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Sample records for relative clonal abundance

  1. Clonal growth and plant species abundance

    PubMed Central

    Herben, Tomáš; Nováková, Zuzana; Klimešová, Jitka

    2014-01-01

    Background and Aims Both regional and local plant abundances are driven by species' dispersal capacities and their abilities to exploit new habitats and persist there. These processes are affected by clonal growth, which is difficult to evaluate and compare across large numbers of species. This study assessed the influence of clonal reproduction on local and regional abundances of a large set of species and compared the predictive power of morphologically defined traits of clonal growth with data on actual clonal growth from a botanical garden. The role of clonal growth was compared with the effects of seed reproduction, habitat requirements and growth, proxied both by LHS (leaf–height–seed) traits and by actual performance in the botanical garden. Methods Morphological parameters of clonal growth, actual clonal reproduction in the garden and LHS traits (leaf-specific area – height – seed mass) were used as predictors of species abundance, both regional (number of species records in the Czech Republic) and local (mean species cover in vegetation records) for 836 perennial herbaceous species. Species differences in habitat requirements were accounted for by classifying the dataset by habitat type and also by using Ellenberg indicator values as covariates. Key Results After habitat differences were accounted for, clonal growth parameters explained an important part of variation in species abundance, both at regional and at local levels. At both levels, both greater vegetative growth in cultivation and greater lateral expansion trait values were correlated with higher abundance. Seed reproduction had weaker effects, being positive at the regional level and negative at the local level. Conclusions Morphologically defined traits are predictive of species abundance, and it is concluded that simultaneous investigation of several such traits can help develop hypotheses on specific processes (e.g. avoidance of self-competition, support of offspring) potentially

  2. Wide Dispersion and Diversity of Clonally Related Inhibitory Interneurons

    PubMed Central

    Harwell, Corey C.; Fuentealba, Luis C.; Gonzalez-Cerrillo, Adrian; Parker, Phillip R.L.; Gertz, Caitlyn C.; Mazzola, Emanuele; Turrero Garcia, Miguel; Alvarez-Buylla, Arturo; Cepko, Constance L.; Kriegstein, Arnold

    2015-01-01

    The mammalian neocortex is composed of two major neuronal cell types with distinct origins: excitatory pyramidal neurons and inhibitory interneurons, generated in dorsal and ventral progenitor zones of the embryonic telencephalon respectively. Thus, inhibitory neurons migrate relatively long distances to reach their destination in the developing forebrain. The role of lineage in the organization and circuitry of interneurons is still not well understood. Utilizing a combination of genetics, retroviral fate mapping and lineage-specific retroviral barcode labeling, we find that clonally related interneurons can be widely dispersed while unrelated interneurons can be closely clustered. These data suggest that migratory mechanisms related to the clustering of interneurons occur largely independent of their clonal origin. PMID:26299474

  3. Wide Dispersion and Diversity of Clonally Related Inhibitory Interneurons.

    PubMed

    Harwell, Corey C; Fuentealba, Luis C; Gonzalez-Cerrillo, Adrian; Parker, Phillip R L; Gertz, Caitlyn C; Mazzola, Emanuele; Garcia, Miguel Turrero; Alvarez-Buylla, Arturo; Cepko, Constance L; Kriegstein, Arnold R

    2015-09-01

    The mammalian neocortex is composed of two major neuronal cell types with distinct origins: excitatory pyramidal neurons and inhibitory interneurons, generated in dorsal and ventral progenitor zones of the embryonic telencephalon, respectively. Thus, inhibitory neurons migrate relatively long distances to reach their destination in the developing forebrain. The role of lineage in the organization and circuitry of interneurons is still not well understood. Utilizing a combination of genetics, retroviral fate mapping, and lineage-specific retroviral barcode labeling, we find that clonally related interneurons can be widely dispersed while unrelated interneurons can be closely clustered. These data suggest that migratory mechanisms related to the clustering of interneurons occur largely independent of their clonal origin. PMID:26299474

  4. Clonally related uterine leiomyomas are common and display branched tumor evolution.

    PubMed

    Mehine, Miika; Heinonen, Hanna-Riikka; Sarvilinna, Nanna; Pitkänen, Esa; Mäkinen, Netta; Katainen, Riku; Tuupanen, Sari; Bützow, Ralf; Sjöberg, Jari; Aaltonen, Lauri A

    2015-08-01

    Uterine leiomyomas are extremely frequent benign smooth muscle tumors often presenting as multiple concurrent lesions and causing symptoms such as abnormal menstrual bleeding, abdominal pain and infertility. While most leiomyomas are believed to arise independently, a few studies have encountered separate lesions harboring identical genetic changes, suggesting a common clonal origin. To investigate the frequency of clonally related leiomyomas, genome-wide tools need to be utilized, and thus little is known about this phenomenon. Using MED12 sequencing and SNP arrays, we searched for clonally related uterine leiomyomas in a set of 103 tumors from 14 consecutive patients who entered hysterectomy owing to symptomatic lesions. Whole-genome sequencing was also utilized to study the genomic architecture of clonally related tumors. This revealed four patients to have two or more tumors that were clonally related, all of which lacked MED12 mutations. Furthermore, some tumors were composed of genetically distinct subclones, indicating a nonlinear, branched model of tumor evolution. DEPDC5 was discovered as a novel tumor suppressor gene playing a role in the progression of uterine leiomyomas. Perhaps counterintuitively—considering Knudson's two-hit hypothesis—a large shared deletion was followed by different truncating DEPDC5 mutations in four clonally related leiomyomas. This study provides insight into the intratumor heterogeneity of these tumors and suggests that a shared clonal origin is a common feature of leiomyomas that do not carry an MED12 mutation. These observations also offer one explanation to the common occurrence of multiple concurrent lesions. PMID:25964426

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

    USGS Publications Warehouse

    Forester, R.M.

    1977-01-01

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

  6. Clonal diversity and estimation of relative clone age: application to agrobiodiversity of yam (Dioscorea rotundata)

    PubMed Central

    2013-01-01

    Background Clonal propagation is a particular reproductive system found in both the plant and animal kingdoms, from human parasites to clonally propagated crops. Clonal diversity provides information about plant and animal evolutionary history, i.e. how clones spread, or the age of a particular clone. In plants, this could provide valuable information about agrobiodiversity dynamics and more broadly about the evolutionary history of a particular crop. We studied the evolutionary history of yam, Dioscorea rotundata. In Africa, Yam is cultivated by tuber clonal propagation. Results We used 12 microsatellite markers to identify intra-clonal diversity in yam varieties. We then used this diversity to assess the relative ages of clones. Using simulations, we assessed how Approximate Bayesian Computation could use clonal diversity to estimate the age of a clone depending on the size of the sample, the number of independent samples and the number of markers. We then applied this approach to our particular dataset and showed that the relative ages of varieties could be estimated, and that each variety could be ranked by age. Conclusions We give a first estimation of clone age in an approximate Bayesian framework. However the precise estimation of clone age depends on the precision of the mutation rate. We provide useful information on agrobiodiversity dynamics and suggest recurrent creation of varietal diversity in a clonally propagated crop. PMID:24219837

  7. Long-term in vitro maintenance of clonal abundance and leukaemia-initiating potential in acute lymphoblastic leukaemia

    PubMed Central

    Pal, D; Blair, H J; Elder, A; Dormon, K; Rennie, K J; Coleman, D J L; Weiland, J; Rankin, K S; Filby, A; Heidenreich, O; Vormoor, J

    2016-01-01

    Lack of suitable in vitro culture conditions for primary acute lymphoblastic leukaemia (ALL) cells severely impairs their experimental accessibility and the testing of new drugs on cell material reflecting clonal heterogeneity in patients. We show that Nestin-positive human mesenchymal stem cells (MSCs) support expansion of a range of biologically and clinically distinct patient-derived ALL samples. Adherent ALL cells showed an increased accumulation in the S phase of the cell cycle and diminished apoptosis when compared with cells in the suspension fraction. Moreover, surface expression of adhesion molecules CD34, CDH2 and CD10 increased several fold. Approximately 20% of the ALL cells were in G0 phase of the cell cycle, suggesting that MSCs may support quiescent ALL cells. Cellular barcoding demonstrated long-term preservation of clonal abundance. Expansion of ALL cells for >3 months compromised neither feeder dependence nor cancer initiating ability as judged by their engraftment potential in immunocompromised mice. Finally, we demonstrate the suitability of this co-culture approach for the investigation of drug combinations with luciferase-expressing primograft ALL cells. Taken together, we have developed a preclinical platform with patient-derived material that will facilitate the development of clinically effective combination therapies for ALL. PMID:27109511

  8. Relative Abundance Measurements in Plumes and Interplumes

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

    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.

  9. Synchrony of clonal cell proliferation and contiguity of clonally related cells: production of mosaicism in the ventricular zone of developing mouse neocortex

    NASA Technical Reports Server (NTRS)

    Cai, L.; Hayes, N. L.; Nowakowski, R. S.

    1997-01-01

    We have analyzed clonal cell proliferation in the ventricular zone (VZ) of the early developing mouse neocortex with a replication-incompetent retrovirus encoding human placental alkaline phosphatase (AP). The retrovirus was injected into the lateral ventricles on embryonic day 11 (E11), i.e., at the onset of neuronogenesis. Three days postinjection, on E14, a total of 259 AP-labeled clones of various sizes were found in 7 fetal brains. There are approximately 7 cell cycles between E11 and E14 (), and there is a 1-2 cell cycle delay between retroviral injection and the production of a retrovirally labeled "founder" cell; thus, we estimate that the "age" of the clones was about 5-6 cell cycles. Almost one-half of the clones (48.3%) identified were pure proliferating clones containing cells only in the VZ. Another 18.5% contained both proliferating and postproliferative cells, and 33.2% contained only postproliferative cells. It was striking that over 90% of the clonally related proliferating cells occurred in clusters of two or more apparently contiguous cells, and about 73% of the proliferating cells occurred in clusters of three or more cells. Regardless of the number of cells in the clone, these clusters were tightly packed and confined to a single level of the VZ. This clustering of proliferating cells indicates that clonally related cells maintain neighbor-neighbor relationships as they undergo interkinetic nuclear migration and progress through several cell cycles, and, as a result, the ventricular zone is a mosaic of small clusters of clonally related and synchronously cycling cells. In addition, cells in the intermediate zone and the cortical plate were also frequently clustered, indicating that they became postproliferative at a similar time and that the output of the VZ is influenced by its mosaic structure.

  10. Cell migration leads to spatially distinct but clonally related airway cancer precursors

    PubMed Central

    Pipinikas, Christodoulos P; Kiropoulos, Theodoros S; Teixeira, Vitor H; Brown, James M; Varanou, Aikaterini; Falzon, Mary; Capitanio, Arrigo; Bottoms, Steven E; Carroll, Bernadette; Navani, Neal; McCaughan, Frank; George, Jeremy P; Giangreco, Adam; Wright, Nicholas A; McDonald, Stuart A C; Graham, Trevor A; Janes, Sam M

    2014-01-01

    Background Squamous cell carcinoma of the lung is a common cancer with 95% mortality at 5 years. These cancers arise from preinvasive lesions, which have a natural history of development progressing through increasing severity of dysplasia to carcinoma in situ (CIS), and in some cases, ending in transformation to invasive carcinoma. Synchronous preinvasive lesions identified at autopsy have been previously shown to be clonally related. Methods Using autofluorescence bronchoscopy that allows visual observation of preinvasive lesions within the upper airways, together with molecular profiling of biopsies using gene sequencing and loss-of-heterozygosity analysis from both preinvasive lesions and from intervening normal tissue, we have monitored individual lesions longitudinally and documented their visual, histological and molecular relationship. Results We demonstrate that rather than forming a contiguous field of abnormal tissue, clonal CIS lesions can develop at multiple anatomically discrete sites over time. Further, we demonstrate that patients with CIS in the trachea have invariably had previous lesions that have migrated proximally, and in one case, into the other lung over a period of 12 years. Conclusions Molecular information from these unique biopsies provides for the first time evidence that field cancerisation of the upper airways can occur through cell migration rather than via local contiguous cellular expansion as previously thought. Our findings urge a clinical strategy of ablating high-grade premalignant airway lesions with subsequent attentive surveillance for recurrence in the bronchial tree. PMID:24550057

  11. 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...

  12. 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...

  13. Investigating the Relation between Stochastic Differentiation, Homeostasis and Clonal Expansion in Intestinal Crypts via Multiscale Modeling

    PubMed Central

    De Matteis, Giovanni; Antoniotti, Marco

    2014-01-01

    Colorectal tumors originate and develop within intestinal crypts. Even though some of the essential phenomena that characterize crypt structure and dynamics have been effectively described in the past, the relation between the differentiation process and the overall crypt homeostasis is still only partially understood. We here investigate this relation and other important biological phenomena by introducing a novel multiscale model that combines a morphological description of the crypt with a gene regulation model: the emergent dynamical behavior of the underlying gene regulatory network drives cell growth and differentiation processes, linking the two distinct spatio-temporal levels. The model relies on a few a priori assumptions, yet accounting for several key processes related to crypt functioning, such as: dynamic gene activation patterns, stochastic differentiation, signaling pathways ruling cell adhesion properties, cell displacement, cell growth, mitosis, apoptosis and the presence of biological noise. We show that this modeling approach captures the major dynamical phenomena that characterize the regular physiology of crypts, such as cell sorting, coordinate migration, dynamic turnover, stem cell niche correct positioning and clonal expansion. All in all, the model suggests that the process of stochastic differentiation might be sufficient to drive the crypt to homeostasis, under certain crypt configurations. Besides, our approach allows to make precise quantitative inferences that, when possible, were matched to the current biological knowledge and it permits to investigate the role of gene-level perturbations, with reference to cancer development. We also remark the theoretical framework is general and may be applied to different tissues, organs or organisms. PMID:24869488

  14. Industry view on the relative importance of "clonality" of biopharmaceutical-producing cell lines.

    PubMed

    Frye, Christopher; Deshpande, Rohini; Estes, Scott; Francissen, Kathy; Joly, John; Lubiniecki, Anthony; Munro, Trent; Russell, Reb; Wang, Tongtong; Anderson, Karin

    2016-03-01

    Recently, several health authorities have requested substantial detail from sponsor firms regarding the practices employed to generate the production cell line for recombinant DNA-(rDNA) derived biopharmaceuticals. Two possible inferences from these regulatory agency questions are that (1) assurance of "clonality" of the production cell line is of major importance to assessing the safety and efficacy of the product and (2), without adequate proof of "clonality", additional studies of the cell line and product are often required to further ensure the product's purity and homogeneity. Here we address the topic of "clonality" in the broader context of product quality assurance by current technologies and practices, as well as discuss some of the relevant science and historical perspective. We agree that the clonal derivation of a production cell line is one factor with potential impact, but it is only one of many factors. Further, we believe that regulatory emphasis should be primarily placed on ensuring product quality of the material actually administered to patients, and on ensuring process consistency and implementing appropriate control strategies through the life cycle of the products. PMID:26852257

  15. Relative resource abundance explains butterfly biodiversity in island communities

    PubMed Central

    Yamamoto, Naoaki; Yokoyama, Jun; Kawata, Masakado

    2007-01-01

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

  16. 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.

  17. Estimating relative abundances of proteins from shotgun proteomics data

    PubMed Central

    2012-01-01

    Background Spectral counting methods provide an easy means of identifying proteins with differing abundances between complex mixtures using shotgun proteomics data. The crux spectral-counts command, implemented as part of the Crux software toolkit, implements four previously reported spectral counting methods, the spectral index (SIN), the exponentially modified protein abundance index (emPAI), the normalized spectral abundance factor (NSAF), and the distributed normalized spectral abundance factor (dNSAF). Results We compared the reproducibility and the linearity relative to each protein’s abundance of the four spectral counting metrics. Our analysis suggests that NSAF yields the most reproducible counts across technical and biological replicates, and both SIN and NSAF achieve the best linearity. Conclusions With the crux spectral-counts command, Crux provides open-source modular methods to analyze mass spectrometry data for identifying and now quantifying peptides and proteins. The C++ source code, compiled binaries, spectra and sequence databases are available at http://noble.gs.washington.edu/proj/crux-spectral-counts. PMID:23164367

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

    PubMed

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

    2016-06-01

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

  19. Divergent modes of clonal spread and intraperitoneal mixing in high-grade serous ovarian cancer.

    PubMed

    McPherson, Andrew; Roth, Andrew; Laks, Emma; Masud, Tehmina; Bashashati, Ali; Zhang, Allen W; Ha, Gavin; Biele, Justina; Yap, Damian; Wan, Adrian; Prentice, Leah M; Khattra, Jaswinder; Smith, Maia A; Nielsen, Cydney B; Mullaly, Sarah C; Kalloger, Steve; Karnezis, Anthony; Shumansky, Karey; Siu, Celia; Rosner, Jamie; Chan, Hector Li; Ho, Julie; Melnyk, Nataliya; Senz, Janine; Yang, Winnie; Moore, Richard; Mungall, Andrew J; Marra, Marco A; Bouchard-Côté, Alexandre; Gilks, C Blake; Huntsman, David G; McAlpine, Jessica N; Aparicio, Samuel; Shah, Sohrab P

    2016-07-01

    We performed phylogenetic analysis of high-grade serous ovarian cancers (68 samples from seven patients), identifying constituent clones and quantifying their relative abundances at multiple intraperitoneal sites. Through whole-genome and single-nucleus sequencing, we identified evolutionary features including mutation loss, convergence of the structural genome and temporal activation of mutational processes that patterned clonal progression. We then determined the precise clonal mixtures comprising each tumor sample. The majority of sites were clonally pure or composed of clones from a single phylogenetic clade. However, each patient contained at least one site composed of polyphyletic clones. Five patients exhibited monoclonal and unidirectional seeding from the ovary to intraperitoneal sites, and two patients demonstrated polyclonal spread and reseeding. Our findings indicate that at least two distinct modes of intraperitoneal spread operate in clonal dissemination and highlight the distribution of migratory potential over clonal populations comprising high-grade serous ovarian cancers. PMID:27182968

  20. Clonal reproduction in fungi

    PubMed Central

    Taylor, John W.; Hann-Soden, Christopher; Branco, Sara; Sylvain, Iman; Ellison, Christopher E.

    2015-01-01

    Research over the past two decades shows that both recombination and clonality are likely to contribute to the reproduction of all fungi. This view of fungi is different from the historical and still commonly held view that a large fraction of fungi are exclusively clonal and that some fungi have been exclusively clonal for hundreds of millions of years. Here, we first will consider how these two historical views have changed. Then we will examine the impact on fungal research of the concept of restrained recombination [Tibayrenc M, Ayala FJ (2012) Proc Natl Acad Sci USA 109 (48):E3305–E3313]. Using animal and human pathogenic fungi, we examine extrinsic restraints on recombination associated with bottlenecks in genetic variation caused by geographic dispersal and extrinsic restraints caused by shifts in reproductive mode associated with either disease transmission or hybridization. Using species of the model yeast Saccharomyces and the model filamentous fungus Neurospora, we examine intrinsic restraints on recombination associated with mating systems that range from strictly clonal at one extreme to fully outbreeding at the other and those that lie between, including selfing and inbreeding. We also consider the effect of nomenclature on perception of reproductive mode and a means of comparing the relative impact of clonality and recombination on fungal populations. Last, we consider a recent hypothesis suggesting that fungi thought to have the most severe intrinsic constraints on recombination actually may have the fewest. PMID:26195774

  1. Dissemination of clonally related multidrug-resistant Klebsiella pneumoniae in Ireland.

    PubMed

    Morris, D; O'Connor, M; Izdebski, R; Corcoran, M; Ludden, C E; McGrath, E; Buckley, V; Cryan, B; Gniadkowski, M; Cormican, M

    2016-01-01

    In October 2012, an outbreak of gentamicin-resistant, ciprofloxacin non-susceptible extended-spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae occurred in a neonatal intensive care unit in Ireland. In order to determine whether the outbreak strain was more widely dispersed in the country, 137 isolates of K. pneumoniae with this resistance phenotype collected from 17 hospitals throughout Ireland between January 2011 and July 2013 were examined. ESBL production was confirmed phenotypically and all isolates were screened for susceptibility to 19 antimicrobial agents and for the presence of genes encoding bla TEM, bla SHV, bla OXA, and bla CTX-M; 22 isolates were also screened for bla KPC, bla NDM, bla VIM, bla IMP and bla OXA-48 genes. All isolates harboured bla SHV and bla CTX-M and were resistant to ciprofloxacin, gentamicin, nalidixic acid, amoxicillin-clavulanate, and cefpodoxime; 15 were resistant to ertapenem, seven to meropenem and five isolates were confirmed as carbapenemase producers. Pulsed-field gel electrophoresis of all isolates identified 16 major clusters, with two clusters comprising 61% of the entire collection. Multilocus sequence typing of a subset of these isolates identified a novel type, ST1236, a single locus variant of ST48. Data suggest that two major clonal groups, ST1236/ST48 (CG43) and ST15/ST14 (CG15) have been circulating in Ireland since at least January 2011. PMID:26113052

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

    PubMed Central

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

    2015-01-01

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

  3. Clonal Characteristics of Circulating B Lymphocyte Repertoire in Primary Biliary Cholangitis.

    PubMed

    Tan, Yan-Guo; Wang, Yu-Qi; Zhang, Ming; Han, Ying-Xin; Huang, Chun-Yang; Zhang, Hai-Ping; Li, Zhuo-Min; Wu, Xiao-Lei; Wang, Xiao-Feng; Dong, Yan; Zhu, Hong-Mei; Zhu, Shi-da; Li, Hong-Mei; Li, Ning; Yan, Hui-Ping; Gao, Zu-Hua

    2016-09-01

    Primary biliary cholangitis (PBC) is an autoimmune liver disease characterized by elevated serum anti-mitochondrial Ab and lymphocyte-mediated bile duct damage. This study was designed to reveal the clonal characteristics of B lymphocyte repertoire in patients with PBC to facilitate better understanding of its pathogenesis and better management of these patients. Using high-throughput sequencing of Ig genes, we analyzed the repertoire of circulating B lymphocytes in 43 patients with PBC, and 34 age- and gender-matched healthy controls. Compared with healthy controls, PBC patients showed 1) a gain of 14 new clones and a loss of 8 clones; 2) a significant clonal expansion and increased relative IgM abundance, which corresponded with the elevated serum IgM level; 3) a significant reduction of clonal diversity and somatic hypermutations in class-switched sequences, which suggested a general immunocompromised status; 4) the reduction of clonal diversity and enhancement of clonal expansion were more obvious at the cirrhotic stage; and 5) treatment with ursodeoxycholic acid could increase the clonal diversity and reduce clonal expansion of the IgM repertoire, with no obvious effect on the somatic hypermutation level. Our data suggest that PBC is a complex autoimmune disease process with evidence of B lymphocyte clonal gains and losses, Ag-dependent ogligoclonal expansion, and a generally compromised immune reserve. This new insight into the pathogenesis of PBC opens up the prospect of studying disease-relevant B cells to better diagnose and treat this devastating disease. PMID:27430717

  4. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2008-05-01

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

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

    PubMed Central

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

    2012-01-01

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

  7. 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.

  8. Antibody arrays for determination of relative protein abundances.

    PubMed

    Chaga, Grigoriy S

    2008-01-01

    As a large number of genome-sequencing projects reached completion, the attention of the scientific community is turning toward understanding the structure-functions of gene translation products-the proteins as well as the complete complement of proteins-the proteome. One goal of proteomics is to correlate changes in protein abundance with biological processes and disease states. To help accelerate this avenue of proteomics, a significant effort has been devoted to the development of multiplexed methods for protein analyses. We have developed an Antibody Microarray, a chip-based technology for multiparallel determination of relative abundance of hundreds of proteins. The Antibody Microarray is composed of hundreds of distinct monoclonal antibodies printed at high density on a glass slide. It utilizes a novel experimental setup and data analysis algorithm, which enables scientists to assay hundreds of cytosolic, nuclear, and membrane-bound proteins with a single experiment. Examples of biological samples that are analyzed on the Antibody Microarray include tissue samples, cell cultures, and body fluids. PMID:18370316

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

    USGS Publications Warehouse

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

    2016-01-01

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

  10. Patterns of relative species abundance in rainforests and coral reefs.

    PubMed

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

    2007-11-01

    A formidable many-body problem in ecology is to understand the complex of factors controlling patterns of relative species abundance (RSA) in communities of interacting species. Unlike many problems in physics, the nature of the interactions in ecological communities is not completely known. Although most contemporary theories in ecology start with the basic premise that species interact, here we show that a theory in which all interspecific interactions are turned off leads to analytical results that are in agreement with RSA data from tropical forests and coral reefs. The assumption of non-interacting species leads to a sampling theory for the RSA that yields a simple approximation at large scales to the exact theory. Our results show that one can make significant theoretical progress in ecology by assuming that the effective interactions among species are weak in the stationary states in species-rich communities such as tropical forests and coral reefs. PMID:17972874

  11. 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.

  12. 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

  13. PCR techniques for clonality assays.

    PubMed

    Diaz-Cano, S J; Blanes, A; Wolfe, H J

    2001-03-01

    Clonal overgrowths represent the hallmark of neoplastic proliferations, and their demonstration has been proved useful clinically for the diagnosis of malignant lymphomas based on the detection of specific and dominant immunoglobulin and/or T-cell receptor gene rearrangements. Nonrandom genetic alterations can also be used to test clonal expansions and the clonal evolution of neoplasms, especially analyzing hypervariable deoxyribonucleic acid (DNA) regions from patients heterozygous for a given marker. These tests rely basically on the demonstration of loss of heterozygosity (LOH) resulting from either hemizygosity (nonrandom interstitial DNA deletions) or homozygosity of mutant alleles observed in neoplasms. LOH analyses identify clonal expansions of a tumor cell population, and point to monoclonal proliferation when multiple and consistent LOH are demonstrated. Based on the methylation-related inactivation of one X chromosome in female subjects, X-linked markers (e.g., androgen receptor gene) will provide clonality information using LOH analyses after DNA digestion with methylation-sensitive restriction endonucleases. Therefore, both non-X-linked and X-linked analyses give complementary information, related and not related to the malignant transformation pathway respectively. Applied appropriately, these tools can establish the clonal evolution of tumor cell populations (tumor heterogeneity), identify early relapses, distinguish recurrent tumors from other metachronic neoplasms, and differentiate field transformation from metastatic tumor growths in synchronic and histologically identical neoplasms. PMID:11277392

  14. Neutral theory and relative species abundance in ecology

    NASA Astrophysics Data System (ADS)

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

    2003-08-01

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

  15. Clonal Expansion of Staphylococcus epidermidis Strains Causing Hickman Catheter-Related Infections in a Hemato-Oncologic Department

    PubMed Central

    Nouwen, Jan L.; van Belkum, Alex; de Marie, Siem; Sluijs, Jacqueline; Wielenga, Jenne J.; Kluytmans, Jan A. J. W.; Verbrugh, Henri A.

    1998-01-01

    The detailed analysis of 411 strains of coagulase-negative staphylococci (CoNS) obtained from 40 neutropenic hemato-oncologic patients (61 Hickman catheter episodes) on intensive chemotherapy is described. By random amplification of polymorphic DNA (RAPD) analysis, a total of 88 different genotypes were detected: 51 in air samples and 30 in skin cultures prior to insertion, 12 in blood cultures after insertion, and only 5 involved in catheter-related infections (CRI). Two RAPD genotypes of Staphylococcus epidermidis predominated, and their prevalence increased during patient hospitalization. At insertion, these clones constituted 11 of 86 (13%) CoNS isolated from air samples and 33 of 75 (44%) CoNS isolated from skin cultures. After insertion, their combined prevalence increased to 33 of 62 (53%) in catheters not associated with CRI and 139 of 188 (74%) in catheters associated with CRI (P = 0.0041). These two predominant S. epidermidis clones gave rise to a very high incidence of CRI (6.0 per 1,000 catheter days) and a very high catheter removal rate for CRI, 70%, despite prompt treatment with vancomycin. A likely source of S. epidermidis strains involved in CRI appeared to be the skin flora in 75% of cases. The validity of these observations was confirmed by pulsed-field gel electrophoresis (PFGE) of SmaI DNA macrorestriction fragments of blood culture CoNS isolates. Again, two predominant CoNS genotypes were found (combined prevalence, 60%). RAPD and PFGE yielded concordant results in 75% of cases. Retrospectively, the same two predominant CoNS clones were also found among blood culture CoNS isolates from the same hematology department in the period 1991 to 1993 (combined prevalence, 42%) but not in the period 1978 to 1982. These observations underscore the pathogenic potential of clonal CoNS types that have successfully and persistently colonized patients in this hemato-oncology department. PMID:9705416

  16. Ecological Consequences of Clonal Integration in Plants

    PubMed Central

    Liu, Fenghong; Liu, Jian; Dong, Ming

    2016-01-01

    Clonal plants are widespread throughout the plant kingdom and dominate in diverse habitats. Spatiotemporal heterogeneity of environment is pervasive at multiple scales, even at scales relevant to individual plants. Clonal integration refers to resource translocation and information communication among the ramets of clonal plants. Due to clonal integration, clonal plant species possess a series of peculiar attributes: plasticity in response to local and non-local conditions, labor division with organ specialization for acquiring locally abundant resources, foraging behavior by selective placement of ramets in resource-rich microhabitats, and avoidance of intraclonal competition. Clonal integration has very profound ecological consequences for clonal plants. It allows them to efficiently cope with environmental heterogeneity, by alleviating local resource shortages, buffering environmental stresses and disturbances, influencing competitive ability, increasing invasiveness, and altering species composition and invasibility at the community level. In this paper, we present a comprehensive review of research on the ecological consequences of plant clonal integration based on a large body of literature. We also attempt to propose perspectives for future research. PMID:27446093

  17. The Relative Importance of Genetic Diversity and Phenotypic Plasticity in Determining Invasion Success of a Clonal Weed in the USA and China

    PubMed Central

    Geng, Yupeng; van Klinken, Rieks D.; Sosa, Alejandro; Li, Bo; Chen, Jiakuan; Xu, Cheng-Yuan

    2016-01-01

    Phenotypic plasticity has been proposed as an important adaptive strategy for clonal plants in heterogeneous habitats. Increased phenotypic plasticity can be especially beneficial for invasive clonal plants, allowing them to colonize new environments even when genetic diversity is low. However, the relative importance of genetic diversity and phenotypic plasticity for invasion success remains largely unknown. Here, we performed molecular marker analyses and a common garden experiment to investigate the genetic diversity and phenotypic plasticity of the globally important weed Alternanthera philoxeroides in response to different water availability (terrestrial vs. aquatic habitats). This species relies predominantly on clonal propagation in introduced ranges. We therefore expected genetic diversity to be restricted in the two sampled introduced ranges (the USA and China) when compared to the native range (Argentina), but that phenotypic plasticity may allow the species' full niche range to nonetheless be exploited. We found clones from China had very low genetic diversity in terms of both marker diversity and quantitative variation when compared with those from the USA and Argentina, probably reflecting different introduction histories. In contrast, similar patterns of phenotypic plasticity were found for clones from all three regions. Furthermore, despite the different levels of genetic diversity, bioclimatic modeling suggested that the full potential bioclimatic distribution had been invaded in both China and USA. Phenotypic plasticity, not genetic diversity, was therefore critical in allowing A. philoxeroides to invade diverse habitats across broad geographic areas. PMID:26941769

  18. The Relative Importance of Genetic Diversity and Phenotypic Plasticity in Determining Invasion Success of a Clonal Weed in the USA and China.

    PubMed

    Geng, Yupeng; van Klinken, Rieks D; Sosa, Alejandro; Li, Bo; Chen, Jiakuan; Xu, Cheng-Yuan

    2016-01-01

    Phenotypic plasticity has been proposed as an important adaptive strategy for clonal plants in heterogeneous habitats. Increased phenotypic plasticity can be especially beneficial for invasive clonal plants, allowing them to colonize new environments even when genetic diversity is low. However, the relative importance of genetic diversity and phenotypic plasticity for invasion success remains largely unknown. Here, we performed molecular marker analyses and a common garden experiment to investigate the genetic diversity and phenotypic plasticity of the globally important weed Alternanthera philoxeroides in response to different water availability (terrestrial vs. aquatic habitats). This species relies predominantly on clonal propagation in introduced ranges. We therefore expected genetic diversity to be restricted in the two sampled introduced ranges (the USA and China) when compared to the native range (Argentina), but that phenotypic plasticity may allow the species' full niche range to nonetheless be exploited. We found clones from China had very low genetic diversity in terms of both marker diversity and quantitative variation when compared with those from the USA and Argentina, probably reflecting different introduction histories. In contrast, similar patterns of phenotypic plasticity were found for clones from all three regions. Furthermore, despite the different levels of genetic diversity, bioclimatic modeling suggested that the full potential bioclimatic distribution had been invaded in both China and USA. Phenotypic plasticity, not genetic diversity, was therefore critical in allowing A. philoxeroides to invade diverse habitats across broad geographic areas. PMID:26941769

  19. Clonal Integration Enhances the Performance of a Clonal Plant Species under Soil Alkalinity Stress

    PubMed Central

    Sun, Juanjuan; Chen, Jishan; Zhang, Yingjun

    2015-01-01

    Clonal plants have been shown to successfully survive in stressful environments, including salinity stress, drought and depleted nutrients through clonal integration between original and subsequent ramets. However, relatively little is known about whether clonal integration can enhance the performance of clonal plants under alkalinity stress. We investigated the effect of clonal integration on the performance of a typical rhizomatous clonal plant, Leymus chinensis, using a factorial experimental design with four levels of alkalinity and two levels of rhizome connection treatments, connected (allowing integration) and severed (preventing integration). Clonal integration was estimated by comparing physiological and biomass features between the rhizome-connected and rhizome-severed treatments. We found that rhizome-connected treatment increased the biomass, height and leaf water potential of subsequent ramets at highly alkalinity treatments but did not affect them at low alkalinity treatments. However, rhizome-connected treatment decreased the root biomass of subsequent ramets and did not influence the photosynthetic rates of subsequent ramets. The biomass of original ramets was reduced by rhizome-connected treatment at the highest alkalinity level. These results suggest that clonal integration can increase the performance of clonal plants under alkalinity stress. Rhizome-connected plants showed dramatically increased survival of buds with negative effects on root weight, indicating that clonal integration influenced the resource allocation pattern of clonal plants. A cost-benefit analysis based on biomass measures showed that original and subsequent ramets significantly benefited from clonal integration in highly alkalinity stress, indicating that clonal integration is an important adaptive strategy by which clonal plants could survive in local alkalinity soil. PMID:25790352

  20. How clonal are bacteria over time?

    PubMed

    Shapiro, B Jesse

    2016-06-01

    Bacteria and archaea reproduce clonally (vertical descent), but exchange genes by recombination (horizontal transfer). Recombination allows adaptive mutations or genes to spread rapidly within (or even between) species, and reduces the burden of deleterious mutations. Clonality-defined here as the balance between vertical and horizontal inheritance-is therefore a key microbial trait, determining how quickly a population can adapt and the size of its gene pool. Here, I discuss whether clonality varies over time and if it can be considered a stable trait of a given population. I show that, in some cases, clonality is clearly not static. For example, non-clonal (highly recombining) populations can give rise to clonal expansions, often of pathogens. However, an analysis of time-course metagenomic data from a lake suggests that a bacterial population's past clonality (as measured by its genetic diversity) is a good predictor of its future clonality. Clonality therefore appears to be relatively-but not completely-stable over evolutionary time. PMID:27057964

  1. [Fitness analysis of seed- and vegetative reproduction of clonal tree Symplocos laurina].

    PubMed

    Zhang, Yunchun; Du, Xiaojun; Zhang, Qiaoying; Gao, Xianming; Su, Zhixian

    2005-09-01

    There are two ways in Symplocos laurina propagation, clonal and sexual reproduction. The study showed that under different habitat conditions, Symplocos laurina could adopt different ways to propagate and occupy space. In conditions with abundant water and nutrient resources, such as in evergreen broad-leaved forests or bamboo forests, the survival rate and space-occupying ability of both ramets and sexual seedlings were relatively high, with clonal ramets took advantage in terms of number and space, suggesting that clonal propagation was the dominant way in such environments. Oppositely, in habitats lack of sufficient nutrition, the survival rate and space-occupying ability of seedlings were low, and grown-up plantlets would preempt in number and space occupation. Bottleneck in sexual propagation appeared in the stage from seed to seedling, while clonal propagation appeared during the period from seedling to ramet. The way of Symplocos laurina invasion was to settle a plantlet, and then occupied the space rapidly by clonal growth, with clonal seedlings dominated in initial stage and lost the advantage after 15 ages. PMID:16355784

  2. 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

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

    NASA Technical Reports Server (NTRS)

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

    1974-01-01

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

  4. 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. Clonally related methicillin-resistant Staphylococcus aureus isolated from short-finned pilot whales (Globicephala macrorhynchus), human volunteers, and a bayfront cetacean rehabilitation facility.

    PubMed

    Hower, Suzanne; Phillips, Matthew C; Brodsky, Micah; Dameron, Adrienne; Tamargo, Manuel A; Salazar, Norma C; Jackson, Charlene R; Barrett, John B; Davidson, Maureen; Davis, Johnnie; Mukherjee, Sampa; Ewing, Ruth Y; Gidley, Maribeth L; Sinigalliano, Christopher D; Johns, Lisa; Johnson, Frank E; Adebanjo, Olufunmilola; Plano, Lisa R W

    2013-05-01

    In May of 2011, a live mass stranding of 26 short-finned pilot whales (Globicephala macrorhynchus) occurred in the lower Florida Keys. Five surviving whales were transferred from the original stranding site to a nearby marine mammal rehabilitation facility where they were constantly attended to by a team of volunteers. Bacteria cultured during the routine clinical care of the whales and necropsy of a deceased whale included methicillin-sensitive and methicillin-resistant Staphylococcus aureus (MSSA and MRSA). In order to investigate potential sources or reservoirs of MSSA and MRSA, samples were obtained from human volunteers, whales, seawater, and sand from multiple sites at the facility, nearby recreational beaches, and a canal. Samples were collected on 3 days. The second collection day was 2 weeks after the first, and the third collection day was 2 months after the last animal was removed from the facility. MRSA and MSSA were isolated on each day from the facility when animals and volunteers were present. MSSA was found at an adjacent beach on all three collection days. Isolates were characterized by utilizing a combination of quantitative real-time PCR to determine the presence of mecA and genes associated with virulence, staphylococcal protein A typing, staphylococcal cassette chromosome mec typing, multilocus sequence typing, and pulsed field gel electrophoresis (PFGE). Using these methods, clonally related MRSA were isolated from multiple environmental locations as well as from humans and animals. Non-identical but genetically similar MSSA and MRSA were also identified from distinct sources within this sample pool. PFGE indicated that the majority of MRSA isolates were clonally related to the prototype human strain USA300. These studies support the notion that S. aureus may be shed into an environment by humans or pilot whales and subsequently colonize or infect exposed new hosts. PMID:23508733

  7. A Predominant Multidrug-Resistant Salmonella enterica Serovar Saintpaul Clonal Line in German Turkey and Related Food Products▿

    PubMed Central

    Beutlich, Janine; Rodríguez, Irene; Schroeter, Andreas; Käsbohrer, Annemarie; Helmuth, Reiner; Guerra, Beatriz

    2010-01-01

    Recently, Salmonella enterica subsp. enterica serovar Saintpaul has increasingly been observed in several countries, including Germany. However, the pathogenic potential and epidemiology of this serovar are not very well known. This study describes biological attributes of S. Saintpaul isolates obtained from turkeys in Germany based on characterization of their pheno- and genotypic properties. Fifty-five S. Saintpaul isolates from German turkeys and turkey-derived food products isolated from 2000 to 2007 were analyzed by using antimicrobial agent, organic solvent, and disinfectant susceptibility tests, isoelectric focusing, detection of resistance determinants, plasmid profiling, pulsed-field gel electrophoresis (PFGE), and hybridization experiments. These isolates were compared to an outgroup consisting of 24 S. Saintpaul isolates obtained from humans and chickens in Germany and from poultry and poultry products (including turkeys) in Netherlands. A common core resistance pattern was detected for 27 German turkey and turkey product isolates. This pattern included resistance (full or intermediate) to ampicillin, amoxicillin-clavulanic acid, gentamicin, kanamycin, nalidixic acid, streptomycin, spectinomycin, and sulfamethoxazole and intermediate resistance or decreased susceptibility to ciprofloxacin (MIC, 2 or 1 μg/ml, respectively) and several third-generation cephalosporins (including ceftiofur and cefoxitin [MIC, 4 to 2 and 16 to 2 μg/ml, respectively]). These isolates had the same core resistance genotype, with blaTEM-1, aadB, aadA2, sul1, a Ser83→Glu83 mutation in the gyrA gene, and a chromosomal class 1 integron carrying the aadB-aadA2 gene cassette. Their XbaI, BlnI, and combined XbaI-BlnI PFGE patterns revealed levels of genetic similarity of 93, 75, and 90%, respectively. This study revealed that a multiresistant S. Saintpaul clonal line is widespread in turkeys and turkey products in Germany and was also detected among German human fecal and Dutch

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

    NASA Technical Reports Server (NTRS)

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

    1978-01-01

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

  9. Incorporating clonal growth form clarifies the role of plant height in response to nitrogen addition.

    PubMed

    Gough, Laura; Gross, Katherine L; Cleland, Elsa E; Clark, Christopher M; Collins, Scott L; Fargione, Joseph E; Pennings, Steven C; Suding, Katharine N

    2012-08-01

    Nutrient addition to grasslands consistently causes species richness declines and productivity increases. Competition, particularly for light, is often assumed to produce this result. Using a long-term dataset from North American herbaceous plant communities, we tested whether height and clonal growth form together predict responses to fertilization because neither trait alone predicted species loss in a previous analysis. Species with a tall-runner growth form commonly increased in relative abundance in response to added nitrogen, while short species and those with a tall-clumped clonal growth form often decreased. The ability to increase in size via vegetative spread across space, while simultaneously occupying the canopy, conferred competitive advantage, although typically only the abundance of a single species within each height-clonal growth form significantly responded to fertilization in each experiment. Classifying species on the basis of two traits (height and clonal growth form) increases our ability to predict species responses to fertilization compared to either trait alone in predominantly herbaceous plant communities. Electronic supplementary material The online version of this article (doi:10.1007/s00442-012-2264-5) contains supplementary material, which is available to authorized users. PMID:22302512

  10. 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.

  11. 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. PMID:21635644

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

    PubMed

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

    2016-01-01

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

  13. 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

  14. Defining Clonal Color in Fluorescent Multi-Clonal Tracking

    PubMed Central

    Wu, Juwell W.; Turcotte, Raphaël; Alt, Clemens; Runnels, Judith M.; Tsao, Hensin; Lin, Charles P.

    2016-01-01

    Clonal heterogeneity and selection underpin many biological processes including development and tumor progression. Combinatorial fluorescent protein expression in germline cells has proven its utility for tracking the formation and regeneration of different organ systems. Such cell populations encoded by combinatorial fluorescent proteins are also attractive tools for understanding clonal expansion and clonal competition in cancer. However, the assignment of clonal identity requires an analytical framework in which clonal markings can be parameterized and validated. Here we present a systematic and quantitative method for RGB analysis of fluorescent melanoma cancer clones. We then demonstrate refined clonal trackability of melanoma cells using this scheme. PMID:27073117

  15. 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., Jr.; 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.

  16. Enforced Clonality Confers a Fitness Advantage

    PubMed Central

    Martínková, Jana; Klimešová, Jitka

    2016-01-01

    In largely clonal plants, splitting of a maternal plant into potentially independent plants (ramets) is usually spontaneous; however, such fragmentation also occurs in otherwise non-clonal species due to application of external force. This process might play an important yet largely overlooked role for otherwise non-clonal plants by providing a mechanism to regenerate after disturbance. Here, in a 5-year garden experiment on two short-lived, otherwise non-clonal species, Barbarea vulgaris and Barbarea stricta, we compared the fitness of plants fragmented by simulated disturbance (“enforced ramets”) both with plants that contemporaneously originate in seed and with individuals unscathed by the disturbance event. Because the ability to regrow from fragments is related to plant age and stored reserves, we compared the effects of disturbance applied during three different ontogenetic stages of the plants. In B. vulgaris, enforced ramet fitness was higher than the measured fitness values of both uninjured plants and plants established from seed after the disturbance. This advantage decreased with increasing plant age at the time of fragmentation. In B. stricta, enforced ramet fitness was lower than or similar to fitness of uninjured plants and plants grown from seed. Our results likely reflect the habitat preferences of the study species, as B. vulgaris occurs in anthropogenic, disturbed habitats where body fragmentation is more probable and enforced clonality thus more advantageous than in the more natural habitats preferred by B. stricta. Generalizing from our results, we see that increased fitness yielded by enforced clonality would confer an evolutionary advantage in the face of disturbance, especially in habitats where a seed bank has not been formed, e.g., during invasion or colonization. Our results thus imply that enforced clonality should be taken into account when studying population dynamics and life strategies of otherwise non-clonal species in disturbed

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

    PubMed

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

    2011-03-01

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

  18. Clonally diverse rfb gene clusters are involved in expression of a family of related D-galactan O antigens in Klebsiella species.

    PubMed Central

    Kelly, R F; Whitfield, C

    1996-01-01

    Klebsiella species express a family of structurally related lipopolysaccharide O antigens which share a common backbone known as D-galactan I. Serotype specificity results from modification of D-galactan I by addition of domains of altered structure or by substitution with O-acetyl and/or alpha-D-Galp side groups with various linkages and stoichiometries. In the prototype, Klebsiella serotype O1, the his-linked rfb gene cluster is required for synthesis of D-galactan I, but genes conferring serotype specificity are unlinked. The D-galactan I part of the O polysaccharide is O acetylated in Klebsiella serotype O8. By cloning the rfb region from Klebsiella serotype O8 and analyzing the O polysaccharide synthesized in Escherichia coli K-12 hosts, we show that, like rfbO1, the rfbO8 region directs formation of unmodified D-galactan I. The rfbAB genes encode an ATP-binding cassette transporter required for export of polymeric D-galactan I across the plasma membrane prior to completion of the lipopolysaccharide molecule by ligation of the O polysaccharide to lipid A-core. Complementation experiments show that the rfbAB gene products in serotypes O1 and O8 are functionally equivalent and interchangeable. Hybridization experiments and physical mapping of the rfb regions in related Klebsiella serotypes suggest the existence of shared rfb genes with a common organization. However, despite the functional equivalence of these rfb gene clusters, at least three distinct clonal groups were detected in different Klebsiella species and subspecies, on the basis of Southern hybridization experiments carried out under high-stringency conditions. The clonal groups cannot be predicted by features of the O-antigen structure. To examine the relationships in more detail, the complete nucleotide sequence of the serotype O8 rfb cluster was determined and compared with that of the serotype O1 prototype. The nucleotide sequences for the six rfb genes showed variations in moles percent G

  19. 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

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

    PubMed Central

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

    2014-01-01

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

  1. Clonal expansion of double-positive intraepithelial lymphocytes by MHC class I-related chain A expressed in mouse small intestinal epithelium.

