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Sample records for nonrodent test species

  1. The Use of Minipig in Drug Discovery and Development: Pros and Cons of Minipig Selection and Strategies to Use as a Preferred Nonrodent Species.

    Science.gov (United States)

    Heining, Peter; Ruysschaert, Tristan

    2016-04-01

    The pig was introduced more than 20 years ago in drug development following attempts of finding a species that shares better homology with human than the dog, based on biophysiological parameters. However, miniaturization, standardized breeding, and health status control were required before the pig could find a broader than niche application in pharmaceutical industry. During the years of experience with minipigs in pharmaceutical research and the science evolving rapidly, the selection of a nonrodent animal species for preclinical safety testing became primarily driven by pharmacological (target expression homologous function), pharmacokinetic, and biophysiological considerations. This offered a broad field of application for the minipig, besides the well-established use in dermal projects in all areas of drug development but also in novel approaches including genetically modified animals. In this article, we look at recent approaches and requirements in the optimal selection of a nonrodent model in pharmaceutical development and critically ask how good a choice the minipig offers for the scientist, how did the testing environment evolve, and what are the key requirements for a broader use of the minipig compared to the other well-established nonrodent species like dog or monkey. © The Author(s) 2015.

  2. Animal models of toxicology testing: the role of pigs.

    Science.gov (United States)

    Helke, Kristi L; Swindle, Marvin Michael

    2013-02-01

    In regulatory toxicological testing, both a rodent and non-rodent species are required. Historically, dogs and non-human primates (NHP) have been the species of choice of the non-rodent portion of testing. The pig is an appropriate option for these tests based on metabolic pathways utilized in xenobiotic biotransformation. This review focuses on the Phase I and Phase II biotransformation pathways in humans and pigs and highlights the similarities and differences of these models. This is a growing field and references are sparse. Numerous breeds of pigs are discussed along with specific breed differences in these enzymes that are known. While much available data are presented, it is grossly incomplete and sometimes contradictory based on methods used. There is no ideal species to use in toxicology. The use of dogs and NHP in xenobiotic testing continues to be the norm. Pigs present a viable and perhaps more reliable model of non-rodent testing.

  3. Modelling hemoglobin and hemoglobin:haptoglobin complex clearance in a non-rodent species– pharmacokinetic and therapeutic implications

    Directory of Open Access Journals (Sweden)

    Felicitas S Boretti

    2014-10-01

    Full Text Available Preclinical studies suggest that haptoglobin (Hp supplementation could be an effective therapeutic modality during acute or chronic hemolytic diseases. Hp prevents Hb extravasation and neutralizes Hb’s oxidative and NO scavenging activity in the vasculature. Small animal models such as mouse, rat and guinea pig appear to be valuable to provide proof-of-concept for Hb neutralization by Hp in diverse pre-clinical conditions. However, these species differ significantly from human in the clearance of Hb:Hp complexes, which leads to long persistence of circulating Hb:Hp complexes after administration of human plasma derived Hp. Alternative animal models must therefore be explored to guide pre-clinical development of these potential therapeutics. In contrast to rodents, dogs have high Hp plasma concentrations comparable to human. In this study we show that like human macrophages, dog peripheral blood monocyte derived macrophages express a glucocorticoid inducible endocytic clearance pathways with a high specificity for the Hb:Hp complex. Evaluating the Beagle dog as a non-rodent model species we provide the first pharmacokinetic parameter estimates of free Hb and Hb:Hp phenotype complexes. The data reflect a drastically reduced volume of distribution (Vc of the complex compared to free Hb, increased exposures (Cmax and AUC and significantly reduced total body clearance (CL with a terminal half-life (t1/2 of approximately 12 hours. Distribution and clearance was identical for dog and human Hb (± glucocorticoid stimulation and for dimeric and multimeric Hp preparations bound to Hb. Collectively, our study supports the dog as a non-rodent animal model to study pharmacological and pharmacokinetic aspects of Hb clearance systems and apply the model to studying Hp therapeutics.

  4. CRC DEPLETION CALCULATIONS FOR THE NON-RODDED ASSEMBLIES IN BATCHES 8 AND 9 CRYSTAL RIVER UNIT 3

    International Nuclear Information System (INIS)

    Wilson, Michael L.

    2001-01-01

    The purpose of this design analysis is to document the SAS2H depletion calculations of certain non-rodded fuel assemblies from batches 8 and 9 of the Crystal River Unit 3 pressurized water reactor (PWR) that are required for Commercial Reactor Critical (CRC) evaluations to support the development of the disposal criticality methodology. A non-rodded assembly is one which never contains a control rod assembly (CRA) or an axial power shaping rod assembly (APSRA) during its irradiation history. The objective of this analysis is to provide SAS2H generated isotopic compositions for each fuel assembly's depleted fuel and depleted burnable poison materials. These SAS2H generated isotopic compositions are acceptable for use in CRC benchmark reactivity calculations containing the various fuel assemblies

  5. CRC DEPLETION CALCULATIONS FOR THE NON-RODDED ASSEMBLIES IN BATCHES 4 AND 5 OF CRYSTAL RIVER UNIT 3

    International Nuclear Information System (INIS)

    Wright, Kenneth D.

    1997-01-01

    The purpose of this design analysis is to document the SAS2H depletion calculations of certain non-rodded fuel assemblies from batches 4 and 5 of the Crystal River Unit 3 pressurized water reactor (PWR) that are required for commercial Reactor Critical (CRC) evaluations to support the development of the disposal criticality methodology. A non-rodded assembly is one which never contains a control rod assembly (CRA) or an axial power shaping rod assembly (APSRA) during its irradiation history. The objective of this analysis is to provide SAS2H generated isotopic compositions for each fuel assembly's depleted fuel and depleted burnable poison materials. These SAS2H generated isotopic compositions are acceptable for use in CRC benchmark reactivity calculations containing the various fuel assemblies

  6. CRC DEPLETION CALCULATIONS FOR THE NON-RODDED ASSEMBLIES IN BATCHES 4 AND 5 OF CRYSTAL RIVER UNIT 3

    Energy Technology Data Exchange (ETDEWEB)

    Kenneth D. Wright

    1997-07-30

    The purpose of this design analysis is to document the SAS2H depletion calculations of certain non-rodded fuel assemblies from batches 4 and 5 of the Crystal River Unit 3 pressurized water reactor (PWR) that are required for commercial Reactor Critical (CRC) evaluations to support the development of the disposal criticality methodology. A non-rodded assembly is one which never contains a control rod assembly (CRA) or an axial power shaping rod assembly (APSRA) during its irradiation history. The objective of this analysis is to provide SAS2H generated isotopic compositions for each fuel assembly's depleted fuel and depleted burnable poison materials. These SAS2H generated isotopic compositions are acceptable for use in CRC benchmark reactivity calculations containing the various fuel assemblies.

  7. CRC DEPLETION CALCULATIONS FOR THE NON-RODDED ASSEMBLIES IN BATCHES 1, 2, AND 3 OF CRYSTAL RIVER UNIT 3

    International Nuclear Information System (INIS)

    Wright, Kenneth D.

    1997-01-01

    The purpose of this design analysis is to document the SAS2H depletion calculations of certain non-rodded fuel assemblies from batches 1, 2, and 3 of the Crystal River Unit 3 pressurized water reactor (PWR) that are required for Commercial Reactor Critical (CRC) evaluations to support development of the disposal criticality methodology. A non-rodded assembly is one which never contains a control rod assembly (CRA) or an axial power shaping rod assembly (APSRA) during its irradiation history. The objective of this analysis is to provide SAS2H generated isotopic compositions for each fuel assembly's depleted fuel and depleted burnable poison materials. These SAS2H generated isotopic compositions are acceptable for use in CRC benchmark reactivity calculations containing the various fuel assemblies

  8. Comparison of rat and rabbit embryo-fetal developmental toxicity data for 379 pharmaceuticals: on the nature and severity of developmental effects (Critical Reviews in Toxicology)

    Science.gov (United States)

    Regulatory non-clinical safety testing of human pharmaceutical compounds typically requires embryo fetal developmental toxicity (EFDT) testing in two species, (one rodent and one non-rodent, usually the rat and the rabbit). The question has been raised whether under some conditio...

  9. Teratology studies in the rabbit.

    Science.gov (United States)

    Allais, Linda; Reynaud, Lucie

    2013-01-01

    The rabbit is generally the non-rodent species or second species after the rat recommended by the regulatory authorities and is part of the package of regulatory reproductive studies for the detection of potential embryotoxic and/or teratogenic effects of pharmaceuticals, chemicals, food additives, and other compounds, including vaccines (see Chapters 1-7).Its availability, practicality in housing and in mating as well as its large size makes the rabbit the preferred choice as a non-rodent species. The study protocols are essentially similar to those established for the rat (Chapter 9), with some particularities. The study designs are well defined in guidelines and are relatively standardized between testing laboratories across the world.As for the rat, large litter sizes and extensive background data in the rabbit are valuable criteria for an optimal assessment of in utero development of the embryo or fetus and for the detection of potential external or internal fetal malformations.

  10. Social housing of non-rodents during cardiovascular recordings in safety pharmacology and toxicology studies.

    Science.gov (United States)

    Prior, Helen; Bottomley, Anna; Champéroux, Pascal; Cordes, Jason; Delpy, Eric; Dybdal, Noel; Edmunds, Nick; Engwall, Mike; Foley, Mike; Hoffmann, Michael; Kaiser, Robert; Meecham, Ken; Milano, Stéphane; Milne, Aileen; Nelson, Rick; Roche, Brian; Valentin, Jean-Pierre; Ward, Gemma; Chapman, Kathryn

    2016-01-01

    The Safety Pharmacology Society (SPS) and National Centre for the Replacement, Refinement & Reduction of Animals in Research (NC3Rs) conducted a survey and workshop in 2015 to define current industry practices relating to housing of non-rodents during telemetry recordings in safety pharmacology and toxicology studies. The aim was to share experiences, canvas opinion on the study procedures/designs that could be used and explore the barriers to social housing. Thirty-nine sites, either running studies (Sponsors or Contract Research Organisations, CROs) and/or outsourcing work responded to the survey (51% from Europe; 41% from USA). During safety pharmacology studies, 84, 67 and 100% of respondents socially house dogs, minipigs and non-human primates (NHPs) respectively on non-recording days. However, on recording days 20, 20 and 33% of respondents socially house the animals, respectively. The main barriers for social housing were limitations in the recording equipment used, study design and animal temperament/activity. During toxicology studies, 94, 100 and 100% of respondents socially house dogs, minipigs and NHPs respectively on non-recording days. However, on recording days 31, 25 and 50% of respondents socially house the animals, respectively. The main barriers for social housing were risk of damage to and limitations in the recording equipment used, food consumption recording and temperament/activity of the animals. Although the majority of the industry does not yet socially house animals during telemetry recordings in safety pharmacology and toxicology studies, there is support to implement this refinement. Continued discussions, sharing of best practice and data from companies already socially housing, combined with technology improvements and investments in infrastructure are required to maintain the forward momentum of this refinement across the industry. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  11. Pigs in Toxicology: Breed Differences in Metabolism and Background Findings.

    Science.gov (United States)

    Helke, Kristi L; Nelson, Keith N; Sargeant, Aaron M; Jacob, Binod; McKeag, Sean; Haruna, Julius; Vemireddi, Vimala; Greeley, Melanie; Brocksmith, Derek; Navratil, Nicole; Stricker-Krongrad, Alain; Hollinger, Charlotte

    2016-06-01

    Both a rodent and a nonrodent species are required for evaluation in nonclinical safety studies conducted to support human clinical trials. Historically, dogs and nonhuman primates have been the nonrodent species of choice. Swine, especially the miniature swine or minipigs, are increasingly being used in preclinical safety as an alternate nonrodent species. The pig is an appropriate option for these toxicology studies based on metabolic pathways utilized in xenobiotic biotransformation. Both similarities and differences exist in phase I and phase II biotransformation pathways between humans and pigs. There are numerous breeds of pigs, yet only a few of these breeds are characterized with regard to both xenobiotic-metabolizing enzymes and background pathology findings. Some specific differences in these enzymes based on breed and sex are known. Although swine have been used extensively in biomedical research, there is also a paucity of information in the current literature detailing the incidence of background lesions and differences between commonly used breeds. Here, the xenobiotic-metabolizing enzymes are compared between humans and pigs, and minipig background pathology changes are reviewed with emphasis on breed differences. © The Author(s) 2016.

  12. Teratology studies in the minipig.

    Science.gov (United States)

    McAnulty, Peter A

    2013-01-01

    The minipig is a suitable species for regulatory teratology testing and may be regarded as an alternative to the rabbit, dog, and primate. The first successful regulatory teratology studies in the minipig were performed in the 1990s. It became clear that minipigs have several benefits over the other non-rodents, as they are purpose-bred for laboratory use, they are sexually mature at approximately 5 months of age, and they produce multiple offspring. The minipig has subsequently gained regulatory acceptance in the teratology testing of new drugs.

  13. Current nonclinical testing paradigm enables safe entry to First-In-Human clinical trials: The IQ consortium nonclinical to clinical translational database.

    Science.gov (United States)

    Monticello, Thomas M; Jones, Thomas W; Dambach, Donna M; Potter, David M; Bolt, Michael W; Liu, Maggie; Keller, Douglas A; Hart, Timothy K; Kadambi, Vivek J

    2017-11-01

    The contribution of animal testing in drug development has been widely debated and challenged. An industry-wide nonclinical to clinical translational database was created to determine how safety assessments in animal models translate to First-In-Human clinical risk. The blinded database was composed of 182 molecules and contained animal toxicology data coupled with clinical observations from phase I human studies. Animal and clinical data were categorized by organ system and correlations determined. The 2×2 contingency table (true positive, false positive, true negative, false negative) was used for statistical analysis. Sensitivity was 48% with a 43% positive predictive value (PPV). The nonhuman primate had the strongest performance in predicting adverse effects, especially for gastrointestinal and nervous system categories. When the same target organ was identified in both the rodent and nonrodent, the PPV increased. Specificity was 84% with an 86% negative predictive value (NPV). The beagle dog had the strongest performance in predicting an absence of clinical adverse effects. If no target organ toxicity was observed in either test species, the NPV increased. While nonclinical studies can demonstrate great value in the PPV for certain species and organ categories, the NPV was the stronger predictive performance measure across test species and target organs indicating that an absence of toxicity in animal studies strongly predicts a similar outcome in the clinic. These results support the current regulatory paradigm of animal testing in supporting safe entry to clinical trials and provide context for emerging alternate models. Copyright © 2017 Elsevier Inc. All rights reserved.

  14. Single-step generation of rabbits carrying a targeted allele of the tyrosinase gene using CRISPR/Cas9.

    Science.gov (United States)

    Honda, Arata; Hirose, Michiko; Sankai, Tadashi; Yasmin, Lubna; Yuzawa, Kazuaki; Honsho, Kimiko; Izu, Haruna; Iguchi, Atsushi; Ikawa, Masahito; Ogura, Atsuo

    2015-01-01

    Targeted genome editing of nonrodent mammalian species has provided the potential for highly accurate interventions into gene function in humans and the generation of useful animal models of human diseases. Here we show successful clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR-associated (Cas)-mediated gene targeting via circular plasmid injection in rabbits. The rabbit tyrosinase gene (TYR) was effectively disrupted, and we confirmed germline transmission by pronuclear injection of a circular plasmid expressing humanized Cas9 (hCas9) and single-guide RNA. Direct injection into pronuclear stage zygotes was possible following an in vitro validation assay. Neither off-target mutagenesis nor hCas9 transgenesis was detected in any of the genetically targeted pups and embryos examined. Gene targeting with this rapid and simplified strategy will help accelerate the development of translational research using other nonrodent mammalian species.

  15. Species composition of a soil invertebrate multi-species test system determines the level of ecotoxicity

    International Nuclear Information System (INIS)

    Sechi, Valentina; D'Annibale, Alessandra; Maraldo, Kristine; Johansen, Anders; Bossi, Rossana; Jensen, John; Krogh, Paul Henning

    2014-01-01

    A soil multi-species, SMS, experimental test system consisting of the natural microbial community, five collembolan species and a predatory mite along with either Enchytraeus crypticus or the earthworm Eisenia fetida were exposed to α-cypermethrin. A comparison of the performance of these two types of SMSs is given to aid the development of a standard test system. E. fetida had a positive effect on the majority of the species, reducing the negative insecticide effect. E. fetida affected the species sensitivity and decreased the degradation of the insecticide due to the organic matter incorporation of earthworm food. After 8 weeks, the EC50 was 0.76 mg kg −1 for enchytraeids and ranged between 2.7 and 18.9 mg kg −1 for collembolans, more sensitive than previously observed with single species. Changes observed in the community structure and function illustrates the strength of a multi-species test system as an ecotoxicological tool compared to single species tests. -- Highlights: • Degradation of alpha-cypermethrin was faster with enchytraeids than with earthworms. • Lumbricid castings and bioturbation explains bioavailability of α-cypermethrin. • Pesticide effects on soil arthropods alter with the community composition. • Multispecies test systems are feasible with either an enchytraeid or a lumbricid. • Collembolans are more sensitive to cypermethrin with enchytraeids than with earthworms. -- Soil ecotoxicological fate and effects in multispecies test systems are affected by earthworm activity

  16. Proceedings of the Mongolian Biodiversity Databank Workshop: Assessing the Conservation Status of Mongolian Mammals and Fishes: II – Mam- mals: Assessment Results and Threats.

    Directory of Open Access Journals (Sweden)

    Emma L. Clark

    2005-12-01

    Full Text Available The Mongolian Biodiversity Databank Workshop was held at the National University of Mongolia and Hustai National Park from 1 st October to 4 th November, 2005. As part of the workshop, participants assessed the conservation status of all Mongolian mammal species using the IUCN Categories and Cri - teria. Of the 128 species assessed, 2% were Critically Endangered (CR, 11% Endangered (EN and 4% Vulnerable (VU. A further 5% were categorised as Near Threatened (NT and 36% categorised as Data Deficient (DD. Ungulates were the most highly impacted: 79% were threatened with extinction. Twelve percent of carnivore species and 12% of rodent species were threatened. No non-rodent small mammal species were listed in a threatened category. Rodents and non-rodent small mammals were less well known, with 44% and 43% respectively found to be Data Deficient. This may have affected the threat assessment of these species. Greatest species richness of Mongolian mammals was found in the northern and western part of the country. The greatest number of threatened species also inhabit the north of the country, as well as the south-west. The main threat affecting most mammals in Mongolia was hunting, with lack of enforcement of legislation also considered a problem.

  17. Glial cell line-derived neurotrophic factor and endothelial cells promote self-renewal of rabbit germ cells with spermatogonial stem cell properties.

    Science.gov (United States)

    Kubota, Hiroshi; Wu, Xin; Goodyear, Shaun M; Avarbock, Mary R; Brinster, Ralph L

    2011-08-01

    Previous studies suggest that exogenous factors crucial for spermatogonial stem cell (SSC) self-renewal are conserved among several mammalian species. Since glial cell line-derived neurotrophic factor (GDNF) and fibroblast growth factor 2 (FGF2) are critical for rodent SSC self-renewal, we hypothesized that they might promote self-renewal of nonrodent SSCs. Therefore, we cultured testicular germ cells from prepubertal rabbits in the presence of GDNF and FGF2 and found they proliferated indefinitely as cellular clumps that displayed characteristics previously identified for rodent SSCs. The rabbit germ cells could not be maintained on mouse embryonic fibroblast (STO) feeders that support rodent SSC self-renewal in vitro but were rather supported on mouse yolk sac-derived endothelial cell (C166) feeder layers. Proliferation of rabbit germ cells was dependent on GDNF. Of critical importance was that clump-forming rabbit germ cells colonized seminiferous tubules of immunodeficient mice, proliferated for at least 6 mo, while retaining an SSC phenotype in the testes of recipient mice, indicating that they were rabbit SSCs. This study demonstrates that GDNF is a mitogenic factor promoting self-renewal that is conserved between rodent and rabbit SSCs; with an evolutionary separation of ∼ 60 million years. These findings provide a foundation to study the mechanisms governing SSC self-renewal in nonrodent species.

  18. Reconnaissance On Chi-Square Test Procedure For Determining Two Species Association

    Science.gov (United States)

    Marisa, Hanifa

    2008-01-01

    Determining the assosiation of two species by using chi-square test has been published. Utility of this procedure to plants species at certain location, shows that the procedure could not find "ecologically" association. Tens sampling units have been made to record some weeds species in Indralaya, South Sumatera. Chi square test; Xt2 = N[|(ad)-(bc)|-(N/2)]2/mnrs (Eq:1) on two species (Cleome sp and Eleusine indica) of the weeds shows positive assosiation; while ecologically in nature, there is no relationship between them. Some alternatives are proposed to this problem; simplified chi-square test steps, make further study to find out ecologically association, or at last, ignore it.

  19. A REVIEW OF SINGLE SPECIES TOXICITY TESTS: ARE THE TESTS RELIABLE PREDICTORS OF AQUATIC ECOSYSTEM COMMUNITY RESPONSES?

    Science.gov (United States)

    This document provides a comprehensive review to evaluate the reliability of indicator species toxicity test results in predicting aquatic ecosystem impacts, also called the ecological relevance of laboratory single species toxicity tests.

