, Sm, Eu and Dy. For the object HD 89668, we present the first abundance analyses results. Enhancement of heavy elements relative to Fe, a characteristic property of CH stars is evident from our analyses in the case of four objects, HD 92545, HD 104979, HD 107574 and HD 204613. A parametric-model-based study is performed to understand the relative contributions from the s- and r-process to the abundances of the heavy elements.

  7. Label-free relative quantification method for low-abundance glycoproteins in human serum by micrOTOF-Q.

    PubMed

    Hao, Piliang; Ren, Yan; Xie, Yongming

    2009-06-01

    In this study, a label-free relative quantification strategy was developed for quantifying low-abundance glycoproteins in human serum. It included three steps: (1) immunodepletion of 12 high-abundance proteins, (2) enrichment of low-abundance glycoproteins by multi-lectin column, (3) relative quantification of them between different samples by micrOTOF-Q. We also evaluated the specificity and efficiency of immunodepletion, the accuracy of protein quantification and the possible influence of immunodepletion, glycoprotein enrichment, trypsin digestion and peptide ionization on quantification. In conclusion, the relative quantification method can be effectively applied to the screening of low-abundance biomarkers.

  8. 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.

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

    PubMed

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

    2006-06-01

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

  10. 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.

  11. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  13. 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.

  14. The relative importance of resources and natural enemies in determining herbivore abundance: thistles, tephritids and parasitoids.

    PubMed

    Walker, Matthew; Hartley, Susan E; Jones, T Hefin

    2008-09-01

    1. The relative importance of host-plant resources and natural enemies in influencing the abundance of insect herbivores was investigated in potted plant and natural population experiments, using tephritid (Diptera: Tephritidae) flies, their host plant, creeping thistle Cirsium arvense, and their Hymenoptera parasitoids. 2. Experimental manipulation of host-plant quality (i.e. levels of host-plant nutrients) and resource availability (i.e. the number of buds) increased tephritid abundance. There was no evidence that the seed-feeding tephritid fly Xyphosia miliaria preferentially oviposited on fertilized C. arvense. 3. At low thistle densities, X. miliaria showed a constant rate of resource exploitation. At higher thistle densities, a threshold was detected, above which additional buds were not attacked. 4. Parasitism attack was variable across host (tephritid) densities but levels of parasitism were consistently higher on the fertilized thistles. 5. Experimental manipulation of host-plant quality and resource availability (quantity) not only directly affects the tephritid population but also, indirectly, leads to high rates of parasitism. Both chemical and physical characteristics of host plants affect the performance of natural enemies. 6. Both top-down and bottom-up forces act to influence tephritid abundance, with bottom-up influences appearing to be the most important.

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

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

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

  16. 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.

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

    PubMed Central

    Rashid, Mamoon; Pain, Arnab

    2013-01-01

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

  18. The Faber-Jackson relation and Fundamental Plane from halo abundance matching

    NASA Astrophysics Data System (ADS)

    Desmond, Harry; Wechsler, Risa H.

    2017-02-01

    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 that 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. This implies that additional correlations between galaxy and halo variables may be required to fully reconcile these models with elliptical galaxy scaling relations.

  19. Helminth parasitism in two closely related South African rodents: abundance, prevalence, species richness and impinging factors.

    PubMed

    Spickett, Andrea; Junker, Kerstin; Krasnov, Boris R; Haukisalmi, Voitto; Matthee, Sonja

    2017-04-01

    We investigated patterns of helminth infection in two closely related rodents (social Rhabdomys pumilio occurring mainly in xeric habitats and solitary R. dilectus occurring mainly in mesic habitats) at 20 localities in different biomes of South Africa and asked if between-species differences were mainly caused by difference in sociality or difference in environmental conditions of their respective habitats. Helminths recovered from the gastrointestinal tract totalled 11 nematode and 5 cestode species from R. pumilio and 19 nematode and 7 cestode species from R. dilectus. In both hosts, mean abundance and prevalence of nematodes were higher compared to cestodes. Cestode infection as well as nematode abundance, species richness or prevalence did not differ between the two rodents. However, incidence of nematode infection was significantly higher in R. dilectus than in R. pumilio. Moreover, nematode numbers and species richness in infracommunities of R. pumilio inhabiting the relatively more xeric Karoo biome were significantly lower than in those inhabiting the relatively less xeric Fynbos biome. Although we could not unequivocally distinguish between effects of host sociality and environmental factors on the number of individuals and species of helminths in the two hosts, differences in the incidence of nematode infection between R. pumilio and R. dilectus as well as differences in the number of nematode individuals and species between R. pumilio from the Fynbos and the Karoo suggested the effect of environmental conditions on helminth infection to be more important than that of sociality.

  20. The Hobby-Eberly Telescope Chemical Abundances of Stars in the Halo (CASH) Project III. Abundance Analysis of Three Bright Hamburg/ESO Survey Stars

    NASA Astrophysics Data System (ADS)

    Davies, L. A.; Frebel, A.; Cowan, J. J.; Allende Prieto, C.; Sneden, C.

    2008-08-01

    We present an abundance analysis of three newly discovered stars from the Hamburg/ESO survey for which HET observations have been obtained as part of the CASH project. Light elemental abundances of all three stars agree with those of other metal-poor stars. This means that they likely formed from well-mixed gas. Upper limits on the heavier neutron-capture abundances have not eliminated the possibility that these stars are r-process enhanced. However, the measured barium abundances are rather low.

  1. Seasonal variations in developmental competence and relative abundance of gene transcripts in buffalo (Bubalus bubalis) oocytes.

    PubMed

    Abdoon, Ahmed S; Gabler, Christoph; Holder, Christoph; Kandil, Omaima M; Einspanier, Ralf

    2014-11-01

    Hot season is a major constraint to production and reproduction in buffaloes. The present work aimed to investigate the effect of season on ovarian function, developmental competence, and the relative abundance of gene expression in buffalo oocytes. Three experiments were conducted. In experiment 1, pairs of buffalo ovaries were collected during cold season (CS, autumn and winter) and hot season (HS, spring and summer), and the number of antral follicles was recorded. Cumulus oocyte complexes (COCs) were aspirated and evaluated according to their morphology into four Grades. In experiment 2, Grade A and B COCs collected during CS and HS were in vitro matured (IVM) for 24 hours under standard conditions at 38.5 °C in a humidified air of 5% CO2. After IVM, cumulus cells were removed and oocytes were fixed, stained with 1% aceto-orcein, and evaluated for nuclear configuration. In vitro matured buffalo oocytes harvested during CS or HS were in vitro fertilized (IVF) using frozen-thawed buffalo semen and cultured in vitro to the blastocyst stage. In experiment 3, buffalo COCs and in vitro matured oocytes were collected during CS and HS, and then snap frozen in liquid nitrogen for gene expression analysis. Total RNA was extracted from COCs and in vitro matured oocytes, and complementary DNA was synthesized; quantitative Reverse Transcription-Polymerase Chain Reaction was performed for eight candidate genes including GAPDH, ACTB, B2M, GDF9, BMP15, HSP70, and SOD2. The results indicated that HS significantly (P < 0.01) decreased the number of antral follicles and the number of COCs recovered per ovary. The number of Grade A, B, and C COCs was lower (P < 0.05) during HS than CS. In vitro maturation of buffalo oocytes during HS significantly (P < 0.01) reduced the number of oocytes reaching the metaphase II stage and increased the percentage of degenerated oocytes compared with CS. Oocytes collected during HS also showed signs of cytoplasmic degeneration. After IVF

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

    USGS Publications Warehouse

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

    2002-01-01

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

  3. 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.

  4. A toy model of prebiotic peptide evolution: the possible role of relative amino acid abundances.

    PubMed

    Polanco, Carlos; Buhse, Thomas; Samaniego, José Lino; Castañón González, Jorge Alberto

    2013-01-01

    This paper presents a mathematical-computational toy model based on the assumed dynamic principles of prebiotic peptide evolution. Starting from a pool of amino acid monomers, the model describes in a generalized manner the generation of peptides and their sequential information. The model integrates the intrinsic and dynamic key elements of the initiation of biopolymerization, such as the relative amino acid abundances and polarities, as well as the oligomer reversibility, i.e. fragmentation and recombination, and peptide self-replication. Our modeling results suggest that the relative amino acid abundances, as indicated by Miller-Urey type electric discharge experiments, played a principal role in the early sequential information of peptide profiles. Moreover, the computed profiles display an astonishing similarity to peptide profiles observed in so-called biological common ancestors found in the following three microorganisms; E. coli, M. jannaschii, and S. cereviasiae. The prebiotic peptide fingerprint was obtained by the so-called polarity index method that was earlier reported as a tool for the identification of cationic amphipathic antibacterial short peptides.

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

    PubMed Central

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

    1995-01-01

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

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

    SciTech Connect

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

    2010-07-15

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

  7. Long-term abundance patterns of macroalgae in relation to environmental variables in the Tagus Estuary (Portugal)

    NASA Astrophysics Data System (ADS)

    Sousa-Dias, Abel; Melo, Ricardo A.

    2008-01-01

    Seasonal and inter-annual patterns of macroalgal abundance in a Tagus Estuary oyster reef are described. Macroalgal abundance was estimated as canopy percent cover by three permanent point intercept transects over a 7-year period. Four categories were defined, corresponding to bare substrate and three different macroalgal functional-form groups: (1) ULVA, foliose group, included Ulva spp.; (2) GRACIL, terete corticated macrophyte group, included only Gracilaria gracilis; and (3) FILAM, small (<10 cm) filamentous group, including eight species. A canonical correspondence analysis (CCA) showed that: (1) ULVA were associated with long and hot days, being usually dominant during spring and especially summer; (2) FILAM were associated with mild temperatures and relatively long days, abundant in spring but showed frequent peaks in summer; and (3) GRACIL were also favoured by spring season, although associated to lower temperature and less daylight hours than FILAM. GRACIL and FILAM were present throughout the year. On the contrary, ULVA were absent or with low cover during colder periods. A negative correlation between GRACIL and FILAM seems to indicate competition between the two categories. The applied models explained 23.3% of the temporal variance in category abundance. Rainfall negatively affected macroalgal cover, as indicated by the positive correlation between rainfall and bare substrate. Our conclusions are in agreement with previous studies that consider algae as excellent environmental integrators, even on a small scale, due to a strong link between the macroalgal communities and relevant environmental variables. It is also relevant that this study used open-access databases of environmental variables, which open up new possibilities for mining existing data resources in new ways. Due to large inter-annual variability, long-term studies are essential to understand population dynamics in estuarine phytobenthic communities.

  8. Abundance analysis of the halo giant HD 122563 with three-dimensional model stellar atmospheres

    NASA Astrophysics Data System (ADS)

    Collet, R.; Nordlund, Å.; Asplund, M.; Hayek, W.; Trampedach, R.

    We present a preliminary local thermodynamic equilibrium (LTE) abundance analysis of the template halo red giant HD122563 based on a realistic, three-dimensional (3D), time-dependent, hydrodynamical model atmosphere of the very metal-poor star. We compare the results of the 3D analysis with the abundances derived by means of a standard LTE analysis based on a classical, 1D, hydrostatic model atmosphere of the star. Due to the different upper photospheric temperature stratifications predicted by 1D and 3D models, we find large, negative, 3D-1D LTE abundance differences for low-excitation OH and Fe I lines. We also find trends with lower excitation potential in the derived Fe LTE abundances from Fe I lines, in both the 1D and 3D analyses. Such trends may be attributed to the neglected departures from LTE in the spectral line formation calculations.

  9. A Differential Abundance Analysis of the Wide Binary Pair HD 219542 A and B

    NASA Astrophysics Data System (ADS)

    Sadakane, Kozo; Ohkubo, Michiko; Honda, Satoshi

    2003-10-01

    The abundances of 22 elements (Li through Zr) in the A and B components of the visual pair HD 219542 were determined and compared using a differential analysis technique. Both components were found to be metal rich, [Fe/H] = +0.13, in the brighter component (A) and [Fe/H] = +0.08 in the fainter component (B). The abundances of three elements (Sc, Ti, and Fe) are definitely higher (by 0.05dex) in component A than in component B. On the other hand, both components have nearly identical abundances of the light element Si. No evidence has been found for differences in the abundances for C, O, Na, Mg, Al, S, Ca, V, Cr, Mn, Co, Ni, Cu, Zn, Sr, Y, and Zr. No clear correlation has been found between the differences in the abundance between the two components and the condensation temperature (Tc).

  10. Statistical analysis from recent abundance determinations in HgMn stars

    NASA Astrophysics Data System (ADS)

    Ghazaryan, S.; Alecian, G.

    2016-08-01

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

  11. 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.

  12. 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.

  13. Species richness and abundance of forest birds in relation to radiation at Chernobyl.

    PubMed

    Moller, A P; Mousseau, T A

    2007-10-22

    The effects of low-level radiation on the abundance of animals are poorly known, as are the effects on ecosystems and their functioning. Recent conclusions from the UN Chernobyl forum and reports in the popular media concerning the effects of radiation from Chernobyl on animals have left the impression that the Chernobyl exclusion zone is a thriving ecosystem, filled with an increasing number of rare species. Surprisingly, there are no standardized censuses of common animals in relation to radiation, leaving the question about the ecological effects of radiation unresolved. We conducted standardized point counts of breeding birds at forest sites around Chernobyl differing in level of background radiation by over three orders of magnitude. Species richness, abundance and population density of breeding birds decreased with increasing level of radiation, even after controlling statistically for the effects of potentially confounding factors such as soil type, habitat and height of the vegetation. This effect was differential for birds eating soil invertebrates living in the most contaminated top soil layer. These results imply that the ecological effects of Chernobyl on animals are considerably greater than previously assumed.

  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. Ion Mobility Mass Spectrometry Direct Isotope Abundance Analysis

    SciTech Connect

    Manuel J. Manard, Stephan Weeks, Kevin Kyle

    2010-05-27

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

  16. Helium Abundance of Saturn from Cassini VIMS and CIRS Combined Analysis

    NASA Astrophysics Data System (ADS)

    Banfield, D. J.; Gierasch, P. J.; Conrath, B. J.; Nicholson, P. D.; Hedman, M. M.

    2013-12-01

    The Cassini VIMS instrument has obtained about 11 stellar occultations of sufficient quality that they can be used to infer the atmospheric structure where the stellar light cuts through Saturn's atmosphere on its way to thespacecraft. For 5 of these stellar occultations, the Cassini CIRS instrument obtained spectra of Saturn's limb at nearly the same time and place. By combining these observations, we have previously demonstrated that we can produce an estimate of the Helium abundance on Saturn (e.g., Banfield et al., DPS BAAS, 2011). The Helium abundance of Saturn is of great interest due to its leverage on our understanding of the formation and internal evolution processes of the giant planets in our Solar System, as well as giant exoplanets in other solar systems. The Helium abundance is also of significant interest due to a long-standing discrepancy between estimates obtained using a combined IR Spectra/Radio Science Occultation technique (He/H2~0.03, Conrath et al., '84) and those obtained using IR spectra alone (He/H2~0.13, Conrath & Gautier, '00). We will present our results from the Cassini VIMS/CIRS analysis of this problem. The technique uses the Cassini CIRS limb spectra to produce an estimate of the temperature profile between about 0.01 mbar and 5 mbar. The VIMS stellar occultations are used to produce a scale height profile over a similar vertical region, but with much better information content (and thus tighter constraints) between about 1 mbar and 5 mbar. By comparing these two results and demanding consistency we can infer the mean molecular mass of the atmosphere (and thus the Helium abundance) in the region of overlap (~1mbar to 5 mbar). Realistically, both sets of observations are quite challenging to perform. The signal levels are relatively low for the CIRS limb spectra (compared to nadir spectra), making calibration especially challenging. Not all VIMS occultations are successful with variable stellar baselines or stray light corrupting the

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

    PubMed

    Riley, S J; Malecki, R A

    2001-09-01

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

  18. 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.

  19. 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.

  20. 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.

  1. Global Analysis of Condition-specific Subcellular Protein Distribution and Abundance*

    PubMed Central

    Jung, Sunhee; Smith, Jennifer J.; von Haller, Priska D.; Dilworth, David J.; Sitko, Katherine A.; Miller, Leslie R.; Saleem, Ramsey A.; Goodlett, David R.; Aitchison, John D.

    2013-01-01

    Cellular control of protein activities by modulation of their abundance or compartmentalization is not easily measured on a large scale. We developed and applied a method to globally interrogate these processes that is widely useful for systems-level analyses of dynamic cellular responses in many cell types. The approach involves subcellular fractionation followed by comprehensive proteomic analysis of the fractions, which is enabled by a data-independent acquisition mass spectrometry approach that samples every available mass to charge channel systematically to maximize sensitivity. Next, various fraction-enrichment ratios are measured for all detected proteins across different environmental conditions and used to group proteins into clusters reflecting changes in compartmentalization and relative conditional abundance. Application of the approach to characterize the response of yeast proteins to fatty acid exposure revealed dynamics of peroxisomes and novel dynamics of MCC/eisosomes, specialized plasma membrane domains comprised of membrane compartment occupied by Can1 (MCC) and eisosome subdomains. It also led to the identification of Fat3, a fatty acid transport protein of the plasma membrane, previously annotated as Ykl187. PMID:23349476

  2. 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.

  3. THE RELATIVE ABUNDANCE OF ISOLATED CLUSTERS AS A PROBE OF DARK ENERGY

    SciTech Connect

    Lee, Jounghun

    2012-06-10

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

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

    NASA Astrophysics Data System (ADS)

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

    2004-12-01

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

  5. MGA (Multi-Group Analysis): A gamma-ray spectrum analysis code for determining plutonium isotopic abundances

    SciTech Connect

    Gunnink, R

    1990-04-03

    Nondestructive measurements of x-ray and gamma-ray emissions can be used to analyze a sample for plutonium. This report describes the methods and algorithms we have developed for analyzing gamma-ray spectra obtained by using a germanium detector system to accurately determine the relative abundances of various actinide isotopes in a sample. Our methodology requires no calibrations and can be used to measure virtually any size and type of plutonium sample. Measurement times can be as short as a few minutes; measurements are frequently accurate to within 1%. Our methods have been programmed into a computerized analysis code called MGA (Multi-Group Analysis). Our current versions can be run on personal computers (IBM type) and on the DEC VAX microcomputer. Spectral analysis times are usually far less than a minute. 28 refs., 26 figs., 1 tab.

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

    SciTech Connect

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

    2009-12-01

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

  7. The relative influence of abundance and priority effects on colonization success in a coral-reef fish

    NASA Astrophysics Data System (ADS)

    Geange, Shane W.; Poulos, Davina E.; Stier, Adrian C.; McCormick, Mark I.

    2017-03-01

    The sequence of species colonization is increasingly recognized as an important determinant of community structure, yet the significance of sequence of arrival relative to colonizer abundance is seldom assessed. We manipulated the magnitude and timing of coral-reef fish settlement to investigate whether the competitive dominance of early-arriving Ambon damselfish (i.e., a priority effect) decreased in strength with increasing abundance of late-arriving lemon damselfish. Sequence of arrival had a stronger effect on survival than the number of competing individuals. Relative to when both species arrived simultaneously, lemon damselfish were less aggressive, avoided competitive interactions more frequently and experienced depressed survival when they arrived later than Ambon damselfish, with these effects occurring independently of lemon damselfish abundance. These results suggest priority effects are more important than colonizer abundance and should motivate the integration of priority effects into future studies of density dependence to determine their relative importance.

  8. 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.

  9. Individual differences in relative hemispheric alpha abundance and cognitive responses to persuasive communications.

    PubMed

    Cacioppo, J T; Petty, R E; Quintanar, L R

    1982-09-01

    Three experiments are reported investigating individual differences in interhemispheric electroencephalogram (EEG) activity and cognitive responses to persuasion. Experiment 1 indicated that subjects who were characterized by relative left hemispheric EEG activity over the parietal areas also produced a less affectively polarized profile of thought listings about the persuasive communication. Moreover, this individual difference emerged only when subjects were confronted by the forewarning and message; the basal patterns of interhemispheric EEG activity, which were obtained prior to the announcement of the attitudinal recommendation, did not portend distinguishable profiles of cognitive responding. Experiment 2 replicated the major findings of Experiment 1 using different topics and a within-subjects rather than a between-subjects design. Further analyses suggested that thinking about an attitude issue rather than responding to a persuasive communication was sufficient to obtain the above relationship between interhemispheric EEG alpha abundance and cognitive response. Experiment 3 used Tesser's time-to-think procedure to assess interhemispheric EEG patterning as a function of the affective polarization of topic-relevant thinking. The results supported the expectation that as subjects thought longer about attitude issues they exhibited a shifting of relative hemispheric EEG activity from the left toward the right parietal areas of the cerebral hemispheres. The significance and limitations of these findings for research on attitude change and the utility of including psychophysiological approaches to elusive research problems in personality and social psychology are discussed.

  10. 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.

  11. Relative abundance and distribution of fisheries influence risk of seabird bycatch

    PubMed Central

    Soriano-Redondo, Andrea; Cortés, Verónica; Reyes-González, José Manuel; Guallar, Santi; Bécares, Juan; Rodríguez, Beneharo; Arcos, José Manuel; González-Solís, Jacob

    2016-01-01

    Fisheries provide an abundant and predictable food source for many pelagic seabirds through discards, but also pose a major threat to them through bycatch, threatening their populations worldwide. The reform of the European Common Fisheries Policy (CFP), which intends to ban discards through the landing obligation of all catches, may force seabirds to seek alternative food sources, such as baited hooks from longlines, increasing bycatch rates. To test this hypothesis we performed a combined analysis of seabird-fishery interactions using as a model Scopoli’s shearwaters Calonectris diomedea in the Mediterranean. Tracking data showed that the probability of shearwaters attending longliners increased exponentially with a decreasing density of trawlers. On-board observations and mortality events corroborated this result: the probability of birds attending longliners increased 4% per each trawler leaving the longliner proximity and bird mortality increased tenfold when trawlers were not operating. Therefore, the implementation of the landing obligation in EU waters will likely cause a substantial increase in bycatch rates in longliners, at least in the short-term, due to birds switching from trawlers to longliners. Thus the implementation of the landing obligation must be carefully monitored and counterbalanced with an urgent implementation of bycatch mitigation measures in the longline fleet. PMID:27876852

  12. Relative abundance and distribution of fisheries influence risk of seabird bycatch.

    PubMed

    Soriano-Redondo, Andrea; Cortés, Verónica; Reyes-González, José Manuel; Guallar, Santi; Bécares, Juan; Rodríguez, Beneharo; Arcos, José Manuel; González-Solís, Jacob

    2016-11-23

    Fisheries provide an abundant and predictable food source for many pelagic seabirds through discards, but also pose a major threat to them through bycatch, threatening their populations worldwide. The reform of the European Common Fisheries Policy (CFP), which intends to ban discards through the landing obligation of all catches, may force seabirds to seek alternative food sources, such as baited hooks from longlines, increasing bycatch rates. To test this hypothesis we performed a combined analysis of seabird-fishery interactions using as a model Scopoli's shearwaters Calonectris diomedea in the Mediterranean. Tracking data showed that the probability of shearwaters attending longliners increased exponentially with a decreasing density of trawlers. On-board observations and mortality events corroborated this result: the probability of birds attending longliners increased 4% per each trawler leaving the longliner proximity and bird mortality increased tenfold when trawlers were not operating. Therefore, the implementation of the landing obligation in EU waters will likely cause a substantial increase in bycatch rates in longliners, at least in the short-term, due to birds switching from trawlers to longliners. Thus the implementation of the landing obligation must be carefully monitored and counterbalanced with an urgent implementation of bycatch mitigation measures in the longline fleet.

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

    PubMed

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

    2014-01-01

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

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

    PubMed

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

    2016-05-01

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

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

    PubMed

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

    2011-08-01

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

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

    PubMed

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

    2016-01-01

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

  17. An optical region elemental abundance analysis of the chemically peculiar HgMn star chi Lupi

    NASA Technical Reports Server (NTRS)

    Wahlgren, Glenn M.; Adelman, Saul J.; Robinson, Richard D.

    1994-01-01

    The optical spectrum of the chemically peculiar HgMn type binary star chi Lupi has been analyzed to determine atmospheric parameters and elemental abundances. Echelle spectra were obtained with the 3.9 m Anglo-Australian telescope to exploit the extreme shape-lined nature of the spectrum. This study was undertaken in support of ultraviolet analyses currently underway that utilize echell spectra obtained with the Hubble Space Telescope. For the B9.5 V primary star we obtain T(sub eff) = 10650 K, log g = 3.9, and xi = 0 km/s, while for the A2 V secondary, T(sub eff) = 9200 K, log g = 4.0, and xi = 2 km/s. Most of the elemental abundances are typical of HgMn stars with similar T(sub eff) showing an overall iron-peak elemental abundance distribution that is basically solar in nature with enhancement of the light elements Si, P, and S, as well as all detected elements heavier than the iron group. Abundances for several elements have been determined for the first time in this star, including several of the rare-earths. The secondary star spectrum shows Am star characteristics. We also discuss the relative merits of the equivalent width and synthetic spectrum techniques in determining the elemental abundences, concluding that the synthetic spectrum technique is necessary for obtaining abundances with the utmost accuracy.

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

    NASA Technical Reports Server (NTRS)

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

    1985-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Krasnopolsky, Vladimir

    2000-12-01

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

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

    USGS Publications Warehouse

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

    2007-01-01

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

  1. Hydrocarbons and fuels analyses with the supersonic gas chromatography mass spectrometry--the novel concept of isomer abundance analysis.

    PubMed

    Fialkov, Alexander B; Gordin, Alexander; Amirav, Aviv

    2008-06-27

    Hydrocarbon analysis with standard GC-MS is confronted by the limited range of volatile compounds amenable for analysis and by the similarity of electron ionization mass spectra for many compounds which show weak or no molecular ions for heavy hydrocarbons. The use of GC-MS with supersonic molecular beams (Supersonic GC-MS) significantly extends the range of heavy hydrocarbons that can be analyzed, and provides trustworthy enhanced molecular ion to all hydrocarbons. In addition, unique isomer mass spectral features are obtained in the ionization of vibrationally cold hydrocarbons. The availability of molecular ions for all hydrocarbons results in the ability to obtain unique chromatographic isomer distribution patterns that can serve as a new method for fuel characterization and identification. Examples of the applicability and use of this novel isomer abundance analysis (IAA) method to diesel fuel, kerosene and oil analyses are shown. It is suggested that in similarity to the "three ions method" for identification purposes, three isomer abundance patterns can serve for fuel characterization. The applications of the Supersonic GC-MS for engine motor oil analysis and transformer oil analysis are also demonstrated and discussed, including the capability to achieve fast 1-2s sampling without separation for oil and fuel fingerprinting. The relatively fast analysis of biodiesel is described, demonstrating the provision of molecular ions to heavy triglycerides. Isomer abundance analysis with the Supersonic GC-MS could find broad range of applications including petrochemicals and fuel analysis, arson analysis, environmental oil/fuel spill analysis, fuel adulteration analysis and motor oil analysis.

  2. [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.

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

    USGS Publications Warehouse

    Keeley, Jon E.

    2003-01-01

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

  4. 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.

  5. Zooplankton abundance in relation to state and type of intrusions onto the southeastern United States shelf during summer

    SciTech Connect

    Paffenhoefer, G.A.; Wester, B.T.; Nicholas, W.D.

    1984-01-01

    The vertical distribution of zooplankton on the continental shelf of northeastern Florida was determined in and around upwelling events and related to concentrations of particulate matter. Doliolida and the cladoceran Penilia avirostris were significantly more abundant in upwelled water < 22/sup 0/C and the cyclopoid genus Oncaea more abundant at warmer temperatures. The abundance of doliolida, Oithona and Oncaea in intrusions and the thermocline was significantly higher in older than in recently upwelled waters. The vertical sequences of the abundance of zooplankton and particulate matter (2-114 ..mu..m ESD) were identical. Zooplankton maxima co-occurred primarily with maxima in phytoplankton biomass (chlorophyll a) and only partly with primary productivity. 27 references, 16 figures, 6 tables.

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

    USGS Publications Warehouse

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

    1993-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-04-01

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

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

    SciTech Connect

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

    2015-07-20

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

  9. Comparative Analysis of Mars Odyssey GRS Chemical Abundances with Other Mission Global Datasets

    NASA Astrophysics Data System (ADS)

    Hahn, B. C.; McLennan, S. M.; Odyssey GRS Science Team

    2006-12-01

    The 2001 Mars Odyssey Gamma-Ray Spectrometer (GRS) instrument package has returned chemical abundance maps of the Martian surface for a suite of elements (Fe, Si, Cl, H, K, Th). Due to a low resolution (>250 km footprint), smoothing effects inherent to the instruments, and the data processing methods, analysis of smaller geologic features can be statistically problematic. However, mean elemental abundances can be determined for larger geologic provinces and specifically defined regions with enough areal extent to produce sufficiently robust statistics. Here we compare GRS-derived element abundances to other Martian global datasets in order to evaluate statistically and geologically meaningful differences. Although outlier regions exist, GRS data reveal a Martian surface more chemically homogeneous than the surfaces of the Earth or moon. Chemical variations are often subtle and difficult to discern. However, even with muted variation and large uncertainties, comparing GRS elemental means and other datasets still reveal statistically robust differences using standard z-statistic tests at high confidence intervals. Note that "statistically significant" differences may not be geologically significant. This method has been employed to determine subtle but statistically significant variations in several element abundances with apparent surface age (e.g., Fe and Cl abundances increase with younger ages; K and Th decrease with younger ages) revealing possible constraints on crustal evolution and surficial processes. We also compared the variations in elemental abundances to variations in specific mineralogies and dust abundance as determined by the Mars Global Surveyor (MGS) Thermal Emission Spectrometer (TES) instrument. This allows an important link between chemistry and mineralogy and further helps constrain the effects of surface dust on remote sensing data.

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

    PubMed

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

    2014-08-28

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

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

    PubMed Central

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

    2015-01-01

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

  12. Relative abundances in the low-metallicity dwarf irregular galaxy UGC 4483

    NASA Technical Reports Server (NTRS)

    Skillman, Evan D.

    1991-01-01

    UGC 4483 is a dwarf irregular galaxy in the M 81 group. Narrow-band optical imaging has revealed an H II region in UGC 4483 with an H-alpha flux of about 2 x 10 to the -13th erg/sq cm per A per s. Optical, UV and NIR spectroscopy of this H II region yield He, C, N, O, Ne, and S abundances for the ISM in this galaxy. With an oxygen abundance of 0.000021 12 + log(O/H) = 7.3, this galaxy is among the most metal-poor dwarf irregulars known to date. A comparison of the S/O abundance ratio in this galaxy with that in I Zw 18 supports the claim by Garnett (1990) that the S/O ratio is consistent with the solar ratio for low-metallicity dwarf irregulars. The C/O ratio in UGC 4483 is lower than that derived for I Zw 18 and, therefore, more in line with the trend seen in higher metallicity H II regions. The derived helium abundance is He/H = 0.075, which converts to a He mass fraction of 0.23, consistent with earlier determinations of the primordial He abundance.

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

    SciTech Connect

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

    2011-02-01

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

  14. Distribution and relative abundance of humpback whales in relation to environmental variables in coastal British Columbia and adjacent waters

    NASA Astrophysics Data System (ADS)

    Dalla Rosa, Luciano; Ford, John K. B.; Trites, Andrew W.

    2012-03-01

    Humpback whales are common in feeding areas off British Columbia (BC) from spring to fall, and are widely distributed along the coast. Climate change and the increase in population size of North Pacific humpback whales may lead to increased anthropogenic impact and require a better understanding of species-habitat relationships. We investigated the distribution and relative abundance of humpback whales in relation to environmental variables and processes in BC waters using GIS and generalized additive models (GAMs). Six non-systematic cetacean surveys were conducted between 2004 and 2006. Whale encounter rates and environmental variables (oceanographic and remote sensing data) were recorded along transects divided into 4 km segments. A combined 3-year model and individual year models (two surveys each) were fitted with the mgcv R package. Model selection was based primarily on GCV scores. The explained deviance of our models ranged from 39% for the 3-year model to 76% for the 2004 model. Humpback whales were strongly associated with latitude and bathymetric features, including depth, slope and distance to the 100-m isobath. Distance to sea-surface-temperature fronts and salinity (climatology) were also constantly selected by the models. The shapes of smooth functions estimated for variables based on chlorophyll concentration or net primary productivity with different temporal resolutions and time lags were not consistent, even though higher numbers of whales seemed to be associated with higher primary productivity for some models. These and other selected explanatory variables may reflect areas of higher biological productivity that favor top predators. Our study confirms the presence of at least three important regions for humpback whales along the BC coast: south Dixon Entrance, middle and southwestern Hecate Strait and the area between La Perouse Bank and the southern edge of Juan de Fuca Canyon.

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

    USGS Publications Warehouse

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

    2015-01-01

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

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

    SciTech Connect

    Jacobson, Heather R.; Frebel, Anna

    2015-07-20

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

  17. Spatial distribution of planktivorous fish schools in relation to krill abundance and local hydrography off Otago, New Zealand

    NASA Astrophysics Data System (ADS)

    O'Driscoll, Richard L.; McClatchie, Sam

    Side-scan sonar allows mapping of near-surface schools of fish, but it has seldom been used for this purpose. Data were collected off the coast of Otago, New Zealand for 21 days during 1994 to 1996 using a 130 kHz Klein 595 digital side-scan sonar. A total of 2198 schools were detected. Of these, 348 schools of barracouta ( Thyrsites atun), 67 schools of jack mackerel ( Trachurus murphyi), and 17 schools of slender tuna ( Allothunnus fallai) were identified. Barracouta schools were significantly smaller than schools of jack mackerel or slender tuna, but the size of schools was not related to state of tide, location, water depth, salinity, temperature, or density of krill. Fish schools were detected throughout daylight hours, but dispersed at night. Analysis of stomach contents revealed barracouta, jack mackerel and slender tuna were feeding on krill, Nyctiphanes australis, and fish schools occurred in areas with high densities of N. australis. Variability in the abundance of N. australis was related to salinity; catches were highest in a band of low-salinity water which was present in the study area following periods of high river runoff.

  18. Dynamin-related proteins Vps1p and Dnm1p control peroxisome abundance in Saccharomyces cerevisiae.

    PubMed

    Kuravi, Kasinath; Nagotu, Shirisha; Krikken, Arjen M; Sjollema, Klaas; Deckers, Markus; Erdmann, Ralf; Veenhuis, Marten; van der Klei, Ida J

    2006-10-01

    Saccharomyces cerevisiae contains three dynamin-related-proteins, Vps1p, Dnm1p and Mgm1p. Previous data from glucose-grown VPS1 and DNM1 null mutants suggested that Vps1p, but not Dnm1p, plays a role in regulating peroxisome abundance. Here we show that deletion of DNM1 also results in reduction of peroxisome numbers. This was not observed in glucose-grown dnm1 cells, but was evident in cells grown in the presence of oleate. Similar observations were made in cells lacking Fis1p, a protein involved in Dnm1p function. Fluorescence microscopy of cells producing Dnm1-GFP or GFP-Fis1p demonstrated that both proteins had a dual localization on mitochondria and peroxisomes. Quantitative analysis revealed a greater reduction in peroxisome number in oleate-induced vps1 cells relative to dnm1 or fis1 cells. A significant fraction of oleate-induced vps1 cells still contained two or more peroxisomes. Conversely, almost all cells of a dnm1 vps1 double-deletion strain contained only one, enlarged peroxisome. This suggests that deletion of DNM1 reinforces the vps1 peroxisome phenotype. Time-lapse imaging indicated that during budding of dnm1 vps1 cells, the single peroxisome present in the mother cell formed long protrusions into the developing bud. This organelle divided at a very late stage of the budding process, possibly during cytokinesis.