    PubMed

    Park, Eun Jeong; Takahashi, Ichiro; Ikeda, Junko; Kawahara, Kazuko; Okamoto, Tetsuji; Kweon, Mi-Na; Fukuyama, Satoshi; Groh, Veronika; Spies, Thomas; Obata, Yuichi; Miyazaki, Jun-Ichi; Kiyono, Hiroshi

    2003-10-15

    Expression of a distant homologue MHC class I molecule, MHC class I-related chain A (MICA), has been found to be stress inducible and limited to the intestinal epithelium. This nonclassical MHC molecule is associated with various carcinomas in humans. To understand the biological consequences of MICA expression in the gut, we generated transgenic (Tg) mice (T3(b)-MICA Tg) under the control of the T3(b) promoter. The T3(b)-MICA Tg mice expressed MICA selectively in the intestine and had an increased number of TCRalphabeta CD4CD8alphaalpha, double-positive (DP) intraepithelial lymphocytes (IELs) in the small bowel. These MICA-expanded DP IELs exhibited a bias to Vbeta8.2 and overlapped motifs of the complementarity-determining region 3 region among various Tg mice. Hence, the overexpression of MICA resulted in a clonal expansion of DP IELs. Studies in model of inflammatory bowel disease showed that transgenic MICA was able to attenuate the acute colitis induced by dextran sodium sulfate administration. Therefore, this unique in vivo model will enable investigation of possible influences of stress-inducible MICA on the gut immune surveillance. PMID:14530335

  2. 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

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

    PubMed Central

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

    2012-01-01

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

  4. 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.

  5. Relation between rainfall intensity and savanna tree abundance explained by water use strategies.

    PubMed

    Xu, Xiangtao; Medvigy, David; Rodriguez-Iturbe, Ignacio

    2015-10-20

    Tree abundance in tropical savannas exhibits large and unexplained spatial variability. Here, we propose that differentiated tree and grass water use strategies can explain the observed negative relation between maximum tree abundance and rainfall intensity (defined as the characteristic rainfall depth on rainy days), and we present a biophysical tree-grass competition model to test this idea. The model is founded on a premise that has been well established in empirical studies, namely, that the relative growth rate of grasses is much higher compared with trees in wet conditions but that grasses are more susceptible to water stress and lose biomass more quickly in dry conditions. The model is coupled with a stochastic rainfall generator and then calibrated and tested using field observations from several African savanna sites. We show that the observed negative relation between maximum tree abundance and rainfall intensity can be explained only when differentiated water use strategies are accounted for. Numerical experiments reveal that this effect is more significant than the effect of root niche separation. Our results emphasize the importance of vegetation physiology in determining the responses of tree abundance to climate variations in tropical savannas and suggest that projected increases in rainfall intensity may lead to an increase in grass in this biome. PMID:26438847

  6. Differential ablation of cosmic dust and implications for the relative abundances of atmospheric metals

    NASA Astrophysics Data System (ADS)

    McNeil, William J.; Lai, Shu T.; Murad, Edmond

    1998-05-01

    Although it is generally accepted that extraterrestrial material is the source of metals in the upper atmosphere, the relative abundances of mesospheric metal atoms and ions present us with a conundrum. Lidar observations have consistently shown that the abundances of neutral metals in the atmosphere and the abundances of these metals in the meteoric material that falls to Earth are significantly disproportionate. The column density of neutral sodium is perhaps 2 orders of magnitude larger than that of calcium, while the abundances in meteorites are approximately equal. By contrast, ion mass spectroscopy has shown that the abundances of the meteoric ions match reasonably well those in the meteorites. We present here a model that attempts to address these discrepancies. At the heart of the model is the concept of differential ablation, which suggests that more volatile metals sublimate earlier in the descent of a cosmic dust particle than do the less volatile components. We model three different meteoric metals: sodium, magnesium, and calcium. Results suggest that sodium ablates to a greater extent than does calcium and that it ablates at a substantially higher altitude. Deposition at lower altitudes leads to more rapid conversion of the atomic calcium into complexes through three-body reactions. Thus the depletion of calcium arises from both a decrease in deposition and an increase in the rate of removal of that which is deposited. We examine the behavior of the model in several respects, comparing predicted results with measurements and finding reasonable agreement. We argue that the success of this model indicates that differential ablation is a key factor in the determination of the relative abundances of meteoric metals in the mesosphere.

  7. 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

    2013-01-01

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

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

    PubMed Central

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

    2013-01-01

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

  9. Phenotypic comparisons between wild relatives and cultivars of kiwifruit, persimmon, mulberry, and olive at the National Clonal Germplasm Repository, Davis, CA

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Phenotypic traits were characterized for 23 wild species and 4 cultivars of 4 clonal fruit crops including, Kiwifruit (Actinidia), Persimmon (Diospyros), Mulberry (Morus) and Olive (Olea). Across all four crops, the wild species varied distinctly, especially when compared with the cultivars. The wil...

  10. 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.

  11. Determination of relative protein abundance by internally normalized ratio algorithm with antibody arrays.

    PubMed

    Andersson, Oskar; Kozlowski, Mark; Garachtchenko, Tatiana; Nikoloff, Corina; Lew, Nancy; Litman, David J; Chaga, Grigoriy

    2005-01-01

    In this paper, we report an experimental setup and mathematical algorithm for determination of relative protein abundance from directly labeled native protein samples applied to an array of antibodies. The application of the proposed experimental system compensates internally at each array element for a number of deficiencies in array experiments such as differential labeling efficiency in dual color assay systems, differential solubility of protein molecules in dual color assay systems, and differential affinity of capture reagents toward proteins labeled with two different fluorescent dyes. This system offers full compensation for variable amounts of capture reagents on separate array structures, as well as limited compensation for nonspecific interactions between capture reagents and analytes. The proposed experimental strategy enables the use of a large number of capture reagents to develop a true multiplex analysis system that will yield complete relative protein abundance information in two biological systems. PMID:15952723

  12. 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. PMID:23949745

  13. 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.

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

    PubMed

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

    2006-02-01

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

  15. 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.

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

    NASA Astrophysics Data System (ADS)

    McNeil, W. J.

    1997-09-01

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

  17. 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

  18. A metastable equilibrium model for the relative abundances of microbial phyla in a hot spring.

    PubMed

    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

  19. An invasive clonal plant benefits from clonal integration more than a co-occurring native plant in nutrient-patchy and competitive environments.

    PubMed

    You, Wenhua; Fan, Shufeng; Yu, Dan; Xie, Dong; Liu, Chunhua

    2014-01-01

    Many notorious invasive plants are clonal, however, little is known about the different roles of clonal integration effects between invasive and native plants. Here, we hypothesize that clonal integration affect growth, photosynthetic performance, biomass allocation and thus competitive ability of invasive and native clonal plants, and invasive clonal plants benefit from clonal integration more than co-occurring native plants in heterogeneous habitats. To test these hypotheses, two stoloniferous clonal plants, Alternanthera philoxeroides (invasive), Jussiaea repens (native) were studied in China. The apical parts of both species were grown either with or without neighboring vegetation and the basal parts without competitors were in nutrient- rich or -poor habitats, with stolon connections were either severed or kept intact. Competition significantly reduced growth and photosynthetic performance of the apical ramets in both species, but not the biomass of neighboring vegetation. Without competition, clonal integration greatly improved the growth and photosynthetic performance of both species, especially when the basal parts were in nutrient-rich habitats. When grown with neighboring vegetation, growth of J. repens and photosynthetic performance of both species were significantly enhanced by clonal integration with the basal parts in both nutrient-rich and -poor habitats, while growth and relative neighbor effect (RNE) of A. philoxeroides were greatly improved by clonal integration only when the basal parts were in nutrient-rich habitats. Moreover, clonal integration increased A. philoxeroides's biomass allocation to roots without competition, but decreased it with competition, especially when the basal ramets were in nutrient-rich sections. Effects of clonal integration on biomass allocation of J. repens was similar to that of A. philoxeroides but with less significance. These results supported our hypothesis that invasive clonal plants A. philoxeroides benefits

  20. An Invasive Clonal Plant Benefits from Clonal Integration More than a Co-Occurring Native Plant in Nutrient-Patchy and Competitive Environments

    PubMed Central

    You, Wenhua; Fan, Shufeng; Yu, Dan; Xie, Dong; Liu, Chunhua

    2014-01-01

    Many notorious invasive plants are clonal, however, little is known about the different roles of clonal integration effects between invasive and native plants. Here, we hypothesize that clonal integration affect growth, photosynthetic performance, biomass allocation and thus competitive ability of invasive and native clonal plants, and invasive clonal plants benefit from clonal integration more than co-occurring native plants in heterogeneous habitats. To test these hypotheses, two stoloniferous clonal plants, Alternanthera philoxeroides (invasive), Jussiaea repens (native) were studied in China. The apical parts of both species were grown either with or without neighboring vegetation and the basal parts without competitors were in nutrient- rich or -poor habitats, with stolon connections were either severed or kept intact. Competition significantly reduced growth and photosynthetic performance of the apical ramets in both species, but not the biomass of neighboring vegetation. Without competition, clonal integration greatly improved the growth and photosynthetic performance of both species, especially when the basal parts were in nutrient-rich habitats. When grown with neighboring vegetation, growth of J. repens and photosynthetic performance of both species were significantly enhanced by clonal integration with the basal parts in both nutrient-rich and -poor habitats, while growth and relative neighbor effect (RNE) of A. philoxeroides were greatly improved by clonal integration only when the basal parts were in nutrient-rich habitats. Moreover, clonal integration increased A. philoxeroides's biomass allocation to roots without competition, but decreased it with competition, especially when the basal ramets were in nutrient-rich sections. Effects of clonal integration on biomass allocation of J. repens was similar to that of A. philoxeroides but with less significance. These results supported our hypothesis that invasive clonal plants A. philoxeroides benefits

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

    NASA Technical Reports Server (NTRS)

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

    1974-01-01

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

  2. Relative isotopic abundances of zirconium in R Cygni and V CANCRI

    NASA Astrophysics Data System (ADS)

    Zook, A. C.

    1985-02-01

    The relative abundances of the isotopes of Zr in the S stars R Cyg and V Cnc are calculated by determining isotopic splitting at the head of the 1Pi - 1Sigma (0, 1) band of ZrO in spectra obtained at resolution 30 pm on hypersensitized 127-O4 plates with a Varo tube on the 51-cm camera at the Coude focus of the 3-m telescope at Lick Observatory. The data reduction techniques and the fit to the model synthetic spectra of Kurucz (1970) are described, and the ratio (Zr-90):(Zr-91):(Zr-92):(Zr-93):(Zr-94):(Zr-96) is given as 47:10:17:6:20:00 percent. The presence of the long-lived unstable isotope Zr-93 is interpreted as evidence for recent nucleosynthesis, and the abundances found are shown to be consistent with s-process nucleosynthesis.

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

    PubMed

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

    2015-03-01

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

  4. Kin Recognition in a Clonal Fish, Poecilia formosa.

    PubMed

    Makowicz, Amber M; Tiedemann, Ralph; Steele, Rachel N; Schlupp, Ingo

    2016-01-01

    Relatedness strongly influences social behaviors in a wide variety of species. For most species, the highest typical degree of relatedness is between full siblings with 50% shared genes. However, this is poorly understood in species with unusually high relatedness between individuals: clonal organisms. Although there has been some investigation into clonal invertebrates and yeast, nothing is known about kin selection in clonal vertebrates. We show that a clonal fish, the Amazon molly (Poecilia formosa), can distinguish between different clonal lineages, associating with genetically identical, sister clones, and use multiple sensory modalities. Also, they scale their aggressive behaviors according to the relatedness to other females: they are more aggressive to non-related clones. Our results demonstrate that even in species with very small genetic differences between individuals, kin recognition can be adaptive. Their discriminatory abilities and regulation of costly behaviors provides a powerful example of natural selection in species with limited genetic diversity. PMID:27483372

  5. Kin Recognition in a Clonal Fish, Poecilia formosa

    PubMed Central

    Makowicz, Amber M.; Tiedemann, Ralph; Schlupp, Ingo

    2016-01-01

    Relatedness strongly influences social behaviors in a wide variety of species. For most species, the highest typical degree of relatedness is between full siblings with 50% shared genes. However, this is poorly understood in species with unusually high relatedness between individuals: clonal organisms. Although there has been some investigation into clonal invertebrates and yeast, nothing is known about kin selection in clonal vertebrates. We show that a clonal fish, the Amazon molly (Poecilia formosa), can distinguish between different clonal lineages, associating with genetically identical, sister clones, and use multiple sensory modalities. Also, they scale their aggressive behaviors according to the relatedness to other females: they are more aggressive to non-related clones. Our results demonstrate that even in species with very small genetic differences between individuals, kin recognition can be adaptive. Their discriminatory abilities and regulation of costly behaviors provides a powerful example of natural selection in species with limited genetic diversity. PMID:27483372

  6. Inferring Clonal Composition from Multiple Sections of a Breast Cancer

    PubMed Central

    Hu, Alex; Weber, Kris; Smith, Josh; Nickerson, Debbie; Song, ChaoZhong; Witten, Daniela; Blau, C. Anthony; Noble, William Stafford

    2014-01-01

    Cancers arise from successive rounds of mutation and selection, generating clonal populations that vary in size, mutational content and drug responsiveness. Ascertaining the clonal composition of a tumor is therefore important both for prognosis and therapy. Mutation counts and frequencies resulting from next-generation sequencing (NGS) potentially reflect a tumor's clonal composition; however, deconvolving NGS data to infer a tumor's clonal structure presents a major challenge. We propose a generative model for NGS data derived from multiple subsections of a single tumor, and we describe an expectation-maximization procedure for estimating the clonal genotypes and relative frequencies using this model. We demonstrate, via simulation, the validity of the approach, and then use our algorithm to assess the clonal composition of a primary breast cancer and associated metastatic lymph node. After dividing the tumor into subsections, we perform exome sequencing for each subsection to assess mutational content, followed by deep sequencing to precisely count normal and variant alleles within each subsection. By quantifying the frequencies of 17 somatic variants, we demonstrate that our algorithm predicts clonal relationships that are both phylogenetically and spatially plausible. Applying this method to larger numbers of tumors should cast light on the clonal evolution of cancers in space and time. PMID:25010360

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

    NASA Astrophysics Data System (ADS)

    Hoyle, Jo; Hicks, Murray; Kilroy, Cathy

    2013-04-01

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

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

    PubMed Central

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

    1990-01-01

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

  9. The population genetics of clonal and partially clonal diploids.

    PubMed Central

    Balloux, François; Lehmann, Laurent; de Meeûs, Thierry

    2003-01-01

    The consequences of variable rates of clonal reproduction on the population genetics of neutral markers are explored in diploid organisms within a subdivided population (island model). We use both analytical and stochastic simulation approaches. High rates of clonal reproduction will positively affect heterozygosity. As a consequence, nearly twice as many alleles per locus can be maintained and population differentiation estimated as F(ST) value is strongly decreased in purely clonal populations as compared to purely sexual ones. With increasing clonal reproduction, effective population size first slowly increases and then points toward extreme values when the reproductive system tends toward strict clonality. This reflects the fact that polymorphism is protected within individuals due to fixed heterozygosity. Contrarily, genotypic diversity smoothly decreases with increasing rates of clonal reproduction. Asexual populations thus maintain higher genetic diversity at each single locus but a lower number of different genotypes. Mixed clonal/sexual reproduction is nearly indistinguishable from strict sexual reproduction as long as the proportion of clonal reproduction is not strongly predominant for all quantities investigated, except for genotypic diversities (both at individual loci and over multiple loci). PMID:12930767

  10. 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.

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

    SciTech Connect

    Panasyuk, M.I.

    1986-03-01

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

  12. Visual habitat geometry predicts relative morph abundance in the colour-polymorphic ornate rainbowfish

    PubMed Central

    Hancox, Daniel; Wilson, Robbie S.; White, Craig R.

    2013-01-01

    During colour signalling in aquatic environments, the colour of the ambient light, the background against which signals are viewed and signal transmission through the environment can all have profound impacts on the efficacy of a given signal. In colour-polymorphic species, where alternative morphs persist owing to a balance in the natural and sexual selection for each, changes to the visual context can have large effects on the local success and relative abundance of competing phenotypes. The ornate rainbowfish, Rhadinocentrus ornatus, is composed of populations that vary in the relative frequency of red and blue individuals, and inhabit sites that vary in water transmittance from clear (white) to heavily tannin-stained (red-shifted). Using spectroradiometry, we measured the downwelling and sidewelling irradiance, bank radiance and water transmittance of 10 R. ornatus habitats. We found that the relative local abundance of each morph was predicted not by water transmittance but by chromatic differences between the vertical (downwelling light) and horizontal (bank colour) components of the habitat. This visual habitat geometry should increase contrast between the colour signal and background, with large potential to influence the strength of natural and sexual selection in this system. PMID:23222447

  13. Is Bordetella pertussis clonal?

    PubMed Central

    Khattak, M. N.; Matthews, R. C.; Burnie, J. P.

    1992-01-01

    OBJECTIVE--To establish whether Bordetella pertussis is essentially clonal. DESIGN--Analysis of restriction fragments of XbaI digests of DNA from clinical and control isolates of B pertussis by pulse field gel electrophoresis. MATERIALS--105 isolates of B pertussis: 67 clinical isolates from throughout the United Kingdom and 23 from Germany (collected during the previous 18 months); vaccine strains 2991 and 3700; and 13 control isolates from Manchester University's culture collection. MAIN OUTCOME MEASURES--Frequency of DNA types according to country of origin and classical serotyping. RESULTS--17 DNA types were identified on the basis of the variation in 11 fragments, banding at 200-412 kilobases; 15 types were found in the clinical and control isolates from the United Kingdom and seven in those from Germany. There was no correlation with serotype. DNA type 1 was the commonest overall (22/105 strains, 22%), predominating in serotypes 1,2 and 1,2,3 and including the vaccine strains but not the isolates from Germany. CONCLUSIONS--Current infections due to B pertussis are not caused by a clonal pathogen as multiple strains are circulating in a given population at one time. There is also considerable epidemiological variation in the pathogen population between countries. These findings may have implications for the design of acellular vaccines. Images FIG 1 FIG 2 FIG 3 PMID:1392709

  14. 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. PMID:23741717

  15. 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.

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

    PubMed Central

    Jeong, Sangkyun; Yu, Hyunjoo; Pfeifer, Karl

    2012-01-01

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

  17. 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.

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

    PubMed

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

    2016-05-01

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

  19. Relative abundances of secondary and primary cosmic rays at high energies

    NASA Technical Reports Server (NTRS)

    Swordy, Simon P.; Mueller, Dietrich; Meyer, Peter; L'Heureux, Jacques; Grunsfeld, John M.

    1990-01-01

    New results on the energy spectra of the cosmic-ray nuclei boron, carbon, nitrogen, and oxygen up to energies around 1 TeV per amu are described. The measurements were performed on the Spacelab 2 mission of the Space Shuttle in 1985. Carbon and oxygen are essentially primary cosmic rays, while boron is purely secondary, and nitrogen has secondary as well as primary contributions. Therefore, the relative abundances of these nuclei provide sensitive information on the propagation of cosmic rays through the Galaxy. It is found that the flux of the secondary cosmic rays continues to decrease relative to that of the primaries over the energy range covered with this observation, and that the mean escape length near 1 TeV per amu is about 1 g/sq cm.

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

    PubMed

    Reisen, W K; Milby, M M

    1986-02-01

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

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

    PubMed Central

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

    2009-01-01

    Colony collapse disorder (CCD) is a mysterious disappearance of honey bees that has beset beekeepers in the United States since late 2006. Pathogens and other environmental stresses, including pesticides, have been linked to CCD, but a causal relationship has not yet been demonstrated. Because the gut acts as a primary interface between the honey bee and its environment as a site of entry for pathogens and toxins, we used whole-genome microarrays to compare gene expression between guts of bees from CCD colonies originating on both the east and west coasts of the United States and guts of bees from healthy colonies sampled before the emergence of CCD. Considerable variation in gene expression was associated with the geographical origin of bees, but a consensus list of 65 transcripts was identified as potential markers for CCD status. Overall, elevated expression of pesticide response genes was not observed. Genes involved in immune response showed no clear trend in expression pattern despite the increased prevalence of viruses and other pathogens in CCD colonies. Microarray analysis revealed unusual ribosomal RNA fragments that were conspicuously more abundant in the guts of CCD bees. The presence of these fragments may be a possible consequence of picorna-like viral infection, including deformed wing virus and Israeli acute paralysis virus, and may be related to arrested translation. Ribosomal fragment abundance and presence of multiple viruses may prove to be useful diagnostic markers for colonies afflicted with CCD. PMID:19706391

  2. 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. PMID:19706391

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

    PubMed Central

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

    2010-01-01

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

  4. 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.

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

    USGS Publications Warehouse

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

    2005-01-01

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

  6. Molecular Evolution of the Escherichia Coli Chromosome. III. Clonal Frames

    PubMed Central

    Milkman, R.; Bridges, M. M.

    1990-01-01

    PCR fragments, 1500-bp, from 15 previously sequenced regions in the Escherichia coli chromosome have been compared by restriction analysis in a large set of wild (ECOR) strains. Prior published observations of segmental clonality are confirmed: each of several sequence types is shared by a number of strains. The rate of recombinational replacement and the average size of the replacements are estimated in a set of closely related strains in which a clonal frame is dotted with occasional stretches of DNA belonging to other clones. A clonal hierarchy is described. Some new comparative sequencing data are presented. PMID:1979037

  7. Identification of Prophages in Bacterial Genomes by Dinucleotide Relative Abundance Difference

    PubMed Central

    Srividhya, K. V.; Alaguraj, V.; Poornima, G.; Kumar, Dinesh; Singh, G. P.; Raghavenderan, L.; Katta, A. V. S. K. Mohan; Mehta, Preeti; Krishnaswamy, S.

    2007-01-01

    Background Prophages are integrated viral forms in bacterial genomes that have been found to contribute to interstrain genetic variability. Many virulence-associated genes are reported to be prophage encoded. Present computational methods to detect prophages are either by identifying possible essential proteins such as integrases or by an extension of this technique, which involves identifying a region containing proteins similar to those occurring in prophages. These methods suffer due to the problem of low sequence similarity at the protein level, which suggests that a nucleotide based approach could be useful. Methodology Earlier dinucleotide relative abundance (DRA) have been used to identify regions, which deviate from the neighborhood areas, in genomes. We have used the difference in the dinucleotide relative abundance (DRAD) between the bacterial and prophage DNA to aid location of DNA stretches that could be of prophage origin in bacterial genomes. Prophage sequences which deviate from bacterial regions in their dinucleotide frequencies are detected by scanning bacterial genome sequences. The method was validated using a subset of genomes with prophage data from literature reports. A web interface for prophage scan based on this method is available at http://bicmku.in:8082/prophagedb/dra.html. Two hundred bacterial genomes which do not have annotated prophages have been scanned for prophage regions using this method. Conclusions The relative dinucleotide distribution difference helps detect prophage regions in genome sequences. The usefulness of this method is seen in the identification of 461 highly probable loci pertaining to prophages which have not been annotated so earlier. This work emphasizes the need to extend the efforts to detect and annotate prophage elements in genome sequences. PMID:18030328

  8. 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.

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

    PubMed Central

    Serra, François; Becher, Verónica; Dopazo, Hernán

    2013-01-01

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

  10. 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.

  11. 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.

  12. Observations of solar wind stream with high abundance of heavy ions and relation with coronal conditions

    NASA Astrophysics Data System (ADS)

    Zastenker, G. N.; Yermolaev, Yu. I.

    1981-11-01

    Long intervals, during which heavy ions were detected in the high energy tail of the energy spectra of solar wind ions, were recorded by the plasma spectrometer SCS onboard the Prognoz-7 satellite. In particular, such a region with unusual features - low velocity, high density, low temperature of protons and, especially, low temperature of alpha-particles - was observed during 10-13 December 1978. The time dependence of these parameters makes it possible to recognize this event as 'noncompressive density enhancement'. In this region heavy ions such as O(6+), O(7+), Si(7+), Si(8+), Si(9+) and a group of iron from Fe(6+) to Fe(13+) were identified by the electrostatic analyzer. The abundance of these ions relative to protons was about ten times higher than had previously been observed. The coronal temperature, estimated from the ratios of the ion fluxes with different ionization states, is higher than that estimated earlier for the oxygen ions.

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

    NASA Astrophysics Data System (ADS)

    Rauch, B. F.

    2014-05-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2005-12-01

    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.

  15. 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.

  16. Relative abundance of the light ions in the winter nighttime topside ionosphere

    NASA Technical Reports Server (NTRS)

    Sanatani, S.; Breig, E. L.

    1984-01-01

    Ion concentration measurements with the retarding potential analyzer onboard OGO 6 satellite have served as basis for investigation of the distribution of the light ions, H(+) and He(+), relative to that of O(+) in the 500- to 800-km height range in the winter nighttime ionosphere. This concentration ratio exhibits distinct large-scale horizontal variations, with a relative depression in the ratio observed over a broad region about -45 deg longitude northward of approximately 40 deg dip latitude. The lower ratios are associated primarily with well-defined relative increases in the abundance of O(+), and occur in the same longitude sector that has been characterized in an earlier study by both an observed concurrent relative enhancement in ion temperature and the presence of large fluxes of energetic electrons. Comparisons are presented for the altitude distributions of the concentration ratio between regions representing extremes of the horizontal variation. A simple diffusive-equilibrium model demonstrates that the effects of ion temperature on the O(+) vertical distribution are a significant factor leading to the observed variation of the concentration ratio.

  17. The clonal origin and clonal evolution of epithelial tumours

    PubMed Central

    Garcia, Sergio Britto; Novelli, Marco; Wright, Nicholas A

    2000-01-01

    While the origin of tumours, whether from one cell or many, has been a source of fascination for experimental oncologists for some time, in recent years there has been a veritable explosion of information about the clonal architecture of tumours and their antecedents, stimulated, in the main, by the ready accessibility of new molecular techniques. While most of these new results have apparently confirmed the monoclonal origin of human epithelial (and other) tumours, there are a significant number of studies in which this conclusion just cannot be made. Moreover, analysis of many articles show that the potential impact of such considerations as patch size and clonal evolution on determinations of clonality have largely been ignored, with the result that a number of these studies are confounded. However, the clonal architecture of preneoplastic lesions provide some interesting insights — many lesions which might have been hitherto regarded as hyperplasias are apparently clonal in derivation. If this is indeed true, it calls into some question our hopeful corollary that a monoclonal origin presages a neoplastic habitus. Finally, it is clear, for many reasons, that methods of analysis which involve the disaggregation of tissues, albeit microdissected, are far from ideal and we should be putting more effort into techniques where the clonal architecture of normal tissues, preneoplastic and preinvasive lesions and their derivative tumours can be directly visualized in situ. PMID:10762440

  18. Solar wind elemental abundances related to the Sun's open magnetic flux

    NASA Astrophysics Data System (ADS)

    Wang, X.; Klecker, B.; Wurz, P.

    2009-10-01

    Context: We present an investigation of the effects of solar magnetic field on the elemental abundance ratios of heavy ions in the solar wind. Aims: We compare the elemental abundance ratios Fe/O, Si/O, Mg/O, Ne/O, and C/O over the 23rd solar cycle, attention being given to the varying fraction of open magnetic flux on the visible side of the solar disc. Methods: We use ACE solar wind data, the current sheet source surface (CSSS) model of the corona, and SoHO/MDI data to relate solar wind compositional properties with the fraction of open magnetic flux on the Sun. We include both a quasi-stationary and intermittent solar wind. Results: For the six investigated solar wind speed ranges, the elemental composition shows a similar FIP-bias of the quasi-stationary solar wind composition with respect to the photosphere but with three plateaus separating low-, mid-, and high-FIP elements. The average enrichment factor for the low-FIP element group (Mg, Fe, Si) with respect to the photospheric values is between 1.67 and 2.47 when the fraction of open magnetic flux on the visible side of the solar disc is above 14%, and it ranges from 2.78 to 4.15 when this fraction is less than 7%. They are close to the enrichment of low-FIP elements with respect to the photospheric values in quasi-stationary fast- and slow- solar wind, which implies similar fractionation mechanisms for the stationary solar wind and the intermittent solar wind. In the low alpha (<7%) case (alpha is the fraction of open magnetic flux on the visible side of the solar disc), the enrichment of heavy elements for the fast solar wind is well correlated with the high fraction of CMEs. In addition, both the charge state ratios and the elemental abundance ratios exhibit a lower dependence on alpha in a slow solar wind than in a fast solar wind. The dependence of the charge state ratios on alpha is correlated with FIP, which implies that solar magnetic effects play a non-negligible role in the elemental fractionation

  19. 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., Jr.

    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.

  20. TEMPERATURE CONDITIONING ALTERS TRANSCRIPT ABUNDANCE OF GENES RELATED TO CHILLING STRESS IN GRAPEFRUIT.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Grapefruit (Citrus paradisi) are susceptible to chilling injury (CI) if held at temperatures below about 10C. Changes in transcript abundance for a number of genes have been correlated with chilling stress in citrus fruit. We tested the hypothesis that conditioning affects transcript abundance of ...

  1. Roles of Clonal Integration in both Heterogeneous and Homogeneous Habitats

    PubMed Central

    Zhang, Haijie; Liu, Fenghong; Wang, Renqing; Liu, Jian

    2016-01-01

    Many studies have shown that clonal integration can promote the performance of clonal plants in heterogeneous habitats, but the roles of clonal integration in both heterogeneous and homogeneous habitats were rarely studied simultaneously. Ramet pairs of Alternanthera philoxeroides (Mart.) Griseb were placed in two habitats either heterogeneous or homogeneous in soil nutrient availability, with stolon connections left intact or severed. Total biomass, total length of stolons, and number of new ramets of distal (relatively young) ramets located in low-nutrient environments were significantly greater when the distal ramets were connected to than when they were disconnected from proximal (relatively old) ramets located in high-nutrient environments. Total length of stolons of proximal ramets growing in low-nutrient environments was significantly higher when the proximal ramets were connected to than when they were disconnected from the distal ramets growing in high-nutrient environments, but stolon connection did not affect total biomass or number of new ramets of the proximal ramets. Stolon severing also did not affect the growth of the whole ramet pairs in heterogeneous environments. In homogeneous high-nutrient environments stolon severing promoted the growth of the proximal ramets and the ramet pairs, but in homogeneous low-nutrient environments it did not affect the growth of the proximal or distal ramets. Hence, for A. philoxeroides, clonal fragmentation appears to be more advantageous than clonal integration in resource-rich homogeneous habitats, and clonal integration becomes beneficial in heterogeneous habitats. Our study contributes to revealing roles of clonal integration in both heterogeneous and homogeneous habitats and expansion patterns of invasive clonal plants such as A. philoxeroides in multifarious habitats. PMID:27200026

  2. Roles of Clonal Integration in both Heterogeneous and Homogeneous Habitats.

    PubMed

    Zhang, Haijie; Liu, Fenghong; Wang, Renqing; Liu, Jian

    2016-01-01

    Many studies have shown that clonal integration can promote the performance of clonal plants in heterogeneous habitats, but the roles of clonal integration in both heterogeneous and homogeneous habitats were rarely studied simultaneously. Ramet pairs of Alternanthera philoxeroides (Mart.) Griseb were placed in two habitats either heterogeneous or homogeneous in soil nutrient availability, with stolon connections left intact or severed. Total biomass, total length of stolons, and number of new ramets of distal (relatively young) ramets located in low-nutrient environments were significantly greater when the distal ramets were connected to than when they were disconnected from proximal (relatively old) ramets located in high-nutrient environments. Total length of stolons of proximal ramets growing in low-nutrient environments was significantly higher when the proximal ramets were connected to than when they were disconnected from the distal ramets growing in high-nutrient environments, but stolon connection did not affect total biomass or number of new ramets of the proximal ramets. Stolon severing also did not affect the growth of the whole ramet pairs in heterogeneous environments. In homogeneous high-nutrient environments stolon severing promoted the growth of the proximal ramets and the ramet pairs, but in homogeneous low-nutrient environments it did not affect the growth of the proximal or distal ramets. Hence, for A. philoxeroides, clonal fragmentation appears to be more advantageous than clonal integration in resource-rich homogeneous habitats, and clonal integration becomes beneficial in heterogeneous habitats. Our study contributes to revealing roles of clonal integration in both heterogeneous and homogeneous habitats and expansion patterns of invasive clonal plants such as A. philoxeroides in multifarious habitats. PMID:27200026

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

    PubMed

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

    2016-01-01

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

  4. 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. PMID:26940771

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed Central

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

    2016-01-01

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

  7. 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.

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

    PubMed

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

    2011-08-01

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

  9. 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.

  10. 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

  11. 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

  12. 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.

  13. Anomalous Relative Ar/Ca Coronal Abundances Observed by the Hinode/EUV Imaging Spectrometer Near Sunspots

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

    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.

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

    USGS Publications Warehouse

    Keeley, J.E.

    2003-01-01

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

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

    USGS Publications Warehouse

    Nelms, C.O.; Twedt, D.J.

    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

  16. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2012-01-01

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

  18. 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

  19. 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.

  20. 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.

  1. Synthetic clonal reproduction through seeds.

    PubMed

    Marimuthu, Mohan P A; Jolivet, Sylvie; Ravi, Maruthachalam; Pereira, Lucie; Davda, Jayeshkumar N; Cromer, Laurence; Wang, Lili; Nogué, Fabien; Chan, Simon W L; Siddiqi, Imran; Mercier, Raphaël

    2011-02-18

    Cloning through seeds has potential revolutionary applications in agriculture, because it would allow vigorous hybrids to be propagated indefinitely. However, asexual seed formation or apomixis, avoiding meiosis and fertilization, is not found in the major food crops. To develop de novo synthesis of apomixis, we crossed Arabidopsis MiMe and dyad mutants that produce diploid clonal gametes to a strain whose chromosomes are engineered to be eliminated after fertilization. Up to 34% of the progeny were clones of their parent, demonstrating the conversion of clonal female or male gametes into seeds. We also show that first-generation cloned plants can be cloned again. Clonal reproduction through seeds can therefore be achieved in a sexual plant by manipulating two to four conserved genes. PMID:21330535

  2. 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

  3. Effects of clonality on the genetic variability of rare, insular species: the case of Ruta microcarpa from the Canary Islands

    PubMed Central

    Meloni, M; Reid, A; Caujapé-Castells, J; Marrero, Á; Fernández-Palacios, J M; Mesa-Coelo, R A; Conti, E

    2013-01-01

    Many plant species combine sexual and clonal reproduction. Clonal propagation has ecological costs mainly related to inbreeding depression and pollen discounting; at the same time, species able to reproduce clonally have ecological and evolutionary advantages being able to persist when conditions are not favorable for sexual reproduction. The presence of clonality has profound consequences on the genetic structure of populations, especially when it represents the predominant reproductive strategy in a population. Theoretical studies suggest that high rate of clonal propagation should increase the effective number of alleles and heterozygosity in a population, while an opposite effect is expected on genetic differentiation among populations and on genotypic diversity. In this study, we ask how clonal propagation affects the genetic diversity of rare insular species, which are often characterized by low levels of genetic diversity, hence at risk of extinction. We used eight polymorphic microsatellite markers to study the genetic structure of the critically endangered insular endemic Ruta microcarpa. We found that clonality appears to positively affect the genetic diversity of R. microcarpa by increasing allelic diversity, polymorphism, and heterozygosity. Moreover, clonal propagation seems to be a more successful reproductive strategy in small, isolated population subjected to environmental stress. Our results suggest that clonal propagation may benefit rare species. However, the advantage of clonal growth may be only short-lived for prolonged clonal growth could ultimately lead to monoclonal populations. Some degree of sexual reproduction may be needed in a predominantly clonal species to ensure long-term viability. PMID:23789068

  4. 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.

  5. Liana Abundance, Diversity, and Distribution on Barro Colorado Island, Panama

    PubMed Central

    Schnitzer, Stefan A.; Mangan, Scott A.; Dalling, James W.; Baldeck, Claire A.; Hubbell, Stephen P.; Ledo, Alicia; Muller-Landau, Helene; Tobin, Michael F.; Aguilar, Salomon; Brassfield, David; Hernandez, Andres; Lao, Suzanne; Perez, Rolando; Valdes, Oldemar; Yorke, Suzanne Rutishauser

    2012-01-01

    Lianas are a key component of tropical forests; however, most surveys are too small to accurately quantify liana community composition, diversity, abundance, and spatial distribution – critical components for measuring the contribution of lianas to forest processes. In 2007, we tagged, mapped, measured the diameter, and identified all lianas ≥1 cm rooted in a 50-ha plot on Barro Colorado Island, Panama (BCI). We calculated liana density, basal area, and species richness for both independently rooted lianas and all rooted liana stems (genets plus clones). We compared spatial aggregation patterns of liana and tree species, and among liana species that varied in the amount of clonal reproduction. We also tested whether liana and tree densities have increased on BCI compared to surveys conducted 30-years earlier. This study represents the most comprehensive spatially contiguous sampling of lianas ever conducted and, over the 50 ha area, we found 67,447 rooted liana stems comprising 162 species. Rooted lianas composed nearly 25% of the woody stems (trees and lianas), 35% of woody species richness, and 3% of woody basal area. Lianas were spatially aggregated within the 50-ha plot and the liana species with the highest proportion of clonal stems more spatially aggregated than the least clonal species, possibly indicating clonal stem recruitment following canopy disturbance. Over the past 30 years, liana density increased by 75% for stems ≥1 cm diameter and nearly 140% for stems ≥5 cm diameter, while tree density on BCI decreased 11.5%; a finding consistent with other neotropical forests. Our data confirm that lianas contribute substantially to tropical forest stem density and diversity, they have highly clumped distributions that appear to be driven by clonal stem recruitment into treefall gaps, and they are increasing relative to trees, thus indicating that lianas will play a greater role in the future dynamics of BCI and other neotropical forests. PMID:23284889

  6. 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

  7. 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. PMID:23667699

  8. Phytoplankton composition and abundance in relation to free-floating Antarctic icebergs

    NASA Astrophysics Data System (ADS)

    Cefarelli, Adrián O.; Vernet, María; Ferrario, Martha E.

    2011-06-01

    Free-drifting icebergs in the Weddell Sea are expected to affect the surrounding marine ecosystem. Sampling associated with iceberg C-18a, a large tabular, free-drifting iceberg in the NW Weddell Sea, carried out from 10 March to 7 April 2009, was designed to test the hypothesis that the iceberg's presence modified phytoplankton composition and abundance. Areas that define a gradient of possible iceberg influence were sampled for phytoplankton: stations close (<1 km) and far (18 km) from iceberg C-18a, an area with numerous small icebergs, Iceberg Alley, and a control site 74 km away. Quantitative samples were obtained from Niskin bottles and counted with an inverted microscope for species abundance. Qualitative samples were collected with nets from the ship's seawater intake. Taxonomic determinations were performed with light and electron microscopy. Overall, diatoms dominated in the mixed layer (surface-˜40 m) and unidentified small flagellated and coccid cells at depth (˜100 m). Fragilariopsis nana, a diatom 2.4-15.5 μm in length, dominated numerically the phytoplankton and was most abundant at the control area. The iceberg's effect on phytoplankton composition was consistent with the hypothesis that they facilitate phytoplankton communities enriched in diatoms, as found in other productive areas of Antarctica. Near the iceberg, diatoms were most abundant, principally at depth, while small flagellate concentration diminished. However, total phytoplankton abundance was lowest at Iceberg Alley in the area of highest meltwater contribution, as indicated by low mean temperature in the mixed layer, and highest at the control site. These results suggest that during austral fall, low growth or high zooplankton grazing could be counteracting the positive effect by icebergs on phytoplankton biomass, otherwise observed in summer months.

  9. 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.

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

    USGS Publications Warehouse

    Merten, Eric C.; Hemstad, Nathaniel A.; Eggert, 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.

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

    USGS Publications Warehouse

    Merten, Eric C.; Hemstad, Nathaniel A.; Eggert, 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.

  12. Emergence of clonally related multidrug resistant Haemophilus influenzae with penicillin-binding protein 3-mediated resistance to extended-spectrum cephalosporins, Norway, 2006 to 2013.

    PubMed

    Skaare, D; Anthonisen, I L; Kahlmeter, G; Matuschek, E; Natås, O B; Steinbakk, M; Sundsfjord, A; Kristiansen, B E

    2014-01-01

    Resistance to cephalosporins in Haemophilus influenzae is usually caused by characteristic alterations in penicillin-binding protein 3 (PBP3), encoded by the ftsI gene. Resistance to extended-spectrum cephalosporins is associated with high-level PBP3-mediated resistance (high-rPBP3), defined by the second stage S385T substitution in addition to a first stage substitution (R517H or N526K). The third stage L389F substitution is present in some high-rPBP3 strains. High-rPBP3 H. influenzae are considered rare outside Japan and Korea. In this study, 30 high-rPBP3 isolates from Norway, collected between 2006 and 2013, were examined by serotyping, multilocus sequence typing (MLST), ftsI sequencing, detection of beta-lactamase genes and minimum inhibitory concentration (MIC) determination. MICs were interpreted according to clinical breakpoints from the European Committee on Antimicrobial Susceptibility Testing (EUCAST). Respiratory isolates predominated (proportion: 24/30). The 30 isolates included one serotype f isolate, while the remaining 29 lacked polysaccharide capsule genes. Resistance to extended-spectrum cephalosporins (cefixime, 29 isolates/30 isolates; cefepime, 28/30; cefotaxime, 26 /30; ceftaroline, 26/30; ceftriaxone, 14/30), beta-lactamase production (11/30) and co-resistance to non-beta-lactams (trimethoprim-sulfamethoxazole, 13/30; tetracycline, 4/30; chloramphenicol, 4/30; ciprofloxacin, 3/30) was frequent. The N526K substitution in PBP3 was present in 23 of 30 isolates; these included a blood isolate which represents the first invasive S385T + N526K isolate reported from Europe. The L389F substitution, present in 16 of 30 isolates, coincided with higher beta-lactam MICs. Non-susceptibility to meropenem was frequent in S385T + L389F + N526K isolates (8/12). All 11 beta-lactamase positive isolates were TEM-1. Five clonal groups of two to 10 isolates with identical MLST-ftsI allelic profiles were observed, including the first reported high-rPBP3

  13. 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.

  14. Propagule Pressure, Habitat Conditions and Clonal Integration Influence the Establishment and Growth of an Invasive Clonal Plant, Alternanthera philoxeroides

    PubMed Central

    You, Wen-Hua; Han, Cui-Min; Fang, Long-Xiang; Du, Dao-Lin

    2016-01-01

    Many notorious invasive plants are clonal, spreading mainly by vegetative propagules. Propagule pressure (the number of propagules) may affect the establishment, growth, and thus invasion success of these clonal plants, and such effects may also depend on habitat conditions. To understand how propagule pressure, habitat conditions and clonal integration affect the establishment and growth of the invasive clonal plants, an 8-week greenhouse with an invasive clonal plant, Alternanthera philoxeroides was conducted. High (five fragments) or low (one fragment) propagule pressure was established either in bare soil (open habitat) or dense native vegetation of Jussiaea repens (vegetative habitat), with the stolon connections either severed from or connected to the relatively older ramets. High propagule pressure greatly increased the establishment and growth of A. philoxeroides, especially when it grew in vegetative habitats. Surprisingly, high propagule pressure significantly reduced the growth of individual plants of A. philoxeroides in open habitats, whereas it did not affect the individual growth in vegetative habitats. A shift in the intraspecific interaction on A. philoxeroides from competition in open habitats to facilitation in vegetative habitats may be the main reason. Moreover, clonal integration significantly improved the growth of A. philoxeroides only in open habitats, especially with low propagule pressure, whereas it had no effects on the growth and competitive ability of A. philoxeroides in vegetative habitats, suggesting that clonal integration may be of most important for A. philoxeroides to explore new open space and spread. These findings suggest that propagule pressure may be crucial for the invasion success of A. philoxeroides, and such an effect also depends on habitat conditions. PMID:27200041

  15. Propagule Pressure, Habitat Conditions and Clonal Integration Influence the Establishment and Growth of an Invasive Clonal Plant, Alternanthera philoxeroides.