  20. Testing for Polytomies in Phylogenetic Species Trees Using Quartet Frequencies.

    Science.gov (United States)

    Sayyari, Erfan; Mirarab, Siavash

    2018-02-28

    Phylogenetic species trees typically represent the speciation history as a bifurcating tree. Speciation events that simultaneously create more than two descendants, thereby creating polytomies in the phylogeny, are possible. Moreover, the inability to resolve relationships is often shown as a (soft) polytomy. Both types of polytomies have been traditionally studied in the context of gene tree reconstruction from sequence data. However, polytomies in the species tree cannot be detected or ruled out without considering gene tree discordance. In this paper, we describe a statistical test based on properties of the multi-species coalescent model to test the null hypothesis that a branch in an estimated species tree should be replaced by a polytomy. On both simulated and biological datasets, we show that the null hypothesis is rejected for all but the shortest branches, and in most cases, it is retained for true polytomies. The test, available as part of the Accurate Species TRee ALgorithm (ASTRAL) package, can help systematists decide whether their datasets are sufficient to resolve specific relationships of interest.

  1. Testing for Polytomies in Phylogenetic Species Trees Using Quartet Frequencies

    Science.gov (United States)

    Sayyari, Erfan

    2018-01-01

    Phylogenetic species trees typically represent the speciation history as a bifurcating tree. Speciation events that simultaneously create more than two descendants, thereby creating polytomies in the phylogeny, are possible. Moreover, the inability to resolve relationships is often shown as a (soft) polytomy. Both types of polytomies have been traditionally studied in the context of gene tree reconstruction from sequence data. However, polytomies in the species tree cannot be detected or ruled out without considering gene tree discordance. In this paper, we describe a statistical test based on properties of the multi-species coalescent model to test the null hypothesis that a branch in an estimated species tree should be replaced by a polytomy. On both simulated and biological datasets, we show that the null hypothesis is rejected for all but the shortest branches, and in most cases, it is retained for true polytomies. The test, available as part of the Accurate Species TRee ALgorithm (ASTRAL) package, can help systematists decide whether their datasets are sufficient to resolve specific relationships of interest. PMID:29495636

  2. Species composition of a soil invertebrate multi-species test system determines the level of ecotoxicity

    DEFF Research Database (Denmark)

    Sechi, Valentina; D'Annibale, Alessandra; Maraldo, Kristine

    2014-01-01

    A soil multi-species, SMS, experimental test system consisting of the natural microbial community, five collembolan species and a predatory mite along with either Enchytraeus crypticus or the earthworm Eisenia fetida were exposed to α-cypermethrin. A comparison of the performance of these two typ...

  3. Development of rearing and testing protocols for a new freshwater sediment test species: the gastropod Valvata piscinalis.

    Science.gov (United States)

    Ducrot, Virginie; Cognat, Claudine; Mons, Raphaël; Mouthon, Jacques; Garric, Jeanne

    2006-03-01

    This paper aimed at proposing rearing and testing protocols for Valvata piscinalis, a new potential species for sediment toxicity testing. Such tests were developed since this species reliably represents the bio/ecological characteristics of other gastropods. It may thus be representative of their sensitivity to chemicals. V. piscinalis was successfully cultured in our laboratory for six generations. Cultures provided a high productivity for a low working time and low costs. The tests conditions we proposed seemed to be relevant for the development of reliable tests with this species. Indeed, hatching probability of egg-capsules, as well as embryo, newborn and juvenile survival rates, were close to 100%. Moreover, growth rates and fecundity were significantly higher than in field and in other laboratory studies. Partial life-cycle tests on clean sediments were achieved for various feeding levels to determine survival, growth and reproduction patterns, ad libitum feeding level and life cycle parameters values. Ad libitum feeding levels for newborn, juveniles and adults were 0.1, 0.4 and 0.8 mg Tetramin/individual/working day. Growth tests with zinc-spiked sediments provided a no-effect concentration and a lowest effect concentration of respectively 200 and 624 mg zinc/kg dry sediment. Other growth tests on spiked sediments we ran at our laboratory with second, third and fourth instars larvae of Chironomus riparius pointed out that V. piscinalis was more sensible to zinc than the chironomid, which is a routine test species in ecotoxicology. According to these results, V. piscinalis is a promising candidate species for sediment toxicity testing.

  4. Duration of Acute and Chronic Toxicity Testing in Animals (ICH S4A and S4B)

    DEFF Research Database (Denmark)

    Spindler, Per; Van Cauteren, Herman

    2013-01-01

    regions in 1991; whereas the process of harmonising the duration of non-rodent studies was initiated. The US FDA originally required studies of at least 12 months duration, whereas in Japan and EU studies of 6 months duration were considered acceptable as an ICH objective. In this chapter, the background...

  5. Assessing contaminant sensitivity of endangered and threatened aquatic species: Part III. Effluent toxicity tests

    Science.gov (United States)

    Dwyer, F.J.; Hardesty, D.K.; Henke, C.E.; Ingersoll, C.G.; Whites, D.W.; Augspurger, T.; Canfield, T.J.; Mount, D.R.; Mayer, F.L.

    2005-01-01

    Toxicity tests using standard effluent test procedures described by the U.S. Environmental Protection Agency were conducted with Ceriodaphnia dubia, fathead minnows (Pimephales promelas), and seven threatened and endangered (listed) fish species from four families: (1) Acipenseridae: shortnose sturgeon (Acipenser brevirostrum); (2) Catostomidae; razorback sucker (Xyrauchen texanus); (3) Cyprinidae: bonytail chub (Gila elegans), Cape Fear shiner (Notropis mekistocholas) Colorado pikeminnow (Ptychocheilus lucius), and spotfin chub (Cyprinella monacha); and (4) Poecillidae: Gila topminnow (Poeciliopsis occidentalis). We conducted 7-day survival and growth studies with embryo-larval fathead minnows and analogous exposures using the listed species. Survival and reproduction were also determined with C. dubia. Tests were conducted with carbaryl, ammonia-or a simulated effluent complex mixture of carbaryl, copper, 4-nonylphenol, pentachlorophenol and permethrin at equitoxic proportions. In addition, Cape Fear shiners and spotfin chub were tested using diazinon, copper, and chlorine. Toxicity tests were also conducted with field-collected effluents from domestic or industrial facilities. Bonytail chub and razorback suckers were tested with effluents collected in Arizona whereas effluent samples collected from North Carolina were tested with Cape Fear shiner, spotfin chub, and shortnose sturgeon. The fathead minnow 7-day effluent test was often a reliable estimator of toxic effects to the listed fishes. However, in 21 % of the tests, a listed species was more sensitive than fathead minnows. More sensitive species results varied by test so that usually no species was always more or less sensitive than fathead minnows. Only the Gila topminnow was consistently less sensitive than the fathead minnow. Listed fish species were protected 96% of the time when results for both fathead minnows and C. dubia were considered, thus reinforcing the value of standard whole

  6. A test of five mechanisms of species coexistence between rodents in ...

    African Journals Online (AJOL)

    A test of five mechanisms of species coexistence between rodents in a southern African savanna. M.R. Perrin, B.P. Kotler. Abstract. The operation of five different mechanisms of species coexistence in a community of rodents was examined in a semi-arid Kalahari savanna in southern Africa. The two most common species ...

  7. Comparison of rat and rabbit embryo-fetal developmental ...

    Science.gov (United States)

    Regulatory non-clinical safety testing of human pharmaceutical compounds typically requires embryo fetal developmental toxicity (EFDT) testing in two species, (one rodent and one non-rodent, usually the rat and the rabbit). The question has been raised whether under some conditions EFDT testing could be limited to one species, or whether the need for testing in a second species could be decided on a case by case basis. As part of an RIVM/CBG-MEB/HESI/US EPA consortium initiative, we built and queried a database of 379 EFDT studies conducted for marketed and non-marketed pharmaceutical compounds. The animal models (rat and rabbit) were assessed for their potential for adverse developmental and maternal outcomes. The database was analyzed for the prevalence of EFDT incidence and the nature and severity of adverse findings in the two species. Some manifestation of EFDT in either one or both species (rat and rabbit) was demonstrated for 282 compounds (74%), and EFDT was detected in only one species (rat or rabbit) in almost a third (31%, 118 compounds), with approximately 58% rat and 42% rabbit studies identifying an EFDT signal among the 379 compounds tested. For 24 compounds (6%), fetal malformations were observed in one species (rat or rabbit) in the absence of any EFDT in the second species. In general, growth retardation, fetal variations, and malformations were more prominent in the rat, whereas embryo-fetal death was observed more often in the rabbit. Discor

  8. A five-amino-acid motif in the undefined region of the TLR8 ectodomain is required for species-specific ligand recognition.

    Science.gov (United States)

    Liu, Jin; Xu, Congfeng; Hsu, Li-Chung; Luo, Yunping; Xiang, Rong; Chuang, Tsung-Hsien

    2010-02-01

    Toll-like receptors play important roles in regulating immunity against microbial infections. Toll-like receptor 8 (TLR8) belongs to a subfamily comprising TLR7, TLR8 and TLR9. Human TLR8 mediates anti-viral immunity by recognizing ssRNA viruses, and triggers potent anti-viral and antitumor immune responses upon ligation by synthetic small molecular weight ligands. Interestingly, distinct from human TLR8, mouse TLR8 was not responsive to ligand stimulation in the absence of polyT-oligodeoxynucleotides (polyT-ODN). The molecular basis for this distinct ligand recognition is still unclear. In the present study, we compared the activation of TLR8 from different species including mouse, rat, human, bovine, porcine, horse, sheep, and cat by ligand ligations. Only the TLR8s from the rodent species (i.e., mouse and rat TLR8s) failed to respond to ligand stimulation in the absence of polyT-ODN. Multiple sequence alignment analysis suggested that these two rodent TLR8s lack a five-amino-acid motif that is conserved in the non-rodent species with varied sequence. This small motif is located in an undefined region of the hTLR8 ectodomain, immediately following LRR-14. Deletion mutation analysis suggested that this motif is essential for the species-specific ligand recognition of hTLR8, whereas it is not required for self-dimerization and intracellular localization of this receptor. (c) 2009 Elsevier Ltd. All rights reserved.

  9. The minipig as a platform for new technologies in toxicology

    DEFF Research Database (Denmark)

    Forster, Roy; Ancian, Philippe; Fredholm, Merete

    2010-01-01

    The potential of the minipig as a platform for future developments in genomics, high density biology, transgenic technology, in vitro toxicology and related emerging technologies was reviewed. Commercial interests in the pig as an agricultural production species have driven scientific progress...... pigs and humans suggest that minipigs will be useful for the testing of biotechnology products (and possibly for in silico toxicology) and (iii) the minipig is the only non-rodent toxicology model where transgenic animals can be readily generated, and reproductive technologies are well developed...... in the pig. These properties should also make the minipig an interesting model for the testing of biotechnology products. These factors all support the idea that the minipig is well placed to meet the challenges of the emerging technologies and the toxicology of the future; it also seems likely...

  10. Competition for light between phytoplankton species : Experimental tests of mechanistic theory

    NARCIS (Netherlands)

    Huisman, J.; Jonker, R.R.; Zonneveld, C.; Weissing, F.J.

    1999-01-01

    According to recent competition theory, the population dynamics of phytoplankton species in monoculture can be used to make a priori predictions of the dynamics and outcome of competition for light. The species with lowest "critical light intensity" should be the superior light competitor. To test

  11. An overview to the investigative approach to species testing in wildlife forensic science

    Science.gov (United States)

    2011-01-01

    The extent of wildlife crime is unknown but it is on the increase and has observable effects with the dramatic decline in many species of flora and fauna. The growing awareness of this area of criminal activity is reflected in the increase in research papers on animal DNA testing, either for the identification of species or for the genetic linkage of a sample to a particular organism. This review focuses on the use of species testing in wildlife crime investigations. Species identification relies primarily on genetic loci within the mitochondrial genome; focusing on the cytochrome b and cytochrome oxidase 1 genes. The use of cytochrome b gained early prominence in species identification through its use in taxonomic and phylogenetic studies, while the gene sequence for cytochrome oxidase was adopted by the Barcode for Life research group. This review compares how these two loci are used in species identification with respect to wildlife crime investigations. As more forensic science laboratories undertake work in the wildlife area, it is important that the quality of work is of the highest standard and that the conclusions reached are based on scientific principles. A key issue in reporting on the identification of a particular species is a knowledge of both the intraspecies variation and the possible overlap of sequence variation from one species to that of a closely related species. Recent data showing this degree of genetic separation in mammalian species will allow greater confidence when preparing a report on an alleged event where the identification of the species is of prime importance. The aim of this review is to illustrate aspects of species testing in wildlife forensic science and to explain how a knowledge of genetic variation at the genus and species level can aid in the reporting of results. PMID:21232099

  12. A likelihood ratio test for species membership based on DNA sequence data

    DEFF Research Database (Denmark)

    Matz, Mikhail V.; Nielsen, Rasmus

    2005-01-01

    DNA barcoding as an approach for species identification is rapidly increasing in popularity. However, it remains unclear which statistical procedures should accompany the technique to provide a measure of uncertainty. Here we describe a likelihood ratio test which can be used to test if a sampled...... sequence is a member of an a priori specified species. We investigate the performance of the test using coalescence simulations, as well as using the real data from butterflies and frogs representing two kinds of challenge for DNA barcoding: extremely low and extremely high levels of sequence variability....

  13. Identification of cytosolic peroxisome proliferator binding protein as a member of the heat shock protein HSP70 family.

    OpenAIRE

    Alvares, K; Carrillo, A; Yuan, P M; Kawano, H; Morimoto, R I; Reddy, J K

    1990-01-01

    Clofibrate and many of its structural analogues induce proliferation of peroxisomes in the hepatic parenchymal cells of rodents and certain nonrodent species including primates. This induction is tissue specific, occurring mainly in the liver parenchymal cells and to a lesser extent in the kidney cortical epithelium. The induction of peroxisomes is associated with a predictable pleiotropic response, characterized by hepatomegaly, and increased activities and mRNA levels of certain peroxisomal...

  14. Adaptive Management Plan for Sensitive Plant Species on the Nevada Test Site

    International Nuclear Information System (INIS)

    Wills, C. A.

    2001-01-01

    The Nevada Test Site supports numerous plant species considered sensitive because of their past or present status under the Endangered Species Act and with federal and state agencies. In 1998, the U.S. Department of Energy, Nevada Operation Office (DOE/NV) prepared a Resource Management Plan which commits to protects and conserve these sensitive plant species and to minimize accumulative impacts to them. This document presents the procedures of a long-term adaptive management plan which is meant to ensure that these goals are met. It identifies the parameters that are measured for all sensitive plant populations during long-term monitoring and the adaptive management actions which may be taken if significant threats to these populations are detected. This plan does not, however, identify the current list of sensitive plant species know to occur on the Nevada Test Site. The current species list and progress on their monitoring is reported annually by DOE/NV in the Resource Management Plan

  15. Evaluation of the usefulness of novel biomarkers for drug-induced acute kidney injury in beagle dogs

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Xiaobing [National Center for Safety Evaluation of Drugs, National Institutes for Food and Drug Control, A8 Hongda Middle Street, Beijing Economic-Technological Development Area, Beijing 100176 (China); Graduate School of Peking Union Medical College, Dongcheng District, Beijing, 100730 (China); Ma, Ben; Lin, Zhi; Qu, Zhe; Huo, Yan; Wang, Jufeng [National Center for Safety Evaluation of Drugs, National Institutes for Food and Drug Control, A8 Hongda Middle Street, Beijing Economic-Technological Development Area, Beijing 100176 (China); Li, Bo, E-mail: libo@nifdc.org.cn [National Center for Safety Evaluation of Drugs, National Institutes for Food and Drug Control, A8 Hongda Middle Street, Beijing Economic-Technological Development Area, Beijing 100176 (China); Graduate School of Peking Union Medical College, Dongcheng District, Beijing, 100730 (China)

    2014-10-01

    As kidney is a major target organ affected by drug toxicity, early detection of renal injury is critical in preclinical drug development. In past decades, a series of novel biomarkers of drug-induced nephrotoxicity were discovered and verified in rats. However, limited data regarding the performance of novel biomarkers in non-rodent species are publicly available. To increase the applicability of these biomarkers, we evaluated the performance of 4 urinary biomarkers including neutrophil gelatinase-associated lipocalin (NGAL), clusterin, total protein, and N-acetyl-β-D-glucosaminidase (NAG), relative to histopathology and traditional clinical chemistry in beagle dogs with acute kidney injury (AKI) induced by gentamicin. The results showed that urinary NGAL and clusterin levels were significantly elevated in dogs on days 1 and 3 after administration of gentamicin, respectively. Gene expression analysis further provided mechanistic evidence to support that NGAL and clusterin are potential biomarkers for the early assessment of drug-induced renal damage. Furthermore, the high area (both AUCs = 1.000) under receiver operator characteristics (ROC) curve also indicated that NGAL and clusterin were the most sensitive biomarkers for detection of gentamicin-induced renal proximal tubular toxicity. Our results also suggested that NAG may be used in routine toxicity testing due to its sensitivity and robustness for detection of tissue injury. The present data will provide insights into the preclinical use of these biomarkers for detection of drug-induced AKI in non-rodent species. - Highlights: • Urinary NGAL, clusterin and NAG levels were significantly elevated in canine AKI. • NGAL and clusterin gene expression were increased following treatment with gentamicin. • NGAL and clusterin have high specificity and sensitivity for detection of AKI.

  16. The incidence of congenital malformations and variations in Göttingen minipigs.

    Science.gov (United States)

    Ellemann-Laursen, S; Marsden, E; Peter, B; Downes, N; Coulby, D; Grossi, A B

    2016-09-01

    Knowledge of the incidence of spontaneous congenital abnormalities is critical for the accurate interpretation of findings in teratogenicity studies in any species. In this paper, results of the examination of 1739 neonatal Göttingen Minipigs are presented. Over the 2-year period under consideration, the incidence of external and visceral malformations was less than 0.2 and 0.1%, respectively. The most common external malformations were syndactyly, limb hyperflexion, domed head and scoliosis. The most common internal malformations were undescended testes, ventricular septal defect, diaphragmatic hernia and atrial septal defects. Pentadactyly and variation in the aortic arch's bifurcation (absent truncus bicaroticus) were the most common variations. These data will help support the use of the Göttingen Minipig as a non-rodent species in embryofetal development studies where concerns persist about the availability of background data. Copyright © 2016 Elsevier Inc. All rights reserved.

  17. Seed viability of five wild Saudi Arabian species by germination and X-ray tests.

    Science.gov (United States)

    Al-Hammad, B A; Al-Ammari, B S

    2017-09-01

    Our objective was to evaluate the usefulness of the germination vs. the X-ray test in determining the initial viability of seeds of five wild species ( Moringa peregrina , Abrus precatorius , Arthrocnemum macrostachyum , Acacia ehrenbergiana and Acacia tortilis ) from Saudi Arabia. Usually several days were required to determine the viability of all five species via germination tests. However, X-ray test will give immediate results on filled/viable seeds. Seeds of all species, except Acacia ehrenbergiana and Acacia tortilis showed high viability in both germination (96-72% at 25/15 °C, 94-70% at 35/25 °C) and X-ray (100-80%) test. Furthermore, there was a general agreement between the germination (19%, 14% at 25/15 °C and 17% and 12% at 35/25 °C) and X-ray (8%, 4%) tests in which seed viability of Acacia ehrenbergiana and Acacia tortilis was very low due to insect damaged embryo as shown in X-ray analysis. Seeds of Abruspreca torius have physical dormancy, which was broken by scarification in concentrated sulfuric acid (10 min), and they exhibited high viability in both the germination (83% at 25/15 °C and 81% at 35/25 °C) and X-ray (96%) tests. Most of the nongerminated seeds of the five species except those of Acacia ehrenbergiana and Acacia tortilis , were alive as judged by the tetrazolium test (TZ). Thus, for the five species examined, the X-ray test was proved to be a good and rapid predictor of seed viability.

  18. Ecotoxicity of the veterinary pharmaceutical ivermectin tested in a soil multi-species (SMS) system

    International Nuclear Information System (INIS)

    Jensen, John; Scott-Fordsmand, Janeck J.

    2012-01-01

    The present study tests the effect of antiparasitic compound ivermectin in a constructed food-web system, a soil multi-species (SMS) higher tier test system. Mutualism, competition and predation within the SMS system were introduced by the addition of five collembolan species, one enchytraeid and a predatory mite species. Bait lamina sticks were incorporated as a measure of functional toxicity, attempting to the integrated feeding activity of the invertebrates. The study showed that on the community level all treatments were significantly affecting the community abundance and composition and that the decrease in abundance corresponded well with increasing exposure concentration for all species. Since all concentrations had significant adverse effect on the community structure, the community-based no-effect-concentration is below the lowest test concentration of 0.25 mg kg −1 , whereas the EC10 for the individual species were as low as 0.05 mg kg −1 . The bait lamina respond was only affected at the highest exposure concentration. - Highlights: ► A multi-species test system was used to evaluate the impact of hazardous substances. ► The pharmaceutical ivermectin was toxic to a wide set of soil invertebrates. ► The toxicity to springtails was higher when exposed in co-existence with a predator. ► Structural endpoints were more sensitive than functional ditto measured by Bait lamina. - Hazardous substances are shown more toxic to soil dwelling invertebrates when exposed in co-existence with other species including a predator.