  19. Foraging ranges of insectivorous bats shift relative to changes in mosquito abundance.

    PubMed

    Gonsalves, Leroy; Law, Brad; Webb, Cameron; Monamy, Vaughan

    2013-01-01

    The need to develop effective management strategies for insectivorous bat populations requires an understanding of factors influencing habitat use. Availability of pest prey, such as mosquitoes is likely to be one such factor. To assess whether this is the case, we radio-tracked Vespadelus vulturnus Thomas (little forest bat), a predator of Aedes vigilax Skuse (saltmarsh mosquito), in saltmarsh and adjacent coastal swamp forest during periods of high and low Ae. vigilax abundance. When mosquito abundance in structurally-open saltmarsh was similar to the more cluttered coastal swamp forest, use of saltmarsh by V. vulturnus was disproportionately greater than its availability, with saltmarsh selected preferentially for foraging. However, at times of low Ae. vigilax abundance in saltmarsh, use of saltmarsh by V. vulturnus was reduced and all habitats were used in proportion to availability in the study area. This is the first radio-tracking study to demonstrate a shift in foraging range by an insectivorous bat species correlated with fluctuations in the distribution and abundance of a particular prey resource. The shift in foraging range by V. vulturnus, corresponding with a spatio-temporal variation in abundance of Ae. vigilax highlights the importance of mosquitoes as a dietary item. Broadscale pest control of Ae. vigilax may have ecological implications for the diet and habitat use of V. vulturnus. An adaptive management approach is proposed, whereby careful monitoring of insectivorous bat populations is recommended before and after any application of broadscale mosquito control measures. We also suggest a precautionary approach is taken such that broadscale control of mosquitoes avoids the lactation period of bats, a time when their energetic demands are greatest and when there is reduced risk of contracting mosquito-borne diseases transmitted by Ae. vigilax.

  20. Landscape level variation in tick abundance relative to seasonal migration in red deer.

    PubMed

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

    2013-01-01

    Partial migration is common among northern ungulates, typically involving an altitudinal movement for seasonally migratory individuals. The main driving force behind migration is the benefit of an extended period of access to newly emerged, high quality forage along the green up gradient with increasing altitude; termed the forage maturation hypothesis. Any other limiting factor spatially correlated with this gradient may provide extra benefits or costs to migration, without necessarily being the cause of it. A common ectoparasite on cervids in Europe is the sheep tick (Ixodes ricinus), but it has not been tested whether migration may lead to the spatial separation from these parasites and thus potentially provide an additional benefit to migration. Further, if there is questing of ticks in winter ranges in May before spring migration, deer migration may also play a role for the distribution of ticks. We quantified the abundance of questing sheep tick within winter and summer home ranges of migratory (n=42) and resident red deer (Cervus elaphus) individuals (n=32) in two populations in May and August 2009-2012. Consistent with predictions, there was markedly lower abundance of questing ticks in the summer areas of migrating red deer (0.6/20 m(2)), both when compared to the annual home range of resident deer (4.9/20 m(2)) and the winter home ranges of migrants (5.8/20 m(2)). The reduced abundances within summer home ranges of migrants were explained by lower abundance of ticks with increasing altitude and distance from the coast. The lower abundance of ticks in summer home ranges of migratory deer does not imply that ticks are the main driver of migration (being most likely the benefits expected from forage maturation), but it suggests that ticks may add to the value of migration in some ecosystems and that it may act to spread ticks long distances in the landscape.

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. Offspring production and self-superparasitism in the solitary ectoparasitoid Spalangia cameroni (Hymenoptera: Pteromalidae) in relation to host abundance.

    PubMed

    Böckmann, E A; Tormos, J; Beitia, F; Fischer, K

    2012-04-01

    Parasitoid fitness strongly depends on the availability and quality of hosts, which provide all resources required for larval development. Several factors, such as host size and previous parasitation, may affect host quality. Because self-superparasitism induces competition among a female's offspring, it should only occur if there is an imperfect recognition of self-parasitized hosts or if there is a fitness advantage to self-superparasitism. Against this background, we investigated self-superparasitism and offspring production in Spalangia cameroni (Hymenoptera: Pteromalidae) in relation to the abundance of a novel host, Ceratitis capitata (Diptera: Tephritidae). Individual pairs of parasitoids were provided with either two (low host abundance) or ten (high host abundance) pupae per day. Under high host abundance, lifetime fecundity (number of eggs laid), offspring number, number of pupae parasitized and hosts killed were greater than under low host abundance, whereas the number of eggs per host was lower; and the proportion of hosts that did not produce offspring tended to be lower. The latter suggests the occurrence of ovicide, when hosts are scarce due to an at least imperfect recognition of previously self-parasitized hosts. Offspring production per parasitized pupa was higher when hosts were scarce and levels of self-superparasitism high, suggesting the existence of beneficial effects of self-superparasitism.

  7. Zeptosens' protein microarrays: a novel high performance microarray platform for low abundance protein analysis.

    PubMed

    Pawlak, Michael; Schick, Eginhard; Bopp, Martin A; Schneider, Michael J; Oroszlan, Peter; Ehrat, Markus

    2002-04-01

    Protein microarrays are considered an enabling technology, which will significantly expand the scope of current protein expression and protein interaction analysis. Current technologies, such as two-dimensional gel electrophoresis (2-DE) in combination with mass spectrometry, allowing the identification of biologically relevant proteins, have a high resolving power, but also considerable limitations. As was demonstrated by Gygi et al. (Proc. Nat. Acad. Sci. USA 2000,97, 9390-9395), most spots in 2-DE, observed from whole cell extracts, are from high abundance proteins, whereas low abundance proteins, such as signaling molecules or kinases, are only poorly represented. Protein microarrays are expected to significantly expedite the discovery of new markers and targets of pharmaceutical interest, and to have the potential for high-throughput applications. Key factors to reach this goal are: high read-out sensitivity for quantification also of low abundance proteins, functional analysis of proteins, short assay analysis times, ease of handling and the ability to integrate a variety of different targets and new assays. Zeptosens has developed a revolutionary new bioanalytical system based on the proprietary planar waveguide technology which allows us to perform multiplexed, quantitative biomolecular interaction analysis with highest sensitivity in a microarray format upon utilizing the specific advantages of the evanescent field fluorescence detection. The analytical system, comprising an ultrasensitive fluorescence reader and microarray chips with integrated microfluidics, enables the user to generate a multitude of high fidelity data in applications such as protein expression profiling or investigating protein-protein interactions. In this paper, the important factors for developing high performance protein microarray systems, especially for targeting low abundant messengers of relevant biological information, will be discussed and the performance of the system will

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

    NASA Astrophysics Data System (ADS)

    Ivanov, Mikhail A.; Head, James W.

    2004-10-01

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

  9. Sulfate-reducing bacteria in marine sediment (Aarhus Bay, Denmark): abundance and diversity related to geochemical zonation.

    PubMed

    Leloup, Julie; Fossing, Henrik; Kohls, Katharina; Holmkvist, Lars; Borowski, Christian; Jørgensen, Bo Barker

    2009-05-01

    In order to better understand the main factors that influence the distribution of sulfate-reducing bacteria (SRB), their population size and their metabolic activity in high- and low-sulfate zones, we studied the SRB diversity in 3- to 5-m-deep sediment cores, which comprised the entire sulfate reduction zone and the upper methanogenic zone. By combining EMA (ethidium monoazide that can only enter damaged/dead cells and may also bind to free DNA) treatment with real-time PCR, we determined the distributions of total intact bacteria (16S rDNA genes) and intact SRB (dsrAB gene), their relative population sizes, and the proportion of dead cells or free DNA with depth. The abundance of SRB corresponded in average to 13% of the total bacterial community in the sulfate zone, 22% in the sulfate-methane transition zone and 8% in the methane zone. Compared with the total bacterial community, there were relatively less dead/damaged cells and free DNA present than among the SRB and this fraction did not change systematically with depth. By DGGE analysis, based on the amplification of the dsrA gene (400 bp), we found that the richness of SRB did not change with depth through the geochemical zones; but the clustering was related to the chemical zonation. A full-length clone library of the dsrAB gene (1900 bp) was constructed from four different depths (20, 110, 280 and 500 cm), and showed that the dsrAB genes in the near-surface sediment (20 cm) was mainly composed of sequences close to the Desulfobacteraceae, including marine complete and incomplete oxidizers such as Desulfosarcina, Desulfobacterium and Desulfococcus. The three other libraries were predominantly composed of Gram-positive SRB.

  10. Quantitative Analysis of the Spectrum of the B3 Abundance Standard iota Herculis

    NASA Astrophysics Data System (ADS)

    Peters, Geraldine J.; Adelman, S. J.; Gulliver, A.

    2010-01-01

    Iota Herculis is an ultrasharp-lined B3IV star that historically has been considered as an abundance standard for the early B stars. New abundances of the lighter and Fe group elements have been determined with the aid of high resolution spectral data from HST/STIS and the Dominion Astrophysical Observatory. The HST spectra were obtained with the STIS E140M and E230M gratings and cover the region 1160-2350 A with a 2-pixel spectral resolution that varies from 0.03-0.08 A. The DAO spectral atlas covers 3820-5350 A in the second order with a 2-pixel resolution 0.072 A. We compare theoretical spectra computed from the NLTE code TLUSTY/SYNSPEC (I. Hubeny & T. Lanz, ApJ, 439,875,1995) and the LTE code ATLAS9/SYNTHE (R. Kurucz, 1993, CD-ROMs 13 & 18) with the observations. The model parameters adopted for the star are Teff = 17,500 K, log g = 3.75, Vturb = 0 km/s, and vsin i = 5 km/s. Solar abundances appear to prevail for the lighter elements but the abundances of Fe group elements are 0.1-0.3 dex below the solar values given by Asplund, Grevesse, & Sauval (2005). In general the NLTE calculations fit the observations better, especially for lines formed high in the atmosphere such as the C I lines near 1260 A. The detailed analysis of the spectrum of this standard star not only allows one to determine the abundances in the atmosphere of a typical field B star but also presents the opportunity to assess the accuracy of atomic parameters for UV lines and find astrophysical f-values. The authors appreciate support from NASA and STScI grants NAG5-11802 and GO-09848. SJA was a guest observer at DAO.

  11. 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.

  12. Relative abundances of methane- and sulphur-oxidising symbionts in the gills of a cold seep mussel and link to their potential energy sources.

    PubMed

    Duperron, S; Guezi, H; Gaudron, S M; Pop Ristova, P; Wenzhöfer, F; Boetius, A

    2011-11-01

    Bathymodiolus mussels are key species in many deep-sea chemosynthetic ecosystems. They often harbour two types of endosymbiotic bacteria in their gills, sulphur- and methane oxidisers. These bacteria take up sulphide and methane from the environment and provide energy to their hosts, supporting some of the most prolific ecosystems in the sea. In this study, we tested whether symbiont relative abundances in Bathymodiolus gills reflect variations in the highly spatially dynamic chemical environment of cold seep mussels. Samples of Bathymodiolus aff. boomerang were obtained from two cold seeps of the deep Gulf of Guinea, REGAB (5°47.86S, 9°42.69E, 3170 m depth) and DIAPIR (6°41.58S, 10°20.94E, 2700 m depth). Relative abundances of both symbiont types were measured by means of 3D fluorescence in situ hybridisation and image analysis and compared considering the local sulphide and methane concentrations and fluxes assessed via benthic chamber incubations. Specimens inhabiting areas with highest methane content displayed higher relative abundances of methane oxidisers. The bacterial abundances correlated also with carbon stable isotope signatures in the mussel tissue, suggesting a higher contribution of methane-derived carbon to the biomass of mussels harbouring higher densities of methane-oxidising symbionts. A dynamic adaptation of abundances of methanotrophs and thiotrophs in the gill could be a key factor optimising the energy yield for the symbiotic system and could explain the success of dual symbiotic mussels at many cold seeps and hydrothermal vents of the Atlantic and Gulf of Mexico.

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

    SciTech Connect

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

    2002-11-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

  15. 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

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

    USGS Publications Warehouse

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

    2011-01-01

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

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

    PubMed Central

    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.

    2015-01-01

    Background 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. Methods and Results At one or more visits among 675 older men from the Normative Aging Study (observations=1,252), 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 (SD) increase in 28-day BC moving average (MA) was associated with 1.97 mm Hg (95%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 (SBP) BP, respectively. Positive BC-BP associations existed throughout all time windows. BC MAs (5-day to 28-day) were associated with increased mtDNA/nDNA; every SD increase in 28-day BC MA was associated with 0.12 SD (95%CI, 0.03–0.20; P=0.007) higher mtDNA/nDNA. High mtDNA/nDNA significantly attenuated the BC-SBP association throughout all time windows. The estimated effect of 28-day BC MA on SBP 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), compared to the top quartile midpoint (2.40 mm Hg; 95%CI, 0.81–3.99; P=0.003). Conclusions In older adults, short- 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. PMID:26660284

  18. 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.

  19. 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.

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

    PubMed

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

    2016-09-29

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

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

    PubMed Central

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

    2016-01-01

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

  2. Spectra edited by relative signs of homonuclear couplings of low abundance nuclei.

    PubMed

    Blechta, Vratislav; Kurfürst, Milan; Schraml, Jan

    2012-02-01

    The proposed homonuclear coupling sign edited (HCSE) experiment can detect signed homonuclear couplings between low abundant nuclei like (13)C, (29)Si and (15)N in linear spin systems, that is, in systems where two nuclei are coupled by the measured coupling, and one of them is coupled by a second coupling to a nucleus of different kind. The third nucleus is usually high abundant hydrogen. Two spectra are measured during the HCSE experiment. Their weighed sum and difference yield two other spectra, one containing peaks coupled only by positive measured couplings and the other having peaks coupled by negative measured couplings. The usual E.COSY-type experiment requires all three couplings in the three spin system (triangular spin system) and not only two couplings as the HCSE experiment. The experiment was successfully tested on known carbon-carbon and silicon-silicon two bond couplings. A set of six simple siloxanes with |(2) J(Si-O-Si)| couplings ranging from 0.5 to 9.0 Hz was measured for the first time, and all the couplings were found to be positive.

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

    SciTech Connect

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

    2010-06-01

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

  4. 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.

  5. 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.

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

    SciTech Connect

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

    2014-02-01

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

  7. Shotgun proteomics to unravel the complexity of the Leishmania infantum exoproteome and the relative abundance of its constituents.

    PubMed

    Braga, Micheline Soares; Neves, Leandro Xavier; Campos, Jonatan Marques; Roatt, Bruno Mendes; de Oliveira Aguiar Soares, Rodrigo Dian; Braga, Samuel Leôncio; de Melo Resende, Daniela; Reis, Alexandre Barbosa; Castro-Borges, William

    2014-06-01

    The exoproteome of some Leishmania species has revealed important insights into host-parasite interaction, paving the way for the proposal of novel disease-oriented interventions. The focus of the present investigation constituted the molecular profile of the L. infantum exoproteome revealed by a shotgun proteomic approach. Promastigotes under logarithmic phase of growth were obtained and harvested by centrifugation at different time points. Cell integrity was evaluated through the counting of viable parasites using propidium iodide labeling, followed by flow cytometry analysis. The 6h culture supernatant, operationally defined here as exoproteome, was then conditioned to in solution digestion and the resulting peptides submitted to mass spectrometry. A total of 102 proteins were identified and categorized according to their cellular function. Their relative abundance index (emPAI) allowed inference that the L. infantum exoproteome is a complex mixture dominated by molecules particularly involved in nucleotide metabolism and antioxidant activity. Bioinformatic analyses support that approximately 60% of the identified proteins are secreted, of which, 85% possibly reach the extracellular milieu by means of non-classic pathways. At last, sera from naturally infected animals, carriers of differing clinical forms of Canine Visceral Leishmaniasis (CVL), were used to test the immunogenicity associated to the L. infantum exoproteome. Western blotting experiments revealed that this sub-proteome was useful at discriminating symptomatic animals from those exhibiting other clinical forms of the disease. Collectively, the molecular characterization of the L. infantum exoproteome and the preliminary immunoproteomic assays opened up new research avenues related to treatment, prognosis and diagnosis of CVL.

  8. 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.

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

    PubMed

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

    2015-02-01

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

  10. Effect of oocyte quality on the relative abundance of specific gene transcripts in bovine mature oocytes and 16-cell embryos

    PubMed Central

    Bilodeau-Goeseels, Sylvie

    2003-01-01

    Although the developmental potential of oocytes is related to oocyte quality, whether the expression of specific genes is altered in oocytes of different quality and in resulting embryos is not known. Semi-quantitative reverse transcription-polymerase chain reaction was used to compare the relative abundance of 2 transcripts for housekeeping proteins (β-actin and ribosomal protein L30) and 3 transcripts for growth factor ligand or receptors (platelet derived growth factor receptor α (PDGFRα), basic fibroblast growth factor (bFGF)), in mature bovine oocytes of high versus low developmental potential. The transcripts for L30, PDGFRα, and bFGF in 16-cell embryos originating from these oocytes were also examined. No significant effect of oocyte quality was detected for any of the transcripts examined from oocytes or 16-cell embryos. In conclusion, a lower developmental potential of oocytes with advanced signs of atresia, was not associated with a lower level of abundance of the transcripts examined. PMID:12760483

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

    USGS Publications Warehouse

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

    2006-01-01

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

  12. Patchy reaction-diffusion and population abundance: the relative importance of habitat amount and arrangement.

    PubMed

    Flather, Curtis H; Bevers, Michael

    2002-01-01

    A discrete reaction-diffusion model was used to estimate long-term equilibrium populations of a hypothetical species inhabiting patchy landscapes to examine the relative importance of habitat amount and arrangement in explaining population size. When examined over a broad range of habitat amounts and arrangements, population size was largely determined by a pure amount effect (proportion of habitat in the landscape accounted for >96% of the total variation compared to <1% for the arrangement main effect). However, population response deviated from a pure amount effect as coverage was reduced below 30%-50%. That deviation coincided with a persistence threshold as indicated by a rapid decline in the probability of landscapes supporting viable populations. When we partitioned experimental landscapes into sets of "above" and "below" persistence threshold, habitat arrangement became an important factor in explaining population size below threshold conditions. Regression analysis on below-threshold landscapes using explicit measures of landscape structure (after removing the covariation with habitat amount) indicated that arrangement variables accounted for 33%-39% of the variation in population size, compared to 27%-49% for habitat amount. Thus, habitat arrangement effects became important when species persistence became uncertain due to dispersal mortality.

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2014-01-07

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

  15. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

  17. An approach to remove albumin for the proteomic analysis of low abundance biomarkers in human serum.

    PubMed

    Ahmed, Nuzhat; Barker, Gillian; Oliva, Karen; Garfin, David; Talmadge, Kenneth; Georgiou, Harry; Quinn, Michael; Rice, Greg

    2003-10-01

    Proteomic technologies are being used to discover and identify disease-associated biomarkers. The application of these technologies in the search for potential diagnostic/prognostic biomarkers in the serum of patients has been limited by the presence of highly abundant albumin and immunoglobulins that constitute approximately 60-97% of the total serum proteins. The purpose of the study was to evaluate whether treatment of human serum with Affi-Gel Blue alone or in combination with Protein A (Aurum serum protein mini kit, Bio-Rad) before two-dimensional gel electrophoresis (2-DE) analysis removed high abundance proteins to allow the visualization of low abundant proteins. Serum samples were treated with either Affi-Gel Blue or Aurum kit and then subjected to 2-DE using 11 cm, pH 4-7 isoelectric focussing strips for the first dimension and 10% sodium dodecyl sulfate-polyacrylamide gel electrophoresis for second dimension. Protein spots were visualized using a fluorescent protein dye (SYPRO Ruby, Bio-Rad). Comparison between treatment methods showed significant removal of albumin by both Affi-Gel Blue and Aurum kit and considerable differences in the protein profile of the gels after each treatment. Direct comparison between treatments revealed twenty-eight protein spots unique to Affi-Gel Blue while only two spots were unique after Aurum kit treatment. Unique spots in Affi-Gel Blue and Aurum kit treated serum were not visualized in untreated serum. Sixteen hours of Affi-Gel Blue treatment resulted in enhanced visualization of fifty-three protein spots by two-fold, thirty-one by five-fold, twelve by ten-fold and six by twenty-fold. In parallel after Aurum kit treatment two-, five-, ten- and twenty-fold enhancements of thirty, thirteen, eight and five protein spots, respectively, were observed. The pattern of increased visualization of protein spots with both treatment methods was similar. In conclusion, treatment of serum samples with Affi-Gel Blue or Aurum kit before

  18. Relative abundance of G protein-coupled receptor 30 and localization in testis and epididymis of sheep at different developmental stages.

    PubMed

    Lu, Peiyao; Wang, Fuchuan; Song, Xianyi; Liu, Yang; Zhang, Kai; Cao, Ningxian

    2016-12-01

    The G protein-coupled receptor 30 (GPR30) is a transmembrane estrogen receptor that binds to estrogen, and has been confirmed to have an important role in testicular cell proliferation and development. The main objective of this study was to examine GPR30 gene expression and localization in the testis and epididymis of sheep at different developmental stages. Testes, including the epididymis, were collected from Polled Dorset x Mongolian cross rams at one (n=4; wt), three (n=4; wt), six (n=4; wt), nine (n=4; wt) and 12 (n=4; wt) months of age. The 12-month-old hybrid crossbred sheep were exsanguinated via puncture of the jugular vein. Relative abundance of GPR30 mRNA was detected by quantitative PCR, and localization of the protein was examined by immunohistochemistry. Semi-quantitative analysis of GPR30 protein was performed by western blotting. The relative abundance of GPR30 mRNA was similar in the epididymis tail for rams at 6, 9, and 12mo of age. Further, relative abundance of GPR30 mRNA in the testes and caput epididymis of 1-, 3-, 6-, 9-, and 12-month-old crossbred rams did not increase with age. The GPR30 mRNA was detected in epididymal interstitial and principal cells, and in the epididymal cavity, spermatocytes, spermatogonial stem cells, Sertoli and Leydig cells, and spermatozoon of ram testes. Western blotting indicated the GPR30 protein was present in 9- and 12-month-old crossbred sheep corpus, cauda epididymis (P<0.05). The results suggest that relative abundance of GPR30 mRNA is time-dependent and localization-specific.

  19. Prevalence patterns of avian Plasmodium and Haemoproteus parasites and the influence of host relative abundance in southern China.

    PubMed

    Zhang, Yanhua; Wu, Yuchun; Zhang, Qiang; Su, Dongdong; Zou, Fasheng

    2014-01-01

    Infectious diseases threaten the health and survival of wildlife populations. Consequently, relationships between host diversity, host abundance, and parasite infection are important aspects of disease ecology and conservation research. Here, we report on the prevalence patterns of avian Plasmodium and Haemoproteus infections and host relative abundance influence based on sampling 728 wild-caught birds representing 124 species at seven geographically widespread sites in southern China. The overall prevalence of two haemoprotozoan parasites, Plasmodium and Haemoproteus, was 29.5%, with 22.0% attributable to Haemoproteus and 7.8% to Plasmodium. Haemoproteus prevalence differed significantly among different avian host families, with the highest prevalence in Nectariniidae, Pycnonotidae and Muscicapidae, whereas Plasmodium prevalence varied significantly among host species. Seventy-nine mitochondrial lineages including 25 from Plasmodium and 54 from Haemoproteus were identified, 80% of which were described here for the first time. The phylogenetic relationships among these parasites indicated stronger host-species specificity for Haemoproteus than Plasmodium. Well-supported host-family (Timaliidae) specific clades were found in both Plasmodium and Haemoproteus. The Haemoproteus tree shows regional subclades, whereas the Plasmodium clades are "scattered" among different geographical regions. Interestingly, there were statistically significant variations in the prevalence of Plasmodium and Haemoproteus among the geographical regions. Furthermore, the prevalence of Plasmodium and Haemoproteus were not significantly correlated with host relative abundance. Further efforts will focus on exploring the relationships between parasite prevalence and sex, age, and immune defense of the host.

  20. Prevalence Patterns of Avian Plasmodium and Haemoproteus Parasites and the Influence of Host Relative Abundance in Southern China

    PubMed Central

    Zhang, Yanhua; Wu, Yuchun; Zhang, Qiang; Su, Dongdong; Zou, Fasheng

    2014-01-01

    Infectious diseases threaten the health and survival of wildlife populations. Consequently, relationships between host diversity, host abundance, and parasite infection are important aspects of disease ecology and conservation research. Here, we report on the prevalence patterns of avian Plasmodium and Haemoproteus infections and host relative abundance influence based on sampling 728 wild-caught birds representing 124 species at seven geographically widespread sites in southern China. The overall prevalence of two haemoprotozoan parasites, Plasmodium and Haemoproteus, was 29.5%, with 22.0% attributable to Haemoproteus and 7.8% to Plasmodium. Haemoproteus prevalence differed significantly among different avian host families, with the highest prevalence in Nectariniidae, Pycnonotidae and Muscicapidae, whereas Plasmodium prevalence varied significantly among host species. Seventy-nine mitochondrial lineages including 25 from Plasmodium and 54 from Haemoproteus were identified, 80% of which were described here for the first time. The phylogenetic relationships among these parasites indicated stronger host-species specificity for Haemoproteus than Plasmodium. Well-supported host-family (Timaliidae) specific clades were found in both Plasmodium and Haemoproteus. The Haemoproteus tree shows regional subclades, whereas the Plasmodium clades are “scattered” among different geographical regions. Interestingly, there were statistically significant variations in the prevalence of Plasmodium and Haemoproteus among the geographical regions. Furthermore, the prevalence of Plasmodium and Haemoproteus were not significantly correlated with host relative abundance. Further efforts will focus on exploring the relationships between parasite prevalence and sex, age, and immune defense of the host. PMID:24911323

  1. An approach to remove alpha amylase for proteomic analysis of low abundance biomarkers in human saliva.

    PubMed

    Deutsch, Omer; Fleissig, Yoram; Zaks, Batia; Krief, Guy; Aframian, Doron J; Palmon, Aaron

    2008-11-01

    Proteomic characterization of human whole saliva for the identification of disease-specific biomarkers is guaranteed to be an easy-to-use and powerful diagnostic tool for defining the onset, progression and prognosis of human systemic diseases and, in particular, oral diseases. The high abundance of proteins, mainly alpha amylase, hampers the detection of low abundant proteins appearing in the disease state and therefore should be removed. In the present study a 2-DE was used to analyze human whole saliva following the removal of alpha amylase by affinity adsorption to potato starch. After alpha amylase removal whole saliva was analyzed by SDS-PAGE showing at least sixfold removal efficiency and by an alpha amylase activity assay showing 97% reduced activity. MS identification of the captured alpha amylase after elution demonstrated specific removal; 2-DE analysis showed the selective removal of alpha amylase and consequently increased gel resolution. MS identification of protein spots in the 60 kDa area revealed 15 proteins, which were masked before alpha amylase removal. In conclusion, treatment of human whole saliva with an alpha amylase removal device increases gel resolution and enables a higher protein sample for analysis.

  2. Use of Multiple Endmember Spectral Mixture Analysis and Radiative Transfer Model to Derive Lunar Mineral Abundance Maps

    NASA Astrophysics Data System (ADS)

    Li, L.; Lucey, P. G.

    2009-03-01

    A new approach combining multiple endmemeber spectral mixture analysis (MESMA) and radiative transfer model (RTM) is proposed to generate lunar global mineral abundance maps from Clementine 1 km UVVIS data.

  3. 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.

  4. The relative protein abundance of UGT1A alternative splice variants as a key determinant of glucuronidation activity in vitro.

    PubMed

    Rouleau, Mélanie; Roberge, Joannie; Falardeau, Sarah-Ann; Villeneuve, Lyne; Guillemette, Chantal

    2013-04-01

    Alternative splicing (AS) is one of the most significant components of the functional complexity of human UDP-glucuronosyltransferase enzymes (UGTs), particularly for the UGT1A gene, which represents one of the best examples of a drug-metabolizing gene regulated by AS. Shorter UGT1A isoforms [isoform 2 (i2)] are deficient in glucuronic acid transferase activity but function as negative regulators of enzyme activity through protein-protein interaction. Their abundance, relative to active UGT1A enzymes, is expected to be a determinant of the global transferase activity of cells and tissues. Here we tested whether i2-mediated inhibition increases with greater abundance of the i2 protein relative to the isoform 1 (i1) enzyme, using the extrahepatic UGT1A7 as a model and a series of 23 human embryonic kidney 293 clonal cell lines expressing variable contents of i1 and i2 proteins. Upon normalization for i1, a significant reduction of 7-ethyl-10-hydroxycamptothecin glucuronide formation was observed for i1+i2 clones (mean of 53%) compared with the reference i1 cell line. In these clones, the i2 protein content varied greatly (38-263% relative to i1) and revealed two groups: 17 clones with i2 < i1 (60% ± 3%) and 6 clones with i2 ≥ i1 (153% ± 24%). The inhibition induced by i2 was more substantial for clones displaying i2 ≥ i1 (74.5%; P = 0.001) compared with those with i2 < i1 (45.5%). Coimmunoprecipitation supports a more substantial i1-i2 complex formation when i2 exceeds i1. We conclude that the relative abundance of regulatory i2 proteins has the potential to drastically alter the local drug metabolism in the cells, particularly when i2 surpasses the protein content of i1.

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

    USGS Publications Warehouse

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

    1999-01-01

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

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

    USGS Publications Warehouse

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

    1999-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  8. Development competence and relative transcript abundance of oocytes derived from small and medium follicles of prepubertal gilts.

    PubMed

    Kohata, Chiyuki; Izquierdo-Rico, María José; Romar, Raquel; Funahashi, Hiroaki

    2013-12-01

    The objective of this study was to examine the competence of mature oocytes aspirated from small follicles (SF, <2 mm in diameter) and medium follicles (MF, 3-6 mm) of abattoir-derived prepubertal gilt ovaries. Oocytes were selected by the presence of the first polar body (1pb) after IVM in a chemically defined medium, for sperm penetration, pronuclear formation, cleavage rate, and development to the blastocyst stage. Relative transcript abundance of genes associated with regulation of oocyte maturation (AURKA, AURKB, and MOS), fertilization (ZP3 and ZP4), maternal effect (NALP9 and HSF1), and anti-apoptosis (BCL2) were also examined in oocytes at germinal vesicle (GV) and metaphase-II (MII) stages. In SF, compared with MF, the maturation rate post-IVM was lower (P < 0.05), but there were no differences in sperm penetration rate (78.2% and 68.5% at 6 hours after insemination and 90.8% and 91.9% at 9 hours after insemination, P = 0.51 and P = 0.67, respectively), the percentage of oocytes that formed both female and male pronuclei (27.9% and 25.8% at 6 hours after insemination and 79.4% and 76.1% at 9 hours after insemination), or cleavage rate at 48 hours after insemination (85.9% and 89.7%, respectively, P = 0.46), whereas blastocyst formation rate was lower (P < 0.05) in oocytes from SF versus MF (14.7% and 31.0%). Transcript abundances decreased (P < 0.05) in all genes examined between the GV and MII stages, although only transcript abundance for MOS was lower (P < 0.05) in GV oocytes from SF versus MF. In conclusion, mature oocytes from SF and MF of prepubertal gilts with a visible 1pb had similar fertilizability in vitro and relative transcript abundance of nine genes. However, follicle size affected meiotic competence, early embryonic development to the blastocyst stage, and transcript abundance of the MOS gene.

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

    PubMed Central

    Qiu, Shanlian; Chen, Guoyuan; Zhou, Yiyong

    2010-01-01

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

  10. Mycelial abundance and other factors related to truffle productivity in Tuber melanosporum-Quercus ilex orchards.

    PubMed

    Suz, Laura M; Martín, María P; Oliach, Daniel; Fischer, Christine R; Colinas, Carlos

    2008-08-01

    Relative quantification of DNA from Tuber melanosporum mycelia was performed by conventional and real-time PCR in soil from trees in three truffle orchards of different ages to determine: (1) whether burn appearance is related to the amount of T. melanosporum mycelium in soil, and (2) whether productivity onset and truffle production are related to (a) the amount of T. melanosporum mycelium in soil, (b) tree height and diameter, (c) burn extension and (d) surface rock cover. The burn seems to appear only after a certain amount of mycelium has formed. Precociously productive trees presented higher quantities of mycelium than nonproductive trees in the productivity onset study, while highly productive trees presented less quantities of mycelium than nonproductive trees in the productivity study. Trees with high but not excessive surface rock cover showed greater truffle production. Larger trees tended to display a burn earlier than smaller trees.

  11. CN and CH Abundance Analysis in a Sample of Eight Galactic Globular Clusters

    NASA Astrophysics Data System (ADS)

    Smolinski, Jason P.; Lee, Y.; Beers, T. C.; Martell, S. L.; An, D.; Sivarani, T.

    2011-01-01

    Galactic globular clusters exhibit star-to-star variations in their light element abundances that are not predicted by formation and evolution models involving single stellar generations. Recently it has been suggested that internal pollution from early supernovae and AGB winds may have played important roles in forming a second generation of enriched stars. We present updated results of a CN and CH abundance analysis of stars from the base to the tip of the red giant branch, and in some cases down onto the main sequence, for eight globular clusters with available photometric and spectroscopic data from SDSS-I and SDSS-II/SEGUE. These results include a discussion of the radial distribution of CN enrichment and how this may impact the current paradigm. Funding for SDSS-I and SDSS-II has been provided by the Alfred P. Sloan Foundation, the Participating Institutions, the National Science Foundation, the U.S. Department of Energy, the National Aeronautics and Space Administration, the Japanese Monbukagakusho, the Max Planck Society, and the Higher Education Funding Council for England. The SDSS Web Site is http://www.sdss.org/. This work was supported in part by grants PHY 02-16783 and PHY 08-22648: Physics Frontiers Center/Joint Institute for Nuclear Astrophysics (JINA), awarded by the U.S. National Science Foundation.

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

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

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

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

    PubMed Central

    Gundry, Michael; Vijg, Jan

    2011-01-01

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

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

    PubMed

    Gundry, Michael; Vijg, Jan

    2012-01-03

    DNA mutations are the source of genetic variation within populations. The majority of mutations with observable effects are deleterious. In humans mutations in the germ line can cause genetic disease. In somatic cells multiple rounds of mutations and selection lead to cancer. The study of genetic variation has progressed rapidly since the completion of the draft sequence of the human genome. Recent advances in sequencing technology, most importantly the introduction of massively parallel sequencing (MPS), have resulted in more than a hundred-fold reduction in the time and cost required for sequencing nucleic acids. These improvements have greatly expanded the use of sequencing as a practical tool for mutation analysis. While in the past the high cost of sequencing limited mutation analysis to selectable markers or small forward mutation targets assumed to be representative for the genome overall, current platforms allow whole genome sequencing for less than $5000. This has already given rise to direct estimates of germline mutation rates in multiple organisms including humans by comparing whole genome sequences between parents and offspring. Here we present a brief history of the field of mutation research, with a focus on classical tools for the measurement of mutation rates. We then review MPS, how it is currently applied and the new insight into human and animal mutation frequencies and spectra that has been obtained from whole genome sequencing. While great progress has been made, we note that the single most important limitation of current MPS approaches for mutation analysis is the inability to address low-abundance mutations that turn somatic tissues into mosaics of cells. Such mutations are at the basis of intra-tumor heterogeneity, with important implications for clinical diagnosis, and could also contribute to somatic diseases other than cancer, including aging. Some possible approaches to gain access to low-abundance mutations are discussed, with a brief

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

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

  16. Homogeneous abundance analysis of FGK dwarf, subgiant, and giant stars with and without giant planets

    NASA Astrophysics Data System (ADS)

    da Silva, Ronaldo; Milone, André de C.; Rocha-Pinto, Helio J.