    PubMed

    You, Wen-Hua; Han, Cui-Min; Fang, Long-Xiang; Du, Dao-Lin

    2016-01-01

    Many notorious invasive plants are clonal, spreading mainly by vegetative propagules. Propagule pressure (the number of propagules) may affect the establishment, growth, and thus invasion success of these clonal plants, and such effects may also depend on habitat conditions. To understand how propagule pressure, habitat conditions and clonal integration affect the establishment and growth of the invasive clonal plants, an 8-week greenhouse with an invasive clonal plant, Alternanthera philoxeroides was conducted. High (five fragments) or low (one fragment) propagule pressure was established either in bare soil (open habitat) or dense native vegetation of Jussiaea repens (vegetative habitat), with the stolon connections either severed from or connected to the relatively older ramets. High propagule pressure greatly increased the establishment and growth of A. philoxeroides, especially when it grew in vegetative habitats. Surprisingly, high propagule pressure significantly reduced the growth of individual plants of A. philoxeroides in open habitats, whereas it did not affect the individual growth in vegetative habitats. A shift in the intraspecific interaction on A. philoxeroides from competition in open habitats to facilitation in vegetative habitats may be the main reason. Moreover, clonal integration significantly improved the growth of A. philoxeroides only in open habitats, especially with low propagule pressure, whereas it had no effects on the growth and competitive ability of A. philoxeroides in vegetative habitats, suggesting that clonal integration may be of most important for A. philoxeroides to explore new open space and spread. These findings suggest that propagule pressure may be crucial for the invasion success of A. philoxeroides, and such an effect also depends on habitat conditions. PMID:27200041

  16. 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

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

    PubMed

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

    2016-01-01

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

  18. Female and male fitness consequences of clonal growth in a dwarf bamboo population with a high degree of clonal intermingling

    PubMed Central

    Matsuo, Ayumi; Tomimatsu, Hiroshi; Suzuki, Jun-Ichirou; Saitoh, Tomoyuki; Shibata, Shozo; Makita, Akifumi; Suyama, Yoshihisa

    2014-01-01

    Background and Aims Although many studies have reported that clonal growth interferes with sexual reproduction as a result of geitonogamous self-pollination and inbreeding depression, the mating costs of clonal growth are expected to be reduced when genets are spatially intermingled with others. This study examined how clonal growth affects both female and male reproductive success by studying a population of a mass-flowering plant, Sasa veitchii var. hirsuta, with a high degree of clonal intermingling. Methods In a 10 × 10 m plot, genets were discriminated based on the multilocus genotypes of 11 nuclear microsatellite loci. The relationships between genet size and the components of reproductive success were then investigated. Male siring success and female and male selfing rates were assessed using paternity analysis. Key Results A total of 111 genets were spatially well intermingled with others. In contrast to previous studies with species forming distinct monoclonal patches, seed production linearly increased with genet size. While male siring success was a decelerating function of genet size, selfing rates were relatively low and not related to genet size. Conclusions The results, in conjunction with previous studies, emphasize the role of the spatial arrangement of genets on both the quantity and quality of offpsring, and suggest that an intermingled distribution of genets can reduce the mating costs of clonal growth and enhance overall fitness, particularly female fitness. PMID:25228034

  19. Plant traits and ecosystem effects of clonality: a new research agenda

    PubMed Central

    Cornelissen, Johannes H. C.; Song, Yao-Bin; Yu, Fei-Hai; Dong, Ming

    2014-01-01

    Background Clonal plants spread laterally by spacers between their ramets (shoot–root units); these spacers can transport and store resources. While much is known about how clonality promotes plant fitness, we know little about how different clonal plants influence ecosystem functions related to carbon, nutrient and water cycling. Approach The response–effect trait framework is used to formulate hypotheses about the impact of clonality on ecosystems. Central to this framework is the degree of correspondence between interspecific variation in clonal ‘response traits’ that promote plant fitness and interspecific variation in ‘effect traits’, which define a plant's potential effect on ecosystem functions. The main example presented to illustrate this concept concerns clonal traits of vascular plant species that determine their lateral extension patterns. In combination with the different degrees of decomposability of litter derived from their spacers, leaves, roots and stems, these clonal traits should determine associated spatial and temporal patterns in soil organic matter accumulation, nutrient availability and water retention. Conclusions This review gives some concrete pointers as to how to implement this new research agenda through a combination of (1) standardized screening of predominant species in ecosystems for clonal response traits and for effect traits related to carbon, nutrient and water cycling; (2) analysing the overlap between variation in these response traits and effect traits across species; (3) linking spatial and temporal patterns of clonal species in the field to those for soil properties related to carbon, nutrient and water stocks and dynamics; and (4) studying the effects of biotic interactions and feedbacks between resource heterogeneity and clonality. Linking these to environmental changes may help us to better understand and predict the role of clonal plants in modulating impacts of climate change and human activities on

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

    USGS Publications Warehouse

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

    2011-01-01

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

  1. 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.

  2. 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.

  3. 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. PMID:23068166

  4. 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. PMID:25423586

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

    USGS Publications Warehouse

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

    2000-01-01

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

  6. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

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

  8. 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

  9. Relative abundance of and composition within fungal orders differ between cheatgrass (Bromus tectorum) and sagebrush (Artemisia tridentate)-associated soils.

    PubMed

    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

  10. Relative abundance of and composition within fungal orders differ between cheatgrass (Bromus tectorum) and sagebrush (Artemisia tridentata)-associated soils.

    PubMed

    Wiber, 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

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

    PubMed

    Damare, Varada; Raghukumar, Seshagiri

    2008-07-01

    Thraustochytrid protists are often abundant in coastal waters. However, their population dynamics and substrate preferences in the oceanic water column are poorly understood. We studied the abundance and distribution of thraustochytrids, bacteria and TEPs in the equatorial Indian Ocean waters during September 2003, October 2004 and September 2006. Thraustochytrids and bacteria were abundant, suggesting high biological productivity of the region. Thraustochytrids were positively related to bacteria during October 2004 but not at other times, suggesting overlapping or varying substrate preferences at different times. Thraustochytrid and bacteria were positively related to TEPs only in a few stations during October 2004, but were mostly positively related to TEPs generated from in situ water in a roller table experiment. TEPs from natural samples during October 2004 had a much greater affinity to the lectin Concanavalin A than to Limulin compared with those in September 2006 and from the roller tank experiments. The chemical composition of TEPs might explain their relationship with thraustochytrids. Thraustochytrids averaged a higher biomass than bacteria in two of the three cruises, but were less frequent and more patchily distributed compared with bacteria. PMID:18510715

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

    NASA Astrophysics Data System (ADS)

    Marboeuf, Ulysse; Schmitt, Bernard

    2014-11-01

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

  13. 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

  14. Complex Antigens Drive Permissive Clonal Selection in Germinal Centers.

    PubMed

    Kuraoka, Masayuki; Schmidt, Aaron G; Nojima, Takuya; Feng, Feng; Watanabe, Akiko; Kitamura, Daisuke; Harrison, Stephen C; Kepler, Thomas B; Kelsoe, Garnett

    2016-03-15

    Germinal center (GC) B cells evolve toward increased affinity by a Darwinian process that has been studied primarily in genetically restricted, hapten-specific responses. We explored the population dynamics of genetically diverse GC responses to two complex antigens-Bacillus anthracis protective antigen and influenza hemagglutinin-in which B cells competed both intra- and interclonally for distinct epitopes. Preferred VH rearrangements among antigen-binding, naive B cells were similarly abundant in early GCs but, unlike responses to haptens, clonal diversity increased in GC B cells as early "winners" were replaced by rarer, high-affinity clones. Despite affinity maturation, inter- and intraclonal avidities varied greatly, and half of GC B cells did not bind the immunogen but nonetheless exhibited biased VH use, V(D)J mutation, and clonal expansion comparable to antigen-binding cells. GC reactions to complex antigens permit a range of specificities and affinities, with potential advantages for broad protection. PMID:26948373

  15. Comparison of bacterial culture and 16S rRNA community profiling by clonal analysis and pyrosequencing for the characterization of the dentine caries-associated microbiome

    PubMed Central

    Schulze-Schweifing, Kathrin; Banerjee, Avijit; Wade, William G.

    2014-01-01

    Culture-independent analyses have greatly expanded knowledge regarding the composition of complex bacterial communities including those associated with oral diseases. A consistent finding from such studies, however, has been the under-reporting of members of the phylum Actinobacteria. In this study, five pairs of broad range primers targeting 16S rRNA genes were used in clonal analysis of 6 samples collected from tooth lesions involving dentine in subjects with active caries. Samples were also subjected to cultural analysis and pyrosequencing by means of the 454 platform. A diverse bacterial community of 229 species-level taxa was revealed by culture and clonal analysis, dominated by representatives of the genera Prevotella, Lactobacillus, Selenomonas, and Streptococcus. The five most abundant species were: Lactobacillus gasseri, Prevotella denticola, Alloprevotella tannerae, S. mutans and Streptococcus sp. HOT 070, which together made up 31.6 % of the sequences. Two samples were dominated by lactobacilli, while the remaining samples had low numbers of lactobacilli but significantly higher numbers of Prevotella species. The different primer pairs produced broadly similar data but proportions of the phylum Bacteroidetes were significantly higher when primer 1387R was used. All of the primer sets underestimated the proportion of Actinobacteria compared to culture. Pyrosequencing analysis of the samples was performed to a depth of sequencing of 4293 sequences per sample which were identified to 264 species-level taxa, and resulted in significantly higher coverage estimates than the clonal analysis. Pyrosequencing, however, also underestimated the relative abundance of Actinobacteria compared to culture. PMID:25429361

  16. Comparison of bacterial culture and 16S rRNA community profiling by clonal analysis and pyrosequencing for the characterization of the dentine caries-associated microbiome.

    PubMed

    Schulze-Schweifing, Kathrin; Banerjee, Avijit; Wade, William G

    2014-01-01

    Culture-independent analyses have greatly expanded knowledge regarding the composition of complex bacterial communities including those associated with oral diseases. A consistent finding from such studies, however, has been the under-reporting of members of the phylum Actinobacteria. In this study, five pairs of broad range primers targeting 16S rRNA genes were used in clonal analysis of 6 samples collected from tooth lesions involving dentine in subjects with active caries. Samples were also subjected to cultural analysis and pyrosequencing by means of the 454 platform. A diverse bacterial community of 229 species-level taxa was revealed by culture and clonal analysis, dominated by representatives of the genera Prevotella, Lactobacillus, Selenomonas, and Streptococcus. The five most abundant species were: Lactobacillus gasseri, Prevotella denticola, Alloprevotella tannerae, S. mutans and Streptococcus sp. HOT 070, which together made up 31.6 % of the sequences. Two samples were dominated by lactobacilli, while the remaining samples had low numbers of lactobacilli but significantly higher numbers of Prevotella species. The different primer pairs produced broadly similar data but proportions of the phylum Bacteroidetes were significantly higher when primer 1387R was used. All of the primer sets underestimated the proportion of Actinobacteria compared to culture. Pyrosequencing analysis of the samples was performed to a depth of sequencing of 4293 sequences per sample which were identified to 264 species-level taxa, and resulted in significantly higher coverage estimates than the clonal analysis. Pyrosequencing, however, also underestimated the relative abundance of Actinobacteria compared to culture. PMID:25429361

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

    PubMed

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

    2016-02-01

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

  18. The role of plant propagation at clonal genebanks

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Clonal genebanks utilize both seed and vegetative propagation techniques. Seed propagation is important for the introduction of new genotypes (accessions), especially crop wild relatives. Additionally, seed may be produced by breeding or to otherwise support research. Temperate tree fruit and nut c...

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

    PubMed Central

    Jiménez-Soto, Luisa F.; Haas, Rainer

    2016-01-01

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

  20. 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.

  1. Relative abundance and behavior of marine mammals exposed to transmissions from the Heard Island Feasibility Test.

    PubMed

    Bowles, A E; Smultea, M; Würsig, B; DeMaster, D P; Palka, D

    1994-10-01

    The Heard Island Feasibility Test source transmitted a hum at 209-220 dB re: 1 microPa at 175-m depth, centered on 57 Hz with a maximum bandwidth of 30 Hz for 1 h of every 3. Experienced marine mammal observers conducted line-transect surveys and monitored marine mammal behavior visually and acoustically in a 70 x 70 km square centered on the transmission site. Thirty-nine groups of cetaceans and 19 of pinnipeds were sighted from both vessels before the start of transmissions. Thirty-nine groups of cetaceans and 23 of pinnipeds were sighted during transmissions. Blue (Balaenoptera musculus), fin (B. physalus), and sperm (Physeter macrocephalus) whales were sighted during the base line period; blue, sperm, and possibly sei (B. borealis) whales were sighted during the transmission period. More schools of hourglass dolphins (Lagenorhynchus cruciger) were sighted during transmissions, but fewer groups of pilot whales (Globicephala melas), southern bottlenose whales (Hyperoodon planifrons), and minke whales (B. acutorostrata). The density of all cetaceans was 0.0157 groups/km2 before the transmissions and 0.0166 groups/km2 during. Antarctic fur seals (Arctocephalus gazella) and southern elephant seals (Mirounga leonina) were seen, but not in sufficient numbers to estimate abundance. One blue whale tracked before, during and after a transmission changed respiration and reorientation rates, but did not avoid the source detectably. Sperm whales and pilot whales were heard in 23% of 1181 min of baseline acoustic surveys; but in none of 1939 min during the transmission period. Both species were heard within 48 h after the end of the test. PMID:7963037

  2. LDL Receptor-related Protein 1 Regulates the Abundance of Diverse Cell-signaling Proteins in the Plasma Membrane Proteome

    PubMed Central

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

    2010-01-01

    LDL receptor-related protein 1 (LRP1) is an endocytic receptor, reported to regulate the abundance of other receptors in the plasma membrane, including uPAR and tissue factor. The goal of this study was to identify novel plasma membrane proteins, involved in cell-signaling, which are regulated by LRP1. Membrane protein ectodomains were prepared from RAW 264.7 cells in which LRP1 was silenced and control cells using protease K. Peptides were identified by LC-MS/MS. By analysis of spectral counts, 31 transmembrane and secreted proteins were regulated in abundance at least 2-fold when LRP1 was silenced. Validation studies confirmed that semaphorin4D (Sema4D), plexin domain-containing protein-1 (Plxdc1), and neuropilin-1 were more abundant in the membranes of LRP1 gene-silenced cells. Regulation of Plxdc1 by LRP1 was confirmed in CHO cells, as a second model system. Plxdc1 co-immunoprecipitated with LRP1 from extracts of RAW 264.7 cells and mouse liver. Although Sema4D did not co-immunoprecipitate with LRP1, the cell-surface level of Sema4D was increased by RAP, which binds to LRP1 and inhibits binding of other ligands. These studies identify Plxdc1, Sema4D, and neuropilin-1 as novel LRP1-regulated cell-signaling proteins. Overall, LRP1 emerges as a generalized regulator of the plasma membrane proteome. PMID:20919742

  3. 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.

  4. 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.

  5. The influence of chemical composition on the properties of Cepheid stars. I. Period-Luminosity relation vs. iron abundance

    NASA Astrophysics Data System (ADS)

    Romaniello, M.; Primas, F.; Mottini, M.; Groenewegen, M.; Bono, G.; François, P.

    2005-01-01

    We have assessed the influence of the stellar iron content on the Cepheid Period-Luminosity (PL) relation by relating the V band residuals from the Freedman et al. (\\cite{fre01}) PL relation to [Fe/H] for 37 Galactic and Magellanic Clouds Cepheids. The iron abundances were measured from FEROS and UVES high-resolution and high-signal to noise optical spectra. Our data indicate that the stars become fainter as metallicity increases, until a plateau or turnover point is reached at about solar metallicity. Our data are incompatible with both no dependence of the PL relation on iron abundance, and with the linearly decreasing behavior often found in the literature (e.g. Kennicutt et al. \\cite{ken98}; Sakai et al. \\cite{sak04}). On the other hand, non-linear theoretical models of Fiorentino et al. (\\cite{fio02}) provide a fairly good description of the data. Based on observations made with ESO Telescopes at La Silla and Paranal Observatories under proposal ID 66.D-0571. Table \\ref{tab:log} is only available in electronic form at http://www.edpsciences.org

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

    PubMed

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

    2012-07-01

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

  7. Influences of clonality on plant sexual reproduction

    PubMed Central

    Barrett, Spencer C. H.

    2015-01-01

    Flowering plants possess an unrivaled diversity of mechanisms for achieving sexual and asexual reproduction, often simultaneously. The commonest type of asexual reproduction is clonal growth (vegetative propagation) in which parental genotypes (genets) produce vegetative modules (ramets) that are capable of independent growth, reproduction, and often dispersal. Clonal growth leads to an expansion in the size of genets and increased fitness because large floral displays increase fertility and opportunities for outcrossing. Moreover, the clonal dispersal of vegetative propagules can assist “mate finding,” particularly in aquatic plants. However, there are ecological circumstances in which functional antagonism between sexual and asexual reproductive modes can negatively affect the fitness of clonal plants. Populations of heterostylous and dioecious species have a small number of mating groups (two or three), which should occur at equal frequency in equilibrium populations. Extensive clonal growth and vegetative dispersal can disrupt the functioning of these sexual polymorphisms, resulting in biased morph ratios and populations with a single mating group, with consequences for fertility and mating. In populations in which clonal propagation predominates, mutations reducing fertility may lead to sexual dysfunction and even the loss of sex. Recent evidence suggests that somatic mutations can play a significant role in influencing fitness in clonal plants and may also help explain the occurrence of genetic diversity in sterile clonal populations. Highly polymorphic genetic markers offer outstanding opportunities for gaining novel insights into functional interactions between sexual and clonal reproduction in flowering plants. PMID:26195747

  8. Demographic consequences of greater clonal than sexual reproduction in Dicentra canadensis.

    PubMed

    Lin, Chia-Hua; Miriti, Maria N; Goodell, Karen

    2016-06-01

    Clonality is a widespread life history trait in flowering plants that may be essential for population persistence, especially in environments where sexual reproduction is unpredictable. Frequent clonal reproduction, however, could hinder sexual reproduction by spatially aggregating ramets that compete with seedlings and reduce inter-genet pollination. Nevertheless, the role of clonality in relation to variable sexual reproduction in population dynamics is often overlooked. We combined population matrix models and pollination experiments to compare the demographic contributions of clonal and sexual reproduction in three Dicentra canadensis populations, one in a well-forested landscape and two in isolated forest remnants. We constructed stage-based transition matrices from 3 years of census data to evaluate annual population growth rates, λ. We used loop analysis to evaluate the relative contribution of different reproductive pathways to λ. Despite strong temporal and spatial variation in seed set, populations generally showed stable growth rates. Although we detected some pollen limitation of seed set, manipulative pollination treatments did not affect population growth rates. Clonal reproduction contributed significantly more than sexual reproduction to population growth in the forest remnants. Only at the well-forested site did sexual reproduction contribute as much as clonal reproduction to population growth. Flowering plants were more likely to transition to a smaller size class with reduced reproductive potential in the following year than similarly sized nonflowering plants, suggesting energy trade-offs between sexual and clonal reproduction at the individual level. Seed production had negligible effects on growth and tuber production of individual plants. Our results demonstrate that clonal reproduction is vital for population persistence in a system where sexual reproduction is unpredictable. The bias toward clonality may be driven by low fitness returns

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

    USGS Publications Warehouse

    Angermeier, Paul L.; Smogor, Roy A.

    1995-01-01

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

  10. Clonal Outbreak of Plasmodium falciparum Infection in Eastern Panama

    PubMed Central

    Obaldia, Nicanor; Baro, Nicholas K.; Calzada, Jose E.; Santamaria, Ana M.; Daniels, Rachel; Wong, Wesley; Chang, Hsiao-Han; Hamilton, Elizabeth J.; Arevalo-Herrera, Myriam; Herrera, Socrates; Wirth, Dyann F.; Hartl, Daniel L.; Marti, Matthias; Volkman, Sarah K.

    2015-01-01

    Identifying the source of resurgent parasites is paramount to a strategic, successful intervention for malaria elimination. Although the malaria incidence in Panama is low, a recent outbreak resulted in a 6-fold increase in reported cases. We hypothesized that parasites sampled from this epidemic might be related and exhibit a clonal population structure. We tested the genetic relatedness of parasites, using informative single-nucleotide polymorphisms and drug resistance loci. We found that parasites were clustered into 3 clonal subpopulations and were related to parasites from Colombia. Two clusters of Panamanian parasites shared identical drug resistance haplotypes, and all clusters shared a chloroquine-resistance genotype matching the pfcrt haplotype of Colombian origin. Our findings suggest these resurgent parasite populations are highly clonal and that the high clonality likely resulted from epidemic expansion of imported or vestigial cases. Malaria outbreak investigations that use genetic tools can illuminate potential sources of epidemic malaria and guide strategies to prevent further resurgence in areas where malaria has been eliminated. PMID:25336725

  11. 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

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

    PubMed

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

    2012-01-01

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

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

    PubMed Central

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

    2013-01-01

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

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

    USGS Publications Warehouse

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

    1991-01-01

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

  15. Effect of iTRAQ labeling on the relative abundance of peptide fragment ions produced by MALDI-MS/MS.

    PubMed

    Gandhi, Tejas; Puri, Pranav; Fusetti, Fabrizia; Breitling, Rainer; Poolman, Bert; Permentier, Hjalmar P

    2012-08-01

    The identification of proteins in proteomics experiments is usually based on mass information derived from tandem mass spectrometry data. To improve the performance of the identification algorithms, additional information available in the fragment peak intensity patterns has been shown to be useful. In this study, we consider the effect of iTRAQ labeling on the fragment peak intensity patterns of singly charged peptides from MALDI tandem MS data. The presence of an iTRAQ-modified basic group on the N-terminus leads to a more pronounced set of b-ion peaks and distinct changes in the abundance of specific peptide types. We performed a simple intensity prediction by using a decision-tree machine learning approach and were able to show that the relative ion abundance in a spectrum can be correctly predicted and distinguished from closely related sequences. This information will be useful for the development of improved method-specific intensity-based protein identification algorithms. PMID:22770492

  16. 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. PMID:24331596

  17. 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

  18. 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

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

    NASA Technical Reports Server (NTRS)

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

    1998-01-01

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

  20. Generation of clonal zebrafish line by androgenesis without egg irradiation.

    PubMed

    Hou, Jilun; Fujimoto, Takafumi; Saito, Taiju; Yamaha, Etsuro; Arai, Katsutoshi

    2015-01-01

    Generation of clonal zebrafish will facilitate large-scale genetic screening and help us to overcome other biological and biotechnological challenges due to their isogenecity. However, protocols for the development of clonal lines have not been optimized. Here, we sought to develop a novel method for generation of clonal zebrafish by androgenesis induced by cold shock. Androgenetic zebrafish doubled haploids (DHs) were induced by cold shock of just-fertilized eggs, and the eggs were then heat shocked to double the chromosome set. The yield rate of putative DHs relative to the total number of eggs used was 1.10% ± 0.19%. Microsatellite genotyping of the putative DHs using 30 loci that covered all 25 linkage groups detected no heterozygous loci, confirming the homozygosity of the DHs. Thus, a clonal line was established from sperm of a DH through a second cycle of cold-shock androgenesis and heat-shock chromosome doubling, followed by genetic verification of the isogenic rate confirming the presence of identical DNA fingerprints by using amplified fragment length polymorphism markers. In addition, our data provided important insights into the cytological mechanisms of cold-shock-induced androgenesis. PMID:26289165

  1. Generation of clonal zebrafish line by androgenesis without egg irradiation

    PubMed Central

    Hou, Jilun; Fujimoto, Takafumi; Saito, Taiju; Yamaha, Etsuro; Arai, Katsutoshi

    2015-01-01

    Generation of clonal zebrafish will facilitate large-scale genetic screening and help us to overcome other biological and biotechnological challenges due to their isogenecity. However, protocols for the development of clonal lines have not been optimized. Here, we sought to develop a novel method for generation of clonal zebrafish by androgenesis induced by cold shock. Androgenetic zebrafish doubled haploids (DHs) were induced by cold shock of just-fertilized eggs, and the eggs were then heat shocked to double the chromosome set. The yield rate of putative DHs relative to the total number of eggs used was 1.10% ± 0.19%. Microsatellite genotyping of the putative DHs using 30 loci that covered all 25 linkage groups detected no heterozygous loci, confirming the homozygosity of the DHs. Thus, a clonal line was established from sperm of a DH through a second cycle of cold-shock androgenesis and heat-shock chromosome doubling, followed by genetic verification of the isogenic rate confirming the presence of identical DNA fingerprints by using amplified fragment length polymorphism markers. In addition, our data provided important insights into the cytological mechanisms of cold-shock–induced androgenesis. PMID:26289165

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

    PubMed

    Tempel, Douglas J; Gutiérrez, R J

    2013-10-01

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

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

    PubMed

    Brunnschweiler, Juerg M; Baensch, Harald

    2011-01-01

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

  4. 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

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

    PubMed

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

    2015-01-01

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

  6. 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

  7. 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

    2015-01-01

    Glycerophospholipids with two, non-equivalent fatty acyl chains can adopt one of two isomeric forms depending on the relative position of substitutions on the glycerol backbone. These so-called sn-positional isomers can have distinct biophysical and biochemical behaviors making it desirable to uniquely assign their regiochemistries. Unambiguous assignment of such similar molecular structures in complex biological extracts is a significant challenge to current analytical technologies. We have recently reported a novel mass spectrometric method that combines collision- and ozone-induced dissociation in series (CID/OzID) to yield product ions characteristic of acyl chain substitution patterns in glycerophospholipids. Here phosphatidylcholines are examined using the CID/OzID protocol combined with desorption electrospray ionization (DESI) to facilitate the rapid exploration of sample arrays comprised of a wide variety of synthetic and biological sources. Comparison of the spectra acquired from different extracts reveals that the sn-positional isomers PC 16:0/18:1 and PC 18:1/16:0 (where the 18:1 chain is present at the sn-2 and sn-1 position of the glycerol backbone, respectively) are most often found together in lipids of either natural or synthetic origin. Moreover, the proportions of the two isomers vary significantly between extracts from different organisms or even between adjacent tissues from the same organism. PMID:25880027

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  9. Strong but diverging clonality - climate relationships of different plant clades explain weak overall pattern across China

    PubMed Central

    Ye, Duo; Liu, Guofang; Song, Yao-Bin; Cornwell, William K.; Dong, Ming; Cornelissen, Johannes H. C.

    2016-01-01

    The clonal strategy should be relatively important in stressful environments (i.e. of low resource availability or harsh climate), e.g. in cold habitats. However, our understanding of the distribution pattern of clonality along environmental gradients is still far from universal. The weakness and inconsistency of overall clonality-climate relationships across taxa, as reported in previous studies, may be due to different phylogenetic lineages having fundamental differences in functional traits other than clonality determining their climate response. Thus, in this study we compared the clonality-climate relationships along a latitudinal gradient within and between different lineages at several taxonomic levels, including four major angiosperm lineages (Magnoliidae, Monocotyledoneae, Superrosidae and Superasteridae), orders and families. To this aim we used a species clonality dataset for 4015 vascular plant species in 545 terrestrial communities across China. Our results revealed clear predictive patterns of clonality proportion in relation to environmental gradients for the predominant representatives of each of the taxonomic levels above, but the relationships differed in shape and strength between the 4 major angiosperm lineages, between the 12 orders and between the 12 families. These different relationships canceled out one another when all lineages at a certain taxonomic level were pooled. Our findings highlight the importance of explicitly accounting for the functional or taxonomic scale for studying variation in plant ecological strategy across environmental gradients. PMID:27246203

  10. Strong but diverging clonality - climate relationships of different plant clades explain weak overall pattern across China.

    PubMed

    Ye, Duo; Liu, Guofang; Song, Yao-Bin; Cornwell, William K; Dong, Ming; Cornelissen, Johannes H C

    2016-01-01

    The clonal strategy should be relatively important in stressful environments (i.e. of low resource availability or harsh climate), e.g. in cold habitats. However, our understanding of the distribution pattern of clonality along environmental gradients is still far from universal. The weakness and inconsistency of overall clonality-climate relationships across taxa, as reported in previous studies, may be due to different phylogenetic lineages having fundamental differences in functional traits other than clonality determining their climate response. Thus, in this study we compared the clonality-climate relationships along a latitudinal gradient within and between different lineages at several taxonomic levels, including four major angiosperm lineages (Magnoliidae, Monocotyledoneae, Superrosidae and Superasteridae), orders and families. To this aim we used a species clonality dataset for 4015 vascular plant species in 545 terrestrial communities across China. Our results revealed clear predictive patterns of clonality proportion in relation to environmental gradients for the predominant representatives of each of the taxonomic levels above, but the relationships differed in shape and strength between the 4 major angiosperm lineages, between the 12 orders and between the 12 families. These different relationships canceled out one another when all lineages at a certain taxonomic level were pooled. Our findings highlight the importance of explicitly accounting for the functional or taxonomic scale for studying variation in plant ecological strategy across environmental gradients. PMID:27246203

  11. Strong but diverging clonality - climate relationships of different plant clades explain weak overall pattern across China

    NASA Astrophysics Data System (ADS)

    Ye, Duo; Liu, Guofang; Song, Yao-Bin; Cornwell, William K.; Dong, Ming; Cornelissen, Johannes H. C.

    2016-06-01

    The clonal strategy should be relatively important in stressful environments (i.e. of low resource availability or harsh climate), e.g. in cold habitats. However, our understanding of the distribution pattern of clonality along environmental gradients is still far from universal. The weakness and inconsistency of overall clonality-climate relationships across taxa, as reported in previous studies, may be due to different phylogenetic lineages having fundamental differences in functional traits other than clonality determining their climate response. Thus, in this study we compared the clonality-climate relationships along a latitudinal gradient within and between different lineages at several taxonomic levels, including four major angiosperm lineages (Magnoliidae, Monocotyledoneae, Superrosidae and Superasteridae), orders and families. To this aim we used a species clonality dataset for 4015 vascular plant species in 545 terrestrial communities across China. Our results revealed clear predictive patterns of clonality proportion in relation to environmental gradients for the predominant representatives of each of the taxonomic levels above, but the relationships differed in shape and strength between the 4 major angiosperm lineages, between the 12 orders and between the 12 families. These different relationships canceled out one another when all lineages at a certain taxonomic level were pooled. Our findings highlight the importance of explicitly accounting for the functional or taxonomic scale for studying variation in plant ecological strategy across environmental gradients.

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

    NASA Astrophysics Data System (ADS)

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

    2005-04-01

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

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

    PubMed

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

    2015-09-01

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

  14. Clonal Plasticity of Aquatic Plant Species Submitted to Mechanical Stress: Escape versus Resistance Strategy

    PubMed Central

    Puijalon, Sara; Bouma, Tjeerd J.; Van Groenendael, Jan; Bornette, Gudrun

    2008-01-01

    Background and Aims The plastic alterations of clonal architecture are likely to have functional consequences, as they affect the spatial distribution of ramets over patchy environments. However, little is known about the effect of mechanical stresses on the clonal growth. The aim of the present study was to investigate the clonal plasticity induced by mechanical stress consisting of continuous water current encountered by aquatic plants. More particularly, the aim was to test the capacity of the plants to escape this stress through clonal plastic responses. Methods The transplantation of ramets of the same clone in two contrasting flow velocity conditions was carried out for two species (Potamogeton coloratus and Mentha aquatica) which have contrasting clonal growth forms. Relative allocation to clonal growth, to creeping stems in the clonal biomass, number and total length of creeping stems, spacer length and main creeping stem direction were measured. Key Results For P. coloratus, plants exposed to water current displayed increased total length of creeping stems, increased relative allocation to creeping stems within the clonal dry mass and increased spacer length. For M. aquatica, plants exposed to current displayed increased number and total length of creeping stems. Exposure to current induced for both species a significant increase of the proportion of creeping stems in the downstream direction to the detriment of creeping stems perpendicular to flow. Conclusions This study demonstrates that mechanical stress from current flow induced plastic variation in clonal traits for both species. The responses of P. coloratus could lead to an escape strategy, with low benefits with respect to sheltering and anchorage. The responses of M. aquatica that may result in a denser canopy and enhancement of anchorage efficiency could lead to a resistance strategy. PMID:18854376

  15. Clonal Evolution in Multiple Myeloma.

    PubMed

    Fakhri, Bita; Vij, Ravi

    2016-08-01

    Multiple myeloma (MM) is the second most common hematologic malignancy encountered among patients in the United States. The last decade has seen incremental improvements in the survival of patients with MM. These advances are, to a large extent, attributable to the addition of proteasome inhibitors and immunomodulatory drugs to the armamentarium of treatment options. The adoption of these drug classes was the result of an empiric research paradigm. However, with the application of next generation sequencing technologies, we are now starting to unravel the genomic landscape of MM. It is hoped that this will allow us to better disentangle the biology of the disease and allow for identification of new therapeutic targets. In this article, we review what we have learned to date about the mutational profile, clonal architecture, and evolution of the disease, and discuss the potential clinical implications of these findings. PMID:27521309

  16. African 2, a Clonal Complex of Mycobacterium bovis Epidemiologically Important in East Africa▿ †

    PubMed Central

    Berg, Stefan; Garcia-Pelayo, M. Carmen; Müller, Borna; Hailu, Elena; Asiimwe, Benon; Kremer, Kristin; Dale, James; Boniotti, M. Beatrice; Rodriguez, Sabrina; Hilty, Markus; Rigouts, Leen; Firdessa, Rebuma; Machado, Adelina; Mucavele, Custodia; Ngandolo, Bongo Nare Richard; Bruchfeld, Judith; Boschiroli, Laura; Müller, Annélle; Sahraoui, Naima; Pacciarini, Maria; Cadmus, Simeon; Joloba, Moses; van Soolingen, Dick; Michel, Anita L.; Djønne, Berit; Aranaz, Alicia; Zinsstag, Jakob; van Helden, Paul; Portaels, Françoise; Kazwala, Rudovick; Källenius, Gunilla; Hewinson, R. Glyn; Aseffa, Abraham; Gordon, Stephen V.; Smith, Noel H.

    2011-01-01

    We have identified a clonal complex of Mycobacterium bovis isolated at high frequency from cattle in Uganda, Burundi, Tanzania, and Ethiopia. We have named this related group of M. bovis strains the African 2 (Af2) clonal complex of M. bovis. Af2 strains are defined by a specific chromosomal deletion (RDAf2) and can be identified by the absence of spacers 3 to 7 in their spoligotype patterns. Deletion analysis of M. bovis isolates from Algeria, Mali, Chad, Nigeria, Cameroon, South Africa, and Mozambique did not identify any strains of the Af2 clonal complex, suggesting that this clonal complex of M. bovis is localized in East Africa. The specific spoligotype pattern of the Af2 clonal complex was rarely identified among isolates from outside Africa, and the few isolates that were found and tested were intact at the RDAf2 locus. We conclude that the Af2 clonal complex is localized to cattle in East Africa. We found that strains of the Af2 clonal complex of M. bovis have, in general, four or more copies of the insertion sequence IS6110, in contrast to the majority of M. bovis strains isolated from cattle, which are thought to carry only one or a few copies. PMID:21097608

  17. Clonal reproduction shapes evolution in the lizard malaria parasite Plasmodium floridense.

    PubMed

    Falk, Bryan G; Glor, Richard E; Perkins, Susan L

    2015-06-01

    The preponderant clonal evolution hypothesis (PCE) predicts that frequent clonal reproduction (sex between two clones) in many pathogens capable of sexual recombination results in strong linkage disequilibrium and the presence of discrete genetic subdivisions characterized by occasional gene flow. We expand on the PCE and predict that higher rates of clonal reproduction will result in: (1) morphologically cryptic species that exhibit (2) low within-species variation and (3) recent between-species divergence. We tested these predictions in the Caribbean lizard malaria parasite Plasmodium floridense using 63 single-infection samples in lizards collected from across the parasite's range, and sequenced them at two mitochondrial, one apicoplast, and five nuclear genes. We identified 11 provisionally cryptic species within P. floridense, each of which exhibits low intraspecific variation and recent divergence times between species (some diverged approximately 110,000 years ago). Our results are consistent with the hypothesis that clonal reproduction can profoundly affect diversification of species capable of sexual recombination, and suggest that clonal reproduction may have led to a large number of unrecognized pathogen species. The factors that may influence the rates of clonal reproduction among pathogens are unclear, and we discuss how prevalence and virulence may relate to clonal reproduction. PMID:25959003

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

    NASA Technical Reports Server (NTRS)

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

    2003-01-01

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

  19. 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. PMID:27126608

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

    PubMed

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

    2014-12-01

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

  1. 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

  2. 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

  3. Contrasting clonal structure among Pocillopora (Scleractinia) communities at two environmentally distinct sites in the Gulf of California

    NASA Astrophysics Data System (ADS)

    Pinzón, J. H.; Reyes-Bonilla, H.; Baums, I. B.; LaJeunesse, T. C.

    2012-09-01

    The contributions of sexual versus asexual reproduction are thought to play an important role in the abundance and ecological success of corals, especially in marginal habitats. Pocillopora corals are distributed throughout the Indo-Pacific and dominate shallow hard-bottom communities in the eastern Pacific where broad seasonal fluctuations in temperature and water turbidity create suboptimal conditions for reef community development. Previous work had revealed three genetic clades in the eastern Pacific that show little correspondence with colony morphology; the broad distribution of type 1 extends into the subtropical southern Gulf of California. Here we examine genetic and clonal structure of two type 1 communities separated by 10 km with microsatellite data. Samples were collected randomly in six 10 m radius circular plots (20 colonies per plot, 3 plots per site). Sites differed in their relative clonality because clonemates (ramets) from a single clone (genet) dominated a large portion (90.9 m long) of the protected leeward side of Gaviota Island (Number of genets/Number of samples = 0.35; observed Genotypic diversity/expected Genotypic diversity = 0.087), while an exposed community at the entrance to La Paz Bay, Punta Galeras, exhibited high genotypic diversity ( N g / N = 0.85; G o / G e = 0.714). Gene flow was unrestricted between sites indicating these communities comprised a single population. The relative proportion of asexual colonies found between community aggregations of Pocillopora in the Gulf of California differed significantly and suggests factors at local, not regional, scales affect these patterns. The possibility that heterogeneity in clonal structure is common throughout the eastern Pacific and across the west Indo-Pacific requires further study. Finally, since morphological variation in Pocillopora has been underappreciated and is in need of taxonomic revision, the use of a consistent field-sampling protocol and high-resolution makers will

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

    USGS Publications Warehouse

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

    2008-01-01

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

  5. Relative abundance and patterns of correlation among six cytokines in pleural fluid measured by cytometric bead array.

    PubMed

    Aoe, Keisuke; Hiraki, Akio; Murakami, Tomoyuki; Murakami, Kazuo; Makihata, Kiyoshi; Takao, Kazushi; Eda, Ryosuke; Maeda, Tadashi; Sugi, Kazuro; Darzynkiewicz, Zbigniew; Takeyama, Hiroyasu

    2003-08-01

    Several cytokines play significant roles in the development and pathogenesis of pleural effusion. Little is known, however, about possible interactions between individual cytokines in terms of regulation of their relative abundance in the effusion. We studied 93 patients presenting with pleural effusion to the National Sanyo Hospital (68 men and 25 women; mean age, 64 years). Twenty-two patients had tuberculous pleurisy, 40 had malignant pleuritis, and 31 had effusions due to an etiology other than tuberculosis or cancer (miscellaneous). Pleural fluid concentrations of IL-2, IL-4, IL-5, IL-10, TNF-alpha, and INF-gamma were simultaneously measured by cytometric bead array (CBA). The ratios of IL-4/IL-5, IL-4/TNF-alpha, IL-2/TNF-alpha, and IL-10/TNF-alpha were lower in patients with tuberculosis pleurisy compared with other patients. In all three groups of patients significant correlation was seen between abundance of IL-2 vs. IL-4, IL-5, IL-10, or TNF-alpha, between IL-4 vs. IL-10, and between TNF-alpha vs. INF-gamma. In malignant pleural fluid patients, the significant correlation was between IL-2 vs. IL-4, TNF-alpha, or INF-gamma, between IL-4 vs. INF-gamma, and between TNF-alpha vs. INF-gamma. In tuberculosis pleural fluid patients, the significant correlation was between IL-2 vs. TNF-alpha, between IL-4 vs. IL-10, and between TNF-alpha vs. INF-gamma. In miscellaneous pleural fluid patients, the significant correlation was between IL-2 vs. IL-4, IL-10, or TNF-alpha, between IL-4 vs. IL-10, TNF-alpha, and between IL-10 vs. TNF-alpha. No significant correlation was observed between other pairs of cytokines. Strong correlation in abundance between particular cytokines in pleural fluids suggests cross-talk between them, in terms that an altered level of one of them provides a feedback mechanism regulating synthesis and/or secretion of another one. Such interactions may play important roles in pathogenesis and severity of the effusion. The CBA methodology provides a

  6. Distribution, relative abundance and size composition of the threatened serranid Epinephelus daemelii in New South Wales, Australia.

    PubMed

    Harasti, D; Malcolm, H

    2013-08-01

    The aim of this study was to undertake baseline surveys on the distribution, relative abundance and total lengths (LT ) of a threatened epinephelid species, black cod Epinephelus daemelii, in New South Wales (NSW), Australia, their westernmost distribution. Diving surveys at 83 sites where E. daemelii were expected to occur were undertaken from 2009 to 2011 using 45 min roving diver counts. Sites were spread through northern NSW, including Lord Howe Island (LHI). Individual fish were measured using stereo-video, enabling accurate length measurement. Surveys were repeated at a sub-set of sites to assess temporal variation across days, seasons and years. A total of 117 E. daemelii were recorded during baseline surveys, occurring at 42% of the surveyed sites. Across all surveys, the highest numbers recorded (14-18 individuals at a site) were at the outer Solitary Islands and Fish Rock (Smoky Cape). Fewer E. daemelii were found southwards, but two sites in the Port Stephens-Great Lakes Marine Park had consistent numbers (three to six) over four annual surveys. Only 12 E. daemelii were recorded from eight of the 18 sites at LHI. The numbers observed at re-surveyed sites were generally stable over years. There were latitudinal and cross-shelf differences in LT . Individuals in the north were found to be significantly larger than those further south, and fish offshore were significantly larger than those inshore. The largest measured fish was 135 cm, smaller than the maximum LT (c. 170 cm) recorded for this species. The smallest fish was 26 cm. Overall, it is considered that the abundance of E. daemelii is low compared to anecdotal data even though they have been protected for c. 30 years in NSW. These findings provide an essential benchmark to assess ongoing status and response to protective management. PMID:23902312

  7. 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.

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

    PubMed

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

    2014-08-01

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

  9. 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.

  10. 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

    . Fifteen fields (~11%) appear to be synchronous with regional plains, and eleven fields (~8%) postdate the plains. Nine fields (~6%) display ambiguous relationships with regional plains and their relative age is uncertain, and eight fields (~6%) represent unclear cases when fields are covered by crater-related materials or by young lava flows or are not in contact with regional plains. The results of our study provide evidence for a distinct change of volcanic style from the mode of formation of globally abundant small shields to the mode of emplacement of vast regional plains in many areas on Venus. This systematic change of volcanic style appears to be inconsistent with the ``nondirectional'' or quasi steady state character of the geologic record of Venus. Although individual small shields were formed throughout the majority of the visible geologic history of Venus, in the syn- and postregional plains time the small-shields style of volcanism was significantly reduced in abundance. The shield fields that predate regional plains do not display a strong tendency to form a single group or a few groups and can be found virtually in all places on Venus. We interpret this observation to mean that these shield fields were globally distributed before the emplacement of regional plains. This interpretation means that the shield fields embayed by regional plains represent exposures of a specific, globally widespread unit, shield plains (psh). In contrast, shield fields that postdate regional plains occur preferentially in the Beta-Atla-Themis region on Venus, well known for its concentration of relatively young volcanic and tectonic activity. The spatial association of relatively young fields with the large centers of young volcanism suggests a genetic link of these fields with the formation and development of the large-scale volcanic centers. The abrupt decrease of the number of shields that postdate the formation of shield plains (psh) strongly suggests a major change of the

  11. Inverse relation between disease severity and expression of the streptococcal cysteine protease, SpeB, among clonal M1T1 isolates recovered from invasive group A streptococcal infection cases.

    PubMed

    Kansal, R G; McGeer, A; Low, D E; Norrby-Teglund, A; Kotb, M

    2000-11-01

    The streptococcal cysteine protease (SpeB) is one of the major virulence factors produced by group A streptococci (GAS). In this study we investigated if differences exist in SpeB production by clonally related M1T1 clinical isolates derived from patients with invasive infections. Twenty-nine of these isolates were from nonsevere cases and 48 were from severe cases, including streptococcal toxic shock syndrome (STSS) and necrotizing fasciitis (NF) cases. The expression and amount of the 28-kDa SpeB protein produced were determined by quantitative Western blotting, and protease activity was measured by a fluorescent enzymatic assay. A high degree of variation in SpeB expression was seen among the isolates, and this variation seemed to correlate with the severity and/or clinical manifestation of the invasive infection. The mean amount of 28-kDa SpeB protein and cysteine protease activity produced by isolates from nonsevere cases was significantly higher than that from STSS cases (P = 0.001). This difference was partly due to the fact that 41% of STSS isolates produced little or no SpeB compared to only 14% of isolates recovered in nonsevere cases. Moreover, the cysteine protease activity among those isolates that expressed SpeB was significantly lower for STSS isolates than for isolates from nonsevere cases (P = 0.001). Increased SpeB production was also inversely correlated with intact M protein expression, and inhibition of cysteine protease activity blocked the cleavage of the surface M protein. Together, the data support the existence of both an "on-off" and a posttranslational regulatory mechanism(s) controlling SpeB production, and they suggest that isolates with the speB gene in the "off" state are more likely to spare the surface M protein and to be isolated from cases of severe rather than nonsevere invasive infection. These findings may have important implications for the role of SpeB in host-pathogen interactions via regulation of the expression of GAS

  12. Inverse Relation between Disease Severity and Expression of the Streptococcal Cysteine Protease, SpeB, among Clonal M1T1 Isolates Recovered from Invasive Group A Streptococcal Infection Cases

    PubMed Central

    Kansal, Rita G.; McGeer, Allison; Low, Donald E.; Norrby-Teglund, Anna; Kotb, Malak

    2000-01-01

    The streptococcal cysteine protease (SpeB) is one of the major virulence factors produced by group A streptococci (GAS). In this study we investigated if differences exist in SpeB production by clonally related M1T1 clinical isolates derived from patients with invasive infections. Twenty-nine of these isolates were from nonsevere cases and 48 were from severe cases, including streptococcal toxic shock syndrome (STSS) and necrotizing fasciitis (NF) cases. The expression and amount of the 28-kDa SpeB protein produced were determined by quantitative Western blotting, and protease activity was measured by a fluorescent enzymatic assay. A high degree of variation in SpeB expression was seen among the isolates, and this variation seemed to correlate with the severity and/or clinical manifestation of the invasive infection. The mean amount of 28-kDa SpeB protein and cysteine protease activity produced by isolates from nonsevere cases was significantly higher than that from STSS cases (P = 0.001). This difference was partly due to the fact that 41% of STSS isolates produced little or no SpeB compared to only 14% of isolates recovered in nonsevere cases. Moreover, the cysteine protease activity among those isolates that expressed SpeB was significantly lower for STSS isolates than for isolates from nonsevere cases (P = 0.001). Increased SpeB production was also inversely correlated with intact M protein expression, and inhibition of cysteine protease activity blocked the cleavage of the surface M protein. Together, the data support the existence of both an “on-off” and a posttranslational regulatory mechanism(s) controlling SpeB production, and they suggest that isolates with the speB gene in the “off” state are more likely to spare the surface M protein and to be isolated from cases of severe rather than nonsevere invasive infection. These findings may have important implications for the role of SpeB in host-pathogen interactions via regulation of the expression of

  13. 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

  14. 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.