  19. Identification of campylobacteria isolated from Danish broilers by phenotypic tests and species-specific PCR assays

    DEFF Research Database (Denmark)

    Wainø, M.; Bang, Dang Duong; Lund, Marianne

    2003-01-01

    campylobacterial cultures, 108 Campylobacter jejuni cultures and 351 campylobacterial cultures other than Camp. jejuni were subjected to various species-specific PCR assays. On the basis of the genotypic tests, it was demonstrated that Camp. jejuni and Camp. coli constituted approx. 99% of all cultures, while...... other species identified were Helicobacter pullorum, Camp. lari and Camp. upsaliensis. However, 29% of the 309 Camp. coli cultures identified by phenotypic tests were hippurate-variable or negative Camp. jejuni cultures, whereas some Camp. lari cultures and unspeciated campylobacter cultures belonged...... and Impact of the Study: Future phenotypic test schemes should be designed to allow a more accurate differentiation of Campylobacter and related species. Preferably, the phenotypic tests should be supplemented with a genotypic strategy to disclose the true campylobacterial species diversity in broilers....

  20. Seed viability of five wild Saudi Arabian species by germination and X-ray tests

    Directory of Open Access Journals (Sweden)

    B.A. Al-Hammad

    2017-09-01

    Full Text Available Our objective was to evaluate the usefulness of the germination vs. the X-ray test in determining the initial viability of seeds of five wild species (Moringa peregrina, Abrus precatorius, Arthrocnemum macrostachyum, Acacia ehrenbergiana and Acacia tortilis from Saudi Arabia. Usually several days were required to determine the viability of all five species via germination tests. However, X-ray test will give immediate results on filled/viable seeds. Seeds of all species, except Acacia ehrenbergiana and Acacia tortilis showed high viability in both germination (96–72% at 25/15 °C, 94–70% at 35/25 °C and X-ray (100–80% test. Furthermore, there was a general agreement between the germination (19%, 14% at 25/15 °C and 17% and 12% at 35/25 °C and X-ray (8%, 4% tests in which seed viability of Acacia ehrenbergiana and Acacia tortilis was very low due to insect damaged embryo as shown in X-ray analysis. Seeds of Abruspreca torius have physical dormancy, which was broken by scarification in concentrated sulfuric acid (10 min, and they exhibited high viability in both the germination (83% at 25/15 °C and 81% at 35/25 °C and X-ray (96% tests. Most of the nongerminated seeds of the five species except those of Acacia ehrenbergiana and Acacia tortilis, were alive as judged by the tetrazolium test (TZ. Thus, for the five species examined, the X-ray test was proved to be a good and rapid predictor of seed viability.

  1. Development of an improved species specific PCR test for detection of Haemophilus parasuis

    DEFF Research Database (Denmark)

    Angen, Øystein; Oliveira, Simone; Ahrens, Peter

    2007-01-01

    , the present PCR test was found to be 100% species specific for H. parasuis, in contrast to the PCR test of Oliveira et al., which also tested positive for strains belonging to A. indolicus, A. porcinus, and A. minor, species commonly occurring in the upper respiratory tract. However, when the PCR test...... with representatives of H. parasuis. The test was further evaluated on 55 clinical samples from 16 Danish pigs suspected for being infected with H. parasuis, showing polyserositis or septicemia at autopsy as well as on 492 nasal swabs. The test was compared with the performance of a PCR test earlier published...... by Oliveira et al. [Oliveira, S., Galina, L., Pijoan, C., 2001. Development of a PCR test to diagnose Haemophilus parasuis infections. J. Vet. Diagn. Invest. 13, 495-501]. The sensitivity of the present PCR test was found to be slightly lower when applied on clinical samples from diseased pigs and 10-fold...

  2. Identification of medically relevant Nocardia species with an abbreviated battery of tests.

    Science.gov (United States)

    Kiska, Deanna L; Hicks, Karen; Pettit, David J

    2002-04-01

    Identification of Nocardia to the species level is useful for predicting antimicrobial susceptibility patterns and defining the pathogenicity and geographic distribution of these organisms. We sought to develop an identification method which was accurate, timely, and employed tests which would be readily available in most clinical laboratories. We evaluated the API 20C AUX yeast identification system as well as several biochemical tests and Kirby-Bauer susceptibility patterns for the identification of 75 isolates encompassing the 8 medically relevant Nocardia species. There were few biochemical reactions that were sufficiently unique for species identification; of note, N. nova were positive for arylsulfatase, N. farcinica were positive for opacification of Middlebrook 7H11 agar, and N. brasiliensis and N. pseudobrasiliensis were the only species capable of liquefying gelatin. API 20C sugar assimilation patterns were unique for N. transvalensis, N. asteroides IV, and N. brevicatena. There was overlap among the assimilation patterns for the other species. Species-specific patterns of susceptibility to gentamicin, tobramycin, amikacin, and erythromycin were obtained for N. nova, N. farcinica, and N. brevicatena, while there was overlap among the susceptibility patterns for the other isolates. No single method could identify all Nocardia isolates to the species level; therefore, a combination of methods was necessary. An algorithm utilizing antibiotic susceptibility patterns, citrate utilization, acetamide utilization, and assimilation of inositol and adonitol accurately identified all isolates. The algorithm was expanded to include infrequent drug susceptibility patterns which have been reported in the literature but which were not seen in this study.

  3. Determination of seed viability of eight wild Saudi Arabian species by germination and X-ray tests.

    Science.gov (United States)

    Al-Turki, Turki A; Baskin, Carol C

    2017-05-01

    Our purpose was to evaluate the usefulness of the germination vs. the X-ray test in determining the initial viability of seeds of eight wild species ( Salvia spinosa , Salvia aegyptiaca , Ochradenus baccatus , Ochradenus arabicus , Suaeda aegyptiaca , Suaeda vermiculata , Prosopisfarcta and Panicumturgidum ) from Saudi Arabia. Several days were required to determine viability of all eight species via germination tests, while immediate results on filled/viable seeds were obtained with the X-ray test. Seeds of all the species, except Sa.aegyptiaca , showed high viability in both the germination (98-70% at 25/15 °C, 93-66% at 35/25 °C) and X-ray (100-75%) test. Furthermore, there was general agreement between the germination (10% at 25/15 °C and 8% at 35/25 °C) and X-ray (5%) tests that seed viability of Sa.aegyptiaca was very low, and X-ray analysis revealed that this was due to poor embryo development. Seeds of P.farcta have physical dormancy, which was broken by scarification in concentrated sulfuric acid (10 min), and they exhibited high viability in both the germination (98% at 25/15 °C and 93% at 35/25 °C) and X-ray (98%) test. Most of the nongerminated seeds of the eight species except those of Sa.aegyptiaca were alive as judged by the tetrazolium test (TZ). Thus, for the eight species examined, the X-ray test was a good and rapid predictor of seed viability.

  4. Taxonomic separation of hippocampal networks: principal cell populations and adult neurogenesis

    Directory of Open Access Journals (Sweden)

    Roelof Maarten evan Dijk

    2016-03-01

    Full Text Available While many differences in hippocampal anatomy have been described between species, it is typically not clear if they are specific to a particular species and related to functional requirements or if they are shared by species of larger taxonomic units. Without such information, it is difficult to infer how anatomical differences may impact on hippocampal function, because multiple taxonomic levels need to be considered to associate behavioral and anatomical changes. To provide information on anatomical changes within and across taxonomic ranks, we present a quantitative assessment of hippocampal principal cell populations in 20 species or strain groups, with emphasis on rodents, the taxonomic group that provides most animals used in laboratory research. Of special interest is the importance of adult hippocampal neurogenesis in species-specific adaptations relative to other cell populations. Correspondence analysis of cell numbers shows that across taxonomic units, phylogenetically related species cluster together, sharing similar proportions of principal cell populations. CA3 and hilus are strong separators that place rodent species into a tight cluster based on their relatively large CA3 and small hilus while non-rodent species (including humans and non-human primates are placed on the opposite side of the spectrum. Hilus and CA3 are also separators within rodents, with a very large CA3 and rather small hilar cell populations separating mole-rats from other rodents that, in turn, are separated from each other by smaller changes in the proportions of CA1 and granule cells. When adult neurogenesis is included, the relatively small populations of young neurons, proliferating cells and hilar neurons become main drivers of taxonomic separation within rodents. The observations provide challenges to the computational modeling of hippocampal function, suggest differences in the organization of hippocampal information streams in rodent and non-rodent

  5. Species-energy relationship in the deep sea: A test using the Quaternary fossil record

    Science.gov (United States)

    Hunt, G.; Cronin, T. M.; Roy, K.

    2005-01-01

    Little is known about the processes regulating species richness in deep-sea communities. Here we take advantage of natural experiments involving climate change to test whether predictions of the species-energy hypothesis hold in the deep sea. In addition, we test for the relationship between temperature and species richness predicted by a recent model based on biochemical kinetics of metabolism. Using the deep-sea fossil record of benthic foraminifera and statistical meta-analyses of temperature-richness and productivity-richness relationships in 10 deep-sea cores, we show that temperature but not productivity is a significant predictor of species richness over the past c. 130 000 years. Our results not only show that the temperature-richness relationship in the deep-sea is remarkably similar to that found in terrestrial and shallow marine habitats, but also that species richness tracks temperature change over geological time, at least on scales of c. 100 000 years. Thus, predicting biotic response to global climate change in the deep sea would require better understanding of how temperature regulates the occurrences and geographical ranges of species. ??2005 Blackwell Publishing Ltd/CNRS.

  6. B chromosomes are more frequent in mammals with acrocentric karyotypes: support for the theory of centromeric drive.

    Science.gov (United States)

    Palestis, Brian G; Burt, Austin; Jones, R Neil; Trivers, Robert

    2004-02-07

    The chromosomes of mammals tend to be either mostly acrocentric (having one long arm) or mostly bi-armed, with few species having intermediate karyotypes. The theory of centromeric drive suggests that this observation reflects a bias during female meiosis, favouring either more centromeres or fewer, and that the direction of this bias changes frequently over evolutionary time. B chromosomes are selfish genetic elements found in some individuals within some species. B chromosomes are often harmful, but persist because they drive (i.e. they are transmitted more frequently than expected). We predicted that species with mainly acrocentric chromosomes would be more likely to harbour B chromosomes than those with mainly bi-armed chromosomes, because female meiosis would favour more centromeres over fewer in species with one-armed chromosomes. Our results show that B chromosomes are indeed more common in species with acrocentric chromosomes, across all mammals, among rodents, among non-rodents and in a test of independent taxonomic contrasts. These results provide independent evidence supporting the theory of centromeric drive and also help to explain the distribution of selfish DNA across species. In addition, we demonstrate an association between the shape of the B chromosomes and the shape of the typical ('A') chromosomes.

  7. Evaluation of the Thermo Scientific SureTect Listeria species assay. AOAC Performance Tested Method 071304.

    Science.gov (United States)

    Cloke, Jonathan; Evans, Katharine; Crabtree, David; Hughes, Annette; Simpson, Helen; Holopainen, Jani; Wickstrand, Nina; Kauppinen, Mikko; Leon-Velarde, Carlos; Larson, Nathan; Dave, Keron

    2014-01-01

    The Thermo Scientific SureTect Listeria species Assay is a new real-time PCR assay for the detection of all species of Listeria in food and environmental samples. This validation study was conducted using the AOAC Research Institute (RI) Performance Tested Methods program to validate the SureTect Listeria species Assay in comparison to the reference method detailed in International Organization for Standardization 11290-1:1996 including amendment 1:2004 in a variety of foods plus plastic and stainless steel. The food matrixes validated were smoked salmon, processed cheese, fresh bagged spinach, cantaloupe, cooked prawns, cooked sliced turkey meat, cooked sliced ham, salami, pork frankfurters, and raw ground beef. All matrixes were tested by Thermo Fisher Scientific, Microbiology Division, Basingstoke, UK. In addition, three matrixes (pork frankfurters, fresh bagged spinach, and stainless steel surface samples) were analyzed independently as part of the AOAC-RI-controlled independent laboratory study by the University ofGuelph, Canada. Using probability of detection statistical analysis, a significant difference in favour of the SureTect assay was demonstrated between the SureTect and reference method for high level spiked samples of pork frankfurters, smoked salmon, cooked prawns, stainless steel, and low-spiked samples of salami. For all other matrixes, no significant difference was seen between the two methods during the study. Inclusivity testing was conducted with 68 different isolates of Listeria species, all of which were detected by the SureTect Listeria species Assay. None of the 33 exclusivity isolates were detected by the SureTect Listeria species Assay. Ruggedness testing was conducted to evaluate the performance of the assay with specific method deviations outside of the recommended parameters open to variation, which demonstrated that the assay gave reliable performance. Accelerated stability testing was additionally conducted, validating the assay

  8. Testing the Relationships between Diversification, Species Richness, and Trait Evolution.

    Science.gov (United States)

    Kozak, Kenneth H; Wiens, John J

    2016-11-01

    Understanding which traits drive species diversification is essential for macroevolutionary studies and to understand patterns of species richness among clades. An important tool for testing if traits influence diversification is to estimate rates of net diversification for each clade, and then test for a relationship between traits and diversification rates among clades. However, this general approach has become very controversial. Numerous papers have now stated that it is inappropriate to analyze net diversification rates in groups in which clade richness is not positively correlated with clade age. Similarly, some have stated that variation in net diversification rates does not explain variation in species richness patterns among clades across the Tree of Life. Some authors have also suggested that strong correlations between richness and diversification rates are a statistical artifact and effectively inevitable. If this latter point is true, then correlations between richness and diversification rates would be uninformative (or even misleading) for identifying how much variation in species richness among clades is explained by variation in net diversification rates. Here, we use simulations (based on empirical data for plethodontid salamanders) to address three main questions. First, how is variation in net diversification rates among clades related to the relationship between clade age and species richness? Second, how accurate are these net diversification rate estimators, and does the age-richness relationship have any relevance to their accuracy? Third, is a relationship between species richness and diversification rates an inevitable, statistical artifact? Our simulations show that strong, positive age-richness relationships arise when diversification rates are invariant among clades, whereas realistic variation in diversification rates among clades frequently disrupts this relationship. Thus, a significant age-richness relationship should not be a

  9. Sensitivity, specificity and comparison of three commercially available immunological tests in the diagnosis of Cryptosporidium species in animals.

    Science.gov (United States)

    Danišová, Olga; Halánová, Monika; Valenčáková, Alexandra; Luptáková, Lenka

    The study was conducted to compare the specificity of immunological diagnostic methods used for the diagnosis of Cryptosporidium species capable of causing life-threatening infection in both immunosuppressed and immunocompetent patients. For the detection of Cryptosporidium species in 79 animals with diarrhoea, we used three Copro-antigen tests: RIDASCREEN ® Cryptosporidium test, Cryptosporidium 2nd Generation (ELISA) and RIDA ® QUICK Cryptosporidium. For immunoassays we used positive and negative samples detected by means of polymerase chain reaction and validated by sequencing and nested polymerase chain reaction to confirm the presence six different species of Cryptosporidium species. Prevalence of cryptosporidiosis in the entire group determined by enzyme immunoassay, enzyme linked immunosorbent assay, immuno-chromatographic test and polymerase chain reaction was 34.17%, 27.84%, 6.33% and 27.84%, respectively. Sensitivity of animal samples with enzyme immunoassay, enzyme linked immunosorbent assay, and immuno-chromatographic test was 63.6%, 40.9% and 22.7%, resp., when questionable samples were considered positive, whereas specificity of enzyme immunoassay, enzyme linked immunosorbent assay and immuno-chromatographic test was 75.9%, 78.9% and 100%, respectively. Positive predictive values and negative predictive values were different for all the tests. These differences results are controversial and therefore reliability and reproducibility of immunoassays as the only diagnostic method is questionable. The use of various Cryptosporidium species in diagnosis based on immunological testing and different results obtained by individual tests indicate potential differences in Copro-antigens produced by individual Cryptosporidium species. Copyright © 2017 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

  10. Threatened plant species of the Nevada Test Site, Ash Meadows, central-southern Nevada

    Energy Technology Data Exchange (ETDEWEB)

    Beatley, J.C.

    1977-04-01

    This report is a companion one to Endangered Plant Species of the Nevada Test Site, Ash Meadows, and Central-Southern Nevada (COO-2307-11) and deals with the threatened plant species of the same area. The species are those cited in the Federal Register, July 1, 1975, and include certain ones listed as occurring only in California or Arizona, but which occur also in central-southern Nevada. As with the earlier report, the purpose of this one is to record in detail the location of the past plant collections which constitute the sole or principal basis for defining the species' distributions and frequency of occurrence in southern Nye County, Nevada, and to recommend the area of the critical habitat where this is appropriate. Many of the species occur also in southern California, and for these the central-southern Nevada records are presented for consideration of the overall status of the species throughout its range.

  11. Species delineation using Bayesian model-based assignment tests: a case study using Chinese toad-headed agamas (genus Phrynocephalus

    Directory of Open Access Journals (Sweden)

    Fu Jinzhong

    2010-06-01

    Full Text Available Abstract Background Species are fundamental units in biology, yet much debate exists surrounding how we should delineate species in nature. Species discovery now requires the use of separate, corroborating datasets to quantify independently evolving lineages and test species criteria. However, the complexity of the speciation process has ushered in a need to infuse studies with new tools capable of aiding in species delineation. We suggest that model-based assignment tests are one such tool. This method circumvents constraints with traditional population genetic analyses and provides a novel means of describing cryptic and complex diversity in natural systems. Using toad-headed agamas of the Phrynocephalus vlangalii complex as a case study, we apply model-based assignment tests to microsatellite DNA data to test whether P. putjatia, a controversial species that closely resembles P. vlangalii morphologically, represents a valid species. Mitochondrial DNA and geographic data are also included to corroborate the assignment test results. Results Assignment tests revealed two distinct nuclear DNA clusters with 95% (230/243 of the individuals being assigned to one of the clusters with > 90% probability. The nuclear genomes of the two clusters remained distinct in sympatry, particularly at three syntopic sites, suggesting the existence of reproductive isolation between the identified clusters. In addition, a mitochondrial ND2 gene tree revealed two deeply diverged clades, which were largely congruent with the two nuclear DNA clusters, with a few exceptions. Historical mitochondrial introgression events between the two groups might explain the disagreement between the mitochondrial and nuclear DNA data. The nuclear DNA clusters and mitochondrial clades corresponded nicely to the hypothesized distributions of P. vlangalii and P. putjatia. Conclusions These results demonstrate that assignment tests based on microsatellite DNA data can be powerful tools

  12. Glyceria maxima as new test species for the EU risk assessment for herbicides: a microcosm study.

    Science.gov (United States)

    Mohr, S; Schott, J; Hoenemann, L; Feibicke, M

    2015-03-01

    In its recent guidance document on tiered risk assessment for plant protection products for aquatic organisms, the European Food Safety Authority (EFSA) proposed to use Glyceria maxima as monocotyledonous grass species for the testing of special herbicide groups. However, published toxicity data for this species is very limited and there is no test guideline for Glyceria sp. For this reason a microcosm study was conducted in order to gain experience on the degree of sensitivity of G. maxima to the herbicidal substances clodinafop-propargyl (grass herbicide) and fluroxypyr (auxin) in comparison to the already established test organism water milfoil Myriophyllum spicatum and the duckweed species Landoltia punctata. Five concentrations without replicates were tested for each test substance using 10 microcosms and three microcosms served as controls. The experiment was run for 8 weeks. Morphological endpoints were used to determine growth and EC50 values. The results show that M. spicatum was most sensitive to fluroxypyr (37 days EC50 for roots: 62 µg/L) and G. maxima most sensitive to clodinafop-propargyl (22 days EC50 for total shoot length: 48 µg/L) whereas the duckweed species was considerable less sensitive. Hence, G. maxima turns out to be a good candidate for testing grass specific herbicides, supporting its inclusion as an additional macrophyte test for the risk assessment of herbicides as proposed by the EFSA.

  13. Comparison of methods for in vitro testing of susceptibility of porcine Mycoplasma species to antimicrobial agents.

    OpenAIRE

    Ter Laak, E A; Pijpers, A; Noordergraaf, J H; Schoevers, E C; Verheijden, J H

    1991-01-01

    The MICs of 18 antimicrobial agents used against strains of three porcine Mycoplasma species were determined by a serial broth dilution method. Twenty field strains of M. hyorhinis, ten field strains of M. hyopneumoniae, six field strains of M. flocculare, and the type strains of these species were tested. Twelve field strains and the type strain of M. hyorhinis were also tested by an agar dilution method. Tests were read at various time points. When the broth dilution method was used, the fi...

  14. Comparison of agar dilution and antibiotic gradient strip test with broth microdilution for susceptibility testing of swine Brachyspira species.

    Science.gov (United States)

    Mirajkar, Nandita S; Gebhart, Connie J

    2016-03-01

    Production-limiting diseases in swine caused by Brachyspira are characterized by mucohemorrhagic diarrhea (B. hyodysenteriae and "B. hampsonii") or mild colitis (B. pilosicoli), while B. murdochii is often isolated from healthy pigs. Emergence of novel pathogenic Brachyspira species and strains with reduced susceptibility to commonly used antimicrobials has reinforced the need for standardized susceptibility testing. Two methods are currently used for Brachyspira susceptibility testing: agar dilution (AD) and broth microdilution (BMD). However, these tests have primarily been used for B. hyodysenteriae and rarely for B. pilosicoli. Information on the use of commercial susceptibility testing products such as antibiotic gradient strips is lacking. Our main objective was to validate and compare the susceptibility results, measured as the minimum inhibitory concentration (MIC), of 6 antimicrobials for 4 Brachyspira species (B. hyodysenteriae, "B. hampsonii", B. pilosicoli, and B. murdochii) by BMD and AD (tiamulin, valnemulin, lincomycin, tylosin, and carbadox) or antibiotic gradient strip (doxycycline) methods. In general, the results of a high percentage of all 4 Brachyspira species differed by ±1 log2 dilution or less by BMD and AD for tiamulin, valnemulin, lincomycin, and tylosin, and by BMD and antibiotic gradient strip for doxycycline. The carbadox MICs obtained by BMD were 1-5 doubling dilutions different than those obtained by AD. BMD for Brachyspira was quicker to perform with less ambiguous interpretation of results when compared with AD and antibiotic gradient strip methods, and the results confirm the utility of BMD in routine diagnostics. © 2016 The Author(s).