    2015-08-01

    Aims: We have analyzed high-resolution and high signal-to-noise-ratio optical spectra of nearby FGK stars with and without detected giant planets in order to homogeneously measure their photospheric parameters, mass, age, and the abundances of volatile (C, N, and O) and refractory (Na, Mg, Si, Ca, Ti, V, Mn, Fe, Ni, Cu, and Ba) elements. Our sample contains 309 stars from the solar neighborhood (up to the distance of 100 pc), out of which 140 are dwarfs, 29 are subgiants, and 140 are giants. Methods: The photospheric parameters are derived from the equivalent widths of Fe i and Fe ii lines. Masses and ages come from the interpolation in evolutionary tracks and isochrones on the Hertzsprung-Russell diagram. The abundance determination is based on the equivalent widths of selected atomic lines of the refractory elements and on the spectral synthesis of C2, CN, C i, O i, and Na i features. We apply a set of statistical methods to analyze the abundances derived for the three subsamples. Results: Our results show that: i) giant stars systematically exhibit underabundance in [C/Fe] and overabundance in [N/Fe] and [Na/Fe] in comparison with dwarfs, a result that is normally attributed to evolution-induced mixing processes in the envelope of evolved stars; ii) for solar analogs alone, the abundance trends with the condensation temperature of the elements are correlated with age and anticorrelated with the surface gravity, which agrees with recent studies; iii) as in the case of [Fe/H], dwarf stars with giant planets are systematically enriched in [X/H] for all the analyzed elements, except for O and Ba (the former due to limitations of statistics), confirming previous findings in the literature that it is not only iron that has an important relation with the planetary formation; and iv) giant planet hosts are also significantly overabundant for the same metallicity when the elements from Mg to Cu are combined. Based on public data from the ELODIE archive (Moultaka et al

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

    PubMed

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

    2012-01-01

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

  18. 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

  19. Size-related bacterial diversity and tetracycline resistance gene abundance in the air of concentrated poultry feeding operations.

    PubMed

    Gao, Min; Jia, Ruizhi; Qiu, Tianlei; Han, Meilin; Wang, Xuming

    2017-01-01

    Concentrated animal-feeding operations (CAFOs) are considered a source of airborne human pathogens and antibiotic resistance genes. Although bacterial abundance and diversity have been well studied, limited information on the size distribution of bioaerosols has prevented a clear understanding of the health effects of exposure to bioaerosols from CAFOs. Here, different sizes of particles were sampled from the inside and outside of atmospheric environments of layer and broiler feeding operations using 8-stage Andersen samplers. The quantitative real-time polymerase chain reaction (qPCR) and 16S rDNA-based sequencing were used to analyze the characteristics of biological abundance and diversity, respectively, according to size. The results indicated that size-related differences occurred in terms of airborne bacterial richness, diversity, and concentration at poultry-feeding operations. The richness of biological genera in the urban atmospheric environment was lower than in concentrated poultry-feeding operations. The biological diversity of airborne bacterial genera, including genera associated with potential pathogens, varied according to size. The bacterial lineages of bioaerosols present in the 7 size stages for layers clustered apart from those for broilers, suggesting that the type of poultry house is a more important factor than the particle size in shaping the microbial communities. In most cases, the concentrations of the 16S rDNA, Escherichia coli, tetW, and tetL genes increased as the particle size increased, with the geometric mean diameters varying from 4.7 to 5.8 μm. These results regarding the size-related differences in the diversity and abundance of bioaerosols will facilitate a better understanding of the potential health impact on both poultry and humans working in such environments.

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

    SciTech Connect

    Gunnink, R

    1991-09-01

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

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

    PubMed

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

    2016-01-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

  4. VizieR Online Data Catalog: Extended abundance analysis of cool stars (Brewer+, 2016)

    NASA Astrophysics Data System (ADS)

    Brewer, J. M.; Fischer, D. A.; Valenti, J. A.; Piskunov, N.

    2016-10-01

    The stellar spectra in this study were all collected using the HIRES spectrograph (R~70000) on the Keck I telescope as part of one or more radial-velocity planet-search programs under the collaborative umbrella known as the California Planet Survey (CPS; Howard+ 2010ApJ...721.1467H). In addition to stellar spectra, our data also include 20 spectra of four different asteroids (4 Vesta, 1036 Ganymed, 3 Juno, and 10 Hygiea) from five epochs throughout the 10-year period covered by the observations in our sample. These spectra provided disk-integrated solar spectra and were obtained to help calibrate our analysis by providing small zero-point offsets for solar parameters and abundances. (4 data files).

  5. Aryl Polyenes, a Highly Abundant Class of Bacterial Natural Products, Are Functionally Related to Antioxidative Carotenoids.

    PubMed

    Schöner, Tim A; Gassel, Sören; Osawa, Ayako; Tobias, Nicholas J; Okuno, Yukari; Sakakibara, Yui; Shindo, Kazutoshi; Sandmann, Gerhard; Bode, Helge B

    2016-02-02

    Bacterial pigments of the aryl polyene type are structurally similar to the well-known carotenoids with respect to their polyene systems. Their biosynthetic gene cluster is widespread in taxonomically distant bacteria, and four classes of such pigments have been found. Here we report the structure elucidation of the aryl polyene/dialkylresorcinol hybrid pigments of Variovorax paradoxus B4 by HPLC-UV-MS, MALDI-MS and NMR. Furthermore, we show for the first time that this pigment class protects the bacterium from reactive oxygen species, similarly to what is known for carotenoids. An analysis of the distribution of biosynthetic genes for aryl polyenes and carotenoids in bacterial genomes is presented; it shows a complementary distribution of these protective pigments in bacteria.

  6. Soil freezing and N deposition: transient vs multi-year effects on plant productivity and relative species abundance.

    PubMed

    Vankoughnett, Mathew R; Henry, Hugh A L

    2014-06-01

    Plant responses to increased atmospheric nitrogen (N) deposition must be considered in the context of a rapidly changing climate. Reductions in snow cover with climate warming can increase the exposure of herbaceous plants to freezing, but it is unclear how freezing damage may interact with increased N availability, and to what extent freezing effects may extend over multiple years. We explored potential interactions between freezing damage and N availability in the context of plant productivity and relative species abundance in a temperate old field using both snow removal and mesocosm experiments, and assessed the legacy effects of the freezing damage over 3 yr. As expected, N addition increased productivity and freezing damage decreased productivity, but these factors were nonadditive; N addition increased productivity disproportionately in the snow removal plots, whereas extreme freezing diminished N addition responses in the mesocosm experiment. Freezing altered relative species abundances, although only the most severe freezing treatments exhibited legacy effects on total productivity over multiple growing seasons. Our results emphasize that while both increased N deposition and freezing damage can have multi-year effects on herbaceous communities, the interactions between these global change factors are contingent on the intensities of the treatments.

  7. 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.

  8. [Effects of relative abundance of Quercus mongolica acorns on five tree species seed dispersal in Xiaoxing' an Mountains, Northeast China].

    PubMed

    Yu, Fei; Shi, Xiao-Xiao; Yi, Xian-Feng; Wang, De-Xiang

    2013-06-01

    An investigation was conducted in a forest farm in the Xiaoxing' an Mountains in autumn, 2009 and 2010 to study the effects of Quercus mongolica acorn quantity and rodent density on the seed dispersal of five tree species (Juglans mandshurica, Pinus koraiensis, Corylus mandshurica, Corylus heterophylla, and Q. mongolica). In the farm, there was an annual change in rodent density. The total capture rate of small rodents in 2009 (31.0%) was significantly higher than that in 2010 (16.7%). The acorn quantity and relative seed abundance (per capita rodent) of Quercus mongolica in 2009 (6.2 +/- 2.1 acorns x m(-2) and 20.0, respectively) were significantly lower than those in 2010 (26.7 +/- 10.2 acorns x m(-2) and 160.0, respectively). In 2009, all the seeds of the five tree species except J. mandshurica were dispersed or eaten in situ, among which, the acorns of Q. mongolica were scatter-hoarded most, and their average dispersal distance was the furthest. In 2010, the seeds of J. mandshurica were scatter-hoarded most, and their average dispersal distance was the furthest. The relative seed abundance of Q. mongolica could be the key factor determining the seed dispersal of the other tree species in the study area.

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

    PubMed

    Tempel, Douglas J; Gutiérrez, R J

    2013-10-01

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

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

    PubMed

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

    2015-04-02

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

  11. Electroantennogram response of the parasitoid, Microplitis croceipes to host-related odors: The discrepancy between relative abundance and level of antennal responses to volatile compound

    PubMed Central

    Morawo, Tolulope; Burrows, Matthew; Fadamiro, Henry

    2017-01-01

    Herbivores emit volatile organic compounds (VOCs) after feeding on plants. Parasitoids exploit these VOCs as odor cues to locate their hosts. In nature, host-related odors are emitted as blends of various compounds occurring in different proportions, and minor blend components can sometimes have profound effects on parasitoid responses. In a previous related study, we identified and quantified VOCs emitted by cotton plant-fed Heliothis virescens (Lepidoptera: Noctuidae) larvae, an herbivore host of the parasitoid Microplitis croceipes (Hymenoptera: Braconidae). In the present study, the olfactory response of female M. croceipes to synthetic versions of 15 previously identified compounds was tested in electroantennogram (EAG) bioassays. Using M. croceipes as a model species, we further asked the question: does the relative abundance of a volatile compound match the level of antennal response in parasitoids? Female M. croceipes showed varying EAG responses to test compounds, indicating different levels of bioactivity in the insect antenna. Eight compounds, including decanal, 1-octen-3-ol, 3-octanone, 2-ethylhexanol, tridecane, tetradecane, α-farnesene and bisabolene, elicited EAG responses above or equal to the 50 th percentile rank of all responses. Interestingly, decanal, which represented only 1% of the total amount of odors emitted by cotton-fed hosts, elicited the highest (0.82 mV) EAG response in parasitoids. On the other hand, ( E)-β-caryophyllene, the most abundant (29%) blend component, elicited a relatively low (0.17 mV) EAG response. The results suggest that EAG response to host-related volatiles in parasitoids is probably more influenced by the ecological relevance or functional role of the compound in the blend, rather than its relative abundance. PMID:28232862

  12. Electroantennogram response of the parasitoid, Microplitis croceipes to host-related odors: The discrepancy between relative abundance and level of antennal responses to volatile compound.

    PubMed

    Morawo, Tolulope; Burrows, Matthew; Fadamiro, Henry

    2016-01-01

    Herbivores emit volatile organic compounds (VOCs) after feeding on plants. Parasitoids exploit these VOCs as odor cues to locate their hosts. In nature, host-related odors are emitted as blends of various compounds occurring in different proportions, and minor blend components can sometimes have profound effects on parasitoid responses. In a previous related study, we identified and quantified VOCs emitted by cotton plant-fed Heliothis virescens (Lepidoptera: Noctuidae) larvae, an herbivore host of the parasitoid Microplitis croceipes (Hymenoptera: Braconidae). In the present study, the olfactory response of female M. croceipes to synthetic versions of 15 previously identified compounds was tested in electroantennogram (EAG) bioassays. Using M. croceipes as a model species, we further asked the question: does the relative abundance of a volatile compound match the level of antennal response in parasitoids? Female M. croceipes showed varying EAG responses to test compounds, indicating different levels of bioactivity in the insect antenna. Eight compounds, including decanal, 1-octen-3-ol, 3-octanone, 2-ethylhexanol, tridecane, tetradecane, α-farnesene and bisabolene, elicited EAG responses above or equal to the 50 (th) percentile rank of all responses. Interestingly, decanal, which represented only 1% of the total amount of odors emitted by cotton-fed hosts, elicited the highest (0.82 mV) EAG response in parasitoids. On the other hand, ( E)-β-caryophyllene, the most abundant (29%) blend component, elicited a relatively low (0.17 mV) EAG response. The results suggest that EAG response to host-related volatiles in parasitoids is probably more influenced by the ecological relevance or functional role of the compound in the blend, rather than its relative abundance.

  13. 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.

  14. 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.

  15. 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

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

    NASA Astrophysics Data System (ADS)

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

    2004-12-01

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

  17. Increasing nitrogen abundance relative to phosphorus in the northwestern Pacific Ocean due to anthropogenic nitrogen deposition

    NASA Astrophysics Data System (ADS)

    Kim, T.; Lee, K.; Najjar, R. G.; Jeong, H.

    2011-12-01

    The increased uses of fossil fuel and agricultural fertilizer have rapidly altered nitrogen availability in many ecosystems over the last several decades. In particular, the coastal waters downwind of highly populated and industrialized areas have been receiving ever higher inputs of anthropogenic nitrogen via rivers and the atmosphere. One of those areas is the coastal and marginal seas of the Northwestern Pacific, which includes the East China Sea, the Yellow Sea and the East/Japan Sea. In this study, we document increases in the availability of nitrogen over phosphorus in these seas by analyzing temporal trend of surface (<50 m) N* (N - RN:P × P, where N, P and RN:P are nitrate concentration, phosphorus concentration, and the mean N:P ratio, respectively). The nutrient data used in the study were collected by the National Fisheries Research and Development Institute in Korea and the Japan Meteorological Agency during the past three decades. The observed N* increase, which was mainly due to an increase in nitrate concentration, was attributed to the riverine and atmospheric input of anthropogenic nitrogen. The N* values in two major rivers (Changjiang and Han River) discharging to the East China Sea and Yellow Sea have increased to >100 μM over the last thirty years. The riverine N* values were compared to those in the selected sea areas where riverine influence is probably greatest and found significant correlations in downstream of the Changjiang River (but not in the Han River). However, the influence of nitrogen flux from the Changjiang River appears to be confined to its estuary based on the analysis of plume extent and nutrient distribution in summer 1998 when the Changjiang River discharge was the greatest observed since the 1950s. We estimated atmospheric nitrogen deposition in the three air monitoring stations in Korea and one in Japan using the data measured by the Acid Deposition Monitoring Network in East Asia and the Korea Meteorological

  18. Hydropathic influences on the quantification of equine heart cytochrome c using relative ion abundance measurements by electrospray ionization fourier transform ion cyclotron resonance mass spectrometry.

    PubMed

    Gordon, E F; Mansoori, B A; Carroll, C F; Muddiman, D C

    1999-10-01

    The number of publications documenting the utility of electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) for the analysis of biological molecules has increased in geometric proportion spanning diverse areas of research. Currently, we are investigating the capabilities of ESI-FTICR to quantify relative molecular ion abundances of biopolymers, an area which has not been explored rigorously. We present here the results of an investigation of a two-component system utilizing equine heart cytochrome c (EH) as the analyte and bovine heart cytochrome c (BH) as a constant concentration internal standard. As these compounds are relatively large ( approximately 12 kDa), they will become multiply charged during the electrospray process. Using appropriate solution and instrument conditions, the 7(+) and 8(+) charge states were enhanced for both cytochrome c species. We report that using the average of the ion abundances for the two charge states observed for each species, the linear curve (intensity ratio vs concentration ratio) had a dynamic range of 0.045-2.348 microM (1.7 orders of magnitude). Linear least-squares regression analysis (LLSRA) of these averaged ion abundances (i.e. [(EH + 7H(+))(7+)/(BH + 7H(+))(7+) + (EH + 8H(+))(8+)/(BH + 8H(+))(8+)]/2) yielded the equation y = 1.005x + 0.027. The slope of the line with its calculated precision, reported as one standard deviation, is 1.005 +/- 0.0150, which is statistically ideal (i.e. equal to unity). However, LLSRA of the ion abundances of the two individual charge states were significantly different (i.e. the slope of the (EH + 7H(+))(7+)/(BH + 7H(+))(7+) peak intensity ratio vs molar ratio data was 0.885 +/- 0.0183 and the slope of the (EH + 8H(+))(8+)/(BH + 8H(+))(8+) data was 1.125 +/- 0.0308). We attribute this difference to the variation in primary amino acid sequence for the two cytochrome c species. Both have 104 amino acids, but there are three residue

  19. 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.

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

    PubMed

    Chew, Gina; Walczyk, Thomas

    2013-04-02

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

  1. Rapid determination of bacterial abundance, biovolume, morphology, and growth by neural network-based image analysis

    PubMed

    Blackburn; Hagstrom; Wikner; Cuadros-Hansson; Bjornsen

    1998-09-01

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

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

    PubMed Central

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

    1998-01-01

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

  3. Impact of a short exposure to levofloxacin on faecal densities and relative abundance of total and quinolone-resistant Enterobacteriaceae.

    PubMed

    Bernard, J; Armand-Lefèvre, L; Luce, E; El Mniai, A; Chau, F; Casalino, E; Andremont, A; Ruppé, E

    2016-07-01

    Emergence of resistant Enterobacteriaceae in the intestinal microbiota during antibiotic treatment is well documented but its early dynamic is not. Here, we compared the densities of total Enterobacteriaceae and relative abundance (RA) of quinolone-resistant Enterobacteriaceae (QRE) in the first stool passed by patients who had a short exposure to levofloxacin (levofloxacin, n=12) or not (control, n=8). Mean densities (SD) (log CFU/g stool) of total Enterobacteriaceae were lower in the levofloxacin group than in the control group-3.4 (1.6) versus 6.7 (1.7), respectively, p <0.001. Conversely, mean RA (SD) of QRE was significantly higher in the levofloxacin group than in the control group-49.7% (23.4) versus 0.1% (3.2), respectively, p <0.05). In conclusion, even a short exposure to levofloxacin has a profound impact on the densities of total Enterobacteriaceae and the QRE-RA.

  4. Evaluation of accurate mass and relative isotopic abundance measurements in the LTQ-orbitrap mass spectrometer for further metabolomics database building.

    PubMed

    Xu, Ying; Heilier, Jean-François; Madalinski, Geoffrey; Genin, Eric; Ezan, Eric; Tabet, Jean-Claude; Junot, Christophe

    2010-07-01

    Recently, high-resolution mass spectrometry has been largely employed for compound identification, thanks to accurate mass measurements. As additional information, relative isotope abundance (RIA) is often needed to reduce the number of candidates prior to tandem MS(n). Here, we report on the evaluation of the LTQ-Orbitrap, in terms of accurate mass and RIA measurements for building further metabolomics spectral databases. Accurate mass measurements were achieved in the ppm range, using external calibration within 24 h, and remained at <5 ppm over a one-week period. The experimental relative abundances of (M+1) isotopic ions were evaluated in different data sets. First of all, 137 solutions of commercial compounds were analyzed by flow injection analysis in both the positive and negative ion modes. It was found that the ion abundance was the main factor impacting the accuracy of RIA measurements. It was possible to define some intensity thresholds above which errors were systematically <20% of their theoretical values. The same type of results were obtained with analyses from two biological media. Otherwise, no significant effect of ion transmission between the LTQ ion trap and the Orbitrap analyzer on RIA measurement errors was found, whereas the reliability of RIA measurements was dramatically improved by reducing the mass detection window. It was also observed that the signal integration method had a significant impact on RIA measurement errors, with the most-reliable results being obtained with peak height integrations. Finally, automatic integrations using the data preprocessing software XCMS and MZmine gave results similar to those obtained by manual integration, suggesting that it is relevant to use the RIA information in automatic elemental composition determination software from metabolomic peak tables.

  5. 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

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

    PubMed

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

    2011-08-01

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

  8. 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 ...

  9. 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.

  10. Modified spectral count index (mSCI) for estimation of protein abundance by protein relative identification possibility (RIPpro): a new proteomic technological parameter.

    PubMed

    Sun, Aihua; Zhang, Jiyang; Wang, Chunping; Yang, Dong; Wei, Handong; Zhu, Yunping; Jiang, Ying; He, Fuchu

    2009-11-01

    Peptides Count (SC) was widely used for protein abundance estimation in proteomics. On the basis of that, Mann and co-workers corrected the SC by dividing spectrum counts by the number of observable peptides per protein and named it PAI. Here we present modified spectral count index (mSCI) for protein abundance estimation, which was defined as the number of observed peptides divided by protein relative identification possibility (RIPpro). RIPpro was derived from 6788 mRNA and protein expression data (collected from human liver samples) and related to proteins' three physical and chemical properties (MW/pI/Hp). For 46 proteins in mouse neuro2a cells, mSCI shows a linear relationship with the actual protein concentration, similar or better than PAI abundance. Also, multiple linear regressions were performed to quantitative assess several factors' impact on the mRNA/protein abundance correlation. Our results shown that the primary factor affecting protein levels was mRNA abundance (32-37%), followed by variability in protein measurement, MW and protein turnover (7-12%,7-9% and 2-3%, respectively). Interestingly, we found that the concordance between mRNA transcripts and protein expression was not consistent among all protein functional categories. This correlation was lower for signaling proteins as compared to metabolism genes. It was determined that RIPpro was the primary factor affecting signaling protein abundance (23% on average), followed by mRNA abundance (17%). In contrast, only 5% (on average) of the variability of metabolic protein abundance was explained by RIPpro, much lower than mRNA abundance (40%). These results provide the impetus for further investigation of the biological significance of mechanisms regulating the mRNA/protein abundance correlation and provide additional insight into the relative importance of the technological parameter (RIPpro) in mRNA/protein correlation research.

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

    NASA Astrophysics Data System (ADS)

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

    2008-02-01

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

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

    USGS Publications Warehouse

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

    2010-01-01

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

  13. High-resolution elemental abundance analysis of the open cluster IC 4756

    NASA Astrophysics Data System (ADS)

    Ting, Yuan-Sen; De Silva, Gayandhi M.; Freeman, Kenneth C.; Parker, Stacey Jo

    2012-11-01

    We present detailed elemental abundances of 12 subgiants in the open cluster IC 4756 including Na, Al, Mg, Si, Ca, Ti, Cr, Ni, Fe, Zn and Ba. We measure the cluster to have [Fe/H] = -0.01 ± 0.10. Most of the measured star-to-star [X/H] abundance variation is below σ < 0.03, as expected from a coeval stellar population preserving natal abundance patterns, supporting the use of elemental abundances as a probe to reconstruct dispersed clusters. We find discrepancies between Cr I and Cr II abundances as well as between Ti I and Ti II abundances, where the ionized abundances are larger by about 0.2 dex. This follows other such studies which demonstrate the effects of overionization in cool stars. IC 4756 are supersolar in Mg, Si, Na and Al, but are solar in the other elements. The fact that IC 4756 is supersolar in some α-elements (Mg, Si) but solar in the others (Ca, Ti) suggests that the production of α-elements is not simply one dimensional and could be exploited for chemical tagging.

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

    NASA Technical Reports Server (NTRS)

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

    2012-01-01

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

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

    SciTech Connect

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

    2012-09-20

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

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

    USGS Publications Warehouse

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

    1999-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Gooding, J. L.; Keil, K.

    1981-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-11-01

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

  19. 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

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

    PubMed Central

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

    2015-01-01

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

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

    SciTech Connect

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

    2012-02-10

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

  2. The dusty nova V1065 centauri (nova cen 2007) : a spectroscopic analysis of abundances and dust properties.

    SciTech Connect

    Helton, L. A.; Woodward, C. E.; Walter, F. M.; Vanlandingham, K.; Schwarz, G. J.; Evans, A.; Ness, J.-U.; Geballe, T. R.; Gehrz, R. D.; Greenhouse, M.; Krautter, J.; Liller, W.; Lynch, D. K.; Rudy, R. J.; Shore, S. N.; Starrfield, S.; Truran, J.

    2010-10-14

    We examine the ejecta evolution of the classical nova V1065 Centauri, constructing a detailed picture of the system based on spectrophotometric observations obtained from 9 to approximately 900 days post-outburst with extensive coverage from optical to mid-infrared wavelengths. We estimate a reddening toward the system of E(B-V) = 0.5 {+-} 0.1, based upon the B-V color and analysis of the Balmer decrement, and derive a distance estimate of 8.7{sub -2.1}{sup +2.8} kpc. The optical spectral evolution is classified as P{sub fe}{sup o} N{sub ne}A{sub 0} according to the CTIO Nova Classification system of Williams et al. Photoionization modeling yields absolute abundance values by number, relative to solar of He/H = 1.6 {+-} 0.3, N/H = 144 {+-} 34, O/H = 58 {+-} 18, and Ne/H = 316 {+-} 58 for the ejecta. We derive an ejected gas mass of M{sub g} = (1.6 {+-} 0.2) x 10{sup -4} M{circle_dot}. The infrared excess at late epochs in the evolution of the nova arises from dust condensed in the ejecta composed primarily of silicate grains. We estimate a total dust mass, Md , of order (0.2-3.7) x 10{sup -7} M{circle_dot}, inferred from modeling the spectral energy distribution observed with the Spitzer IRS and Gemini-South GNIRS spectrometers. Based on the speed class, neon abundance, and the predominance of silicate dust, we classify V1065 Cen as an ONe-type classical nova.

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

    NASA Astrophysics Data System (ADS)

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

    2014-01-01

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

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

    PubMed

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

    2015-03-05

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

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

    PubMed Central

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

    2015-01-01

    Network theory has provided a general way to understand mutualistic plant–animal interactions at the community level. However, the mechanisms responsible for interaction patterns remain controversial. In this study we use a combination of statistical models and probability matrices to evaluate the relative importance of species morphological and nutritional (phenotypic) traits and species abundance in determining interactions between fleshy-fruited plants and birds that disperse their seeds. The models included variables associated with species abundance, a suite of variables associated with phenotypic traits (fruit diameter, bird bill width, fruit nutrient compounds), and the species identity of the avian disperser. Results show that both phenotypic traits and species abundance are important determinants of pairwise interactions. However, when considered separately, fruit diameter and bill width were more important in determining seed dispersal interactions. The effect of fruit compounds was less substantial and only important when considered together with abundance-related variables and/or the factor ‘animal species’. PMID:25750409

  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, A.I.; Parsley, M.J.

    1999-01-01

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

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

    USGS Publications Warehouse

    Allen, M. Brady; Connolly, Patrick J.

    2011-01-01

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

  8. 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.

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

    USGS Publications Warehouse

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

    2002-01-01

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

  10. A rapid method for depletion of Rubisco from soybean (Glycine max) leaf for proteomic analysis of lower abundance proteins.

    PubMed

    Krishnan, Hari B; Natarajan, Savithiry S

    2009-12-01

    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 CO(2) fixation enzyme Rubisco. Resolution can be improved through depletion of Rubisco using fractionation techniques based upon different physiological or biochemical principles. We have developed a fast and simple fractionation technique using 10 mM Ca(2+) and 10 mM phytate to precipitate Rubisco from soybean leaf soluble protein extract. This method is not only rapid, but also inexpensive, and capable of removing 85% of the extremely abundant Rubisco enzyme from soybean leaf soluble protein extract. This method allowed for roughly 230 previously inconspicuous protein spots in soybean leaf to be more easily detectable (3-fold increase in vol%) using fluorescent detection and allowed 28 phosphorylated proteins previously undetected, to be isolated and identified by MALDI-TOF-MS.

  11. Bathyal meiobenthos of the western Coral Sea: distribution and abundance in relation to microbial standing stocks and environmental factors

    NASA Astrophysics Data System (ADS)

    Alongi, Daniel M.; Pichon, Michel

    1988-04-01

    The distribution and abundance of meiobenthos in relation to microbial densities and environmental factors were examined at 24 stations in a bathyal (298-1610 m) region of the western Coral Sea. Densities of metazoan meiofauna were low ( overlinex = 57 ; range: 19-170 individuals 10 cm -2) compared with other bathyal communtiesm but when densities of living Foraminifera ( overlinex = 560 ; range: 0-3410 individuals 10 cm -2) were included, total faunal densities were high ( overlinex = 610 10 cm-2) and ranged from 73 to 3465 individuals 10 cm -2. Soft-bodied (non-chitinous) taxa (e.g. turbellarians) were not detected beyond the continental slope. Densities of all metazoan taxa, excluding nematodes, decreased significantly with bathymetric depth. When the effect of ocean depth was held constant, only a few significant correlations of meiobenthos with microbes and sediment characteristics were found. Our data, coupled with earlier findings of low bacterial densities and organic conditions, suggest that low densities of metazoan meiobenthos in the western Coral Sea are due to low rates of detrital input. However, densities of Foraminifera and other protozoans increased with bathymetric depth ( ALONGI, 1987, Deep-Sea Research, 34, 1245-1254), indicating their ability to exploit oligotrophic conditions and to gain numerical dominance in benthic food webs of the deep sea.

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

    PubMed

    Wallace, Robert; Ayala, Guido; Viscarra, Maria

    2012-12-01

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

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

    SciTech Connect

    Sundaralingam, N.

    1993-06-08

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

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

    USGS Publications Warehouse

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

    2010-01-01

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

  15. A family of abundant plasma membrane-associated glycoproteins related to the arabinogalactan proteins is unique to flowering plants

    PubMed Central

    1989-01-01

    We have identified a family of abundant peripheral plasma membrane glycoproteins that is unique to flowering plants. They are identified by a monoclonal antibody, MAC 207, that recognizes an epitope containing L-arabinose and D-glucuronic acid. Immunofluorescence and immunogold labeling studies locate the MAC 207 epitope to the outer surface of the plasma membrane both in protoplasts and in intact tissues. In some cells MAC 207 also binds to the vacuolar membrane, probably reflecting the movement of the plasma membrane glycoproteins in the endocytic pathway. The epitope recognized by MAC 207 is also present on a distinct soluble proteoglycan secreted into the growth medium by carrot (Daucus carota) suspension culture cells. Biochemical evidence identifies this neutral proteoglycan as a member of the large class of arabinogalactan proteins (AGPs), and suggests a structural relationship between it and the plasma membrane glycoproteins. AGPs have the property of binding to beta-glycans, and we therefore propose that one function of the AGP-related, plasma membrane-associated glycoproteins may be to act as cell surface attachment sites for cell wall matrix polysaccharides. PMID:2469683

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

    PubMed

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

    2016-01-01

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

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

    PubMed Central

    Zipf, Alexander

    2016-01-01

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

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

    PubMed

    Bara, Jeffrey J; Muturi, Ephantus J

    2015-05-01

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

  19. 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.

  20. 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

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

    PubMed

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

    2014-01-01

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

  2. 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

  3. Paleodietary reconstruction using stable isotopes and abundance analysis of bovids from the Shungura Formation of South Omo, Ethiopia.

    PubMed

    Negash, Enquye W; Alemseged, Zeresenay; Wynn, Jonathan G; Bedaso, Zelalem K

    2015-11-01

    Preservation of the stable carbon isotopic composition of fossil tooth enamel enables us to estimate the relative proportion of C3 versus C4 vegetation in an animal's diet, which, combined with analysis of faunal abundance, may provide complementary methods of paleoenvironmental reconstruction. To this end, we analyzed stable carbon isotopic composition (δ(13)C values) of tooth enamel from four bovid tribes (Tragelaphini, Aepycerotini, Reduncini, and Alcelaphini) derived from six members of the Shungura Formation (Members B, C, D, F, G, and L; ages from ca. 2.90-1.05 Ma (millions of years ago) in the Lower Omo Valley of southwestern Ethiopia. The bovids show a wide range of δ(13)C values within taxa and stratigraphic members, as well as temporal changes in the feeding strategies of taxa analyzed throughout the middle to late Pliocene and early Pleistocene. Such variation suggests that the use of actualistic approaches for paleoenvironmental reconstruction may not always be warranted. Alcelaphini was the only taxon analyzed that retained a consistent dietary preference throughout the sequence, with entirely C4-dominated diets. Reduncini had a mixed C3/C4 to C4-dominated diet prior to 2.4 Ma, after which this taxon shifted to a largely C4-dominated diet. Aepycerotini generally showed a mixed C3/C4 diet, with a period of increased C4 diet from 2.5 to 2.3 Ma. Tragelaphini showed a range of mixed C3/C4 diets, with a median value that was briefly nearer the C4 end member from 2.9 to 2.4 Ma but was otherwise towards the C3 end member. These isotopic results, combined with relative abundance data for these bovids, imply that the environment of the Lower Omo Valley consisted of a mosaic of closed woodlands, with riverine forests and open grasslands. However, our data also signify that the overall environment gradually became more open, and that C4 grasses became more dominant. Finally, these results help document the range and extent of environments and potential diets

  4. Seasonal trends and spatial relations between environmental/meteorological factors and leishmaniosis sand fly vector abundances in Central Spain.

    PubMed

    Gálvez, R; Descalzo, M A; Miró, G; Jiménez, M I; Martín, O; Dos Santos-Brandao, F; Guerrero, I; Cubero, E; Molina, R

    2010-01-01

    This paper reports on an entomological survey performed over the period 2006-2008 in Central Spain (mainly in the Madrid province) where canine leishmaniosis (CanL) is endemic. The study area was selected on the grounds of its wide altitude range, which determines both broad climate and vegetation ranges that could affect sand fly distributions. This area was surveyed from NE to SW across its mountain range (Sistema Central) and plateau area using sticky traps mainly on embankments. In 2006 and 2007, 123 sites were sampled (9557 sand flies captured) to establish possible relations between environmental or meteorological factors and vector densities (Phlebotomus perniciosus and Phlebotomus ariasi). The factors correlated with higher vector densities were: a sample site between villages or at the edge of a village, the lack of a paved road, a rural habitat, an east or south-facing wall or wall sheltered from the wind, the presence of livestock or birds, a holm-oak wood vegetation, a lower summer mean temperature and lower annual mean precipitation. This study was followed by a seasonal survey conducted at 16 selected sites (14,353 sand flies) sampled them monthly from May to November 2008. P. perniciosus showed a diphasic seasonal trend with two abundance peaks in July and September whereas P. ariasi showed a monophasic trend with one peak in August. Comparing with data from studies performed in 1991 in the same area, vector densities are significantly higher. A possible explanation for this is that the vectors (mainly P. ariasi) are moving towards higher altitudes perhaps because of global change. This increasing trend could have an impact on CanL and its geographical distribution.

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

    USGS Publications Warehouse

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

    2016-01-01

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

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

    PubMed

    Ptolemy, Adam S; Britz-McKibbin, Philip

    2005-09-01

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

  7. 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.

  8. 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.

  9. Abundances of heavy elements in metal deficient stars II. Detailed spectroscopic analysis

    NASA Astrophysics Data System (ADS)

    Zhao, Gang

    1994-01-01

    In this paper, we determine the abundances of a number of neutron capture elements in metal-poor dwarfs and subgiants. The strontium, yttrium, zirconium, barium, lanthanum, cerium and europium abundances are deduced in a sample of 10 to 20 stars on the basis of high resolution, high signal-to-noise spectra. The main results are: (1) The elements of the first peak, strontium-yttrium-zirconium, show the odd-even effect: strontium and zirconium are less deficient than yttrium in Population II stars. (2) The yttrium abundance is constant ([ Y/Fe] = -0.06) for all stars with [ Fe/H] > -2.5 . (3) The barium overdeficiency increases with decreasing metallicity when [ Fe/H] < -1.7 . (4) Lanthanum and cerium are overdeficient with respect to iron. (5) Europium is overabundant for -1 > [ Fe/H] > -2 . (6) There is a real cosmic scatter in [ Y/Fe] , [ Zr/Fe] and [ Ba/Fe] , of the order of 0.1 dex.

  10. A critical analysis of interstellar Zn and Cr as galactic abundance benchmarks for quasar absorbers

    NASA Technical Reports Server (NTRS)

    Sembach, Kenneth R.; Steidel, Charles C.; Macke, Robert J.; Meyer, David M.

    1995-01-01

    We present interstellar gas-phase abundances of zinc and chromium in the Milky Way for comparison with the abundances of these elements in damped Ly-alpha systems at redshifts near z approximately 2. We make use of both IUE (International Ultraviolet Explorer) and GHRS (Goddard High Resolution Spectrograph) archival information in deriving the Milky Way values and find that the average difference in (Zn/H) and (Cr/Zn) between the Milky Way and damped Ly-alpha systems at large N(H1) is about 0.9 dex. The Zn/H values we find for the Milky Way are approximately -0.2 to -0.7 dex below solar and are due in large part to depletion of Zn onto dust grains. The amount of this gas-phase depletion is variable and depends upon the H1 column density and molecular fraction of the gas. Milky Way sight lines having low molecular fractions have values of (Zn/H) within approximately 0.2 dex of the solar value. Combined with larger values of (Cr/Zn) found for the damped Ly-alpha systems, this result confirms that measures of (Zn/H) should accurately reflect the lower gas-phase abundances of Zn found in these systems.

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

    PubMed

    Naicy, Thomas; Venkatachalapathy, R Thirupathy; Aravindakshan, T V; Raghavan, K C; Mini, M; Shyama, K

    2016-10-01

    Nerve Growth Factor (NGF) promotes the development of pre-antral ovarian follicles through ovarian innervations and regulation of ovarian response to gonadotropins. The present study was conducted to study the tissue gene expression profile, to characterize the genetic variants, find associations of the NGF gene with prolificacy in the prolific Malabari and less prolific Attappady Black goats because NGF has an important role in reproduction by augmenting ovarian folliculogenesis. Relative abundance of NGF mRNA was greatest in reproductive tissues signifying its role in reproduction. The PCR-SSCP analysis of a 251bp fragment of Exon 3 of the NGF gene from the 277 goats revealed four diplotypes (EE, EF, FF and EG) with respective frequencies of 0.76, 0.22, 0.01 and 0.01. Sequencing of the representative samples revealed one synonymous and one novel non synonymous mutations (g.705G>A and g.715C>T). Statistical analysis indicated that the SNP g.705G>A was associated with litter size in Attappady Black goats (P<0.05) and a PCR-RFLP was designed using the restriction enzyme, BpiI, for rapid screening of the SNP. The results of the present study suggest that the NGF gene is a primary candidate gene affecting prolificacy in goats and may be used for Marker Assisted Selection (MAS) in goats, especially in lowly prolific Attappady Black goats.