  15. 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

  16. Clonal origins and parallel evolution of regionally synchronous colorectal adenoma and carcinoma

    PubMed Central

    Rhee, Je-Keun; Jung, Seung-Hyun; Lee, Sung Hak; Baek, In-Pyo; Kim, Min Sung; Lee, Sug Hyung; Chung, Yeun-Jun

    2015-01-01

    Although the colorectal adenoma-to-carcinoma sequence represents a classical cancer progression model, the evolution of the mutational landscape underlying this model is not fully understood. In this study, we analyzed eight synchronous pairs of colorectal high-grade adenomas and carcinomas, four microsatellite-unstable (MSU) and four -stable (MSS) pairs, using whole-exome sequencing. In the MSU adenoma-carcinoma pairs, we observed no subclonal mutations in adenomas that became fixed in paired carcinomas, suggesting a ‘parallel’ evolution of synchronous adenoma-to-carcinoma, rather than a ‘stepwise’ evolution. The abundance of indel (in MSU and MSS pairs) and microsatellite instability (in MSU pairs) was noted in the later adenoma- or carcinoma-specific mutations, indicating that the mutational processes and functional constraints operative in early and late colorectal carcinogenesis are different. All MSU cases exhibited clonal, truncating mutations in ACVR2A, TGFBR2, and DNA mismatch repair genes, but none were present in APC or KRAS. In three MSS pairs, both APC and KRAS mutations were identified as both early and clonal events, often accompanying clonal copy number changes. An MSS case uniquely exhibited clonal ERBB2 amplification, followed by APC and TP53 mutations as carcinoma-specific events. Along with the previously unrecognized clonal origins of synchronous colorectal adenoma-carcinoma pairs, our study revealed that the preferred sequence of mutational events during colorectal carcinogenesis can be context-dependent. PMID:26336987

  17. Clonal origins and parallel evolution of regionally synchronous colorectal adenoma and carcinoma.

    PubMed

    Kim, Tae-Min; An, Chang Hyeok; Rhee, Je-Keun; Jung, Seung-Hyun; Lee, Sung Hak; Baek, In-Pyo; Kim, Min Sung; Lee, Sug Hyung; Chung, Yeun-Jun

    2015-09-29

    Although the colorectal adenoma-to-carcinoma sequence represents a classical cancer progression model, the evolution of the mutational landscape underlying this model is not fully understood. In this study, we analyzed eight synchronous pairs of colorectal high-grade adenomas and carcinomas, four microsatellite-unstable (MSU) and four-stable (MSS) pairs, using whole-exome sequencing. In the MSU adenoma-carcinoma pairs, we observed no subclonal mutations in adenomas that became fixed in paired carcinomas, suggesting a 'parallel' evolution of synchronous adenoma-to-carcinoma, rather than a 'stepwise' evolution. The abundance of indel (in MSU and MSS pairs) and microsatellite instability (in MSU pairs) was noted in the later adenoma- or carcinoma-specific mutations, indicating that the mutational processes and functional constraints operative in early and late colorectal carcinogenesis are different. All MSU cases exhibited clonal, truncating mutations in ACVR2A, TGFBR2, and DNA mismatch repair genes, but none were present in APC or KRAS. In three MSS pairs, both APC and KRAS mutations were identified as both early and clonal events, often accompanying clonal copy number changes. An MSS case uniquely exhibited clonal ERBB2 amplification, followed by APC and TP53 mutations as carcinoma-specific events. Along with the previously unrecognized clonal origins of synchronous colorectal adenoma-carcinoma pairs, our study revealed that the preferred sequence of mutational events during colorectal carcinogenesis can be context-dependent. PMID:26336987

  18. Longevity of clonal plants: why it matters and how to measure it

    PubMed Central

    de Witte, Lucienne C.; Stöcklin, Jürg

    2010-01-01

    Background Species' life-history and population dynamics are strongly shaped by the longevity of individuals, but life span is one of the least accessible demographic traits, particularly in clonal plants. Continuous vegetative reproduction of genets enables persistence despite low or no sexual reproduction, affecting genet turnover rates and population stability. Therefore, the longevity of clonal plants is of considerable biological interest, but remains relatively poorly known. Scope Here, we critically review the present knowledge on the longevity of clonal plants and discuss its importance for population persistence. Direct life-span measurements such as growth-ring analysis in woody plants are relatively easy to take, although, for many clonal plants, these methods are not adequate due to the variable growth pattern of ramets and difficult genet identification. Recently, indirect methods have been introduced in which genet size and annual shoot increments are used to estimate genet age. These methods, often based on molecular techniques, allow the investigation of genet size and age structure of whole populations, a crucial issue for understanding their viability and persistence. However, indirect estimates of clonal longevity are impeded because the process of ageing in clonal plants is still poorly understood and because their size and age are not always well correlated. Alternative estimators for genet life span such as somatic mutations have recently been suggested. Conclusions Empirical knowledge on the longevity of clonal species has increased considerably in the last few years. Maximum age estimates are an indicator of population persistence, but are not sufficient to evaluate turnover rates and the ability of long-lived clonal plants to enhance community stability and ecosystem resilience. In order to understand the dynamics of populations it will be necessary to measure genet size and age structure, not only life spans of single individuals, and to

  19. Clonal complex Pseudomonas aeruginosa in horses.

    PubMed

    Kidd, Timothy J; Gibson, Justine S; Moss, Susan; Greer, Ristan M; Cobbold, Rowland N; Wright, John D; Ramsay, Kay A; Grimwood, Keith; Bell, Scott C

    2011-05-01

    Pseudomonas aeruginosa is associated with infectious endometritis in horses. Although infectious endometritis is often considered a venereal infection, there is relatively limited genotypic-based evidence to support this mode of transmission. The study sought to determine the relatedness between genital P. aeruginosa isolates collected from a limited geographical region using molecular strain typing. Enterobacterial repetitive intergenic consensus PCR typing was performed on 93 isolates collected between 2005 and 2009 from 2058 thoroughbred horses (including 18 stallions) at 66 studs. While P. aeruginosa was not detected in the stallions, 53/93 (57%) mares harbouring P. aeruginosa had clonally related strains, which included a single dominant genotype detected in 42 (45%) mares from 13 different studs. These novel findings suggest that most equine genital P. aeruginosa infections in this region may have been acquired from mechanisms other than direct horse to horse transmission. Instead, other potential acquisition pathways, as well as strain specific adaptation to the equine genital tract, should be investigated. PMID:21183294

  20. 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.

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

    PubMed Central

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

    2013-01-01

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

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

    USGS Publications Warehouse

    Todd, Thomas N.; Davis, Bruce M.

    1995-01-01

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

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

    PubMed

    Wallace, Robert; Ayala, Guido; Viscarra, Maria

    2012-12-01

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

  4. 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.

  5. The Hayflick Limit May Determine the Effective Clonal Diversity of Naive T Cells.

    PubMed

    Ndifon, Wilfred; Dushoff, Jonathan

    2016-06-15

    Having a large number of sufficiently abundant T cell clones is important for adequate protection against diseases. However, as shown in this paper and elsewhere, between young adulthood and >70 y of age the effective clonal diversity of naive CD4/CD8 T cells found in human blood declines by a factor of >10. (Effective clonal diversity accounts for both the number and the abundance of T cell clones.) The causes of this observation are incompletely understood. A previous study proposed that it might result from the emergence of certain rare, replication-enhancing mutations in T cells. In this paper, we propose an even simpler explanation: that it results from the loss of T cells that have attained replicative senescence (i.e., the Hayflick limit). Stochastic numerical simulations of naive T cell population dynamics, based on experimental parameters, show that the rate of homeostatic T cell proliferation increases after the age of ∼60 y because naive T cells collectively approach replicative senescence. This leads to a sharp decline of effective clonal diversity after ∼70 y, in agreement with empirical data. A mathematical analysis predicts that, without an increase in the naive T cell proliferation rate, this decline will occur >50 yr later than empirically observed. These results are consistent with a model in which exhaustion of the proliferative capacity of naive T cells causes a sharp decline of their effective clonal diversity and imply that therapeutic potentiation of thymopoiesis might either prevent or reverse this outcome. PMID:27183600

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

    USGS Publications Warehouse

    Bell, J.F., III; 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).

  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. PMID:25017697

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

    PubMed

    Bara, Jeffrey J; Muturi, Ephantus J

    2015-05-01

    Ochlerotatus triseriatus (Say), the primary vector of La Crosse virus (LAC), develops in a variety of natural and artificial aquatic containers where it often co-occurs with larvae of other mosquito species. We conducted a field study at two woodlots (South Farms and Trelease Woods) in Urbana, IL, to examine how container type influences vector abundance, body size, and susceptibility to LAC. Mosquito pupae were collected from tree holes, plastic bins, and waste tires, and eclosing adults were identified to species morphologically. Oc. triseriatus and Ochlerotatus japonicus (Theobald) females were orally challenged with LAC and midgut infection rate, disseminated infection rate, and body titer were determined by reverse-transcriptase real-time PCR. Oc. triseriatus was the dominant species collected in tree holes while Oc. japonicus and Culex restuans (Theobald) were mostly dominant in artificial containers. Female Oc. triseriatus and Oc. japonicus collected from plastic bins were significantly larger than those collected from tree holes or waste tires. Oc. japonicus females from South Farms were also significantly larger than those from Trelease Woods. Oc. triseriatus females collected from plastic bins and waste tires were significantly more susceptible to LAC infection relative to females collected from tree holes. In addition, Oc. triseriatus females from waste tires had significantly higher LAC titer relative to Oc. triseriatus from tree holes. For each container type and study site, wing length was not correlated to infection or dissemination rates. These findings suggest that the container type in which Oc.triseriatus develop may contribute to the spatial and temporal dynamics of LAC transmission. PMID:26334821

  9. Contrasting the CO2-He Isotope and Relative Abundance Systematics of the Central American and IBM Arcs

    NASA Astrophysics Data System (ADS)

    Hilton, D. R.; Fischer, T. P.; Shaw, A. M.; Hauri, E.; Walker, J.

    2006-12-01

    We report CO2 and He isotope and relative abundance data obtained utilizing high-T fumaroles, geothermal wells, boiling mud pots, hot springs and phenocryst-bearing lavas from both MARGINS-targeted regions. In Central America, we collected ~140 fluid and ~30 lava samples covering a total of 41 volcanic centers in Costa Rica (7), Nicaragua (8), El Salvador (10), Honduras (9) and Guatemala (7). Along the IBM arc, we sampled the islands of Uracas, Agrigan, Pagan and Alamagan in the CNMI and Oshima, Niijima, Shikinajima, Hachijojima and Aogashima in the Izu islands. Helium isotope ratios (3He/4He) reach a maximum of 8RA (where RA = air 3He/4He) with most values > 5 RA. The majority of samples have CO2/3He ratios between 1010 and 1011, as at other arcs. The δ13C of the CO2 for the majority of samples fall between -5 and 0 ‰ (PDB) consistent with a major slab input to the carbon inventory. The entire database has been assessed to identify samples unmodified by localised crustal processes (~75% of total), thereby defining the He and C systematics of the underlying mantle source. At both arcs, we utilize along-strike He-C variations to consider the relative influence of various subduction zone forcing functions on the output C-flux. We show that subducted sediment lithology, particularly down-hole C distribution and the nature (oxidized/reduced) of the C, is a major control on the output as opposed to other factors such as angle of slab dip, convergence rate, and thickness of overlying arc crust.

  10. NSAIDs modulate clonal evolution in Barrett's esophagus.

    PubMed

    Kostadinov, Rumen L; Kuhner, Mary K; Li, Xiaohong; Sanchez, Carissa A; Galipeau, Patricia C; Paulson, Thomas G; Sather, Cassandra L; Srivastava, Amitabh; Odze, Robert D; Blount, Patricia L; Vaughan, Thomas L; Reid, Brian J; Maley, Carlo C

    2013-06-01

    Cancer is considered an outcome of decades-long clonal evolution fueled by acquisition of somatic genomic abnormalities (SGAs). Non-steroidal anti-inflammatory drugs (NSAIDs) have been shown to reduce cancer risk, including risk of progression from Barrett's esophagus (BE) to esophageal adenocarcinoma (EA). However, the cancer chemopreventive mechanisms of NSAIDs are not fully understood. We hypothesized that NSAIDs modulate clonal evolution by reducing SGA acquisition rate. We evaluated thirteen individuals with BE. Eleven had not used NSAIDs for 6.2±3.5 (mean±standard deviation) years and then began using NSAIDs for 5.6±2.7 years, whereas two had used NSAIDs for 3.3±1.4 years and then discontinued use for 7.9±0.7 years. 161 BE biopsies, collected at 5-8 time points over 6.4-19 years, were analyzed using 1Million-SNP arrays to detect SGAs. Even in the earliest biopsies there were many SGAs (284±246 in 10/13 and 1442±560 in 3/13 individuals) and in most individuals the number of SGAs changed little over time, with both increases and decreases in SGAs detected. The estimated SGA rate was 7.8 per genome per year (95% support interval [SI], 7.1-8.6) off-NSAIDs and 0.6 (95% SI 0.3-1.5) on-NSAIDs. Twelve individuals did not progress to EA. In ten we detected 279±86 SGAs affecting 53±30 Mb of the genome per biopsy per time point and in two we detected 1,463±375 SGAs affecting 180±100 Mb. In one individual who progressed to EA we detected a clone having 2,291±78 SGAs affecting 588±18 Mb of the genome at three time points in the last three of 11.4 years of follow-up. NSAIDs were associated with reduced rate of acquisition of SGAs in eleven of thirteen individuals. Barrett's cells maintained relative equilibrium level of SGAs over time with occasional punctuations by expansion of clones having massive amount of SGAs. PMID:23785299

  11. NSAIDs Modulate Clonal Evolution in Barrett's Esophagus

    PubMed Central

    Kostadinov, Rumen L.; Kuhner, Mary K.; Li, Xiaohong; Sanchez, Carissa A.; Galipeau, Patricia C.; Paulson, Thomas G.; Sather, Cassandra L.; Srivastava, Amitabh; Odze, Robert D.; Blount, Patricia L.; Vaughan, Thomas L.; Reid, Brian J.; Maley, Carlo C.

    2013-01-01

    Cancer is considered an outcome of decades-long clonal evolution fueled by acquisition of somatic genomic abnormalities (SGAs). Non-steroidal anti-inflammatory drugs (NSAIDs) have been shown to reduce cancer risk, including risk of progression from Barrett's esophagus (BE) to esophageal adenocarcinoma (EA). However, the cancer chemopreventive mechanisms of NSAIDs are not fully understood. We hypothesized that NSAIDs modulate clonal evolution by reducing SGA acquisition rate. We evaluated thirteen individuals with BE. Eleven had not used NSAIDs for 6.2±3.5 (mean±standard deviation) years and then began using NSAIDs for 5.6±2.7 years, whereas two had used NSAIDs for 3.3±1.4 years and then discontinued use for 7.9±0.7 years. 161 BE biopsies, collected at 5–8 time points over 6.4–19 years, were analyzed using 1Million-SNP arrays to detect SGAs. Even in the earliest biopsies there were many SGAs (284±246 in 10/13 and 1442±560 in 3/13 individuals) and in most individuals the number of SGAs changed little over time, with both increases and decreases in SGAs detected. The estimated SGA rate was 7.8 per genome per year (95% support interval [SI], 7.1–8.6) off-NSAIDs and 0.6 (95% SI 0.3–1.5) on-NSAIDs. Twelve individuals did not progress to EA. In ten we detected 279±86 SGAs affecting 53±30 Mb of the genome per biopsy per time point and in two we detected 1,463±375 SGAs affecting 180±100 Mb. In one individual who progressed to EA we detected a clone having 2,291±78 SGAs affecting 588±18 Mb of the genome at three time points in the last three of 11.4 years of follow-up. NSAIDs were associated with reduced rate of acquisition of SGAs in eleven of thirteen individuals. Barrett's cells maintained relative equilibrium level of SGAs over time with occasional punctuations by expansion of clones having massive amount of SGAs. PMID:23785299

  12. Enhancing cancer clonality analysis with integrative genomics

    PubMed Central

    2015-01-01

    Introduction It is understood that cancer is a clonal disease initiated by a single cell, and that metastasis, which is the spread of cancer from the primary site, is also initiated by a single cell. The seemingly natural capability of cancer to adapt dynamically in a Darwinian manner is a primary reason for therapeutic failures. Survival advantages may be induced by cancer therapies and also occur as a result of inherent cell and microenvironmental factors. The selected "more fit" clones outmatch their competition and then become dominant in the tumor via propagation of progeny. This clonal expansion leads to relapse, therapeutic resistance and eventually death. The goal of this study is to develop and demonstrate a more detailed clonality approach by utilizing integrative genomics. Methods Patient tumor samples were profiled by Whole Exome Sequencing (WES) and RNA-seq on an Illumina HiSeq 2500 and methylation profiling was performed on the Illumina Infinium 450K array. STAR and the Haplotype Caller were used for RNA-seq processing. Custom approaches were used for the integration of the multi-omic datasets. Results Reported are major enhancements to CloneViz, which now provides capabilities enabling a formal tumor multi-dimensional clonality analysis by integrating: i) DNA mutations, ii) RNA expressed mutations, and iii) DNA methylation data. RNA and DNA methylation integration were not previously possible, by CloneViz (previous version) or any other clonality method to date. This new approach, named iCloneViz (integrated CloneViz) employs visualization and quantitative methods, revealing an integrative genomic mutational dissection and traceability (DNA, RNA, epigenetics) thru the different layers of molecular structures. Conclusion The iCloneViz approach can be used for analysis of clonal evolution and mutational dynamics of multi-omic data sets. Revealing tumor clonal complexity in an integrative and quantitative manner facilitates improved mutational

  13. Plant Clonal Integration Mediates the Horizontal Redistribution of Soil Resources, Benefiting Neighboring Plants

    PubMed Central

    Ye, Xue-Hua; Zhang, Ya-Lin; Liu, Zhi-Lan; Gao, Shu-Qin; Song, Yao-Bin; Liu, Feng-Hong; Dong, Ming

    2016-01-01

    Resources such as water taken up by plants can be released into soils through hydraulic redistribution and can also be translocated by clonal integration within a plant clonal network. We hypothesized that the resources from one (donor) microsite could be translocated within a clonal network, released into different (recipient) microsites and subsequently used by neighbor plants in the recipient microsite. To test these hypotheses, we conducted two experiments in which connected and disconnected ramet pairs of Potentilla anserina were grown under both homogeneous and heterogeneous water regimes, with seedlings of Artemisia ordosica as neighbors. The isotopes [15N] and deuterium were used to trace the translocation of nitrogen and water, respectively, within the clonal network. The water and nitrogen taken up by P. anserina ramets in the donor microsite were translocated into the connected ramets in the recipient microsites. Most notably, portions of the translocated water and nitrogen were released into the recipient microsite and were used by the neighboring A. ordosica, which increased growth of the neighboring A. ordosica significantly. Therefore, our hypotheses were supported, and plant clonal integration mediated the horizontal hydraulic redistribution of resources, thus benefiting neighboring plants. Such a plant clonal integration-mediated resource redistribution in horizontal space may have substantial effects on the interspecific relations and composition of the community and consequently on ecosystem processes. PMID:26904051

  14. B-cell clonality and infection with Helicobacter pylori: implications for development of gastric lymphoma.

    PubMed Central

    Sorrentino, D; Ferraccioli, G F; DeVita, S; Avellini, C; Beltrami, C A; Labombarda, A; Bernardis, V; De Biase, F; Trevisi, A; Pivetta, B; Boiocchi, M; Bartoli, E

    1996-01-01

    BACKGROUND: Although Helicobacter pylori has been implicated in the pathogenesis of gastric mucosa associated lymphoid tissue (MALT) and MALT lymphoma, it is not known how it may trigger these lesions and whether there is an identifiable pre-neoplastic stage. AIMS: To investigate the relation between MALT, H pylori infection, and B-cell clonality (a potential marker of pre-neoplastic lesions). PATIENTS: 141 subjects with simple dyspepsia. METHODS: Gastric biopsy specimens from all patients were examined for MALT and H pylori. Of these, 25 consecutive MALT positive specimens were scored for features of MALT lymphoma and VDJ clonality studied by polymerase chain reaction. RESULTS: Overall, prevalence was 62% for H pylori and 46% for MALT. VDJ clonality was frequent in the sub-group studied (nine of 25), mostly associated with lymphoid follicles (eight of nine or 89%), and with a high scoring for MALT lymphoma. VDJ clonality was equally frequent in patients with and without H pylori (seven of 20 and two of five or 35% and 40% respectively). CONCLUSIONS: B-cell clonality is unexpectedly common in subjects with simple dyspepsia and MALT raising clinical management questions. These findings also suggest that the cascade MALT formation--B-cell clonality--MALT lymphoma may not be uniquely associated with H pylori infection. PMID:8984020

  15. Divergent clonal selection dominates medulloblastoma at recurrence

    PubMed Central

    Morrissy, A. Sorana; Garzia, Livia; Shih, David J. H.; Zuyderduyn, Scott; Huang, Xi; Skowron, Patryk; Remke, Marc; Cavalli, Florence M. G.; Ramaswamy, Vijay; Lindsay, Patricia E.; Jelveh, Salomeh; Donovan, Laura K.; Wang, Xin; Luu, Betty; Zayne, Kory; Li, Yisu; Mayoh, Chelsea; Thiessen, Nina; Mercier, Eloi; Mungall, Karen L.; Ma, Yusanne; Tse, Kane; Zeng, Thomas; Shumansky, Karey; Roth, Andrew J. L.; Shah, Sohrab; Farooq, Hamza; Kijima, Noriyuki; Holgado, Borja L.; Lee, John J. Y.; Matan-Lithwick, Stuart; Liu, Jessica; Mack, Stephen C.; Manno, Alex; Michealraj, K. A.; Nor, Carolina; Peacock, John; Qin, Lei; Reimand, Juri; Rolider, Adi; Thompson, Yuan Y.; Wu, Xiaochong; Pugh, Trevor; Ally, Adrian; Bilenky, Mikhail; Butterfield, Yaron S. N.; Carlsen, Rebecca; Cheng, Young; Chuah, Eric; Corbett, Richard D.; Dhalla, Noreen; He, An; Lee, Darlene; Li, Haiyan I.; Long, William; Mayo, Michael; Plettner, Patrick; Qian, Jenny Q.; Schein, Jacqueline E.; Tam, Angela; Wong, Tina; Birol, Inanc; Zhao, Yongjun; Faria, Claudia C.; Pimentel, José; Nunes, Sofia; Shalaby, Tarek; Grotzer, Michael; Pollack, Ian F.; Hamilton, Ronald L.; Li, Xiao-Nan; Bendel, Anne E.; Fults, Daniel W.; Walter, Andrew W.; Kumabe, Toshihiro; Tominaga, Teiji; Collins, V. Peter; Cho, Yoon-Jae; Hoffman, Caitlin; Lyden, David; Wisoff, Jeffrey H.; Garvin, James H.; Stearns, Duncan S.; Massimi, Luca; Schüller, Ulrich; Sterba, Jaroslav; Zitterbart, Karel; Puget, Stephanie; Ayrault, Olivier; Dunn, Sandra E.; Tirapelli, Daniela P. C.; Carlotti, Carlos G.; Wheeler, Helen; Hallahan, Andrew R.; Ingram, Wendy; MacDonald, Tobey J.; Olson, Jeffrey J.; Van Meir, Erwin G.; Lee, Ji-Yeoun; Wang, Kyu-Chang; Kim, Seung-Ki; Cho, Byung-Kyu; Pietsch, Torsten; Fleischhack, Gudrun; Tippelt, Stephan; Ra, Young Shin; Bailey, Simon; Lindsey, Janet C.; Clifford, Steven C.; Eberhart, Charles G.; Cooper, Michael K.; Packer, Roger J.; Massimino, Maura; Garre, Maria Luisa; Bartels, Ute; Tabori, Uri; Hawkins, Cynthia E.; Dirks, Peter; Bouffet, Eric; Rutka, James T.; Wechsler-Reya, Robert J.; Weiss, William A.; Collier, Lara S.; Dupuy, Adam J.; Korshunov, Andrey; Jones, David T. W.; Kool, Marcel; Northcott, Paul A.; Pfister, Stefan M.; Largaespada, David A.; Mungall, Andrew J.; Moore, Richard A.; Jabado, Nada; Bader, Gary D.; Jones, Steven J. M.; Malkin, David; Marra, Marco A.; Taylor, Michael D.

    2016-01-01

    The development of targeted anti-cancer therapies through the study of cancer genomes is intended to increase survival rates and decrease treatment-related toxicity. We treated a transposon–driven, functional genomic mouse model of medulloblastoma with ‘humanized’ in vivo therapy (microneurosurgical tumour resection followed by multi-fractionated, image-guided radiotherapy). Genetic events in recurrent murine medulloblastoma exhibit a very poor overlap with those in matched murine diagnostic samples (<5%). Whole-genome sequencing of 33 pairs of human diagnostic and post-therapy medulloblastomas demonstrated substantial genetic divergence of the dominant clone after therapy (<12% diagnostic events were retained at recurrence). In both mice and humans, the dominant clone at recurrence arose through clonal selection of a pre-existing minor clone present at diagnosis. Targeted therapy is unlikely to be effective in the absence of the target, therefore our results offer a simple, proximal, and remediable explanation for the failure of prior clinical trials of targeted therapy. PMID:26760213

  16. Divergent clonal selection dominates medulloblastoma at recurrence.

    PubMed

    Morrissy, A Sorana; Garzia, Livia; Shih, David J H; Zuyderduyn, Scott; Huang, Xi; Skowron, Patryk; Remke, Marc; Cavalli, Florence M G; Ramaswamy, Vijay; Lindsay, Patricia E; Jelveh, Salomeh; Donovan, Laura K; Wang, Xin; Luu, Betty; Zayne, Kory; Li, Yisu; Mayoh, Chelsea; Thiessen, Nina; Mercier, Eloi; Mungall, Karen L; Ma, Yusanne; Tse, Kane; Zeng, Thomas; Shumansky, Karey; Roth, Andrew J L; Shah, Sohrab; Farooq, Hamza; Kijima, Noriyuki; Holgado, Borja L; Lee, John J Y; Matan-Lithwick, Stuart; Liu, Jessica; Mack, Stephen C; Manno, Alex; Michealraj, K A; Nor, Carolina; Peacock, John; Qin, Lei; Reimand, Juri; Rolider, Adi; Thompson, Yuan Y; Wu, Xiaochong; Pugh, Trevor; Ally, Adrian; Bilenky, Mikhail; Butterfield, Yaron S N; Carlsen, Rebecca; Cheng, Young; Chuah, Eric; Corbett, Richard D; Dhalla, Noreen; He, An; Lee, Darlene; Li, Haiyan I; Long, William; Mayo, Michael; Plettner, Patrick; Qian, Jenny Q; Schein, Jacqueline E; Tam, Angela; Wong, Tina; Birol, Inanc; Zhao, Yongjun; Faria, Claudia C; Pimentel, José; Nunes, Sofia; Shalaby, Tarek; Grotzer, Michael; Pollack, Ian F; Hamilton, Ronald L; Li, Xiao-Nan; Bendel, Anne E; Fults, Daniel W; Walter, Andrew W; Kumabe, Toshihiro; Tominaga, Teiji; Collins, V Peter; Cho, Yoon-Jae; Hoffman, Caitlin; Lyden, David; Wisoff, Jeffrey H; Garvin, James H; Stearns, Duncan S; Massimi, Luca; Schüller, Ulrich; Sterba, Jaroslav; Zitterbart, Karel; Puget, Stephanie; Ayrault, Olivier; Dunn, Sandra E; Tirapelli, Daniela P C; Carlotti, Carlos G; Wheeler, Helen; Hallahan, Andrew R; Ingram, Wendy; MacDonald, Tobey J; Olson, Jeffrey J; Van Meir, Erwin G; Lee, Ji-Yeoun; Wang, Kyu-Chang; Kim, Seung-Ki; Cho, Byung-Kyu; Pietsch, Torsten; Fleischhack, Gudrun; Tippelt, Stephan; Ra, Young Shin; Bailey, Simon; Lindsey, Janet C; Clifford, Steven C; Eberhart, Charles G; Cooper, Michael K; Packer, Roger J; Massimino, Maura; Garre, Maria Luisa; Bartels, Ute; Tabori, Uri; Hawkins, Cynthia E; Dirks, Peter; Bouffet, Eric; Rutka, James T; Wechsler-Reya, Robert J; Weiss, William A; Collier, Lara S; Dupuy, Adam J; Korshunov, Andrey; Jones, David T W; Kool, Marcel; Northcott, Paul A; Pfister, Stefan M; Largaespada, David A; Mungall, Andrew J; Moore, Richard A; Jabado, Nada; Bader, Gary D; Jones, Steven J M; Malkin, David; Marra, Marco A; Taylor, Michael D

    2016-01-21

    The development of targeted anti-cancer therapies through the study of cancer genomes is intended to increase survival rates and decrease treatment-related toxicity. We treated a transposon-driven, functional genomic mouse model of medulloblastoma with 'humanized' in vivo therapy (microneurosurgical tumour resection followed by multi-fractionated, image-guided radiotherapy). Genetic events in recurrent murine medulloblastoma exhibit a very poor overlap with those in matched murine diagnostic samples (<5%). Whole-genome sequencing of 33 pairs of human diagnostic and post-therapy medulloblastomas demonstrated substantial genetic divergence of the dominant clone after therapy (<12% diagnostic events were retained at recurrence). In both mice and humans, the dominant clone at recurrence arose through clonal selection of a pre-existing minor clone present at diagnosis. Targeted therapy is unlikely to be effective in the absence of the target, therefore our results offer a simple, proximal, and remediable explanation for the failure of prior clinical trials of targeted therapy. PMID:26760213

  17. Clonality and intracellular polyploidy in virus evolution and pathogenesis.

    PubMed

    Perales, Celia; Moreno, Elena; Domingo, Esteban

    2015-07-21

    In the present article we examine clonality in virus evolution. Most viruses retain an active recombination machinery as a potential means to initiate new levels of genetic exploration that go beyond those attainable solely by point mutations. However, despite abundant recombination that may be linked to molecular events essential for genome replication, herein we provide evidence that generation of recombinants with altered biological properties is not essential for the completion of the replication cycles of viruses, and that viral lineages (near-clades) can be defined. We distinguish mechanistically active but inconsequential recombination from evolutionarily relevant recombination, illustrated by episodes in the field and during experimental evolution. In the field, recombination has been at the origin of new viral pathogens, and has conferred fitness advantages to some viruses once the parental viruses have attained a sufficient degree of diversification by point mutations. In the laboratory, recombination mediated a salient genome segmentation of foot-and-mouth disease virus, an important animal pathogen whose genome in nature has always been characterized as unsegmented. We propose a model of continuous mutation and recombination, with punctuated, biologically relevant recombination events for the survival of viruses, both as disease agents and as promoters of cellular evolution. Thus, clonality is the standard evolutionary mode for viruses because recombination is largely inconsequential, since the decisive events for virus replication and survival are not dependent on the exchange of genetic material and formation of recombinant (mosaic) genomes. PMID:26195777

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

    SciTech Connect

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

    2011-04-20

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

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

    USGS Publications Warehouse

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

    2016-01-01

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

  20. 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.

  1. Two wheat (Triticum aestivum) pathogenesis-related 10 (PR-10) transcripts with distinct patterns of abundance in different organs.

    PubMed

    Mohammadi, Mohsen; Srivastava, Sanjeeva; Hall, Jocelyn C; Kav, Nat N V; Deyholos, Michael K

    2012-06-01

    PR-10 genes encode small, acidic, intracellular proteins that respond to abiotic and biotic stimuli. Transgenic expression of PR-10 genes has been shown to enhance early seedling growth of dicots in saline environments. To identify candidate PR-10 genes in cereals for increasing stress tolerance, we conducted phylogenetic analyses and real-time polymerase chain reaction of representatives of the two major clades of putative PR-10 genes in wheat. We observed that the abundance of BQ752893 was generally greater than the abundance of CV778999, particularly when measured in roots across four wheat genotypes. However, CV778999 transcripts were more abundant than BQ752893 in flag leaves. These data suggest that the transcripts define two functionally divergent groups of PR-10 type genes in wheat, both of which may be suitable targets for biotechnological manipulation under different circumstances. PMID:21818707

  2. 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.

  3. 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...

  4. Phenology and Abundance of Bean Leaf Beetle (Coleoptera: Chrysomelidae) in Eastern South Dakota on Alfalfa and Soybean Relative to Tillage, Fertilization and Yield

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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 a...

  5. 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.

  6. Cell abundance and fluorescence of picoplankton in relation to growth irradiance and nitrogen availability in the red sea

    NASA Astrophysics Data System (ADS)

    Veldhuis, Marcel J. W.; Kraay, Gijsbert W.

    The vertical distribution and cellular fluorescence characteristics (chlorophyll and phycoerythrin, PE) of picoplankton (cyanobacteria and prochlorophytes) in the southern Red Sea were investigated in relation to physico-chemical properties of the water column. At all stations two subpopulations of Synechococcus sp. (type A and B) co-occurred, with maximal numbers up to 75 000·cm -3. Type B, with dim fluorescence signals, dominated the surface waters whereas type A, with bright fluorescence signals, dominated at greater depth. The divinyl a and b containing Prochlorococcus sp. peaked below the cyanobacteria at the deep chlorophyll maximum (DCM) with maximal cell numbers of 276 000·cm -3. Due to thermal stratification the cellular fluorescence (chlorophyll and phycoerythrin) increased with decreasing growth (PAR) irradiance, in an S-shaped manner, but magnitude and slope for the three picoplankters differed. The Synechococcus sp. type B had only a moderate increase in chlorophyll and phycoerythrin fluorescence signals with depth (3.4 and 6.6 fold, respectively), with values saturating at 3% (L d) of the surface irradiance. The deeper-water type not only possessed much higher values for cellular fluorescence than the B type, but the increase with decreasing light level was also much higer (for chlorophyll by a factor of 11 and PE increased by a factor of 23). In addition, maximal values for these fluorescence signals occurred at an isolume of 1 to 0.5%. These differences in concentrations and responses of the pigment content to the prevailing light climate explain the variation in abundance of both types over the water column. Although the prochlorophytes dominated almost the entire euphotic zone, their adaptation to low light levels was even better than in the two types of cyanobacteria. With depth their increase in chlorophyll fluorescence was similar to that observed in the cyanobacteria (with an increase from surface to bottom of the euphotic zone by a factor

  7. Evolutionary perspectives on clonal reproduction in vertebrate animals

    PubMed Central

    Avise, John C.

    2015-01-01

    A synopsis is provided of different expressions of whole-animal vertebrate clonality (asexual organismal-level reproduction), both in the laboratory and in nature. For vertebrate taxa, such clonal phenomena include the following: human-mediated cloning via artificial nuclear transfer; intergenerational clonality in nature via parthenogenesis and gynogenesis; intergenerational hemiclonality via hybridogenesis and kleptogenesis; intragenerational clonality via polyembryony; and what in effect qualifies as clonal replication via self-fertilization and intense inbreeding by simultaneous hermaphrodites. Each of these clonal or quasi-clonal mechanisms is described, and its evolutionary genetic ramifications are addressed. By affording an atypical vantage on standard vertebrate reproduction, clonality offers fresh perspectives on the evolutionary and ecological significance of recombination-derived genetic variety. PMID:26195735

  8. 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.

  9. Phylogenetic Meta-Analysis of the Functional Traits of Clonal Plants Foraging in Changing Environments

    PubMed Central

    Xie, Xiu-Fang; Song, Yao-Bin; Zhang, Ya-Lin; Pan, Xu; Dong, Ming

    2014-01-01

    Foraging behavior, one of the adaptive strategies of clonal plants, has stimulated a tremendous amount of research. However, it is a matter of debate whether there is any general pattern in the foraging traits (functional traits related to foraging behavior) of clonal plants in response to diverse environments. We collected data from 97 published papers concerning the relationships between foraging traits (e.g., spacer length, specific spacer length, branch intensity and branch angle) of clonal plants and essential resources (e.g., light, nutrients and water) for plant growth and reproduction. We incorporated the phylogenetic information of 85 plant species to examine the universality of foraging hypotheses using phylogenetic meta-analysis. The trends toward forming longer spacers and fewer branches in shaded environments were detected in clonal plants, but no evidence for a relation between foraging traits and nutrient availability was detected, except that there was a positive correlation between branch intensity and nutrient availability in stoloniferous plants. The response of the foraging traits of clonal plants to water availability was also not obvious. Additionally, our results indicated that the foraging traits of stoloniferous plants were more sensitive to resource availability than those of rhizomatous plants. In consideration of plant phylogeny, these results implied that the foraging traits of clonal plants (notably stoloniferous plants) only responded to light intensity in a general pattern but did not respond to nutrient or water availability. In conclusion, our findings on the effects of the environment on the foraging traits of clonal plants avoided the confounding effects of phylogeny because we incorporated phylogeny into the meta-analysis. PMID:25216101

  10. Clonal deletion and clonal anergy in the thymus induced by cellular elements with different radiation sensitivities

    SciTech Connect

    Roberts, J.L.; Sharrow, S.O.; Singer, A. )

    1990-03-01

    The present study demonstrates that immune tolerance can be achieved in the thymus both by clonal deletion and by clonal inactivation, but that the two tolerant states are induced by cellular elements with different radiation sensitivities. TCR engagement of self antigens on bone marrow-derived, radiation-sensitive (presumably dendritic) cells induces clonal deletion of developing thymocytes, whereas TCR engagement of self antigens on radiation-resistant cellular elements, such as thymic epithelium, induces clonal anergy. The nondeleted, anergic thymocytes can express IL-2-Rs but are unable to proliferate in response to either specific antigen or anti-TCR antibodies, and do develop into phenotypically mature cells that emigrate out of the thymus and into the periphery.

  11. Seasonal dynamics of prokaryotic abundance and activities in relation to environmental parameters in a transitional aquatic ecosystem (Cape Peloro, Italy).

    PubMed

    Zaccone, R; Azzaro, M; Azzaro, F; Bergamasco, A; Caruso, G; Leonardi, M; La Ferla, R; Maimone, G; Mancuso, M; Monticelli, L S; Raffa, F; Crisafi, E

    2014-01-01

    This study examines the effects of temporal changes on microbial parameters in a brackish aquatic ecosystem. To this aim, the abundances of prokaryotes and vibrios together with the rates of enzymatic hydrolysis of proteins by leucine aminopeptidase (LAP), polysaccharides by β-glucosidase (GLU) and organic phosphates by alkaline phosphatase (AP), heterotrophic prokaryotic production (HPP), respiration (R), were seasonally investigated, during a 2-year period in the coastal area of Cape Peloro (Messina, Italy), constituted by two brackish lakes (Faro and Ganzirri). In addition, physical and chemical parameters (temperature, salinity, nutrients) and particulate organic carbon and nitrogen (POC, PN) were measured. The influence of multiple factors on prokaryotic abundances and activities was analysed. The results showed that Cape Peloro area is characterised by high seasonal variability of the microbial parameters that is higher than the spatial one. Combined changes in particulate matter and temperature (T), could explain the variability in vibrios abundance, GLU and R activities in both lakes, indicating a direct stimulation of the warm season on the heterotrophic prokaryotic metabolism. Positive correlations between T (from 13.3 to 29.6 °C) and HPP, LAP, AP, POC, PN are also observed in Ganzirri Lake. Moreover, the trophic status index and most of the microbial parameters show significant seasonal differences. This study demonstrates that vibrios abundance and microbial activities are responsive to the spatial and seasonal changes of examined area. The combined effects of temperature and trophic conditions on the microbial parameters lead us to suggest their use as potential indicators of the prokaryotic response to climate changes in temperate brackish areas. PMID:24158689

  12. 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.

  13. Quality improvement in Vignoles through clonal selection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Our goal is to select an improved, loose-clustered clone of Vignoles that will contribute to an integrated approach to disease control. Clonal selection has historically proven useful in reducing cluster compactness through a variety of mechanisms, including decreased berry size, lengthening of the ...

  14. Plant Diseases Impact USDA Clonal Vaccinium Genebank

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The USDA Agricultural Research Service maintains a diverse collection of Vaccinium genotypes at the National Clonal Germplasm Repository, a temperate fruit and nut genebank in Corvallis, Oregon. Vaccinium species are hosts for two emerging diseases in the U.S. Pacific Northwest that impact the colle...

  15. 'Sharpe', a clonal plum rootstock for peach

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sharpe clonal rootstock for peach is jointly released for grower trial by the U.S. Department of Agriculture, Agricultural Research Service (Byron, GA), and Florida Agricultural Experiment Station. Sharpe, previously tested as FLA1-1, was discovered in the wild and appears to be a hybrid of Chickas...

  16. HIV genetic information and clonal growth

    Cancer.gov

    Based on an analysis of blood cells from five HIV-infected individuals, NCI researchers have identified more than 2,400 HIV DNA insertion sites. Analysis of these sites showed that there is extensive clonal expansion (growth) of HIV infected cells.

  17. Ephemeral clonal integration in Calathea marantifolia (Marantaceae): Evidence of diminished integration over time.

    PubMed

    Matlaga, David P; da S L Sternberg, Leonel

    2009-02-01

    A major advantage of clonal growth forms is the intergenerational transfer of resources through vascular connections (clonal integration). Connections linking ramets can be persistent or ephemeral. For species with ephemeral connections, whether the extent of clonal integration changes over time is unclear. To address this issue, we tracked water movement using an isotopic label and assessed the demographic performance of parent and offspring ramets over time in a severing experiment. Our study system was the understory herb Calathea marantifolia, which has parent ramets that produce vegetative bulbils (clonal offspring) that pass through distinct pre- and post-rooting stages. Little water was transported between parents and offspring, and the direction of movement was primarily from parent to pre-rooting offspring. Anatomical observations of inter-ramet connections showed that vascular bundles were twice as abundant in parent stems compared to inter-ramet connections. Severing inter-ramet connections reduced the growth of offspring ramets but not parents. Survival of pre-rooting offspring was reduced by 10% due to severing, but post-rooting offspring were not affected. Our results suggest that offspring ramets of C. marantifolia are weaned from their parent as they progress from pre- to post-rooting stages. PMID:21628198

  18. Clonal analysis and virulent traits of pathogenic extraintestinal Escherichia coli isolates from swine in China

    PubMed Central

    2012-01-01

    Background Extraintestinal pathogenic Escherichia coli (ExPEC) can cause a variety of infections outside the gastrointestinal tract in humans and animals. Infections due to swine ExPECs have been occurring with increasing frequency in China. These ExPECs may now be considered a new food-borne pathogen that causes cross-infections between humans and pigs. Knowledge of the clonal structure and virulence genes is needed as a framework to improve the understanding of phylogenetic traits of porcine ExPECs. Results Multilocus sequence typing (MLST) data showed that the isolates investigated in this study could be placed into four main clonal complexes, designated as CC10, CC1687, CC88 and CC58. Strains within CC10 were classified as phylogroup A, and these accounted for most of our porcine ExPEC isolates. Isolates in the CC1687 clonal complex, formed by new sequence types (STs), was classified as phylogroup D, with CC88 isolates considered as B2 and CC58 isolates as B1. Porcine ExPECs in these four clonal complexes demonstrated significantly different virulence gene patterns. A few porcine ExPECs were indentified in phylogroup B2, the phylogroup in which human ExPECs mainly exist. However some STs in the four clonal groups of porcine ExPECs were reported to cause extraintestinal infections in human, based on data in the MLST database. Conclusion Porcine ExPECs have different virulence gene patterns for different clonal complexes. However, these strains are mostly fell in phylogenentic phylogroup A, B1 and D, which is different from human ExPECs that concentrate in phylogroup B2. Our findings provide a better understanding relating to the clonal structure of ExPECs in diseased pigs and indicate a need to re-evaluate their contribution to human ExPEC diseases. PMID:22909380

  19. Clonal hematopoiesis in acquired aplastic anemia.

    PubMed

    Ogawa, Seishi

    2016-07-21

    Clonal hematopoiesis (CH) in aplastic anemia (AA) has been closely linked to the evolution of late clonal disorders, including paroxysmal nocturnal hemoglobinuria and myelodysplastic syndromes (MDS)/acute myeloid leukemia (AML), which are common complications after successful immunosuppressive therapy (IST). With the advent of high-throughput sequencing of recent years, the molecular aspect of CH in AA has been clarified by comprehensive detection of somatic mutations that drive clonal evolution. Genetic abnormalities are found in ∼50% of patients with AA and, except for PIGA mutations and copy-neutral loss-of-heterozygosity, or uniparental disomy (UPD) in 6p (6pUPD), are most frequently represented by mutations involving genes commonly mutated in myeloid malignancies, including DNMT3A, ASXL1, and BCOR/BCORL1 Mutations exhibit distinct chronological profiles and clinical impacts. BCOR/BCORL1 and PIGA mutations tend to disappear or show stable clone size and predict a better response to IST and a significantly better clinical outcome compared with mutations in DNMT3A, ASXL1, and other genes, which are likely to increase their clone size, are associated with a faster progression to MDS/AML, and predict an unfavorable survival. High frequency of 6pUPD and overrepresentation of PIGA and BCOR/BCORL1 mutations are unique to AA, suggesting the role of autoimmunity in clonal selection. By contrast, DNMT3A and ASXL1 mutations, also commonly seen in CH in the general population, indicate a close link to CH in the aged bone marrow, in terms of the mechanism for selection. Detection and close monitoring of somatic mutations/evolution may help with prediction and diagnosis of clonal evolution of MDS/AML and better management of patients with AA. PMID:27121470

  20. Consequences of clonality for sexual fitness: Clonal expansion enhances fitness under spatially restricted dispersal

    PubMed Central

    Van Drunen, Wendy E.; van Kleunen, Mark; Dorken, Marcel E.

    2015-01-01

    Clonality is a pervasive feature of sessile organisms, but this form of asexual reproduction is thought to interfere with sexual fitness via the movement of gametes among the modules that comprise the clone. This within-clone movement of gametes is expected to reduce sexual fitness via mate limitation of male reproductive success and, in some cases, via the production of highly inbred (i.e., self-fertilized) offspring. However, clonality also results in the spatial expansion of the genetic individual (i.e., genet), and this should decrease distances gametes and sexually produced offspring must travel to avoid competing with other gametes and offspring from the same clone. The extent to which any negative effects of clonality on mating success might be offset by the positive effects of spatial expansion is poorly understood. Here, we develop spatially explicit models in which fitness was determined by the success of genets through their male and female sex functions. Our results indicate that clonality serves to increase sexual fitness when it is associated with the outward expansion of the genet. Our models further reveal that the main fitness benefit of clonal expansion might occur through the dispersal of offspring over a wider area compared with nonclonal phenotypes. We conclude that, instead of interfering with sexual reproduction, clonal expansion should often serve to enhance sexual fitness. PMID:26195748

  1. Evaluating Clonal Expansion of HIV-Infected Cells: Optimization of PCR Strategies to Predict Clonality

    PubMed Central

    Laskey, Sarah B.; Pohlmeyer, Christopher W.; Bruner, Katherine M.; Siliciano, Robert F.