  15. Testing Dragonflies as Species Richness Indicators in a Fragmented Subtropical Atlantic Forest Environment.

    Science.gov (United States)

    Renner, S; Sahlén, G; Périco, E

    2016-06-01

    We surveyed 15 bodies of water among remnants of the Atlantic Forest biome in southern Brazil for adult dragonflies and damselflies to test whether an empirical selection method for diversity indicators could be applied in a subtropical ecosystem, where limited ecological knowledge on species level is available. We found a regional species pool of 34 species distributed in a nested subset pattern with a mean of 11.2 species per locality. There was a pronounced difference in species composition between spring, summer, and autumn, but no differences in species numbers between seasons. Two species, Homeoura chelifera (Selys) and Ischnura capreolus (Hagen), were the strongest candidates for regional diversity indicators, being found only at species-rich localities in our surveyed area and likewise in an undisturbed national forest reserve, serving as a reference site for the Atlantic Forest. Using our selection method, we found it possible to obtain a tentative list of diversity indicators without having detailed ecological information of each species, providing a reference site is available for comparison. The method thus allows for indicator species to be selected in blanco from taxonomic groups that are little known. We hence argue that Odonata can already be incorporated in ongoing assessment programs in the Neotropics, which would also increase the ecological knowledge of the group and allow extrapolation to other taxa.

  16. Status of endangered and threatened plant species on Tonopah Test Range: a survey

    International Nuclear Information System (INIS)

    Rhoads, W.A.; Cochrane, S.A.; Williams, M.P.

    1979-10-01

    Six species under consideration by the US Fish and Wildlife Service (FWS) for endangered or threatened status were found on or near the Tonopah Test Range (TTR) in southern central Nevada. Based on recognized threats to these species, their overall distribution, rarity, and other factors, status recommendations were prepared for Sandia Corporation. In addition, ten species that occur in the vicinity of TTR, and which may yet be found on TTR, are discussed in brief. Each species is discussed in relation to distribution, rarity, taxonomy, habitat requirements, endangerment, assessment of status, and proposed protection and monitoring needs. Construction activities and off-road vehicle travel are the most prominent man-caused threats to species on TTR; habitat destruction by trampling and over-grazing by feral horses and non-permit cattle significantly modifies habitats of certain species. We recommend two kinds of protective measures. First is the planning of activities so that habitats, particularly the suggested protected habitats, are not disturbed. Second, and directed to the same end, off-road traffic should be curtailed in the regions of the proposed protected habitats

  17. [Altitudinal patterns of species richness and species range size of vascular plants in Xiaolong- shan Reserve of Qinling Mountain: a test of Rapoport' s rule].

    Science.gov (United States)

    Zheng, Zhi; Gong, Da-Jie; Sun, Cheng-Xiang; Li, Xiao-Jun; Li, Wan-Jiang

    2014-09-01

    Altitudinal patterns of species richness and species range size and their underlying mechanisms have long been a key topic in biogeography and biodiversity research. Rapoport's rule stated that the species richness gradually declined with the increasing altitude, while the species ranges became larger. Using altitude-distribution database from Xiaolongshan Reverse, this study explored the altitudinal patterns of vascular plant species richness and species range in Qinling Xiaolongshan Reserve, and examined the relationships between species richness and their distributional middle points in altitudinal bands for different fauna, taxonomic units and growth forms and tested the Rapoport's rule by using Stevens' method, Pagel's method, mid-point method and cross-species method. The results showed that the species richness of vascular plants except small-range species showed a unimodal pattern along the altitude in Qinling Xiaolongshan Reserve and the highest proportion of small-range species was found at the lower altitudinal bands and at the higher altitudinal bands. Due to different assemblages and examining methods, the relationships between species distributing range sizes and the altitudes were different. Increasing taxonomic units was easier to support Rapoport's rule, which was related to niche differences that the different taxonomic units occupied. The mean species range size of angiosperms showed a unimodal pattern along the altitude, while those of the gymnosperms and pteridophytes were unclearly regular. The mean species range size of the climbers was wider with the increasing altitude, while that of the shrubs which could adapt to different environmental situations was not sensitive to the change of altitude. Pagel's method was easier to support the Rapoport's rule, and then was Steven's method. On the contrary, due to the mid-domain effect, the results of the test by using the mid-point method showed that the mean species range size varied in a unimodal

  18. Perch Selection by Three Cooccurring Species of Celithemis (Odonata: Libellulidae: Testing for a Competitive Hierarchy among Similar Species

    Directory of Open Access Journals (Sweden)

    Wade B. Worthen

    2016-01-01

    Full Text Available In many communities of perching dragonflies (Odonata: Libellulidae, a size-dependent competitive hierarchy creates a positive relationship between male body size and perch height. We tested for this pattern among three similar-sized species: Celithemis elisa, C. fasciata, and C. ornata. Males were caught and photographed from May to July 2015 at Ashmore Heritage Preserve, Greenville County, SC, USA, and perch heights and perch distance to open water were measured. Five indices of body size were measured with ImageJ software: abdomen length, forewing length, hindwing length, area of forewing, and area of hindwing. Celithemis fasciata was significantly larger than the other two species for all five anatomical characters and used perches that were significantly taller and closer to open water than the other species, though these differences changed over the summer. Aggressive interactions between and within species were tallied and compared to expected distributions based on mean relative abundances derived from hourly abundance counts. Patterns of interspecific aggression were also consistent with a size-dependent hierarchy: the large C. fasciata was attacked less frequently, and the small C. ornata more frequently, than predicted by their relative abundances. We conclude that even small differences in body size may contribute to niche partitioning in perch selection.

  19. Adaptation of the fish juvenile growth test (OECD TG 215, 2000) to the marine species Dicentrarchus labrax.

    Science.gov (United States)

    Tornambè, A; Manfra, L; Canepa, S; Oteri, F; Martuccio, G; Cicero, A M; Magaletti, E

    2018-02-01

    The OECD TG 215 method (2000) (C.14 method of EC Regulation 440/2008) was developed on the rainbow trout (Oncorynchus mykiss) to assess chronic toxicity (28d) of chemicals on fish juveniles. It contemplates to use other well documented species identifying suitable conditions to evaluate their growth. OECD proposes the European sea bass (Dicentrarchus labrax, L. 1758) as Mediterranean species among vertebrates recommended in the OECD guidelines for the toxicity testing of chemicals. In this context, our study is aimed to proposing the adaptation of the growth test (OECD TG 215, 2000) to D. labrax. For this purpose toxicity tests were performed with sodium dodecyl sulfate, a reference toxicant commonly used in fish toxicity assays. The main aspects of the testing procedure were reviewed: fish size (weight), environmental conditions, dilution water type, experimental design, loading rate and stocking density, feeding (food type and ration), test validity criteria. The experience gained from growth tests with the sea bass allows to promote its inclusion among the species to be used for the C.14 method. Copyright © 2016. Published by Elsevier Inc.

  20. Testing species distribution models across space and time: high latitude butterflies and recent warming

    DEFF Research Database (Denmark)

    Eskildsen, Anne; LeRoux, Peter C.; Heikkinen, Risto K.

    2013-01-01

    changes at expanding range margins can be predicted accurately. Location. Finland. Methods. Using 10-km resolution butterfly atlas data from two periods, 1992–1999 (t1) and 2002–2009 (t2), with a significant between-period temperature increase, we modelled the effects of climatic warming on butterfly...... butterfly distributions under climate change. Model performance was lower with independent compared to non-independent validation and improved when land cover and soil type variables were included, compared to climate-only models. SDMs performed less well for highly mobile species and for species with long......Aim. To quantify whether species distribution models (SDMs) can reliably forecast species distributions under observed climate change. In particular, to test whether the predictive ability of SDMs depends on species traits or the inclusion of land cover and soil type, and whether distributional...

  1. Species-specific considerations in using the fish embryo test as an alternative to identify endocrine disruption.

    Science.gov (United States)

    Schiller, Viktoria; Zhang, Xiaowei; Hecker, Markus; Schäfers, Christoph; Fischer, Rainer; Fenske, Martina

    2014-10-01

    A number of regulations have been implemented that aim to control the release of potentially adverse endocrine disrupters into the aquatic environment based on evidence from laboratory studies. Currently, such studies rely on testing approaches with adult fish because reliable alternatives have not been validated so far. Fish embryo tests have been proposed as such an alternative, and here we compared two species (medaka and zebrafish) to determine their suitability for the assessment of substances with estrogenic and anti-androgenic activity. Changes in gene expression (in here the phrase gene expression is used synonymously to gene transcription, although it is acknowledged that gene expression is additionally regulated, e.g., by translation and protein stability) patterns between the two species were compared in short term embryo exposure tests (medaka: 7-day post fertilization [dpf]; zebrafish: 48 and 96h post fertilization [hpf]) by using relative quantitative real-time RT-PCR. The tested genes were related to the hypothalamic-gonadal-axis and early steroidogenesis. Test chemicals included 17α-ethinylestradiol and flutamide as estrogenic and anti-androgenic reference compounds, respectively, as well as five additional substances with endocrine activities, namely bisphenol A, genistein, prochloraz, linuron and propanil. Estrogenic responses were comparable in 7-dpf medaka and 48/96-hpf zebrafish embryos and included transcriptional upregulation of aromatase b, vitellogenin 1 as well as steroidogenic genes, suggesting that both species reliably detected exposure to estrogenic compounds. However, anti-androgenic responses differed between the two species, with each species providing specific information concerning the mechanism of anti-androgenic disruption in fish embryos. Although small but significant changes in the expression of selected genes was observed in 48-hpf zebrafish embryos, exposure prolonged to 96hpf was necessary to obtain a response indicative

  2. Testing projected wild bee distributions in agricultural habitats: predictive power depends on species traits and habitat type.

    Science.gov (United States)

    Marshall, Leon; Carvalheiro, Luísa G; Aguirre-Gutiérrez, Jesús; Bos, Merijn; de Groot, G Arjen; Kleijn, David; Potts, Simon G; Reemer, Menno; Roberts, Stuart; Scheper, Jeroen; Biesmeijer, Jacobus C

    2015-10-01

    Species distribution models (SDM) are increasingly used to understand the factors that regulate variation in biodiversity patterns and to help plan conservation strategies. However, these models are rarely validated with independently collected data and it is unclear whether SDM performance is maintained across distinct habitats and for species with different functional traits. Highly mobile species, such as bees, can be particularly challenging to model. Here, we use independent sets of occurrence data collected systematically in several agricultural habitats to test how the predictive performance of SDMs for wild bee species depends on species traits, habitat type, and sampling technique. We used a species distribution modeling approach parametrized for the Netherlands, with presence records from 1990 to 2010 for 193 Dutch wild bees. For each species, we built a Maxent model based on 13 climate and landscape variables. We tested the predictive performance of the SDMs with independent datasets collected from orchards and arable fields across the Netherlands from 2010 to 2013, using transect surveys or pan traps. Model predictive performance depended on species traits and habitat type. Occurrence of bee species specialized in habitat and diet was better predicted than generalist bees. Predictions of habitat suitability were also more precise for habitats that are temporally more stable (orchards) than for habitats that suffer regular alterations (arable), particularly for small, solitary bees. As a conservation tool, SDMs are best suited to modeling rarer, specialist species than more generalist and will work best in long-term stable habitats. The variability of complex, short-term habitats is difficult to capture in such models and historical land use generally has low thematic resolution. To improve SDMs' usefulness, models require explanatory variables and collection data that include detailed landscape characteristics, for example, variability of crops and

  3. Evaluation of the Thermo Scientific SureTect Salmonella species assay. AOAC Performance Tested Method 051303.

    Science.gov (United States)

    Cloke, Jonathan; Clark, Dorn; Radcliff, Roy; Leon-Velarde, Carlos; Larson, Nathan; Dave, Keron; Evans, Katharine; Crabtree, David; Hughes, Annette; Simpson, Helen; Holopainen, Jani; Wickstrand, Nina; Kauppinen, Mikko

    2014-01-01

    The Thermo Scientific SureTect Salmonella species Assay is a new real-time PCR assay for the detection of Salmonellae in food and environmental samples. This validation study was conducted using the AOAC Research Institute (RI) Performance Tested Methods program to validate the SureTect Salmonella species Assay in comparison to the reference method detailed in International Organization for Standardization 6579:2002 in a variety of food matrixes, namely, raw ground beef, raw chicken breast, raw ground pork, fresh bagged lettuce, pork frankfurters, nonfat dried milk powder, cooked peeled shrimp, pasteurized liquid whole egg, ready-to-eat meal containing beef, and stainless steel surface samples. With the exception of liquid whole egg and fresh bagged lettuce, which were tested in-house, all matrixes were tested by Marshfield Food Safety, Marshfield, WI, on behalf of Thermo Fisher Scientific. In addition, three matrixes (pork frankfurters, lettuce, and stainless steel surface samples) were analyzed independently as part of the AOAC-RI-controlled laboratory study by the University of Guelph, Canada. No significant difference by probability of detection or McNemars Chi-squared statistical analysis was found between the candidate or reference methods for any of the food matrixes or environmental surface samples tested during the validation study. Inclusivity and exclusivity testing was conducted with 117 and 36 isolates, respectively, which demonstrated that the SureTect Salmonella species Assay was able to detect all the major groups of Salmonella enterica subspecies enterica (e.g., Typhimurium) and the less common subspecies of S. enterica (e.g., arizoniae) and the rarely encountered S. bongori. None of the exclusivity isolates analyzed were detected by the SureTect Salmonella species Assay. Ruggedness testing was conducted to evaluate the performance of the assay with specific method deviations outside of the recommended parameters open to variation (enrichment time

  4. Comparison of methods for in vitro testing of susceptibility of porcine Mycoplasma species to antimicrobial agents.

    Science.gov (United States)

    Ter Laak, E A; Pijpers, A; Noordergraaf, J H; Schoevers, E C; Verheijden, J H

    1991-02-01

    The MICs of 18 antimicrobial agents used against strains of three porcine Mycoplasma species were determined by a serial broth dilution method. Twenty field strains of M. hyorhinis, ten field strains of M. hyopneumoniae, six field strains of M. flocculare, and the type strains of these species were tested. Twelve field strains and the type strain of M. hyorhinis were also tested by an agar dilution method. Tests were read at various time points. When the broth dilution method was used, the final MIC had to be read 2 days after color changes had stopped. MICs of tetracycline, oxytetracycline, doxycycline, and minocycline were low for the three Mycoplasma species tested. MICs of chlortetracycline were 8 to 16 times higher than MICs of the other tetracyclines. Spiramycin, tylosin, kitasamycin, spectinomycin, tiamulin, lincomycin, and clindamycin were effective against all strains of M. hyorhinis and M. hyopneumoniae. The quinolones were highly effective against M. hyopneumoniae but less effective against M. hyorhinis. The susceptibility patterns for M. hyopneumoniae and M. flocculare were similar.

  5. An experimental test of fitness variation across a hydrologic gradient predicts willow and poplar species distributions.

    Science.gov (United States)

    Wei, Xiaojing; Savage, Jessica A; Riggs, Charlotte E; Cavender-Bares, Jeannine

    2017-05-01

    Environmental filtering is an important community assembly process influencing species distributions. Contrasting species abundance patterns along environmental gradients are commonly used to provide evidence for environmental filtering. However, the same abundance patterns may result from alternative or concurrent assembly processes. Experimental tests are an important means to decipher whether species fitness varies with environment, in the absence of dispersal constraints and biotic interactions, and to draw conclusions about the importance of environmental filtering in community assembly. We performed an experimental test of environmental filtering in 14 closely related willow and poplar species (family Salicaceae) by transplanting cuttings of each species into 40 common gardens established along a natural hydrologic gradient in the field, where competition was minimized and herbivory was controlled. We analyzed species fitness responses to the hydrologic environment based on cumulative growth and survival over two years using aster fitness models. We also examined variation in nine drought and flooding tolerance traits expected to contribute to performance based on a priori understanding of plant function in relation to water availability and stress. We found substantial evidence that environmental filtering along the hydrologic gradient played a critical role in determining species distributions. Fitness variation of each species in the field experiment was used to model their water table depth optima. These optima predicted 68% of the variation in species realized hydrologic niches based on peak abundance in naturally assembled communities in the surrounding region. Multiple traits associated with water transport efficiency and water stress tolerance were correlated with species hydrologic niches, but they did not necessarily covary with each other. As a consequence, species occupying similar hydrologic niches had different combinations of trait values

  6. Germination and root elongation bioassays in six different plant species for testing Ni contamination in soil.

    Science.gov (United States)

    Visioli, Giovanna; Conti, Federica D; Gardi, Ciro; Menta, Cristina

    2014-04-01

    In vitro short-term chronic phytotoxicity germination and root elongation test were applied to test the effects of nickel (Ni) in seed germination and root elongation in six plants species: Cucumis sativus (Cucurbitaceae), Lepidium sativum and Brassica nigra (Brassicaceae), Trifolium alexandrinum and Medicago sativa (Fabaceae), Phacelia tanacetifolia (Boraginaceae). A naturally Ni rich soil was used to compare the results obtained. Unlike root elongation, germination was not affected by Ni in any of the six species tested. EC50 values, calculated on the root elongation, showed that Ni toxicity decreases in the following order: P. tanacetifolia > B. nigra > C. sativus > L. sativum > M. sativa > T. alexandrinum. The test conducted using soil elutriate revealed a significantly lower effect in both seed germination and root elongation when compared to the results obtained using untreated soil. Conversely, the test performed on soil confirmed the high sensitivity of C. sativus, P. tanacetifolia and L. sativum to Ni.

  7. Standard test method for distribution coefficients of inorganic species by the batch method

    CERN Document Server

    American Society for Testing and Materials. Philadelphia

    2010-01-01

    1.1 This test method covers the determination of distribution coefficients of chemical species to quantify uptake onto solid materials by a batch sorption technique. It is a laboratory method primarily intended to assess sorption of dissolved ionic species subject to migration through pores and interstices of site specific geomedia. It may also be applied to other materials such as manufactured adsorption media and construction materials. Application of the results to long-term field behavior is not addressed in this method. Distribution coefficients for radionuclides in selected geomedia are commonly determined for the purpose of assessing potential migratory behavior of contaminants in the subsurface of contaminated sites and waste disposal facilities. This test method is also applicable to studies for parametric studies of the variables and mechanisms which contribute to the measured distribution coefficient. 1.2 The values stated in SI units are to be regarded as standard. No other units of measurement a...

  8. Evaluation of the Leptospira species microscopic agglutination test in experimentally vaccinated cats and Leptospira species seropositivity in aged azotemic client-owned cats.

    Science.gov (United States)

    Shropshire, Sarah B; Veir, Julia K; Morris, Arianne K; Lappin, Michael R

    2016-10-01

    The objectives of this study were to validate the microscopic agglutination test (MAT) using feline sera, determine cross-reactivity of Borrelia burgdorferi antibodies in the MAT, and evaluate if there is an association between Leptospira species seropositivity in aged (⩾10 years) client-owned cats with and without azotemia (creatinine >2 g/dl). A four-serovar canine leptospiral vaccine was administered to two specific pathogen-free (SPF) cats on days 0 and 14. The MAT was performed intermittently until day 42 for the serovars Canicola, Grippotyphosa, Hardjo, Icterohaemorrhagiae, Pomona and Bratislava, with a cut-off value of ⩾1:100. Five purpose-bred cats were infested with wild-caught Ixodes scapularis adults with an average B burgdorferi infection rate of 50%, and tested for antibodies against B burgdorferi C6 peptide and DNA in skin biopsies, as well as by MAT. Sera from 66 azotemic and 75 non-azotemic cats ⩾10 years of age were tested for Leptospira species antibodies using the MAT and results were compared by the χ(2) test. Both SPF cats seroconverted by week 3 and formed antibodies against at least one serovar. There was no cross-reactivity in the MAT using samples from cats with antibodies to B burgdorferi. MAT results were positive for 4/66 azotemic cats and 8/75 non-azotemic cats; these results were not statistically different. The MAT can be interpreted using feline serum and does not appear to cross-react in cats with B burgdorferi antibodies. There was no association between Leptospira species MAT results and azotemia in this group of aged client-owned cats but further studies are needed to determine if leptospirosis contributes to feline chronic kidney disease. © The Author(s) 2015.

  9. Identification of Eastern United States Reticulitermes Termite Species via PCR-RFLP, Assessed Using Training and Test Data

    Directory of Open Access Journals (Sweden)

    Ryan C. Garrick

    2015-06-01

    Full Text Available Reticulitermes termites play key roles in dead wood decomposition and nutrient cycling in forests. They also damage man-made structures, resulting in considerable economic loss. In the eastern United States, five species (R. flavipes, R. virginicus, R. nelsonae, R. hageni and R. malletei have overlapping ranges and are difficult to distinguish morphologically. Here we present a molecular tool for species identification. It is based on polymerase chain reaction (PCR amplification of a section of the mitochondrial cytochrome oxidase subunit II gene, followed by a three-enzyme restriction fragment length polymorphism (RFLP assay, with banding patterns resolved via agarose gel electrophoresis. The assay was designed using a large set of training data obtained from a public DNA sequence database, then evaluated using an independent test panel of Reticulitermes from the Southern Appalachian Mountains, for which species assignments were determined via phylogenetic comparison to reference sequences. After refining the interpretive framework, the PCR-RFLP assay was shown to provide accurate identification of four co-occurring species (the fifth species, R. hageni, was absent from the test panel, so accuracy cannot yet be extended to training data. The assay is cost- and time-efficient, and will help improve knowledge of Reticulitermes species distributions.