  12. Age- and Activity-Related Differences in the Abundance of Myosin Essential and Regulatory Light Chains in Human Muscle

    PubMed Central

    Cobley, James N.; Ab. Malik, Zulezwan; Morton, James P.; Close, Graeme L.; Edwards, Ben J.; Burniston, Jatin G.

    2016-01-01

    Traditional methods for phenotyping skeletal muscle (e.g., immunohistochemistry) are labor-intensive and ill-suited to multixplex analysis, i.e., assays must be performed in a series. Addressing these concerns represents a largely unmet research need but more comprehensive parallel analysis of myofibrillar proteins could advance knowledge regarding age- and activity-dependent changes in human muscle. We report a label-free, semi-automated and time efficient LC-MS proteomic workflow for phenotyping the myofibrillar proteome. Application of this workflow in old and young as well as trained and untrained human skeletal muscle yielded several novel observations that were subsequently verified by multiple reaction monitoring (MRM). We report novel data demonstrating that human ageing is associated with lesser myosin light chain 1 content and greater myosin light chain 3 content, consistent with an age-related reduction in type II muscle fibers. We also disambiguate conflicting data regarding myosin regulatory light chain, revealing that age-related changes in this protein more closely reflect physical activity status than ageing per se. This finding reinforces the need to control for physical activity levels when investigating the natural process of ageing. Taken together, our data confirm and extend knowledge regarding age- and activity-related phenotypes. In addition, the MRM transitions described here provide a methodological platform that can be fine-tuned to suite multiple research needs and thus advance myofibrillar phenotyping. PMID:28248225

  13. Relative abundance and prevalence of selected Borrelia infections in Ixodes scapularis and Amblyomma americanum (Acari: Ixodidae) from publicly owned lands in Monmouth County, New Jersey.

    PubMed

    Schulze, Terry L; Jordan, Robert A; Healy, Sean P; Roegner, Vivien E; Meddis, Michael; Jahn, Margaret B; Guthrie, Douglas L

    2006-11-01

    To evaluate their potential importance in the transmission of ixodid tick-borne borrelioses in Monmouth County, NJ, we collected host-seeking Ixodes scapularis Say and Amblyomma americanum (L.) (Acari: Ixodidae) adults and nymphs to determine relative encounter frequencies and the infection prevalence of selected Borrelia spp. in their respective tick vectors. We also reviewed records of all ticks submitted for identification by the public in Monmouth County during 2001-2005. Relative abundance of the two species varied markedly among sites. Adult encounter frequencies for the two species were similar; however, A. americanum nymphs were encountered 3 times more frequently than I. scapularis nymphs. Of 435 ticks submitted by the public, 50.1 and 38.9% were I. scapularis and A. americanum, respectively. However, during May through August, the peak Lyme disease transmission season in New Jersey, significantly more submitted ticks were A. americanum (55.9%), compared with I. scapularis (34.1%). Polymerase chain reaction analysis of 94 1. scapularis and 103 A. americanum adults yielded infection prevalences of 31.9% for B. burgdorferi and 5.8% for B. lonestari, respectively. Although the infection prevalence of B. burgdorferi in I. scapularis was considerably higher than the infection prevalence of B. lonestari in A. americanum, the higher encounter frequencies for A. americanum compared with I. scapularis observed in this and other studies may result in increased risk of acquiring exposure to A. americanum-transmitted pathogens. The potential public health implications of these results are discussed.

  14. 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...

  15. {sup 39}Ar Detection at the 10{sup -16} Isotopic Abundance Level with Atom Trap Trace Analysis

    SciTech Connect

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

    2011-03-11

    Atom trap trace analysis, a laser-based atom counting method, has been applied to analyze atmospheric {sup 39}Ar (half-life=269 yr), a cosmogenic isotope with an isotopic abundance of 8x10{sup -16}. In addition to the superior selectivity demonstrated in this work, the counting rate and efficiency of atom trap trace analysis have been improved by 2 orders of magnitude over prior results. The significant applications of this new analytical capability lie in radioisotope dating of ice and water samples and in the development of dark matter detectors.

  16. 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.

  17. Preliminary Results of Detailed Chemical Abundance Analysis of Milky Way Satellite Galaxy Reticulum II Discovered in the Dark Energy Survey

    NASA Astrophysics Data System (ADS)

    Nagasawa, Daniel; Marshall, Jennifer L.; Li, Ting; Dark Energy Survey Milky Way Science Group

    2016-01-01

    We present preliminary results from abundance analysis of stars in Milky Way satellite galaxies found in the Dark Energy Survey (DES). DES has discovered 16 candidate satellite galaxies of the Milky Way in its first two years of operation. Since January 2015, three candidates have subsequently been revealed to be dark matter-dominated by spectroscopic follow-up studies of their kinematics, confirming their status as satellite galaxies. Spectroscopic follow-up of the remaining 13 candidates is underway. We have analyzed high resolution VLT/GIRAFFE spectra of member stars in one of these satellite galaxies, Reticulum II. Using equivalent width measurement and spectral synthesis methods, we measure the abundances of Iron and other species in order to begin to understand the chemical content of these Milky Way satellites.

  18. 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.

  19. Distribution and abundance of stream fishes in relation to barriers: implications for monitoring stream recovery after barrier removal

    USGS Publications Warehouse

    Zydlewski, Joseph; Coghlan Jr., Stephen M.; Gardner, C.; Saunders, R.

    2011-01-01

    Dams are ubiquitous in coastal regions and have altered stream habitats and the distribution and abundance of stream fishes in those habitats by disrupting hydrology, temperature regime and habitat connectivity. Dam removal is a common restoration tool, but often the response of the fish assemblage is not monitored rigorously. Sedgeunkedunk Stream, a small tributary to the Penobscot River (Maine, USA), has been the focus of a restoration effort that includes the removal of two low-head dams. In this study, we quantified fish assemblage metrics along a longitudinal gradient in Sedgeunkedunk Stream and also in a nearby reference stream. By establishing pre-removal baseline conditions and associated variability and the conditions and variability immediately following removal, we can characterize future changes in the system associated with dam removal. Over 2 years prior to dam removal, species richness and abundance in Sedgeunkedunk Stream were highest downstream of the lowest dam, lowest immediately upstream of that dam and intermediate farther upstream; patterns were similar in the reference stream. Although seasonal and annual variation in metrics within each site was substantial, the overall upstream-to-downstream pattern along the stream gradient was remarkably consistent prior to dam removal. Immediately after dam removal, we saw significant decreases in richness and abundance downstream of the former dam site and a corresponding increase in fish abundance upstream of the former dam site. No such changes occurred in reference sites. Our results show that by quantifying baseline conditions in a small stream before restoration, the effects of stream restoration efforts on fish assemblages can be monitored successfully. These data set the stage for the long-term assessment of Sedgeunkedunk Stream and provide a simple methodology for assessment in other restoration projects.

  20. Seasonal fecundity is not related to geographic position across a species' global range despite a central peak in abundance.

    PubMed

    Ruskin, Katharine J; Etterson, Matthew A; Hodgman, Thomas P; Borowske, Alyssa C; Cohen, Jonathan B; Elphick, Chris S; Field, Christopher R; Kern, Rebecca A; King, Erin; Kocek, Alison R; Kovach, Adrienne I; O'Brien, Kathleen M; Pau, Nancy; Shriver, W Gregory; Walsh, Jennifer; Olsen, Brian J

    2017-01-01

    The range of a species is determined by the balance of its demographic rates across space. Population growth rates are widely hypothesized to be greatest at the geographic center of the species range, but indirect empirical support for this pattern using abundance as a proxy has been mixed, and demographic rates are rarely quantified on a large spatial scale. Therefore, the texture of how demographic rates of a species vary over its range remains an open question. We quantified seasonal fecundity of populations spanning the majority of the global range of a single species, the saltmarsh sparrow (Ammodramus caudacutus), which demonstrates a peak of abundance at the geographic center of its range. We used a novel, population projection method to estimate seasonal fecundity inclusive of seasonal and spatial variation in life history traits that contribute to seasonal fecundity. We replicated our study over 3 years, and compared seasonal fecundity to latitude and distance among plots. We observed large-scale patterns in some life history traits that contribute to seasonal fecundity, such as an increase in clutch size with latitude. However, we observed no relationship between latitude and seasonal fecundity. Instead, fecundity varied greatly among plots separated by as little as 1 km. Our results do not support the hypothesis that demographic rates are highest at the geographic and abundance center of a species range, but rather they suggest that local drivers strongly influence saltmarsh sparrow fecundity across their global range.

  1. A study of Culicoides in Rondônia, in the Brazilian Amazon: species composition, relative abundance and potential vectors.

    PubMed

    Carvalho, L P C; Pereira Júnior, A M; Farias, E S; Almeida, J F; Rodrigues, M S; Resadore, F; Pessoa, F A C; Medeiros, J F

    2017-03-01

    There is very little information available about Culicoides species (Diptera: Ceratopogonidae) in the western Brazilian Amazon. However, studies of the fauna of this region are essential to knowledge of the species and potential vectors within it. Thus, the present study aims to evaluate the abundance, richness and composition of Culicoides species in rural areas in the state of Rondônia, Brazil. Culicoides specimens were collected in forest and pasture environments in the municipality of Porto Velho, using light traps. A total of 1708 individuals (1136 females and 572 males) belonging to 33 species were collected; 28 of these samples represent new records for the state of Rondônia and include the first record of Culicoides contubernalis in Brazil. Culicoides insignis was the most abundant species (86.1%). Species richness was greater in forest areas (32 species, 96.96%), whereas pastures presented the greatest number of Culicoides captured (n = 1540, 90.1%). This study shows that Culicoides populations differ between forest and pasture environments and indicates that the abundance of C. insignis is an important factor in epidemiological vigilance studies in the region.

  2. Relative abundance and distribution of fishes and crayfish at Ash Meadows National Wildlife Refuge, Nye County, Nevada, 2007-08

    USGS Publications Warehouse

    Scoppettone, G. Gary; Rissler, Peter; Johnson, Danielle; Hereford, Mark

    2011-01-01

    swamp crayfish and western mosquitofish was in water with temperature greater than 26 degrees C near the springhead, and in shallow (depths less than 10 centimeters) grassy marshes. Among 177 sampling stations within the range of Warm Springs Amargosa pupfish, red swamp crayfish were collected at 96 stations and western mosquitofish were collected at 49 stations. Removal of convict cichlid (Amatitlania nigrofasciata) from Fairbanks Spring was followed by a substantial increase in Ash Meadows Amargosa pupfish (Cyprinodon nevadensis mionectes) captures from 910 pre-removal to 3,056 post-removal. Red swamp crayfish was continually removed from Bradford 1 Spring, which seemed to cause an increase in the speckled dace population. Restoration of Kings Pool and Jackrabbit Springs promoted the success of native fishes with the greatest densities in restored reaches. Ongoing restoration of Carson Slough and its tributaries, as well as control and elimination of invasive species, is expected to increase abundance and distribution of Ash Meadows' native fish populations. Further analysis of data from this study will help determine the habitat characteristic(s) that promote native species and curtail non-native species.

  3. Changes in tumorigenesis- and angiogenesis-related gene transcript abundance profiles in ovarian cancer detected by tailored high density cDNA arrays.

    PubMed Central

    Martoglio, A. M.; Tom, B. D.; Starkey, M.; Corps, A. N.; Charnock-Jones, D. S.; Smith, S. K.

    2000-01-01

    BACKGROUND: Complementary DNA array analysis of gene expression has a potential application for clinical diagnosis of disease processes. However, accessibility, affordability, reproducibility of results, and management of the data generated remain issues of concern. Use of cDNA arrays tailored for studies of specific pathways, tissues, or disease states may render a cost- and time-effective method to define potential hallmark genotype alterations. MATERIALS AND METHODS: We produced a 332-membered human cDNA array on nylon membranes tailored for studies of angiogenesis and tumorigenesis in reproductive disease. We tested the system for reproducibility using a novel statistical approach for analysis of array data and employed the arrays to investigate gene expression alterations in ovarian cancer. RESULTS: Intra-assay analysis and removal of agreement outliers was shown to be a critical step prior to interpretation of cDNA array data. The system revealed highly reproducible results, with intermembrane coefficient of reproducibility of +/- 0.98. Comparison of placental and ovarian sample data confirmed expected differences in angiogenic profiles and tissue-specific markers, such as human placental lactogen (hPL). Analysis of expression profiles of five normal ovary and four poorly differentiated serous papillary ovarian adenocarcinoma samples revealed an overall increase in angiogenesis-related markers, including vascular endothelial growth factor (VEGF) and angiopoietin-1 in the diseased tissue. These were accompanied by increases in immune response mediators (e.g. HLA-DR, Ron), apoptotic and neoplastic markers (e.g. BAD protein, b-myb), and novel potential markers of ovarian cancer, such as cofilin, moesin, and neuron-restrictive silencer factor (REST) protein. CONCLUSIONS: In-house production of tailored cDNA arrays, coupled to comprehensive analysis of resulting hybridization profiles, provides an accessible, reliable, and highly effective method of applying array

  4. Elemental abundance analysis of the early-type members of the open cluster M6: Preliminary results

    NASA Astrophysics Data System (ADS)

    Kılıçoǧlu, T.; Monier, R.; Fossati, L.

    2014-11-01

    Differences in chemical composition among main sequence stars within a given cluster are probably due to differences in their masses and other effects such as radiative diffusion, magnetic field, rotation, mixing mechanisms, mass loss, accretion and multiplicity. The early type main-sequence members of open clusters of different ages support studies of the competition between radiative diffusion and mixing mechanisms. We have analysed low- and high-resolution spectra covering the spectral range λ 4500-5840 Å of late B-, A- and F-type members of the open cluster M6 (age ˜100 Myr). The spectra were obtained with the FLAMES/GIRAFFE spectrograph mounted at UT2, the 8-m VLT telescope. The effective temperatures, surface gravities and microturbulent velocities of the stars were derived from both photometric and spectral methods. We have also performed a chemical abundance analysis using synthetic spectra. Abundances were determined for the elements C, O, Mg, Si, Ca, Sc, Ti, Cr, Mn, Fe, Ni, Y and Ba. The star-to-star variations in element abundances among the members of M6 are discussed.

  5. Estimating stellar atmospheric parameters, absolute magnitudes and elemental abundances from the LAMOST spectra with Kernel-based principal component analysis

    NASA Astrophysics Data System (ADS)

    Xiang, M.-S.; Liu, X.-W.; Shi, J.-R.; Yuan, H.-B.; Huang, Y.; Luo, A.-L.; Zhang, H.-W.; Zhao, Y.-H.; Zhang, J.-N.; Ren, J.-J.; Chen, B.-Q.; Wang, C.; Li, J.; Huo, Z.-Y.; Zhang, W.; Wang, J.-L.; Zhang, Y.; Hou, Y.-H.; Wang, Y.-F.

    2017-01-01

    Accurate determination of stellar atmospheric parameters and elemental abundances is crucial for Galactic archaeology via large-scale spectroscopic surveys. In this paper, we estimate stellar atmospheric parameters - effective temperature Teff, surface gravity log g and metallicity [Fe/H], absolute magnitudes MV and MKs, α-element to metal (and iron) abundance ratio [α/M] (and [α/Fe]), as well as carbon and nitrogen abundances [C/H] and [N/H] from the Large Sky Area Multi-Object Fibre Spectroscopic Telescope (LAMOST) spectra with a multivariate regression method based on kernel-based principal component analysis, using stars in common with other surveys (Hipparcos, Kepler, Apache Point Observatory Galactic Evolution Experiment) as training data sets. Both internal and external examinations indicate that given a spectral signal-to-noise ratio (SNR) better than 50, our method is capable of delivering stellar parameters with a precision of ˜100 K for Teff, ˜0.1 dex for log g, 0.3-0.4 mag for MV and MKs, 0.1 dex for [Fe/H], [C/H] and [N/H], and better than 0.05 dex for [α/M] ([α/Fe]). The results are satisfactory even for a spectral SNR of 20. The work presents first determinations of [C/H] and [N/H] abundances from a vast data set of LAMOST, and, to our knowledge, the first reported implementation of absolute magnitude estimation directly based on a vast data set of observed spectra. The derived stellar parameters for millions of stars from the LAMOST surveys will be publicly available in the form of value-added catalogues.

  6. Spatial Analysis of Spectra from Galactic Planetary Nebulae and Extragalactic H II Regions: Testing for Abundance Variations

    NASA Astrophysics Data System (ADS)

    Miller, Timothy R.

    2017-01-01

    Presented here is a spatial analysis of spectra for seven planetary nebulae (NGC 2440, NGC 3242, NGC 5315, NGC 5882, NGC 7662, IC 2165, and IC 3568) as well as H II regions from six nearly face-on, spiral galaxies (NGC 2403, NGC 3310, NGC 4321, NGC 5194, NGC 5236, and NGC 5457). The two main goals of the study were (1) to investigate whether or not each planetary nebula (PN) is chemically homogeneous; and (2) to search for evidence of azimuthal abundance gradients in the disks of the galaxies. Each of these test the validity of assumptions commonly made for these two object types, i.e., (1) Ejecta from asymptotic giant branch stars are well mixed and (2) elements returned to the interstellar medium of a spiral galaxy are “instantaneously” distributed around the disk for a fixed distance from the center.The PN homogeneity problem was addressed by spatially dividing each long-slit HST/STIS spectrum into many smaller regions across each object and calculating the abundances of each region. The major result is that the ejecta are indeed homogeneous in each planetary nebula for the elements probed. A secondary goal was to constrain the temperature and luminosity of each PN central star, which was accomplished by modeling each object using the photoionization code CLOUDY.The spectra for the galaxies are from the VIRUS-P spectrograph, an integral field unit consisting of 246 fibers arranged in a square, with the observations centered on or near the nuclear bulge, covering a full 360 degrees around each galaxy and encompassing numerous H II regions located near the bulge. Additional goals for each galaxy included obtaining radial abundance gradients and accurate carbon and neon abundances for high metallicity H II regions.

  7. Cetacean distribution and relative abundance on the central eastern and the southeastern Bering Sea shelf with reference to oceanographic domains

    NASA Astrophysics Data System (ADS)

    Moore, S. E.; Waite, J. M.; Friday, N. A.; Honkalehto, T.

    2002-10-01

    Visual line-transect surveys for cetaceans were conducted in the central-eastern Bering Sea (CEBS) from 5 July to 5 August 1999, and in the southeastern Bering Sea (SEBS) from 10 June to 3 July 2000, in association with a pollock stock assessment survey aboard the NOAA ship Miller Freeman. Observers scanned for cetaceans with 25× (Big Eye) binoculars from the flying bridge (platform height=12 m) at survey speeds of 18.5-22 km h -1 (10-12 knots). Transect survey effort was 1761 km in 1999, in a study area 196,885 km 2; and 2194 km in 2000, in a study area 158,561 km 2. An additional 609 and 402 km of trackline was surveyed in 1999 and 2000, respectively, while in transit to or from pollock survey way points. Fin whales ( Balaenoptera physalus) were the most common large whale, and Dall’s porpoise ( Phocoenoides dalli) the most common small cetacean in both regions. In the CEBS (1999), uncorrected cetacean abundance estimates were: 3368 (CV=0.29) fin whales, 810 (CV=0.36) minke whales ( B. acutorostrata), 14,312 (CV=0.26) Dall’s porpoise and 693 (CV=0.53) harbor porpoise ( Phocoenaphocoena). In the SEBS (2000), uncorrected abundance estimates were: 683 (CV=0.32) fin whales, 102 (CV=0.50) humpback whales ( Megaptera novaeangliae), 1003 (CV=0.26) minke whales, 9807 (CV=0.20) Dall’s porpoise and 1958 (CV=0.21) harbor porpoise. These are the first estimates of cetacean abundance that can be directly compared between two regions of the eastern Bering Sea. Distributions of some species were associated with bathymetric features, and there were occasions when prey associations were obvious. For example, in the SEBS, fin whales occurred on the Middle Shelf (50-100 m) and on the Outer Shelf (100-200 m) near the Pribilof canyon, but in the CEBS fin whales occurred primarily on the Outer Shelf along the 200 m isobath (i.e. the Green Belt). Fin whales were sometimes associated with echo-sounder backscatter from a mixture of fish schools and zooplankton. Humpback whales

  8. Differential chemical abundance analysis of a 47 Tucanæ asymptotic giant branch star with respect to Arcturus

    NASA Astrophysics Data System (ADS)

    Worley, C. C.; Cottrell, P. L.; Freeman, K. C.; Wylie-de Boer, E. C.

    2009-12-01

    This study resolves a discrepancy in the abundance of Zr in the 47 Tucanæ asymptotic giant branch (AGB) star Lee 2525. This star was observed using the echelle spectrograph on the 2.3-m telescope at Siding Spring Observatory. The analysis was undertaken by calibrating Lee 2525 with respect to the standard giant star Arcturus. This work emphasizes the importance of using a standard star with stellar parameters comparable to the star under analysis rather than a calibration with respect to the Sun as in Koch & McWilliam. Systematic errors in the analysis process are then minimized due to the similarity in atmospheric structure between the standard and programme stars. The abundances derived for Lee 2525 were found to be in general agreement with the Brown & Wallerstein values except for Zr. In this study Zr has a similar enhancement ([Zr/Fe] = +0.51 dex) to another light s-process element, Y ([Y/Fe] = +0.53 dex), which reflects current theory regarding the enrichment of s-process elements by nuclear processes within AGB stars. This is contrary to the results of Brown & Wallerstein where Zr was underabundant ([Zr/Fe] = -0.51 dex) and Y was overabundant ([Y/Fe] = +0.50 dex) with respect to Fe.

  9. Relative abundances of sandfly species (Diptera: Phlebotominae) in two villages in the same area of Campeche, in southern Mexico.

    PubMed

    Rebollar-Téllez, E A; Tun-Ku, E; Manrique-Saide, P C; Andrade-Narvaez, F J

    2005-03-01

    Leishmania mexicana is the parasite causing most cases of human cutaneous leishmaniasis in southern Mexico, where Lutzomyia olmeca olmeca and Lu. cruciata are the most probable vectors. In the present study, sandflies were collected during one transmission season (November 2001-March 2002) in the village of La Guadalupe and the nearby village of Dos Naciones, in the southern Mexican county of Calakmul. Using Shannon traps, Disney traps and CDC light traps, 5983 sandflies (Brumptomyia and Lutzomyia) were caught. In Dos Naciones the numbers of Lu. panamensis caught in Shannon or CDC traps outnumbered those of the other sandfly species. In La Guadalupe, in contrast, the most abundant species in the collections made with Shannon or CDC traps was Lu. cruciata , followed by Lu. olmeca olmeca and Lu. deleoni. In both locations, the numbers of sandflies attracted to Shannon traps peaked between 18.00 and 22.00 hours. Given the abundance of Lu. olmeca olmeca in the collections made with Shannon and Disney traps (it was the only species caught in the latter), this species is probably the primary vector of Le. mexicana in Calakmul county.

  10. Relative abundance of American badger (Taxidea taxus) and red fox (Vulpes vulpes) in landscapes with high and low rodenticide poisoning levels.

    PubMed

    Proulx, Gilbert; MacKenzie, Neil

    2012-03-01

    Over the past decade, extensive poisoning campaigns have been conducted in southern Saskatchewan to control Richardson's ground squirrel Spermophilus richardsonii (Sabine, 1822) populations. Such campaigns might impact on predator abundance by decreasing prey levels, and also through secondary poisoning. Using spotlighting, we investigated the relative abundance of American badgers Taxidea taxus (Schreber, 1777) and red fox Vulpes vulpes (Linnaeus, 1758) in 2 study areas with road access and crops, but with different levels of poisoning. In the study area with relatively low poisoning (19.6% of the area traversed by roads), there were 2.2 times more American badgers per km of road and 6.4 times more red foxes per km than in the study area with high poisoning (89.7% of the area). It is recommended that an Integrated Pest Management program be developed to conserve natural predators across landscapes.

  11. Relative abundances of methane- and sulfur-oxidizing symbionts in gills of the deep-sea hydrothermal vent mussel Bathymodiolus azoricus under pressure

    NASA Astrophysics Data System (ADS)

    Szafranski, Kamil M.; Piquet, Bérénice; Shillito, Bruce; Lallier, François H.; Duperron, Sébastien

    2015-07-01

    The deep-sea mussel Bathymodiolus azoricus dominates hydrothermal vent fauna in the Azores region. The gills of this species house methane- and sulfur-oxidizing bacteria that fulfill most of the mussel's nutritional requirements. Previous studies suggested that the ratio between methane- and sulfur-oxidizers could vary in response to the availability of electron donors in their environment, and this flexibility is considered a key factor in explaining the ecological success of the species. However, previous studies were based on non-isobaric recovery of specimens, with experiments at atmospheric pressure which may have induced artifacts. This study investigates the effect of pressure-related stress during recovery and experimentation on the relative abundances of bacterial symbionts. Mussel specimens were recovered for the first time using the pressure-maintaining device PERISCOP. Specimens were subsequently transferred into pressurized vessels and exposed to various chemical conditions. Using optimized fluorescence in situ hybridization-based approaches, relative abundance of symbionts were measured. Our results show that the recovery method (isobaric versus non-isobaric) does not influence the abundances of bacterial symbionts. Significant differences occur among specimens sampled from two contrasting sites. Exposure of mussels from the deeper site to sulfide and bicarbonate, and to bicarbonate alone, both resulted in a rapid and significant increase in the relative abundance of sulfur-oxidizers. Results reported herein are congruent with those from previous reports investigating mussels originating from shallow sites and kept at ambient pressure. Isobaric recovery and maintenance allowed us to perform in vivo experiments in specimens from a deeper site that could not be maintained alive at ambient pressure, and will greatly improve the chances of identifying the molecular mechanisms underlying the dialogue between bathymodioline hosts and symbionts.

  12. Novel low abundance and transient RNAs in yeast revealed by tiling microarrays and ultra high-throughput sequencing are not conserved across closely related yeast species.

    PubMed

    Lee, Albert; Hansen, Kasper Daniel; Bullard, James; Dudoit, Sandrine; Sherlock, Gavin

    2008-12-01

    A complete description of the transcriptome of an organism is crucial for a comprehensive understanding of how it functions and how its transcriptional networks are controlled, and may provide insights into the organism's evolution. Despite the status of Saccharomyces cerevisiae as arguably the most well-studied model eukaryote, we still do not have a full catalog or understanding of all its genes. In order to interrogate the transcriptome of S. cerevisiae for low abundance or rapidly turned over transcripts, we deleted elements of the RNA degradation machinery with the goal of preferentially increasing the relative abundance of such transcripts. We then used high-resolution tiling microarrays and ultra high-throughput sequencing (UHTS) to identify, map, and validate unannotated transcripts that are more abundant in the RNA degradation mutants relative to wild-type cells. We identified 365 currently unannotated transcripts, the majority presumably representing low abundance or short-lived RNAs, of which 185 are previously unknown and unique to this study. It is likely that many of these are cryptic unstable transcripts (CUTs), which are rapidly degraded and whose function(s) within the cell are still unclear, while others may be novel functional transcripts. Of the 185 transcripts we identified as novel to our study, greater than 80 percent come from regions of the genome that have lower conservation scores amongst closely related yeast species than 85 percent of the verified ORFs in S. cerevisiae. Such regions of the genome have typically been less well-studied, and by definition transcripts from these regions will distinguish S. cerevisiae from these closely related species.

  13. Sims Analysis of Water Abundance and Hydrogen Isotope in Lunar Highland Plagioclase

    NASA Technical Reports Server (NTRS)

    Hui, Hejiu; Guan, Yunbin; Chen, Yang; Peslier, Anne H.; Zhang, Youxue; Liu, Yang; Rossman, George R.; Eiler, John M.; Neal, Clive R.

    2015-01-01

    The detection of indigenous water in mare basaltic glass beads has challenged the view established since the Apollo era of a "dry" Moon. Since this discovery, measurements of water in lunar apatite, olivine-hosted melt inclusions, agglutinates, and nominally anhydrous minerals have confirmed that lunar igneous materials contain water, implying that some parts of lunar mantle may have as much water as Earth's upper mantle. The interpretation of hydrogen (H) isotopes in lunar samples, however, is controversial. The large variation of H isotope ratios in lunar apatite (delta Deuterium = -202 to +1010 per mille) has been taken as evidence that water in the lunar interior comes from the lunar mantle, solar wind protons, and/or comets. The very low deuterium/H ratios in lunar agglutinates indicate that solar wind protons have contributed to their hydrogen content. Conversely, H isotopes in lunar volcanic glass beads and olivine-hosted melt inclusions being similar to those of common terrestrial igneous rocks, suggest a common origin for water in both Earth and Moon. Lunar water could be inherited from carbonaceous chondrites, consistent with the model of late accretion of chondrite-type materials to the Moon as proposed by. One complication about the sources of lunar water, is that geologic processes (e.g., late accretion and magmatic degassing) may have modified the H isotope signatures of lunar materials. Recent FTIR analyses have shown that plagioclases in lunar ferroan anorthosite contain approximately 6 ppm H2O. So far, ferroan anorthosite is the only available lithology that is believed to be a primary product of the lunar magma ocean (LMO). A possible consequence is that the LMO could have contained up to approximately 320 ppm H2O. Here we examine the possible sources of water in the LMO through measurements of water abundances and H isotopes in plagioclase of two ferroan anorthosites and one troctolite from lunar highlands.

  14. Computational analysis reveals abundance of potential glycoproteins in Archaea, Bacteria and Eukarya.

    PubMed

    Zafar, Sadia; Nasir, Arshan; Bokhari, Habib

    2011-01-01

    Glycosylation is the most common type of post-translational modification (PTM) and is known to affect protein stability, folding and activity. Inactivity of enzymes mediating glycosylation can result in serious disorders including colon cancer and brain disorders. Out of five main types of glycosylation, N-linked glycosylation is most abundant and characterized by the addition of a sugar group to an Asparagine residue at the N-X-S/T motif. Enzyme mediating such transfer is known as oligosaccharyl transferase (OST). It has been hypothesized before that a significant number of proteins serve as glycoproteins. In this study, we used programming implementations of Python to statistically quantify the representation of glycoproteins by scanning all the available proteome sequence data at ExPASy server for the presence of glycoproteins and also the enzyme which plays critical role in glycosylation i.e. OST. Our results suggest that more than 50% of the proteins carry N-X-S/T motif i.e. they could be potential glycoproteins. Furthermore, approximately 28-36% (1/3) of proteins possesses signature motifs which are characteristic features of enzyme OST. Quantifying this bias individually reveals that both the number of proteins tagged with N-X-S/T motif and the average number of motifs per protein is significantly higher in case of eukaryotes when compared to prokaryotes. In the light of these results we conclude that there is a significant bias in the representation of glycoproteins in the proteomes of all species and is manifested substantially in eukaryotes and claim for glycosylation to be the most common and ubiquitous PTM in cells, especially in eukaryotes.

  15. A robust method for ammonium nitrogen isotopic analysis in freshwater and seawater at natural abundance levels

    NASA Astrophysics Data System (ADS)

    Zhang, L.; Altabet, M. A.; Wu, T.; Hadas, O.

    2006-12-01

    Natural ammonium N isotopic abundance has been increasingly used in studies of marine and freshwater biogeochemistry. However, current methods are time-consuming, subject to interference from DON, and not reliable at low concentrations. Our new method for determining the δ15N of ammonium overcomes these difficulties by employing the oxidation of ammonium to nitrite followed by conversion of nitrite to nitrous oxide. In the first step, ammonium is quantitatively oxidized by hypobromite at pH~12. After the addition of sodium arsenite to consume excess hypobromite, yield is verified by colorimetric NO2-measurement using sulfanilamide and naphthyl ethylenediamine (NED). Nitrite is further reduced to N2O by a 1:1 sodium azide and acetic acid buffer solution using previously established procedures. Buffer concentration can be varied according to sample matrix to ensure that a reaction pH between 2 and 4 is reached. The product nitrous oxide is then isotopically analyzed using a continuous flow purge and cryogenic trap system coupled to an isotope ratio mass spectrometer. Reliable δ15N values (±0.31‰) are obtained over a concentration range of 0.5 μM to 20 μM using 20 ml volumes of either fresh or seawater samples. Reagent blanks are very low, about 0.05 μM. There is no interference from any of the nitrogen containing compounds tested except short chain aliphatic amino acid (i.e. glycine) which typically are not present at sufficiently high environmental concentrations to pose a problem.

  16. Dimensional Analysis and General Relativity

    ERIC Educational Resources Information Center

    Lovatt, Ian

    2009-01-01

    Newton's law of gravitation is a central topic in the first-year physics curriculum. A lecturer can go beyond the physical details and use the history of gravitation to discuss the development of scientific ideas; unfortunately, the most recent chapter in this history, general relativity, is not covered in first-year courses. This paper discusses…

  17. Relative abundance of biotic communities of plankton and zoobenthos in three ox-bow lakes of Eastern India

    NASA Astrophysics Data System (ADS)

    Chakrabarty, Debajyoti; Biswas, Probir; Das, Sanjib Kumar

    2010-07-01

    We made comparative studies of three tropical ox-bow lakes in India with different trophic states. The species number of zooplanktons was negatively correlated with the degree of water eutrophication, and lakes of similar trophic status had higher similarity of species. The most significant differences of species composition were observed with rotifers and zoobenthos. The density and biomass of phytoplankton, rotifers, oligochaetes and chironomids tended to increase with increasing nutrients. We observed a significant difference of dominant species in different waters, especially the eutrophic lake, which was dominated by a few species of oligochaetes. The abundance of Tanypus bilobatus showed a highly significant correlation with the degree of eutrophication. Rotifers and zoobenthos showed considerably lower biodiversity in the eutrophic lake.

  18. Can heavy isotopes increase lifespan? Studies of relative abundance in various organisms reveal chemical perspectives on aging

    PubMed Central

    2016-01-01

    Stable heavy isotopes co‐exist with their lighter counterparts in all elements commonly found in biology. These heavy isotopes represent a low natural abundance in isotopic composition but impose great retardation effects in chemical reactions because of kinetic isotopic effects (KIEs). Previous isotope analyses have recorded pervasive enrichment or depletion of heavy isotopes in various organisms, strongly supporting the capability of biological systems to distinguish different isotopes. This capability has recently been found to lead to general decline of heavy isotopes in metabolites during yeast aging. Conversely, supplementing heavy isotopes in growth medium promotes longevity. Whether this observation prevails in other organisms is not known, but it potentially bears promise in promoting human longevity. PMID:27554342

  19. Phenology and abundance in relation to climatic variation in a sub-arctic insect herbivore-mountain birch system.

    PubMed

    Mjaaseth, Ragnhild R; Hagen, Snorre B; Yoccoz, Nigel G; Ims, Rolf A

    2005-08-01

    The two forest-defoliating geometrid moth species Operophtera brumata and Epirrita autumnata are known to exhibit different altitudinal distribution patterns in northern birch forests. One possible explanation for this is that altitudinal climatic variation differentially affects the performance of two species through mismatching larval and host plant phenology. We explored this hypothesis by investigating the relationship between larval phenology and leaf phenology of Betula pubescens, which is the main host plant of both moth species, along ten replicate altitudinal transects during two springs with contrasting climate in northern Norway. There was a distinct monotonous cline in host plant phenology with increasing altitude in both years of the study, but the development of the leaves were generally 14 days later in the first of the 2 years due to cold spring weather. We found that larval development of both species closely tracked host plant leaf phenology independent of altitude and year. However, at the time of sampling, E. autumnata was approximately one instar ahead of O. brumata at all altitudes, probably reflecting that E. autumnata has faster early instar growth than O. brumata. The abundance of O. brumata was lowest at the altitudinal forest-line, while E. autumnata was lowest near sea level. Our results do not indicate that the altitudinal distribution patterns of the two moth species is due to any phenological mismatch between larval and host plant phenology. We suggest rather that natural enemies at low altitudes limit larval survival and thus abundance of E. autumnata, while an early onset of winter at the forest limit reduces survival of late eclosing adults of O. brumata.