    2016-01-01

    In HIV-infected individuals receiving suppressive antiretroviral therapy, the virus persists indefinitely in a reservoir of latently infected cells. The proliferation of these cells may contribute to the stability of the reservoir and thus to the lifelong persistence of HIV-1 in infected individuals. Because the HIV-1 replication process is highly error-prone, the detection of identical viral genomes in distinct host cells provides evidence for the clonal expansion of infected cells. We evaluated alignments of unique, near-full-length HIV-1 sequences to determine the relationship between clonality in a short region and clonality in the full genome. Although it is common to amplify and sequence short, subgenomic regions of the viral genome for phylogenetic analysis, we show that sequence identity of these amplicons does not guarantee clonality across the full viral genome. We show that although longer amplicons capture more diversity, no subgenomic region can recapitulate the diversity of full viral genomes. Consequently, some identical subgenomic amplicons should be expected even from the analysis of completely unique viral genomes, and the presence of identical amplicons alone is not proof of clonally expanded HIV-1. We present a method for evaluating evidence of clonal expansion in the context of these findings. PMID:27494508

  2. Evaluating Clonal Expansion of HIV-Infected Cells: Optimization of PCR Strategies to Predict Clonality.

    PubMed

    Laskey, Sarah B; Pohlmeyer, Christopher W; Bruner, Katherine M; Siliciano, Robert F

    2016-08-01

    In HIV-infected individuals receiving suppressive antiretroviral therapy, the virus persists indefinitely in a reservoir of latently infected cells. The proliferation of these cells may contribute to the stability of the reservoir and thus to the lifelong persistence of HIV-1 in infected individuals. Because the HIV-1 replication process is highly error-prone, the detection of identical viral genomes in distinct host cells provides evidence for the clonal expansion of infected cells. We evaluated alignments of unique, near-full-length HIV-1 sequences to determine the relationship between clonality in a short region and clonality in the full genome. Although it is common to amplify and sequence short, subgenomic regions of the viral genome for phylogenetic analysis, we show that sequence identity of these amplicons does not guarantee clonality across the full viral genome. We show that although longer amplicons capture more diversity, no subgenomic region can recapitulate the diversity of full viral genomes. Consequently, some identical subgenomic amplicons should be expected even from the analysis of completely unique viral genomes, and the presence of identical amplicons alone is not proof of clonally expanded HIV-1. We present a method for evaluating evidence of clonal expansion in the context of these findings. PMID:27494508

  3. Temporal changes in euphausiid distribution and abundance in North Atlantic cold-core rings in relation to the surrounding waters

    NASA Astrophysics Data System (ADS)

    Endo, Yoshinari; Wiebe, Peter H.

    2007-02-01

    The species composition of euphausiids was investigated in relationship to the hydrographic conditions in the North Atlantic cold-core rings (CCR) and adjacent waters to elucidate species succession in evolving water masses. Using data, dating back to the 1970s, from as many CCRs as possible and selecting typical cases where no major physical perturbations occurred, a general pattern of euphausiid succession and change in vertical distribution in rings with time was obtained. This pattern was related to the general distribution of euphausiids in the northwestern North Atlantic Ocean, aiming at providing basic information on probable response of North Atlantic marine ecosystem to global warming. Of the 34 euphausiid species identified, 5 were cold-water species, 17 were warm-water species, 6 were wide-ranging warm-water species, 1 was transitional, 4 were cosmopolitan and the remaining was Thysanoessa parva. Among cold-water species, Euphausia krohni and Nematoscelis megalops were dominant in CCRs. E. krohni became rare in rings older than 6 months, whereas N. megalops survived longer, being abundant in some rings of 9 months or older, by staying within its preferred temperature range as the CCR elevated isotherms sank to depths where they are normally found in the Sargasso Sea and because it is an omnivore-carnivore. Among warm-water species, epipelagic species appeared first in rings, corresponding to the physical change occurring most rapidly in the surface layers. Mesopelagic species appeared later. Cold-water species made up 65-85% of the total euphausiid population in number in younger rings (1-5 months old), while warm-water species contributed only 2-7%. Wide-ranging warm-water species made up about up to one fourth of the total in rings 5 and 7 months old. Warm-water species, mainly E. brevis, increased in older rings (9 months old or older) and made up 50% of the total in the oldest ring. The contribution of cold-water species decreased to 14% in older

  4. A comparison of 454 sequencing and clonal sequencing for the characterization of hepatitis C virus NS3 variants.

    PubMed

    Ho, Cynthia K Y; Welkers, Matthijs R A; Thomas, Xiomara V; Sullivan, James C; Kieffer, Tara L; Reesink, Henk W; Rebers, Sjoerd P H; de Jong, Menno D; Schinkel, Janke; Molenkamp, Richard

    2015-07-01

    We compared 454 amplicon sequencing with clonal sequencing for the characterization of intra-host hepatitis C virus (HCV) NS3 variants. Clonal and 454 sequences were obtained from 12 patients enrolled in a clinical phase I study for telaprevir, an NS3-4a protease inhibitor. Thirty-nine datasets were used to compare the consensus sequence, average pairwise distance, normalized Shannon entropy, phylogenetic tree topology and the number and frequency of variants derived from both sequencing techniques. In general, a good concordance was observed between both techniques for the majority of datasets. Discordant results were observed for 5 out of 39 clonal and 454 datasets, which could be attributed to primer-related selective amplification used for clonal sequencing. Both 454 and clonal datasets consisted of a few major variants and a large number of low-frequency variants. Telaprevir resistance-associated variants were observed in low frequencies and were detected more often by 454. We conclude that performance of 454 and clonal sequencing is comparable for the characterization of intra-host virus populations. Not surprisingly, 454 is superior for the detection of low frequency resistance-associated variants. However, despite the greater coverage, 454 failed to detect some low frequency variants detected by clonal sequencing. PMID:25818622

  5. Size-related variation in protein abundance in the brain and abdominal tissue of bumble bee workers.

    PubMed

    Wolschin, F; Shpigler, H; Amdam, G V; Bloch, G

    2012-06-01

    Female bumble bee workers of the same species often show a profound body size variation that is linked to a division of labour. Large individuals are more likely to forage whereas small individuals are more likely to perform in-nest activities. A higher sensory sensitivity, stronger circadian rhythms as well as better learning and memory performances appear to better equip large individuals for outdoor activities compared to their smaller siblings. The molecular mechanisms underlying worker functional polymorphism remain unclear. Proteins are major determinants of an individual's morphology and behaviour. We hypothesized that the abundance of proteins such as metabolic enzymes as well as proteins involved in neuronal functions would differ with body size and provide insights into the mechanisms underlying size-dependent physiological specialization in bumble bee workers. We conducted protein quantification measurements based on liquid chromatography coupled with tandem mass spectrometry on tissue samples derived from small and large Bombus impatiens and Bombus terrestris workers. Proteins found to differ significantly in abundance between small and large workers belong to the categories of structure, energy metabolism and stress response. These findings provide the first proteomic insight into mechanisms associated with size-based division of labour in social insects. PMID:22568679

  6. 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.

  7. Clonal relationships in recurrent B-cell lymphomas.

    PubMed

    Lee, Seung Eun; Kang, So Young; Yoo, Hae Yong; Kim, Seok Jin; Kim, Won Seog; Ko, Young Hyeh

    2016-03-15

    Immunoglobulin (Ig) gene rearrangements remain largely unmodified during the clonal expansion of neoplastic cells. We investigated the clonal relationships between lymphoma components at diagnosis and at relapse by analyzing Ig gene rearrangements. A BIOMED-2 multiplex polymerase chain reaction (PCR) assay was performed in 27 patients using formalin-fixed paraffin embedded tissues, with subsequent cloning and sequencing of the amplified Ig genes in 17 patients. All 27 cases of primary and corresponding relapsed tumors showed monoclonal rearrangements of the Ig genes by BIOMED-2 PCR. Whereas IgVH or IgVK fragment lengths were identical in 8/27 pairs (30%), fragment lengths differed in 19/27 pairs (70%). In 17 cases analyzed by sequencing, an identical VDJ gene rearrangement was confirmed in 4/4 pairs (100%) with the same fragment lengths and in 10/13 pairs (77%) with different fragment lengths. Four of 17 primary lymphomas had multiple VDJ rearrangements, and three of them showed an unrelated relapse. Unrelated relapse was observed in 1/8 mantle cell lymphomas, 1/5 diffuse large B-cell lymphomas, and a large B cell lymphoma developed in a patient with a small lymphocytic lymphoma. Unrelated relapses developed after a longer disease-free interval and tended to show poorer outcome compared with related relapse. In summary, relapse of a lymphoma from an unrelated clone is uncommon, but can occur in B-cell lymphomas. Clonal relationships should be determined by sequencing of the Ig genes, and not just by comparing the PCR product size. PMID:26848863

  8. Clonal relationships in recurrent B-cell lymphomas

    PubMed Central

    Lee, Seung Eun; Kang, So Young; Yoo, Hae Yong; Kim, Seok Jin; Kim, Won Seog; Ko, Young Hyeh

    2016-01-01

    Immunoglobulin (Ig) gene rearrangements remain largely unmodified during the clonal expansion of neoplastic cells. We investigated the clonal relationships between lymphoma components at diagnosis and at relapse by analyzing Ig gene rearrangements. A BIOMED-2 multiplex polymerase chain reaction (PCR) assay was performed in 27 patients using formalin-fixed paraffin embedded tissues, with subsequent cloning and sequencing of the amplified Ig genes in 17 patients. All 27 cases of primary and corresponding relapsed tumors showed monoclonal rearrangements of the Ig genes by BIOMED-2 PCR. Whereas IgVH or IgVK fragment lengths were identical in 8/27 pairs (30%), fragment lengths differed in 19/27 pairs (70%). In 17 cases analyzed by sequencing, an identical VDJ gene rearrangement was confirmed in 4/4 pairs (100%) with the same fragment lengths and in 10/13 pairs (77%) with different fragment lengths. Four of 17 primary lymphomas had multiple VDJ rearrangements, and three of them showed an unrelated relapse. Unrelated relapse was observed in 1/8 mantle cell lymphomas, 1/5 diffuse large B-cell lymphomas, and a large B cell lymphoma developed in a patient with a small lymphocytic lymphoma. Unrelated relapses developed after a longer disease-free interval and tended to show poorer outcome compared with related relapse. In summary, relapse of a lymphoma from an unrelated clone is uncommon, but can occur in B-cell lymphomas. Clonal relationships should be determined by sequencing of the Ig genes, and not just by comparing the PCR product size. PMID:26848863

  9. The relative abundance of a salivary protein, bSP30, is correlated with susceptibility to bloat in cattle herds selected for high or low bloat susceptibility.

    PubMed

    Rajan, G H; Morris, C A; Carruthers, V R; Wilkins, R J; Wheeler, T T

    1996-12-01

    Pasture bloat is a serious economic and animal welfare problem in cattle grazed on legumes in New Zealand. Analysis of salivary proteins from dairy cattle in herds bred for either low or high susceptibility to bloat has resulted in the identification of a 30 kilodalton protein, which we term bSP30, whose relative abundance is negatively correlated with bloat score (r = -0.40 +/- 0.12). From 74 animals sampled, relative abundance of bSP30 was 66 +/- 15% higher in the low-susceptibility herd than in the high-susceptibility herd. Relative abundance of bSP30 also varied significantly within individuals, according to feeding or time of day, and from day to day. A sequence homology search of 38 amino acids derived from three tryptic fragments of the protein suggests that the amino acid sequence of bSP30 has not been described previously. Amino acid analysis indicates that bSP30 is not a member of the proline-rich family of salivary proteins. The function of bSP30 is unknown but it is conceivable that it plays a role in the aetiology of bloat. PMID:9022155

  10. Different Growth Promoting Effects of Endophytic Bacteria on Invasive and Native Clonal Plants

    PubMed Central

    Dai, Zhi-Cong; Fu, Wei; Wan, Ling-Yun; Cai, Hong-Hong; Wang, Ning; Qi, Shan-Shan; Du, Dao-Lin

    2016-01-01

    The role of the interactions between endophytes and alien plants has been unclear yet in plant invasion. We used a completely germ-free culture system to quantify the plant growth-promoting (PGP) effects of endophytic bacteria Bacillus sp. on aseptic seedlings of Wedelia trilobata and of its native clonal congener W. chinensis. The endophytic bacteria did not affect the growth of W. chinensis, but they significantly promoted the growth of W. trilobata. With the PGP effects of endophytic bacteria, relative change ratios of the clonal traits and the ramets’ growth traits of W. trilobata were significantly greater than those of W. chinensis. Our results indicate that the growth-promoting effects of endophytes may differ between invasive and native clonal plants, and the endophytes of invasive plant may be host-specific to facilitate plant invasion. PMID:27252722

  11. Different Growth Promoting Effects of Endophytic Bacteria on Invasive and Native Clonal Plants.

    PubMed

    Dai, Zhi-Cong; Fu, Wei; Wan, Ling-Yun; Cai, Hong-Hong; Wang, Ning; Qi, Shan-Shan; Du, Dao-Lin

    2016-01-01

    The role of the interactions between endophytes and alien plants has been unclear yet in plant invasion. We used a completely germ-free culture system to quantify the plant growth-promoting (PGP) effects of endophytic bacteria Bacillus sp. on aseptic seedlings of Wedelia trilobata and of its native clonal congener W. chinensis. The endophytic bacteria did not affect the growth of W. chinensis, but they significantly promoted the growth of W. trilobata. With the PGP effects of endophytic bacteria, relative change ratios of the clonal traits and the ramets' growth traits of W. trilobata were significantly greater than those of W. chinensis. Our results indicate that the growth-promoting effects of endophytes may differ between invasive and native clonal plants, and the endophytes of invasive plant may be host-specific to facilitate plant invasion. PMID:27252722

  12. Annual cycle in abundance, distribution, and size in relation to hydrography of important copepod species in the western Arctic Ocean

    NASA Astrophysics Data System (ADS)

    Ashjian, Carin J.; Campbell, Robert G.; Welch, Harold E.; Butler, Mari; Van Keuren, Donna

    2003-10-01

    A yearlong study of the zooplankton biomass and the abundance, vertical distribution, life stage proportions, and body size and condition for five target copepod species ( Calanus glacialis, C. hyperboreus, Metridia longa, Microcalanus pygmaeus, Oithona similis) was conducted from October 1997 to October 1998 in the Western Arctic Ocean. The research was staged from Ice Station SHEBA that drifted from Canadian Basin over the Northwind Ridge and Chukchi Plateau and back over the Basin during this period. Four hydrographic regimes were surveyed during the period of the study. Zooplankton biomass was least over the basin during the fall and winter and greatest over the Chukchi Plateau during summer, with most biomass in the 200-1500 m depth interval except during summer when greatest biomass was present in the upper 200 m. The five copepod species followed two general life history strategies: (1) sustained reproduction with all life stages present throughout the year and constant depth distribution ( M. longa, M. pygmaeus, O. similis) and (2) pulsed reproduction with overlapping cohorts present and ontogenetic redistribution of preferred depths through the year ( C. glacialis, C. hyperboreus). Body size and condition did not demonstrate consistent temporal or regional patterns. Based on population age structure, both C. hyperboreus and C. glacialis were reproducing in the Arctic Ocean. However, extremely low abundances of C. glacialis suggested that this species may not be self-sustaining in the Arctic Ocean. Plankton biomass was consistent with that observed in recent studies and supported an emerging paradigm of a more productive Arctic Ocean than traditionally believed.

  13. 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. PMID:26056318

  14. 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

  15. Detectable Clonal Mosaicism in the Human Genome

    PubMed Central

    Machiela, Mitchell J.; Chanock, Stephen J.

    2013-01-01

    Human genetic mosaicism is the presence of two or more cellular populations with distinct genotypes in an individual who developed from a single fertilized ovum. While initially observed across a spectrum of rare genetic disorders, detailed assessment of data from genome-wide association studies now reveal that detectable clonal mosaicism involving large structural alterations (> 2 Mb) can also be seen in populations of apparently healthy individuals. The first generation of descriptive studies have generated new interest in understanding the molecular basis of the affected genomic regions, percent of the cellular subpopulation involved, and developmental timing of the underlying mutational event, which could reveal new insights into the initiation, clonal expansion and phenotypic manifestations of mosaic events. Early evidence indicates detectable clonal mosaicism increases in frequency with age and could preferentially occur in males. The observed pattern of recurrent events affecting specific chromosomal regions indicates some regions are more susceptible to these events, which could reflect inter-individual differences in genomic stability. Moreover, it is also plausible that the presence of large structural events could be associated with cancer risk. The characterization of detectable genetic mosaicism reveals that there could be important dynamic changes in the human genome associated with the aging process, which could be associated with risk for common disorders, such as cancer, cardiovascular disease, diabetes, and neurological disorders. PMID:24246702

  16. Unexpected abundance and long-term relative stability of the brown alga Cystoseira amentacea, hitherto regarded as a threatened species, in the north-western Mediterranean Sea.

    PubMed

    Thibaut, Thierry; Blanfuné, Aurélie; Markovic, Laurent; Verlaque, Marc; Boudouresque, Charles F; Perret-Boudouresque, Michèle; Maćic, Vesna; Bottin, Lorraine

    2014-12-15

    Cystoseira amentacea is a Mediterranean endemic alga thriving on very shallow rocky substrates. It has been considered as a threatened species, having experienced a steady decline and is therefore protected by international conventions. The historical distribution of the species has been assessed along the French Mediterranean coast, on the basis of 467 articles and herbarium vouchers. We have produced an accurate map of its current distribution and abundance along 1832 km of coastline, through in situ surveys. C. amentacea was observed along 1125 km of shoreline, including 33% of almost continuous or continuous belt. In most of its range, there is no evidence of loss, except in 4 areas of Provence, French Riviera and Corsica. A significant relation was found between the absence or low abundance of C. amentacea and the vicinity of ports and large sewage outfalls. The status of conservation of the species should therefore be reassessed. PMID:25440190

  17. Abundance of ticks (Acari: Ixodidae) infesting the western fence lizard, Sceloporus occidentalis, in relation to environmental factors.

    PubMed

    Tälleklint-Eisen, L; Eisen, R J

    1999-09-01

    We examined the impact of environmental characteristics, such as habitat type, topographic exposure and presence of leaf litter, on the abundance of Ixodes pacificus ticks infesting the western fence lizard (Sceloporus occidentalis) at the University of California Hopland Research and Extension Center (HREC), Mendocino County, California. A total of 383 adult lizards were slip-noosed and examined for tick infestation in April and May 1998. At least 94% of the lizards were infested by ticks and at least 20% of the females and 33% of the males carried > 15 ticks. This intensive utilization of western fence lizards (which do not serve as natural reservoirs for Lyme disease spirochetes) by subadult ticks, is probably the primary reason for the low prevalence of infection with Borrelia burgdorferi in I. pacificus nymphs and adults previously recorded at the HREC. Tick loads were higher on male than female lizards. Also, male lizards were generally more heavily infested in late April than in late May. The prevalence of tick infestation exceeded 88% in all habitat types but males collected in woodland and grass/woodland edges had higher tick loads than those collected in open grassland. Male lizards captured in open, exposed grassland tended to carry heavier tick loads in northern/eastern, as compared to southern/western, exposures, and when leaf litter was present. PMID:10581712

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

    PubMed

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

    2012-10-15

    A survey of invertebrates in drinking water from treatment works, internal taps and hydrants on mains was carried out by almost all water companies in the Netherlands from September 1993 to August 1995. Aquatic sow bugs (Asellidae, 1-12 mm) and oligochaeta worms (Oligochaeta, 1-100 mm), both known to have caused rare though embarrassing consumer complaints, were found to form 98% of the mean biomass in water flushed from mains. Their numbers in the mains water ranged up to 1500 (mean 37) Asellidae m(-3) and up to 9900 (mean 135) Oligochaeta m(-3). Smaller crustaceans (0.5-2 mm) dominated the numbers in water from mains. e.g. water fleas (Cladocera and Copepoda up to 14,000 m(-3)). Common invertebrates in treated water and in tap water were Rotifera (<1 mm) and nematode worms (Nematoda, <2 mm). No Asellidae, large Oligochaeta (>5 mm) or other large invertebrates were found in 1560 samples of 200 l treated water or tap water. Large variations in invertebrate abundance were found within and between distribution systems. Of the variability of mean biomass in mains per system, 55%, 60% and 63% could statistically be explained by differences in the Biofilm Formation Rate, non-particulate organic matter and the permanganate index of the treated water of the treatment works respectively. A similar correlation was found between mean invertebrate biomass and mean sediment volumes in the distribution systems (R(2) = 52%). PMID:22840474

  19. 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.

  20. The 20Ne(d,p)21Ne transfer reaction in relation to the s-process abundances

    NASA Astrophysics Data System (ADS)

    Nsangu, C. T.; Laird, A. M.; Parikh, A.; Adsley, P.; Birch, M. D.; Chen, A. A.; Faestermann, T.; Fox, S. P.; Fulton, B. R.; Hertenberger, R.; Irvine, D.; Kay, B. P.; Longland, R.; Manwell, S.; Murphy, A. St. J.; Schmitt, K.; de Séréville, N.; Tomlinson, J. R.; Wirth, H.-F.

    2016-01-01

    A study of the 20Ne(d,p)21Ne transfer reaction was performed using the Quadrupole Dipole Dipole Dipole (Q3D) magnetic spectrograph in Garching, Germany. The experiment probed excitation energies in 21Ne ranging from 6.9 MeV to 8.5 MeV. The aim was to investigate the spectroscopic information of 21Ne within the Gamow window of core helium burning in massive stars. Further information in this region will help reduce the uncertainties on the extrapolation down to Gamow window cross sections of the 17O(α,γ)21Ne reaction. In low metallicity stars, this reaction has a direct impact on s-process abundances by determining the fate of 16O as either a neutron poison or a neutron absorber. The experiment used a 22-MeV deuteron beam, with intensities varying from 0.5-1 μA, and an implanted target of 20Ne of 7 μg/cm2 in 40 μg/cm2 carbon foils. Sixteen 21Ne peaks have been identified in the Ex = 6.9-8.5 MeV range, of which only thirteen peaks correspond to known states. Only the previously-known Ex = 7.960 MeV state was observed within the Gamow window.

  1. 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

  2. Do attacks by jaguars Panthera onca and pumas Puma concolor (Carnivora: Felidae) on livestock correlate with species richness and relative abundance of wild prey?

    PubMed

    Burgas, Albert; Amit, Ronit; Lopez, Bernat C

    2014-12-01

    Abstract: Attacks by big cats on livestock are one of the major causes of human-felid conflicts and, therefore, an important factor in the conservation of these species. It has been argued that a reduction in natural prey abundance promotes attacks on domestic species, but few studies have tested this statement, and some have delivered contradictory results. We investigated whether the occurrence of attacks to livestock by jaguar and puma relates to the abundance and richness of their natural prey. In the rainy season 2009, we tracked potential prey species counting signs of presence along linear transects in 14 non-attacked cattle farms (control) and in 14 attacked cattle farms in NW Costa Rica. There was a negative relationship between the occurrence of attacks and both species richness (p = 0.0014) and abundance (p = 0.0012) of natural prey. Our results support the establishment of actions to promote support and recovery of natural prey, in order to diminish attacks on livestock, while maintaining jaguar and puma populations. PMID:25720180

  3. 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

  4. Distribution and Abundance of Human Specific Bacteroides and Relation to Traditional Indicators in an Urban Tropical Catchment

    NASA Astrophysics Data System (ADS)

    Nshimyimana, J.; Shanahan, P.; Thompson, J. R.; Ekklesia, E.; Chua Hock Chye, L.

    2012-12-01

    The Singapore government through its Public Utilities Board is interested in opening Kranji Reservoir to recreational use. However, water courses within the Kranji Reservoir catchment contain human fecal indicator bacteria above recreational water quality criteria; their sources and distribution are unknown. The primary goals of this study were to determine the distribution of fecal indicator bacteria in drainages and water bodies in the Kranji reservoir catchment area. Total coliforms, E. coli, and the DNA-based HF marker (targeting a human specific strain of Bacteroides) were quantified in 27 samples collected in January 2009 and 54 samples collected in July 2009. Correlation of HF marker cell equivalents (CE) and E. coli abundance (colony forming units (CFU) or Most Probable Number (MPN)) to different land-use categories revealed potential sources of fecal contamination to the Kranji reservoir. Notably, areas designated as farming/agricultural were associated with the highest levels of E. coli (geometric mean 30,500 CFU/100 ml) and HF marker (1.23±1.13x106 CE/100 ml ± S.D.) while in general lower HF marker and E. coli levels were observed in residential areas, undeveloped areas, and within the Kranji reservoir (i.e. Kranji Reservoir had 2 to 17 MPN/100 ml of E. coli and 103 to 105 HF marker CE/100 ml). A partial survey of potential point sources for fecal contamination within the farming area revealed a wastewater effluent stream with HF marker levels exceeding 107 CE/100ml. As observed in previous studies, total coliforms and E. coli levels were weakly (R<0.4), or anti- correlated to HF marker concentrations across different land uses. Weak correspondence between traditional indicators (E. coli, total coliforms) and molecular indicators (HF marker) may be explained by differences in the ability of the respective organisms to grow or survive under aerated tropical conditions. The HF marker sequence matches that of Bacteroides dorei, an obligate anaerobe that

  5. 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.

  6. Genetic distance and age affect the cuticular chemical profiles of the clonal ant Cerapachys biroi.

    PubMed

    Teseo, Serafino; Lecoutey, Emmanuel; Kronauer, Daniel J C; Hefetz, Abraham; Lenoir, Alain; Jaisson, Pierre; Châline, Nicolas

    2014-05-01

    Although cuticular hydrocarbons (CHCs) have received much attention from biologists because of their important role in insect communication, few studies have addressed the chemical ecology of clonal species of eusocial insects. In this study we investigated whether and how differences in CHCs relate to the genetics and reproductive dynamics of the parthenogenetic ant Cerapachys biroi. We collected individuals of different ages and subcastes from several colonies belonging to four clonal lineages, and analyzed their cuticular chemical signature. CHCs varied according to colonies and clonal lineages in two independent data sets, and correlations were found between genetic and chemical distances between colonies. This supports the results of previous research showing that C. biroi workers discriminate between nestmates and non-nestmates, especially when they belong to different clonal lineages. In C. biroi, the production of individuals of a morphological subcaste specialized in reproduction is inversely proportional to colony-level fertility. As chemical signatures usually correlate with fertility and reproductive activity in social Hymenoptera, we asked whether CHCs could function as fertility-signaling primer pheromones determining larval subcaste fate in C. biroi. Interestingly, and contrary to findings for several other ant species, fertility and reproductive activity showed no correlation with chemical signatures, suggesting the absence of fertility related CHCs. This implies that other cues are responsible for subcaste differentiation in this species. PMID:24756691

  7. Plant and soil natural abundance delta (15)N: indicators of relative rates of nitrogen cycling in temperate forest ecosystems.

    PubMed

    Templer, Pamela H; Arthur, Mary A; Lovett, Gary M; Weathers, Kathleen C

    2007-08-01

    Watersheds within the Catskill Mountains, New York, receive among the highest rates of nitrogen (N) deposition in the northeastern United States and are beginning to show signs of N saturation. Despite similar amounts of N deposition across watersheds within the Catskill Mountains, rates of soil N cycling and N retention vary significantly among stands of different tree species. We examined the potential use of delta (15)N of plants and soils as an indicator of relative forest soil N cycling rates. We analyzed the delta (15)N of foliage, litterfall, bole wood, surface litter layer, fine roots and organic soil from single-species stands of American beech (Fagus grandifolia), eastern hemlock (Tsuga canadensis), red oak (Quercus rubra), and sugar maple (Acer saccharum). Fine root and organic soil delta (15)N values were highest within sugar maple stands, which correlated significantly with higher rates of net mineralization and nitrification. Results from this study suggest that fine root and organic soil delta (15)N can be used as an indicator of relative rates of soil N cycling. Although not statistically significant, delta (15)N was highest within foliage, wood and litterfall of beech stands, a tree species associated with intermediate levels of soil N cycling rates and forest N retention. Our results show that belowground delta (15)N values are a better indicator of relative rates of soil N cycling than are aboveground delta (15)N values. PMID:17479293

  8. 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

  9. The feature of distribution and clonality of TCR γ/δ subfamilies T cells in patients with B-cell non-Hodgkin lymphoma.

    PubMed

    Wang, Liang; Xu, Meng; Wang, Chunyan; Zhu, Lihua; Hu, Junyan; Chen, Shaohua; Wu, Xiuli; Li, Bo; Li, Yangqiu

    2014-01-01

    Restricted T-cell receptor (TCR) Vα/Vβ repertoire expression and clonal expansion of αβ T cells especially for putative tumor-associated antigens were observed in patients with hematological malignancies. To further characterize the γδ T-cell immune status in B-cell non-Hodgkin lymphoma (B-NHL), we investigated the distribution and clonality of TCR Vγ/Vδ repertoire in peripheral blood (PB), bone marrow (BM), and lymph node (LN) from patients with B-NHL. Four newly diagnosed B-NHL cases, including three with diffuse large B-cell lymphoma (DLBCL) and one with small lymphocytic lymphoma (SLL), were enrolled. The restrictive expression of TCR Vγ/Vδ subfamilies with different distribution patterns could be detected in PB, BM, or LN from all of four patients, and partial subfamily T cells showed clonal proliferation. At least one clonally expanded Vδ subfamily member was found in PB from each patient. However, the expression pattern and clonality of TCR Vγ/Vδ changed in different immune organs and showed individual feature in different patients. The clonally expanded Vδ5, Vδ6, and Vδ8 were detected only in PB but neither in BM nor LN while clonally expanded Vδ2 and Vδ3 could be detected in both PB and BM/LN. In conclusion, the results provide a preliminary profile of distribution and clonality of TCR γ/δ subfamilies T cells in PB, BM, and LN from B-NHL; similar clonally expanded Vδ subfamily T cells in PB and BM may be related to the same B-cell lymphoma-associated antigens, while the different reactive clonally expanded Vγ/Vδ T cells may be due to local immune response. PMID:24963496

  10. 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

  11. Changes in the relative abundance and movement of insect pollinators during the flowering cycle of Brassica rapa crops: implications for gene flow.

    PubMed

    Mesa, Laura A; Howlett, Bradley G; Grant, Jan E; Didham, Raphael K

    2013-01-01

    The potential movement of transgenes from genetically modified crops to non-genetically modified crops via insect-mediated pollen dispersal has been highlighted as one of the areas of greatest concern in regards to genetically modified crops. Pollen movement depends sensitively on spatial and temporal variation in the movement of insect pollinators between crop fields. This study tested the degree of variation in the diversity and relative abundance of flower-visiting insects entering versus leaving pak choi, Brassica rapa var. chinensis L. (Brassicales: Brassicaceae), crops throughout different stages of the flowering cycle. The relative abundance of flower-visiting insects varied significantly with Brassica crop phenology. Greater numbers of flower-visiting insects were captured inside rather than outside the crop fields, with the highest capture rates of flower-visitors coinciding with the peak of flowering in both spring-flowering and summer-flowering crops. Moreover, the ratio of flower-visiting insects entering versus leaving crop fields also varied considerably with changing crop phenology. Despite high variation in relative capture rates, the data strongly indicate non-random patterns of variation in insect movement in relation to crop phenology, with early-season aggregation of flower-visiting insects entering and remaining in the crop, and then mass emigration of flower-visiting insects leaving the crop late in the flowering season. Although pollen movement late in the flowering cycle might contribute relatively little to total seed set (and hence crop production), the findings here suggest that extensive late-season pollinator redistribution in the landscape could contribute disproportionately to long-distance gene movement between crops. PMID:23937538

  12. Inter-annual variations in the abundance of young-of-the-year of migratory fishes in the Upper Paraná River floodplain: relations with hydrographic attributes.

    PubMed

    Suzuki, H I; Agostinho, A A; Bailly, D; Gimenes, M F; Júlio, H F; Gomes, L C

    2009-06-01

    In this study, we identified and characterized the hydrographic attributes related to the success of recruitment of migratory fishes in the Upper Paraná River floodplain. To achieve our objectives, we analyzed inter-annual variations in the abundance of young-of-the-year (YOY; index of recruitment) of six migratory species and their relations with hydrographic attributes. Recruitment was related to the intensity, duration (in different fluviometrical levels), elasticity, number of pulses, greater uninterrupted overflow and delay of the floods (all obtained using the PULSO software). Collections of fish were conducted in the period between January 1987 and November 2007 in distinct environments (river channels, secondary channels and connected and disconnected floodplain lakes) distributed along three subsystems (Paraná, Baía and Ivinheima). Relations between recruitment and the attributes of interest were determined through analysis of covariance. In the studied period, the highest abundances of YOY were registered in 2007, followed by 1992, 1993, 2005 and 1988. The abundance of YOY was positively correlated with an intensity of high water levels (potamophase) and the duration of potamophase 1 and negatively with the duration of low water levels (limnophase) and a delay of flood. Higher hydrometric levels (540 and 610 cm for Paraná and 325 and 450 cm for Ivinheima) and greatest uninterrupted overflow presented different relations (significant interactions) among subsystems, but all with positive effects on recruitment. Results evidenced that recruitment responded better when floods started in January with potamophase intensities above 610 cm and water levels above 450 cm over a period of 50 days and repeated every two years (or > 610 cm for 38 days and repeated every two or three years). Therefore, artificial control of the floods at intervals of two or three years by manipulating the discharge of dams located upstream from the floodplain in a way that promotes

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

    NASA Technical Reports Server (NTRS)

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

    1982-01-01

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

  14. 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

  15. [Molecular Mechanism and Malignant Clonal Evolution of Multiple Myeloma].

    PubMed

    Ding, Fei; Zhu, Ping; Wu, Xue-Qiang

    2015-10-01

    Almost all patients with multiple myeloma (MM) have chromosomal translocation which can result in genetic variation. There are mainly five types of chromosomal translocations, involving the IGH gene translocation to 11q13 (CCND1), 4p16 (FGFR/MMSET), 16q23 (MAF), 6p21 (CCND3) and 20q11 (MAFB). It is possible that all IGH translocations converge on a common cell cycle signal pathway. Some MM develops through a multistep transformation from monoclonal gammopathy of undetermined significance (MGUS) to smoldering MM (SMM) and eventually to MM and plasma cell leukemia (PCL). Similarly to what Darwin proposed in the mid-19th century-random genetic variation and natural selection in the context of limited resources, MM clonal evolution follow branching and nonlinear mode. The failure of MM treatment is usually related with the minimal subclone which is hardly found at newlydiagnosed. PMID:26524068

  16. Environmental gradients structure Daphnia pulex × pulicaria clonal distribution.

    PubMed

    Pantel, J H; Juenger, T E; Leibold, M A

    2011-04-01

    The rarity of eukaryotic asexual reproduction is frequently attributed to the disadvantage of reduced genetic variation relative to sexual reproduction. However, parthenogenetic lineages that evolved repeatedly from sexual ancestors can generate regional pools of phenotypically diverse clones. Various theories to explain the maintenance of this genetic diversity as a result of environmental and spatial heterogeneity [frozen niche variation (FNV), general-purpose genotype] are conceptually similar to community ecological explanations for the maintenance of regional species diversity. We employed multivariate statistics common in community ecological research to study population genetic structure in the freshwater crustacean, Daphnia pulex × pulicaria. This parthenogenetic hybrid arose repeatedly from sexual ancestors. Daphnia pulex × pulicaria populations harboured substantial genetic variation among populations and the clonal composition at each pond corresponded to nutrient levels and invertebrate predator densities. The interclonal selection process described by the FNV hypothesis likely structured our D. pulex × pulicaria populations. PMID:21288271

  17. 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.

  18. 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.

  19. Clonality Testing in Veterinary Medicine: A Review With Diagnostic Guidelines.

    PubMed

    Keller, S M; Vernau, W; Moore, P F

    2016-07-01

    The accurate distinction of reactive and neoplastic lymphoid proliferations can present challenges. Given the different prognoses and treatment strategies, a correct diagnosis is crucial. Molecular clonality assays assess rearranged lymphocyte antigen receptor gene diversity and can help differentiate reactive from neoplastic lymphoid proliferations. Molecular clonality assays are commonly used to assess atypical, mixed, or mature lymphoid proliferations; small tissue fragments that lack architecture; and fluid samples. In addition, clonality testing can be utilized to track neoplastic clones over time or across anatomic sites. Molecular clonality assays are not stand-alone tests but useful adjuncts that follow clinical, morphologic, and immunophenotypic assessment. Even though clonality testing provides valuable information in a variety of situations, the complexities and pitfalls of this method, as well as its dependency on the experience of the interpreter, are often understated. In addition, a lack of standardized terminology, laboratory practices, and interpretational guidelines hinders the reproducibility of clonality testing across laboratories in veterinary medicine. The objectives of this review are twofold. First, the review is intended to familiarize the diagnostic pathologist or interested clinician with the concepts, potential pitfalls, and limitations of clonality testing. Second, the review strives to provide a basis for future harmonization of clonality testing in veterinary medicine by providing diagnostic guidelines. PMID:26933096

  20. Infection Efficiency of Four Phytophthora infestans Clonal Lineages and DNA-Based Quantification of Sporangia

    PubMed Central

    Fall, Mamadou Lamine; Tremblay, David Mathieu; Gobeil-Richard, Mélanie; Couillard, Julie; Rocheleau, Hélène; Van der Heyden, Hervé; Lévesque, Camile André; Beaulieu, Carole; Carisse, Odile

    2015-01-01

    The presence and abundance of pathogen inoculum is with host resistance and environmental conditions a key factor in epidemic development. Therefore, several spore-sampling devices have been proposed to monitor pathogen inoculum above fields. However, to make spore sampling more reliable as a management tool and to facilitate its adoption, information on infection efficiency and molecular tools for estimating airborne sporangia concentration are needed. Experiments were thus undertaken in a growth chamber to study the infection efficiency of four clonal lineages of P. infestans (US-8, US-11, US-23, and US-24) by measuring the airborne sporangia concentration and resulting disease intensity. The relationship between the airborne sporangia concentration and the number of lesions per leaf was exponential. For the same concentration, the sporangia of US-23 caused significantly more lesions than the sporangia of the other clonal lineages did. Under optimal conditions, an airborne sporangia concentration of 10 sporangia m−3 for US-23 was sufficient to cause one lesion per leaf, whereas for the other clonal lineages, it took 15 to 25 sporangia m−3 to reach the same disease intensity. However, in terms of diseased leaf area, there was no difference between clonal lineages US-8, US-23 and US-24. Also, a sensitive quantitative real-time polymerase chain reaction (qPCR) tool was developed to quantify P. infestans airborne sporangia with detection sensitivity of one sporangium. The specificity of the qPCR assay was rigorously tested for airborne inoculum and was either similar to, or an improvement on, other published PCR assays. This assay allows rapid and reliable detection and quantification of P. infestans airborne sporangia and thereby, facilitates the implementation of spores-sampling network. PMID:26301826

  1. The relative accuracy of standard estimators for macrofaunal abundance and species richness derived from selected intertidal transect designs used to sample exposed sandy beaches

    NASA Astrophysics Data System (ADS)

    Schoeman, transect designs used to sample exposed sandy beaches D. S.; Wheeler, M.; Wait, M.

    2003-10-01

    In order to ensure that patterns detected in field samples reflect real ecological processes rather than methodological idiosyncrasies, it is important that researchers attempt to understand the consequences of the sampling and analytical designs that they select. This is especially true for sandy beach ecology, which has lagged somewhat behind ecological studies of other intertidal habitats. This paper investigates the performance of routine estimators of macrofaunal abundance and species richness, which are variables that have been widely used to infer predictable patterns of biodiversity across a gradient of beach types. To do this, a total of six shore-normal strip transects were sampled on three exposed, oceanic sandy beaches in the Eastern Cape, South Africa. These transects comprised contiguous quadrats arranged linearly between the spring high and low water marks. Using simple Monte Carlo simulation techniques, data collected from the strip transects were used to assess the accuracy of parameter estimates from different sampling strategies relative to their true values (macrofaunal abundance ranged 595-1369 individuals transect -1; species richness ranged 12-21 species transect -1). Results indicated that estimates from the various transect methods performed in a similar manner both within beaches and among beaches. Estimates for macrofaunal abundance tended to be negatively biased, especially at levels of sampling effort most commonly reported in the literature, and accuracy decreased with decreasing sampling effort. By the same token, estimates for species richness were always negatively biased and were also characterised by low precision. Furthermore, triplicate transects comprising a sampled area in the region of 4 m 2 (as has been previously recommended) are expected to miss more than 30% of the species that occur on the transect. Surprisingly, for both macrofaunal abundance and species richness, estimates based on data from transects sampling quadrats

  2. 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.

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

    PubMed

    Srinivasan, R; Jambulingam, P; Vanamail, P

    2013-07-01

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

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

    PubMed

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

    2016-06-01

    Chenab River is one of the most important rivers of Punjab Province (Pakistan) that receives huge input of industrial effluents and municipal sewage from major cities in the Central Punjab, Pakistan. The current study was designed to evaluate the concentration levels and associated ecological risks of USEPA priority polycyclic aromatic hydrocarbons (PAHs) in the surface sediments of Chenab River. Sampling was performed from eight (n = 24) sampling stations of Chenab River and its tributaries. We observed a relatively high abundance of ∑16PAHs during the summer season (i.e. 554 ng g(-1)) versus that in the winter season (i.e. 361 ng g(-1)), with an overall abundance of two-, five- and six-ring PAH congeners. Results also revealed that the nitrate and phosphate contents in the sediments were closely associated with low molecular weight (LMW) and high molecular weight (HMW) PAHs, respectively. Source apportionment results showed that the combustion of fossil fuels appears to be the key source of PAHs in the study area. The risk quotient (RQ) values indicated that seven PAH congeners (i.e. phenanthrene, anthracene, fluoranthene, pyrene, benzo(a)pyrene, chrysene and benzo(a)anthracene) could pose serious threats to the aquatic life of the riverine ecosystem in Pakistan. PMID:27234513

  5. 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.

  6. 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.

  7. 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.

  8. Influence of pregnancy in mid-to-late gestation on circulating metabolites, visceral organ mass, and abundance of proteins relating to energy metabolism in mature beef cows.

    PubMed

    Wood, K M; Awda, B J; Fitzsimmons, C; Miller, S P; McBride, B W; Swanson, K C

    2013-12-01

    In mid-to-late gestation, nutrient demand increases to meet the growth requirements of the conceptus and cows may alter metabolism in response to energy demands of pregnancy. By better understanding the metabolic role of pregnancy, there may be opportunities to better understand maintenance energy costs and improve overall feed efficiency. Eighteen mature Simmental/Angus crossbred cows, pregnant (PREG; n = 9) and nonpregnant (OPEN; n = 9), were used to investigate the effect of pregnancy on BW change, carcass traits, visceral organ mass, and circulating serum metabolites. Cows were blocked by day of expected parturition such that each block was slaughtered 4 to 5 wk before parturition. Cows were individually fed for ad libitum intake using Calan gates for 89 to 105 d. Cows were weighed, ultrasounded for rib (over the 12th and 13th rib) and rump fat, and a serum sample obtained at d 1, 56, and 3 to 5 d before slaughter. At slaughter, organs were removed, trimmed of fat, and weighed. Serum was analyzed for β-hydroxybutyrate (BHBA), NEFA, glucose, urea, total cholesterol, and triiodothyronine (T3). Tissue samples from liver, kidney, sternomandibularis muscle, ruminal papillae, pancreas, and small intestinal mucosa were collected at slaughter and snap frozen in liquid N. Western blots were conducted to quantify abundance of: proliferating cell nuclear antigen (PCNA), ATP synthase, ubiquitin, and Na(+)/K+ ATPase for all tissues; PPARγ, PPARγ coactivator 1α (PGC1-α), 5'-adenosine monophosphate-activated protein kinase (AMPK) and phosphorylated-AMPK (pAMPK) for liver, muscle, and rumen; phosphoenolpyruvate carboxykinase (PEPCK) for liver and kidney; and uncoupling protein 2 (UCP2) for liver. Data were analyzed using PROC MIXED in SAS as a replicated randomized complete block. Liver weights (actual, relative to BW, relative to HCW) were heavier (P ≤ 0.02) in OPEN. Rumen mass and kidney fat weight, both relative to BW, were also greater (P ≤ 0.04) in OPEN. On d 56

  9. The Metal Abundances across Cosmic Time (MACT) Survey. II. Evolution of the Mass–metallicity Relation over 8 Billion Years, Using [OIII]4363AA-based Metallicities

    NASA Astrophysics Data System (ADS)

    Ly, Chun; Malkan, Matthew A.; Rigby, Jane R.; Nagao, Tohru

    2016-09-01

    We present the first results from MMT and Keck spectroscopy for a large sample of 0.1≤slant z≤slant 1 emission-line galaxies selected from our narrowband imaging in the Subaru Deep Field. We measured the weak [O iii] λ4363 emission line for 164 galaxies (66 with at least 3σ detections, and 98 with significant upper limits). The strength of this line is set by the electron temperature for the ionized gas. Because the gas temperature is regulated by the metal content, the gas-phase oxygen abundance is inversely correlated with [O iii] λ4363 line strength. Our temperature-based metallicity study is the first to span ≈ 8 Gyr of cosmic time and ≈ 3 dex in stellar mass for low-mass galaxies, {log}({M}\\star /{M}ȯ )≈ 6.0–9.0. Using extensive multi-wavelength photometry, we measure the evolution of the stellar mass–gas metallicity relation and its dependence on dust-corrected star formation rate (SFR). The latter is obtained from high signal-to-noise Balmer emission-line measurements. Our mass–metallicity relation is consistent with Andrews & Martini at z≤slant 0.3, and evolves toward lower abundances at a given stellar mass, {log}{({{O/H}})\\propto (1+z)}-{2.32-0.26+0.52}. We find that galaxies with lower metallicities have higher SFRs at a given stellar mass and redshift, although the scatter is large (≈ 0.3 dex) and the trend is weaker than seen in local studies. We also compare our mass–metallicity relation against predictions from high-resolution galaxy formation simulations, and find good agreement with models that adopt energy- and momentum-driven stellar feedback. We identified 16 extremely metal-poor galaxies with abundances of less than a tenth of solar; our most metal-poor galaxy at z≈ 0.84 is similar to I Zw 18.