  10. Prodigious polyphyly in imperilled freshwater pearly-mussels (Bivalvia: Unionidae): a phylogenetic test of species and generic designations

    Science.gov (United States)

    Lydeard, Charles; Minton, Russell L.; Williams, James D.

    2000-01-01

    Unionid bivalves or freshwater pearly-mussels (Unionoidea: Unionidae) serve as an exemplary system for examining many of the problems facing systematists and conservation biologists today. Most of the species and genera were described in the late 1800s and early 1900s, but few phylogenetic studies have been conducted to test conventional views of species and classification. Pearly-mussels of Gulf Coastal drainages of the southeastern United States from the Escambia (southern Alabama to Florida) to the Suwannee Rivers (Florida) are a unique fauna comprised of approximately 100 species, with about 30 endemic to the region. In this study, mitochondrial cytochrome c oxidase subunit I and 16S rRNA gene sequences were used to test the monophyly and to estimate evolutionary relationships of five unionid species representing three different genera. The molecular phylogenies depict all three genera as polyphyletic. The prodigious polyphyly exhibited within unionids is due to incorrect notions of homology and false assumptions about missing anatomical data. In contrast, the molecular phylogeny provides evidence to support the recognition of all five unionid species as distinct evolutionary entities. Furthermore, molecular genealogical evidence supports the elevation of Quincuncina infucata (Conrad) of the Suwannee River to species level, for which Q. kleiniana (Lea) is available.

  11. A comparison of dose-response models for death from hematological depression

    International Nuclear Information System (INIS)

    Morris, M.D.; Jones, T.D.

    1987-01-01

    Many radiation-induced lethality experiments that have been published for various mammalian species have been compiled into a database suitable to study interspecific variability of radiosensitivity, dose-rate dependence of sensitivity, dose-response behavior within each experiment, etc. The data compiled were restricted to continuous and nearly continuous exposures to photon radiations having source energies above 100 keV. Also, photon source energy, exposure geometry, and body weight considerations were used to select studies where the dose to hematopoietic marrow was nearly uniform, i.e., < +- 20%. The data base reflects 13 mammalian test species ranging from mouse to cattle. Some 211 studies were compiled but only 105 were documented in adequate detail to be useful in development and evaluation of dose-response models of interest to practical human exposures. Of the 105 studies, 70 were for various rodent species, and 35 were for nonrodent groups ranging from standard laboratory primates (body weight ∼5 kg) to cattle (body weight 375 kg). This paper considers seven different dose-response models which are tested for validity against those 105 studies. The dose-response models included: a right-skewed extreme value, a left-skewed extreme value model, log-logistic, log-probit, logistic, probit, and Weibull models. In general, the log transformed models did not improve model performance and the extreme value models did not seem consistent with the preponderance of the data. Overall, the probit and the logistic models seemed preferable over the Weibull model. 30 refs., 8 tabs

  12. A study of tobacco carcinogenesis XLVIII. Carcinogenicity of N'-nitrosonornicotine in mink (Mustela vison).

    Science.gov (United States)

    Koppang, N; Rivenson, A; Reith, A; Dahle, H K; Evensen, O; Hoffmann, D

    1992-11-01

    During tobacco processing and smoking, nicotine and nornicotine give rise to N'-nitrosonornicotine (NNN), a highly abundant, strong carcinogen. NNN is known to exert carcinogenic activity in mice, rats and hamsters. Major target organs for NNN carcinogenicity in the rat are the esophagus and the nasal mucosa, and in the Syrian golden hamster trachea and nasal mucosa. In comparison with the rat, the mink (Mustela vison) has a markedly expanded nasal mucosa. Therefore, we explored in this study whether the mink could serve as a non-rodent model for nasal carcinogenesis using NNN as the carcinogen. Twenty random-bred mink, beginning at the age of 3 weeks, received twice weekly s.c. injections of NNN, a total dose of 11.9 mM per animal over a 38 week period. All of the 19 mink at risk developed malignant tumors of both the respiratory and the olfactory region of the nose within 3.5 years. In most animals the malignant tumors, primarily esthesioneuroepithelioma, invaded the brain. Remarkably, NNN induced no other tumors in the mink. None of the control animals developed nasal tumors nor tumors at other sites during the 3.5 years of the assay. The historical data from the farm did not reveal any spontaneous occurrence of nasal tumors in mink at any age. This study supports the concept that NNN is a proven carcinogen for multiple species of mammals and that the mink can serve as a non-rodent, non-inbred animal model for nasal carcinogenesis, especially since NNN induces only tumors in the nasal cavity in this species and not at other sites, as it does in mice, rats and hamsters.

  13. Are trade-offs among species' ecological interactions scale dependent? A test using pitcher-plant inquiline species.

    Science.gov (United States)

    Kneitel, Jamie M

    2012-01-01

    Trade-offs among species' ecological interactions is a pervasive explanation for species coexistence. The traits associated with trade-offs are typically measured to mechanistically explain species coexistence at a single spatial scale. However, species potentially interact at multiple scales and this may be reflected in the traits among coexisting species. I quantified species' ecological traits associated with the trade-offs expected at both local (competitive ability and predator tolerance) and regional (competitive ability and colonization rate) community scales. The most common species (four protozoa and a rotifer) from the middle trophic level of a pitcher plant (Sarracenia purpurea) inquiline community were used to link species traits to previously observed patterns of species diversity and abundance. Traits associated with trade-offs (competitive ability, predator tolerance, and colonization rate) and other ecological traits (size, growth rate, and carrying capacity) were measured for each of the focal species. Traits were correlated with one another with a negative relationship indicative of a trade-off. Protozoan and rotifer species exhibited a negative relationship between competitive ability and predator tolerance, indicative of coexistence at the local community scale. There was no relationship between competitive ability and colonization rate. Size, growth rate, and carrying capacity were correlated with each other and the trade-off traits: Size was related to both competitive ability and predator tolerance, but growth rate and carrying capacity were correlated with predator tolerance. When partial correlations were conducted controlling for size, growth rate and carrying capacity, the trade-offs largely disappeared. These results imply that body size is the trait that provides the basis for ecological interactions and trade-offs. Altogether, this study showed that the examination of species' traits in the context of coexistence at different scales

  14. Testing deep-sea biodiversity paradigms on abyssal nematode genera and Acantholaimus species

    Science.gov (United States)

    Lins, Lidia; da Silva, Maria Cristina; Neres, Patrícia; Esteves, André Morgado; Vanreusel, Ann

    2018-02-01

    Biodiversity patterns in the deep sea have been extensively studied in the last decades. In this study, we investigated whether reputable concepts in deep-sea ecology also explain diversity and distribution patterns of nematode genera and species in the abyss. Among them, three paradigms were tackled: (1) the deep sea is a highly diverse environment at a local scale, while on a regional and even larger geographical scale, species and genus turnover is limited; (2) the biodiversity of deep-sea nematode communities changes with the nature and amount of organic matter input from the surface; and (3) patch-mosaic dynamics of the deep-sea environment drive local diversity. To test these hypotheses, diversity and density of nematode assemblages and of species of the genus Acantholaimus were studied along two abyssal E-W transects. These two transects were situated in the Southern Ocean ( 50°S) and the North Atlantic ( 10°N). Four different hierarchical scales were used to compare biodiversity: at the scale of cores, between stations from the same region, and between regions. Results revealed that the deep sea harbours a high diversity at a local scale (alpha diversity), but that turnover can be shaped by different environmental drivers. Therefore, these results question the second part of the paradigm about limited species turnover in the deep sea. Higher surface primary productivity was correlated with greater nematode densities, whereas diversity responses to the augmentation of surface productivity showed no trend. Areas subjected to a constant and low food input revealed similar nematode communities to other oligotrophic abyssal areas, while stations under high productivity were characterized by different dominant genera and Acantholaimus species, and by a generally low local diversity. Our results corroborate the species-energy hypothesis, where productivity can set a limit to the richness of an ecosystem. Finally, we observed no correlation between sediment

  15. Species detection using HyBeacon(®) probe technology: Working towards rapid onsite testing in non-human forensic and food authentication applications.

    Science.gov (United States)

    Dawnay, Nick; Hughes, Rebecca; Court, Denise Syndercombe; Duxbury, Nicola

    2016-01-01

    Identifying individual species or determining species' composition in an unknown sample is important for a variety of forensic applications. Food authentication, monitoring illegal trade in endangered species, forensic entomology, sexual assault case work and counter terrorism are just some of the fields that can require the detection of the biological species present. Traditional laboratory based approaches employ a wide variety of tools and technologies and exploit a number of different species specific traits including morphology, molecular differences and immuno-chemical analyses. A large number of these approaches require laboratory based apparatus and results can take a number of days to be returned to investigating authorities. Having a presumptive test for rapid identification could lead to savings in terms of cost and time and allow sample prioritisation if confirmatory testing in a laboratory is required later. This model study describes the development of an assay using a single HyBeacon(®) probe and melt curve analyses allowing rapid screening and authentication of food products labelled as Atlantic cod (Gadus morhua). Exploiting melt curve detection of species specific SNP sites on the COI gene the test allows detection of a target species (Atlantic cod) and closely related species which may be used as substitutes. The assay has been designed for use with the Field Portable ParaDNA system, a molecular detection platform for non-expert users. The entire process from sampling to result takes approximately 75min. Validation studies were performed on both single source genomic DNA, mixed genomic DNA and commercial samples. Data suggests the assay has a lower limit of detection of 31 pg DNA. The specificity of the assay to Atlantic cod was measured by testing highly processed food samples including frozen, defrosted and cooked fish fillets as well as fish fingers, battered fish fillet and fish pie. Ninety-six (92.7%) of all Atlantic cod food products

  16. Effects of sediment-spiked lufenuron on benthic macroinvertebrates in outdoor microcosms and single-species toxicity tests

    Energy Technology Data Exchange (ETDEWEB)

    Brock, T.C.M., E-mail: theo.brock@wur.nl [Alterra, Wageningen University and Research Centre, P.O. Box 47, 6700 AA Wageningen (Netherlands); Bas, D.A. [Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam (Netherlands); Belgers, J.D.M. [Alterra, Wageningen University and Research Centre, P.O. Box 47, 6700 AA Wageningen (Netherlands); Bibbe, L. [Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam (Netherlands); Boerwinkel, M-C.; Crum, S.J.H. [Alterra, Wageningen University and Research Centre, P.O. Box 47, 6700 AA Wageningen (Netherlands); Diepens, N.J. [Department of Aquatic Ecology and Water Quality Management, Wageningen University, P.O. Box 47, 6700 AA Wageningen (Netherlands); Kraak, M.H.S.; Vonk, J.A. [Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam (Netherlands); Roessink, I. [Alterra, Wageningen University and Research Centre, P.O. Box 47, 6700 AA Wageningen (Netherlands)

    2016-08-15

    Highlights: • In outdoor microcosms constructed with lufenuron-spiked sediment we observed that this insecticide persistent in the sediment compartment. • Sediment exposure to lufenuron caused population-level declines (insects and crustaceans) and increases (mainly oligochaete worms) of benthic invertebrates. • The direct and indirect effects observed in the microcosms were supported by results of sediment-spiked single species tests with Chironomus riparius, Hyalella azteca and Lumbriculus variegatus. • The tier-1 effect assessment procedure for sediment organisms recommended by the European Food Safety Authority is protective for the treatment-related responses observed in the microcosm test. - Abstract: Sediment ecotoxicity studies were conducted with lufenuron to (i) complement the results of a water-spiked mesocosm experiment with this lipophilic benzoylurea insecticide, (ii) to explore the predictive value of laboratory single-species tests for population and community-level responses of benthic macroinvertebrates, and (iii) to calibrate the tier-1 effect assessment procedure for sediment organisms. For this purpose the concentration-response relationships for macroinvertebrates between sediment-spiked microcosms and those of 28-d sediment-spiked single-species toxicity tests with Chironomus riparius, Hyalella azteca and Lumbriculus variegatus were compared. Lufenuron persisted in the sediment of the microcosms. On average, 87.7% of the initial lufenuron concentration could still be detected in the sediment after 12 weeks. Overall, benthic insects and crustaceans showed treatment-related declines and oligochaetes treatment-related increases. The lowest population-level NOEC in the microcosms was 0.79 μg lufenuron/g organic carbon in dry sediment (μg a.s./g OC) for Tanytarsini, Chironomini and Dero sp. Multivariate analysis of the responses of benthic macroinvertebrates revealed a community-level NOEC of 0.79 μg a.s./g OC. The treatment

  17. Modeling hemoglobin and hemoglobin:haptoglobin complex clearance in a non-rodent species–pharmacokinetic and therapeutic implications

    OpenAIRE

    Boretti, Felicitas S.; Baek, Jin Hyen; Palmer, Andre F.; Schaer, Dominik J.; Buehler, Paul W.

    2014-01-01

    Background: Haptoglobin (Hp) prevents hemoglobin (Hb) extravasation and attenuates Hb induced tissue oxidation and vasoconstriction. Small animal models such as mouse, rat and guinea pig appear to demonstrate proof-of-concept for Hb neutralization by Hp in diverse pre-clinical conditions. However, these species differ significantly from humans in the clearance of Hb:Hp and demonstrate long persistence of circulating Hb:Hp complexes. Objective: The focus of this study is to understand Hb:Hp...

  18. Ecology of Floristic Quality Assessment: testing for correlations between coefficients of conservatism, species traits and mycorrhizal responsiveness.

    Science.gov (United States)

    Bauer, Jonathan T; Koziol, Liz; Bever, James D

    2018-02-01

    Many plant species are limited to habitats relatively unaffected by anthropogenic disturbance, so protecting these undisturbed habitats is essential for plant conservation. Coefficients of conservatism (C values) were developed as indicators of a species' sensitivity to anthropogenic disturbance, and these values are used in Floristic Quality Assessment as a means of assessing natural areas and ecological restoration. However, assigning of these values is subjective and improved quantitative validation of C values is needed. We tested whether there are consistent differences in life histories between species with high and low C values. To do this, we grew 54 species of tallgrass prairie plants in a greenhouse and measured traits that are associated with trade-offs on the fast-slow continuum of life-history strategies. We also grew plants with and without mycorrhizal fungi as a test of these species' reliance on this mutualism. We compared these traits and mycorrhizal responsiveness to C values. We found that six of the nine traits we measured were correlated with C values, and together, traits predicted up to 50 % of the variation in C values. Traits including fast growth rates and greater investment in reproduction were associated with lower C values, and slow growth rates, long-lived leaves and high root:shoot ratios were associated with higher C values. Additionally, plants with high C values and a slow life history were more responsive to mutualisms with mycorrhizal fungi. Overall, our results connect C values with life-history trade-offs, indicating that high C value species tend to share a suite of traits associated with a slow life history.

  19. Evaluating ecosystem services provided by non-native species: an experimental test in California grasslands.

    Science.gov (United States)

    Stein, Claudia; Hallett, Lauren M; Harpole, W Stanley; Suding, Katharine N

    2014-01-01

    The concept of ecosystem services--the benefits that nature provides to human's society--has gained increasing attention over the past decade. Increasing global abiotic and biotic change, including species invasions, is threatening the secure delivery of these ecosystem services. Efficient evaluation methods of ecosystem services are urgently needed to improve our ability to determine management strategies and restoration goals in face of these new emerging ecosystems. Considering a range of multiple ecosystem functions may be a useful way to determine such strategies. We tested this framework experimentally in California grasslands, where large shifts in species composition have occurred since the late 1700's. We compared a suite of ecosystem functions within one historic native and two non-native species assemblages under different grazing intensities to address how different species assemblages vary in provisioning, regulatory and supporting ecosystem services. Forage production was reduced in one non-native assemblage (medusahead). Cultural ecosystem services, such as native species diversity, were inherently lower in both non-native assemblages, whereas most other services were maintained across grazing intensities. All systems provided similar ecosystem services under the highest grazing intensity treatment, which simulated unsustainable grazing intensity. We suggest that applying a more comprehensive ecosystem framework that considers multiple ecosystem services to evaluate new emerging ecosystems is a valuable tool to determine management goals and how to intervene in a changing ecosystem.

  20. Habitat, food, and small mammal community structure in Namaqualand

    Directory of Open Access Journals (Sweden)

    M. van Deventer

    2006-12-01

    Full Text Available The effect of habitat differences and food availability on small mammal (rodent and elephant shrew species richness, diversity, density and biomass was investigated in Namaqualand, South Africa. Species richness in the three habitats sampled, namely Upland Succulent Karoo, Dry Riverine Shrub and North-western Mountain Renosterveld was low, with only 2–4 species per habitat. Rodents trapped were predominantly Gerbillurus paeba and Aethomys namaquensis, with fewer Mus minutoides and Petromyscus sp. The only non-rodent was the elephant shrew Elephantulus edwardii. Ten habitat features, the percentage of total plant cover, tree cover, shrub cover, grass cover, plant litter, total basal cover, sand, gravel or rock cover, and the dominant plant height were recorded at 30 randomly chosen points on five sampling grids in each habitat. Small mammal density and biomass was significantly correlated with food availability (green foliage cover, seeds, and relative density and biomass of insects. Species richness and diversity of small mammals were significantly correlated with shrub cover. Numbers and biomass of specific species correlated significantly with different habitat features in each case.

  1. Use of butterflies as nontarget insect test species and the acute toxicity and hazard of mosquito control insecticides.

    Science.gov (United States)

    Hoang, Tham C; Pryor, Rachel L; Rand, Gary M; Frakes, Robert A

    2011-04-01

    Honeybees are the standard insect test species used for toxicity testing of pesticides on nontarget insects for the U.S. Environmental Protection Agency (U.S. EPA) under the Federal Insecticide Fungicide and Rodenticide Act (FIFRA). Butterflies are another important insect order and a valued ecological resource in pollination. The current study conducted acute toxicity tests with naled, permethrin, and dichlorvos on fifth larval instar (caterpillars) and adults of different native Florida, USA, butterfly species to determine median lethal doses (24-h LD50), because limited acute toxicity data are available with this major insect group. Thorax- and wing-only applications of each insecticide were conducted. Based on LD50s, thorax and wing application exposures were acutely toxic to both caterpillars and adults. Permethrin was the most acutely toxic insecticide after thorax exposure to fifth instars and adult butterflies. However, no generalization on acute toxicity (sensitivity) of the insecticides could be concluded based on exposures to fifth instars versus adult butterflies or on thorax versus wing exposures of adult butterflies. A comparison of LD50s of the butterflies from this study (caterpillars and adults) with honeybee LD50s for the adult mosquito insecticides on a µg/organism or µg/g basis indicates that several butterfly species are more sensitive to these insecticides than are honeybees. A comparison of species sensitivity distributions for all three insecticides shows that permethrin had the lowest 10th percentile. Using a hazard quotient approach indicates that both permethrin and naled applications in the field may present potential acute hazards to butterflies, whereas no acute hazard of dichlorvos is apparent in butterflies. Butterflies should be considered as potential test organisms when nontarget insect testing of pesticides is suggested under FIFRA. Copyright © 2011 SETAC.

  2. Distribution of the Chuckwalla, Western Burrowing Owl, and Six Bat Species on the Nevada Test Site

    Energy Technology Data Exchange (ETDEWEB)

    Cathy A. Willis

    1997-05-01

    Field Surveys were conducted in 1996 to determine the current distribution of several animal species of concern on the Nevada Test Site (NTS). They included the chuckwall (Sauromalus obesus), western burrowing owl (Speotyto cunicularia), and six species of bats. Nineteen chuckwallas and 118 scat locations were found during the chuckwalla field study. Eighteen western burrowing owls were found at 12 sighting locations during the 1996 field study. Of the eleven bat species of concern which might occur on the NTS, five, and possibly six, were captured during this survey. The U.S. Department of Energy, Nevada Operations Office, takes certain management actions to protect and conserve the chuckwalla, western burrowing owl, and bats on the NTS. These actions are described and include: (1) conducting surveys at sites of proposed land-disturbing activities (2) altering projects whenever possible to avoid or minimize impacts to these species (3) maintaining a geospatial database of known habitat for species of concern (4) sharing sighting and trap location data gathered on the NTS with other local land and resource managers, and (5) conducting periodic field surveys to monitor these species distribution and relative abundance on the NTS.