  20. 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.

  1. 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

  2. Relative Abundance of Carsonella ruddii (Gamma Proteobacterium) in Females and Males of Cacopsylla pyricola (Hemiptera: Psyllidae) and Bactericera cockerelli (Hemiptera: Triozidae).

    PubMed

    Cooper, W Rodney; Garczynski, Stephen F; Horton, David R

    2015-01-01

    Carsonella ruddii (Gamma Proteobacterium) is an obligate bacterial endosymbiont of psyllids that produces essential amino acids that are lacking in the insect's diet. Accurate estimations of Carsonella populations are important to studies of Carsonella-psyllid interactions and to developing ways to target Carsonella for control of psyllid pests including pear psylla, Cacopsylla pyricola (Förster) (Hemiptera: Psyllidae) and potato psyllid, Bactericera cockerelli (Šulc) (Hemiptera: Triozidae). We used two methods, namely fluorescence in situ hybridization and quantitative polymerase chain reaction (qPCR), to estimate relative abundance of Carsonella in bacteriocytes and whole bodies of psyllids, respectively. Using these two methods, we compared Carsonella populations between female and male insects. Estimations using fluorescence in situ hybridization indicated that Carsonella was more abundant in bacteriocytes of female C. pyricola than in those of males, but Carsonella abundance in bacteriocytes did not differ between sexes of B. cockerelli. Analyses by qPCR using whole-body specimens indicated Carsonella was more abundant in females than in males of both psyllids. Neither fluorescence in situ hybridization nor qPCR indicated that Carsonella populations differed in abundance among adults of different ages (0-3 wk after adult eclosion). Using fluorescence in situ hybridization, Carsonella was observed in ovarioles of newly emerged females and formed an aggregation in the posterior end of mature oocytes. Results of our study indicate that female psyllids harbor greater populations of Carsonella than do males and that sex should be controlled for in studies which require estimations of Carsonella populations.

  3. OXYGEN ABUNDANCES IN CEPHEIDS

    SciTech Connect

    Luck, R. E.; Andrievsky, S. M.; Korotin, S. N.; Kovtyukh, V. V. E-mail: serkor@skyline.od.ua E-mail: scan@deneb1.odessa.ua

    2013-07-01

    Oxygen abundances in later-type stars, and intermediate-mass stars in particular, are usually determined from the [O I] line at 630.0 nm, and to a lesser extent, from the O I triplet at 615.7 nm. The near-IR triplets at 777.4 nm and 844.6 nm are strong in these stars and generally do not suffer from severe blending with other species. However, these latter two triplets suffer from strong non-local thermodynamic equilibrium (NLTE) effects and thus see limited use in abundance analyses. In this paper, we derive oxygen abundances in a large sample of Cepheids using the near-IR triplets from an NLTE analysis, and compare those abundances to values derived from a local thermodynamic equilibrium (LTE) analysis of the [O I] 630.0 nm line and the O I 615.7 nm triplet as well as LTE abundances for the 777.4 nm triplet. All of these lines suffer from line strength problems making them sensitive to either measurement complications (weak lines) or to line saturation difficulties (strong lines). Upon this realization, the LTE results for the [O I] lines and the O I 615.7 nm triplet are in adequate agreement with the abundance from the NLTE analysis of the near-IR triplets.

  4. Relation between mRNA expression and sequence information in Desulfovibrio vulgaris: Combinatorial contributions of upstream regulatory motifs and coding sequence features to variations in mRNA abundance

    SciTech Connect

    Wu, Gang; Nie, Lei; Zhang, Weiwen

    2006-05-26

    ABSTRACT-The context-dependent expression of genes is the core for biological activities, and significant attention has been given to identification of various factors contributing to gene expression at genomic scale. However, so far this type of analysis has been focused whether on relation between mRNA expression and non-coding sequence features such as upstream regulatory motifs or on correlation between mRN abundance and non-random features in coding sequences (e.g. codon usage and amino acid usage). In this study multiple regression analyses of the mRNA abundance and all sequence information in Desulfovibrio vulgaris were performed, with the goal to investigate how much coding and non-coding sequence features contribute to the variations in mRNA expression, and in what manner they act together...

  5. Analysis of the factors that affect the distribution and abundance of three Neobuxbaumia species (Cactaceae) that differ in their degree of rarity

    NASA Astrophysics Data System (ADS)

    Ruedas, Marcela; Valverde, Teresa; Zavala-Hurtado, José Alejandro

    2006-03-01

    We studied three species of columnar cacti in the genus Neobuxbaumia which differ in their degree of rarity: Neobuxbaumia macrocephala (the rarest), Neobuxbaumia tetetzo (intermediate), and Neobuxbaumia mezcalaensis (the most common). To investigate the ecological factors that limit their distribution and abundance, we surveyed 80 localities within the region of Tehuacan-Cuicatlán, in Central Mexico. At each locality we measured several environmental variables, and the density of the Neobuxbaumia populations present. We used a principal component analysis (PCA) to identify the factors that are associated to the presence/absence of each species. Additionally, we carried out multiple regressions between environmental variables and population density to test whether the variation in these variables was related to changes in abundance. The results show that factors significantly affecting the distribution of these species are mean annual temperature, altitude, rainfall, and soil properties such as texture and organic matter content. N. mezcalaensis reaches maximum population densities of 14,740 plants per ha (average density = 3943 plants per ha) and is associated with localities with relatively abundant rainfall. N. tetetzo shows maximum population densities of 14,060 plants per ha (average = 3070 plants per ha), and is associated with sites located at high latitudes and with high phosphorous content in the soil. The rarest species, N. macrocephala, shows maximum densities of 1180 plants per ha (average = 607 plants per ha) and is associated with localities with high soil calcium content. The distribution of this species is limited to sites with specific values of the environmental variables recorded, conferring it a high habitat specificity which accounts for its rarity.

  6. Seasonal occurrence and relative abundance of aphids on potato plants with classical and transgenic characters of resistance to Colorado potato beetle Leptinotarsa decemlineata (Say).

    PubMed

    Ashouri, A

    2004-01-01

    The seasonal abundance and dynamics of potato-infesting aphids were studied in two seasons, on potato Solanum tuberosum L. with various types of transgenic and classical resistance to primary pests, especially the Colorado potato beetle (CPB), Leptinotarsa decemlineata (Say). The lines tested were the NewLeaf potato, a transgenic expressing the Bacillus thuringiensis CryIIIA toxin (BTT); NYL 235-4 a parental line derived from S. berthaultii (NYL) with a high density of glandular trichomes; and a transgenic line expressing oryzacystatln I (OCI), a proteinase inhibitor gene from rice; potatoes from two commercial cultivars, Superior and Kennebec, served as controls. Over the two seasons, Macrosiphum euphorbiae (Thomas) and, to a lesser extent, Myzus persicae (Sulzer) were by far the most abundant aphids observed in the experimental plots. M. persicae was observed relatively late in the season, and was most abundant on the Kennebec-OCI potato. Macrosiphum euphorbiae was more regular over seasons, and its highest densities were observed on the NYL 235-4 line. The population of M. euphorbiae showed markedly different patterns on the five lines studied, which was clearly related to potato plant phenology. Density of M. euphorbiae was observed on the NYL 235-4 line, in late July and early August.

  7. Bottom-up and middle-down proteomics have comparable accuracies in defining histone post-translational modification relative abundance and stoichiometry.

    PubMed

    Sidoli, Simone; Lin, Shu; Karch, Kelly R; Garcia, Benjamin A

    2015-03-17

    Histone proteins are key components of chromatin. Their N-terminal tails are enriched in combinatorial post-translational modifications (PTMs), which influence gene regulation, DNA repair, and chromosome condensation. Mass spectrometry (MS)-based middle-down proteomics has emerged as a technique to analyze co-occurring PTMs, as it allows for the characterization of intact histone tails (>50 aa) rather than short (<20 aa) peptides analyzed by bottom-up. However, a demonstration of its reliability is still lacking. We compared results obtained with the middle-down and the bottom-up strategy in calculating PTM relative abundance and stoichiometry. Since bottom-up was proven to have biases in peptide signal detection such as uneven ionization efficiency, we performed an external correction using a synthetic peptide library with known peptide relative abundance. Corrected bottom-up data were used as reference. Calculated abundances of single PTMs showed similar deviations from the reference when comparing middle-down and uncorrected bottom-up results. Moreover, we show that the two strategies provided similar performance in defining accurate PTM stoichiometry. Collectively, we evidenced that the middle-down strategy is at least equally reliable to bottom-up in quantifying histone PTMs.

  8. 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.

  9. 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

  10. 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

  11. Influence of relative abundance of isotopes on depth resolution for depth profiling of metal coatings by laser ablation inductively coupled plasma mass spectrometry.

    PubMed

    Fariñas, Juan C; Coedo, Aurora G; Dorado, Teresa

    2010-04-15

    A systematic study on the influence of relative abundance of isotopes of elements in the coating (A(c)) and in the substrate (A(s)) on both shape of time-resolved signals and depth resolution (Delta z) was performed for depth profile analysis of metal coatings on metal substrates by ultraviolet (266 nm) nanosecond laser ablation inductively coupled plasma quadrupole mass spectrometry. Five coated samples with coating thicknesses of the same order of magnitude (20-30 microm) were tested: nickel coating on aluminium, chromium and copper, and steel coated with copper and zinc. A laser repetition rate of 1 Hz and a laser fluence of 21 J cm(-2) were used. Five different depth profile types were established, which showed a clear dependence on A(c)/A(s) ratio. In general, depth profiles obtained for ratios above 1-10 could not be used to determine Delta z. We found that Delta z increased non-linearly with A(c)/A(s) ratio. The best depth profile types, leading to highest depth resolution and reproducibility, were attained in all cases by using the isotopes with low/medium A(c) values and with the highest A(s) values. In these conditions, an improvement of up to 4 times in Delta z values was achieved. The average ablation rates were in the range from 0.55 microm pulse(-1) for copper coating on steel to 0.83 microm pulse(-1) for zinc coating on steel, and the Delta z values were between 2.74 microm for nickel coating on chromium and 5.91 microm for nickel coating on copper, with RSD values about 5-8%.

  12. Species richness, relative abundance, and habitat associations of nocturnal birds along the rio grande in Southern texas

    USGS Publications Warehouse

    Skoruppa, M.K.; Woodin, M.C.; Blacklock, G.

    2009-01-01

    The segment of the Rio Grande between International Falcon Reservoir and Del Rio, Texas (distance ca. 350 km), remains largely unexplored ornithologically. We surveyed nocturnal birds monthly during February-June 1998 at 19 stations along the Rio Grande (n = 6) and at upland stock ponds (n = 13) in Webb County, Texas. We conducted 10-min point counts (n = 89) after sunset and before moonset. Four species of owls and five species of nightjars were detected. Nightjars, as a group, were nearly five limes more abundant (mean number/count = 2.63) than owls (mean number = 0.55). The most, common owl, the great horned owl (Bubo virginianus), had a mean number of 0.25/point count. The mean for elf owls (Micrathene whitneyi) was 0.16/point count. The most common nightjars were the common poorwill (Phalaenoptilus nuttallii; 1.21/point count) and lesser nighthawk (Chordeiles acutipennir, 1.16/point count). Survey sites on the river supported more species (mean = 2.2) than did upland stock ponds (mean = 1.4). However, only one species (common pauraque, Nyctidromus albicollis) showed a preference for the river sites. Our results establish this segment of the Rio Grande in southern Texas as an area of high diversity of nightjars in the United States, matched (in numbers of species) only by southeastern Arizona and southwestern New Mexico.

  13. Variability of invertebrate abundance in drinking water distribution systems in the Netherlands in relation to biostability and sediment volumes.

    PubMed

    van Lieverloo, J Hein M; Hoogenboezem, Wim; Veenendaal, Gerrit; van der Kooij, Dick

    2012-10-15

    A survey of invertebrates in drinking water from treatment works, internal taps and hydrants on mains was carried out by almost all water companies in the Netherlands from September 1993 to August 1995. Aquatic sow bugs (Asellidae, 1-12 mm) and oligochaeta worms (Oligochaeta, 1-100 mm), both known to have caused rare though embarrassing consumer complaints, were found to form 98% of the mean biomass in water flushed from mains. Their numbers in the mains water ranged up to 1500 (mean 37) Asellidae m(-3) and up to 9900 (mean 135) Oligochaeta m(-3). Smaller crustaceans (0.5-2 mm) dominated the numbers in water from mains. e.g. water fleas (Cladocera and Copepoda up to 14,000 m(-3)). Common invertebrates in treated water and in tap water were Rotifera (<1 mm) and nematode worms (Nematoda, <2 mm). No Asellidae, large Oligochaeta (>5 mm) or other large invertebrates were found in 1560 samples of 200 l treated water or tap water. Large variations in invertebrate abundance were found within and between distribution systems. Of the variability of mean biomass in mains per system, 55%, 60% and 63% could statistically be explained by differences in the Biofilm Formation Rate, non-particulate organic matter and the permanganate index of the treated water of the treatment works respectively. A similar correlation was found between mean invertebrate biomass and mean sediment volumes in the distribution systems (R(2) = 52%).

  14. Distribution and Abundance of Phlebotominae, Vectors of Leishmaniasis, in Argentina: Spatial and Temporal Analysis at Different Scales

    PubMed Central

    Quintana, María Gabriela; Fernández, María Soledad; Salomón, Oscar Daniel

    2012-01-01

    The spatial-temporal analysis of the abundance of insects, vectors of tegumentary leishmaniasis (TL) and visceral leishmaniasis (VL), was performed in Argentina using spatial-temporal increasing scales. In the microscale (microfocal), the effect of the primary vegetation-crop interface in vector abundance was observed, and also how the shelters, food sources, and other environmental characteristics contribute to habitat microheterogeneity and so to a microheterogeneous vector distribution. In the mesoscale (locality or epidemic focus), the results from different foci of TL (rural and periurban) and VL (urban) suggested a metapopulation structure determined partially by quantifiable habitat variables that could explain the increase of risk associated to an increase of vector-human contact due to climatic or anthropogenic changes. In the macroscale (regional), captures of vectors and records of human cases allowed the construction of risk maps and predictive models of vector distribution. In conclusion, in order to obtain valid results transferrable to control programs from spatial studies, special attention should be paid in order to assure the consistency between the spatial scales of the hypotheses, data, and analytical tools of each experimental or descriptive design. PMID:22315620

  15. The CALIFA survey: Oxygen abundances

    NASA Astrophysics Data System (ADS)

    Sánchez, S. F.; Aff001

    We present here the last results we obtained on the spatial resolved analysis of the ionized gas of disk-dominated galaxies based on CALIFA data. CALIFA is an ongoing IFS survey of galaxies in the Local Univese (0.005 < z < 0.03) that has already obtained spectroscopic information up to ~2.5r e with a spatial resolution better than ~1 kpc for a total number of an statiscal sample of galaxies of different morphological types, covering the CM-diagram up to Mr<-18 mag. With nearly 2000 spectra obtained for each galaxy, CALIFA offer one of the best IFU data to study the starformation histories and chemical enrichment of galaxies. In this article we focus on the main results based on the analysis of the oxygen abundances based on the study of ionized gas in H ii regions and individual spaxels, and their relations with the global properties of galaxies. In summary we have found that: (1) the -Z relation does not present a secondary relation with the star-formation rate, when the abundance is measured at the effective radius; (2) the oxygen abundance present a strong correlation with the stellar surface density (Σ-Z relation); (3) the oxygen abundance profiles present three well defined regimes, (a) an overall negative radial gradient, between 0.5-2 r e , with a characteristic slope of α O/H ~-0.1 dex/r e , (b) an universal flatenning beyond >2r e and (c) an inner drop at <0.5r e which presence depends on the mass. All these results indicates that disk-galaxies present an overall inside-out growth, although with clear deviations from this simple scenario.

  16. The Abundance and Pollen Foraging Behaviour of Bumble Bees in Relation to Population Size of Whortleberry (Vaccinium uliginosum)

    PubMed Central

    Mayer, Carolin; Michez, Denis; Chyzy, Alban; Brédat, Elise; Jacquemart, Anne-Laure

    2012-01-01

    Habitat fragmentation can have severe effects on plant pollinator interactions, for example changing the foraging behaviour of pollinators. To date, the impact of plant population size on pollen collection by pollinators has not yet been investigated. From 2008 to 2010, we monitored nine bumble bee species (Bombus campestris, Bombus hortorum s.l., Bombus hypnorum, Bombus lapidarius, Bombus pascuorum, Bombus pratorum, Bombus soroensis, Bombus terrestris s.l., Bombus vestalis s.l.) on Vaccinium uliginosum (Ericaceae) in up to nine populations in Belgium ranging in size from 80 m2 to over 3.1 ha. Bumble bee abundance declined with decreasing plant population size, and especially the proportion of individuals of large bumble bee species diminished in smaller populations. The most remarkable and novel observation was that bumble bees seemed to switch foraging behaviour according to population size: while they collected both pollen and nectar in large populations, they largely neglected pollen collection in small populations. This pattern was due to large bumble bee species, which seem thus to be more likely to suffer from pollen shortages in smaller habitat fragments. Comparing pollen loads of bumble bees we found that fidelity to V. uliginosum pollen did not depend on plant population size but rather on the extent shrub cover and/or openness of the site. Bumble bees collected pollen only from three plant species (V. uliginosum, Sorbus aucuparia and Cytisus scoparius). We also did not discover any pollination limitation of V. uliginosum in small populations. We conclude that habitat fragmentation might not immediately threaten the pollination of V. uliginosum, nevertheless, it provides important nectar and pollen resources for bumble bees and declining populations of this plant could have negative effects for its pollinators. The finding that large bumble bee species abandon pollen collection when plant populations become small is of interest when considering plant and

  17. The abundance and pollen foraging behaviour of bumble bees in relation to population size of whortleberry (Vaccinium uliginosum).

    PubMed

    Mayer, Carolin; Michez, Denis; Chyzy, Alban; Brédat, Elise; Jacquemart, Anne-Laure

    2012-01-01

    Habitat fragmentation can have severe effects on plant pollinator interactions, for example changing the foraging behaviour of pollinators. To date, the impact of plant population size on pollen collection by pollinators has not yet been investigated. From 2008 to 2010, we monitored nine bumble bee species (Bombus campestris, Bombus hortorum s.l., Bombus hypnorum, Bombus lapidarius, Bombus pascuorum, Bombus pratorum, Bombus soroensis, Bombus terrestris s.l., Bombus vestalis s.l.) on Vaccinium uliginosum (Ericaceae) in up to nine populations in Belgium ranging in size from 80 m(2) to over 3.1 ha. Bumble bee abundance declined with decreasing plant population size, and especially the proportion of individuals of large bumble bee species diminished in smaller populations. The most remarkable and novel observation was that bumble bees seemed to switch foraging behaviour according to population size: while they collected both pollen and nectar in large populations, they largely neglected pollen collection in small populations. This pattern was due to large bumble bee species, which seem thus to be more likely to suffer from pollen shortages in smaller habitat fragments. Comparing pollen loads of bumble bees we found that fidelity to V. uliginosum pollen did not depend on plant population size but rather on the extent shrub cover and/or openness of the site. Bumble bees collected pollen only from three plant species (V.uliginosum, Sorbus aucuparia and Cytisus scoparius). We also did not discover any pollination limitation of V. uliginosum in small populations. We conclude that habitat fragmentation might not immediately threaten the pollination of V. uliginosum, nevertheless, it provides important nectar and pollen resources for bumble bees and declining populations of this plant could have negative effects for its pollinators. The finding that large bumble bee species abandon pollen collection when plant populations become small is of interest when considering plant and

  18. Utilization of interferometric light microscopy for the rapid analysis of virus abundance in a river.

    PubMed

    Roose-Amsaleg, Céline; Fedala, Yasmina; Vénien-Bryan, Catherine; Garnier, Josette; Boccara, Albert-Claude; Boccara, Martine

    2017-03-02

    There is a constant need for direct counting of biotic nanoparticles such as viruses to unravel river functioning. We used, for the first time in freshwater, a new method based on interferometry differentiating viruses from other particles such as membrane vesicles. In the French Marne River, viruses represented between 42 and 72% of the particles. A spring monitoring in 2014 revealed their increase (2.1 × 10(7) to 2.1 × 10(8) mL(-1)) linked to an increase in algal biomass and diversity of bacterial plankton. Predicted virus size distributions were in agreement with transmission electron microscopy analysis suggesting a dominance of large viruses (≥60 nm).

  19. Variation in large-bodied fish-community structure and abundance in relation to water-management regime in a large regulated river.

    PubMed

    Haxton, T J; Findlay, C S

    2009-07-01

    Variation in life-history traits (growth, condition, mortality and recruitment) and relative abundance of 11 large-bodied fish species was investigated among three water-management regimes (unimpounded, run-of-the-river and winter reservoirs) in the large regulated Ottawa River, Canada. If waterpower management had an effect on fishes, then (1) would be expected community structuring among water-management regimes and (2) species with similar life-history traits should be affected in a similar manner. Large-bodied fish communities were assessed using two different standard index-netting techniques, one using trap nets and the other gillnets. Community structure could be discriminated based on species caught in nets using holographic neural networks (78.8% correct overall classification rate using trap nets and 76.0% using gillnets); therefore, water-management regimes affected community structure in the Ottawa River. Littoral zone benthivores were significantly lower in abundance (P < 0.001) or absent in winter reservoirs, whereas the abundance of planktivores or species that were planktivorous at young ages were significantly greater than in unimpounded river reaches. Growth, condition and mortality did not vary among reach types except smallmouth bass Micropterus dolomieu were in better condition in winter reservoirs than unimpounded reaches. Lake sturgeon Acipenser fulvescens recruitment was impaired in run-of-the-river reaches, whereas recruitment for other species that spawn in fast water was not affected.

  20. 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.

  1. 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.

  2. Source apportionment of atmospheric PAHs in the western Balkans by natural abundance radiocarbon analysis.

    PubMed

    Zencak, Zdenek; Klanova, Jana; Holoubek, Ivan; Gustafsson, Orjan

    2007-06-01

    Progress in source apportionment of priority combustion-derived atmospheric pollutants can be made by an inverse approach to inventory emissions, namely, receptor-based compound class-specific radiocarbon analysis (CCSRA) of target pollutants. In the present study, CCSRA of the combustion-derived polycyclic aromatic hydrocarbons (PAHs) present in the atmosphere of the countries of the former republic of Yugoslavia was performed. The carbon stable isotope composition (delta13C) of PAHs varied between -27.68 and -27.19 per thousand, whereas delta14C values ranged from -568 per thousand for PAHs sampled in Kosovo to -288 per thousand for PAHs sampled in the Sarajevo area. The application of an isotopic mass balance model to these delta14C data revealed a significant contribution (35-65%) from the combustion of non-fossil material to the atmospheric PAH pollution, even in urban and industrialized areas. Furthermore, consistency was observed between the isotopic composition of PAHs obtained by high-volume sampling and those collected by passive sampling. This encourages the use of passive samplers for CCSRA applications. This marks the first time that a CCSRA investigation could be executed on a geographically wide scale, providing a quantitative field-based source apportionment, which points out that also non-fossil combustion processes should be targeted for remedial action.

  3. Microbiome analysis reveals the abundance of bacterial pathogens in Rousettus leschenaultii guano

    PubMed Central

    Banskar, Sunil; Bhute, Shrikant S.; Suryavanshi, Mangesh V.; Punekar, Sachin; Shouche, Yogesh S.

    2016-01-01

    Bats are crucial for proper functioning of an ecosystem. They provide various important services to ecosystem and environment. While, bats are well-known carrier of pathogenic viruses, their possible role as a potential carrier of pathogenic bacteria is under-explored. Here, using culture-based approach, employing multiple bacteriological media, over thousand bacteria were cultivated and identified from Rousettus leschenaultii (a frugivorous bat species), the majority of which were from the family Enterobacteriaceae and putative pathogens. Next, pathogenic potential of most frequently cultivated component of microbiome i.e. Escherichia coli was assessed to identify its known pathotypes which revealed the presence of virulent factors in many cultivated E. coli isolates. Applying in-depth bacterial community analysis using high-throughput 16 S rRNA gene sequencing, a high inter-individual variation was observed among the studied guano samples. Interestingly, a higher diversity of bacterial communities was observed in decaying guano representative. The search against human pathogenic bacteria database at 97% identity, a small proportion of sequences were found associated to well-known human pathogens. The present study thus indicates that this bat species may carry potential bacterial pathogens and advice to study the effect of these pathogens on bats itself and the probable mode of transmission to humans and other animals. PMID:27845426

  4. Microbiome analysis reveals the abundance of bacterial pathogens in Rousettus leschenaultii guano.

    PubMed

    Banskar, Sunil; Bhute, Shrikant S; Suryavanshi, Mangesh V; Punekar, Sachin; Shouche, Yogesh S

    2016-11-15

    Bats are crucial for proper functioning of an ecosystem. They provide various important services to ecosystem and environment. While, bats are well-known carrier of pathogenic viruses, their possible role as a potential carrier of pathogenic bacteria is under-explored. Here, using culture-based approach, employing multiple bacteriological media, over thousand bacteria were cultivated and identified from Rousettus leschenaultii (a frugivorous bat species), the majority of which were from the family Enterobacteriaceae and putative pathogens. Next, pathogenic potential of most frequently cultivated component of microbiome i.e. Escherichia coli was assessed to identify its known pathotypes which revealed the presence of virulent factors in many cultivated E. coli isolates. Applying in-depth bacterial community analysis using high-throughput 16 S rRNA gene sequencing, a high inter-individual variation was observed among the studied guano samples. Interestingly, a higher diversity of bacterial communities was observed in decaying guano representative. The search against human pathogenic bacteria database at 97% identity, a small proportion of sequences were found associated to well-known human pathogens. The present study thus indicates that this bat species may carry potential bacterial pathogens and advice to study the effect of these pathogens on bats itself and the probable mode of transmission to humans and other animals.

  5. Source apportionment of atmospheric PAHs in the Western Balkans by natural abundance radiocarbon analysis

    SciTech Connect

    Zdenek Zencak; Jana Klanova; Ivan Holoubek; Oerjan Gustafsson

    2007-06-01

    Progress in source apportionment of priority combustion-derived atmospheric pollutants can be made by an inverse approach to inventory emissions, namely, receptor-based compound class-specific radiocarbon analysis (CCSRA) of target pollutants. In the present study, CCSRA of the combustion-derived polycyclic aromatic hydrocarbons (PAHs) present in the atmosphere of the countries of the former republic of Yugoslavia was performed. The carbon stable isotope composition ({delta}{sup 13}C) of PAHs varied between -27.68 and -27.19{per_thousand}, whereas {Delta}{sup 14}C values ranged from -568{per_thousand} for PAHs sampled in Kosovo to -288{per_thousand} for PAHs sampled in the Sarajevo area. The application of an isotopic mass balance model to these {Delta}{sup 14}C data revealed a significant contribution (35-65%) from the combustion of non-fossil material to the atmospheric PAH pollution, even in urban and industrialized areas. Furthermore, consistency was observed between the isotopic composition of PAHs obtained by high-volume sampling and those collected by passive sampling. This encourages the use of passive samplers for CCSRA applications. This marks the first time that a CCSRA investigation could be executed on a geographically wide scale, providing a quantitative field-based source apportionment, which points out that also non-fossil combustion processes should be targeted for remedial action. 36 refs., 1 fig., 3 tabs.

  6. Protective effects of leucine on redox status and mitochondrial-related gene abundance in the jejunum of intrauterine growth-retarded piglets during early weaning period.

    PubMed

    Huang, Qiang; Xu, Wen; Bai, Kai-Wen; He, Jin-Tian; Ahmad, Hussain; Zhou, Le; Zhang, Li-Li; Wang, Tian

    2017-04-01

    The aim of this study was to investigate the effects of dietary supplementation with 0.35% l-leucine on redox status and gene abundance relating to mitochondrial biogenesis and function in the jejunum of intrauterine growth-retarded (IUGR) piglets during early weaning period. According to a 2 × 2 factorial arrangement, 16 IUGR and 16 normal body weight (NBW) piglets were fed a basal diet without l-leucine supplementation or a basal diet plus 0.35% l-leucine supplementation from the age of 14 to 35 d. The results showed that compared with NBW piglets, IUGR piglets had a lower (p < 0.05) jejunal DNA concentration, a reduced (p < 0.05) manganese superoxide dismutase (MnSOD) and total antioxidant capability (T-AOC) activities and mitochondrial DNA content in the jejunum. Leucine supplementation increased (p < 0.05) MnSOD and T-AOC activities and decreased (p < 0.05) the malondialdehyde content in the jejunum of IUGR piglets. The mRNA gene abundance of nuclear respiratory factor-1 (NRF1), mitochondrial transcription factor A (TFAM), ATP synthase (ATPs), cytochrome c oxidase V (CcOX V), cytochrome c and glucokinase in the jejunum of IUGR piglets was reduced (p < 0.05) compared with NBW piglets. However, NRF1, peroxisome proliferation-activated receptor gamma coactivator-1 alpha, TFAM, ATPs and CcOX I mRNA gene abundance in the jejunum of IUGR piglets were increased (p < 0.05) by diets supplemented with leucine. These data indicate that leucine supplementation has therapeutic potential for attenuating intestinal oxidative stress and mitochondrial dysfunction in IUGR piglets during the early period of life via increasing enzyme activities and up-regulating mRNA gene abundance.

  7. 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

  8. Spatial, temporal, and habitat-related variation in abundance of pelagic fishes in the Gulf of Mexico: potential implications of the deepwater horizon oil spill.

    PubMed

    Rooker, Jay R; Kitchens, Larissa L; Dance, Michael A; Wells, R J David; Falterman, Brett; Cornic, Maëlle

    2013-01-01

    Time-series data collected over a four-year period were used to characterize patterns of abundance for pelagic fishes in the northern Gulf of Mexico (GoM) before (2007-2009) and after (2010) the Deepwater Horizon oil spill. Four numerically dominant pelagic species (blackfin tuna, blue marlin, dolphinfish, and sailfish) were included in our assessment, and larval density of each species was lower in 2010 than any of the three years prior to the oil spill, although larval abundance in 2010 was often statistically similar to other years surveyed. To assess potential overlap between suitable habitat of pelagic fish larvae and surface oil, generalized additive models (GAMs) were developed to evaluate the influence of ocean conditions on the abundance of larvae from 2007-2009. Explanatory variables from GAMs were then linked to environmental data from 2010 to predict the probability of occurrence for each species. The spatial extent of surface oil overlapped with early life habitat of each species, possibly indicating that the availability of high quality habitat was affected by the DH oil spill. Shifts in the distribution of spawning adults is another factor known to influence the abundance of larvae, and the spatial occurrence of a model pelagic predator (blue marlin) was characterized over the same four-year period using electronic tags. The spatial extent of oil coincided with areas used by adult blue marlin from 2007-2009, and the occurrence of blue marlin in areas impacted by the DH oil spill was lower in 2010 relative to pre-spill years.

  9. Abundance and Temperature Dependency of Protein-Protein Interaction Revealed by Interface Structure Analysis and Stability Evolution.

    PubMed

    He, Yi-Ming; Ma, Bin-Guang

    2016-05-25

    Protein complexes are major forms of protein-protein interactions and implement essential biological functions. The subunit interface in a protein complex is related to its thermostability. Though the roles of interface properties in thermal adaptation have been investigated for protein complexes, the relationship between the interface size and the expression level of the subunits remains unknown. In the present work, we studied this relationship and found a positive correlation in thermophiles rather than mesophiles. Moreover, we found that the protein interaction strength in complexes is not only temperature-dependent but also abundance-dependent. The underlying mechanism for the observed correlation was explored by simulating the evolution of protein interface stability, which highlights the avoidance of misinteraction. Our findings make more complete the picture of the mechanisms for protein complex thermal adaptation and provide new insights into the principles of protein-protein interactions.

  10. Abundance and Temperature Dependency of Protein-Protein Interaction Revealed by Interface Structure Analysis and Stability Evolution

    PubMed Central

    He, Yi-Ming; Ma, Bin-Guang

    2016-01-01

    Protein complexes are major forms of protein-protein interactions and implement essential biological functions. The subunit interface in a protein complex is related to its thermostability. Though the roles of interface properties in thermal adaptation have been investigated for protein complexes, the relationship between the interface size and the expression level of the subunits remains unknown. In the present work, we studied this relationship and found a positive correlation in thermophiles rather than mesophiles. Moreover, we found that the protein interaction strength in complexes is not only temperature-dependent but also abundance-dependent. The underlying mechanism for the observed correlation was explored by simulating the evolution of protein interface stability, which highlights the avoidance of misinteraction. Our findings make more complete the picture of the mechanisms for protein complex thermal adaptation and provide new insights into the principles of protein-protein interactions. PMID:27220911

  11. Relativity Concept Inventory: Development, Analysis, and Results

    ERIC Educational Resources Information Center

    Aslanides, J. S.; Savage, C. M.

    2013-01-01

    We report on a concept inventory for special relativity: the development process, data analysis methods, and results from an introductory relativity class. The Relativity Concept Inventory tests understanding of relativistic concepts. An unusual feature is confidence testing for each question. This can provide additional information; for example,…

  12. Changes in the concentration and relative abundance of alkanes and PAHs from the Deepwater Horizon oiling of coastal marshes.

    PubMed

    Turner, R E; Overton, E B; Meyer, B M; Miles, M S; Hooper-Bui, L

    2014-09-15

    We determined changes of 28 alkanes and 43 different PAHs in 418 wetland soil samples collected on ten sampling trips to three Louisiana estuaries before and after they were oiled from the 2010 Deepwater Horizon disaster. There was a significant decline in 22 of the 28 alkane analytes (0.42% day(-1)), no change in 6, over 2.5 years. The concentration of five aromatic petroleum hydrocarbons (PAHs) increased (range 0.25-0.70% day(-1)), whereas the total PAH pool did not change. Of these five, naphthalene and C-1-naphthalenes are suggested to be of higher toxicity than the other three because of their relatively higher volatility or solubility. The relative proportions of alkane analytes, but not PAHs, does not yet resemble that in the pre-oiled marshes after 3 years, The trajectories of nine indicators for degradation/weathering were either inconclusive or misleading (alkanes) or confirmed the relatively meager degradation of PAHs.

  13. Systematic analysis of intron size and abundance parameters in diverse lineages.

    PubMed

    Wu, Jiayan; Xiao, Jingfa; Wang, Lingping; Zhong, Jun; Yin, Hongyan; Wu, Shuangxiu; Zhang, Zhang; Yu, Jun

    2013-10-01

    All eukaryotic genomes have genes with introns in variable sizes. As far as spliceosomal introns are concerned, there are at least three basic parameters to stratify introns across diverse eukaryotic taxa: size, number, and sequence context. The number parameter is highly variable in lower eukaryotes, especially among protozoan and fungal species, which ranges from less than 4% to 78% of the genes. Over greater evolutionary time scales, the number parameter undoubtedly increases as observed in higher plants and higher vertebrates, reaching greater than 12.5 exons per gene in average among mammalian genomes. The size parameter is more complex, where multiple modes appear at work. Aside from intronless genes, there are three other types of intron-containing genes: half-sized, minimal, and size-expandable introns. The half-sized introns have only been found in a limited number of genomes among protozoan and fungal lineages and the other two types are prevalent in all animal and plant genomes. Among the size-expandable introns, the sizes of plant introns are expansion-limited in that the large introns exceeding 1000 bp are fewer in numbers and transposon-free as compared to the large introns among animals, where the larger introns are filled with transposable elements and appear expansion-flexible, reaching several kilobasepairs (kbp) and even thousands of kbp in size. Most of the intron parameters can be studied as signatures of the specific splicing machineries of different eukaryotic lineages and are highly relevant to the regulation of gene expression and functionality. In particular, the transcription-splicing-export coupling of eukaryotic intron dispensing leads to a working hypothesis that all intron parameters are evolved to be efficient and function-related in processing and routing the spliced transcripts.