  10. Influence of 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.

  11. Antioxidant activities from different rosemary clonal lines.

    PubMed

    Ban, Lan; Narasimhamoorthy, Brindha; Zhao, Liuqing; Greaves, John A; Schroeder, William D

    2016-06-15

    Rosemary extract is widely used in food industry and carnosic acid is reported to be the major component that is responsible for its antioxidant activities. However, it is unclear how the numerous plant metabolites interact and contribute to the overall antioxidant activity. In this study, with poultry fat as the model food system, rosemary extract from six clonal lines were evaluated that each represented a different genetic variant. As expected, rosemary extract with higher carnosic acid content had higher antioxidant activity. However, rosemary extract which had carnosic acid removed retained a significant amount of activity. Furthermore, when the individual contributions of carnosic acid and the portion without carnosic acid were evaluated separately, neither was shown to be responsible for the overall level of its stabilization effect from rosemary extract as a whole entity. The interactions among different plant metabolites have a major impact on the overall antioxidant capabilities of rosemary extract. PMID:26868574

  12. Stress-induced changes in abundance differ among obligate and facultative endosymbionts of the soybean aphid.

    PubMed

    Enders, Laramy S; Miller, Nicholas J

    2016-02-01

    Bacterial endosymbionts can drive evolutionary novelty by conferring adaptive benefits under adverse environmental conditions. Among aphid species there is growing evidence that symbionts influence tolerance to various forms of stress. However, the extent to which stress inflicted on the aphid host has cascading effects on symbiont community dynamics remains poorly understood. Here we simultaneously quantified the effect of host-plant induced and xenobiotic stress on soybean aphid (Aphis glycines) fitness and relative abundance of its three bacterial symbionts. Exposure to soybean defensive stress (Rag1 gene) and a neurotoxic insecticide (thiamethoxam) substantially reduced aphid composite fitness (survival × reproduction) by 74 ± 10% and 92 ± 2%, respectively, which in turn induced distinctive changes in the endosymbiont microbiota. When challenged by host-plant defenses a 1.4-fold reduction in abundance of the obligate symbiont Buchnera was observed across four aphid clonal lines. Among facultative symbionts of Rag1-stressed aphids, Wolbachia abundance increased twofold and Arsenophonus decreased 1.5-fold. A similar pattern was observed under xenobiotic stress, with Buchnera and Arsenophonus titers decreasing (1.3-fold) and Wolbachia increasing (1.5-fold). Furthermore, variation in aphid virulence to Rag1 was positively correlated with changes in Arsenophonus titers, but not Wolbachia or Buchnera. A single Arsenophonus multi-locus genotype was found among aphid clonal lines, indicating strain diversity is not primarily responsible for correlated host-symbiont stress levels. Overall, our results demonstrate the nature of aphid symbioses can significantly affect the outcome of interactions under stress and suggests general changes in the microbiome can occur across multiple stress types. PMID:26865969

  13. 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

  14. Stink bug species composition and relative abundance of the redbanded stink bug (Hemiptera: Pentatomidae) in soybean in the upper gulf coast Texas.

    PubMed

    Vyavhare, Suhas S; Way, Michael O; Medina, Raul F

    2014-12-01

    Stink bugs are the primary arthropod soybean pests in the southern United States. Historically, important stink bug species damaging soybeans in the southern United States included the southern green stink bug Nezara viridula (L.), the green stink bug Chinavia hilaris (Say), and the brown stink bug Euschistus servus (Say) (Hemiptera: Pentatomidae). The redbanded stink bug, Piezodorus guildinii (Westwood), has recently become an economic pest of soybean in the southern region of the United States, especially in Louisiana and Texas. Little is known about current stink bug species composition and relative abundance in Texan soybean agro-ecosystems. To fill this gap, commercial soybean fields in the Upper Gulf Coast of Texas were sampled weekly during the growing season using a sweep net throughout R2 (full flowering) to R7 (beginning maturity) from 2011 to 2013. Adults and nymphs (third, fourth, and fifth instars) of redbanded stink bug, southern green stink bug, green stink bug, and brown stink bug were counted per 25 sweeps. The relative abundance of redbanded stink bug was significantly higher than any other stink bug species throughout 2011-2013. Over 65% of the total population of major stink bugs collected during this period were redbanded stink bugs and ≍19% were southern green stink bugs. The highest redbanded stink bug densities and the highest ratio of redbanded stink bug nymphs to adults were recorded at R7. Results from this study show that redbanded stink bug has become the predominant stink bug species in soybean in the Upper Gulf Coast of Texas. PMID:25290375

  15. 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

  16. Stellar Oxygen Abundances

    NASA Astrophysics Data System (ADS)

    King, Jeremy

    1994-04-01

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

  17. Impact of high dietary lipid intake and related metabolic disorders on the abundance and acyl composition of the unique mitochondrial phospholipid, cardiolipin.

    PubMed

    Feillet-Coudray, Christine; Fouret, Gilles; Casas, François; Coudray, Charles

    2014-10-01

    Excessive dietary lipid intake, coupled with lack of exercise, are the major causes of the development and progression of metabolic syndrome features e. g. obesity, hepatic steatosis, insulin resistance, type 2 diabetes and cardiovascular diseases. These metabolic diseases are associated with both structural and functional alterations of mitochondria. Cardiolipin (CL) is a unique phospholipid that is almost exclusively localized in the mitochondrial inner membrane. Cardiolipin is at the heart of mitochondrial metabolism playing a key role in several processes of mitochondrial bioenergetics as well as in mitochondrial membrane stability and dynamics, and in many of the mitochondrial-dependent steps of apoptosis. Indeed, alterations to CL content and acyl chain profile have been associated with mitochondrial dysfunction in multiple tissues in Barth syndrome and in many other physio-pathological conditions. After a brief overview of the biological roles of CL, we highlight the consequences of lipid overload-related nutritional manipulations as well as related metabolic disorders on both CL content and its fatty acid composition in the major metabolic tissues, the heart, muscle and liver. The goal of this review is to fill a void in the CL literature concerning the effects of CL abundance and form that arise following high lipid supplementation and the related metabolic disorders. PMID:24951897

  18. [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. PMID:25720178

  19. Diet of juvenile lake trout in southern Lake Ontario in relation to abundance and size of prey fishes, 1979-1987

    USGS Publications Warehouse

    Elrod, Joseph H.; O'Gorman, Robert

    1991-01-01

    We examined the diet of juvenile lake trout Salvelinus namaycush (<450 mm, total length) in Lake Ontario during four sampling periods (April–May, June, July–August, and October 1979–1987) in relation to changes in prey fish abundance in the depth zone where we caught the lake trout. Over all years combined, slimy sculpins Cottus cognatus contributed the most (39–52%) by wet weight to the diet, followed by alewives Alosa pseudoharengus(3–38%), rainbow smelt Osmerus mordax (17–43%), and johnny darters Etheostoma nigrum(2–10%). Over 90% of alewives eaten during April–May and June were age 1, and 98% of those eaten during October were age 0 (few alewives were eaten in July–August). Mean lengths of rainbow smelt and slimy sculpins in stomachs increased with size of lake trout. Juvenile lake trout generally fed opportunistically—seasonal and annual changes in diet usually reflected seasonal and annual changes in abundance of prey fishes near bottom where we captured the lake trout. Furthermore, diet within a given season varied with depth of capture of lake trout, and changes with depth in proportions of prey species in lake trout stomachs mirrored changes in proportions of the prey species in trawl catches at the same depth. Alewives (ages 0 and 1) were the only prey fish eaten in substantial quantities by both juvenile lake trout and other salmonines, and thus are a potential focus of competition between these predators.

  20. 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.

  1. Effects of clonal integration on the invasive clonal plant Alternanthera philoxeroides under heterogeneous and homogeneous water availability

    PubMed Central

    You, Wen-Hua; Han, Cui-Min; Liu, Chun-Hua; Yu, Dan

    2016-01-01

    Many notorious invasive plants are clonal, living in heterogeneous or homogeneous habitats. To understand how clonal integration affects the performance of these plants in different habitat conditions, an 8-week greenhouse experiment was conducted: ramet pairs of A. philoxeroides were grown in two habitats, either heterogeneous or homogeneous in water availability, with the stolon connections either severed or kept intact. Under heterogeneous water availability, compared with ramets in homogeneous habitats, clonal integration significantly promoted the growth and photosynthetic performance of water-stressed apical ramets, whereas it only increased the photosynthetic performance but did not affect the growth of water-stressed basal ramets. Moreover, clonal integration markedly increased the root/shoot ratios of ramets grown in habitats with high water supply but decreased it under low water availability. Under homogeneous water availability, stolon connection (clonal integration) did not influence the growth, photosynthetic performance and biomass allocation of water-stressed ramets, but it significantly promoted the growth of well-watered ramets in both apical and basal sections. These findings deepen our understanding of the bidirectional and differentiated (mainly acropetal) clonal integration of A. philoxeroides, suggesting that the invasive plant A. philoxeroides can benefit from clonal integration in both heterogeneous and homogeneous habitats. PMID:27416868

  2. Effects of clonal integration on the invasive clonal plant Alternanthera philoxeroides under heterogeneous and homogeneous water availability.

    PubMed

    You, Wen-Hua; Han, Cui-Min; Liu, Chun-Hua; Yu, Dan

    2016-01-01

    Many notorious invasive plants are clonal, living in heterogeneous or homogeneous habitats. To understand how clonal integration affects the performance of these plants in different habitat conditions, an 8-week greenhouse experiment was conducted: ramet pairs of A. philoxeroides were grown in two habitats, either heterogeneous or homogeneous in water availability, with the stolon connections either severed or kept intact. Under heterogeneous water availability, compared with ramets in homogeneous habitats, clonal integration significantly promoted the growth and photosynthetic performance of water-stressed apical ramets, whereas it only increased the photosynthetic performance but did not affect the growth of water-stressed basal ramets. Moreover, clonal integration markedly increased the root/shoot ratios of ramets grown in habitats with high water supply but decreased it under low water availability. Under homogeneous water availability, stolon connection (clonal integration) did not influence the growth, photosynthetic performance and biomass allocation of water-stressed ramets, but it significantly promoted the growth of well-watered ramets in both apical and basal sections. These findings deepen our understanding of the bidirectional and differentiated (mainly acropetal) clonal integration of A. philoxeroides, suggesting that the invasive plant A. philoxeroides can benefit from clonal integration in both heterogeneous and homogeneous habitats. PMID:27416868

  3. Trawls and cooling-water intakes as estuarine fish sampling tools: Comparisons of catch composition, trends in relative abundance, and length selectivity

    NASA Astrophysics Data System (ADS)

    Greenwood, M. F. D.

    2008-01-01

    Fish populations in estuaries are often monitored with traditional sampling gears such as trawls. Trawling is relatively expensive and may be hindered by environmental conditions such as tides and substrates. Power station cooling-water intake screens have been effectively used as estuarine fish sampling devices for many years, but very few quantitative comparisons of intake fish-catch characteristics with samples from other collection methods have been made. Fish collected at the cooling-water intake of a large power station in the lower Forth estuary, UK, were more similar in assemblage composition to fish caught by nearby pelagic trawling than to fish caught by Agassiz (demersal) trawling, mostly because the intake and pelagic-trawl catches were largely composed of clupeids ( Sprattus sprattus and Clupea harengus). The intake catch was typified by pelagic, demersal, and benthic species, however, and was less variable than the catches made by the two trawls. Monthly trends in relative abundance correlated reasonably well between the intake and trawl samples. Fish collected at the intake tended to be significantly smaller than those collected by trawling, which was probably attributable to the intake's smaller mesh size. The study highlighted the utility of a cooling-water intake as an efficient, low-cost fish sampling device, which should be considered as an alternative to trawling as the cost of the latter increases into the future.

  4. ABUNDANCE OF SEAGRASS (ZOSTERA MARINA L.) AND MACROALGAE IN RELATION TO THE SALINITY-TEMPERATURE GRADIENT IN YAQUINA BAY, OREGON, USA

    EPA Science Inventory

    The distribution and abundance of the seagrass, Zostera marina, and the associated macroalgae are described for Yaquina Bay, Oregon, U.S.A. Possible relationships between plant abundance and physical-chemical characteristics of the water column were also explored. Study sites w...

  5. Molecular Mimicry and Clonal Deletion: A Fresh Look

    PubMed Central

    Rose, Noel R.

    2014-01-01

    In this article, I trace the historic background of clonal deletion and molecular mimicry, two major pillars underlying our present understanding of autoimmunity and autoimmune disease. Clonal deletion originated as a critical element of the clonal selection theory of antibody formation in order to explain tolerance of self. If we did have complete clonal deletion, there would be major voids, the infamous “black holes”, in our immune repertoire. For comprehensive, protective adaptive immunity, full deletion is necessarily a rare event. Molecular mimicry, the sharing of epitopes among self and non-self antigens, is extraordinary common and provides the evidence that complete deletion of self-reactive clones is rare. If molecular mimicry were not common, protective adaptive immunity could not be all-encompassing. By taking a fresh look at these two processes together we can envision their evolutionary basis and understand the need for regulatory devices to prevent molecular mimicry from progressing to autoimmune disease. PMID:25172771

  6. GENETIC VARIATION IN CLONAL VERTEBRATES DETECTED BY SIMPLE SEQUENCE FINGERPRINTING

    EPA Science Inventory

    Measurement of clonal heterogeneity is central to understanding evolutionary and population genetics of roughly 50 species of vertebrates lack effective genetic recombination. imple-sequence DNA fingerprinting with oligonucleotide probes (CAG)5 and (GACA)4 was used to detect hete...

  7. Molecular mimicry and clonal deletion: A fresh look.

    PubMed

    Rose, Noel R

    2015-06-21

    In this article, I trace the historic background of clonal deletion and molecular mimicry, two major pillars underlying our present understanding of autoimmunity and autoimmune disease. Clonal deletion originated as a critical element of the clonal selection theory of antibody formation in order to explain tolerance of self. If we did have complete clonal deletion, there would be major voids, the infamous "black holes", in our immune repertoire. For comprehensive, protective adaptive immunity, full deletion is necessarily a rare event. Molecular mimicry, the sharing of epitopes among self and non-self antigens, is extraordinary common and provides the evidence that complete deletion of self-reactive clones is rare. If molecular mimicry were not common, protective adaptive immunity could not be all-encompassing. By taking a fresh look at these two processes together we can envision their evolutionary basis and understand the need for regulatory devices to prevent molecular mimicry from progressing to autoimmune disease. PMID:25172771

  8. Clonal Expansion (CE) Models in Cancer Risk Assessment

    EPA Science Inventory

    Cancer arises when cells accumulate sufficient critical mutations. Carcinogens increase the probability of mutation during cell division or promote clonal expansion within stages. Multistage CE models recapitulate this process and provide a framework for incorporating relevant da...

  9. Clonal integration in Ludwigia hexapetala under different light regimes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Physiological integration among ramets of invasive plant species may support their colonization and spread in novel aquatic environments where growth-limiting resources are spatially heterogeneous. Under contrasting light conditions, we investigated how clonal integration influences growth, biomass...

  10. Species richness and relative species abundance of Nymphalidae (Lepidoptera) in three forests with different perturbations in the North-Central Caribbean of Costa Rica.

    PubMed

    Stephen, Carolyn; Sánchez, Ragde

    2014-09-01

    Measurements of species richness and species abundance can have important implications for regulations and conservation. This study investigated species richness and abundance of butterflies in the family Nymphalidae at undisturbed, and disturbed habitats in Tirimbina Biological Reserve and Nogal Private Reserve, Sarapiquí, Costa Rica. Traps baited with rotten banana were placed in the canopy and the understory of three habitats: within mature forest, at a river/forest border, and at a banana plantation/forest border. In total, 71 species and 487 individuals were caught and identified during May and June 2011 and May 2013. Species richness and species abundance were found to increase significantly at perturbed habitats (p < 0.0001, p < 0.0001, respectively). The edge effect, in which species richness and abundance increase due to greater complementary resources from different habitats, could be one possible explanation for increased species richness and abundance. PMID:25412524

  11. Abundance patterns in early-type galaxies: is there a "knee" in the [Fe/H] vs. [α/Fe] relation?

    NASA Astrophysics Data System (ADS)

    Walcher, C. J.; Coelho, P. R. T.; Gallazzi, A.; Bruzual, G.; Charlot, S.; Chiappini, C.

    2015-10-01

    Early-type galaxies (ETGs) are known to be enhanced in α elements, in accordance with their old ages and short formation timescales. In this contribution we aim to resolve the enrichment histories of ETGs. This means we study the abundance of Fe ([Fe/H]) and the α-element groups ([α/Fe]) separately for stars older than 9.5 Gyr ([Fe/H]o, [α/Fe]o) and for stars between 1.5 and 9.5 Gyr ([Fe/H]i, [α/Fe]i). Through extensive simulation we show that we can indeed recover the enrichment history per galaxy. We then analyze a spectroscopic sample of 2286 early-type galaxies from the SDSS selected to be ETGs. We separate out those galaxies for which the abundance of iron in stars grows throughout the lifetime of the galaxy, i.e. in which [Fe/H]o< [Fe/H]i. We call those consistent with self-enrichment, while the others must have experienced some mergers or significant gas accretion. We confirm earlier work where the [Fe/H] and [α/Fe] parameters are correlated with the mass and velocity dispersion of ETGs. We emphasize that the strongest relation is between [α/Fe] and age. This relation falls into two regimes, one with a steep slope for old galaxies and one with a shallow slope for younger ETGs. The vast majority of ETGs in our sample do not show the "knee" in the plot of [Fe/H] vs. [α/Fe] commonly observed in local group galaxies. This implies that for the vast majority of ETGs, the stars younger than 9.5 Gyr are likely to have been accreted or formed from accreted gas. The properties of the intermediate-age stars in accretion-dominated ETGs indicate that mass growth through late (minor) mergers in ETGs is dominated by galaxies with low [Fe/H] and low [α/Fe]. The method of reconstructing the stellar enrichment histories of ETGs introduced in this paper promises to constrain the star formation and mass assembly histories of large samples of galaxies in a unique way.

  12. Lineage and clonal development of gastric glands.

    PubMed

    Nomura, S; Esumi, H; Job, C; Tan, S S

    1998-12-01

    Individual gastric glands of the stomach are composed of cells of different phenotypes. These are derived from multipotent progenitor stem cells located at the isthmus region of the gland. Previous cell lineage analyses suggest that gastric glands, as in the colon and small intestine, are invariably monoclonal by adult stages. However, little is known about the ontogenetic progression of glandular clonality in the stomach. To examine this issue, we employed an in situ cell lineage marker in female mice heterozygous for an X-linked transgene. We found that stomach glands commence development as polyclonal units, but by adulthood (6 weeks), the majority progressed to monoclonal units. Our analysis suggests that at least three progenitor cells are required to initiate the development of individual gastric glands if they are analyzed just after birth. Hence, unlike the colon and small intestine, stomachs showed a significant fraction (10-25%) of polyclonal glands at adult stages. We suggest that these glands persist from polyclonal glands present in the embryonic stomach and hypothesize that they represent a subpopulation of glands with larger numbers of self-renewing stem cells. PMID:9851847

  13. The Pathogen of the Great Barrier Reef Sponge Rhopaloeides odorabile Is a New Strain of Pseudoalteromonas agarivorans Containing Abundant and Diverse Virulence-Related Genes.

    PubMed

    Choudhury, Jayanta D; Pramanik, Arnab; Webster, Nicole S; Llewellyn, Lyndon E; Gachhui, Ratan; Mukherjee, Joydeep

    2015-08-01

    Sponge diseases have increased dramatically, yet the causative agents of disease outbreaks have eluded identification. We undertook a polyphasic taxonomic analysis of the only confirmed sponge pathogen and identified it as a novel strain of Pseudoalteromonas agarivorans. 16S ribosomal RNA (rRNA) and gyraseB (gyrB) gene sequences along with phenotypic characteristics demonstrated that strain NW4327 was most closely related to P. agarivorans. DNA-DNA hybridization and in silico genome comparisons established NW4327 as a novel strain of P. agarivorans. Genes associated with type IV pili, mannose-sensitive hemagglutinin pili, and curli formation were identified in NW4327. One gene cluster encoding ATP-binding cassette (ABC) transporter, HlyD and TolC, and two clusters related to the general secretion pathway indicated the presence of type I secretion system (T1SS) and type II secretion system (T2SS), respectively. A contiguous gene cluster of at least 19 genes related to type VI secretion system (T6SS) which included all 13 core genes was found. The absence of T1SS and T6SS in nonpathogenic P. agarivorans S816 established NW4327 as the virulent strain. Serine proteases and metalloproteases of the classes S8, S9, M4, M6, M48, and U32 were identified in NW4327, many of which can degrade collagen. Collagenase activity in NW4327 and its absence in the nonpathogenic P. agarivorans KMM 255(T) reinforced the invasiveness of NW4327. This is the first report unambiguously identifying a sponge pathogen and providing the first insights into the virulence genes present in any pathogenic Pseudoalteromonas genome. The investigation supports a theoretical study predicting high abundance of terrestrial virulence gene homologues in marine bacteria. PMID:25837832

  14. 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. PMID:11426717

  15. 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.

  16. Relative abundances of sub-iron to iron nuclei in low energy (50-250 MeV/N) cosmic rays as observed in the SKYLAB experiment

    NASA Astrophysics Data System (ADS)

    Durgaprasad, N.; Yadav, J. S.; Biswas, S.

    1985-08-01

    A Lexan polycarbonate detector exposed on the exterior of Skylab-3 for 73 days during a solar quiet period was used to study the relative abundances of calcium to nickel ions in low energy cosmic rays of 50 to 250 MeV/N. The method of charge identification is based on the measurement of conelength (L) and residual range (R) of these particles in various Lexan sheets. Since more than one cone (sometimes as many as five) is observed and is measured, the charge accuracy becomes precise and accurate. The ratio of (calcium to manganese) to (iron and cobalt) obtained at three energy intervals of 50 to 80, 80 to 150, 150 to 250 and 50 to 250 MeV/N are 7.6 plus or minus 3.8, 2.7 plus or minus 0.8, 1.4 plus or minus 0.6 and 3.3 plus or minus 0.7 respectively. These data thus indicate a large increase of this ratio with decreasing energy. The origin of this strong energy dependence is not understood at present.

  17. Relative abundances of sub-iron to iron nuclei in low energy (50-250 MeV/N) cosmic rays as observed in the Skylab experiment

    NASA Technical Reports Server (NTRS)

    Biswas, S.; Durgaprasad, N.; Yadav, J. S.

    1985-01-01

    A Lexan polycarbonate detector exposed on the exterior of Skylab-3 for 73 days during a solar quiet period was used to study the relative abundances of calcium to nickel ions in low energy cosmic rays of 50 to 250 MeV/N. The method of charge identification is based on the measurement of conelength (L) and residual range (R) of these particles in various Lexan sheets. Since more than one cone (sometimes as many as five) is observed and is measured, the charge accuracy becomes precise and accurate. The ratio of (calcium to manganese) to (iron and cobalt) obtained at three energy intervals of 50 to 80, 80 to 150, 150 to 250 and 50 to 250 MeV/N are 7.6 plus or minus 3.8, 2.7 plus or minus 0.8, 1.4 plus or minus 0.6 and 3.3 plus or minus 0.7 respectively. These data thus indicate a large increase of this ratio with decreasing energy. The origin of this strong energy dependence is not understood at present.

  18. Spatio-temporal variation in small mammal species richness, relative abundance and body mass reveal changes in a coastal wetland ecosystem in Ghana.

    PubMed

    Ofori, Benjamin Y; Attuquayefio, Daniel K; Owusu, Erasmus H; Musah, Yahaya; Ntiamoa-Baidu, Yaa

    2016-06-01

    Coastal wetlands in Ghana are under severe threat of anthropogenic drivers of habitat degradation and climate change, thereby increasing the need for assessment and monitoring to inform targeted and effective conservation of these ecosystems. Here, we assess small mammal species richness, relative abundance and body mass in three habitats at the Muni-Pomadze Ramsar site of Ghana, and compare these to baseline data gathered in 1997 to evaluate changes in the wetland ecosystem. Small mammals were live-trapped using Sherman collapsible and pitfall traps. We recorded 84 individuals of 10 species in 1485 trap-nights, whereas the baseline study recorded 45 individuals of seven species in 986 trap-nights. The overall trap-success was therefore greater in the present study (5.66 %) than the baseline study (4.56 %). The species richness increased from one to four in the forest, and from zero to eight in the thicket, but decreased from six to four in the grassland. The total number of individuals increased in all habitats, with the dominant species in the grassland shifting from Lemniscomys striatus to Mastomys erythroleucus. Three species, Malacomys edwardsi, Grammomys poensis and Praomys tullbergi are the first records for the Muni-Pomadze Ramsar site. Generally, the average body mass of individual species in the grassland was lower in the present study. The considerable changes in small mammal community structure suggest changes in the wetland ecosystem. The conservation implications of our findings are discussed. PMID:27154051

  19. Evaluation of relative isotopic abundance measurements in a quadrupole time-of-flight mass spectrometer for elemental composition determination of natural products in traditional Chinese medicine.

    PubMed

    Wu, Zhi-Jun; Huo, Jia-Li; Chen, Jian-Zhong; Li, Na; Fang, Dong-Mei; Chen, Xiao-Zhen; Zhang, Guo-Lin; Wang, Jian-Hua; Xu, Xiao-Ying

    2013-01-01

    The relative isotopic abundance (RIA) measurement errors of a quadrupole time-of-flight (Q-ToF) instrument incorporating analog-to-digital converter detectors were systemically evaluated by stochastically collecting about 200 data in positive ion mass spectrometry (MS) mode. Errors varied with peak intensities at definite spectral acquisition rates but were very close, even if peak intensities changed sharply at different spectral acquisition rates with the same concentration. Intensity thresholds were systematically defined at 1 Hz of spectral acquisition rates. RIA measurement errors were also evaluated using peak area. It seemed that peak area was better adapted for the high-intensity ions while peak intensity was suited for very low-intensity ions. Several known compounds were selected for RIA measurements for product ions in tandem mass spectropmetry (MS/MS) mode. An extract of a representative traditional Chinese medicinal, Paederia scandens was analyzed with high-performance liquid chromatography-electrospray ionization-QToF-MS/MS. The unique elemental compositions of some compounds could not be identified even with exact masses and MS/MS spectra of measured and reference compounds. RIA errors, especially of (M+2)M(-1), provided vital information for determining the elemental composition. PMID:24261081

  20. Emerging sporotrichosis is driven by clonal and recombinant Sporothrix species.

    PubMed

    Rodrigues, Anderson Messias; de Hoog, GSybren; Zhang, Yu; de Camargo, Zoilo Pires

    2014-05-01

    Sporotrichosis, caused by agents of the fungal genus Sporothrix, occurs worldwide, but the infectious species are not evenly distributed. Sporothrix propagules usually gain entry into the warm-blooded host through minor trauma to the skin from contaminated plant debris or through scratches or bites from felines carrying the disease, generally in the form of outbreaks. Over the last decade, sporotrichosis has changed from a relatively obscure endemic infection to an epidemic zoonotic health problem. We evaluated the impact of the feline host on the epidemiology, spatial distribution, prevalence and genetic diversity of human sporotrichosis. Nuclear and mitochondrial markers revealed large structural genetic differences between S. brasiliensis and S. schenckii populations, suggesting that the interplay of host, pathogen and environment has a structuring effect on the diversity, frequency and distribution of Sporothrix species. Phylogenetic data support a recent habitat shift within S. brasiliensis from plant to cat that seems to have occurred in southeastern Brazil and is responsible for its emergence. A clonal structure was found in the early expansionary phase of the cat-human epidemic. However, the prevalent recombination structure in the plant-associated pathogen S. schenckii generates a diversity of genotypes that did not show any significant increase in frequency as etiological agents of human infection over time. These results suggest that closely related pathogens can follow different strategies in epidemics. Thus, species-specific types of transmission may require distinct public health strategies for disease control. PMID:26038739

  1. Emerging sporotrichosis is driven by clonal and recombinant Sporothrix species

    PubMed Central

    Rodrigues, Anderson Messias; de Hoog, GSybren; Zhang, Yu; de Camargo, Zoilo Pires

    2014-01-01

    Sporotrichosis, caused by agents of the fungal genus Sporothrix, occurs worldwide, but the infectious species are not evenly distributed. Sporothrix propagules usually gain entry into the warm-blooded host through minor trauma to the skin from contaminated plant debris or through scratches or bites from felines carrying the disease, generally in the form of outbreaks. Over the last decade, sporotrichosis has changed from a relatively obscure endemic infection to an epidemic zoonotic health problem. We evaluated the impact of the feline host on the epidemiology, spatial distribution, prevalence and genetic diversity of human sporotrichosis. Nuclear and mitochondrial markers revealed large structural genetic differences between S. brasiliensis and S. schenckii populations, suggesting that the interplay of host, pathogen and environment has a structuring effect on the diversity, frequency and distribution of Sporothrix species. Phylogenetic data support a recent habitat shift within S. brasiliensis from plant to cat that seems to have occurred in southeastern Brazil and is responsible for its emergence. A clonal structure was found in the early expansionary phase of the cat–human epidemic. However, the prevalent recombination structure in the plant-associated pathogen S. schenckii generates a diversity of genotypes that did not show any significant increase in frequency as etiological agents of human infection over time. These results suggest that closely related pathogens can follow different strategies in epidemics. Thus, species-specific types of transmission may require distinct public health strategies for disease control. PMID:26038739

  2. Solar abundance of iridium

    PubMed Central

    Drake, Stephen; Aller, Lawrence H.

    1976-01-01

    By a method of spectrum synthesis, which yields log gfA, where g is the statistical weight of the lower level, f is the oscillator strength, and A is the abundance, an attempt is made to deduce the solar iridium abundance from one relatively unblended, but fairly weak IrI line, λ 3220.78 Å. If the Corliss-Bozman f-value for this line is adopted, we find log A(Ir) = 0.82 on the scale log A(H) = 12.00. The discordance with the value found from carbonaceous chondrites may arise from faulty f-values or from difficulties arising from line blending in this far ultraviolet domain of the solar spectrum. PMID:16578735

  3. Global Molecular Epidemiology of the O15:K52:H1 Extraintestinal Pathogenic Escherichia coli Clonal Group: Evidence of Distribution beyond Europe

    PubMed Central

    Johnson, James R.; Stell, Adam L.; O'Bryan, Timothy T.; Kuskowski, Michael; Nowicki, Bogdan; Johnson, Candice; Maslow, Joel N.; Kaul, Anil; Kavle, Justine; Prats, Guillem

    2002-01-01

    Escherichia coli O15:K52:H1 is a significant extraintestinal pathogen in Europe (G. Prats et al., J. Clin. Microbiol. 38:201-209, 2000). To search for evidence of this clonal group outside of Europe, 75 non-European E. coli isolates of serogroup O15 were compared with five members of the O15:K52:H1 clonal group from Barcelona, Spain, according to genomic background, virulence genotypes, and antimicrobial resistance profiles. Amplification phylotyping showed that 16 (21%) of the 75 non-European O15 isolates corresponded with the O15:K52:H1 clonal group. The 16 non-European O15:K52:H1 clonal group members represented diverse geographic locales. They were isolated almost exclusively from humans with extraintestinal infections and accounted for 50% of all O15 isolates from five human clinical collections studied. Most non-European clonal group members exhibited a consensus virulence factor profile that included the F16 or F7-2 papA alleles (P fimbrial structural subunit), papG allele II (P fimbrial adhesin), iha (putative adhesin siderophore), and iutA (aerobactin receptor). This resembles the virulence profiles of (i) European representatives of the O15:K52:H1 clonal group and (ii) phylogenetically relatedclonal group A,” a recently recognized significant contributor to trimethoprim-sulfamethoxazole resistance in the United States (A. R. Manges et al., N. Engl. J. Med. 345:1007-1013, 2001). Antimicrobial resistance profiles were variable, and resistance was inconsistently transferred by conjugation. These findings indicate that the O15:K52:H1 clonal group is broadly distributed beyond Europe, exhibits previously unrecognized phenotypic and genotypic diversity, and contributes significantly to extraintestinal infections in humans. PMID:12037043

  4. B cell clonality in gastric lymphoid tissues of patients with Sjögren's syndrome.

    PubMed Central

    Ferraccioli, G F; Sorrentino, D; De Vita, S; Casatta, L; Labombarda, A; Avellini, C; Dolcetti, R; Di Luca, D; Beltrami, C A; Boiocchi, M; Bartoli, E

    1996-01-01

    OBJECTIVE: To determine the prevalence of mucosa associated lymphoid tissue (MALT) in the stomach and of a possible antigen driven proliferation, in patients with Sjögren's syndrome (SS). METHODS: Twenty one patients with primary SS and 80 dyspeptic controls underwent upper endoscopy. Lymphoid tissue and Helicobacter pylori were assessed by histopathological analysis. Epstein-Barr virus (EBV) or human herpes virus-6 (HHV-6) genome were studied by polymerase chain reaction (PCR) DNA amplification. Two PCR VDJ procedures were used to detect immunoglobulin heavy chain (IgH) gene rearrangement. RESULTS: Organised MALT was found in 33.3% of the patients, compared with 21.5% of the controls (NS). H pylori infection was seen in 71% of patients and 63% of controls. Genomic EBV or HHV-6 was found in a minor portion of SS gastric tissues. B cell expansion was detected in nine of the 21 patients. Infectious agents in the stomach might have contributed to B cell clonality only in 55.5% of the cases. No strict relationship was found between lymphoid follicles and clonality. CONCLUSION: Lymphoid accumulation in the gastric mucosa is common in Sjögren's syndrome, but full evidence for an antigen driven B cell expansion could not be demonstrated. Only a portion of those with clonal B cell expansion had evidence of an infectious agent. Other unknown infectious agents or factors related to the underlying disease (autoantigen) and its tissue environment may have a further role as possible causes of B clonal expansion in the gastric mucosa. Images PMID:8660105

  5. Disturbance and clonal reproduction determine liana distribution and maintain liana diversity in a tropical forest.

    PubMed

    Ledo, Alicia; Schnitzer, Stefan A

    2014-08-01

    Negative density dependence (NDD) and habitat specialization have received strong empirical support as mechanisms that explain tree species diversity maintenance and distribution in tropical forests. In contrast, disturbance appears to play only a minor role. Previous studies have rarely examined the relative strengths of these diversity maintenance mechanisms concurrently, and few studies have included plant groups other than trees. Here we used a large, spatially explicit data set from Barro Colorado Island, Panama (BCI) to test whether liana and tree species distribution patterns are most consistent with NDD, habitat specialization, or disturbance. We found compelling evidence that trees responded to habitat specialization and NDD; however, only disturbance explained the distribution of the majority of liana species and maintained liana diversity. Lianas appear to respond to disturbance with high vegetative (clonal) reproduction, and liana species' ability to produce clonal stems following disturbance results in a clumped spatial distribution. Thus, clonal reproduction following disturbance explains local liana spatial distribution and diversity maintenance on BCI, whereas negative density dependence and habitat specialization, two prominent mechanisms contributing to tree species diversity and distribution, do not. PMID:25230468

  6. Noise-Driven Phenotypic Heterogeneity with Finite Correlation Time in Clonal Populations

    PubMed Central

    Lee, UnJin; Skinner, John J.; Reinitz, John; Rosner, Marsha Rich; Kim, Eun-Jin

    2015-01-01

    There has been increasing awareness in the wider biological community of the role of clonal phenotypic heterogeneity in playing key roles in phenomena such as cellular bet-hedging and decision making, as in the case of the phage-λ lysis/lysogeny and B. Subtilis competence/vegetative pathways. Here, we report on the effect of stochasticity in growth rate, cellular memory/intermittency, and its relation to phenotypic heterogeneity. We first present a linear stochastic differential model with finite auto-correlation time, where a randomly fluctuating growth rate with a negative average is shown to result in exponential growth for sufficiently large fluctuations in growth rate. We then present a non-linear stochastic self-regulation model where the loss of coherent self-regulation and an increase in noise can induce a shift from bounded to unbounded growth. An important consequence of these models is that while the average change in phenotype may not differ for various parameter sets, the variance of the resulting distributions may considerably change. This demonstrates the necessity of understanding the influence of variance and heterogeneity within seemingly identical clonal populations, while providing a mechanism for varying functional consequences of such heterogeneity. Our results highlight the importance of a paradigm shift from a deterministic to a probabilistic view of clonality in understanding selection as an optimization problem on noise-driven processes, resulting in a wide range of biological implications, from robustness to environmental stress to the development of drug resistance. PMID:26203903

  7. Genotyping the clonal structure of a gorgonian coral, Junceella juncea (Anthozoa: Octocorallia), using microsatellite loci

    NASA Astrophysics Data System (ADS)

    Liu, Shang-Yin Vanson; Yu, Hon-Tsen; Fan, Tung-Yung; Dai, Chang-Feng

    2005-11-01

    The identification of different clones is fundamental to the study of population structure among organisms with mixed reproductive modes such as cnidarians. However, due to the low genetic variation of coral mtDNA and contamination by zooxanthellate DNA, very few molecular markers are available for studying the clonal structure of cnidarians. Herein we used four polymorphic loci of microsatellite DNA isolated from a zooxanthellae-free octocoral, Junceella juncea, to study its clonal structure in seven populations collected from three localities in Taiwan. In total, 40 multilocus genotypes were found among 152 colonies, and the number of genotypes (clones) identified in the seven populations ranged from 2 to 16. Each of the 40 multilocus genotypes was restricted to a single population, even where adjacent populations were only 100 m distant. The ratio of observed to expected genotypic diversity (Go:Ge) ranged from 0.217 to 0.650, and Go showed a significant departure from Ge ( p<0.05) at each site indicating that asexual fragmentation may play a major role in the maintenance of established populations. Mean relatedness ( R) values showed that genotypes within reefs were more closely related than those between regions. The results indicate that microsatellites are useful for discerning the clonal structures among and within populations at different spatial scales.

  8. Subpopulations of Staphylococcus aureus clonal complex 121 are associated with distinct clinical entities.

    PubMed

    Kurt, Kevin; Rasigade, Jean-Philippe; Laurent, Frederic; Goering, Richard V; Žemličková, Helena; Machova, Ivana; Struelens, Marc J; Zautner, Andreas E; Holtfreter, Silva; Bröker, Barbara; Ritchie, Stephen; Reaksmey, Sin; Limmathurotsakul, Direk; Peacock, Sharon J; Cuny, Christiane; Layer, Franziska; Witte, Wolfgang; Nübel, Ulrich

    2013-01-01

    We investigated the population structure of Staphylococcus aureus clonal complex CC121 by mutation discovery at 115 genetic housekeeping loci from each of 154 isolates, sampled on five continents between 1953 and 2009. In addition, we pyro-sequenced the genomes from ten representative isolates. The genome-wide SNPs that were ascertained revealed the evolutionary history of CC121, indicating at least six major clades (A to F) within the clonal complex and dating its most recent common ancestor to the pre-antibiotic era. The toxin gene complement of CC121 isolates was correlated with their SNP-based phylogeny. Moreover, we found a highly significant association of clinical phenotypes with phylogenetic affiliations, which is unusual for S. aureus. All isolates evidently sampled from superficial infections (including staphylococcal scalded skin syndrome, bullous impetigo, exfoliative dermatitis, conjunctivitis) clustered in clade F, which included the European epidemic fusidic-acid resistant impetigo clone (EEFIC). In comparison, isolates from deep-seated infections (abscess, furuncle, pyomyositis, necrotizing pneumonia) were disseminated in several clades, but not in clade F. Our results demonstrate that phylogenetic lineages with distinct clinical properties exist within an S. aureus clonal complex, and that SNPs serve as powerful discriminatory markers, able to identify these lineages. All CC121 genomes harboured a 41-kilobase prophage that was dissimilar to S. aureus phages sequenced previously. Community-associated MRSA and MSSA from Cambodia were extremely closely related, suggesting this MRSA arose in the region. PMID:23505464

  9. Noise-Driven Phenotypic Heterogeneity with Finite Correlation Time in Clonal Populations.

    PubMed

    Lee, UnJin; Skinner, John J; Reinitz, John; Rosner, Marsha Rich; Kim, Eun-Jin

    2015-01-01

    There has been increasing awareness in the wider biological community of the role of clonal phenotypic heterogeneity in playing key roles in phenomena such as cellular bet-hedging and decision making, as in the case of the phage-λ lysis/lysogeny and B. Subtilis competence/vegetative pathways. Here, we report on the effect of stochasticity in growth rate, cellular memory/intermittency, and its relation to phenotypic heterogeneity. We first present a linear stochastic differential model with finite auto-correlation time, where a randomly fluctuating growth rate with a negative average is shown to result in exponential growth for sufficiently large fluctuations in growth rate. We then present a non-linear stochastic self-regulation model where the loss of coherent self-regulation and an increase in noise can induce a shift from bounded to unbounded growth. An important consequence of these models is that while the average change in phenotype may not differ for various parameter sets, the variance of the resulting distributions may considerably change. This demonstrates the necessity of understanding the influence of variance and heterogeneity within seemingly identical clonal populations, while providing a mechanism for varying functional consequences of such heterogeneity. Our results highlight the importance of a paradigm shift from a deterministic to a probabilistic view of clonality in understanding selection as an optimization problem on noise-driven processes, resulting in a wide range of biological implications, from robustness to environmental stress to the development of drug resistance. PMID:26203903

  10. Clonal CD8+ T Cell Persistence and Variable Gene Usage Bias in a Human Transplanted Hand

    PubMed Central

    Kim, Joseph Y.; Balamurugan, Arumugam; Azari, Kodi; Hofmann, Christian; Ng, Hwee L.; Reed, Elaine F.; McDiarmid, Suzanne; Yang, Otto O.

    2015-01-01

    Immune prophylaxis and treatment of transplanted tissue rejection act indiscriminately, risking serious infections and malignancies. Although animal data suggest that cellular immune responses causing rejection may be rather narrow and predictable based on genetic background, there are only limited data regarding the clonal breadth of anti-donor responses in humans after allogeneic organ transplantation. We evaluated the graft-infiltrating CD8+ T lymphocytes in skin punch biopsies of a transplanted hand over 178 days. Profiling of T cell receptor (TCR) variable gene usage and size distribution of the infiltrating cells revealed marked skewing of the TCR repertoire indicating oligoclonality, but relatively normal distributions in the blood. Although sampling limitation prevented complete assessment of the TCR repertoire, sequencing further identified 11 TCR clonal expansions that persisted through varying degrees of clinical rejection and immunosuppressive therapy. These 11 clones were limited to three TCR beta chain variable (BV) gene families. Overall, these data indicate significant oligoclonality and likely restricted BV gene usage of alloreactive CD8+ T lymphocytes, and suggest that changes in rejection status are more due to varying regulation of their activity or number rather than shifts in the clonal populations in the transplanted organ. Given that controlled animal models produce predictable BV usage in T lymphocytes mediating rejection, understanding the determinants of TCR gene usage associated with rejection in humans may have application in specifically targeted immunotherapy. PMID:26287728

  11. A timeline demarcating two waves of clonal deletion and Foxp3 upregulation during thymocyte development.

    PubMed

    Hu, Daniel Y; Yap, Jin Y; Wirasinha, Rushika C; Howard, Debbie R; Goodnow, Christopher C; Daley, Stephen R

    2016-04-01

    Thymocytes that bind strongly to self-antigens are prevented from becoming naive T cells by several mechanisms. They undergo clonal deletion at two stages of development; wave 1 in immature thymocytes lacking the medulla-homing chemokine receptor, CCR7, or wave 2 in more mature CCR7(+) thymocytes. Alternatively, self-reactive thymocytes upregulate Foxp3 to become T-regulatory cells. Here, we describe the differential timing of the two waves of deletion and Foxp3 upregulation relative to the immature proliferating stage. Proliferating thymocytes were pulse-labeled in normal C57BL/6 mice with 5-ethynyl-2'-deoxyuridine (EdU). Thymocytes progressed into wave 1 (CCR7(-)) and wave 2 (CCR7(+)) of clonal deletion ~2 and 5 days after proliferation, respectively. Foxp3 upregulation occurred between 4 and 8 days after proliferation, predominantly in thymocytes with a Helios(+) CCR7(+) phenotype. These findings establish a timeline that suggests that wave 1 of clonal deletion occurs in the thymic cortex, whereas wave 2 and Foxp3 upregulation both occur in the thymic medulla. PMID:26510893

  12. Subpopulations of Staphylococcus aureus Clonal Complex 121 Are Associated with Distinct Clinical Entities

    PubMed Central

    Kurt, Kevin; Rasigade, Jean-Philippe; Laurent, Frederic; Goering, Richard V.; Žemličková, Helena; Machova, Ivana; Struelens, Marc J.; Zautner, Andreas E.; Holtfreter, Silva; Bröker, Barbara; Ritchie, Stephen; Reaksmey, Sin; Limmathurotsakul, Direk; Peacock, Sharon J.; Cuny, Christiane; Layer, Franziska; Witte, Wolfgang; Nübel, Ulrich

    2013-01-01

    We investigated the population structure of Staphylococcus aureus clonal complex CC121 by mutation discovery at 115 genetic housekeeping loci from each of 154 isolates, sampled on five continents between 1953 and 2009. In addition, we pyro-sequenced the genomes from ten representative isolates. The genome-wide SNPs that were ascertained revealed the evolutionary history of CC121, indicating at least six major clades (A to F) within the clonal complex and dating its most recent common ancestor to the pre-antibiotic era. The toxin gene complement of CC121 isolates was correlated with their SNP-based phylogeny. Moreover, we found a highly significant association of clinical phenotypes with phylogenetic affiliations, which is unusual for S. aureus. All isolates evidently sampled from superficial infections (including staphylococcal scalded skin syndrome, bullous impetigo, exfoliative dermatitis, conjunctivitis) clustered in clade F, which included the European epidemic fusidic-acid resistant impetigo clone (EEFIC). In comparison, isolates from deep-seated infections (abscess, furuncle, pyomyositis, necrotizing pneumonia) were disseminated in several clades, but not in clade F. Our results demonstrate that phylogenetic lineages with distinct clinical properties exist within an S. aureus clonal complex, and that SNPs serve as powerful discriminatory markers, able to identify these lineages. All CC121 genomes harboured a 41-kilobase prophage that was dissimilar to S. aureus phages sequenced previously. Community-associated MRSA and MSSA from Cambodia were extremely closely related, suggesting this MRSA arose in the region. PMID:23505464

  13. Genetic diversity in three invasive clonal aquatic species in New Zealand

    PubMed Central

    2010-01-01

    Background Elodea canadensis, Egeria densa and Lagarosiphon major are dioecious clonal species which are invasive in New Zealand and other regions. Unlike many other invasive species, the genetic variation in New Zealand is very limited. Clonal reproduction is often considered an evolutionary dead end, even though a certain amount of genetic divergence may arise due to somatic mutations. The successful growth and establishment of invasive clonal species may be explained not by adaptability but by pre-existing ecological traits that prove advantageous in the new environment. We studied the genetic diversity and population structure in the North Island of New Zealand using AFLPs and related the findings to the number of introductions and the evolution that has occurred in the introduced area. Results Low levels of genetic diversity were found in all three species and appeared to be due to highly homogeneous founding gene pools. Elodea canadensis was introduced in 1868, and its populations showed more genetic structure than those of the more recently introduced of E. densa (1946) and L. major (1950). Elodea canadensis and L. major, however, had similar phylogeographic patterns, in spite of the difference in time since introduction. Conclusions The presence of a certain level of geographically correlated genetic structure in the absence of sexual reproduction, and in spite of random human dispersal of vegetative propagules, can be reasonably attributed to post-dispersal somatic mutations. Direct evidence of such evolutionary events is, however, still insufficient. PMID:20565861

  14. Staphylococcus aureus In Vitro Secretion of Alpha Toxin (hla) Correlates with the Affiliation to Clonal Complexes

    PubMed Central

    Monecke, Stefan; Müller, Elke; Büchler, Joseph; Stieber, Bettina; Ehricht, Ralf

    2014-01-01

    The alpha toxin of Staphylococcus aureus is a pore forming toxin that penetrates host cell membranes causing osmotic swelling, rupture, lysis and subsequently cell death. Haemolysin alpha is toxic to a wide range of different mammalian cells; i.e., neurotoxic, dermonecrotic, haemolytic, and it can cause lethality in a wide variety of animals. In this study, the in vitro alpha toxin production of 648 previously genotyped isolates of S. aureus was measured quantitatively using antibody microarrays. Isolates originated from medical and veterinary settings and were selected in order to represent diverse clonal complexes and defined clinical conditions. Generally, the production of alpha toxin in vitro is related to the clonal complex affiliation. For clonal complexes CC22, CC30, CC45, CC479, CC705 and others, invariably no alpha toxin production was noted under the given in vitro conditions, while others, such as CC1, CC5, CC8, CC15 or CC96 secreted variable or high levels of alpha toxin. There was no correlation between alpha toxin yield and clinical course of the disease, or between alpha toxin yield and host species. PMID:24940872

  15. Adapting populations in space: clonal interference and genetic diversity

    NASA Astrophysics Data System (ADS)

    Weissman, Daniel; Barton, Nick

    Most species inhabit ranges much larger than the scales over which individuals interact. How does this spatial structure interact with adaptive evolution? We consider a simple model of a spatially-extended, adapting population and show that, while clonal interference severely limits the adaptation of purely asexual populations, even rare recombination is enough to allow adaptation at rates approaching those of well-mixed populations. We also find that the genetic hitchhiking produced by the adaptive alleles sweeping through the population has strange effects on the patterns of genetic diversity. In large spatial ranges, even low rates of adaptation cause all individuals in the population to rapidly trace their ancestry back to individuals living in a small region in the center of the range. The probability of fixation of an allele is thus strongly dependent on the allele's spatial location, with alleles from the center favored. Surprisingly, these effects are seen genome-wide (instead of being localized to the regions of the genome undergoing the sweeps). The spatial concentration of ancestry produces a power-law dependence of relatedness on distance, so that even individuals sampled far apart are likely to be fairly closely related, masking the underlying spatial structure.