  3. Rapid diagnostic tests as a source of DNA for Plasmodium species-specific real-time PCR

    Directory of Open Access Journals (Sweden)

    Van Esbroeck Marjan

    2011-03-01

    Full Text Available Abstract Background This study describes the use of malaria rapid diagnostic tests (RDTs as a source of DNA for Plasmodium species-specific real-time PCR. Methods First, the best method to recover DNA from RDTs was investigated and then the applicability of this DNA extraction method was assessed on 12 different RDT brands. Finally, two RDT brands (OptiMAL Rapid Malaria Test and SDFK60 malaria Ag Plasmodium falciparum/Pan test were comprehensively evaluated on a panel of clinical samples submitted for routine malaria diagnosis at ITM. DNA amplification was done with the 18S rRNA real-time PCR targeting the four Plasmodium species. Results of PCR on RDT were compared to those obtained by PCR on whole blood samples. Results Best results were obtained by isolating DNA from the proximal part of the nitrocellulose component of the RDT strip with a simple DNA elution method. The PCR on RDT showed a detection limit of 0.02 asexual parasites/μl, which was identical to the same PCR on whole blood. For all 12 RDT brands tested, DNA was detected except for one brand when a low parasite density sample was applied. In RDTs with a plastic seal covering the nitrocellulose strip, DNA extraction was hampered. PCR analysis on clinical RDT samples demonstrated correct identification for single species infections for all RDT samples with asexual parasites of P. falciparum (n = 60, Plasmodium vivax (n = 10, Plasmodium ovale (n = 10 and Plasmodium malariae (n = 10. Samples with only gametocytes were detected in all OptiMAL and in 10 of the 11 SDFK60 tests. None of the negative samples (n = 20 gave a signal by PCR on RDT. With PCR on RDT, higher Ct-values were observed than with PCR on whole blood, with a mean difference of 2.68 for OptiMAL and 3.53 for SDFK60. Mixed infections were correctly identified with PCR on RDT in 4/5 OptiMAL tests and 2/5 SDFK60 tests. Conclusions RDTs are a reliable source of DNA for Plasmodium real-time PCR. This study demonstrates the

  4. Factors That Modulate Neurogenesis: A Top-Down Approach.

    Science.gov (United States)

    LaDage, Lara D

    2016-08-24

    Although hippocampal neurogenesis in the adult brain has been conserved across the vertebrate lineage, laboratory studies have primarily examined this phenomenon in rodent models. This approach has been successful in elucidating important factors and mechanisms that can modulate rates of hippocampal neurogenesis, including hormones, environmental complexity, learning and memory, motor stimulation, and stress. However, recent studies have found that neurobiological research on neurogenesis in rodents may not easily translate to, or explain, neurogenesis patterns in nonrodent systems, particularly in species examined in the field. This review examines some of the evolutionary and ecological variables that may also modulate neurogenesis patterns. This 'top-down' and more naturalistic approach, which incorporates ecology and natural history, particularly of nonmodel species, may allow for a more comprehensive understanding of the functional significance of neurogenesis. © 2016 S. Karger AG, Basel.

  5. Should the Space Station be an ark?

    Science.gov (United States)

    Wassersug, R

    1994-08-01

    This essay explores the pros and cons of maximizing the number of species that can be maintained on the Space Station. It reviews some of the history of comparative space biology to show that different cultures have different perspectives on the study of non-traditional research organisms (ie non-rodents) in space. Despite these differences, there are simple principles that all international partners in the Space Station endeavour should be able to uphold when deciding what facilities to build and what species to fly. As an argument for maximizing the taxonomic diversity on the Space Station, examples are given to show how very similar organisms may have different reactions to microgravity. At the same time the political pressure in the USA to make the Space Station an institution specifically servicing the 'health, well-being and economic benefits of people on earth', is acknowledged. Ultimately the justification for what species will be on the Space Station should rest with the quality of the scientific questions being asked.

  6. Samd7 is a cell type-specific PRC1 component essential for establishing retinal rod photoreceptor identity.

    Science.gov (United States)

    Omori, Yoshihiro; Kubo, Shun; Kon, Tetsuo; Furuhashi, Mayu; Narita, Hirotaka; Kominami, Taro; Ueno, Akiko; Tsutsumi, Ryotaro; Chaya, Taro; Yamamoto, Haruka; Suetake, Isao; Ueno, Shinji; Koseki, Haruhiko; Nakagawa, Atsushi; Furukawa, Takahisa

    2017-09-26

    Precise transcriptional regulation controlled by a transcription factor network is known to be crucial for establishing correct neuronal cell identities and functions in the CNS. In the retina, the expression of various cone and rod photoreceptor cell genes is regulated by multiple transcription factors; however, the role of epigenetic regulation in photoreceptor cell gene expression has been poorly understood. Here, we found that Samd7, a rod-enriched sterile alpha domain (SAM) domain protein, is essential for silencing nonrod gene expression through H3K27me3 regulation in rod photoreceptor cells. Samd7- null mutant mice showed ectopic expression of nonrod genes including S-opsin in rod photoreceptor cells and rod photoreceptor cell dysfunction. Samd7 physically interacts with Polyhomeotic homologs (Phc proteins), components of the Polycomb repressive complex 1 (PRC1), and colocalizes with Phc2 and Ring1B in Polycomb bodies. ChIP assays showed a significant decrease of H3K27me3 in the genes up-regulated in the Samd7 -deficient retina, showing that Samd7 deficiency causes the derepression of nonrod gene expression in rod photoreceptor cells. The current study suggests that Samd7 is a cell type-specific PRC1 component epigenetically defining rod photoreceptor cell identity.

  7. Evaluating the biodegradability and effects of dispersed oil using Arctic test species and conditions: phase 2 activities

    Energy Technology Data Exchange (ETDEWEB)

    MacFarlin, Kelly M.; Perkins, Robert A. [University of Alaska Fairbanks (United States)], email: raperkins@alaska.edu; Gardiner, William W.; Word, Jack D. [NewFields NorthWest (United States)

    2011-07-01

    In the event of a marine oil spill, managers have to make correct and rapid decisions, weighing a number of possibilities, which include natural attenuation, mechanical recovery, in situ burning, and/or chemical dispersion. To do this, the relative toxicity of physically and chemically dispersed fresh oil and the rates of biodegradation for fresh and weathered oil need to be understood in advance. A joint industry program was established in 2008 to research and discuss these areas. Phase 1 activities included determining the species relevant to the Beaufort and Chukchi Sea ecosystems, creating and setting up a toxicity and biodegradation laboratory with a cold room in Barrow, Alaska, developing collection and culture methods for test organisms, and developing toxicity and biodegradation test protocols. The second phase of this now completed research is discussed in this paper. It consisted of toxicity testing of the local environmentally significant species, the copepod (C. glacialis), Arctic cod (B. saida), and larval sculpin (Myoxocephalus sp.).

  8. Combining and Comparing Coalescent, Distance and Character-Based Approaches for Barcoding Microalgaes: A Test with Chlorella-Like Species (Chlorophyta.

    Directory of Open Access Journals (Sweden)

    Shanmei Zou

    Full Text Available Several different barcoding methods of distinguishing species have been advanced, but which method is the best is still controversial. Chlorella is becoming particularly promising in the development of second-generation biofuels. However, the taxonomy of Chlorella-like organisms is easily confused. Here we report a comprehensive barcoding analysis of Chlorella-like species from Chlorella, Chloroidium, Dictyosphaerium and Actinastrum based on rbcL, ITS, tufA and 16S sequences to test the efficiency of traditional barcoding, GMYC, ABGD, PTP, P ID and character-based barcoding methods. First of all, the barcoding results gave new insights into the taxonomic assessment of Chlorella-like organisms studied, including the clear species discrimination and resolution of potentially cryptic species complexes in C. sorokiniana, D. ehrenbergianum and C. Vulgaris. The tufA proved to be the most efficient barcoding locus, which thus could be as potential "specific barcode" for Chlorella-like species. The 16S failed in discriminating most closely related species. The resolution of GMYC, PTP, P ID, ABGD and character-based barcoding methods were variable among rbcL, ITS and tufA genes. The best resolution for species differentiation appeared in tufA analysis where GMYC, PTP, ABGD and character-based approaches produced consistent groups while the PTP method over-split the taxa. The character analysis of rbcL, ITS and tufA sequences could clearly distinguish all taxonomic groups respectively, including the potentially cryptic lineages, with many character attributes. Thus, the character-based barcoding provides an attractive complement to coalescent and distance-based barcoding. Our study represents the test that proves the efficiency of multiple DNA barcoding in species discrimination of microalgaes.

  9. Combining and Comparing Coalescent, Distance and Character-Based Approaches for Barcoding Microalgaes: A Test with Chlorella-Like Species (Chlorophyta)

    Science.gov (United States)

    Zou, Shanmei; Fei, Cong; Song, Jiameng; Bao, Yachao; He, Meilin; Wang, Changhai

    2016-01-01

    Several different barcoding methods of distinguishing species have been advanced, but which method is the best is still controversial. Chlorella is becoming particularly promising in the development of second-generation biofuels. However, the taxonomy of Chlorella–like organisms is easily confused. Here we report a comprehensive barcoding analysis of Chlorella-like species from Chlorella, Chloroidium, Dictyosphaerium and Actinastrum based on rbcL, ITS, tufA and 16S sequences to test the efficiency of traditional barcoding, GMYC, ABGD, PTP, P ID and character-based barcoding methods. First of all, the barcoding results gave new insights into the taxonomic assessment of Chlorella-like organisms studied, including the clear species discrimination and resolution of potentially cryptic species complexes in C. sorokiniana, D. ehrenbergianum and C. Vulgaris. The tufA proved to be the most efficient barcoding locus, which thus could be as potential “specific barcode” for Chlorella-like species. The 16S failed in discriminating most closely related species. The resolution of GMYC, PTP, P ID, ABGD and character-based barcoding methods were variable among rbcL, ITS and tufA genes. The best resolution for species differentiation appeared in tufA analysis where GMYC, PTP, ABGD and character-based approaches produced consistent groups while the PTP method over-split the taxa. The character analysis of rbcL, ITS and tufA sequences could clearly distinguish all taxonomic groups respectively, including the potentially cryptic lineages, with many character attributes. Thus, the character-based barcoding provides an attractive complement to coalescent and distance-based barcoding. Our study represents the test that proves the efficiency of multiple DNA barcoding in species discrimination of microalgaes. PMID:27092945

  10. Low temperature storage test phase 2 : identification of problem species

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2009-12-15

    The use of renewable fuels such as biodiesel, in motor vehicle fuels is expected to grow rapidly in North America as a result of governmental mandates. Biodiesel is a fuel component made from plant and animal feedstocks via a transesterification process. The fatty acid methyl esters (FAME) of biodiesel have cloud points that range from 5 degrees C to -15 degrees C. The poor low temperature performance of blends containing FAME must be understood in order to avoid operability issues. This paper presented the results of several testing programs conducted by researchers to investigate filter plugging in biodiesel fuels caused by high levels of saturated monoglycerides. The low temperature storage stability of 57 biodiesel fuels comprised of B5 and B20 made with canola methyl ester (CME), soybean methyl ester (SME), tallow methyl ester (TME) and palm methyl ester (PME) was investigated. Filter blocking tests were conducted to assess storage stability. Deposits from the blends were analyzed using gas chromatography and mass spectrometry (GC-MS) in order to identify the problem species. Results of the study confirmed the deleterious impact of saturated mono-glycerides in FAME on the low temperature operability of filters in fuel handling systems. 11 refs., 7 tabs., 5 figs. 9 appendices.

  11. Lichen species preference by reindeer

    Energy Technology Data Exchange (ETDEWEB)

    Holleman, D F; Luick, J R

    1977-08-01

    The preference by reindeer for five species of lichens commonly found on Central Alaska rangelands was tested under controlled laboratory conditions. Results indicate that reindeer are strongly selective species in their lichen grazing habits. The five tested species ranged as follows in order of decreasing acceptibility: Caldonia alpestris, C. rangiferina, Stereocaulon paschale, Cetraria richardsonii, and Peltigera aphthosa.

  12. Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass--Sequence Relationships with an Innovative Metabarcoding Protocol.

    Directory of Open Access Journals (Sweden)

    Vasco Elbrecht

    Full Text Available Metabarcoding is an emerging genetic tool to rapidly assess biodiversity in ecosystems. It involves high-throughput sequencing of a standard gene from an environmental sample and comparison to a reference database. However, no consensus has emerged regarding laboratory pipelines to screen species diversity and infer species abundances from environmental samples. In particular, the effect of primer bias and the detection limit for specimens with a low biomass has not been systematically examined, when processing samples in bulk. We developed and tested a DNA metabarcoding protocol that utilises the standard cytochrome c oxidase subunit I (COI barcoding fragment to detect freshwater macroinvertebrate taxa. DNA was extracted in bulk, amplified in a single PCR step, and purified, and the libraries were directly sequenced in two independent MiSeq runs (300-bp paired-end reads. Specifically, we assessed the influence of specimen biomass on sequence read abundance by sequencing 31 specimens of a stonefly species with known haplotypes spanning three orders of magnitude in biomass (experiment I. Then, we tested the recovery of 52 different freshwater invertebrate taxa of similar biomass using the same standard barcoding primers (experiment II. Each experiment was replicated ten times to maximise statistical power. The results of both experiments were consistent across replicates. We found a distinct positive correlation between species biomass and resulting numbers of MiSeq reads. Furthermore, we reliably recovered 83% of the 52 taxa used to test primer bias. However, sequence abundance varied by four orders of magnitudes between taxa despite the use of similar amounts of biomass. Our metabarcoding approach yielded reliable results for high-throughput assessments. However, the results indicated that primer efficiency is highly species-specific, which would prevent straightforward assessments of species abundance and biomass in a sample. Thus, PCR

  13. Relationships within the Proteobacteria of plant pathogenic Acidovorax species and subspecies, Burkholderia species, and Herbaspirillum rubrisubalbicans by sequence analysis of 16S rDNA, numerical analysis and determinative tests.

    Science.gov (United States)

    Hu, F P; Young, J M; Triggs, C M; Park, D C; Saul, D J

    2001-12-01

    Sequence data for 16S rDNA of the type strains of Acidovorax avenae subsp. avenae, A. avenae subsp. cattleyae, A. avenae subsp. citrulli, A. konjaci and Herbaspirillum rubrisubalbicans were compared with GenBank library accessions of Burkholderia spp., Comamonas sp., Ralstonia solanacearum and Variovorax sp. Maximum Parsimony analysis produced two clusters: 1. Acidovorax spp., Comamonas sp., and Variovorax sp. (all in the Comamonadaceae), and 2. Burkholderia spp., Ralstonia solanacearum, and Herbaspirillum rubrisubalbicans. Maximum Likelihood analysis produced only one cluster (of the Comamonadaceae). Using nutritional and laboratory tests, all Acidovorax spp., Burkholderia spp., and Herbaspirillum rubrisubalbicans were discriminated in distinct clusters at the species level, and could be identified by selected determinative tests. There were no phenotypic tests constituted as a circumscription of the genera and which permitted the allocation of strains to genera. Strain identification as species allowed allocation to genera only by inference. The nomenclatural implications of these data are discussed.

  14. Elimination of Whole Effluent Toxicity NPDES Permit Limits through the Use of an Alternative Testing Species and Reasonable Potential Analysis

    International Nuclear Information System (INIS)

    PAYNE, W.L.

    2004-01-01

    The cladoceran, Ceriodaphnia dubia (C. dubia), is required by the State of South Carolina to be used in whole effluent toxicity (WET) compliance tests in order to meet limits contained within National Pollutant Discharge Elimination System (NPDES) permits. Westinghouse Savannah River Company (WSRC) experienced WET test failures for no clear reason over a long period of time. Toxicity identification examinations on effluents did not indicate the presence of toxicants; therefore, the WET test itself was brought under suspicion. Research was undertaken with an alternate cladoceran, Daphnia ambigua (D. ambigua). It was determined that this species survives better in soft water, so approval was obtained from regulating authorities to use this ''alternate'' species in WET tests. The result was better test results and elimination of non-compliances. The successful use of D. ambigua allowed WSRC to gain approval from the South Carolina Department of Health and Environmental Control (SCDHEC) to remove WET limits from the NPDES permit

  15. Diet before and during Pregnancy and Offspring Health: The Importance of Animal Models and What Can Be Learned from Them.

    Science.gov (United States)

    Chavatte-Palmer, Pascale; Tarrade, Anne; Rousseau-Ralliard, Delphine

    2016-06-14

    This review article outlines epidemiologic studies that support the hypothesis that maternal environment (including early nutrition) plays a seminal role in determining the offspring's long-term health and metabolism, known as the concept of Developmental Origins of Health and Diseases (DOHaD). In this context, current concerns are particularly focused on the increased incidence of obesity and diabetes, particularly in youth and women of child-bearing age. We summarize key similarities, differences and limitations of various animal models used to study fetal programming, with a particular focus on placentation, which is critical for translating animal findings to humans. This review will assist researchers and their scientific audience in recognizing the pros and cons of various rodent and non-rodent animal models used to understand mechanisms involved in fetal programming. Knowledge gained will lead to improved translation of proposed interventional therapies before they can be implemented in humans. Although rodents are essential for fundamental exploration of biological processes, other species such as rabbits and other domestic animals offer more tissue-specific physiological (rabbit placenta) or physical (ovine maternal and lamb birth weight) resemblances to humans. We highlight the important maternal, placental, and fetal/neonatal characteristics that contribute to developmentally programmed diseases, specifically in offspring that were affected in utero by undernutrition, overnutrition or maternal diabetes. Selected interventions aimed at prevention are summarized with a specific focus on the 1000 days initiative in humans, and maternal exercise or modification of the n-3/n-6 polyunsaturated fatty acid (PUFA) balance in the diet, which are currently being successfully tested in animal models to correct or reduce adverse prenatal programming. Animal models are essential to understand mechanisms involved in fetal programming and in order to propose

  16. Diet before and during Pregnancy and Offspring Health: The Importance of Animal Models and What Can Be Learned from Them

    Directory of Open Access Journals (Sweden)

    Pascale Chavatte-Palmer

    2016-06-01

    Full Text Available This review article outlines epidemiologic studies that support the hypothesis that maternal environment (including early nutrition plays a seminal role in determining the offspring’s long-term health and metabolism, known as the concept of Developmental Origins of Health and Diseases (DOHaD. In this context, current concerns are particularly focused on the increased incidence of obesity and diabetes, particularly in youth and women of child-bearing age. We summarize key similarities, differences and limitations of various animal models used to study fetal programming, with a particular focus on placentation, which is critical for translating animal findings to humans. This review will assist researchers and their scientific audience in recognizing the pros and cons of various rodent and non-rodent animal models used to understand mechanisms involved in fetal programming. Knowledge gained will lead to improved translation of proposed interventional therapies before they can be implemented in humans. Although rodents are essential for fundamental exploration of biological processes, other species such as rabbits and other domestic animals offer more tissue-specific physiological (rabbit placenta or physical (ovine maternal and lamb birth weight resemblances to humans. We highlight the important maternal, placental, and fetal/neonatal characteristics that contribute to developmentally programmed diseases, specifically in offspring that were affected in utero by undernutrition, overnutrition or maternal diabetes. Selected interventions aimed at prevention are summarized with a specific focus on the 1000 days initiative in humans, and maternal exercise or modification of the n-3/n-6 polyunsaturated fatty acid (PUFA balance in the diet, which are currently being successfully tested in animal models to correct or reduce adverse prenatal programming. Animal models are essential to understand mechanisms involved in fetal programming and in order to

  17. Survival, Pb-uptake and behaviour of three species of earthworm in Pb treated soils determined using an OECD-style toxicity test and a soil avoidance test

    International Nuclear Information System (INIS)

    Langdon, Caroline J.; Hodson, Mark E.; Arnold, Rebecca E.; Black, Stuart

    2005-01-01

    Mature (clitellate) Eisenia andrei Bouche (ultra epigeic), Lumbricus rubellus Hoffmeister (epigeic), and Aporrectodea caliginosa (Savigny) (endogeic) earthworms were placed in soils treated with Pb(NO 3 ) 2 to have concentrations in the range 1000 to 10 000 mg Pb kg -1 . After 28 days LC50 -95%confidencelimit +95%confidencelimit values were E. andrei5824 -361 +898 mg Pb kg -1 , L. rubellus2867 -193 +145 mg Pb kg -1 and A. caliginosa2747 -304 +239 mg Pb kg -1 and EC50s for weight change were E. andrei2841 -68 +150 mg Pb kg -1 , L. rubellus1303 -201 +240 mg Pb kg -1 and A. caliginosa1208 -206 +212 mg Pb kg -1 . At any given soil Pb concentration, Pb tissue concentrations after 28 days were the same for all three earthworm species. In a soil avoidance test there was no difference between the behaviour of the different species. The lower sensitivity to Pb exhibited by E. andrei is most likely due to physiological adaptations associated with the modes of life of the earthworms, and could have serious implications for the use of this earthworm as the species of choice in standard toxicological testing.

  18. Etest and Sensititre YeastOne Susceptibility Testing of Echinocandins against Candida Species from a Single Center in Austria.

    Science.gov (United States)

    Aigner, Maria; Erbeznik, Thomas; Gschwentner, Martin; Lass-Flörl, Cornelia

    2017-08-01

    Candida species were tested for susceptibility to caspofungin, anidulafungin, and micafungin in order to evaluate the roles of Etest and Sensititre YeastOne in antifungal susceptibility testing for daily routines and to survey resistance. A total of 104 Candida species isolates detected from blood cultures were investigated. With EUCAST broth microdilution as the reference method, essential agreement (EA), categorical agreement (CA), very major errors (VME), major errors (ME), and minor (MIN) errors were assessed by reading MICs at 18, 24, and 48 h. By use of EUCAST broth microdilution and species-specific clinical breakpoints (CBPs), echinocandin resistance was not detected during the study period. Using EUCAST CBPs, MIC readings at 24 h for the Etest and Sensititre YeastOne resulted in CA levels of 99% and 93% for anidulafungin and 99% and 97% for micafungin. Using revised CLSI CBPs for caspofungin, CA levels were 92% and 99% for Etest and Sensititre YeastOne. The Etest proved an excellent, easy-to-handle alternative method for testing susceptibility to anidulafungin and micafungin. Due to misclassifications, the Etest is less suitable for testing susceptibility to caspofungin (8% of isolates falsely tested resistant). The CA levels of Sensititre YeastOne were 93% and 97% for anidulafungin and micafungin (24 h) by use of EUCAST CBPs and increased to 100% for both antifungals if CLSI CBPs were applied and to 100% and 99% if Sensititre YeastOne epidemiological cutoff values (ECOFFs) were applied. No one echinocandin could be demonstrated to be superior to another in vitro Since resistance was lacking among our Candida isolates, we cannot derive any recommendation from accurate resistance detection by the Etest and Sensititre YeastOne. Copyright © 2017 American Society for Microbiology.