  14. [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.

  15. Sodium abundances of AGB and RGB stars in Galactic globular clusters. I. Analysis and results of NGC 2808

    NASA Astrophysics Data System (ADS)

    Wang, Y.; Primas, F.; Charbonnel, C.; Van der Swaelmen, M.; Bono, G.; Chantereau, W.; Zhao, G.

    2016-07-01

    Context. Galactic globular clusters (GC) are known to have multiple stellar populations and be characterised by similar chemical features, e.g. O-Na anti-correlation. While second-population stars, identified by their Na overabundance, have been found from the main sequence turn-off up to the tip of the red giant branch (RGB) in various Galactic GCs, asymptotic giant branch (AGB) stars have rarely been targeted. The recent finding that NGC 6752 lacks an Na-rich AGB star has thus triggered new studies on AGB stars in GCs, since this result questions our basic understanding of GC formation and stellar evolution theory. Aims: We aim to compare the Na abundance distributions of AGB and RGB stars in Galactic GCs and investigate whether the presence of Na-rich stars on the AGB is metallicity-dependent. Methods: With high-resolution spectra obtained with the multi-object high-resolution spectrograph FLAMES on ESO/VLT, we derived accurate Na abundances for 31 AGB and 40 RGB stars in the Galactic GC NGC 2808. Results: We find that NGC 2808 has a mean metallicity of -1.11 ± 0.08 dex, in good agreement with earlier analyses. Comparable Na abundance dispersions are derived for our AGB and RGB samples, with the AGB stars being slightly more concentrated than the RGB stars. The ratios of Na-poor first-population to Na-rich second-population stars are 45:55 in the AGB sample and 48:52 in the RGB sample. Conclusions: NGC 2808 has Na-rich second-population AGB stars, which turn out to be even more numerous - in relative terms - than their Na-poor AGB counterparts and the Na-rich stars on the RGB. Our findings are well reproduced by the fast rotating massive stars scenario and they do not contradict the recent results that there is not an Na-rich AGB star in NGC 6752. NGC 2808 thus joins the larger group of Galactic GCs for which Na-rich second-population stars on the AGB have recently been found. Based on observations made with ESO telescopes at the La Silla Paranal Observatory

  16. Identification of Biodegradation Pathways in a Multi-Process Phytoremediation System (MPPS) Using Natural Abundance 14C Analysis of PLFA

    NASA Astrophysics Data System (ADS)

    Cowie, B. R.; Greenberg, B. M.; Slater, G. F.

    2008-12-01

    Optimizing remediation of petroleum-contaminated soils requires thorough understanding of the mechanisms and pathways involved in a proposed remediation system. In many engineered and natural attenuation systems, multiple degradation pathways may contribute to observed contaminant mass losses. In this study, biodegradation in the soil microbial community was identified as a major pathway for petroleum hydrocarbon removal in a Multi-Process Phytoremediation System (MPPS) using natural abundance 14C analysis of Phospholipid Fatty Acids (PLFA). In contaminated soils, PLFA were depleted in Δ14C to less than -800‰, directly demonstrating microbial uptake and utilization of petroleum derived carbon (Δ14C = -992‰) during bioremediation. Mass balance indicated that more than 80% of microbial carbon was derived from petroleum hydrocarbons and a maximum of 20% was produced from metabolism of modern carbon sources. In contrast, in a nearby uncontaminated control soil, the microbial community maintained a nearly modern 14C signature, suggesting preferential degradation of more labile, recent carbon. Mass balance using δ13C and Δ14C of soil CO2 demonstrated that mineralization of petroleum carbon contributed 60-65% of soil CO2 at the contaminated site. The remainder was derived from atmospheric (27-30%) and decomposition of non- petroleum natural organic carbon (5-10%). The clean control exhibited substantially lower CO2 concentrations that were derived from atmospheric (55%) and natural organic carbon (45%) sources. This study highlights the value of using multiple carbon isotopes to identify degradation pathways in petroleum- contaminated soils undergoing phytoremediation and the power of natural abundance 14C to detect petroleum metabolism in natural microbial communities.

  17. Detection and Characterization of Low Abundance Glycopeptides Via Higher-Energy C-Trap Dissociation and Orbitrap Mass Analysis

    NASA Astrophysics Data System (ADS)

    Hart-Smith, Gene; Raftery, Mark J.

    2012-01-01

    Broad-scale mass spectrometric analyses of glycopeptides are constrained by the considerable complexity inherent to glycoproteomics, and techniques are still being actively developed to address the associated analytical difficulties. Here we apply Orbitrap mass analysis and higher-energy C-trap dissociation (HCD) to facilitate detailed insights into the compositions and heterogeneity of complex mixtures of low abundance glycopeptides. By generating diagnostic oxonium product ions at mass measurement errors of <5 ppm, highly selective glycopeptide precursor ion detections are made at sub-fmol limits of detection: analyses of proteolytic digests of a hen egg glycoprotein mixture detect 88 previously uncharacterized glycopeptides from 666 precursor ions selected for MS/MS, with only one false positive due to co-fragmentation of a non-glycosylated peptide with a glycopeptide. We also demonstrate that by (1) identifying multiple series of glycoforms using high mass accuracy single stage MS spectra, and (2) performing product ion scans at optimized HCD collision energies, the identification of peptide + N-acetylhexosamine (HexNAc) ions (Y1 ions) can be readily achieved at <5 ppm mass measurement errors. These data allow base peptide sequences and glycan compositional information to be attained with high confidence, even for glycopeptides that produce weak precursor ion signals and/or low quality MS/MS spectra. The glycopeptides characterized from low fmol abundances using these methods allow two previously unreported glycosylation sites on the Gallus gallus protein ovoglycoprotein (amino acids 82 and 90) to be confirmed; considerable glycan heterogeneities at amino acid 90 of ovoglycoprotein, and amino acids 34 and 77 of Gallus gallus ovomucoid are also revealed.

  18. Oxygen abundance maps of CALIFA galaxies

    NASA Astrophysics Data System (ADS)

    Zinchenko, I. A.; Pilyugin, L. S.; Grebel, E. K.; Sánchez, S. F.; Vílchez, J. M.

    2016-11-01

    We construct maps of the oxygen abundance distribution across the discs of 88 galaxies using Calar Alto Legacy Integral Field Area survey (CALIFA) Data Release 2 (DR2) spectra. The position of the centre of a galaxy (coordinates on the plate) was also taken from the CALIFA DR2. The galaxy inclination, the position angle of the major axis, and the optical radius were determined from the analysis of the surface brightnesses in the Sloan Digital Sky Survey (SDSS) g and r bands of the photometric maps of SDSS Data Release 9. We explore the global azimuthal abundance asymmetry in the discs of the CALIFA galaxies and the presence of a break in the radial oxygen abundance distribution. We found that there is no significant global azimuthal asymmetry for our sample of galaxies, i.e. the asymmetry is small, usually lower than 0.05 dex. The scatter in oxygen abundances around the abundance gradient has a comparable value, ≲0.05 dex. A significant (possibly dominant) fraction of the asymmetry can be attributed to the uncertainties in the geometrical parameters of these galaxies. There is evidence for a flattening of the radial abundance gradient in the central part of 18 galaxies. We also estimated the geometric parameters (coordinates of the centre, the galaxy inclination and the position angle of the major axis) of our galaxies from the analysis of the abundance map. The photometry-map-based and the abundance-map-based geometrical parameters are relatively close to each other for the majority of the galaxies but the discrepancy is large for a few galaxies with a flat radial abundance gradient.

  19. Distribution and abundance of human-specific Bacteroides and relation to traditional indicators in an urban tropical catchment

    PubMed Central

    Nshimyimana, J P; Ekklesia, E; Shanahan, P; Chua, L H C; Thompson, J R

    2014-01-01

    Aims The study goals were to determine the relationship between faecal indicator bacteria (FIB), the HF183 marker and land use, and the phylogenetic diversity of HF183 marker sequences in a tropical urban watershed. Methods and Results Total coliforms, Escherichia coli, and HF183 were quantified in 81 samples categorized as undeveloped, residential and horticultural from the Kranji Reservoir and Catchment in Singapore. Quantitative-PCR for HF183 followed by analysis of variance indicated that horticultural areas had significantly higher geometric means for marker levels (4·3 × 104 HF183-GE 100 ml−1) than nonhorticultural areas (3·07 × 103 HF183-GE 100 ml−1). E. coli and HF183 were moderately correlated in horticultural areas (R = 0·59, P = 0·0077), but not elsewhere in the catchment. Initial upstream surveys of candidate sources revealed elevated HF183 in a wastewater treatment effluent but not in aquaculture ponds. The HF183 marker was cloned, sequenced and determined by phylogenetic analysis to match the original marker description. Conclusion We show that quantification of the HF183 marker is a useful tool for mapping the spatial distribution and potential sources of human sewage contamination in tropical environments such as Singapore. Significance and Impact A major challenge for assessment of water quality in tropical environments is the natural occurrence and nonconservative behaviour of FIB. The HF183 marker has been employed in temperate environments as an alternative indicator for human sewage contamination. Our study supports the use of the HF183 marker as an indicator for human sewage in Singapore and motivates further work to determine HF183 marker levels that correspond to public health risk in tropical environments. PMID:24460587

  20. Genome analysis of Excretory/Secretory proteins in Taenia solium reveals their Abundance of Antigenic Regions (AAR).

    PubMed

    Gomez, Sandra; Adalid-Peralta, Laura; Palafox-Fonseca, Hector; Cantu-Robles, Vito Adrian; Soberón, Xavier; Sciutto, Edda; Fragoso, Gladis; Bobes, Raúl J; Laclette, Juan P; Yauner, Luis del Pozo; Ochoa-Leyva, Adrián

    2015-05-19

    Excretory/Secretory (ES) proteins play an important role in the host-parasite interactions. Experimental identification of ES proteins is time-consuming and expensive. Alternative bioinformatics approaches are cost-effective and can be used to prioritize the experimental analysis of therapeutic targets for parasitic diseases. Here we predicted and functionally annotated the ES proteins in T. solium genome using an integration of bioinformatics tools. Additionally, we developed a novel measurement to evaluate the potential antigenicity of T. solium secretome using sequence length and number of antigenic regions of ES proteins. This measurement was formalized as the Abundance of Antigenic Regions (AAR) value. AAR value for secretome showed a similar value to that obtained for a set of experimentally determined antigenic proteins and was different to the calculated value for the non-ES proteins of T. solium genome. Furthermore, we calculated the AAR values for known helminth secretomes and they were similar to that obtained for T. solium. The results reveal the utility of AAR value as a novel genomic measurement to evaluate the potential antigenicity of secretomes. This comprehensive analysis of T. solium secretome provides functional information for future experimental studies, including the identification of novel ES proteins of therapeutic, diagnosis and immunological interest.

  1. Correction of precursor and product ion relative abundances in order to standardize CID spectra and improve Ecom50 accuracy for non-targeted metabolomics

    PubMed Central

    Dubey, Ritvik; Hill, Dennis W.; Lai, Steven; Ming-Hui, Chen; Grant, David F.

    2014-01-01

    Quantitative biases in the abundance of precursor and product ions due to mass discrimination in RF-only ion guides results in inaccurate collision induced dissociation (CID) spectra. We evaluated the effects of collision cell RF voltage and collision energy on CID spectra using ten singly protonated compounds (46–854 Da) in an orthogonal acceleration time-of-flight mass spectrometer. The relative ion transfer efficiency, i.e. the relative amount of ions transferred through the ion guide at any particular RF voltage was shown to be dependent on the ion’s m/z. We developed an algorithm to correct for the mass discriminating effects of RF voltage on CID spectra. The algorithm was tested for both precursor and product ions at multiple RF voltages and collision energies in order to ensure reliability. Our results suggest that compounds that generate major product ions with m/z values <150 have peak intensities that deviate substantially from their actual abundance. This has implications for small molecule metabolomics research, particularly for studies that rely on CID spectra matching methods for structure identification. PMID:25960696

  2. Sulfuric acid vapor and other cloud-related gases in the Venus atmosphere - Abundances inferred from observed radio opacity

    NASA Technical Reports Server (NTRS)

    Steffes, P. G.; Eshleman, V. R.

    1982-01-01

    It is suggested that the absorbing characteristics of sulfuric acid vapor appear to reconcile what had been thought to be an inconsistency among measurements and deductions regarding the constituents of the Venus atmosphere and radio occultation, radar reflection, and radio emission measurements of its opacity. Laboratory measurements of sulfuric acid, sulfur dioxide, water vapor, and carbon dioxide are used to model relative contributions to opacity as a function of height in a way that is consistent with observations of the constituents and absorbing properties of the atmosphere. It is concluded that sulfuric acid vapor is likely to be the principal microwave absorber in the 30-50 km altitude range of the middle atmosphere of Venus.

  3. Water table related variations in the abundance of intact archaeal membrane lipids in a Swedish peat bog.

    PubMed

    Weijers, Johan W H; Schouten, Stefan; van der Linden, Marjolein; van Geel, Bas; Damsté, Jaap S Sinninghe

    2004-10-01

    The presence and distribution of isoprenoid glycerol dialkyl glycerol tetraethers (GDGTs), lipids that constitute the membranes of Archaea, have been investigated in a 50-cm long core from a Swedish peat bog. In the acrotelm, the periodically water saturated and thus oxic upper layer of the peat bog, only minor amounts of GDGTs were found. These amounts increase considerably in the catotelm, the continuously water saturated and consequently anoxic lower layer of the peat bog. Based on earlier analyses of GDGTs in different settings and on 16S rDNA results from literature, these lipids are likely derived from methanogenic Archaea. Crenarchaeol, previously only found in marine settings and in fresh water lakes, has also been found in this peat bog. Contrary to the other GDGTs, crenarchaeol concentrations remain relatively constant throughout the peat core, suggesting that they are produced by Crenarchaeota thriving in the oxic part of the peat bog and possibly also in the anoxic part.

  4. A Bayesian hierarchical model of Antarctic fur seal foraging and pup growth related to sea ice and prey abundance.

    PubMed

    Hiruki-Raring, Lisa M; Ver Hoef, Jay M; Boveng, Peter L; Bengtson, John L

    2012-03-01

    We created a Bayesian hierarchical model (BHM) to investigate ecosystem relationships between the physical ecosystem (sea ice extent), a prey measure (krill density), predator behaviors (diving and foraging effort of female Antarctic fur seals, Arctocephalus gazella, with pups) and predator characteristics (mass of maternal fur seals and pups). We collected data on Antarctic fur seals from 1987/1988 to 1994/1995 at Seal Island, Antarctica. The BHM allowed us to link together predators and prey into a model that uses all the data efficiently and accounts for major sources of uncertainty. Based on the literature, we made hypotheses about the relationships in the model, which we compared with the model outcome after fitting the BHM. For each BHM parameter, we calculated the mean of the posterior density and the 95% credible interval. Our model confirmed others' findings that increased sea ice was related to increased krill density. Higher krill density led to reduced dive intensity of maternal fur seals, as measured by dive depth and duration, and to less time spent foraging by maternal fur seals. Heavier maternal fur seals and lower maternal foraging effort resulted in heavier pups at 22 d. No relationship was found between krill density and maternal mass, or between maternal mass and foraging effort on pup growth rates between 22 and 85 days of age. Maternal mass may have reflected environmental conditions prior to the pup provisioning season, rather than summer prey densities. Maternal mass and foraging effort were not related to pup growth rates between 22 and 85 d, possibly indicating that food was not limiting, food sources other than krill were being used, or differences occurred before pups reached age 22 d.

  5. 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

  6. Relating Needs Assessment and Needs Analysis.

    ERIC Educational Resources Information Center

    Kaufman, Roger; Valentine, Glenn

    1989-01-01

    Discusses the necessity of relating needs assessment and needs analysis in performance management. Topics discussed include measurable objectives; the identification and selection of needs; performance improvement; the Organizational Elements Model (OEM), which helps to identify means and ends; and training requirements analysis. (eight…

  7. Relative messenger RNA abundance in bovine oocytes collected in vitro or in vivo before and 20 hr after the preovulatory luteinizing hormone surge.

    PubMed

    Lonergan, Patrick; Gutiérrez-Adán, Alfonso; Rizos, Dimitrios; Pintado, Belen; de la Fuente, Julio; Boland, Maurice P

    2003-11-01

    In the cyclic cow, final maturation of the ovulatory follicle is initiated by the preovulatory luteinizing hormone (LH) surge. During the subsequent 24 hr period, the oocyte nucleus undergoes meiotic progression to metaphase II and several changes in cytoplasmic organization take place. We have previously shown that oocytes recovered at the time of the LH peak and matured in vitro are less competent to reach the blastocyst stage than their counterparts recovered 20 hr later following in vivo maturation, despite both groups undergoing IVF and culture in parallel. The objective of this study was to compare, using real-time quantitative RT-PCR, the relative abundance of various developmentally important gene transcripts in these oocytes. The groups used were mature bovine oocytes originating from: (1) 2-6 mm follicles from slaughterhouse ovaries; (2) preovulatory follicles punctured by ovum pick-up just before the LH surge (i.e., immature) and matured in vitro; or (3) preovulatory follicles punctured 20 hr later, just prior to ovulation (i.e., in vivo matured). In addition, immature oocytes from 2-6 mm follicles were examined. We examined the relative mRNA expression of five enzymes involved in protection against free oxygen radicals (mitochondrial Mn-superoxide dismutase, MnSOD, cytosolic Cu/Zn superoxide dismutase, Cu/ZnSOD, gamma-glutamyl-cysteine transferase, GCS, glutathione peroxidase, GPX, sarcosine oxidase, SOX), a transcript involved in follicular development (growth differentiation factor-9, GDF-9), transcripts involved in glucose metabolism (glucose-6-phosphate dehydrogenase, G6PDH, glucose transporter type-1 and -8, Glut-1, Glut-8) and genes involved in cell cycle events, Cyclin A and B, and poly(A) polymerase (PAP). Transcripts for all genes were detected, irrespective of oocyte origin. While differences were not significant in all cases, variations in levels of transcript abundance between the groups were related to developmental competence. In

  8. Meta-analysis of quantification methods shows that archaea and bacteria have similar abundances in the subseafloor.

    PubMed

    Lloyd, Karen G; May, Megan K; Kevorkian, Richard T; Steen, Andrew D

    2013-12-01

    There is no universally accepted method to quantify bacteria and archaea in seawater and marine sediments, and different methods have produced conflicting results with the same samples. To identify best practices, we compiled data from 65 studies, plus our own measurements, in which bacteria and archaea were quantified with fluorescent in situ hybridization (FISH), catalyzed reporter deposition FISH (CARD-FISH), polyribonucleotide FISH, or quantitative PCR (qPCR). To estimate efficiency, we defined "yield" to be the sum of bacteria and archaea counted by these techniques divided by the total number of cells. In seawater, the yield was high (median, 71%) and was similar for FISH, CARD-FISH, and polyribonucleotide FISH. In sediments, only measurements by CARD-FISH in which archaeal cells were permeabilized with proteinase K showed high yields (median, 84%). Therefore, the majority of cells in both environments appear to be alive, since they contain intact ribosomes. In sediments, the sum of bacterial and archaeal 16S rRNA gene qPCR counts was not closely related to cell counts, even after accounting for variations in copy numbers per genome. However, qPCR measurements were precise relative to other qPCR measurements made on the same samples. qPCR is therefore a reliable relative quantification method. Inconsistent results for the relative abundance of bacteria versus archaea in deep subsurface sediments were resolved by the removal of CARD-FISH measurements in which lysozyme was used to permeabilize archaeal cells and qPCR measurements which used ARCH516 as an archaeal primer or TaqMan probe. Data from best-practice methods showed that archaea and bacteria decreased as the depth in seawater and marine sediments increased, although archaea decreased more slowly.

  9. Proposed Method for Estimating Health-Promoting Glucosinolates and Hydrolysis Products in Broccoli (Brassica oleracea var. italica) Using Relative Transcript Abundance.

    PubMed

    Becker, Talon M; Jeffery, Elizabeth H; Juvik, John A

    2017-01-18

    Due to the importance of glucosinolates and their hydrolysis products in human nutrition and plant defense, optimizing the content of these compounds is a frequent breeding objective for Brassica crops. Toward this goal, we investigated the feasibility of using models built from relative transcript abundance data for the prediction of glucosinolate and hydrolysis product concentrations in broccoli. We report that predictive models explaining at least 50% of the variation for a number of glucosinolates and their hydrolysis products can be built for prediction within the same season, but prediction accuracy decreased when using models built from one season's data for prediction of an opposing season. This method of phytochemical profile prediction could potentially allow for lower phytochemical phenotyping costs and larger breeding populations. This, in turn, could improve selection efficiency for phase II induction potential, a type of chemopreventive bioactivity, by allowing for the quick and relatively cheap content estimation of phytochemicals known to influence the trait.

  10. Relativity concept inventory: Development, analysis, and results

    NASA Astrophysics Data System (ADS)

    Aslanides, J. S.; Savage, C. M.

    2013-06-01

    We report on a concept inventory for special relativity: the development process, data analysis methods, and results from an introductory relativity class. The Relativity Concept Inventory tests understanding of relativistic concepts. An unusual feature is confidence testing for each question. This can provide additional information; for example, high confidence correlated with incorrect answers suggests a misconception. A novel aspect of our data analysis is the use of Monte Carlo simulations to determine the significance of correlations. This approach is particularly useful for small sample sizes, such as ours. Our results show a gender bias that was not present in course assessment, similar to that reported for the Force Concept Inventory.

  11. Abundance and activity of soil microorganisms in Cedrus atlantica forests are more related to land use than to altitude or latitude

    NASA Astrophysics Data System (ADS)

    Ramírez Rojas, Irene; Perez Fernandez, María; Moreno Gallardo, Laura; Lechuga Ordoñez, Victor; Linares, Juan Carlos

    2016-04-01

    Several environmental traits might change the abundance and the function of soil microorganisms in forest soils by plant-mediated reactions. Few studies have related the landscape-scale forest structural diversity with the micro-scale distribution of microorganism and their activities. High mountain environments harbor ecosystems that are very sensitive to global change and hence highly vulnerable, as those of Atlantic cedar. Altitudinal gradients in mountains are orrelated with changes in vegetation. We propose that altitudinal gradients drive shifts in microbial communities and are correlated with land uses. Thus, the latitudinal and longitudinal pattern of abundance and activity of soil micro-organisms was studied in an intercontinental comparison. We investigate soil extractable organic carbon (EOC) and nitrogen and carbon, microbial biomass and microbial metabolic activities at eight different sites along the latitudinal range of Cedrus atlantica, covering different altitudes and soils characteristics both in Southern Spain and Northern Morocco. Analyses of the abundances of total bacteria, (16S rRNA gene), was conducted using the Ilumina metagenomics technique. Results show that the stands at the highest altitudes had distinct microbial and biochemical characteristics compared with other areas. Overall, microbial activity, as measured by soil respiration, is higher in forests subjected to lower human pressure than in stands highly degraded, probably reflecting the quality of litter input that results of the influence of local assemblage of different tree, shrub and annual species, though changes in the soil N and C contents. Indeed, total soil C and N contents explained the microbial properties at every scale. Our results suggest that in contrast to the observed pronounced altitudinal changes, the kind of human-mediate land management has a stronger role in defining changes in microbial composition and activities in the investigated forest systems.

  12. Relative abundance and distribution of fishes within an established Area of Critical Environmental Concern, of the Amargosa River Canyon and Willow Creek, Inyo and San Bernardino Counties, California

    USGS Publications Warehouse

    Scoppettone, G. Gary; Hereford, Mark E.; Rissler, Peter H.; Johnson, Danielle M.; Salgado, Antonio

    2011-01-01

    The Amargosa River Canyon of San Bernardino and Inyo County, California, has been designated by the Bureau of Land Management as an Area of Critical Environmental Concern, due in part to its unique flora and fauna. As a task of the Area of Critical Environmental Concern implementation plan, a survey of native fishes was conducted from June 21 to August 12, 2010. Geographic Information System tools were used to map sampling locations, which were spaced at 50-meter intervals. Global Positioning Systems were used to locate sampling stations, and stations with adequate water for successful trapping were sampled with baited minnow traps. Amargosa River pupfish (Cyprinodon nevadensis amargosae) and speckled dace (Rhinichthys osculus spp.) were widespread throughout Armargosa River Canyon. Throughout the study area 8,558 pupfish were captured at 194 stations; 3,472 speckled dace were captured at 210 stations; 238 red-swamp crayfish (Procambarus clarkia) were captured at 83 stations; and 1,095 western mosquitofish (Gambusia affinus) were captured at 110 stations. Pupfish were most abundant in open water habitat with native riparian vegetation, and they were significantly less abundant where the stream was completely covered by cattails or where saltcedar (Tamarix sp.) dominated the riparian corridor. There was no relationship between stream cover and speckled dace distribution. Non-native western mosquitofish and red-swamp crayfish densities were significantly higher in stream reaches dominated by saltcedar. The continued spread of saltcedar threatens to negatively affect pupfish and potentially reduce speckled dace abundance throughout the Amargosa River Canyon. This study can serve as baseline information for observing native fish populations in the future, as related to potential changes to the Amargosa River Canyon ecosystem.

  13. 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.

  14. The relative abundance and seasonal distribution correspond with the sources of polycyclic aromatic hydrocarbons (PAHs) in the surface sediments of Chenab River, Pakistan.

    PubMed

    Hussain, Imran; Syed, Jabir Hussain; Kamal, Atif; Iqbal, Mehreen; Eqani, Syed-Ali-Mustjab-Akbar-Shah; Bong, Chui Wei; Taqi, Malik Mumtaz; Reichenauer, Thomas G; Zhang, Gan; Malik, Riffat Naseem

    2016-06-01

    Chenab River is one of the most important rivers of Punjab Province (Pakistan) that receives huge input of industrial effluents and municipal sewage from major cities in the Central Punjab, Pakistan. The current study was designed to evaluate the concentration levels and associated ecological risks of USEPA priority polycyclic aromatic hydrocarbons (PAHs) in the surface sediments of Chenab River. Sampling was performed from eight (n = 24) sampling stations of Chenab River and its tributaries. We observed a relatively high abundance of ∑16PAHs during the summer season (i.e. 554 ng g(-1)) versus that in the winter season (i.e. 361 ng g(-1)), with an overall abundance of two-, five- and six-ring PAH congeners. Results also revealed that the nitrate and phosphate contents in the sediments were closely associated with low molecular weight (LMW) and high molecular weight (HMW) PAHs, respectively. Source apportionment results showed that the combustion of fossil fuels appears to be the key source of PAHs in the study area. The risk quotient (RQ) values indicated that seven PAH congeners (i.e. phenanthrene, anthracene, fluoranthene, pyrene, benzo(a)pyrene, chrysene and benzo(a)anthracene) could pose serious threats to the aquatic life of the riverine ecosystem in Pakistan.

  15. Abundance of birds in Fukushima as judged from Chernobyl.

    PubMed

    Møller, Anders Pape; Hagiwara, Atsushi; Matsui, Shin; Kasahara, Satoe; Kawatsu, Kencho; Nishiumi, Isao; Suzuki, Hiroyuki; Ueda, Keisuke; Mousseau, Timothy A

    2012-05-01

    The effects of radiation on abundance of common birds in Fukushima can be assessed from the effects of radiation in Chernobyl. Abundance of birds was negatively related to radiation, with a significant difference between Fukushima and Chernobyl. Analysis of 14 species common to the two areas revealed a negative effect of radiation on abundance, differing between areas and species. The relationship between abundance and radiation was more strongly negative in Fukushima than in Chernobyl for the same 14 species, demonstrating a negative consequence of radiation for birds immediately after the accident on 11 March 2011 during the main breeding season in March-July, when individuals work close to their maximum sustainable level.

  16. Abundances of Volatile - Bearing Species from Evolved Gas Analysis of Samples from the Rocknest Aeolian Bedform in Gale Crater

    NASA Technical Reports Server (NTRS)

    Archer, P. D., Jr.; Franc, H. B.; Sutter, B.; McAdam, A.; Ming, D. W.; Morris, R. V.; Mahaffy, P. R.

    2013-01-01

    The Sample Analysis at Mars (SAM) instrument suite on board the Mars Science Laboratory (MSL) recently ran four samples from an aeolian bedform named Rocknest. SAM detected the evolution of H2O, CO2, O2, and SO2, indicative of the presence of multiple volatile bearing species (Fig 1). The Rocknest bedform is a windblown deposit selected as representative of both the windblown material in Gale crater as well as the globally-distributed martian dust. Four samples of Rocknest material were analyzed by SAM, all from the fifth scoop taken at this location. The material delivered to SAM passed through a 150 m sieve and is assumed to have been well mixed during the sample acquisition/preparation/handoff process. SAM heated the Rocknest samples to approx.835 C at a ramp rate of 35 C/min with a He carrier gas flow rate of apprx.1.5 standard cubic centimeters per minute and at an oven pressure of 30 mbar [1]. Evolved gases were detected by a quadrupole mass spectrometer (QMS). This abstract presents the molar abundances of H2O, CO2, O2, and SO2 as well as their concentration in rocknest samples using an estimated sample mass.

  17. Glycan Degradation (GlyDeR) Analysis Predicts Mammalian Gut Microbiota Abundance and Host Diet-Specific Adaptations

    PubMed Central

    Zarecki, Raphy; Oberhardt, Matthew; Ursell, Luke K.; Kupiec, Martin; Knight, Rob; Gophna, Uri; Ruppin, Eytan

    2014-01-01

    ABSTRACT Glycans form the primary nutritional source for microbes in the human gut, and understanding their metabolism is a critical yet understudied aspect of microbiome research. Here, we present a novel computational pipeline for modeling glycan degradation (GlyDeR) which predicts the glycan degradation potency of 10,000 reference glycans based on either genomic or metagenomic data. We first validated GlyDeR by comparing degradation profiles for genomes in the Human Microbiome Project against KEGG reaction annotations. Next, we applied GlyDeR to the analysis of human and mammalian gut microbial communities, which revealed that the glycan degradation potential of a community is strongly linked to host diet and can be used to predict diet with higher accuracy than sequence data alone. Finally, we show that a microbe’s glycan degradation potential is significantly correlated (R = 0.46) with its abundance, with even higher correlations for potential pathogens such as the class Clostridia (R = 0.76). GlyDeR therefore represents an important tool for advancing our understanding of bacterial metabolism in the gut and for the future development of more effective prebiotics for microbial community manipulation. PMID:25118239

  18. Depth-related distribution and abundance of seastars (Echinodermata: Asteroidea) in the Porcupine Seabight and Porcupine Abyssal Plain, N.E. Atlantic

    NASA Astrophysics Data System (ADS)

    Howell, Kerry L.; Billett, David S. M.; Tyler, Paul A.

    2002-10-01

    The depth-related distribution of seastar (Echinodermata: Asteroidea) species between 150 and 4950 m in the Porcupine Seabight and Porcupine Abyssal Plain is described. 47 species of asteroid were identified from ˜14,000 individuals collected. The bathymetric range of each species is recorded. What are considered quantitative data, from an acoustically monitored epibenthic sledge and supplementary data from otter trawls, are used to display the relative abundance of individuals within their bathymetric range. Asteroid species are found to have very narrow centres of distribution in which they are abundant, despite much wider total adult depth ranges. Centres of distribution may be skewed. This might result from competition for resources or be related to the occurrence of favourable habitats at particular depths. The bathymetric distributions of the juveniles of some species extend outside the adult depth ranges. There is a distinct pattern of zonation with two major regions of faunal change and six distinct zones. An upper slope zone ranges from 150 to ˜700 m depth, an upper bathyal zone between 700 and 1100 m, a mid-bathyal zone from 1100 to1700 m and a lower bathyal zone between 1700 and 2500 m. Below 2500 m the lower continental slope and continental rise have a characteristic asteroid fauna. The abyssal zone starts at about 2800 m. Regions of major faunal change are identified at the boundaries of both upper and mid-bathyal zones and at the transition of bathyal to abyssal fauna. Diversity is greatest at ˜1800 m, decreasing with depth to ˜2600 m before increasing again to high levels at ˜4700 m.

  19. [Variability in the relative abundance, size structure and sex ratio of the dolphinfish Coryphaena hippurus (Pisces: Coryphaenidae) in the Gulf of Tehuantepec, México].

    PubMed

    Alejo-Plata, Carmen; Gómez, José Luis; Serrano-Guzmán, Saúl J

    2014-06-01

    Variability in the relative abundance, size structure and sex ratio of the dolphinfish Coryphaena hippurus (Pisces: Coryphaenidae) in the Gulf of Tehuantepec, México. The dolphinfish (Coryphaena hippurus), is an oceanic epipelagic fish found worldwide in tropical and subtropical waters, with a high dispersal capability via large-scale migrations. This fast-swimming top-level predator is abundant in the Gulf of Tehuantepec, where it is caught incidentally by artisanal fisheries, and represents a target species for both recreational and commercial fisheries in Mexico, Ecuador, Peru and Central America. Nowadays, local fishery information on this species is scarce, thus our objective was to analyze the size structure by sex and the catch-per-unit-effort (CPUE) tendency of dolphinfish caught in the Gulf of Tehuantepec, from 2000 to 2007. For this, fishery catches information was obtained from the artisanal fleet, at six landing sites in the Gulf, and the sex ratio, fork length (FL) and the catch per unit effort (CPUE) were estimated. From all sampling sites, a total of 3 494 females, and 3 877 males were obtained, and dolphinfish size as fork length (FL) ranged from 20.5 to 152cm. Fish size ranged from 25.5 to 148cm furcal length (FL) in males, and 20.5 to 129cm FL in females. The sex ratio (males:females) was 1:1, except in April-May (1:1.5, p < 0.05) and November (1:0.5, p < 0.05). The sex ratio at different size classes showed a significant bias towards females at smaller sizes (< 75cm FL), whereas the males were predominant in larger size classes (> 100cm FL). The size structure was bimodal, with a variation in the size average; the modes were defined as the small group (FL = 50-55cm) and the large size group (FL = 100-110cm). The CPUE showed seasonal changes: values were high for the November-December period, and values were lower for July-August. The seasonal and inter annual variation in the abundance of dolphinfish is probably related to a pre

  20. Method optimization for proteomic analysis of soybean leaf: Improvements in identification of new and low-abundance proteins

    PubMed Central

    Mesquita, Rosilene Oliveira; de Almeida Soares, Eduardo; de Barros, Everaldo Gonçalves; Loureiro, Marcelo Ehlers

    2012-01-01

    The most critical step in any proteomic study is protein extraction and sample preparation. Better solubilization increases the separation and resolution of gels, allowing identification of a higher number of proteins and more accurate quantitation of differences in gene expression. Despite the existence of published results for the optimization of proteomic analyses of soybean seeds, no comparable data are available for proteomic studies of soybean leaf tissue. In this work we have tested the effects of modification of a TCA-acetone method on the resolution of 2-DE gels of leaves and roots of soybean. Better focusing was obtained when both mercaptoethanol and dithiothreitol were used in the extraction buffer simultaneously. Increasing the number of washes of TCA precipitated protein with acetone, using a final wash with 80% ethanol and using sonication to ressuspend the pellet increased the number of detected proteins as well the resolution of the 2-DE gels. Using this approach we have constructed a soybean protein map. The major group of identified proteins corresponded to genes of unknown function. The second and third most abundant groups of proteins were composed of photosynthesis and metabolism related genes. The resulting protocol improved protein solubility and gel resolution allowing the identification of 122 soybean leaf proteins, 72 of which were not detected in other published soybean leaf 2-DE gel datasets, including a transcription factor and several signaling proteins. PMID:22802721

  1. Analysis of Aircraft Fuels and Related Materials

    DTIC Science & Technology

    1982-09-01

    9) Hypodermic syringes and needles (10) Laboratory detergent preparation for glassware 533...AFWAL-TR-82-2082 ANALYSIS OF AIRCR ’ELS AND RELATED MATERIALS F. Neil Hodgson, Edward A. Steinmetz. John D. Tobias, Billy B. Bowles, and Charlotte D...80 Discussion 80 7. Analysis of Rman Spectroscopy Data for Goodness-Of-Fit to Four Statistical Distributions 86 S. Analyses to Determine Cause of

  2. Influence of observers and stream flow on northern two-lined salamander (Eurycea bislineata bislineata) relative abundance estimates in Acadia and Shenandoah National Parks, USA

    USGS Publications Warehouse

    Crocker, J.B.; Bank, M.S.; Loftin, C.S.; Jung Brown, R.E.