  16. Decoding astrocyte heterogeneity: New tools for clonal analysis.

    PubMed

    Bribián, A; Figueres-Oñate, M; Martín-López, E; López-Mascaraque, L

    2016-05-26

    The importance of astrocyte heterogeneity came out as a hot topic in neurosciences especially over the last decades, when the development of new methodologies allowed demonstrating the existence of big differences in morphological, neurochemical and physiological features between astrocytes. However, although the knowledge about the biology of astrocytes is increasing rapidly, an important characteristic that remained unexplored, until the last years, has been the relationship between astrocyte lineages and cell heterogeneity. To fill this gap, a new method called StarTrack was recently developed, a powerful genetic tool that allows tracking astrocyte lineages forming cell clones. Using StarTrack, a single astrocyte progenitor and its progeny can be specifically labeled from its generation, during embryonic development, to its final fate in the adult brain. Because of this specific labeling, astrocyte clones, exhibiting heterogeneous morphologies and features, can be easily analyzed in relation to their ontogenetic origin. This review summarizes how astrocyte heterogeneity can be decoded studying the embryonic development of astrocyte lineages and their clonal relationship. Finally, we discuss about some of the challenges and opportunities emerging in this exciting area of investigation. PMID:25917835

  17. Affected chromosome homeostasis and genomic instability of clonal yeast cultures.

    PubMed

    Adamczyk, Jagoda; Deregowska, Anna; Panek, Anita; Golec, Ewelina; Lewinska, Anna; Wnuk, Maciej

    2016-05-01

    Yeast cells originating from one single colony are considered genotypically and phenotypically identical. However, taking into account the cellular heterogeneity, it seems also important to monitor cell-to-cell variations within a clone population. In the present study, a comprehensive yeast karyotype screening was conducted using single chromosome comet assay. Chromosome-dependent and mutation-dependent changes in DNA (DNA with breaks or with abnormal replication intermediates) were studied using both single-gene deletion haploid mutants (bub1, bub2, mad1, tel1, rad1 and tor1) and diploid cells lacking one active gene of interest, namely BUB1/bub1, BUB2/bub2, MAD1/mad1, TEL1/tel1, RAD1/rad1 and TOR1/tor1 involved in the control of cell cycle progression, DNA repair and the regulation of longevity. Increased chromosome fragility and replication stress-mediated chromosome abnormalities were correlated with elevated incidence of genomic instability, namely aneuploid events-disomies, monosomies and to a lesser extent trisomies as judged by in situ comparative genomic hybridization (CGH). The tor1 longevity mutant with relatively balanced chromosome homeostasis was found the most genomically stable among analyzed mutants. During clonal yeast culture, spontaneously formed abnormal chromosome structures may stimulate changes in the ploidy state and, in turn, promote genomic heterogeneity. These alterations may be more accented in selected mutated genetic backgrounds, namely in yeast cells deficient in proper cell cycle regulation and DNA repair. PMID:26581629

  18. 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%. PMID:20188923

  19. Carbon relations of flowering in a semelparous clonal desert perennial

    SciTech Connect

    Tissue, D.T.; Nobel, P.S. )

    1990-02-01

    Agave deserti is a long-lived, semelparous perennial of the northwestern Sonoran Desert that flowers after {approx} 50-55 yr. Measurements of CO{sub 2} exchange over 24-h periods indicated that leaves of flowering rosettes had 24% more net CO{sub 2} uptake than leaves of adjacent nonflowering rosettes during the first month of inflorescence production. Net CO{sub 2} uptake for leaves of flowering rosettes was 32% less thereafter than for leaves of nonflowering rosettes, as senescing leaves of flowering rosettes exhibited dramatic reductions in nitrogen and chlorophyll contents. During the course of flowering, levels of total nonstructural carbohydrate (TNC) in the leaves of flowering rosettes dropped from 38 to 6% of the leaf dry mass, indicating substantial translocation of stored carbon to the inflorescence. TNC reserves of the rosette provided 70% of the carbon required to produce the 1.53 kg inflorescence, and CO{sub 2} uptake by the leaves and the inflorescence provided the remaining 30%. Rosettes must attain a minimum size (> 1,000 g dry mass) to initiate flowering, unless they are connected to a large flowering rosette. Small rosettes did not produce inflorescences when their rhizome connection to a large rosette was severed {approx} 4 wk before inflorescences emerged, suggesting that a chemical signal is transmitted through the rhizome that induces the small rosette to flower precociously. Small flowering rosettes could not complete formation of the inflorescence unless partially supported by carbon supplied by the connected large rosette. The contribution of the large rosette declined from 74% for a 0-30 g dry mass connected rosette to 35% for a 200-600 g rosette. For both small and large flowering rosettes, the translocation of substantial carbohydrate reserves from the leaves is essential for production of the inflorescence.

  20. Clonal integration in homogeneous environments increases performance of Alternanthera philoxeroides.

    PubMed

    Dong, Bi-Cheng; Alpert, Peter; Zhang, Qian; Yu, Fei-Hai

    2015-10-01

    Physiological integration between connected ramets can increase the performance of clonal plants when ramets experience contrasting levels of resource availabilities in heterogeneous environments. It has generally been shown or assumed that clonal integration has little effect on clonal performance in homogeneous environments. However, a conceptual model suggests that integration could increase performance in a homogeneous environment when connected ramets differ in uptake ability and external resource supply is high. We tested this hypothesis in a greenhouse experiment with the amphibious plant Alternanthera philoxeroides. Ramets in clonal fragments containing three rooted and two unrooted ramets were either left connected or divided into a basal part with two rooted ramets and an apical part with the other ramets. To simulate realistic, homogeneous environments of the species with different levels of resource supply, plants were grown at 0, 20, or 40 cm of water depth. Water depth had a positive effect on most measures of growth, indicating that resource supply increased with depth. Connection had negative to neutral effects on total growth of fragments at a water depth of 0 cm, and neutral to positive effects at 20- and 40-cm depths; effects on the apical part were generally positive and larger at greater depth; effects on the basal part were generally negative and smaller at greater depth. Results largely supported the hypothesis and further suggest that clonal integration of allocation and reproduction may modify benefits of resource sharing in homogeneous environments. PMID:26009243

  1. Multiple disturbances accelerate clonal growth in a potentially monodominant bamboo.

    PubMed

    Gagnon, Paul R; Platt, William J

    2008-03-01

    Organisms capable of rapid clonal growth sometimes monopolize newly freed space and resources. We hypothesize that sequential disturbances might change short-term clonal demography of these organisms in ways that promote formation of monotypic stands. We examined this hypothesis by studying the clonal response of Arundinaria gigantea (giant cane, a bamboo) to windstorm and fire. We studied giant cane growing in both a large tornado-blowdown gap and under forest canopy, in burned and unburned plots, using a split-block design. We measured density of giant cane ramets (culms) and calculated finite rates of increase (lamda) for populations of ramets over three years. Ramet density nearly doubled in stands subjected to both windstorm and fire; the high ramet densities that resulted could inhibit growth in other plants. In comparison, ramet density increased more slowly after windstorm alone, decreased after fire alone, and remained in stasis in controls. We predict that small, sparse stands of giant cane could spread and amalgamate to form dense, monotypic stands (called "canebrakes") that might influence fire return intervals and act as an alternative state to bottomland forest. Other clonal species may similarly form monotypic stands following successive disturbances via rapid clonal growth. PMID:18459325

  2. The Complex, Clonal, and Controversial Nature of Barrett's Esophagus.

    PubMed

    Evans, James A; McDonald, Stuart A C

    2016-01-01

    Barrett's esophagus (BO) is a preneoplastic condition described as the replacement of the stratified squamous epithelium of the distal esophagus with one that histologically presents as a diverse mixture of metaplastic glands resembling gastric or intestinal-type columnar epithelium. The clonal origins of BO are still unclear. More recently, we have begun to investigate the relationship between the various metaplastic gland phenotypes observed in BO, how they evolve, and the cancer risk they bestow. Studies have revealed that glands along the BO segment are clonal units containing a single stem cell clone that can give rise to all the differentiated epithelial cell types in glands. Clonal lineage tracing analysis has revealed that Barrett's glands are capable of bifurcation and this facilitates clonal expansion and competition. In fact, BO in some patients appears to consist of multiple, independently initiated clones that compete with each other for space and possibly resources. This chapter discusses the concepts of clonal competition and expansion in BO and sets out to query what we know about the role of gland diversity and phenotypic evolution within this complex columnar metaplasia. PMID:27573766

  3. Molecular epidemiology of clonal diploids: a quick overview and a short DIY (do it yourself) notice.

    PubMed

    De Meeûs, Thierry; Lehmann, Laurent; Balloux, François

    2006-03-01

    In this short review we report the basic notions needed for understanding the population genetics of clonal diploids. We focus on the consequences of clonality on the distribution of genetic diversity within individuals, between individuals and between populations. We then summarise how to detect clonality in mainly sexual populations, conversely, how to detect sexuality in mainly clonal populations and also how genetic differentiation between populations is affected by clonality in diploids. This information is then used for building recipes on how to analyse and interpret genetic polymorphism data in molecular epidemiology studies of clonal diploids. PMID:16290062

  4. 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

  5. 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.

  6. Late embryogenesis abundant proteins

    PubMed Central

    Olvera-Carrillo, Yadira; Reyes, José Luis

    2011-01-01

    Late Embryogenesis Abundant (LEA) proteins accumulate at the onset of seed desiccation and in response to water deficit in vegetative plant tissues. The typical LEA proteins are highly hydrophilic and intrinsically unstructured. They have been classified in different families, each one showing distinctive conserved motifs. In this manuscript we present and discuss some of the recent findings regarding their role in plant adaptation to water deficit, as well as those concerning to their possible function, and how it can be related to their intrinsic structural flexibility. PMID:21447997

  7. Increase of genetic diversity and clonal replacement of epidemic methicillin-resistant Staphylococcus aureus strains in South-East Austria

    PubMed Central

    Zarfel, Gernot; Luxner, Josefa; Folli, Bettina; Leitner, Eva; Feierl, Gebhard; Kittinger, Clemens; Grisold, Andrea

    2016-01-01

    Spa-typing and microarray techniques were used to study epidemiological changes in methicillin-resistant Staphylococcus aureus (MRSA) in South-East Austria. The population structure of 327 MRSA isolated between 2002 and 2012 was investigated. MRSA was assigned to 58 different spa types and 14 different MLST CC (multilocus sequence type clonal complexes); in particular, between 2007 and 2012, an increasing diversity in MRSA clones could be observed. The most abundant clonal complex was CC5. On the respective SCCmec cassettes, the CC5 isolates differed clearly within this decade and CC5/SCCmecI, the South German MRSA, predominant in 2002, was replaced by CC5/SCCmecII, the Rhine-Hesse MRSA in 2012. Whereas in many European countries MLST CC22-MRSA (EMRSA 15, the Barnim epidemic MRSA) is predominant, this clone occurred in Austria nearly 10 years later than in neighbouring countries. CC45, the Berlin EMRSA, epidemic in Germany, was only sporadically found in South-East Austria. The Irish ST8-MRSA-II represented by spa-type t190 was frequently found in 2002 and 2007, but disappeared in 2012. Our results demonstrate clonal replacement of MRSA clones within the last years in Austria. Ongoing surveillance is warranted for detection of changes within the MRSA population. PMID:27231237

  8. Increase of genetic diversity and clonal replacement of epidemic methicillin-resistant Staphylococcus aureus strains in South-East Austria.

    PubMed

    Zarfel, Gernot; Luxner, Josefa; Folli, Bettina; Leitner, Eva; Feierl, Gebhard; Kittinger, Clemens; Grisold, Andrea

    2016-07-01

    Spa-typing and microarray techniques were used to study epidemiological changes in methicillin-resistant Staphylococcus aureus (MRSA) in South-East Austria. The population structure of 327 MRSA isolated between 2002 and 2012 was investigated. MRSA was assigned to 58 different spa types and 14 different MLST CC (multilocus sequence type clonal complexes); in particular, between 2007 and 2012, an increasing diversity in MRSA clones could be observed. The most abundant clonal complex was CC5. On the respective SCCmec cassettes, the CC5 isolates differed clearly within this decade and CC5/SCCmecI, the South German MRSA, predominant in 2002, was replaced by CC5/SCCmecII, the Rhine-Hesse MRSA in 2012. Whereas in many European countries MLST CC22-MRSA (EMRSA 15, the Barnim epidemic MRSA) is predominant, this clone occurred in Austria nearly 10 years later than in neighbouring countries. CC45, the Berlin EMRSA, epidemic in Germany, was only sporadically found in South-East Austria. The Irish ST8-MRSA-II represented by spa-type t190 was frequently found in 2002 and 2007, but disappeared in 2012. Our results demonstrate clonal replacement of MRSA clones within the last years in Austria. Ongoing surveillance is warranted for detection of changes within the MRSA population. PMID:27231237

  9. Dynamic clonal equilibrium and predetermined cancer risk in Barrett's oesophagus.

    PubMed

    Martinez, Pierre; Timmer, Margriet R; Lau, Chiu T; Calpe, Silvia; Sancho-Serra, Maria Del Carmen; Straub, Danielle; Baker, Ann-Marie; Meijer, Sybren L; Kate, Fiebo J W Ten; Mallant-Hent, Rosalie C; Naber, Anton H J; van Oijen, Arnoud H A M; Baak, Lubbertus C; Scholten, Pieter; Böhmer, Clarisse J M; Fockens, Paul; Bergman, Jacques J G H M; Maley, Carlo C; Graham, Trevor A; Krishnadath, Kausilia K

    2016-01-01

    Surveillance of Barrett's oesophagus allows us to study the evolutionary dynamics of a human neoplasm over time. Here we use multicolour fluorescence in situ hybridization on brush cytology specimens, from two time points with a median interval of 37 months in 195 non-dysplastic Barrett's patients, and a third time point in a subset of 90 patients at a median interval of 36 months, to study clonal evolution at single-cell resolution. Baseline genetic diversity predicts progression and remains in a stable dynamic equilibrium over time. Clonal expansions are rare, being detected once every 36.8 patient years, and growing at an average rate of 1.58 cm(2) (95% CI: 0.09-4.06) per year, often involving the p16 locus. This suggests a lack of strong clonal selection in Barrett's and that the malignant potential of 'benign' Barrett's lesions is predetermined, with important implications for surveillance programs. PMID:27538785

  10. Pretransplant cytotoxic conditioning produces effects consistent with clonal deletion mechanisms.

    PubMed

    Zheng, T L; Johnson, C P; Sutherland, D E

    1987-05-01

    A rat cardiac allograft model (ACl to Lewis) was used to investigate the clonal deletion theory. Twelve groups of Lewis recipients received various combinations of donor-specific blood transfusions (DSTs), immediate post-DST immunosuppression with azathioprine/prednisone, and low-dose cyclosporine (1 mg/kg/day) posttransplant. DSTs and cyclosporine together gave modest prolongation of graft survival (from 6.0 to 17 days). DSTs plus immediate post-DST immunosuppression followed by low-dose cyclosporine prolonged graft survival to an average of 45 days. Third-party transfusions alone and in combination with immunosuppression did not significantly prolong allograft survival. Postoperative cyclosporine was required for the expression of this effect suggesting that clonal depression rather than clonal deletion had occurred. Combining DSTs with brief but intense preoperative immunosuppression may be a more effective method of pretransplant conditioning than DSTs alone. PMID:3295388

  11. Dynamic clonal equilibrium and predetermined cancer risk in Barrett's oesophagus

    PubMed Central

    Martinez, Pierre; Timmer, Margriet R.; Lau, Chiu T.; Calpe, Silvia; Sancho-Serra, Maria del Carmen; Straub, Danielle; Baker, Ann-Marie; Meijer, Sybren L.; Kate, Fiebo J. W. ten; Mallant-Hent, Rosalie C.; Naber, Anton H. J.; van Oijen, Arnoud H. A. M.; Baak, Lubbertus C.; Scholten, Pieter; Böhmer, Clarisse J. M.; Fockens, Paul; Bergman, Jacques J. G. H. M.; Maley, Carlo C.; Graham, Trevor A.; Krishnadath, Kausilia K

    2016-01-01

    Surveillance of Barrett's oesophagus allows us to study the evolutionary dynamics of a human neoplasm over time. Here we use multicolour fluorescence in situ hybridization on brush cytology specimens, from two time points with a median interval of 37 months in 195 non-dysplastic Barrett's patients, and a third time point in a subset of 90 patients at a median interval of 36 months, to study clonal evolution at single-cell resolution. Baseline genetic diversity predicts progression and remains in a stable dynamic equilibrium over time. Clonal expansions are rare, being detected once every 36.8 patient years, and growing at an average rate of 1.58 cm2 (95% CI: 0.09–4.06) per year, often involving the p16 locus. This suggests a lack of strong clonal selection in Barrett's and that the malignant potential of ‘benign' Barrett's lesions is predetermined, with important implications for surveillance programs. PMID:27538785

  12. [Clonal eosinophilia revealed by recurrent Staphylococcus aureus infection].

    PubMed

    Vandenbos, F; Figueredo, M; Dumon-Gubeno, M-C; Nicolle, I; Tarhini, A; Medioni, L-D; Naman, H; Mouroux, J

    2011-06-01

    Acquired eosinophilia is currently classified into secondary (reactional to underlying diseases), clonal (presence of a bone marrow histological, cytogenetic or molecular marker of a myeloid malignancy) and idiopathic (neither secondary nor clonal) categories. We report the case of a 47-year-old male who was admitted to the hospital for Staphylococcus aureus recurring infections. An hypereosinophilia was discovered and led to molecular analysis. The identification of FIP1L1-PDGFRA fusion gene permitted the diagnostic of clonal eosinophilia. Treatment by imatinib mesylate induced an haematological remission, the control of the infection and thoracotomy cicatrization. This case is original because of its infectious presentation and the efficacy of imatinib mesylate to control the infectious process. PMID:21665081

  13. Fine-scale temporal and spatial variation of taxon and clonal structure in the Daphnia longispina hybrid complex in heterogeneous environments

    PubMed Central

    2012-01-01

    Background Cyclical parthenogenetic water fleas of the genus Daphnia have become a prominent model organism in ecology and evolution. In the past, analyses of their population structure have been limited by the prevailing use of allozyme markers, which in general do not allow for the distinction of individual clones. In this study, we used 10 microsatellite markers to track changes in the taxonomic and clonal composition of Daphnia populations, and traced the abundance of the most common clones in two European reservoirs. One of the localities was inhabited by a single species of the Daphnia longispina complex (D. galeata), the other by two parental species (D. galeata and D. longispina) and their interspecific hybrids. The study took place during the transition from summer stratification to autumn mixing, representing a period of major environmental change within lake habitats. Results In both reservoirs, we observed temporal (generation-to-generation) and spatial (along the heterogeneous reservoir environment) changes in Daphnia community structure. In the single-species reservoir, the clonal diversity of D. galeata increased with time, as a few dominant clones were replaced by a higher number of less common clones. A loss in selective advantage for the dominant clones may have been due to gradual changes in the environment, or due to selection acting in a negative frequency-dependent manner. In the multispecies reservoir, there were no apparent temporal trends in clonal diversity but we observed significantly lower clonal diversity in the interspecific hybrids than in the coexisting parental species, supporting the existence of reproductive barriers between the parental genomes. Conclusions Our study, tracing clonal lineages of Daphnia in time and space by the fine-resolution markers, contributes to the understanding of how clonal reproduction impacts community structure in cyclically parthenogenetic organisms. PMID:22280487

  14. Induction of ketosis in rats fed low-carbohydrate, high-fat diets depends on the relative abundance of dietary fat and protein.

    PubMed

    Bielohuby, Maximilian; Menhofer, Dominik; Kirchner, Henriette; Stoehr, Barbara J M; Müller, Timo D; Stock, Peggy; Hempel, Madlen; Stemmer, Kerstin; Pfluger, Paul T; Kienzle, Ellen; Christ, Bruno; Tschöp, Matthias H; Bidlingmaier, Martin

    2011-01-01

    Low-carbohydrate/high-fat diets (LC-HFDs) in rodent models have been implicated with both weight loss and as a therapeutic approach to treat neurological diseases. LC-HFDs are known to induce ketosis; however, systematic studies analyzing the impact of the macronutrient composition on ketosis induction and weight loss success are lacking. Male Wistar rats were pair-fed for 4 wk either a standard chow diet or one of three different LC-HFDs, which only differed in the relative abundance of fat and protein (percentages of fat/protein in dry matter: LC-75/10; LC-65/20; LC-55/30). We subsequently measured body composition by nuclear magnetic resonance (NMR), analyzed blood chemistry and urine acetone content, evaluated gene expression changes of key ketogenic and gluconeogenic genes, and measured energy expenditure (EE) and locomotor activity (LA) during the first 4 days and after 3 wk on the respective diets. Compared with chow, rats fed with LC-75/10, LC-65/20, and LC-55/30 gained significantly less body weight. Reductions in body weight were mainly due to lower lean body mass and paralleled by significantly increased fat mass. Levels of β-hydroxybutyate were significantly elevated feeding LC-75/10 and LC-65/20 but decreased in parallel to reductions in dietary fat. Acetone was about 16-fold higher with LC-75/10 only (P < 0.001). In contrast, rats fed with LC-55/30 were not ketotic. Serum fibroblast growth factor-21, hepatic mRNA expression of hydroxymethylglutaryl-CoA-lyase, peroxisome proliferator-activated receptor-γ coactivator-1α, and peroxisome proliferator-activated receptor-γ coactivator-1β were increased with LC-75/10 only. Expression of phosphoenolpyruvate carboxykinase and glucose-6-phosphatase was downregulated by 50-70% in LC-HF groups. Furthermore, EE and LA were significantly decreased in all groups fed with LC-HFDs after 3 wk on the diets. In rats, the absence of dietary carbohydrates per se does not induce ketosis. LC-HFDs must be high in fat

  15. 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

  16. Relative Abundances of Calcite and Silica in Fracture Coatings as a Possible Indicator of Evaporation in a Thick Unsaturated Zone, Yucca Mountain, Nevada

    NASA Astrophysics Data System (ADS)

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

    2005-12-01

    Yucca Mountain, a ridge of shallowly dipping, Miocene-age volcanic rocks in southwest Nevada, is the proposed site for a nuclear waste repository to be constructed in the 500- to 700-m-thick unsaturated zone (UZ). At the proposed repository, the 300-m-thick Topopah Spring Tuff welded unit (TSw) is overlain by approximately 30 m of nonwelded tuffs (PTn); the Tiva Canyon Tuff welded unit (TCw) overlies the PTn with a range in thickness from 0 to approximately 130 m at the site. The amount of water percolation through the UZ is low and difficult to measure directly, but local seepage into mined tunnels has been observed in the TCw. Past water seepage in the welded tuffs is recorded by widespread, thin (0.3 cm) coatings of calcite and silica on fracture surfaces and within cavities. Abundances of calcite and silica in the coatings were determined by X-ray microfluorescence mapping and subsequent multispectral image analysis of over 200 samples. The images were classified into constituent phases including opal-chalcedony-quartz (secondary silica) and calcite. In the TCw samples, the median calcite/silica ratio is 8; in the TSw samples within 35 m below the PTn, median calcite/silica falls to 2, perhaps reflecting an increase in soluble silica from the presence of glass in the nonwelded tuffs. In the deeper parts of the TSw, median calcite/silica reaches 100 and many samples contain no detectable secondary silica phase. Evaporation and changing pCO2 control precipitation of calcite from water percolating downward in the UZ, but precipitation of opal requires only evaporation. Calcite/silica ratios, therefore, can constrain the relative importance of evaporation in the UZ. Although calcite/silica values scatter widely within the TSw, reflecting the spatial variability of gas and water flow, average calcite/silica ratios increase with stratigraphic depth, indicating less evaporation at the deeper levels of the UZ. Coupled with the much smaller calcite/silica ratios

  17. Critical analysis of the stringent complete response in multiple myeloma: contribution of sFLC and bone marrow clonality

    PubMed Central

    Paiva, Bruno; López-Anglada, Lucía; Mateos, María-Victoria; Cedena, Teresa; Vidríales, María-Belén; Sáez-Gómez, María Auxiliadora; Contreras, Teresa; Oriol, Albert; Rapado, Inmaculada; Teruel, Ana-Isabel; Cordón, Lourdes; Blanchard, María Jesús; Bengoechea, Enrique; Palomera, Luis; de Arriba, Felipe; Cueto-Felgueroso, Cecilia; Orfao, Alberto; Bladé, Joan; San Miguel, Jesús F.; Lahuerta, Juan José

    2015-01-01

    Stringent complete response (sCR) criteria are used in multiple myeloma as a deeper response category compared with CR, but prospective validation is lacking, it is not always clear how evaluation of clonality is performed, and is it not known what the relative clinical influence is of the serum free light chain ratio (sFLCr) and bone marrow (BM) clonality to define more sCR. To clarify this controversy, we focused on 94 patients that reached CR, of which 69 (73%) also fulfilled the sCR criteria. Patients with sCR displayed slightly longer time to progression (median, 62 vs 53 months, respectively; P = .31). On analyzing this contribution to the prognosis of sFLCr or clonality, it was found that the sFLCr does not identify patients in CR at distinct risk; by contrast, low-sensitive multiparametric flow cytometry (MFC) immunophenotyping (2 colors), which is equivalent to immunohistochemistry, identifies a small number of patients (5 cases) with high residual tumor burden and dismal outcome; nevertheless, using traditional 4-color MFC, persistent clonal BM disease was detectable in 36% of patients, who, compared with minimal residual disease-negative cases, had a significantly inferior outcome. These results show that the current definition of sCR should be revised. PMID:26089396

  18. Investigating the effects of topography and clonality on genetic structuring within a large Norwegian population of Arabidopsis lyrata

    PubMed Central

    Lundemo, Sverre; Stenøien, Hans K.; Savolainen, Outi

    2010-01-01

    Background and Aims The gene flow through pollen or seeds governs the extent of spatial genetic structure in plant populations. Another factor that can contribute to this pattern is clonal growth. The perennial species Arabidopsis lyrata ssp. petraea (Brassicaceae) is a self-incompatible, clonal species found in disjunctive populations in central and northern Europe. Methods Fourteen microsatellite markers were employed to study the level of kinship and clonality in a high-altitude mountain valley at Spiterstulen, Norway. The population has a continuous distribution along the banks of the River Visa for about 1·5 km. A total of 17 (10 m × 10 m) squares were laid out in a north–south transect following the river on both sides. Key Results It is shown that clonal growth is far more common than previously shown in this species, although the overall size of the genets is small (mean diameter = 6·4 cm). Across the whole population there is no indication of isolation by distance, and spatial genetic structure is only visible on fine spatial scales. In addition, no effect of the river on the spatial distribution of genotypes was found. Conclusions Unexpectedly, the data show that populations of small perennials like A. lyrata can behave like panmictic units across relatively large areas at local sites, as opposed to earlier findings in central Europe. PMID:20519240

  19. Critical analysis of the stringent complete response in multiple myeloma: contribution of sFLC and bone marrow clonality.

    PubMed

    Martínez-López, Joaquín; Paiva, Bruno; López-Anglada, Lucía; Mateos, María-Victoria; Cedena, Teresa; Vidríales, María-Belén; Sáez-Gómez, María Auxiliadora; Contreras, Teresa; Oriol, Albert; Rapado, Inmaculada; Teruel, Ana-Isabel; Cordón, Lourdes; Blanchard, María Jesús; Bengoechea, Enrique; Palomera, Luis; de Arriba, Felipe; Cueto-Felgueroso, Cecilia; Orfao, Alberto; Bladé, Joan; San Miguel, Jesús F; Lahuerta, Juan José

    2015-08-13

    Stringent complete response (sCR) criteria are used in multiple myeloma as a deeper response category compared with CR, but prospective validation is lacking, it is not always clear how evaluation of clonality is performed, and is it not known what the relative clinical influence is of the serum free light chain ratio (sFLCr) and bone marrow (BM) clonality to define more sCR. To clarify this controversy, we focused on 94 patients that reached CR, of which 69 (73%) also fulfilled the sCR criteria. Patients with sCR displayed slightly longer time to progression (median, 62 vs 53 months, respectively; P = .31). On analyzing this contribution to the prognosis of sFLCr or clonality, it was found that the sFLCr does not identify patients in CR at distinct risk; by contrast, low-sensitive multiparametric flow cytometry (MFC) immunophenotyping (2 colors), which is equivalent to immunohistochemistry, identifies a small number of patients (5 cases) with high residual tumor burden and dismal outcome; nevertheless, using traditional 4-color MFC, persistent clonal BM disease was detectable in 36% of patients, who, compared with minimal residual disease-negative cases, had a significantly inferior outcome. These results show that the current definition of sCR should be revised. PMID:26089396

  20. Colonization history and clonal richness of asexual Daphnia in periglacial habitats of contrasting age in West Greenland.

    PubMed

    Haileselasie, Tsegazeabe H; Mergeay, Joachim; Weider, Lawrence J; Jeppesen, Erik; De Meester, Luc

    2016-07-01

    Due to climate change, Arctic ice sheets are retreating. This leads to the formation of numerous new periglacial ponds and lakes, which are being colonized by planktonic organisms such as the water flea Daphnia. This system provides unique opportunities to test genotype colonization dynamics and the genetic assemblage of populations. Here, we studied clonal richness of the Daphnia pulex species complex in novel periglacial habitats created by glacial retreat in the Jakobshavn Isbrae area of western Greenland. Along a 10 km transect, we surveyed 73 periglacial habitats out of which 61 were colonized by Daphnia pulex. Hence, for our analysis, we used 21 ponds and 40 lakes in two clusters of habitats differing in age (estimated <50 years vs. >150 years). We tested the expectation that genetic diversity would be low in recently formed (i.e. young), small habitats, but would increase with increasing age and size. We identified a total of 42 genetically distinct clones belonging to two obligately asexual species of the D. pulex species complex: D. middendorffiana and the much more abundant D. pulicaria. While regional clonal richness was high, most clones were rare: 16 clones were restricted to a single habitat and the five most widespread clones accounted for 68% of all individuals sampled. On average, 3·2 clones (range: 1-12) coexisted in a given pond or lake. There was no relationship between clonal richness and habitat size when we controlled for habitat age. Whereas clonal richness was statistically higher in the cluster of older habitats when compared with the cluster of younger ponds and lakes, most young habitats were colonized by multiple genotypes. Our data suggest that newly formed (periglacial) ponds and lakes are colonized within decades by multiple genotypes via multiple colonization events, even in the smallest of our study systems (4 m(2) ). PMID:27279332

  1. Phenotypic plasticity or speciation? A case from a clonal marine organism

    PubMed Central

    2008-01-01

    Background Clonal marine organisms exhibit high levels of morphological variation. Morphological differences may be a response to environmental factors but also they can be attributed to accumulated genetic differences due to disruption of gene flow among populations. In this study, we examined the extensive morphological variation (of 14 characters) in natural populations observed in the gorgonian Eunicea flexuosa, a widely distributed Caribbean octocoral. Eco-phenotypic and genetic effects were evaluated by reciprocal transplants of colonies inhabiting opposite ends of the depth gradient and analysis of population genetics of mitochondrial and nuclear genes, respectively. Results Significant differences (P < 0.001) in 14 morphological traits were found among colonies inhabiting 12 locations distributed in seven reefs in southwest Puerto Rico. Results from principal component analysis indicated the presence of two groups based on depth distribution, suggesting the presence of two discrete morphotypes (i.e. shallow type < 5 m and deep type > 17 m). A discriminant function analysis based on a priori univariate and multivariate analyses (which separated the colonies in morphotypes) correctly classified 93% of the colonies for each environment. Light, water motion and sediment transport might influence the distribution of the two morphotypes. Reaction norms of morphological characters of colonies reciprocally transplanted showed gradual significant changes through the 15 months of transplantation. Sclerites of shallow water colonies became larger when transplanted to deeper environments and vice versa, but neither of the two transplanted groups overlapped with the residents' morphology. Genetic analysis of mitochondrial and nuclear genes suggested that such discrete morphology and non-overlapping phenotypic plasticity is correlated with the presence of two independent evolutionary lineages. The distribution of the lineages is non-random and may be related to

  2. Clinical Clostridium difficile: clonality and pathogenicity locus diversity.

    PubMed

    Dingle, Kate E; Griffiths, David; Didelot, Xavier; Evans, Jessica; Vaughan, Alison; Kachrimanidou, Melina; Stoesser, Nicole; Jolley, Keith A; Golubchik, Tanya; Harding, Rosalind M; Peto, Tim E; Fawley, Warren; Walker, A Sarah; Wilcox, Mark; Crook, Derrick W

    2011-01-01

    Clostridium difficile infection (CDI) is an important cause of mortality and morbidity in healthcare settings. The major virulence determinants are large clostridial toxins, toxin A (tcdA) and toxin B (tcdB), encoded within the pathogenicity locus (PaLoc). Isolates vary in pathogenicity from hypervirulent PCR-ribotypes 027 and 078 with high mortality, to benign non-toxigenic strains carried asymptomatically. The relative pathogenicity of most toxigenic genotypes is still unclear, but may be influenced by PaLoc genetic variant. This is the largest study of C. difficile molecular epidemiology performed to date, in which a representative collection of recent isolates (n = 1290) from patients with CDI in Oxfordshire, UK, was genotyped by multilocus sequence typing. The population structure was described using NeighborNet and ClonalFrame. Sequence variation within toxin B (tcdB) and its negative regulator (tcdC), was mapped onto the population structure. The 69 Sequence Types (ST) showed evidence for homologous recombination with an effect on genetic diversification four times lower than mutation. Five previously recognised genetic groups or clades persisted, designated 1 to 5, each having a strikingly congruent association with tcdB and tcdC variants. Hypervirulent ST-11 (078) was the only member of clade 5, which was divergent from the other four clades within the MLST loci. However, it was closely related to the other clades within the tcdB and tcdC loci. ST-11 (078) may represent a divergent formerly non-toxigenic strain that acquired the PaLoc (at least) by genetic recombination. This study focused on human clinical isolates collected from a single geographic location, to achieve a uniquely high density of sampling. It sets a baseline of MLST data for future comparative studies investigating genotype virulence potential (using clinical severity data for these isolates), possible reservoirs of human CDI, and the evolutionary origins of hypervirulent strains

  3. Cetacean distribution and abundance in relation to oceanographic domains on the eastern Bering Sea shelf, June and July of 2002, 2008, and 2010

    NASA Astrophysics Data System (ADS)

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

    2013-10-01

    As part of the Bering Sea Project, cetacean surveys were conducted to describe distribution and estimate abundance on the eastern Bering Sea shelf. Three marine mammal observers conducted visual surveys along transect lines sampled during the Alaska Fisheries Science Center walleye pollock assessment survey in June and July of 2008 and 2010. Distribution and abundance in 2008 and 2010 (cold years) are compared with results from a similar survey conducted in 2002 (a warm year), as the only three years that the entire survey area was sampled; patterns largely match those previously observed. Abundance estimates for comparable areas in 2002, 2008 and 2010 were as follows: humpback whales (Megaptera novaeangliae): 231 (CV=0.63), 436 (CV=0.45), and 675 (CV=0.80); fin whales (Balaenoptera physalus): 419 (CV=0.33), 1368 (CV=0.34), and 1061 (CV=0.38); minke whales (Balaenoptera acutorostrata): 389 (CV=0.52), 517 (CV=0.69), and 2020 (CV=0.73); Dall's porpoise (Phocoenoides dalli): 35,303 (CV=0.53), 14,543 (CV=0.32), and 11,143 (CV=0.32); and harbor porpoise (Phocoena phocoena): 1971 (CV=0.46), 4056 (CV=0.40), and 833 (CV=0.66). It should be noted that these abundance estimates are not corrected for biases due to perception, availability, or responsive movement. Estimates for humpback, fin and minke whales increased from 2002 to 2010, while those for harbor and Dall's porpoise decreased; trends were significant for fin whales. It is likely that changes in estimated abundance are due at least in part to shifts in distribution and not just changes in overall population size. Annual abundance estimates were examined by oceanographic domain. Humpback whales were consistently concentrated in coastal waters north of Unimak Pass. Fin whales were broadly distributed in the outer domain and slope in 2008 and 2010, but sightings were sparse in 2002. Minke whales were distributed throughout the study area in 2002 and 2008, but in 2010 they were concentrated in the outer domain and

  4. Patterns in abundance and size of two deep-water gorgonian octocorals, in relation to depth and substrate features off Nova Scotia

    NASA Astrophysics Data System (ADS)

    Watanabe, Shana; Metaxas, Anna; Sameoto, Jessica; Lawton, Peter

    2009-12-01

    Deep-water corals form unique ecosystems, yet very little is known about factors that regulate their distribution and growth. The abundance and size of two deep-water gorgonian coral species, Paragorgia arborea and Primnoa resedaeformis, and their relationship with depth and substratum cover, were investigated at Northeast Channel, off Nova Scotia, in July 2006. This is the first study to measure abundance and size of these two coral species at depths >500 m in the Canadian Atlantic region. A total of 5 transects between 500 and 1000 m depth were examined using video collected by the remotely operated vehicle ROPOS. Abundance of both species was patchy, but higher at these deeper depths than at <500 m. Abundance generally declined with depth, and was moderately correlated with cover of hard substratum (cobble, boulder, bedrock). These relationships were stronger and less variable for P. resedaeformis than for P. arborea, suggesting that factors such as topographic relief may play an additional role in regulating distributions of P. arborea. Maximum colony height was 125 and 240 cm for P. resedaeformis and P. arborea, respectively, and much greater than recorded for depths <500 m. Overall, colony height and depth relationships were strong for both species, but variable among transects. P. resedaeformis showed a negative relationship with depth, while the opposite was observed for P. arborea, suggesting that the two species are affected differently by factors that vary with depth (e.g. temperature, fishing disturbance). Relationships between colony size and size of attachment stone were stronger for P. arborea, especially for overturned colonies, than for P. resedaeformis, suggesting that availability of suitably coarse substrate may be more important for the long-term persistence of P. arborea colonies.

  5. Anthropogenic soils and land use patterns in relation to small mammal and flea abundance in plague endemic area of Western Usambara Mountains, Tanzania.

    PubMed

    Kimaro, Didas N; Msanya, Balthazar M; Meliyo, Joel; Hieronimo, Proches; Mwango, Sibaway; Kihupi, Nganga I; Gulinck, Hubert; Deckers, Jozef A

    2014-07-01

    Heterogeneity in the landscapes of West Usambara Mountains on land use and human activities has been reported. However, the interface of land use patterns and human modified soils with small mammal and flea abundance for possible explanation of plague has not been explored. This study was carried out to determine the link between anthropogenic soils and land use patterns on small mammal and flea abundance and the occurrence of reported plague in the Western Usambara Mountains in Tanzania. Standard soil survey methods were used to identify and describe soils and land use patterns on lower slopes and valley bottoms on which the surrounding villages are reported to have high and medium plague frequencies. The identified soils were characterised in terms of their morphological and physico-chemical properties and classified according to FAO-World Reference Base for Soil Resources. Small mammals were trapped on the same landscape positions and identified to genus/species level. Fleas were removed from the trapped small mammals, counted and identified to species level. In total 57 small mammals were captured from which 32 fleas were collected. Results show that human settlements and mixed cultivation on lower slopes and continuous vegetable cropping in the valley bottoms are dominant land use types. Intensive use of forest soils, manuring and irrigation on farms in the studied landscapes have contributed to the development of uniquely human modified soils namely Hortic Anthrosols in the lower slopes and Plaggic Irragric Hortic Anthrosols in valley bottoms. The identified anthropogenic soils and land use patterns are associated with high abundance of small mammals (Mastomys natalensis) and flea species (Xenopsylla brasiliensis and Dinopsyllus lypusus). This phenomenon is vividly apparent in the villages with medium to high plague frequencies. The study suggests that plague surveillance programmes should consider the existing relationship between anthropogenic soils, land

  6. Geographical and seasonal variations in mesozooplankton abundance and biomass in relation to environmental parameters in Lake Shinji Ohashi River Lake Nakaumi brackish-water system, Japan

    NASA Astrophysics Data System (ADS)

    Uye, S.; Shimazu, T.; Yamamuro, M.; Ishitobi, Y.; Kamiya, H.

    2000-10-01

    We measured the abundance and biomass of the major taxonomic groups of mesozooplankton at six stations in Lake Shinji-Ohashi River-Lake Nakaumi brackish-water system, Japan, monthly for three full years (1995-1997), except for one station (for 1 year and 9 months). Over the entire area, copepods overwhelmingly dominated the zooplankton community both in terms of abundance (mean: 87.9%) and biomass (83.4%). The remaining taxa were cladocerans (i.e. Diphanosoma brachyurum, Evadone tergestina, Penilia avirostris, Podon leuckarti and Podon polyphemoides), appendicularians ( Oikopleura dioica and Oikopleura longicauda), chaetognaths ( Sagitta crassa) and the larvae of benthos (e.g. polychaetes, bivalves, gastropods and malacostracans). The geographical and seasonal variations of the mesozooplankton community were therefore principally explained by the variations of the copepod community. The geographical difference in copepod species composition was associated with salinity preference or tolerance of respective species. In Lake Shinji, where the salinity was lowest (mean: 4.0), Sinocalanus tenellus was monospecifically abundant with sporadic occurrence of Pseudodiaptomus inopinus. In Ohashi River (mean salinity: 9.9), Acartia hudsonica, Acartia sinjiensis, Eurytemora pacifica and Oithona davisae added to the community. At central and southeast Lake Nakaumi and in Honjo District, where mean salinity ranged from 16.4 to 21.7, these four species became more important than S. tenellus and P. inopinus. At the entrance of Sakai Strait, where the salinity was highest (mean: 24.0), Paracalanus spp. constituted a significant component. Due to large temperature fluctuation with season, the copepods showed remarkable seasonal variations in abundance and biomass, with enormous annual peaks in winter-spring. These annual peaks might be attributed to scarce occurrence of predators.

  7. Intrafamilial cluster of pulmonary tuberculosis due to Mycobacterium bovis of the African 1 clonal complex.

    PubMed

    Godreuil, S; Jeziorski, E; Bañuls, A L; Fraisse, T; Van de Perre, P; Boschiroli, M L

    2010-12-01

    A new clonal complex of Mycobacterium bovis present at high frequency in cattle from west central African countries has been described as the African 1 (Af1) clonal complex. Here, the first intrafamilial cluster of human tuberculosis cases due to M. bovis Af1 clonal complex strains is reported. We discuss hypotheses regarding modes of transmission. PMID:20980573

  8. Cryptic changes in the genetic structure of a highly clonal coral population and the relationship with ecological performance

    NASA Astrophysics Data System (ADS)

    Williams, Dana E.; Miller, M. W.; Baums, I. B.