  19. Short Communication. Comparing flammability traits among fire-stricken (low elevation) and non fire-stricken (high elevation) conifer forest species of Europe: A test of the Mutch hypothesis

    OpenAIRE

    A. P. Dimitrakopoulos; I. D. Mitsopoulos; A. Kaliva

    2013-01-01

    Aim of study. The flammability of the main coniferous forest species of Europe, divided into two groups according to their fire regime and altitudinal distribution, was tested in an effort to detect species-specific differences that may have an influence on community-wide fire regimes.Area of study. Conifer species comprising low- and high-elevation forests in Europe.Materials and Methods. The following conifer species were tested: low elevation; Pinus halepensis (Aleppo pine), Pinus brutia (...

  20. Suitability of seven species of soil-inhabiting invertebrates for testing toxicity of pesticides in soil pore water

    NARCIS (Netherlands)

    Ronday, R.; Houx, N.W.H.

    1996-01-01

    This study assessed the suitability of seven species of soil invertebrates for toxicologically testing pesticides in water. Requirements were that the organisms must survive in water, be easy to handle, be easy to breed, be sensitive to pesticides, and show unambiguous toxicological effects. The

  1. Use of genome sequence data in the design and testing of SSR markers for Phytophthora species

    Directory of Open Access Journals (Sweden)

    Cardle Linda

    2008-12-01

    Full Text Available Abstract Background Microsatellites or single sequence repeats (SSRs are a powerful choice of marker in the study of Phytophthora population biology, epidemiology, ecology, genetics and evolution. A strategy was tested in which the publicly available unigene datasets extracted from genome sequences of P. infestans, P. sojae and P. ramorum were mined for candidate SSR markers that could be applied to a wide range of Phytophthora species. Results A first approach, aimed at the identification of polymorphic SSR loci common to many Phytophthora species, yielded 171 reliable sequences containing 211 SSRs. Microsatellites were identified from 16 target species representing the breadth of diversity across the genus. Repeat number ranged from 3 to 16 with most having seven repeats or less and four being the most commonly found. Trinucleotide repeats such as (AAGn, (AGGn and (AGCn were the most common followed by pentanucleotide, tetranucleotide and dinucleotide repeats. A second approach was aimed at the identification of useful loci common to a restricted number of species more closely related to P. sojae (P. alni, P. cambivora, P. europaea and P. fragariae. This analysis yielded 10 trinucleotide and 2 tetranucleotide SSRs which were repeated 4, 5 or 6 times. Conclusion Key studies on inter- and intra-specific variation of selected microsatellites remain. Despite the screening of conserved gene coding regions, the sequence diversity between species was high and the identification of useful SSR loci applicable to anything other than the most closely related pairs of Phytophthora species was challenging. That said, many novel SSR loci for species other than the three 'source species' (P. infestans, P. sojae and P. ramorum are reported, offering great potential for the investigation of Phytophthora populations. In addition to the presence of microsatellites, many of the amplified regions may represent useful molecular marker regions for other studies as

  2. Three New Soil-inhabiting Species of Trichoderma in the Stromaticum Clade with Test of Their Antagonism to Pathogens.

    Science.gov (United States)

    Chen, Kai; Zhuang, Wen-Ying

    2017-09-01

    Trichoderma is a dominant component of the soil mycoflora. During the field investigations of northern, central, and southwestern China, three new species in the Stromaticum clade were encountered from soil, and named as T. hebeiense, T. sichuanense, and T. verticillatum. Their phylogenetic positions were determined by analyses of the combined two genes: partial sequences of translation elongation factor 1-alpha and the second largest RNA polymerase subunit-encoding genes. Distinctions between the new species and their close relatives were discussed. Trichoderma hebeiense appeared as a separate terminal branch. The species is distinctive by its oblong conidia and aggregated pustules in culture. Trichoderma sichuanense features in concentric colony and produces numerous clean exudates on aerial mycelium in culture. Trichoderma verticillatum is characterized by its verticillium-like synanamorph and production of abundant chlamydospores. In vitro antagonism towards the new species was tested by dual culture technique.

  3. Inducible Clindamycin Resistance in Staphylococcus Species

    International Nuclear Information System (INIS)

    Afridi, F. I.; Zeb, M.; Farooqi, B. J.; Murtaza, G.; Hussain, A.

    2014-01-01

    Objective: To determine the frequency of inducible clindamycin resistance in clinical isolates of Staphylococcus species by phenotypic D-test. Study Design: Observational study. Place and Duration of Study: Ziauddin University Hospital, Karachi, from July to December 2011. Methodology: Consecutive clinical isolates of Staphylococcus species were collected and identified by conventional microbiological techniques. Antimicrobial susceptibility testing and inducible clindamycin resistance was carried out by performing D-test using CLSI criteria. Methicillin resistance was detected by using Cefoxitin disk as a surrogate marker. Statistical analysis was performed by SPSS version-17. Results: A total of 667 clinical isolates of Staphylococcus species were obtained during the study period. In these isolates, 177 (26.5%) were Staphylococcus aureus, and 490 (73.5%) were coagulase negative Staphylococci. The total frequency of inducible clindamycin resistance among isolates of Staphylococcus species was 120/667 (18%). Frequency of inducible clindamycin resistance among coagulase negative Staphylococci group and Staphylococcus aureus group were 18.57% and 16.38% respectively. Median age of patients in D-test positive group was 19.5 (1 - 54) years. Conclusion: The frequency of inducible clindamycin resistance among Staphylococcus species may differ in different hospital setup. Clinical microbiology laboratories should implement testing simple and effective D-test on all Staphylococcus species. D-test positive isolates should be reported clindamycin resistant to decrease treatment failure. (author)

  4. Development of novel microsatellite markers for Holothurian scabra (Holothuriidae), Apostichopus japonicas (Stichopodidae) and cross-species testing in other sea cucumbers

    Science.gov (United States)

    Shangguan, Jingbo; Li, Zhongbao

    2018-03-01

    Thirty-five new microsatellite loci from the sea cucumbers Holothurian scabra (Jaeger, 1833) and Apostichopus japonicas (Selenka, 1867) were screened and characterized using the method of magnetic bead enrichment. Of the twenty-four polymorphic loci tested, eighteen were consistent with Hardy-Weinberg equilibrium after a modified false discovery rate (B-Y FDR) correction, whereas six showed statistically significant deviations (CHS2 and CHS11: Psea cucumbers ( Holothurian scabra, Holothuria leucospilota, Stichopus horrens and Apostichopus japonicas) were tested for mutual cross-amplification using a total of ninety microsatellite loci. Although transferability and universality of all loci were generally low, the results of the cross-species study showed that the markers can be applied to identify individuals to species according to the presence or absence of specific microsatellite alleles. The microsatellite markers reported here will contribute to the study of genetic diversity, assisted breeding, and population conservation in sea cucumbers, as well as allow for the identification of individuals to closely related species.

  5. Comparison of minipig, dog, monkey and human drug metabolism and disposition.

    Science.gov (United States)

    Dalgaard, Lars

    2015-01-01

    This article gives an overview of the drug metabolism and disposition (ADME) characteristics of the most common non-rodent species used in toxicity testing of drugs (minipigs, dogs, and monkeys) and compares these to human characteristics with regard to enzymes mediating the metabolism of drugs and the transport proteins which contribute to the absorption, distribution and excretion of drugs. Literature on ADME and regulatory guidelines of relevance in drug development of small molecules has been gathered. Non-human primates (monkeys) are the species that is closest to humans in terms of genetic homology. Dogs have an advantage due to the ready availability of comprehensive background data for toxicological safety assessment and dogs are easy to handle. Pigs have been used less than dogs and monkeys as a model in safety assessment of drug candidates. However, when a drug candidate is metabolised by aldehyde oxidase (AOX1), N-acetyltransferases (NAT1 and NAT2) or cytochrome (CYP2C9-like) enzymes which are not expressed in dogs, but are present in pigs, this species may be a better choice than dogs, provided that adequate exposure can be obtained in pigs. Conversely, pigs might not be the right choice if sulfation, involving 3-phospho-adenosyl-5-phosphosulphate sulphotransferase (PAPS) is an important pathway in the human metabolism of a drug candidate. In general, the species selection should be based on comparison between in vitro studies with human cell-based systems and animal-cell-based systems. Results from pharmacokinetic studies are also important for decision-making by establishing the obtainable exposure level in the species. Access to genetically humanized mouse models and highly sensitive analytical methods (accelerator mass spectrometry) makes it possible to improve the chance of finding all metabolites relevant for humans before clinical trials have been initiated and, if necessary, to include another animal species before long term toxicity studies are

  6. Antifungal susceptibility testing of Candida species isolated from the immunocompromised patients admitted to ten university hospitals in Iran

    NARCIS (Netherlands)

    Badiee, P.; Badali, H.; Boekhout, T.; Diba, K.; Moghadam, A.G.; Hossaini Nasab, A.; Jafarian, H.; Mohammadi, R.; Mirhendi, H.; Najafzadeh, M.J.; Shamsizadeh, A.; Soltani, J.

    2017-01-01

    Background Antifungal susceptibility testing is a subject of interest in the field of medical mycology. The aim of the present study were the distributions and antifungal susceptibility patterns of various Candida species isolated from colonized and infected immunocompromised patients admitted to

  7. Inferring modes of colonization for pest species using heterozygosity comparisons and a shared-allele test.

    Science.gov (United States)

    Sved, J A; Yu, H; Dominiak, B; Gilchrist, A S

    2003-02-01

    Long-range dispersal of a species may involve either a single long-distance movement from a core population or spreading via unobserved intermediate populations. Where the new populations originate as small propagules, genetic drift may be extreme and gene frequency or assignment methods may not prove useful in determining the relation between the core population and outbreak samples. We describe computationally simple resampling methods for use in this situation to distinguish between the different modes of dispersal. First, estimates of heterozygosity can be used to test for direct sampling from the core population and to estimate the effective size of intermediate populations. Second, a test of sharing of alleles, particularly rare alleles, can show whether outbreaks are related to each other rather than arriving as independent samples from the core population. The shared-allele statistic also serves as a genetic distance measure that is appropriate for small samples. These methods were applied to data on a fruit fly pest species, Bactrocera tryoni, which is quarantined from some horticultural areas in Australia. We concluded that the outbreaks in the quarantine zone came from a heterogeneous set of genetically differentiated populations, possibly ones that overwinter in the vicinity of the quarantine zone.

  8. Sensitivity of species to chemicals: dose-response characteristics for various test types (LC(50), LR(50) and LD(50)) and modes of action.

    Science.gov (United States)

    Hendriks, A Jan; Awkerman, Jill A; de Zwart, Dick; Huijbregts, Mark A J

    2013-11-01

    While variable sensitivity of model species to common toxicants has been addressed in previous studies, a systematic analysis of inter-species variability for different test types, modes of action and species is as of yet lacking. Hence, the aim of the present study was to identify similarities and differences in contaminant levels affecting cold-blooded and warm-blooded species administered via different routes. To that end, data on lethal water concentrations LC50, tissue residues LR50 and oral doses LD50 were collected from databases, each representing the largest of its kind. LC50 data were multiplied by a bioconcentration factor (BCF) to convert them to internal concentrations that allow for comparison among species. For each endpoint data set, we calculated the mean and standard deviation of species' lethal level per compound. Next, the means and standard deviations were averaged by mode of action. Both the means and standard deviations calculated depended on the number of species tested, which is at odds with quality standard setting procedures. Means calculated from (BCF) LC50, LR50 and LD50 were largely similar, suggesting that different administration routes roughly yield similar internal levels. Levels for compounds interfering biochemically with elementary life processes were about one order of magnitude below that of narcotics disturbing membranes, and neurotoxic pesticides and dioxins induced death in even lower amounts. Standard deviations for LD50 data were similar across modes of action, while variability of LC50 values was lower for narcotics than for substances with a specific mode of action. The study indicates several directions to go for efficient use of available data in risk assessment and reduction of species testing. Copyright © 2013 Elsevier Inc. All rights reserved.

  9. Introducing of the methods of pollutants detecting and species used as experiment organisms in testing laboratories (ro

    Directory of Open Access Journals (Sweden)

    Romeo T. Cristina

    2012-12-01

    Full Text Available Zebrafish are vertebrate animals often used in research for wastewaters, environment chemicals, cancer and diabetes drugs due to their speed and ease for handling and obtaining test results. Organisms capacity to detect and avoid contaminated soils reveals soils stressor potential and has an ecological relevance indepted with its direct relationship to soil biodiversity and it’s quality as a habitat for the organism. Soil pollution tests were accomplished on arthropods (Collembola, earthworms, oligochaete worms (Enchytraeidae, this being behavior modification tests, observing which species avoids contaminated soils and if response intensity depends on contamination degree. Using Daphnia sp. for testing it’s possible because of their sensibility to an amount of aquatic pollutants and also for their small sizes involving a use of small volumes of test substance and water for dilution.

  10. Possibilities and limitations of using historic provenance tests to infer forest species growth responses to climate change

    Science.gov (United States)

    Laura P. Leites; Gerald E. Rehfeldt; Andrew P. Robinson; Nicholas L. Crookston; Barry Jaquish

    2012-01-01

    Under projected changes in global climate, the growth and survival of existing forests will depend on their ability to adjust physiologically in response to environmental change. Quantifying their capacity to adjust and whether the response is species- or population-specific is important to guide forest management strategies. New analyses of historic provenance tests...

  11. Use of species-specific PCR for the identification of 10 sea cucumber species

    Science.gov (United States)

    Wen, Jing; Zeng, Ling

    2014-11-01

    We developed a species-specific PCR method to identify species among dehydrated products of 10 sea cucumber species. Ten reverse species-specific primers designed from the 16S rRNA gene, in combination with one forward universal primer, generated PCR fragments of ca. 270 bp length for each species. The specificity of the PCR assay was tested with DNA of samples of 21 sea cucumber species. Amplification was observed in specific species only. The species-specific PCR method we developed was successfully applied to authenticate species of commercial products of dehydrated sea cucumber, and was proven to be a useful, rapid, and low-cost technique to identify the origin of the sea cucumber product.

  12. Comparative sensitivity of five species of macrophytes and six species of algae to atrazine, metribuzin, alachlor, and metolachlor

    Science.gov (United States)

    Fairchild, James F.; Ruessler, Shane; Carlson, A. Ron

    1998-01-01

    This study determined the relative sensitivity of five species of aquatic macrophytes and six species of algae to four commonly used herbicides (atrazine, metribuzin, alachlor, and metolachlor). Toxicity tests consisted of 96-h (duckweed and algae) or 14-d (submerged macrophytes) static exposures. The triazine herbicides (atrazine and metribuzin) were significantly more toxic to aquatic plants than were the acetanilide herbicides (alachlor and metolachlor). Toxicity studies ranked metribuzin > atrazine > alachlor > metolachlor in decreasing order of overall toxicity to aquatic plants. Relative sensitivities of macrophytes to these herbicides decreased in the order of Ceratophyllum > Najas > Elodea > Lemna > Myriophyllum. Relative sensitivities of algae to herbicides decreased in the order of Selenastrum > Chlorella > Chlamydomonas > Microcystis > Scenedesmus > Anabaena. Algae and macrophytes were of similar overall sensitivities to herbicides. Data indicated that Selenastrum, a commonly tested green alga, was generally more sensitive compared to other plant species. Lemna minor, a commonly tested floating vascular plant, was of intermediate sensitivity, and was fivefold less sensitive than Ceratophyllum, which was the most sensitive species tested. The results indicated that no species was consistently most sensitive, and that a suite of aquatic plant test species may be needed to perform accurate risk assessments of herbicides.

  13. Method for aquatic multiple species toxicant testing: acute toxicity of 10 chemicals to 5 vertebrates and 2 invertebrates. [Pimephales promelas; Carassius auratus; Ictalurus punctatus; Lepomis macrochirus; Salmo gairdneri; Orconectes immunis; Aplexa hypnorum

    Energy Technology Data Exchange (ETDEWEB)

    Phipps, G.L.; Holcombe, G.W.

    1985-01-01

    A method was developed to simultaneously ascertain 96 h LC/sub 50/ values for seven freshwater species in a single flow through test with measured concentrations. It allows interspecific comparisons, easy determination of the most sensitive species, and cuts cost of labor, materials and chemical analysis for measured concentration tests. Species tested included fathead minnows Pimephales promelas, goldfish Carassius auratus, channel catfish Ictalurus punctatus, bluegill Lepomis macrochirus, rainbow trout Salmo gairdneri, crayfish Orconectes immunis and snails Aplexa hypnorum. Compounds tested were pentachlorophenol, 2-chloroethanol, 2,4-pentanedione, hexachloroethane, ..cap alpha..-bromo-2',5'-dimethoxyacetophenone, benzaldehyde, 1,3-dichloro-4,6-dinitro-benzene, dursban, sevin and cadmium chloride. The LC/sub 50/ values from these multiple species tests compared favourably with those determined using single species tests at this laboratory, usually within 20%.

  14. Testing the Stress-Gradient Hypothesis at the Roof of the World: Effects of the Cushion Plant Thylacospermum caespitosum on Species Assemblages

    Science.gov (United States)

    Dvorský, Miroslav; Doležal, Jiří; Kopecký, Martin; Chlumská, Zuzana; Janatková, Kateřina; Altman, Jan; de Bello, Francesco; Řeháková, Klára

    2013-01-01

    Many cushion plants ameliorate the harsh environment they inhabit in alpine ecosystems and act as nurse plants, with significantly more species growing within their canopy than outside. These facilitative interactions seem to increase with the abiotic stress, thus supporting the stress-gradient hypothesis. We tested this prediction by exploring the association pattern of vascular plants with the dominant cushion plant Thylacospermum caespitosum (Caryophyllaceae) in the arid Trans-Himalaya, where vascular plants occur at one of the highest worldwide elevational limits. We compared plant composition between 1112 pair-plots placed both inside cushions and in surrounding open areas, in communities from cold steppes to subnival zones along two elevational gradients (East Karakoram: 4850–5250 m and Little Tibet: 5350–5850 m). We used PERMANOVA to assess differences in species composition, Friedman-based permutation tests to determine individual species habitat preferences, species-area curves to assess whether interactions are size-dependent and competitive intensity and importance indices to evaluate plant-plant interactions. No indications for net facilitation were found along the elevation gradients. The open areas were not only richer in species, but not a single species preferred to grow exclusively inside cushions, while 39–60% of 56 species detected had a significant preference for the habitat outside cushions. Across the entire elevation range of T. caespitosum, the number and abundance of species were greater outside cushions, suggesting that competitive rather than facilitative interactions prevail. This was supported by lower soil nutrient contents inside cushions, indicating a resource preemption, and little thermal amelioration at the extreme end of the elevational gradient. We attribute the negative associations to competition for limited resources, a strong environmental filter in arid high-mountain environment selecting the stress-tolerant species

  15. Testing the stress-gradient hypothesis at the roof of the world: effects of the cushion plant Thylacospermum caespitosum on species assemblages.

    Directory of Open Access Journals (Sweden)

    Miroslav Dvorský

    Full Text Available Many cushion plants ameliorate the harsh environment they inhabit in alpine ecosystems and act as nurse plants, with significantly more species growing within their canopy than outside. These facilitative interactions seem to increase with the abiotic stress, thus supporting the stress-gradient hypothesis. We tested this prediction by exploring the association pattern of vascular plants with the dominant cushion plant Thylacospermum caespitosum (Caryophyllaceae in the arid Trans-Himalaya, where vascular plants occur at one of the highest worldwide elevational limits. We compared plant composition between 1112 pair-plots placed both inside cushions and in surrounding open areas, in communities from cold steppes to subnival zones along two elevational gradients (East Karakoram: 4850-5250 m and Little Tibet: 5350-5850 m. We used PERMANOVA to assess differences in species composition, Friedman-based permutation tests to determine individual species habitat preferences, species-area curves to assess whether interactions are size-dependent and competitive intensity and importance indices to evaluate plant-plant interactions. No indications for net facilitation were found along the elevation gradients. The open areas were not only richer in species, but not a single species preferred to grow exclusively inside cushions, while 39-60% of 56 species detected had a significant preference for the habitat outside cushions. Across the entire elevation range of T. caespitosum, the number and abundance of species were greater outside cushions, suggesting that competitive rather than facilitative interactions prevail. This was supported by lower soil nutrient contents inside cushions, indicating a resource preemption, and little thermal amelioration at the extreme end of the elevational gradient. We attribute the negative associations to competition for limited resources, a strong environmental filter in arid high-mountain environment selecting the stress

  16. Why are tropical mountain passes "low" for some species? Genetic and stable-isotope tests for differentiation, migration and expansion in elevational generalist songbirds.