    2007-01-01

    We investigated effects of observers and stream flow on Northern Two-Lined Salamander (Eurycea bislineata bislineata) counts in streams in Acadia (ANP) and Shenandoah National Parks (SNP). We counted salamanders in 22 ANP streams during high flow (May to June 2002) and during low flow (July 2002). We also counted salamanders in SNP in nine streams during high flow (summer 2003) and 11 streams during low flow (summers 2001?02, 2004). In 2002, we used a modified cover-controlled active search method with a first and second observer. In succession, observers turned over 100 rocks along five 1-m belt transects across the streambed. The difference between observers in total salamander counts was not significant. We counted fewer E. b. bislineata during high flow conditions, confirming that detection of this species is reduced during high flow periods and that assessment of stream salamander relative abundance is likely more reliable during low or base flow conditions.

  3. Relative abundance, site fidelity, and survival of adult lake trout in Lake Michigan from 1999 to 2001: Implications for future restoration strategies

    USGS Publications Warehouse

    Bronte, C.R.; Holey, M.E.; Madenjian, C.P.; Jonas, J.L.; Claramunt, R.M.; McKee, P.C.; Toneys, M.L.; Ebener, M.P.; Breidert, B.; Fleischer, G.W.; Hess, R.; Martell, A.W.; Olsen, E.J.

    2007-01-01

    We compared the relative abundance of lake trout Salvelinus namaycush spawners in gill nets during fall 1999–2001 in Lake Michigan at 19 stocked spawning sites with that at 25 unstocked sites to evaluate how effective site-specific stocking was in recolonizing historically important spawning reefs. The abundance of adult fish was higher at stocked onshore and offshore sites than at unstocked sites. This suggests that site-specific stocking is more effective at establishing spawning aggregations than relying on the ability of hatchery-reared lake trout to find spawning reefs, especially those offshore. Spawner densities were generally too low and too young at most sites to expect significant natural reproduction. However, densities were sufficiently high at some sites for reproduction to occur and therefore the lack of recruitment was attributable to other factors. Less than 3% of all spawners could have been wild fish, which indicates that little natural reproduction occurred in past years. Wounding by sea lamprey Petromyzon marinus was generally lower for Seneca Lake strain fish and highest for strains from Lake Superior. Fish captured at offshore sites in southern Lake Michigan had the lowest probability of wounding, while fish at onshore sites in northern Lake Michigan had the highest probability. The relative survival of the Seneca Lake strain was higher than that of the Lewis Lake or the Marquette strains for the older year-classes examined. Survival differences among strains were less evident for younger year-classes. Recaptures of coded-wire-tagged fish of five strains indicated that most fish returned to their stocking site or to a nearby site and that dispersal from stocking sites during spawning was about 100 km. Restoration strategies should rely on site-specific stocking of lake trout strains with good survival at selected historically important offshore spawning sites to increase egg deposition and the probability of natural reproduction in Lake

  4. A Comparative Assessment of Track Plates to Quantify Fine Scale Variations in the Relative Abundance of Norway Rats in Urban Slums.

    PubMed

    Hacker, Kathryn P; Minter, Amanda; Begon, Mike; Diggle, Peter J; Serrano, Soledad; Reis, Mitermayer G; Childs, James E; Ko, Albert I; Costa, Federico

    2016-06-01

    Norway rats (Rattus norvegicus) living in urban environments are a critical public health and economic problem, particularly in urban slums where residents are at a higher risk for rat borne diseases, yet convenient methods to quantitatively assess population sizes are lacking. We evaluated track plates as a method to determine rat distribution and relative abundance in a complex urban slum environment by correlating the presence and intensity of rat-specific marks on track plates with findings from rat infestation surveys and trapping of rats to population exhaustion. To integrate the zero-inflated track plate data we developed a two-component mixture model with one binary and one censored continuous component. Track plate mark-intensity was highly correlated with signs of rodent infestation (all coefficients between 0.61 and 0.79 and all p-values < 0.05). Moreover, the mean level of pre-trapping rat-mark intensity on plates was significantly associated with the number of rats captured subsequently (Odds ratio1.38; 95% CI 1.19-1.61) and declined significantly following trapping (Odds ratio 0.86; 95% CI 0.78-0.95). Track plates provided robust proxy measurements of rat abundance and distribution and detected rat presence even when populations appeared 'trapped out'. Tracking plates are relatively easy and inexpensive methods that can be used to intensively sample settings such as urban slums, where traditional trapping or mark-recapture studies are impossible to implement, and therefore the results can inform and assess the impact of targeted urban rodent control campaigns.

  5. Spatial variation in abundance, size and orientation of juvenile corals related to the biomass of parrotfishes on the Great Barrier Reef, Australia.

    PubMed

    Trapon, Melanie L; Pratchett, Morgan S; Hoey, Andrew S

    2013-01-01

    For species with complex life histories such as scleractinian corals, processes occurring early in life can greatly influence the number of individuals entering the adult population. A plethora of studies have examined settlement patterns of coral larvae, mostly on artificial substrata, and the composition of adult corals across multiple spatial and temporal scales. However, relatively few studies have examined the spatial distribution of small (≤50 mm diameter) sexually immature corals on natural reef substrata. We, therefore, quantified the variation in the abundance, composition and size of juvenile corals (≤50 mm diameter) among 27 sites, nine reefs, and three latitudes spanning over 1000 km on Australia's Great Barrier Reef. Overall, 2801 juveniles were recorded with a mean density of 6.9 (±0.3 SE) ind.m(-2), with Acropora, Pocillopora, and Porites accounting for 84.1% of all juvenile corals surveyed. Size-class structure, orientation on the substrate and taxonomic composition of juvenile corals varied significantly among latitudinal sectors. The abundance of juvenile corals varied both within (6-13 ind.m(-2)) and among reefs (2.8-11.1 ind.m(-2)) but was fairly similar among latitudes (6.1-8.2 ind.m(-2)), despite marked latitudinal variation in larval supply and settlement rates previously found at this scale. Furthermore, the density of juvenile corals was negatively correlated with the biomass of scraping and excavating parrotfishes across all sites, revealing a potentially important role of parrotfishes in determining distribution patterns of juvenile corals on the Great Barrier Reef. While numerous studies have advocated the importance of parrotfishes for clearing space on the substrate to facilitate coral settlement, our results suggest that at high biomass they may have a detrimental effect on juvenile coral assemblages. There is, however, a clear need to directly quantify rates of mortality and growth of juvenile corals to understand the relative

  6. Dietary sunflower oil modulates milk fatty acid composition without major changes in adipose and mammary tissue fatty acid profile or related gene mRNA abundance in sheep.

    PubMed

    Castro-Carrera, T; Frutos, P; Leroux, C; Chilliard, Y; Hervás, G; Belenguer, A; Bernard, L; Toral, P G

    2015-04-01

    There are very few studies in ruminants characterizing mammary and adipose tissue (AT) expression of genes and gene networks for diets causing variations in milk fatty acid (FA) composition without altering milk fat secretion, and even less complementing this information with data on tissue FA profiles. This work was conducted in sheep in order to investigate the response of the mammary gland and the subcutaneous and perirenal AT, in terms of FA profile and mRNA abundance of genes involved in lipid metabolism, to a diet known to modify milk FA composition. Ten lactating Assaf ewes were randomly assigned to two treatments consisting of a total mixed ration based on alfalfa hay and a concentrate (60 : 40) supplemented with 0 (control diet) or 25 (SO diet) g of sunflower oil/kg of diet dry matter for 7 weeks. Milk composition, including FA profile, was analysed after 48 days on treatments. On day 49, the animals were euthanized and tissue samples were collected to analyse FA and mRNA abundance of 16 candidate genes. Feeding SO did not affect animal performance but modified milk FA composition. Major changes included decreases in the concentration of FA derived from de novo synthesis (e.g. 12:0, 14:0 and 16:0) and increases in that of long-chain FA (e.g. 18:0, c9-18:1, trans-18:1 isomers and c9,t11-CLA); however, they were not accompanied by significant variations in the mRNA abundance of the studied lipogenic genes (i.e. ACACA, FASN, LPL, CD36, FABP3, SCD1 and SCD5) and transcription factors (SREBF1 and PPARG), or in the constituent FA of mammary tissue. Regarding the FA composition of AT, the little influence of SO did not appear to be linked to changes in gene mRNA abundance (decreases of GPAM and SREBF1 in both tissues, and of PPARG in the subcutaneous depot). Similarly, the great variation between AT (higher contents of saturated FA and trans-18:1 isomers in the perirenal, and of cis-18:1, c9,t11-CLA and n-3 PUFA in the subcutaneous AT) could not be related to

  7. Effects of sequential feeding of β-adrenergic agonists on cull cow performance, carcass characteristics, and mRNA relative abundance.

    PubMed

    Weber, M J; Dikeman, M E; Unruh, J A; Jaeger, J R; Murray, L; Houser, T A; Johnson, B J

    2012-05-01

    The objectives of this study were to determine the effects of supplementation with a single β-adrenergic agonist (β-AA) or a sequence of β-AA on cow performance, carcass characteristics, and mRNA relative abundance of cull cows implanted and fed a concentrate diet. Sixty cull cows were implanted with Revalor-200 (200 mg of trenbolone acetate and 20 mg of estradiol) and assigned to 1 of 4 treatments (n = 15/treatment): CON = fed a concentrate diet only; RH = supplemented with ractopamine-HCl for the last 25 d before slaughter; ZH = supplemented with zilpaterol-HCl for 20 d before a 3-d withdrawal before slaughter; RH + ZH = supplemented with RH for 25 d, followed by ZH for 20 d before a 3-d withdrawal before slaughter. Ractopamine-HCl was supplemented at a dose of 200 mg·animal(-1)·d(-1), and ZH was supplemented at 8.33 mg/kg (100% DM basis) of feed. All cows were fed a concentrate diet for 74 d. Each treatment had 5 cows per pen and 3 replicate pens. Body weights were collected on d 1, 24, 51, and 72. Muscle biopsies from the LM were collected on d 24, 51, and at slaughter from a subsample of 3 cows per pen. Carcass traits were evaluated postslaughter. The 2 ZH treatments averaged 15.3 kg more BW gain, 0.20 kg greater ADG, and 7.8 cm(2) larger LM area than CON and RH treatments, and 21 kg more HCW than CON, but these differences were not significant (P > 0.10), likely due to a sample size of n = 15/treatment. The sequence of RH followed by ZH tended to optimize the combination of HCW, LM area, percent intramuscular fat, and lean color and maturity compared with the ZH treatment. Abundance of β(2)-adrenergic receptor (AR) mRNA was not altered in the RH + ZH treatment during RH supplementation from d 24 to 51 of feeding. However, the abundance of β(2)-AR mRNA increased (P < 0.05) the last 23 d of feeding for the RH treatment and tended (P = 0.10) to increase in ZH cows during ZH supplementation. For all cows, abundance of type IIa myosin heavy chain (MHC

  8. Abundance estimation and conservation biology

    USGS Publications Warehouse

    Nichols, J.D.; MacKenzie, D.I.

    2004-01-01

    should be focused on relationships between demographic processes such as survival and recruitment, the two quantities responsible for changes in abundance, rather than simply on the magnitudes of these quantities. They describe a type of Jolly–Seber capture–recapture model that permits inference about the underlying relationship between per capita recruitment rates and survival rates (Link & Barker, this volume). Implementation used Bayesian Markov Chain Monte Carlo methods and appeared to work well, yielding inferences about the relationship between recruitment and survival that were robust to selection of prior distribution. We believe that readers will find their arguments compelling, and we expect to see increased use of hierarchical modeling approaches in capture–recapture and related fields. Otto (presentation without paper) also recommended use of hierarchical models in analysis of multiple data sources dealing with population dynamics of North American mallards. He integrated survival inferences from ringing data, abundance information from aerial survey data, and recruitment information based on age ratios from a harvest survey. He used a Leslie matrix population projection model as an integrating framework and obtained estimates of breeding population size using all data.Otto’s approach also permitted inference about biases in estimated quantities. As with the work of Link & Barker (2004), we find Otto’s recommendation to use hierarchical models to integrate data from multiple sources to be very compelling. Alisauskas et al. (2004) report results of an analysis of capture–recapture data for a askatchewan population of white–winged scoters. They used the approach of Pradel (1996) to estimate population growth rate (See the PDF) directly. Estimates for 1975–1985 were quite low, but estimates for the recent period, 2000–2003,increased to values > 1. Parameter estimates for seniority, survival and per capita recruitment (Pradel, 1996) led to the

  9. Pain related inflammation analysis using infrared images

    NASA Astrophysics Data System (ADS)

    Bhowmik, Mrinal Kanti; Bardhan, Shawli; Das, Kakali; Bhattacharjee, Debotosh; Nath, Satyabrata

    2016-05-01

    Medical Infrared Thermography (MIT) offers a potential non-invasive, non-contact and radiation free imaging modality for assessment of abnormal inflammation having pain in the human body. The assessment of inflammation mainly depends on the emission of heat from the skin surface. Arthritis is a disease of joint damage that generates inflammation in one or more anatomical joints of the body. Osteoarthritis (OA) is the most frequent appearing form of arthritis, and rheumatoid arthritis (RA) is the most threatening form of them. In this study, the inflammatory analysis has been performed on the infrared images of patients suffering from RA and OA. For the analysis, a dataset of 30 bilateral knee thermograms has been captured from the patient of RA and OA by following a thermogram acquisition standard. The thermograms are pre-processed, and areas of interest are extracted for further processing. The investigation of the spread of inflammation is performed along with the statistical analysis of the pre-processed thermograms. The objectives of the study include: i) Generation of a novel thermogram acquisition standard for inflammatory pain disease ii) Analysis of the spread of the inflammation related to RA and OA using K-means clustering. iii) First and second order statistical analysis of pre-processed thermograms. The conclusion reflects that, in most of the cases, RA oriented inflammation affects bilateral knees whereas inflammation related to OA present in the unilateral knee. Also due to the spread of inflammation in OA, contralateral asymmetries are detected through the statistical analysis.

  10. [Diversity, relative abundance and activity patterns of medium and large mammals in a tropical deciduous forest in the Isthmus of Tehuantepec, Oaxaca, Mexico].

    PubMed

    Cortés-Marcial, Malinalli; Briones-Salas, Miguel

    2014-12-01

    The use of camera traps and mammal track search are complementary methods to monitoring species of which is not well documented their natural history, as in the case of medium and large mammals. To ensure its conservation and good management, it is necessary to generate information about the structure of the community and their populations. The objective of the present study was to estimate the diversity, relative abundance and activity patterns of medium and large mammals in a tropical deciduous forest located in the Isthmus of Tehuantepec, Oaxaca, Mexico. Samplings were conducted in three month intervals, from September 2011 to May 2013. We used photographic-sampling and track search, two complementary sampling methods. For photographic-sampling, 12 camera traps were placed covering an area of 60 km2, while for the tracks search a monthly tour of four line-transect surveys of three kilometers length each was undertaken. We obtained a total of 344 pictures with 5292 trap-days total sampling effort; in addition, 187 track records in a total of 144 km. With both methods we registered 21 species of mammals, in 13 families and seven orders, and five species resulted in new records to the area. The diversity index of Shannon-Wiener obtained with the method of tracks was H' = 2.41, while the most abundant species were Urocyon cinereoargen- teus (IAR = 0.23) and Pecari tajacu (IAR = 0.20). By the method of trap the most abundant species were P. tajacu (IAR = 2.62) and Nasua narica (IAR = 1.28). In terms of patterns of activity P. tajacu, N. narica and Odocoileus virginianus were primarily diurnal species; Canis latrans and Leopardus pardalis did not show preference for any schedule in particular, and Didelphis virginiana and Dasypus novemcinctus preferred to have nocturnal activity. This information can be of help to the creation of programs of management and conservation of mam- mals of medium and large in the Isthmus of Tehuantepec, Oaxaca, México.

  11. Capella: Structure and Abundances

    NASA Technical Reports Server (NTRS)

    Brickhouse, Nancy S.

    1999-01-01

    This grant covers the analysis of ASCA spectra of the cool star binary system Capella. This project has also required the analysis of simultaneous EUVE data. The ASCA spectrum of Capella could not be fit with standard models; by imposing models based on strong lines observed with EUVE, a problem wavelength region was identified. Correcting the problem required calculations of atomic collision strengths of higher principal quantum number than had ever been calculated, resulting in a paper in process by Liedahl and Brickhouse. With these new models applied to the ASCA spectrum, better fits were obtained. While solar abundance ratios are generally consistent with the ASCA data, the ratio of Ne/Fe is three to four times lower than solar photospheric values. Whether there is a general First Ionization Potential (FIP) effect or a specific neon anomaly cannot be determined from these data. Detailed discussion has been provided to NASA in the most recent annual report (1997). Two poster presentations have been made regarding modeling requirements. A substantial paper is in the final revision form, following review by six co-authors. The results of this work have wide implications, since the newly calculated emission lines almost certainly contribute to other problems in fitting not only other stellar spectra, but also composite supernova remnants, galaxies, and cooling flow clusters of galaxies. Furthermore, Liedahl and Brickhouse have identified other species for which lines of a similar nature (high principal quantum number) will contribute significant flux. For moderate resolution X-ray spectra, lines left out of the models in relatively isolated bands, will be attributed to continuum flux by spectral fitting engines, causing errors in line-to-continuum ratios. Thus addressing the general theoretical problem is of crucial importance.

  12. Age-related changes in transcriptional abundance and circulating levels of anti-Mullerian hormone and Sertoli cell count in crossbred and Zebu bovine males.

    PubMed

    Rajak, S K; Kumaresan, A; Attupuram, N M; Chhillar, S; Baithalu, R K; Nayak, S; Sreela, L; Singh, Raushan K; Tripathi, U K; Mohanty, T K; Yadav, Savita

    2017-02-01

    Age-related changes in peripheral anti-Mullerian hormone (AMH) concentrations and transcriptional abundance of AMH gene in testicular tissue were studied in crossbred (Holstein Friesian × Tharparkar) and Zebu (Tharparkar) males. In both the breeds, basal AMH concentrations were estimated using ELISA method in blood plasma obtained from six males each at 1, 6, 12, 18, and 24 months age. After blood collection at respective ages, all the males were castrated and expression and immunolocalization of AMH was performed in the testicular tissue. The concentration of AMH in blood plasma was found to be highest at 1 month of age in both crossbred and Zebu males, which subsequently decreased with advancing age. Significantly (P < 0.05) lower concentration of AMH was observed in crossbred as compared with Zebu males at 24 months of age. In line with peripheral AMH concentrations, the expression of AMH gene was also higher (P < 0.05) at 1 month of age, which thereafter declined significantly with advancement of age in crossbred males. Furthermore, the expression of AMH gene differed significantly between Zebu and crossbred males at all the age groups studied. Immunolocalization of AMH in testicular tissue also revealed a stronger expression at 1 month age, which gradually decreased till 24 months of age. The true Sertoli cell count was significantly higher in Zebu compared with crossbred males at all age groups studied except at 6 months age. The relationship between Sertoli cell count and circulating AMH concentrations was negative and significant (r = -0.81; P = 0.004). In conclusion, expression of AMH gene in testicular tissue and peripheral blood concentrations of AMH were higher in young compared with adults in both crossbred and Zebu males; however, the transcriptional abundance and circulating levels of AMH were higher in Zebu compared with crossbred males.

  13. Phenology and abundance of bean leaf beetle (Coleoptera: Chrysomelidae) in eastern South Dakota on alfalfa and soybean relative to tillage, fertilization, and yield.

    PubMed

    Hammack, Leslie; Pikul, Joseph L; West, Mark S

    2010-06-01

    Phenology and abundance of bean leaf beetles, Cerotoma trifurcata (Förster), were examined throughout two eastern South Dakota growing seasons in relation to grain yields in chisel- and ridge-tilled soybeans [Glycine max (L.) Merrill] grown in 2-yr rotation with corn (Zea mays L.) with and without added nitrogen (N). Populations were also sampled early and late season in alfalfa (Medicago sativa L.). Beetles were present in alfalfa by late May and most were reproductively active within a week, but their presence in alfalfa did not always precede soybean emergence. Most beetles taken from alfalfa in late fall were teneral; all were previtellogenic and unmated. Reproductively active beetles were detected in soybeans as soon as seedlings emerged. A partial second generation apparently occurred each year. First-generation beetles started to emerge in soybean fields during the first or third week of July but, whether emergence started early or late, most beetles emerging after July seemingly failed to mature their eggs and started leaving soybeans within several weeks of eclosion. This pattern suggested that any second generation arose from only the earliest emerging beetles of the first generation, with later emerging individuals having to overwinter before reproducing. Thus, any factors delaying emergence of the first generation, such as delayed soybean planting, could potentially limit its reproductive capacity through winter mortality. Cumulative seasonal beetle counts were lower in N-treated subplots and in ridge-tilled compared with chisel-tilled plots. Soybean grain yield increased with decreases in peak abundance of first-generation beetles and with N fertilization.

  14. Douglas-fir forests in the Cascade Mountains of Oregon and Washington: is the abundance of small mammals related to stand age and moisture?

    USGS Publications Warehouse

    Coen, P.S.; Bury, R.B.; Spies, T.A.

    1988-01-01

    Red tree voles (Arborimus longicaudus) were the only small mammal strongly associated with old-growth forests, whereas vagrant shrews (Sorex vagrans) were most abundant in young forests. Pacific marsh shrews (S. bendirii) were most abundant in wet old-growth forests, but abundance of this species in young (wet) forests needs further study. Clearcuts had a mammalian fauna distinct from young forest stands. Abundance of several species was correlated to habitat features unique to naturally regenerated forests, indicated an urgent need to study the long-term effects of forest management to nongame wildlife.

  15. In-Depth Global Analysis of Transcript Abundance Levels in Porcine Alveolar Macrophages Following Infection with Porcine Reproductive and Respiratory Syndrome Virus

    PubMed Central

    Miller, Laura C.; Neill, John D.; Harhay, Gregory P.; Lager, Kelly M.; Laegreid, William W.; Kehrli, Marcus E.

    2010-01-01

    Porcine reproductive and respiratory syndrome virus (PRRSV) is a major pathogen of swine worldwide and causes considerable economic loss. Identifying specific cell signaling or activation pathways that associate with variation in PRRSV replication and macrophage function may lead to identification of novel gene targets for the control of PRRSV infection. Serial Analysis of Gene Expression (SAGE) was used to create and survey the transcriptome of in vitro mock-infected and PRRSV strain VR-2332-infected porcine alveolar macrophages (PAM) at 0, 6, 12, 16, and 24 hours after infection. The transcriptome data indicated changes in transcript abundance occurring in PRRSV-infected PAMs over time after infection with more than 590 unique tags with significantly altered transcript abundance levels identified (P < .01). Strikingly, innate immune genes (whose transcript abundances are typically altered in response to other pathogens or insults including IL-8, CCL4, and IL-1β) showed no or very little change at any time point following infection. PMID:22331987

  16. Abundance, behavior, and movement patterns of western gray whales in relation to a 3-D seismic survey, Northeast Sakhalin Island, Russia.

    PubMed

    Gailey, Glenn; Würsig, Bernd; McDonald, Trent L

    2007-11-01

    A geophysical seismic survey was conducted in the summer of 2001 off the northeastern coast of Sakhalin Island, Russia. The area of seismic exploration was immediately adjacent to the Piltun feeding grounds of the endangered western gray whale (Eschrichtius robustus). This study investigates relative abundance, behavior, and movement patterns of gray whales in relation to occurrence and proximity to the seismic survey by employing scan sampling, focal follow, and theodolite tracking methodologies. These data were analyzed in relation to temporal, environmental, and seismic related variables to evaluate potential disturbance reactions of gray whales to the seismic survey. The relative numbers of whales and pods recorded from five shore-based stations were not significantly different during periods when seismic surveys were occurring compared to periods when no seismic surveys were occurring and to the post-seismic period. Univariate analyses indicated no significant statistical correlation between seismic survey variables and any of the eleven movement and behavior variables. Multiple regression analyses indicated that, after accounting for temporal and environmental variables, 6 of 11 movement and behavior variables (linearity, acceleration, mean direction, blows per surfacing, and surface-dive blow rate) were not significantly associated with seismic survey variables, and 5 of 11 variables (leg speed, reorientation rate, distance-from-shore, blow interval, and dive time) were significantly associated with seismic survey variables. In summary, after accounting for environmental variables, no correlation was found between seismic survey variables and the linearity of whale movements, changes in whale swimming speed between theodolite fixes, mean direction of whale movement, mean number of whale exhalations per minute at the surface, mean time at the surface, and mean number of exhalations per minute during a whales surface-to-dive cycle. In contrast, at higher

  17. Variation of morphological and chemical traits of perennial grasses in arid ecosystems. Are these patterns influenced by the relative abundance of shrubs?

    NASA Astrophysics Data System (ADS)

    Moreno, Laura; Bertiller, Mónica B.

    2012-05-01

    We asked whether morphological and chemical traits of perennial grasses in semiarid-arid ecosystems are influenced by the abundance of coexisting shrubs, in northern-central Patagonia, Chubut Province, Argentina. We selected populations of two perennial grass species, highly preferred by herbivores (4 for Festuca pallescens and 8 for Poa ligularis) at 10 sites distributed across a wide range of aridity. We assessed the relative shrub cover (shrub cover as percent of total cover) of each site and randomly collected 5 to 10 bunches of each grass species per site in December 2007 (late vegetative-early reproductive growth period). We measured the height of vegetative tillers, and morphological (length, width, area, dry mass, and specific area) and chemical (N, C, soluble phenolics and lignin concentration) attributes of full expanded green blades in the collected bunches. Further, we computed the aridity index of each site using temperature and precipitation data. The aridity index ranged from 1.07 to 3.9 at F. pallescens sites and from 3.6 to 7.3 at P. ligularis sites. The relative shrub cover increased significantly with aridity varying from 0.01 to 99%. Tiller height, blade length, and blade area of P. ligularis increased significantly with increasing relative shrub cover and aridity. Concentration of soluble phenolics in blades of both species decreased with increasing relative shrub cover and aridity. N concentration in blades of P. ligularis and specific blade area in F. pallescens decreased with increasing relative shrub cover and aridity. We conclude that some traits of perennial grasses (phenolics concentration in green blades in both species, and tiller height and some blade attributes in P. ligularis) were influenced by shrub cover itself. The variation in these traits was opposite to that expected by the effect of aridity and could be associated with escape from herbivores and/or drought, enhanced mesophytism, and reduced chemical defenses.

  18. Evolution of CO 2 , CH 4 , and OCS abundances relative to H 2 O in the coma of comet 67P around perihelion from Rosetta /VIRTIS-H observations

    NASA Astrophysics Data System (ADS)

    Bockelée-Morvan, Dominique; Crovisier, J.; Erard, S.; Capaccioni, F.; Leyrat, C.; Filacchione, G.; Drossart, P.; Encrenaz, T.; Biver, N.; de Sanctis, M.-C.; Schmitt, B.; Kührt, E.; Capria, M.-T.; Combes, M.; Combi, M.; Fougere, N.; Arnold, G.; Fink, U.; Ip, W.; Migliorini, A.; Piccioni, G.; Tozzi, G.

    2016-11-01

    Infrared observations of the coma of 67P/Churyumov-Gerasimenko were carried out from July to September 2015, i.e., around perihelion (13 August 2015), with the high-resolution channel of the VIRTIS instrument onboard Rosetta. We present the analysis of fluorescence emission lines of H$_2$O, CO$_2$, $^{13}$CO$_2$, OCS, and CH$_4$ detected in limb sounding with the field of view at 2.7-5 km from the comet centre. Measurements are sampling outgassing from the illuminated southern hemisphere, as revealed by H$_2$O and CO$_2$ raster maps, which show anisotropic distributions, aligned along the projected rotation axis. An abrupt increase of water production is observed six days after perihelion. In the mean time, CO$_2$, CH$_4$, and OCS abundances relative to water increased by a factor of 2 to reach mean values of 32%, 0.47%, and 0.18%, respectively, averaging post-perihelion data. We interpret these changes as resulting from the erosion of volatile-poor surface layers. Sustained dust ablation due to the sublimation of water ice maintained volatile-rich layers near the surface until at least the end of the considered period, as expected for low thermal inertia surface layers. The large abundance measured for CO$_2$ should be representative of the 67P nucleus original composition, and indicates that 67P is a CO$_2$-rich comet. Comparison with abundance ratios measured in the northern hemisphere shows that seasons play an important role in comet outgassing. The low CO$_2$/H$_2$O values measured above the illuminated northern hemisphere are not original, but the result of the devolatilization of the uppermost layers.

  19. Spatio-temporal analysis of abundances of three malaria vector species in southern Benin using zero-truncated models

    PubMed Central

    2014-01-01

    Background A better understanding of the ecology and spatial-temporal distribution of malaria vectors is essential to design more effective and sustainable strategies for malaria control and elimination. In a previous study, we analyzed presence-absence data of An. funestus, An. coluzzii, and An. gambiae s.s. in an area of southern Benin with high coverage of vector control measures. Here, we further extend the work by analysing the positive values of the dataset to assess the determinants of the abundance of these three vectors and to produce predictive maps of vector abundance. Methods Positive counts of the three vectors were assessed using negative-binomial zero-truncated (NBZT) mixed-effect models according to vector control measures and environmental covariates derived from field and remote sensing data. After 8-fold cross-validation of the models, predictive maps of abundance of the sympatric An. funestus, An. coluzzii, and An. gambiae s.s. were produced. Results Cross-validation of the NBZT models showed a satisfactory predictive accuracy. Almost all changes in abundance between two surveys in the same village were well predicted by the models but abundances for An. gambiae s.s. were slightly underestimated. During the dry season, predictive maps showed that abundance greater than 1 bite per person per night were observed only for An. funestus and An. coluzzii. During the rainy season, we observed both increase and decrease in abundance of An. funestus, which are dependent on the ecological setting. Abundances of both An. coluzzii and An. gambiae s.s. increased during the rainy season but not in the same areas. Conclusions Our models helped characterize the ecological preferences of three major African malaria vectors. This works highlighted the importance to study independently the binomial and the zero-truncated count processes when evaluating vector control strategies. The study of the bio-ecology of malaria vector species in time and space is critical

  20. Relative risk regression analysis of epidemiologic data.

    PubMed

    Prentice, R L

    1985-11-01

    Relative risk regression methods are described. These methods provide a unified approach to a range of data analysis problems in environmental risk assessment and in the study of disease risk factors more generally. Relative risk regression methods are most readily viewed as an outgrowth of Cox's regression and life model. They can also be viewed as a regression generalization of more classical epidemiologic procedures, such as that due to Mantel and Haenszel. In the context of an epidemiologic cohort study, relative risk regression methods extend conventional survival data methods and binary response (e.g., logistic) regression models by taking explicit account of the time to disease occurrence while allowing arbitrary baseline disease rates, general censorship, and time-varying risk factors. This latter feature is particularly relevant to many environmental risk assessment problems wherein one wishes to relate disease rates at a particular point in time to aspects of a preceding risk factor history. Relative risk regression methods also adapt readily to time-matched case-control studies and to certain less standard designs. The uses of relative risk regression methods are illustrated and the state of development of these procedures is discussed. It is argued that asymptotic partial likelihood estimation techniques are now well developed in the important special case in which the disease rates of interest have interpretations as counting process intensity functions. Estimation of relative risks processes corresponding to disease rates falling outside this class has, however, received limited attention. The general area of relative risk regression model criticism has, as yet, not been thoroughly studied, though a number of statistical groups are studying such features as tests of fit, residuals, diagnostics and graphical procedures. Most such studies have been restricted to exponential form relative risks as have simulation studies of relative risk estimation

  1. Species richness and relative species abundance of Nymphalidae (Lepidoptera) in three forests with different perturbations in the North-Central Caribbean of Costa Rica.

    PubMed

    Stephen, Carolyn; Sánchez, Ragde

    2014-09-01

    Measurements of species richness and species abundance can have important implications for regulations and conservation. This study investigated species richness and abundance of butterflies in the family Nymphalidae at undisturbed, and disturbed habitats in Tirimbina Biological Reserve and Nogal Private Reserve, Sarapiquí, Costa Rica. Traps baited with rotten banana were placed in the canopy and the understory of three habitats: within mature forest, at a river/forest border, and at a banana plantation/forest border. In total, 71 species and 487 individuals were caught and identified during May and June 2011 and May 2013. Species richness and species abundance were found to increase significantly at perturbed habitats (p < 0.0001, p < 0.0001, respectively). The edge effect, in which species richness and abundance increase due to greater complementary resources from different habitats, could be one possible explanation for increased species richness and abundance.

  2. Effect of leptin during in vitro maturation of prepubertal calf oocytes: embryonic development and relative mRNA abundances of genes involved in apoptosis and oocyte competence.

    PubMed

    Córdova, Bladimir; Morató, Roser; de Frutos, Celia; Bermejo-Álvarez, Pablo; Paramio, Teresa; Gutiérrez-Adán, Alfonso; Mogas, Teresa

    2011-12-01

    During the in vitro maturation of adult bovine oocytes, leptin has beneficial effects on blastocyst development, apoptosis and transcription levels of developmentally important genes. The present study analyzes the differential effects of leptin on prepubertal bovine oocytes and cumulus cells. Effects were determined of leptin treatment during oocyte maturation on their developmental capacity after fertilization (Exp. 1), incidence of apoptosis in cumulus oocyte complexes (COCs) (Exp. 2) or on relative mRNA abundances of genes in cumulus cells and oocytes (Exp. 3). COCs were matured in serum-free medium containing 1 mg/mL polyvinyl alcohol and 0, 10, 100, or 1000 ng/mL leptin (L0, L10, L100, and L1000, respectively), or in medium supplemented with 10% fetal calf serum (FCS) as a positive control. Addition of leptin during oocyte maturation had no effect on cleavage rates after fertilization (FCS, 68.6%; L0, 62.9%; L10, 66.9%; L100, 63.4%; L1000, 60.9%). Similarly, no significant differences in blastocyst rates were observed when oocytes were matured in the presence of L0 (8.4%), L10 (9.3%), L100 (6.7%), L1000 (8.2%), compared to control FCS (9.4%). In Experiment 2, maturation in the presence of 1000 ng/mL of leptin increased the proportion of TUNEL-positive cumulus cell (6.9%) with respect to those matured in the presence of FCS (4.96%), but not at the lower leptin doses. When relative mRNA abundances were examined for seven genes by qRT-PCR, five (TP53, BAX, DNMT3A, PGTS2 and LEPR) showed differences among groups. LEPR expression was significantly higher in the oocytes matured with FCS compared with the other groups and in those matured with PVA (L0) without leptin compared with the three groups of oocytes matured in the presence of leptin. In conclusion, the addition of leptin to the in vitro maturation medium used for prepubertal bovine oocytes does not increase the development potential of the oocytes or reduce the percentage of apoptosis in cumulus cells

  3. 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.

  4. ANALYSIS OF TWO SMALL MAGELLANIC CLOUD H II REGIONS CONSIDERING THERMAL INHOMOGENEITIES: IMPLICATIONS FOR THE DETERMINATIONS OF EXTRAGALACTIC CHEMICAL ABUNDANCES

    SciTech Connect

    Pena-Guerrero, Maria A.; Peimbert, Antonio; Peimbert, Manuel; Ruiz, Maria Teresa E-mail: antonio@astroscu.unam.mx E-mail: mtruiz@das.uchile.cl

    2012-02-20

    We present long-slit spectrophotometry considering the presence of thermal inhomogeneities (t{sup 2}) of two H II regions in the Small Magellanic Cloud (SMC): NGC 456 and NGC 460. Physical conditions and chemical abundances were determined for three positions in NGC 456 and one position in NGC 460, first under the assumption of uniform temperature and then allowing for the possibility of thermal inhomogeneities. We determined t{sup 2} values based on three different methods: (1) by comparing the temperature derived using oxygen forbidden lines with the temperature derived using helium recombination lines (RLs), (2) by comparing the abundances derived from oxygen forbidden lines with those derived from oxygen RLs, and (3) by comparing the abundances derived from ultraviolet carbon forbidden lines with those derived from optical carbon RLs. The first two methods averaged t{sup 2} = 0.067 {+-} 0.013 for NGC 456 and t{sup 2} = 0.036 {+-} 0.027 for NGC 460. These values of t{sup 2} imply that when gaseous abundances are determined with collisionally excited lines they are underestimated by a factor of nearly two. From these objects and others in the literature, we find that in order to account for thermal inhomogeneities and dust depletion, the O/H ratio in low-metallicity H II regions should be corrected by 0.25-0.45 dex depending on the thermal structure of the nebula or by 0.35 dex if such information is not available.