    2014-09-01

    Elkhorn coral , Acropora palmata, relies heavily on clonal propagation and often displays low genotypic (clonal) diversity. Populations in the Florida Keys experienced rapid declines in tissue cover between 2004 and 2006, largely due to hurricanes and disease, but remained stable from 2006 to 2010. All elkhorn colonies in 150 m2 permanent study plots were genotyped in 2006 ( n = 15 plots) and 2010 ( n = 24 plots), and plots sampled in both years were examined for changes in allelic and genotypic diversity during this period of stable ecological abundance. Overall, genetic diversity of Florida plots was low and declined further over the 4-yr period; seven of the 36 original genets and two of 67 alleles (among five microsatellite loci) were lost completely from the sampled population, and an additional 15 alleles were lost from individual reefs. In 2010, Florida plots (~19 colonies) contained an average of 2.2 ± 1.38 (mean ± SD) genets with a significant negative correlation between colony abundance and genotypic diversity. When scaled to total tissue abundance, genotypic diversity is even lower, with 43 % of genets below the size of sexual maturity. We examined the hypothesized positive relationship of local genotypic diversity with ecological performance measures. In Florida plots ( n = 15), genotypic diversity was not significantly correlated with tissue loss associated with chronic predation, nor with acute disease and storm-fragmentation events, though this relationship may be obscured by the low range of observed diversity and potential confounding with abundance. When more diverse plots in Curaçao ( n = 9) were examined, genotypic diversity was not significantly correlated with resistance during an acute storm disturbance or rate of recovery following disturbance. Cryptic loss of genetic diversity occurred in the apparently stable Florida population and confirms that stable or even increasing abundance does not necessarily indicate genetic stability.

  9. Clonal diversity of recurrently mutated genes in myelodysplastic syndromes

    PubMed Central

    Walter, MJ; Shen, D; Shao, J; Ding, L; White, BS; Kandoth, C; Miller, CA; Niu, B; McLellan, MD; Dees, ND; Fulton, R; Elliot, K; Heath, S; Grillot, M; Westervelt, P; Link, DC; DiPersio, JF; Mardis, E; Ley, TJ; Wilson, RK; Graubert, TA

    2013-01-01

    Recent studies suggest that most cases of myelodysplastic syndrome (MDS) are clonally heterogeneous, with a founding clone and multiple subclones. It is not known whether specific gene mutations typically occur in founding clones or subclones. We screened a panel of 94 candidate genes in a cohort of 157 patients with MDS or secondary acute myeloid leukemia (sAML). This included 150 cases with samples obtained at MDS diagnosis and 15 cases with samples obtained at sAML transformation (8 were also analyzed at the MDS stage). We performed whole-genome sequencing (WGS) to define the clonal architecture in eight sAML genomes and identified the range of variant allele frequencies (VAFs) for founding clone mutations. At least one mutation or cytogenetic abnormality was detected in 83% of the 150 MDS patients and 17 genes were significantly mutated (false discovery rate ≤0.05). Individual genes and patient samples displayed a wide range of VAFs for recurrently mutated genes, indicating that no single gene is exclusively mutated in the founding clone. The VAFs of recurrently mutated genes did not fully recapitulate the clonal architecture defined by WGS, suggesting that comprehensive sequencing may be required to accurately assess the clonal status of recurrently mutated genes in MDS. PMID:23443460

  10. Quantification of Clonal Circulating Plasma cells in Relapsed Multiple Myeloma

    PubMed Central

    Gonsalves, Wilson I; Morice, William G; Rajkumar, S. Vincent; Gupta, Vinay; Timm, Michael M; Dispenzieri, Angela; Buadi, Francis K; Lacy, Martha Q; Singh, Preet P; Kapoor, Prashant; Gertz, Morie A; Kumar, Shaji K

    2014-01-01

    The presence of clonal circulating plasma cells (cPCs) remains a marker of high-risk disease in newly diagnosed multiple myeloma (MM) patients. However, its prognostic utility in MM patients with previously treated disease is unknown. We studied 647 consecutive patients with previously treated MM seen at the Mayo Clinic, Rochester who had their peripheral blood evaluated for cPCs by multi-parameter flow cytometry. Of these patients, 145 had actively relapsing disease while the remaining 502 had disease that was in a plateau and included 68 patients in complete remission (CR) and 434 patients with stable disease. Patients with actively relapsing disease were more likely to have clonal cPCs than those in a plateau (P < 0.001). None of the patients in CR had any clonal cPCs detected. Among patients whose disease was in a plateau, the presence of clonal cPCs predicted for a worse median survival (22 months vs. not reached; P=0.004). Among actively relapsing patients, the presence of ≥100 cPCs predicted for a worse survival after flow cytometry analysis (12 months vs. 33 months; P<0.001). Future studies are needed to determine the role of these findings in developing a risk-adapted treatment approach in MM patients with actively relapsing disease. PMID:25113422

  11. Genomic Aberrations Drive Clonal Evolution of Neuroendocrine Tumors.

    PubMed

    Kaushik, Akash Kumar; Sreekumar, Arun

    2016-05-01

    Molecular features of castration-resistant neuroendocrine prostate cancer (CRPC-NE) are not well characterized. A recent study that investigated genomic aberrations of CRPC-NE tumors suggests their clonal evolution from CRPC adenocarcinoma. Furthermore, the existence of a distinct DNA methylation profile in CRPC-NE implicates a critical role for epigenetic modification in the development of CRPC-NE. PMID:27037211

  12. Phenotypic differences among three clonal lineages of Phytophthora ramorum

    Technology Transfer Automated Retrieval System (TEKTRAN)

    There are three major clonal lineages of Phytophthora ramorum present in North America and Europe named NA1, NA2, and EU1. Twenty-three isolates representing all three lineages were evaluated for phenotype including (i) aggressiveness on detached Rhododendron leaves and (ii) growth rate at minimum, ...

  13. Comparative organogenic responses of six clonal apple rootstock cultivars

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The organogenesis potential is different among cultivars and must be optimized for individual genotypes. Shoot organogenesis capacity from leaf explants and root organogenesis capacity of in vitro shoots in six clonal apple rootstock cultivars were compared. The shoot organogenesis capacity was hi...

  14. Flare Plasma Iron Abundance

    NASA Technical Reports Server (NTRS)

    Dennis, Brian R.; Dan, Chau; Jain, Rajmal; Schwartz, Richard A.; Tolbert, Anne K.

    2008-01-01

    The equivalent width of the iron-line complex at 6.7 keV seen in flare X-ray spectra suggests that the iron abundance of the hottest plasma at temperatures >approx.10 MK may sometimes be significantly lower than the nominal coronal abundance of four times the photospheric value that is commonly assumed. This conclusion is based on X-ray spectral observations of several flares seen in common with the Ramaty High Energy Solar Spectroscopic Imager (RHESSI) and the Solar X-ray Spectrometer (SOXS) on the second Indian geostationary satellite, GSAT-2. The implications of this will be discussed as it relates to the origin of the hot flare plasma - either plasma already in the corona that is directly heated during the flare energy release process or chromospheric plasma that is heated by flare-accelerated particles and driven up into the corona. Other possible explanations of lower-than-expected equivalent widths of the iron-line complex will also be discussed.

  15. Clonal Origin of Hepatocellular Carcinoma and Recurrence After Liver Transplantation.

    PubMed

    Wang, Zhenglu; Gong, Weihua; Shou, Dawei; Zhang, Luzhou; Gu, Xiangqian; Wang, Yuliang; Teng, Dahong; Zheng, Hong

    2016-01-01

    BACKGROUND This study aimed to determine whether patterns of tumor clonal origin in pluri-nodular hepatocellular carcinoma (PNHC) could serve as an indicator of tumor recurrence following liver transplantation. MATERIAL AND METHODS Tumor tissue samples from 60 PNHC patients who underwent liver transplantation were examined. The diagnosis of patients conformed to the University of California San Francisco (UCSF) standards for pluri-nodular hepatocellular carcinoma. We performed loss of heterozygosity tests at multiple microsatellite sites to determine the clonal origins of the tumors. Clinical information, pathological data, preoperative serum alpha-feto protein (AFP) and postoperative follow-ups were obtained and correlations between the clonal origin of the tumor, tumor-free survival, pathological characteristics, and AFP levels in serum were studied. RESULTS A total of 165 tumor nodules were collected. Tumor clonal origins were identified as intrahepatic metastasis (IM; 41.67%), multicentric occurrence (MO; 55%) or unidentified (3.33%). Three-year tumor-free survival for the IM group was 48% compared to 75.76% in the MO group (p<0.05), while the occurrence of microscopic tumor thrombus was 100% and 3.03% (p<0.05) for these groups, respectively. The degree of tumor differentiation was 80% for the IM group and 18.18% for the MO group (p<0.05), while the mean AFP concentration for these groups was 226.80 μg/L (2.78-3000 μg/L) and 24.59 μg/L (1.16-531. 30 μg/L; p<0.05), respectively. CONCLUSIONS Clonal origin patterns can serve as important indicators to predict the recurrence of PNHC following liver transplantation. Taken together with pathological characteristics and preoperative serum AFP levels, the risk of recurrence can be established in advance. PMID:27487734

  16. Clonal relatedness is a predictor of spontaneous multidrug efflux pump gene overexpression in Staphylococcus aureus.

    PubMed

    Schindler, Bryan D; Jacinto, Pauline L; Buensalido, Joseph Adrian L; Seo, Susan M; Kaatz, Glenn W

    2015-05-01

    Increased expression of genes encoding multidrug resistance efflux pumps (MDR-EPs) contributes to antimicrobial agent and biocide resistance in Staphylococcus aureus. Previously identified associations between norA overexpression and spa type t002 meticillin-resistant S. aureus (MRSA), and a similar yet weaker association between mepA overexpression and type t008 meticillin-susceptible S. aureus (MSSA), in clinical isolates are suggestive of clonal dissemination. It is also possible that related strains are prone to mutations resulting in overexpression of specific MDR-EP genes. Exposure of non-MDR-EP-overexpressing clinical isolates to biocides and dyes can select for MDR-EP-overexpressing mutants. spa types t002 and t008 isolates are predominated by multilocus sequencing typing sequence types (STs) 5 and 8, respectively. In this study, non-MDR-EP gene-overexpressing clinical isolates (MRSA and MSSA) representing ST5 and ST8 were subjected to single exposures of ethidium bromide (EtBr) to select for EtBr-resistant mutants. Measurements of active EtBr transport among mutants were used to demonstrate an efflux-proficient phenotype. Using quantitative reverse-transcription PCR, it was found that EtBr-resistant mutants of ST5 and ST8 parental strains predominantly overexpressed mepA (100%) and mdeA (83%), respectively, regardless of meticillin sensitivity. Associations between clonal lineage and MDR-EP gene overexpression differed from those previously observed and suggest the latter is due to clonal spread of efflux-proficient strains. The predilection of in vitro-selected mutants of related strains to overexpress the same MDR-EP gene indicates the presence of a consistent mutational process. PMID:25548027

  17. Long telomeres are associated with clonality in wild populations of the fissiparous starfish Coscinasterias tenuispina.

    PubMed

    Garcia-Cisneros, A; Pérez-Portela, R; Almroth, B C; Degerman, S; Palacín, C; Sköld, H Nilsson

    2015-11-01

    Telomeres usually shorten during an organism's lifespan and have thus been used as an aging and health marker. When telomeres become sufficiently short, senescence is induced. The most common method of restoring telomere length is via telomerase reverse transcriptase activity, highly expressed during embryogenesis. However, although asexual reproduction from adult tissues has an important role in the life cycles of certain species, its effect on the aging and fitness of wild populations, as well as its implications for the long-term survival of populations with limited genetic variation, is largely unknown. Here we compare relative telomere length of 58 individuals from four populations of the asexually reproducing starfish Coscinasterias tenuispina. Additionally, 12 individuals were used to compare telomere lengths in regenerating and non-regenerating arms, in two different tissues (tube feet and pyloric cecum). The level of clonality was assessed by genotyping the populations based on 12 specific microsatellite loci and relative telomere length was measured via quantitative PCR. The results revealed significantly longer telomeres in Mediterranean populations than Atlantic ones as demonstrated by the Kruskal-Wallis test (K=24.17, significant value: P-value<0.001), with the former also characterized by higher levels of clonality derived from asexual reproduction. Telomeres were furthermore significantly longer in regenerating arms than in non-regenerating arms within individuals (pyloric cecum tissue: Mann-Whitney test, V=299, P-value<10(-6); and tube feet tissue Student's t=2.28, P-value=0.029). Our study suggests that one of the mechanisms responsible for the long-term somatic maintenance and persistence of clonal populations is telomere elongation. PMID:25990879

  18. Dramatic increase in the relative abundance of large male dungeness crabs Cancer magister following closure of commercial fishing in Glacier Bay, Alaska

    USGS Publications Warehouse

    Taggart, S.J.; Shirley, T.C.; O'Clair, C. E.; Mondragon, J.

    2004-01-01

    The size structure of the population of the Dungeness crab Cancer magister was studied at six sites in or near Glacier Bay, Alaska, before and after the closure of commercial fishing. Seven years of preclosure and 4 years of postclosure data are presented. After the closure of Glacier Bay to commercial fishing, the number and size of legal-sized male Dungeness crabs increased dramatically at the experimental sites. Female and sublegal-sized male crabs, the portions of the population not directly targeted by commercial fishing, did not increase in size or abundance following the closure. There was not a large shift in the size-abundance distribution of male crabs at the control site that is still open to commercial fishing. Marine protected areas are being widely promoted as effective tools for managing fisheries while simultaneously meeting marine conservation goals and maintaining marine biodiversity. Our data demonstrate that the size of male Dungeness crabs can markedly increase in a marine reserve, which supports the concept that marine reserves could help maintain genetic diversity in Dungeness crabs and other crab species subjected to size-limit fisheries and possibly increase the fertility of females. ?? 2004 by the American Fisheries Society.

  19. Relative distribution and abundance of fishes and crayfish in 2010 and 2014 prior to saltcedar (Tamarix ssp.) removal in the Amargosa River Canyon, southeastern California

    USGS Publications Warehouse

    Hereford, Mark E.

    2016-01-01

    The Amargosa River Canyon, located in the Mojave Desert of southeastern California, contains the longest perennial reach of the Amargosa River. Because of its diverse flora and fauna, it has been designated as an Area of Critical Environmental Concern and a Wild and Scenic River by the Bureau of Land Management. A survey of fishes conducted in summer 2010 indicated that endemic Amargosa River pupfish (Cyprinodon nevadensis amargosae) and speckled dace (Rhinichthys osculus spp.) were abundant and occurred throughout the Amargosa River Canyon. The 2010 survey reported non-native red swamp crayfish (Procambarus clarkii) and western mosquitofish (Gambusia affinis) captures were significantly higher, whereas pupfish captures were lower, in areas dominated by non-native saltcedar (Tamarix ssp.). Based on the 2010 survey, it was hypothesized that the invasion of saltcedar could result in a decrease in native species. In an effort to maintain and enhance native fish populations, the Bureau of Land Management removed saltcedar from a 1,550 meter reach of stream on the Amargosa River in autumn 2014 and autumn 2015. Prior to the removal of saltcedar, a survey of fishes and crayfish using baited minnow traps was conducted in the treatment reach to serve as a baseline for future comparisons with post-saltcedar removal surveys. During the 2014 survey, 1,073 pupfish and 960 speckled dace were captured within the treatment reach. Catch per unit effort of pupfish and speckled dace in the treatment reach was less in 2014 than in 2010, although differences could be owing to seasonal variation in capture probability. Non-native mosquitofish catch per unit effort decreased from 2010 to 2014; however, the catch per unit effort of crayfish increased from 2010 to 2014. Future monitoring efforts of this reach should be conducted at the same time period to account for potential seasonal fluctuations of abundance and distribution of fishes and crayfish. A more robust study design that

  20. Eupalopsellidae and Stigmaeidae (Acari: Prostigmata) within citrus orchards in Florida: species distribution, relative and seasonal abundance within trees, associated vines, and ground cover plants.

    PubMed

    Childers, Carl C; Ueckermann, Eduard A

    2014-10-01

    Seven citrus orchards on reduced- to no-pesticide spray programs were sampled for predacious mites in the families Eupalopsellidae and Stigmaeidae (Acari: Prostigmata) in central and south central Florida. Inner and outer canopy leaves, fruit, twigs, and trunk scrapings were sampled monthly between August 1994 and January 1996. Open flowers were sampled in March from five of the sites. Two species of eupalopsellid mites (Exothorhis caudata Summers and Saniosulus harteni (van-Dis and Ueckermann)) were identified from 252 specimens collected within citrus tree canopies within the seven citrus orchards of which 249 were E. caudata. Only two E. caudata were collected from ground cover plants within five of the seven orchards. Eight species of Stigmaeidae were identified from 5,637 specimens: Agistemus floridanus Gonzalez, A. terminalis Gonzalez, Eustigmaeus arcuata (Chandhri), E. sp. near arcuata, E. segnis (Koch), Mediostigmaeus citri (Rakha and McCoy), Stigmaeus seminudus Wood, and Zetzellia languida Gonzalez were collected from within citrus tree canopies from seven orchard sites. Agistemus floridanus was the only species in either family that was abundant with 5,483 collected from within citrus tree canopies compared with only 39 from vine or ground cover plants. A total of 431 samples from one or more of 82 vines and ground cover plants were sampled monthly between September 1994 and January 1996 in five of these orchards and one or more eupalopsellids or stigmaeids were collected from 19 of these plants. Richardia brasiliensis (Meg.) Gomez had nine A. floridanus from 5 of 25 samples collected from this plant. Solanum sp. had five A. floridanus from three samples taken. Both eupalopsellid and stigmaeid species numbers represented <1 % of the total numbers of phytoseiid species taken from the same plants. The two remaining orchards were on full herbicide programs and ground cover plants were absent. Agistemus floridanus was more abundant in the citrus orchards

  1. Physiological Integration Ameliorates Negative Effects of Drought Stress in the Clonal Herb Fragaria orientalis

    PubMed Central

    Zhang, Yunchun; Zhang, Qiaoying; Sammul, Marek

    2012-01-01

    Clonal growth allows plants to spread horizontally and to establish ramets in sites of contrasting resource status. If ramets remain physiologically integrated, clones in heterogeneous environments can act as cooperative systems – effects of stress on one ramet can be ameliorated by another connected ramet inhabiting benign conditions. But little is known about the effects of patch contrast on physiological integration of clonal plants and no study has addressed its effects on physiological traits like osmolytes, reactive oxygen intermediates and antioxidant enzymes. We examined the effect of physiological integration on survival, growth and stress indicators such as osmolytes, reactive oxygen intermediates (ROIs) and antioxidant enzymes in a clonal plant, Fragaria orientalis, growing in homogenous and heterogeneous environments differing in patch contrast of water availability (1 homogeneous (no contrast) group; 2 low contrast group; 3 high contrast group). Drought stress markedly reduced the survival and growth of the severed ramets of F. orientalis, especially in high contrast treatments. Support from a ramet growing in benign patch considerably reduced drought stress and enhanced growth of ramets in dry patches. The larger the contrast between water availability, the larger the amount of support the depending ramet received from the supporting one. This support strongly affected the growth of the supporting ramet, but not to an extent to cause increase in stress indicators. We also found indication of costs related to maintenance of physiological connection between ramets. Thus, the net benefit of physiological integration depends on the environment and integration between ramets of F. orientalis could be advantageous only in heterogeneous conditions with a high contrast. PMID:22957054

  2. Clonal types of Toxoplasma gondii among immune compromised and immune competent individuals in Accra, Ghana.

    PubMed

    Ayi, Irene; Kwofie, Kofi Dadzie; Blay, Emmanuel Awusah; Osei, Joseph Harold Nyarko; Frempong, Kwadwo Kyeremeh; Koku, Roberta; Ghansah, Anita; Lartey, Margaret; Suzuki, Takashi; Boakye, Daniel Adjei; Koram, Kwadwo Ansah; Ohta, Nobuo

    2016-06-01

    There are three major clonal lineages, types I, II, and III, of Toxoplasma gondii known to cause human toxoplasmosis worldwide. Toxoplasma gondii infections have, however, not been genotyped in Ghana. This study detected the clonal types infecting immune compromised and immune competent individuals in Accra, Ghana. Blood samples were obtained from 148 HIV seropositive pre-antiretroviral therapy individuals (0≤CD4(+) T-cell count/μl blood ≤200) at the Fevers Unit and 149 HIV seronegative apparently healthy blood donors at the blood bank, all of the Korle-Bu Teaching Hospital. Genomic DNA was extracted and multilocus genotyping conducted by nested PCR-RFLP analysis using GRA6, SAG3, and BTUB gene markers. Among the HIV seropositive participants, 54.7% (81/148) were T. gondii DNA positive for any of the markers. Out of the 81, 42.0% (34) were positive for SAG3 only, 30.9% (25) for GRA6 only, 24.7% (20) for both SAG3 and GRA6, and 2.5% (2) for SAG3, GRA6, and BTUB. Overall, 93.8% of the positives were of clonal type II, 1.2% type I, while 4.9% (4) were atypical or mixed types (I and II). In the healthy blood donors, prevalence of T. gondii DNA positivity was 3.4% (5/149) by SAG3 and/or GRA6; among them, 60.0% (3/5) were type I, and the remaining 40.0%, type II. This study showed a relatively high prevalence of active T. gondii infections in immune compromised patients and low prevalence in immune competent individuals in Accra. Type II was highly prevalent. Detection of T. gondii in blood donors raises public health concerns and screening for T. gondii should be considered. PMID:26775819

  3. Clonal Diversification and Changes in Lipid Traits and Colony Morphology in Mycobacterium abscessus Clinical Isolates.

    PubMed

    Park, In Kwon; Hsu, Amy P; Tettelin, Hervé; Shallom, Shamira J; Drake, Steven K; Ding, Li; Wu, Un-In; Adamo, Nick; Prevots, D Rebecca; Olivier, Kenneth N; Holland, Steven M; Sampaio, Elizabeth P; Zelazny, Adrian M

    2015-11-01

    The smooth-to-rough colony morphology shift in Mycobacterium abscessus has been implicated in loss of glycopeptidolipid (GPL), increased pathogenicity, and clinical decline in cystic fibrosis (CF) patients. However, the evolutionary phenotypic and genetic changes remain obscure. Serial isolates from nine non-CF patients with persistent M. abscessus infection were characterized by colony morphology, lipid profile via thin-layer chromatography and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), sequencing of eight genes in the GPL locus, and expression level of fadD23, a key gene involved in the biosynthesis of complex lipids. All 50 isolates were typed as M. abscessus subspecies abscessus and were clonally related within each patient. Rough isolates, all lacking GPL, predominated at later disease stages, some showing variation within rough morphology. While most (77%) rough isolates harbored detrimental mutations in mps1 and mps2, 13% displayed previously unreported mutations in mmpL4a and mmpS4, the latter yielding a putative GPL precursor. Two isolates showed no deleterious mutations in any of the eight genes sequenced. Mixed populations harboring different GPL locus mutations were detected in 5 patients, demonstrating clonal diversification, which was likely overlooked by conventional acid-fast bacillus (AFB) culture methods. Our work highlights applications of MALDI-TOF MS beyond identification, focusing on mycobacterial lipids relevant in virulence and adaptation. Later isolates displayed accumulation of triacylglycerol and reduced expression of fadD23, sometimes preceding rough colony onset. Our results indicate that clonal diversification and a shift in lipid metabolism, including the loss of GPL, occur during chronic lung infection with M. abscessus. GPL loss alone may not account for all traits associated with rough morphology. PMID:26292297

  4. Solar abundance of osmium

    PubMed Central

    Jacoby, George; Aller, Lawrence H.

    1976-01-01

    The abundance parameter, log gfA, where g is the statistical weight of the lower level, f is the oscillator strength, and A is the abundance (by numbers of atoms with respect to hydrogen), has been derived for three lines of osmium by a method of spectrum synthesis. An apparent discordance of the derived abundance with that found from the carbonaceous chondrites is probably to be attributed primarily to errors in the f-values, and blending with unknown contributors. PMID:16592314

  5. Long-Term Efficacy and Patterns of Failure After Accelerated Partial Breast Irradiation: A Molecular Assay-Based Clonality Evaluation

    SciTech Connect

    Vicini, Frank A. . E-mail: fvicini@beaumont.edu; Antonucci, J. Vito; Wallace, Michelle R.N.; Gilbert, Samuel; Goldstein, Neal S.; Kestin, Larry; Chen, Peter; Kunzman, Jonathan; Boike, Thomas; Benitez, Pamela; Martinez, Alvaro

    2007-06-01

    Purpose: To determine the long-term efficacy and cosmetic results of accelerated partial breast irradiation (APBI) by reviewing our institution's experience. Methods and Materials: A total of 199 patients with early-stage breast cancer were treated prospectively with adjuvant APBI after lumpectomy using interstitial brachytherapy. All patients had negative margins, 82% had Stage I disease, median tumor size was 1.1 cm, and 12% had positive lymph nodes. The median follow-up for surviving patients was 8.6 years. Fifty-three patients (27%) have been followed for {>=}10 years. Results: Six ipsilateral breast tumor recurrences (IBTRs) were observed, for a 5-year and 10-year actuarial rate of 1.6% and 3.8%, respectively. A total of three regional nodal failures were observed, for a 10-year actuarial rate of 1.6%. Five contralateral breast cancers developed, for a 5- and 10-year actuarial rate of 2.2% and 5.2%, respectively. The type of IBTR (clonally related vs. clonally distinct) was analyzed using a polymerase chain reaction-based loss of heterozygosity assay. Eighty-three percent of IBTRs (n = 5) were classified as clonally related. Multiple clinical, pathologic, and treatment-related factors were analyzed for an association with the development of an IBTR, regional nodal failure, or contralateral breast cancer. On multivariate analysis, no variable was associated with any of these events. Cosmetic results were rated as excellent/good in 99% of patients. Conclusions: Long-term results with APBI using interstitial brachytherapy continue to demonstrate excellent long-term local and regional control rates and cosmetic results. According to a polymerase chain reaction-based loss of heterozygosity assay, 83% of recurrences were classified as clonally related.

  6. Rapid Emergence and Clonal Dissemination of CTX-M-15-Producing Salmonella enterica Serotype Virchow, South Korea.

    PubMed

    Kim, Jin Seok; Yun, Young-Sun; Kim, Soo Jin; Jeon, Se-Eun; Lee, Deog-yong; Chung, Gyung Tae; Yoo, Cheon-Kwon; Kim, Junyoung

    2016-01-01

    The prevalence of cefotaxime-resistant Salmonella enterica serotype Virchow has dramatically increased in South Korea since the first isolation in 2011. Of 68 isolates collected over 10 years, 28 cefotaxime-resistant isolates harbored the bla(CTX-M-15) extended-spectrum β-lactamase gene and were closely related genetically, demonstrating the clonal dissemination of CTX-M-15-producing Salmonella Virchow in South Korea. PMID:26674083

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

    NASA Astrophysics Data System (ADS)

    Zhang, Y.

    2015-12-01

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

  8. Thysanoptera (Thrips) Within Citrus Orchards in Florida: Species Distribution, Relative and Seasonal Abundance Within Trees, and Species on Vines and Ground Cover Plants

    PubMed Central

    Childers, Carl C.; Nakahara, Sueo

    2006-01-01

    crops in Florida. The five most abundant thrips species collected within citrus tree canopies were: A. fasciapennis, F. bispinosa, C. orchidii, K. flavipes, and D. trifasciatus. In comparison, the following five thrips species were most abundant on vines or ground cover plants: F. bispinosa, H. gowdeyi, F. cephalica, M. abdominalis, and F. gossypiana. Fifty-eight species of vines or ground cover plants in 26 families were infested with one or more of 27 species of thrips. PMID:20233100

  9. [Phenomenon of the evolution of clonal chromosomal abnormalities in childhood acute myeloid leukemia].

    PubMed

    Andreeva, S V; Drozdova, V D; Kavardakova, N V

    2010-01-01

    Analysis of chromosomal abnormalities in bone marrow cells in 116 children with diagnosis of acute myeloid leukemia (AML) was performed. Frequency of evolution of clonal chromosome abnormalities in AML constituted 42,3%. The most abundant among them were numerical abnormalities of chromosomes 8, 9, and 21 as well as secondary structural abnormalities in region 12p12, 9p22, 9q22, 9q34, 11q14-23, and 16q22. Numerical abnormalities were registered in 26,7% cases. The basic mechanism of leukemic clone evolution was trisomy, deletion and monosomy. The frequency of evolution was 7 times higher in the age group up to 2 years and twice higher in the age group up to 5 years. The high frequency of evolution was established at t(15;17)(q22;q22) and the absence at inv(16)(p13q22). The patients with clonal evolution died earlier, before reaching remission, that can be connected with heavy initial state and high frequency of relapse. Conception of abnormality clone evolution was proposed at some stages: I--appearance of balanced rearrangement; II--trisomy; III--lose of chromosomal material. Appearance of unbalanced genome in evolution possess an advantage in proliferate activity and can be connected with the answer on chemotherapy. Identity of abnormal chromosome structure at diagnosis and relapse of disease can be an evidence of the influence of chemical agent on establishment of some types of evolution of chromosome abnormalities in leukemic cells in AML in children. PMID:20608159

  10. Common clonal origin of central and resident memory T cells following skin immunization

    PubMed Central

    Gaide, Olivier; Emerson, Ryan O.; Jiang, Xiaodong; Gulati, Nicholas; Nizza, Suzanne; Desmarais, Cindy; Robins, Harlan; Krueger, James G.; Clark, Rachael A.; Kupper, Thomas S.

    2015-01-01

    Central memory T (TCM) cells in lymph nodes (LN) and resident memory T (TRM) cells in peripheral tissues play distinct roles in protective immunity1-5. Both are generated after primary infections, but the clonal origin of TRM and TCM cells is unclear. To address this question, mice were immunized through the skin with either a protein antigen, a chemical hapten, or a non-replicating poxvirus. We then analyzed antigen activated T cells from different tissues using high-throughput sequencing (HTS) of the gene (Tcrbv) encoding T cell receptor gene β chain CDR3 region to simultaneously track thousands of unique T cells6. For every abundant TRM clone generated in the skin, an abundant TCM clone bearing the identical TCR was present in lymph nodes (LN). Thus antigen reactive skin TRM and LN TCM clones were derived from a common naive T cell precursor after skin immunization, generating overlapping TCR repertoires. Although they bore the same TCR, TRM mediated rapid contact hypersensitivity (CHS)7 responses in mice, whereas TCM mediated delayed and attenuated responses. Studies in human subjects confirmed the generation of skin TRM in allergic contact dermatitis. Thus, immunization through skin simultaneously generates skin TRM and LN TCM in similar numbers from the same naïve T cells. PMID:25962122

  11. Lithium Abundance in Planet Search Stars

    NASA Astrophysics Data System (ADS)

    Myles, Justin; Yale Exoplanets

    2016-01-01

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

  12. Coronal abundances and their variation

    NASA Technical Reports Server (NTRS)

    Saba, Julia L. R.

    1995-01-01

    This contract supports the investigation of elemental abundances in the solar corona, principally through analysis of high-resolution soft X-ray spectra from the Flat Crystal Spectrometer on the Solar Maximum Mission. The goals of the study are a characterization of the mean values of relative abundances of elements accessible in the FCS data, and information on the extent and circumstances of their variability. This report is a summation of the data analysis and reporting activities which occurred during the period of 15 April 1994 to 15 April 1995.

  13. Chemical Abundances of Symbiotic Giants

    NASA Astrophysics Data System (ADS)

    Gałan, C.; Mikołajewska, J.; Hinkle, K. H.; Joyce, R. R.

    2015-12-01

    High resolution (R ˜ 50000), near-IR spectra were used to measure photospheric abundances of CNO and elements around the iron peak for 24 symbiotic giants. Spectrum synthesis was employed using local thermal equilibrium and hydrostatic model atmospheres. The metallicities are distributed in a wide range with maximum around [Fe/H] ˜-0.4 - - 0.3 dex. Enrichment in 14N indicates that all the sample giants have experienced the first dredge-up. The relative abundance of [Ti/Fe] is generally large in red symbiotic systems.

  14. Coronal Abundances and Their Variation

    NASA Technical Reports Server (NTRS)

    Saba, Julia L. R.

    1996-01-01

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

  15. Improved Clonal Selection Algorithm Combined with Ant Colony Optimization

    NASA Astrophysics Data System (ADS)

    Gao, Shangce; Wang, Wei; Dai, Hongwei; Li, Fangjia; Tang, Zheng

    Both the clonal selection algorithm (CSA) and the ant colony optimization (ACO) are inspired by natural phenomena and are effective tools for solving complex problems. CSA can exploit and explore the solution space parallely and effectively. However, it can not use enough environment feedback information and thus has to do a large redundancy repeat during search. On the other hand, ACO is based on the concept of indirect cooperative foraging process via secreting pheromones. Its positive feedback ability is nice but its convergence speed is slow because of the little initial pheromones. In this paper, we propose a pheromone-linker to combine these two algorithms. The proposed hybrid clonal selection and ant colony optimization (CSA-ACO) reasonably utilizes the superiorities of both algorithms and also overcomes their inherent disadvantages. Simulation results based on the traveling salesman problems have demonstrated the merit of the proposed algorithm over some traditional techniques.

  16. Clonal forestry, heterosis and advanced-generation breeding

    SciTech Connect

    Tuskan, G.A.

    1997-08-01

    This report discusses the clonal planting stock offers many advantages to the forest products industry. Advanced-generation breeding strategies should be designed to maximize within-family variance and at the same time allow the capture of heterosis. Certainly there may be a conflict in the choice of breeding strategy based on the trait of interest. It may be that the majority of the traits express heterosis due to overdominance. Alternatively, disease resistance is expressed as the lack of a specific metabolite or infection court then the homozygous recessive genotype may be the most desirable. Nonetheless, as the forest products industry begins to utilize the economic advantages of clonal forestry, breeding strategies will have to be optimized for these commercial plant materials. Here, molecular markers can be used to characterize the nature of heterosis and therefore define the appropriate breeding strategy.

  17. Mechanisms of clonal evolution in childhood acute lymphoblastic leukemia

    PubMed Central

    Park, Eugene; Papaemmanuil, Elli; Ford, Anthony; Kweon, Soo-Mi; Trageser, Daniel; Hasselfeld, Brian; Henke, Nadine; Mooster, Jana; Geng, Huimin; Schwarz, Klaus; Kogan, Scott C.; Casellas, Rafael; Schatz, David G.; Lieber, Michael R; Greaves, Mel F.; Müschen, Markus

    2015-01-01

    Childhood acute lymphoblastic leukemia can often be retraced to a pre-leukemic clone carrying a prenatal genetic lesion. Postnatally acquired mutations then drive clonal evolution towards overt leukemia. RAG1-RAG2 and AID enzymes, the diversifiers of immunoglobulin genes, are strictly segregated to early and late stages of B-lymphopoiesis, respectively. Here, we identified small pre-BII cells as a natural subset of increased genetic vulnerability owing to concurrent activation of these enzymes. Consistent with epidemiological findings on childhood ALL etiology, susceptibility to genetic lesions during B-lymphopoiesis at the large to small pre-BII transition is exacerbated by abnormal cytokine signaling and repetitive inflammatory stimuli. We demonstrate that AID and RAG1-RAG2 drive leukemic clonal evolution with repeated exposure to inflammatory stimuli, paralleling chronic infections in childhood. PMID:25985233

  18. Distinguishing clonal apple rootstocks by isozymes banding patterns.

    PubMed

    Kaushal, K; Modgil, M; Sharma, D R

    2001-11-01

    Molecular characterisation of clonal apple rootstocks using isozymes was carried out to identify isozyme polymorphism in seven clonal apple rootstocks and to identify the most characteristic and stable enzyme markers for each individual rootstock. Five enzyme systems were studied out of which polyphenol oxidase, malate dehydrogenase, acid phosphatase and peroxidase were useful in discriminating among the rootstocks. The peroxidase enzyme system showed maximum variation and esterase showed the least variation among the rootstocks. Out of seven rootstocks, three were distinguished on the basis of one enzyme system only (M.3 with MDH or PER, M.7 with PPO or PER and MM. 111 with MDH). Out of the sixteen loci studied seven were found to be polymorphic. Genetic variation among the rootstocks was explained on the basis of various parameters. The percentage of polymorphic loci varied from 13.33 to 35.71 per cent. PMID:11906109

  19. Clonal analysis of limbal epithelial stem cell populations.

    PubMed

    Schlötzer-Schrehardt, Ursula

    2013-01-01

    While convincing data clearly suggest the presence of stem cells in the basal limbal epithelium in vivo, testing the proliferation, self-renewal, and differentiation capacity of stem cells relies on the development of methodologies that allow for their isolation and extensive propagation in vitro. Clonal analysis involving differentiation between short-lived transient cell clones and long-lived stem cell clones is an invaluable technique to identify stem cells in vitro, and allows cells to be expanded over multiple passages. This chapter describes a protocol for the isolation, expansion, and clonal analysis of limbal epithelial stem cells. The cultivation method described may be essential for long-term restoration of the damaged ocular surface in patients with limbal stem cell deficiency. PMID:23690004

  20. Clonal development and organization of the adult Drosophila central brain

    PubMed Central

    Yu, Hung-Hsiang; Awasaki, Takeshi; Schroeder, Mark David; Long, Fuhui; Yang, Jacob S.; He, Yisheng; Ding, Peng; Kao, Jui-Chun; Wu, Gloria Yueh-Yi; Peng, Hanchuan; Myers, Gene; Lee, Tzumin

    2013-01-01

    Summary Background The insect brain can be divided into neuropils that are formed by neurites of both local and remote origin. The complexity of the interconnections obscures how these neuropils are established and interconnected through development. The Drosophila central brain develops from a fixed number of neuroblasts (NBs) that deposit neurons in regional clusters. Results By determining individual NB clones and pursuing their projections into specific neuropils we unravel the regional development of the brain neural network. Exhaustive clonal analysis revealed 95 stereotyped neuronal lineages with characteristic cell body locations and neurite trajectories. Most clones show complex projection patterns, but despite the complexity, neighboring clones often co-innervate the same local neuropil(s) and further target a restricted set of distant neuropils. Conclusions These observations argue for regional clonal development of both neuropils and neuropil connectivity throughout the Drosophila central brain. PMID:23541733

  1. Defining the clonal dynamics leading to mouse skin tumour initiation.

    PubMed

    Sánchez-Danés, Adriana; Hannezo, Edouard; Larsimont, Jean-Christophe; Liagre, Mélanie; Youssef, Khalil Kass; Simons, Benjamin D; Blanpain, Cédric

    2016-08-18

    The changes in cell dynamics after oncogenic mutation that lead to the development of tumours are currently unknown. Here, using skin epidermis as a model, we assessed the effect of oncogenic hedgehog signalling in distinct cell populations and their capacity to induce basal cell carcinoma, the most frequent cancer in humans. We found that only stem cells, and not progenitors, initiated tumour formation upon oncogenic hedgehog signalling. This difference was due to the hierarchical organization of tumour growth in oncogene-targeted stem cells, characterized by an increase in symmetric self-renewing divisions and a higher p53-dependent resistance to apoptosis, leading to rapid clonal expansion and progression into invasive tumours. Our work reveals that the capacity of oncogene-targeted cells to induce tumour formation is dependent not only on their long-term survival and expansion, but also on the specific clonal dynamics of the cancer cell of origin. PMID:27459053

  2. Local genetic structure in a clonal dioecious angiosperm.

    PubMed

    Ruggiero, M V; Reusch, T B H; Procaccini, G

    2005-04-01

    We used seven microsatellite loci to characterize genetic structure and clonal architecture at three different spatial scales (from meters to centimetres) of a Cymodocea nodosa population. C. nodosa exhibits both sexual reproduction and vegetative propagation by rhizome elongation. Seeds remain buried in the sediment nearby the mother plant in a dormant stage until germination. Seed dispersal potential is therefore expected to be extremely restricted. High clonal diversity (up to 67% of distinct genotypes) and a highly intermingled configuration of genets at different spatial scales were found. No significant differences in genetic structure were found among the three spatial scales, indicating that genetic diversity is evenly distributed along the meadow. Autocorrelation analyses of kinship estimates confirmed the absence of spatial clumping of genets at small spatial scale and the expectations of a very restricted seed dispersal (observed dispersal range 1-21 m) in this species. PMID:15773928

  3. Locally Confined Clonal Complexes of Mycobacterium ulcerans in Two Buruli Ulcer Endemic Regions of Cameroon

    PubMed Central

    Kerber, Sarah; Minyem, Jacques C.; Um Boock, Alphonse; Vogel, Moritz; Bayi, Pierre Franklin; Junghanss, Thomas; Brites, Daniela; Harris, Simon R.; Parkhill, Julian; Pluschke, Gerd; Lamelas Cabello, Araceli

    2015-01-01

    Background Mycobacterium ulcerans is the causative agent of the necrotizing skin disease Buruli ulcer (BU), which has been reported from over 30 countries worldwide. The majority of notified patients come from West African countries, such as Côte d’Ivoire, Ghana, Benin and Cameroon. All clinical isolates of M. ulcerans from these countries are closely related and their genomes differ only in a limited number of single nucleotide polymorphisms (SNPs). Methodology/Principal Findings We performed a molecular epidemiological study with clinical isolates from patients from two distinct BU endemic regions of Cameroon, the Nyong and the Mapé river basins. Whole genome sequencing of the M. ulcerans strains from these two BU endemic areas revealed the presence of two phylogenetically distinct clonal complexes. The strains from the Nyong river basin were genetically more diverse and less closely related to the M. ulcerans strain circulating in Ghana and Benin than the strains causing BU in the Mapé river basin. Conclusions Our comparative genomic analysis revealed that M. ulcerans clones diversify locally by the accumulation of SNPs. Case isolates coming from more recently emerging BU endemic areas, such as the Mapé river basin, may be less diverse than populations from longer standing disease foci, such as the Nyong river basin. Exchange of strains between distinct endemic areas seems to be rare and local clonal complexes can be easily distinguished by whole genome sequencing. PMID:26046531

  4. Clonal evolution of B cells in transformation from low- to high-grade lymphoma

    PubMed Central

    Matolcsy, András; Schattner, Elaine J.; Knowles, Daniel M.; Casali, Paolo

    2015-01-01

    An outcome of low-grade B cell non-Hodgkins's lymphomas is the transformation to high-grade diffuse large B cell lymphomas (DLBL). To investigate the mechanisms of clonal evolution in the transformation to DLBL, we performed longitudinal molecular analyses of immunoglobulin (Ig), VHDJH gene sequences expressed in cases of chronic lymphocytic leukemia (CLL), small lymphocytic lymphoma (SLL), and follicular lymphoma (FL) that transformed to DLBL. Among the neoplastic CLL and SLL cells and their respective high-grade transformants, there was no evidence for a clonotypic shift or acquired mutations in the expressed Ig VHDJH gene segments, as further confirmed by a specific and sensitive PCR-single strand polymorphism analysis. In contrast, among the FL cells there was a high degree of intraclonal diversification with highly divergent VHDJH gene sequences. Despite this intraclonal heterogeneity, the related DLBL expressed a collinear but unique VHDJH gene sequence. The intraclonal genealogical tree for the FL case demonstrated that the DLBL emerged in association with unique VHDJH gene mutational events. Among the intraclonal FL and related DLBL transformants, the nature and distribution of the Ig VHDJH gene mutations were consistent with antigenic selection. Thus, clonal evolution in the transformation from low- to high-grade B cell lymphoma may involve distinct pathways which vary according to the cellular origin and the type of the progenitor B cell tumor. PMID:10229093

  5. Massively Parallel Sequencing-Based Clonality Analysis of Synchronous Endometrioid Endometrial and Ovarian Carcinomas.

    PubMed

    Schultheis, Anne M; Ng, Charlotte K Y; De Filippo, Maria R; Piscuoglio, Salvatore; Macedo, Gabriel S; Gatius, Sonia; Perez Mies, Belen; Soslow, Robert A; Lim, Raymond S; Viale, Agnes; Huberman, Kety H; Palacios, Jose C; Reis-Filho, Jorge S; Matias-Guiu, Xavier; Weigelt, Britta

    2016-06-01

    Synchronous early-stage endometrioid endometrial carcinomas (EECs) and endometrioid ovarian carcinomas (EOCs) are associated with a favorable prognosis and have been suggested to represent independent primary tumors rather than metastatic disease. We subjected sporadic synchronous EECs/EOCs from five patients to whole-exome massively parallel sequencing, which revealed that the EEC and EOC of each case displayed strikingly similar repertoires of somatic mutations and gene copy number alterations. Despite the presence of mutations restricted to the EEC or EOC in each case, we observed that the mutational processes that shaped their respective genomes were consistent. High-depth targeted massively parallel sequencing of sporadic synchronous EECs/EOCs from 17 additional patients confirmed that these lesions are clonally related. In an additional Lynch Syndrome case, however, the EEC and EOC were found to constitute independent cancers lacking somatic mutations in common. Taken together, sporadic synchronous EECs/EOCs are clonally related and likely constitute dissemination from one site to the other. PMID:26832770

  6. Seasonal abundance of soil-surface arthropods in relation to some meteorological and edaphic variables of the grassland and tree-planted areas in a tropical semi-arid savanna

    NASA Astrophysics Data System (ADS)

    Vikram Reddy, M.; Venkataiah, B.

    1990-03-01

    Seasonality of relative population abundance in different groups of soil-surface arthropods was investigated monthly by pit-fall traps during a 2-year period in the grassland and tree-planted areas of a tropical semi-arid savanna at Warangal (south India). Densities of most groups were lowest during summer and highest during the rainy season. They were less abundant during winter. Arthropods were recorded in higher numbers in tree-planted compared to grassland areas. Certain arthropods that were found only during part of the year were recorded for a longer period in the tree-planted area. Formicidae, Monomorium indicum Forel, Crematogaster sp. and Pachycondyla? tesserinoda (Emery), and Coleoptera, Pachycera sp. reached maximum densities in the rainy season and minimum numbers during winter and summer in the grassland area. However, these species had lower densities during the rainy season and reached maximum densities during winter and summer in the tree-planted area. The seasonal abundance of arthropods showed significant linear correlations with different abiotic environmental variables such as rainfall, soil moisture, organic matter, soil and air temperatures, soil pH, relative humidity at the soil surface, and potassium and phosphorus of surface soil. Soil moisture and rainfall were generally the strongest correlates with densities, particularly in the grassland area.

  7. Molecular Markers Reveal Exclusively Clonal Reproduction in Trichophyton rubrum

    PubMed Central

    Gräser, Y.; Kühnisch, J.; Presber, W.

    1999-01-01

    Genotypic variability among 96 Trichophyton rubrum strains which displayed different colony morphologies and were collected from four continents was investigated. Twelve markers representing 57 loci were analyzed by PCR fingerprinting, amplified fragment length polymorphism, and random amplified monomorphic DNA markers. Interestingly, none of the methods used revealed any DNA polymorphism, indicating a strictly clonal mode of reproduction and a strong adaptation to human skin. PMID:10523582

  8. 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 (