  5. Environmental occurrence, abundance, and potential toxicity of polychlorinated biphenyl congeners: considerations for a congener-specific analysis.

    PubMed

    McFarland, V A; Clarke, J U

    1989-05-01

    Polychlorinated biphenyls (PCBs) as environmental contaminants often cannot be adequately described by reference to Aroclors or to total PCBs. Although there are 209 possible PCB configurations (congeners), perhaps half that number account for nearly all of the environmental contamination attributable to PCBs. Still fewer congeners are both prevalent and either demonstrably or potentially toxic. If potential toxicity, environmental prevalence, and relative abundance in animal tissues are used as criteria, the number of environmentally threatening PCB congeners reduces to about thirty-six. Twenty-five of these account for 50 to 75% of total PCBs in tissue samples of fish, invertebrates, birds, and mammals. A few PCB congeners that are sterically similar to 2,3,7,8-tetrachlorodibenzo-p-dioxin (2,3,7,8-TCDD) are directly toxic. Other PCB congeners, as well as those that are directly toxic, may also be involved in toxicity indirectly by stimulating the production of (inducing) bioactivating enzyme systems. The most consequential of these have the ability to induce aryl hydrocarbon metabolizing mixed-function oxidases (MFOs). A result can be an increased capacity for bioactivation of otherwise nontoxic foreign compounds such as certain polynuclear aromatic hydrocarbons (PAH) to cytotoxic or genotoxic metabolites. The effectiveness of specific PCB congeners as inducers of different types of cytochrome P-450-dependent MFO systems is determined by their stereochemistry. Although MFO induction is not a proximate cause, it is a strong correlate of certain kinds of toxicities. Structural patterns can thus be used to discriminate among PCB congeners on the basis of toxic potential, if not entirely on toxicity per se. Congeners that demonstrate 3-methylcholanthrene-type (3-MC-type) and mixed-type MFO induction have the greatest toxic potential. These congeners most closely resemble 2,3,7,8-TCDD in their structures and in their toxic effects. The larger group of phenobarbital

  6. The Abundance of Interstellar Fluorine

    NASA Technical Reports Server (NTRS)

    Lauroesch, James T.

    2005-01-01

    The primary objective of this program was to obtain FUSE observations of the interstellar absorption lines of F I at 951 and 954 Angstroms to derive the abundance of fluorine toward the star HD 164816. The nucleosynthetic source(s) of fluorine are still a matter of debate - the present day abundance of fluorine can potentially constrain models for pulsationally driven dredge-up in asymptotic giant branch stars. An accurate measure for the depletion behavior of fluorine will determine whether it may be detectable in QSO absorption line systems - an unambiguous detection of fluorine at suitably high redshifts would provide the best evidence to date for the neutrino process in massive stars. Furthermore, due to its extreme reactivity, measurement of the gas-phase interstellar fluorine abundance is important for models of grain chemistry. Despite the importance of measuring the interstellar fluorine abundance, at the time of our proposal only one previous detection has been made due to the low relative abundance of fluorine, the lack of lines outside the far-UV, and the blending of the available F I transitions with lines of Hz. The star HD 164816 is associated with the Lagoon nebula (M8), and at a distance of approximately 1.5 kpc probes both distant and local gas. Beginning April 8th, 2004 FUSE FP-Split observations of the star HD 164816 were obtained for this program. This data became available in the FUSE data archive May 21, 2004, and these observations were then downloaded and we began our analysis. Our analysis procedure has involved (1) fitting stellar models to the FUSE spectra, (2) using the multiple lines of Hz and N I at other wavelengths in the FUSE bandpass to derive column densities for the lines of H2 and N I which are blended with the F I features at 951 and 954 angstroms (3) the measurement of the column densities of F I and the species O I and C1 I which are important species for the dis-entangling of dust and nucleosynthetic effects. As discussed in

  7. Seasonal studies on commensal rats and their ectoparasites in a rural area of Egypt: the relationship of ectoparasites to the species, locality, and relative abundance of the host.

    PubMed

    Soliman, S; Main, A J; Marzouk, A S; Montasser, A A

    2001-06-01

    The present study was carried out in 3 villages, namely Kafr Ayoub Soliman, Kafr Ibrahim El-Aidi, and El-Sa'adat, Sharqiya Governorate, Egypt. A total of 519 rats was collected from the 3 study sites: 46.6% Rattus rattus, and 53.4% Rattus norvegicus. A total of 20,643 ectoparasites was recovered from R. rattus: 33.3% mites, 33.8% fleas, and 32.9% lice. From R. norvegicus a total of 40,997 ectoparasites was recovered: 28.9% mites, 31% fleas, and 40.1% lice. Three common mite species were recovered from both rat hosts, i.e., Ornithonyssus bacoti, Radfordia ensifera, and Laelaps nuttalli. Three common flea species were also recovered from both rat hosts, i.e., Echidnophaga gallinacea, Leptopsylla segnis, and Xenopsylla cheopis. Polyplax spinulosa was the only dominant louse species that infested both rat hosts. Rats did not show a definite breeding season, and the seasonal rat indices were generally low in different study sites. There were no significant differences between the prevalence of each of mites, fleas, and lice in both rat species. The total general indices of mites and fleas, on the other hand, was significantly higher in R. norvegicus. The general index of X. cheopis was high and ranged between 5.9 in R. rattus and 14.5 in R. norvegicus. Season-related changes were observed in the general index of each of L. segnis infesting both rat species and R. ensifera and O. bacoti infesting R. norvegicus. The prevalence and general indices of some ectoparasites showed differences related to the locality of their rat hosts. Seasonal changes in the general indices of some ectoparasites paralleled seasonal changes in the relative abundance of their rat hosts.

  8. Permafrost response to increasing Arctic shrub abundance depends on the relative influence of shrubs on local soil cooling versus large-scale climate warming

    NASA Astrophysics Data System (ADS)

    Lawrence, David M.; Swenson, Sean C.

    2011-10-01

    Deciduous shrub abundance is increasing across the Arctic in response to climatic warming. In a recent field manipulation experiment in which shrubs were removed from a plot and compared to a control plot with shrubs, Blok et al (2010 Glob. Change Biol. 16 1296-305) found that shrubs protect the ground through shading, resulting in a ~ 9% shallower active layer thickness (ALT) under shrubs compared to grassy-tundra, which led them to argue that continued Arctic shrub expansion could mitigate future permafrost thaw. We utilize the Community Land Model (CLM4) coupled to the Community Atmosphere Model (CAM4) to evaluate this hypothesis. CLM4 simulates shallower ALT (~- 11 cm) under shrubs, consistent with the field manipulation study. However, in an idealized pan-Arctic + 20% shrub area experiment, atmospheric heating, driven mainly by surface albedo changes related to protrusion of shrub stems above the spring snowpack, leads to soil warming and deeper ALT (~+ 10 cm). Therefore, if climate feedbacks are considered, shrub expansion may actually increase rather than decrease permafrost vulnerability. When we account for blowing-snow redistribution from grassy-tundra to shrubs, shifts in snowpack distribution in low versus high shrub area simulations counter the climate warming impact, resulting in a grid cell mean ALT that is unchanged. These results reinforce the need to consider vegetation dynamics and blowing-snow processes in the permafrost thaw model projections.

  9. Spatio-temporal variation in small mammal species richness, relative abundance and body mass reveal changes in a coastal wetland ecosystem in Ghana.

    PubMed

    Ofori, Benjamin Y; Attuquayefio, Daniel K; Owusu, Erasmus H; Musah, Yahaya; Ntiamoa-Baidu, Yaa

    2016-06-01

    Coastal wetlands in Ghana are under severe threat of anthropogenic drivers of habitat degradation and climate change, thereby increasing the need for assessment and monitoring to inform targeted and effective conservation of these ecosystems. Here, we assess small mammal species richness, relative abundance and body mass in three habitats at the Muni-Pomadze Ramsar site of Ghana, and compare these to baseline data gathered in 1997 to evaluate changes in the wetland ecosystem. Small mammals were live-trapped using Sherman collapsible and pitfall traps. We recorded 84 individuals of 10 species in 1485 trap-nights, whereas the baseline study recorded 45 individuals of seven species in 986 trap-nights. The overall trap-success was therefore greater in the present study (5.66 %) than the baseline study (4.56 %). The species richness increased from one to four in the forest, and from zero to eight in the thicket, but decreased from six to four in the grassland. The total number of individuals increased in all habitats, with the dominant species in the grassland shifting from Lemniscomys striatus to Mastomys erythroleucus. Three species, Malacomys edwardsi, Grammomys poensis and Praomys tullbergi are the first records for the Muni-Pomadze Ramsar site. Generally, the average body mass of individual species in the grassland was lower in the present study. The considerable changes in small mammal community structure suggest changes in the wetland ecosystem. The conservation implications of our findings are discussed.

  10. On the relative abundance of LiH and LiH+ molecules in the early universe: new results from quantum reactions

    NASA Astrophysics Data System (ADS)

    Bovino, S.; Tacconi, M.; Gianturco, F.

    2011-05-01

    The chemistry of Li in the early universe has been discussed in the past, reaching contrasting conclusions (see e.g., SLD96; BG97; GP98; Vonlanthen et al. 2009). Of critical relevance, is the uncertainty in the knowledge of reliable reaction rates for the destruction of LiH and LiH^+ molecules formed by radiative recombination (Dickinson & Gadéa 2000) via strongly exothermic reactions without entrance barriers: LiH + H → Li + H_2 LiH + H^+ → Li + H_2^+ and LiH^+ + H → Li^+ + H_2. Therefore, it is an accurate knowledge of the reaction rates for the above processes, at low redshift values, that can ultimately tell us what the end-role of the LiH/LiH^+ systems could be as efficient coolants under early universe conditions. The task of the present work is to show that the reaction rates recently determined from fully ab-initio quantum methods (Bovino et al. 2009, 2010a, 2010b), which also employ accurate interaction forces between partners, have a significant impact on the evolution of LiH and LiH^+ during the post-recombination era of the early universe. We shall further show that a more realistic description of the rates for a neutralization process LiH^+ + e^- → Li + H could substantially change the relative abundance of the ionic molecular species.

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

    NASA Technical Reports Server (NTRS)

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

    1973-01-01

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

  12. Foetal life protein provision of mink (Neovison vison) changes the relative mRNA abundance of some hepatic enzymes regulating fat metabolism.

    PubMed

    Matthiesen, Connie Frank; Casañas, Maria Arantzazu Aguinaga; Tauson, Anne-Helene

    2014-01-01

    The nutrient provision to pregnant females has high impact on the growth and metabolism of their offspring. The objective was to investigate if the expression of hepatic enzymes regulating the fat metabolism was affected in foetuses and adult female mink born by dams fed either a low or an adequate level of protein during late gestation. The relative abundances of acetyl coenzyme A carboxylase (ACC), fatty acid synthase (FAS) and carnitine palmitoyl transferase 1 (CPT1) mRNA were determined by qualitative polymerase chain reaction in the livers of F₀- and F₁-generation dams and in F₁-generation foetuses. Low protein provision during foetal life resulted in a lower expression of FAS in foetal liver but a tendency towards increased expression in the liver of adult dams. There was a tendency towards an effect of life stage of the animal on the expression of ACC resulting in a higher expression among F₁ foetuses exposed to low protein during foetal life than F₀ dams fed a low protein diet during late gestation. The expression of CPT1 was significantly lower among dams exposed to low protein provision during foetal life than controls, possibly indicating a lower rate of mitochondrial β-oxidation. Further investigations are needed to clarify the consequences of these changes for the fat metabolism.

  13. AUTOMATED DECONVOLUTION OF COMPOSITE MASS SPECTRA OBTAINED WITH AN OPEN-AIR IONIZATIONS SOURCE BASED ON EXACT MASSES AND RELATIVE ISOTIPIC ABUNDANCES

    EPA Science Inventory

    Chemicals dispersed by accidental, deliberate, or weather-related events must be rapidly identified to assess health risks. Mass spectra from high levels of analytes obtained using rapid, open-air ionization by a Direct Analysis in Real Time (DART®) ion source often contain

  14. Distribution, abundance, biomass and diversity of benthic infauna in the Northeast Chukchi Sea, Alaska: Relation to environmental variables and marine mammals

    NASA Astrophysics Data System (ADS)

    Schonberg, Susan V.; Clarke, Janet T.; Dunton, Kenneth H.

    2014-04-01

    In summer 2009 and 2010, as part of Chukchi Sea Offshore Monitoring in Drilling Area - Chemical and Benthos (COMIDA CAB) program, we performed a quantitative assessment of the biomass, abundance, and community structure of benthic infaunal populations of the Northeastern Chukchi Sea. This analysis documented a benthic species inventory of 361 taxa collected from 142 individual van Veen grab samples (0.1 m-2) at 52 stations. Infaunal abundance was dominated by Polychaeta, Mollusca, and Crustacea. Large concentrations of bivalves (up to 1235 m-2; 920.2 gww m-2) were collected south of Hanna Shoal where flow from two water masses converge and deposit labile carbon to the seafloor, as indicated by low surface sediment C:N ratios. Amphipods (up to 1640 m-2; 26.0 gww m-2), and polychaetes (up to 4665 m-2; 114.7 gww m-2) were documented from multiple stations west of and within Barrow Canyon. This high productivity was most likely due to the "canyon effect", where marine and coastal detrital carbon supplies are channeled by the canyon structure, enhancing carbon deposition and flux, which supports rich benthic communities within the canyon and surrounding areas. To examine the relationships between infaunal distributions of all collected taxa with the physical environment, we used a Biota and Environment matching (BIO-ENV) routine. A combination of water depth, bottom-water temperature and salinity, surface sediment total organic nitrogen (TON) and sediment C:N molar ratios correlated closest with infaunal abundance distribution (ρ=0.54), indicating that multiple factors influence the success of benthic communities. BIO-ENV routines produced similar correlation results when performed on targeted walrus prey items (bivalves (ρ=0.50), polychaetes (ρ=0.53), but gray whale prey items (amphipods) were not strongly correlated to any combination of physical environmental factors (ρ=0.24). Distributions of primary prey items for gray whales (amphipods) and walruses (bivalves

  15. 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.

  16. Tracing magma sources in an arc-arc collision zone: Helium and carbon isotope and relative abundance systematics of the Sangihe Arc, Indonesia

    NASA Astrophysics Data System (ADS)

    Jaffe, Lillie A.; Hilton, David R.; Fischer, Tobias P.; Hartono, Udi

    2004-04-01

    The Sangihe Arc is presently colliding with the Halmahera Arc in northeastern Indonesia, forming the world's only extant example of an arc-arc collision zone. We report the first helium and carbon isotopic and relative abundance data from the Sangihe Arc volcanoes as a means to trace magma origins in this complicated tectonic region. Results of this study define a north-south trend in 3He/4He, CO2/3He, and δ13C, suggesting that there are variations in primary magma source characteristics along the strike of the arc. The northernmost volcanoes (Awu and Karangetang) have higher CO2/3He and δ13C (up to 179 × 109 and -0.4‰, respectively) and lower 3He/4He (˜5.4 RA) than the southernmost volcanoes (Ruang, Lokon, and Mahawu). Resolving the arc CO2 into component structures (mantle-derived, plus slab-derived organic and carbonate CO2), the northern volcanoes contain an unusually high (>90%) contribution of CO2 derived from isotopically heavy carbonate associated with the subducting slab (sediment and altered oceanic basement). Furthermore, the overall slab contribution (CO2 of carbonate and organic origin) relative to carbon of mantle wedge origin is significantly enhanced in the northern segment of the arc. These observations may be caused by greater volumes of sediment subduction in the northern arc, along-strike variability in subducted sediment composition, or enhanced slab-derived fluid/melt production resulting from the superheating of the slab as collision progresses southward.

  17. Elemental Abundances from Very Low Abundance HII Regions

    NASA Astrophysics Data System (ADS)

    Skillman, Evan D.; Terlevich, Roberto J.; Terlevich, Elena

    1992-12-01

    In 1987 we initiated a program to mitigate the deficiency of known low metallicity galaxies. Following our discoveries of very low abundance H II regions in nearby dwarf galaxies (Skillman et al. 1988, 1989a,b), we used the IDS on the INT to to collect spectra of dwarf galaxies in the Second Byurakan Survey (SBS) of UV excess galaxies. Our survey of over 40 SBS galaxies was completed in January 1990 and we have identified roughly one dozen very low metallicity H II galaxies. Now, with a significant sample of these galaxies, several observational programs are possible; foremost of these is the measurement of the primordial helium abundance (eg., Pagel et al. 1992). We report here on observations from March 1991 and 1992 using the ISIS spectrograph on the WHT to obtain very high quality spectra of 8 of these newly discovered metal-poor galaxies. The ISIS double spectrograph allows simultaneous observations of the blue (3600 - 5100 Angstroms) and red (6300 - 6800 Angstroms). Thus, He, N, O, Ne and S abundances can be derived with relatively small observational uncertainties. We compare our new observations with those in the literature. Our preliminary analysis indicates a slightly larger scatter in He/H at low O/H than had been seen previously. The small scatter may have been due simply to the paucity of observations at low metallicity. References: Pagel, B.E.J., Simonson, E.A., Terlevich, R.J., & Edmunds, M.G. 1992, MNRAS, 255, 325 Skillman, E.D., Kennicutt, R.C., & Hodge, P.W. 1989a, ApJ, 347, 875 Skillman, E.D., Melnick, J., Terlevich, R., & Moles, M. 1988, A&A, 196, 31 Skillman, E.D., Terlevich, R., & Melnick, J. 1989b, MNRAS, 240, 563

  18. Identifying related journals through log analysis

    PubMed Central

    Lu, Zhiyong; Xie, Natalie; Wilbur, W. John

    2009-01-01

    Motivation: With the explosion of biomedical literature and the evolution of online and open access, scientists are reading more articles from a wider variety of journals. Thus, the list of core journals relevant to their research may be less obvious and may often change over time. To help researchers quickly identify appropriate journals to read and publish in, we developed a web application for finding related journals based on the analysis of PubMed log data. Availability: http://www.ncbi.nlm.nih.gov/IRET/Journals Contact: luzh@ncbi.nlm.nih.gov Supplementary information: Supplementary data are available at Bioinformatics online. PMID:19734155

  19. Integrated analysis of transcriptomic and proteomic data of Desulfovibrio vulgaris: Zero-Inflated Poisson regression models to predict abundance of undetected proteins

    SciTech Connect

    Nie, Lei; Wu, Gang; Brockman, Fred J.; Zhang, Weiwen

    2006-05-04

    Abstract Advances in DNA microarray and proteomics technologies have enabled high-throughput measurement of mRNA expression and protein abundance. Parallel profiling of mRNA and protein on a global scale and integrative analysis of these two data types could provide additional insight into the metabolic mechanisms underlying complex biological systems. However, because protein abundance and mRNA expression are affected by many cellular and physical processes, there have been conflicting results on the correlation of these two measurements. In addition, as current proteomic methods can detect only a small fraction of proteins present in cells, no correlation study of these two data types has been done thus far at the whole-genome level. In this study, we describe a novel data-driven statistical model to integrate whole-genome microarray and proteomic data collected from Desulfovibrio vulgaris grown under three different conditions. Based on the Poisson distribution pattern of proteomic data and the fact that a large number of proteins were undetected (excess zeros), Zero-inflated Poisson models were used to define the correlation pattern of mRNA and protein abundance. The models assumed that there is a probability mass at zero representing some of the undetected proteins because of technical limitations. The models thus use abundance measurements of transcripts and proteins experimentally detected as input to generate predictions of protein abundances as output for all genes in the genome. We demonstrated the statistical models by comparatively analyzing D. vulgaris grown on lactate-based versus formate-based media. The increased expressions of Ech hydrogenase and alcohol dehydrogenase (Adh)-periplasmic Fe-only hydrogenase (Hyd) pathway for ATP synthesis were predicted for D. vulgaris grown on formate.

  20. The abundances of H-3 and C-14 in the solar wind. [measured by lunar soil analysis

    NASA Technical Reports Server (NTRS)

    Fireman, E. L.; Defelice, J.; Damico, J.

    1976-01-01

    Tritium is measured as a function of depth in a Surveyor 3 sample. The upper limit for solar-wind-implanted tritium gives a H-3/H-1 limit for the solar wind of 1 part in one hundred billion. The temperature release patterns of C-14 from lunar soils are measured. The C-14 release patterns from surface soils differ from a trench-bottom soil and give evidence for the presence of C-14 in the solar wind with a C-14/H-1 ratio of approximately 4 parts in one hundred billion. The implications of these radionuclide abundances in the solar wind are discussed.

  1. Surprising abundance of Gallionella-related iron oxidizers in creek sediments at pH 4.4 or at high heavy metal concentrations

    PubMed Central

    Fabisch, Maria; Beulig, Felix; Akob, Denise M.; Küsel, Kirsten

    2013-01-01

    We identified and quantified abundant iron-oxidizing bacteria (FeOB) at three iron-rich, metal-contaminated creek sites with increasing sediment pH from extremely acidic (R1, pH 2.7), to moderately acidic (R2, pH 4.4), to slightly acidic (R3, pH 6.3) in a former uranium-mining district. The geochemical parameters showed little variations over the 1.5 year study period. The highest metal concentrations found in creek sediments always coincided with the lowest metal concentrations in creek water at the slightly acidic site R3. Sequential extractions of R3 sediment revealed large portions of heavy metals (Ni, Cu, Zn, Pb, U) bound to the iron oxide fraction. Light microscopy of glass slides exposed in creeks detected twisted stalks characteristic of microaerobic FeOB of the family Gallionellaceae at R3 but also at the acidic site R2. Sequences related to FeOB such as Gallionella ferruginea, Sideroxydans sp. CL21, Ferritrophicum radicicola, and Acidovorax sp. BrG1 were identified in the sediments. The highest fraction of clone sequences similar to the acidophilic “Ferrovum myxofaciens” was detected in R1. Quantitative PCR using primer sets specific for Gallionella spp., Sideroxydans spp., and “Ferrovum myxofaciens” revealed that ~72% (R2 sediment) and 37% (R3 sediment) of total bacterial 16S rRNA gene copies could be assigned to groups of FeOB with dominance of microaerobic Gallionella spp. at both sites. Gallionella spp. had similar and very high absolute and relative gene copy numbers in both sediment communities. Thus, Gallionella-like organisms appear to exhibit a greater acid and metal tolerance than shown before. Microaerobic FeOB from R3 creek sediment enriched in newly developed metal gradient tubes tolerated metal concentrations of 35 mM Co, 24 mM Ni, and 1.3 mM Cd, higher than those in sediments. Our results will extend the limited knowledge of FeOB at contaminated, moderately to slightly acidic environments. PMID:24385973

  2. Surprising abundance of Gallionella-related iron oxidizers in creek sediments at pH 4.4 or at high heavy metal concentrations

    USGS Publications Warehouse

    Fabisch, Maria; Beulig, Felix; Akob, Denise M.; Küsel, Kirsten

    2013-01-01

    We identified and quantified abundant iron-oxidizing bacteria (FeOB) at three iron-rich, metal-contaminated creek sites with increasing sediment pH from extremely acidic (R1, pH 2.7), to moderately acidic (R2, pH 4.4), to slightly acidic (R3, pH 6.3) in a former uranium-mining district. The geochemical parameters showed little variations over the 1.5 year study period. The highest metal concentrations found in creek sediments always coincided with the lowest metal concentrations in creek water at the slightly acidic site R3. Sequential extractions of R3 sediment revealed large portions of heavy metals (Ni, Cu, Zn, Pb, U) bound to the iron oxide fraction. Light microscopy of glass slides exposed in creeks detected twisted stalks characteristic of microaerobic FeOB of the family Gallionellaceae at R3 but also at the acidic site R2. Sequences related to FeOB such as Gallionella ferruginea, Sideroxydans sp. CL21, Ferritrophicum radicicola, and Acidovorax sp. BrG1 were identified in the sediments. The highest fraction of clone sequences similar to the acidophilic “Ferrovum myxofaciens” was detected in R1. Quantitative PCR using primer sets specific for Gallionella spp., Sideroxydans spp., and “Ferrovum myxofaciens” revealed that ~72% (R2 sediment) and 37% (R3 sediment) of total bacterial 16S rRNA gene copies could be assigned to groups of FeOB with dominance of microaerobic Gallionella spp. at both sites. Gallionella spp. had similar and very high absolute and relative gene copy numbers in both sediment communities. Thus, Gallionella-like organisms appear to exhibit a greater acid and metal tolerance than shown before. Microaerobic FeOB from R3 creek sediment enriched in newly developed metal gradient tubes tolerated metal concentrations of 35 mM Co, 24 mM Ni, and 1.3 mM Cd, higher than those in sediments. Our results will extend the limited knowledge of FeOB at contaminated, moderately to slightly acidic environments.

  3. High-resolution abundance analysis of red giants in the metal-poor bulge globular cluster HP 1

    NASA Astrophysics Data System (ADS)

    Barbuy, B.; Cantelli, E.; Vemado, A.; Ernandes, H.; Ortolani, S.; Saviane, I.; Bica, E.; Minniti, D.; Dias, B.; Momany, Y.; Hill, V.; Zoccali, M.; Siqueira-Mello, C.

    2016-06-01

    Context. The globular cluster HP 1 is projected at only 3.̊33 from the Galactic center. Together with its distance, this makes it one of the most central globular clusters in the Milky Way. It has a blue horizontal branch (BHB) and a metallicity of [Fe/H] ≈ -1.0. This means that it probably is one of the oldest objects in the Galaxy. Abundance ratios can reveal the nucleosynthesis pattern of the first stars as well as the early chemical enrichment and early formation of stellar populations. Aims: High-resolution spectra obtained for six stars were analyzed to derive the abundances of the light elements C, N, O, Na, and Al, the alpha-elements Mg, Si, Ca, and Ti, and the heavy elements Sr, Y, Zr, Ba, La, and Eu. Methods: High-resolution spectra of six red giants that are confirmed members of the bulge globular cluster HP 1 were obtained with the 8 m VLT UT2-Kueyen telescope with the UVES spectrograph in FLAMES-UVES configuration. The spectroscopic parameter derivation was based on the excitation and ionization equilibrium of Fe i and Fe ii. Results: We confirm a mean metallicity of [Fe/H] = -1.06 ± 0.10, by adding the two stars that were previously analyzed in HP 1. The alpha-elements O and Mg are enhanced by about +0.3 ≲ [O,Mg/Fe] ≲ +0.5 dex, Si is moderately enhanced with +0.15 ≲ [Si/Fe] ≲ +0.35 dex, while Ca and Ti show lower values of -0.04 ≲ [Ca,Ti/Fe] ≲ +0.28 dex. The r-element Eu is also enhanced with [Eu/Fe] ≈ +0.4, which together with O and Mg is indicative of early enrichment by type II supernovae. Na and Al are low, but it is unclear if Na-O are anticorrelated. The heavy elements are moderately enhanced, with -0.20 < [La/Fe] < +0.43 dex and 0.0 < [Ba/Fe] < +0.75 dex, which is compatible with r-process formation. The spread in Y, Zr, Ba, and La abundances, on the other hand, appears to be compatible with the spinstar scenario or other additional mechanisms such as the weak r-process. Observations collected at the European Southern

  4. Chemical abundances and kinematics of barium stars

    NASA Astrophysics Data System (ADS)

    de Castro, D. B.; Pereira, C. B.; Roig, F.; Jilinski, E.; Drake, N. A.; Chavero, C.; Sales Silva, J. V.

    2016-07-01

    In this paper, we present an homogeneous analysis of photospheric abundances based on high-resolution spectroscopy of a sample of 182 barium stars and candidates. We determined atmospheric parameters, spectroscopic distances, stellar masses, ages, luminosities and scaleheight, radial velocities, abundances of the Na, Al, α-elements, iron-peak elements, and s-process elements Y, Zr, La, Ce, and Nd. We employed the local thermodynamic equilibrium model atmospheres of Kurucz and the spectral analysis code MOOG. We found that the metallicities, the temperatures and the surface gravities for barium stars cannot be represented by a single Gaussian distribution. The abundances of α-elements and iron peak elements are similar to those of field giants with the same metallicity. Sodium presents some degree of enrichment in more evolved stars that could be attributed to the NeNa cycle. As expected, the barium stars show overabundance of the elements created by the s-process. By measuring the mean heavy-element abundance pattern as given by the ratio [s/Fe], we found that the barium stars present several degrees of enrichment. We also obtained the [hs/ls] ratio by measuring the photospheric abundances of the Ba-peak and the Zr-peak elements. Our results indicated that the [s/Fe] and the [hs/ls] ratios are strongly anticorrelated with the metallicity. Our kinematical analysis showed that 90 per cent of the barium stars belong to the thin disc population. Based on their luminosities, none of the barium stars are luminous enough to be an asymptotic giant branch star, nor to become self-enriched in the s-process elements. Finally, we determined that the barium stars also follow an age-metallicity relation.

  5. Sequence-Based Analysis Uncovers an Abundance of Non-Coding RNA in the Total Transcriptome of Mycobacterium tuberculosis

    PubMed Central

    Arnvig, Kristine B.; Comas, Iñaki; Thomson, Nicholas R.; Houghton, Joanna; Boshoff, Helena I.; Croucher, Nicholas J.; Rose, Graham; Perkins, Timothy T.; Parkhill, Julian; Dougan, Gordon; Young, Douglas B.

    2011-01-01

    RNA sequencing provides a new perspective on the genome of Mycobacterium tuberculosis by revealing an extensive presence of non-coding RNA, including long 5’ and 3’ untranslated regions, antisense transcripts, and intergenic small RNA (sRNA) molecules. More than a quarter of all sequence reads mapping outside of ribosomal RNA genes represent non-coding RNA, and the density of reads mapping to intergenic regions was more than two-fold higher than that mapping to annotated coding sequences. Selected sRNAs were found at increased abundance in stationary phase cultures and accumulated to remarkably high levels in the lungs of chronically infected mice, indicating a potential contribution to pathogenesis. The ability of tubercle bacilli to adapt to changing environments within the host is critical to their ability to cause disease and to persist during drug treatment; it is likely that novel post-transcriptional regulatory networks will play an important role in these adaptive responses. PMID:22072964

  6. Relative Fecal Abundance of Extended-Spectrum-β-Lactamase-Producing Escherichia coli Strains and Their Occurrence in Urinary Tract Infections in Women

    PubMed Central

    Lixandru, Brandusa; Cojocaru, Radu; Büke, Çağrı; Paramythiotou, Elisabeth; Angebault, Cécile; Visseaux, Claire; Djuikoue, Ingrid; Erdem, Esra; Burduniuc, Olga; El Mniai, Assiya; Marcel, Candice; Perrier, Marion; Kesteman, Thomas; Clermont, Olivier; Denamur, Erick; Armand-Lefèvre, Laurence; Andremont, Antoine

    2013-01-01

    Extended-spectrum-beta-lactamase (ESBL)-producing Escherichia coli (ESBL E. coli) strains are of major concern because few antibiotics remain active against these bacteria. We investigated the association between the fecal relative abundance (RA) of ESBL-producing E. coli (ESBL-RA) and the occurrence of ESBL E. coli urinary tract infections (UTIs). The first stool samples passed after suspicion of UTI from 310 women with subsequently confirmed E. coli UTIs were sampled and tested for ESBL-RA by culture on selective agar. Predictive values of ESBL-RA for ESBL E. coli UTI were analyzed for women who were not exposed to antibiotics when the stool was passed. ESBL E. coli isolates were characterized for ESBL type, phylogroup, relatedness, and virulence factors. The prevalence of ESBL E. coli fecal carriage was 20.3%, with ESBL E. coli UTIs being present in 12.3% of the women. The mean ESBL-RA (95% confidence interval [CI]) was 13-fold higher in women exposed to antibiotics at the time of sampling than in those not exposed (14.3% [range, 5.6% to 36.9%] versus 1.1% [range, 0.32% to 3.6%], respectively; P < 0.001) and 18-fold higher in women with ESBL E. coli UTI than in those with another E. coli UTI (10.0% [range, 0.54% to 100%] versus 0.56% [range, 0.15% to 2.1%[, respectively; P < 0.05). An ESBL-RA of <0.1% was 100% predictive of a non-ESBL E. coli UTI. ESBL type, phylogroup, relatedness, and virulence factors were not found to be associated with ESBL-RA. In conclusion, ESBL-RA was linked to the occurrence of ESBL E. coli UTI in women who were not exposed to antibiotics and who had the same clone of E. coli in urine samples and fecal samples. Especially, a low ESBL-RA appeared to be associated with a low risk of ESBL E. coli infection. PMID:23836184

  7. Relative Abundance and Plasmodium Infection Rates of Malaria Vectors in and around Jabalpur, a Malaria Endemic Region in Madhya Pradesh State, Central India

    PubMed Central

    Singh, Neeru; Mishra, Ashok K.; Chand, Sunil K.; Bharti, Praveen K.; Singh, Mrigendra P.; Nanda, Nutan; Singh, Om P.; Sodagiri, Kranti; Udhyakumar, Venkatachalam

    2015-01-01

    Background This study was undertaken in two Primary Health Centers (PHCs) of malaria endemic district Jabalpur in Madhya Pradesh (Central India). Methods In this study we had investigated the relative frequencies of the different anopheline species collected within the study areas by using indoor resting catches, CDC light trap and human landing methods. Sibling species of malaria vectors were identified by cytogenetic and molecular techniques. The role of each vector and its sibling species in the transmission of the different Plasmodium species was ascertained by using sporozoite ELISA. Results A total of 52,857 specimens comprising of 17 anopheline species were collected by three different methods (39,964 by indoor resting collections, 1059 by human landing and 11,834 by CDC light trap). Anopheles culicifacies was most predominant species in all collections (55, 71 and 32% in indoor resting, human landing and light trap collections respectively) followed by An. subpictus and An. annularis. All five sibling species of An. culicifacies viz. species A, B, C, D and E were found while only species T and S of An. fluviatilis were collected. The overall sporozoite rate in An. culicifacies and An. fluviatilis were 0.42% (0.25% for P. falciparum and 0.17% for P. vivax) and 0.90% (0.45% for P. falciparum and 0.45% for P. vivax) respectively. An. culicifacies and An. fluviatilis were found harbouring both P. vivax variants VK-210 and VK-247, and P. falciparum. An. culicifacies sibling species C and D were incriminated as vectors during most part of the year while sibling species T of An. fluviatilis was identified as potential vector in monsoon and post monsoon season. Conclusions An. culicifacies species C (59%) was the most abundant species followed by An. culicifacies D (24%), B (8.7%), E (6.7%) and A (1.5%). Among An. fluviatilis sibling species, species T was common (99%) and only few specimens of S were found. Our study provides crucial information on the prevalence

  8. Induction of ketosis in rats fed low-carbohydrate, high-fat diets depends on the relative abundance of dietary fat and protein.

    PubMed

    Bielohuby, Maximilian; Menhofer, Dominik; Kirchner, Henriette; Stoehr, Barbara J M; Müller, Timo D; Stock, Peggy; Hempel, Madlen; Stemmer, Kerstin; Pfluger, Paul T; Kienzle, Ellen; Christ, Bruno; Tschöp, Matthias H; Bidlingmaier, Martin

    2011-01-01

    Low-carbohydrate/high-fat diets (LC-HFDs) in rodent models have been implicated with both weight loss and as a therapeutic approach to treat neurological diseases. LC-HFDs are known to induce ketosis; however, systematic studies analyzing the impact of the macronutrient composition on ketosis induction and weight loss success are lacking. Male Wistar rats were pair-fed for 4 wk either a standard chow diet or one of three different LC-HFDs, whi