    Science.gov (United States)

    Gadek, Chauncey R; Newsome, Seth D; Beckman, Elizabeth J; Chavez, Andrea N; Galen, Spencer C; Bautista, Emil; Witt, Christopher C

    2018-05-01

    Most tropical bird species have narrow elevational ranges, likely reflecting climatic specialization. This is consistent with Janzen's Rule, the tendency for mountain passes to be effectively "higher" in the tropics. Hence, those few tropical species that occur across broad elevational gradients (elevational generalists) represent a contradiction to Janzen's Rule. Here, we aim to address the following questions. Are elevational generalists being sundered by diversifying selection along the gradient? Does elevational movement cause these species to resist diversification or specialization? Have they recently expanded, suggesting that elevational generalism is short-lived in geological time? To answer these questions, we tested for differentiation, movement and expansion in four elevational generalist songbird species on the Andean west slope. We used morphology and mtDNA to test for genetic differentiation between high- and low-elevation populations. To test for elevational movements, we measured hydrogen isotope (δ 2 H) values of metabolically inert feathers and metabolically active liver. Morphology differed for House Wren (Troglodytes aedon) and Hooded Siskin (Spinus magellanicus), but not for Cinereous Conebill (Conirostrum cinereum) and Rufous-collared Sparrow (Zonotrichia capensis) respectively. mtDNA was structured by elevation only in Z. capensis. δ 2 H data indicated elevational movements by two tree- and shrub-foraging species with moderate-to-high vagility (C. cinereum and S. magellanicus), and sedentary behaviour by two terrestrial-foraging species with low-to-moderate vagility (T. aedon and Z. capensis). In S. magellanicus, elevational movements and lack of mtDNA structure contrast with striking morphological divergence, suggesting strong diversifying selection on body proportions across the c. 50 km gradient. All species except C. cinereum exhibited mtDNA haplotype variation consistent with recent population expansion across the elevational

  17. Comparative toxicity of ten organic chemicals to four earthworm species

    Energy Technology Data Exchange (ETDEWEB)

    Neuhauser, E.F.; Durkin, P.R.; Malecki, M.R.; Anatra, M.

    1986-01-01

    Ten organic chemicals were tested for toxicity to four earthworm species: Allolobophora tuberculata, Eisenia fetida, Eudrilus eugeniae and Perionyx excavatus, using the European Economic Community's (EEC) earthworm artificial soil and contact testing procedure. The phenols were the most toxic chemicals tested, followed by the amine, substituted benzenes, halogenated aliphatic hydrocarbon, polycyclic aromatic hydrocarbon and phthalate as the least toxic chemical tested. Correlations among species within each type of test for a given chemical were extremely high, suggesting that the selection of earthworm test species does not markedly affect the assessment of a chemical's toxicity. The correlation between the two tests was low for all test species. The contact test LC50 for a given chemical cannot be directly correlated to an artificial soil test LC50 for the same earthworm species.

  18. Molecular and Morphological Differentiation of Common Dolphins (Delphinus sp.) in the Southwestern Atlantic: Testing the Two Species Hypothesis in Sympatry

    Science.gov (United States)

    Cunha, Haydée A.; de Castro, Rocio Loizaga; Secchi, Eduardo R.; Crespo, Enrique A.; Lailson-Brito, José; Azevedo, Alexandre F.; Lazoski, Cristiano; Solé-Cava, Antonio M.

    2015-01-01

    The taxonomy of common dolphins (Delphinus sp.) has always been controversial, with over twenty described species since the original description of the type species of the genus (Delphinus delphis Linnaeus, 1758). Two species and four subspecies are currently accepted, but recent molecular data have challenged this view. In this study we investigated the molecular taxonomy of common dolphins through analyses of cytochrome b sequences of 297 individuals from most of their distribution. We included 37 novel sequences from the Southwestern Atlantic Ocean, a region where the short- and long-beaked morphotypes occur in sympatry, but which had not been well sampled before. Skulls of individuals from the Southwestern Atlantic were measured to test the validity of the rostral index as a diagnostic character and confirmed the presence of the two morphotypes in our genetic sample. Our genetic results show that all common dolphins in the Atlantic Ocean belong to a single species, Delphinus delphis. According to genetic data, the species Delphinus capensis is invalid. Long-beaked common dolphins from the Northeastern Pacific Ocean may constitute a different species. Our conclusions prompt the need for revision of currently accepted common dolphin species and subspecies and of Delphinus delphis distribution. PMID:26559411

  19. Molecular and Morphological Differentiation of Common Dolphins (Delphinus sp. in the Southwestern Atlantic: Testing the Two Species Hypothesis in Sympatry.

    Directory of Open Access Journals (Sweden)

    Haydée A Cunha

    Full Text Available The taxonomy of common dolphins (Delphinus sp. has always been controversial, with over twenty described species since the original description of the type species of the genus (Delphinus delphis Linnaeus, 1758. Two species and four subspecies are currently accepted, but recent molecular data have challenged this view. In this study we investigated the molecular taxonomy of common dolphins through analyses of cytochrome b sequences of 297 individuals from most of their distribution. We included 37 novel sequences from the Southwestern Atlantic Ocean, a region where the short- and long-beaked morphotypes occur in sympatry, but which had not been well sampled before. Skulls of individuals from the Southwestern Atlantic were measured to test the validity of the rostral index as a diagnostic character and confirmed the presence of the two morphotypes in our genetic sample. Our genetic results show that all common dolphins in the Atlantic Ocean belong to a single species, Delphinus delphis. According to genetic data, the species Delphinus capensis is invalid. Long-beaked common dolphins from the Northeastern Pacific Ocean may constitute a different species. Our conclusions prompt the need for revision of currently accepted common dolphin species and subspecies and of Delphinus delphis distribution.

  20. Helminth community structure and diet of three Afrotropical anuran species: a test of the interactive-versus-isolationist parasite communities hypothesis

    Directory of Open Access Journals (Sweden)

    G. C. Akani

    2011-09-01

    Full Text Available The interactive-versus-isolationist hypothesis predicts that parasite communities should be depauperated and weakly structured by interspecific competition in amphibians. A parasitological survey was carried out to test this hypothesis using three anuran species from Nigeria, tropical Africa (one Bufonidae; two Ranidae. High values of parasite infection parameters were found in all three species, which were infected by nematodes, cestodes and trematodes. Nonetheless, the parasite communities of the three anurans were very depauperated in terms of number of species (4 to 6. Interspecific competition was irrelevant in all species, as revealed by null models and Monte Carlo permutations. Cluster analyses revealed that, in terms of parasite community composition, the two Ranidae were similar, whereas the Bufonidae was more different. However, when prevalence, intensity, and abundance of parasites are combined into a multivariate analysis, each anuran species was clearly spaced apart from the others, thus revealing considerable species-specific differences in terms of their parasite communities. All anurans were generalists and probably opportunistic in terms of dietary habits, and showed no evidence of interspecific competition for food. Overall, our data are widely consistent with expectations driven from the interactive-versus-isolationist parasite communities hypothesis.

  1. Species delimitation of the Hyphydrus ovatus complex in western Palaearctic with an update of species distributions (Coleoptera, Dytiscidae

    Directory of Open Access Journals (Sweden)

    Johannes Bergsten

    2017-06-01

    Full Text Available The species status of Hyphydrus anatolicus Guignot, 1957 and H. sanctus Sharp, 1882, previously often confused with the widespread H. ovatus (Linnaeus, 1760, are tested with molecular and morphological characters. Cytochrome c oxidase subunit 1 (CO1 was sequenced for 32 specimens of all three species. Gene-trees were inferred with parsimony, time-free bayesian and strict clock bayesian analyses. The GMYC model was used to estimate species limits. All three species were reciprocally monophyletic with CO1 and highly supported. The GMYC species delimitation analysis unequivocally delimited the three species with no other than the three species solution included in the confidence interval. A likelihood ratio test rejected the one-species null model. Important morphological characters distinguishing the species are provided and illustrated. New distributional data are given for the following species: Hyphydrus anatolicus from Slovakia and Ukraine, and H. aubei Ganglbauer, 1891, and H. sanctus from Turkey.

  2. Single-locus species delimitation: a test of the mixed Yule–coalescent model, with an empirical application to Philippine round-leaf bats

    OpenAIRE

    Esselstyn, Jacob A.; Evans, Ben J.; Sedlock, Jodi L.; Anwarali Khan, Faisal Ali; Heaney, Lawrence R.

    2012-01-01

    Prospects for a comprehensive inventory of global biodiversity would be greatly improved by automating methods of species delimitation. The general mixed Yule–coalescent (GMYC) was recently proposed as a potential means of increasing the rate of biodiversity exploration. We tested this method with simulated data and applied it to a group of poorly known bats (Hipposideros) from the Philippines. We then used echolocation call characteristics to evaluate the plausibility of species boundaries s...

  3. Distribution of Plasmodium species on the island of Grande Comore on the basis of DNA extracted from rapid diagnostic tests

    Directory of Open Access Journals (Sweden)

    Papa Mze Nasserdine

    2016-01-01

    Full Text Available In the Union of Comoros, interventions for combating malaria have contributed to a spectacular decrease in the prevalence of the disease. We studied the current distribution of Plasmodium species on the island of Grande Comore using nested PCR. The rapid diagnostic tests (RDTs currently used in the Comoros are able to identify Plasmodium falciparum but no other Plasmodium species. In this study, we tested 211 RDTs (158 positive and 53 negative. Among the 158 positive RDTs, 22 were positive for HRP2, 3 were positive only for pLDH, and 133 were positive for HRP2 and pLDH. DNA was extracted from a proximal part of the nitrocellulose membrane of RDTs. A total of 159 samples were positive by nested PCR. Of those, 156 (98.11% were positive for P. falciparum, 2 (1.25% were positive for P. vivaxI, and 1 (0.62% was positive for P. malariae. None of the samples were positive for P. ovale. Our results show that P. falciparum is still the most dominant species on the island of Grande Comore, but P. vivax and P. malariae are present at a low prevalence.

  4. Confronting species distribution model predictions with species functional traits.

    Science.gov (United States)

    Wittmann, Marion E; Barnes, Matthew A; Jerde, Christopher L; Jones, Lisa A; Lodge, David M

    2016-02-01

    Species distribution models are valuable tools in studies of biogeography, ecology, and climate change and have been used to inform conservation and ecosystem management. However, species distribution models typically incorporate only climatic variables and species presence data. Model development or validation rarely considers functional components of species traits or other types of biological data. We implemented a species distribution model (Maxent) to predict global climate habitat suitability for Grass Carp (Ctenopharyngodon idella). We then tested the relationship between the degree of climate habitat suitability predicted by Maxent and the individual growth rates of both wild (N = 17) and stocked (N = 51) Grass Carp populations using correlation analysis. The Grass Carp Maxent model accurately reflected the global occurrence data (AUC = 0.904). Observations of Grass Carp growth rate covered six continents and ranged from 0.19 to 20.1 g day(-1). Species distribution model predictions were correlated (r = 0.5, 95% CI (0.03, 0.79)) with observed growth rates for wild Grass Carp populations but were not correlated (r = -0.26, 95% CI (-0.5, 0.012)) with stocked populations. Further, a review of the literature indicates that the few studies for other species that have previously assessed the relationship between the degree of predicted climate habitat suitability and species functional traits have also discovered significant relationships. Thus, species distribution models may provide inferences beyond just where a species may occur, providing a useful tool to understand the linkage between species distributions and underlying biological mechanisms.

  5. Isolation of Candida Species from Gastroesophageal Lesions among Pediatrics in Isfahan, Iran: Identification and Antifungal Susceptibility Testing of Clinical Isolates by E-test

    Directory of Open Access Journals (Sweden)

    Fatemeh Salehi

    2017-01-01

    Full Text Available Background: Candida species can become opportunistic pathogens causing local or systemic invasive infections. Gastroesophageal candidiasis may depend on the Candida colonization and local damage of the mucosal barrier. Risk factors are gastric acid suppression, diabetes mellitus, chronic debilitating states such as carcinomas, and the use of systemic antibiotics and corticosteroids. The aim of this study is collection and molecular identification of Candida species from gastroesophageal lesions among pediatrics in Isfahan, and determination of minimum inhibitory concentration (MIC ranges for clinical isolates. Materials and Methods: A total of 200 patients underwent endoscopy (130 specimens from gastritis and 70 samples from esophagitis were included in this study between April 2015 and November 2015. All specimens were subcultured on sabouraud dextrose agar, and genomic DNA of all strains was extracted using boiling method. Polymerase chain reaction and DNA sequencing of the ITS1-5.8SrDNA-ITS2 region were used for the identification of all Candida strains. MIC ranges were determined for itraconazole (ITC, amphotericin B (AmB, and fluconazole (FLU by E-test. Results: Twenty of 200 suspected patients (10% were positive by direct microscopy and culture. Candida albicans was the most common species (60% followed by Candida glabrata (30%, Candida parapsilosis (5%, and Candida kefyr (5%. MIC ranges were determined for FLU (0.125–8 μg/mL, ITC (0.008–0.75 μg/mL, and AmB (0.008–0.75 μg/mL, respectively. Conclusion: Every colonization of Candida species should be considered as a potentially factor of mucocutaneous candidiasis and should be treated with antifungal drugs.

  6. Reproductive/developmental toxicity and immunotoxicity assessment in the nonhuman primate model

    International Nuclear Information System (INIS)

    Buse, Eberhard; Habermann, Gunnar; Osterburg, Ingrid; Korte, Rainhart; Weinbauer, Gerhard F.

    2003-01-01

    Nonhuman primates are being used increasingly as a non-rodent animal model during preclinical toxicology and safety assessment on the basis of proven similarity and comparability between nonhuman primates and humans. The validity of the nonhuman primate models applies to many aspects of toxicological testing and holds particularly true for the evaluation of reproductive toxicology and developmental toxicology. More recently, the advent of humanized antibodies and vaccines imposed further demand on nonhuman primate models since many immunotherapeutics do not interact with rodent receptors but frequently only cross-react with primate tissue. In this paper we discuss the suitability of primate models for reproductive, developmental and immunotoxicology testing, and present our initial data on the development of lymphatic organs and immune system in a nonhuman primate model

  7. Testing decision rules for categorizing species' extinction risk to help develop quantitative listing criteria for the U.S. Endangered Species Act.

    Science.gov (United States)

    Regan, Tracey J; Taylor, Barbara L; Thompson, Grant G; Cochrane, Jean Fitts; Ralls, Katherine; Runge, Michael C; Merrick, Richard

    2013-08-01

    Lack of guidance for interpreting the definitions of endangered and threatened in the U.S. Endangered Species Act (ESA) has resulted in case-by-case decision making leaving the process vulnerable to being considered arbitrary or capricious. Adopting quantitative decision rules would remedy this but requires the agency to specify the relative urgency concerning extinction events over time, cutoff risk values corresponding to different levels of protection, and the importance given to different types of listing errors. We tested the performance of 3 sets of decision rules that use alternative functions for weighting the relative urgency of future extinction events: a threshold rule set, which uses a decision rule of x% probability of extinction over y years; a concave rule set, where the relative importance of future extinction events declines exponentially over time; and a shoulder rule set that uses a sigmoid shape function, where relative importance declines slowly at first and then more rapidly. We obtained decision cutoffs by interviewing several biologists and then emulated the listing process with simulations that covered a range of extinction risks typical of ESA listing decisions. We evaluated performance of the decision rules under different data quantities and qualities on the basis of the relative importance of misclassification errors. Although there was little difference between the performance of alternative decision rules for correct listings, the distribution of misclassifications differed depending on the function used. Misclassifications for the threshold and concave listing criteria resulted in more overprotection errors, particularly as uncertainty increased, whereas errors for the shoulder listing criteria were more symmetrical. We developed and tested the framework for quantitative decision rules for listing species under the U.S. ESA. If policy values can be agreed on, use of this framework would improve the implementation of the ESA by

  8. Photoactivated toxicity of PAH to endangered fishes and standard laboratory test species

    International Nuclear Information System (INIS)

    Buckler, D.R.; Mount, D.R.; Tillitt, D.E.

    1994-01-01

    Polynuclear aromatic hydrocarbons (PAH) have been detected in water and sediment from the San Juan River Basin, located in the Four Corners area of the southwestern US. In addition to possessing extensive oil and gas deposits, the San Juan contains several threatened or endangered fish species such as Colorado squawfish and razorback suckers. Proposed expansion of oil and gas development in the basin has sparked concerns that potential increases in PAH loading may jeopardize these and other native fishes. In response, the authors conducted laboratory exposures of threatened and endangered species to various PAH both with and without accompanying exposure to UV light. As predicted from the literature, exposure to UV light caused a marked photo-activated toxicity response in all species; however, the sensitivity to PAH both with and without UV exposure varied among species and lifestages. Supplemental studies were conducted to evaluate the physiological mechanisms for variation in sensitivity between species and lifestage

  9. 40 CFR 798.3260 - Chronic toxicity.

    Science.gov (United States)

    2010-07-01

    ... and mucous membranes, respiratory, circulatory, autonomic and central nervous systems, somatomotor... period. Blood samples should be drawn for clinical chemistry measurements from all non-rodents and at..., 3rd Printing 1975) pp. 60-67. (5) National Academy of Sciences. “Principles and Procedures for...

  10. Species used for drug testing reveal different inhibition susceptibility for 17beta-hydroxysteroid dehydrogenase type 1.

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    Gabriele Möller

    Full Text Available Steroid-related cancers can be treated by inhibitors of steroid metabolism. In searching for new inhibitors of human 17beta-hydroxysteroid dehydrogenase type 1 (17beta-HSD 1 for the treatment of breast cancer or endometriosis, novel substances based on 15-substituted estrone were validated. We checked the specificity for different 17beta-HSD types and species. Compounds were tested for specificity in vitro not only towards recombinant human 17beta-HSD types 1, 2, 4, 5 and 7 but also against 17beta-HSD 1 of several other species including marmoset, pig, mouse, and rat. The latter are used in the processes of pharmacophore screening. We present the quantification of inhibitor preferences between human and animal models. Profound differences in the susceptibility to inhibition of steroid conversion among all 17beta-HSDs analyzed were observed. Especially, the rodent 17beta-HSDs 1 were significantly less sensitive to inhibition compared to the human ortholog, while the most similar inhibition pattern to the human 17beta-HSD 1 was obtained with the marmoset enzyme. Molecular docking experiments predicted estrone as the most potent inhibitor. The best performing compound in enzymatic assays was also highly ranked by docking scoring for the human enzyme. However, species-specific prediction of inhibitor performance by molecular docking was not possible. We show that experiments with good candidate compounds would out-select them in the rodent model during preclinical optimization steps. Potentially active human-relevant drugs, therefore, would no longer be further developed. Activity and efficacy screens in heterologous species systems must be evaluated with caution.

  11. Iodine metabolism and thyroid functions in various species of domestic animals and poultry birds. I - Species difference in thyroid status as reflected by triiodothyronine 131I uptake test

    International Nuclear Information System (INIS)

    Setia, M.S.; Parshad, Omkar; Varman, P.N.

    1974-01-01

    In vitro triiodothyronine- 131 I uptake, by red blood cells was studied in buffaloes, buffaloe calves, cross-bred calves, rams, goats, piglets and also in pure white leg horn and cross-bred birds. Results revealed that buffalo calves have the lowest uptake values, whereas piglets appeared to have the highest values as compared to other species. Distinct differences in the uptake of T 3 - 131 I by the erythrocytes were observed to exist within as well as amongst the species of farm animals and poultry birds studied. Cross-breds exhibited higher degree of T 3 - 131 I uptake as compared to pure-breds. This test offers promise where more tedious methods may not be possible for conducting the survey on the thyroid status and iodine metabolism on large population of live-stock. (author)

  12. Valuing local endangered species. The role of intra-species substitutes

    Energy Technology Data Exchange (ETDEWEB)

    Loureiro, Maria L. [Department of Economic Analysis, Universidade de Santiago (Spain); IDEGA, Universidade de Santiago de Compostela, Campus Sur, Avda das Ciencias, S/N. 15782, Santiago de Compostela (Spain); Ojea, Elena [IDEGA, Universidade de Santiago de Compostela, Campus Sur, Avda das Ciencias, S/N. 15782, Santiago de Compostela (Spain)

    2008-12-01

    Valuation of endangered species is important in many circumstances, and particularly when assessing the impact of large accidental oil spills. Previous studies have tested the effects of including in the contingent valuation survey reminders about the existence of diverse substitutes (in terms of other natural resources also in danger of extinction in the same area, other programs to be valued, or alternative uses of money). We include a reminder about the existence of the same biological species not being under danger of extinction elsewhere. We believe this reminder allows individuals to make an easy assessment of the biological scarcity of the species they are supposed to value. Thus, the key difference with previous studies is that valuation of endangered species is combined with an assessment of preferences towards conservation of local and native species. Our WTP results are not sensitive to the information provided about other foreign substitutes. Implications of this finding are discussed. (author)

  13. Valuing local endangered species. The role of intra-species substitutes

    International Nuclear Information System (INIS)

    Loureiro, Maria L.; Ojea, Elena

    2008-01-01

    Valuation of endangered species is important in many circumstances, and particularly when assessing the impact of large accidental oil spills. Previous studies have tested the effects of including in the contingent valuation survey reminders about the existence of diverse substitutes (in terms of other natural resources also in danger of extinction in the same area, other programs to be valued, or alternative uses of money). We include a reminder about the existence of the same biological species not being under danger of extinction elsewhere. We believe this reminder allows individuals to make an easy assessment of the biological scarcity of the species they are supposed to value. Thus, the key difference with previous studies is that valuation of endangered species is combined with an assessment of preferences towards conservation of local and native species. Our WTP results are not sensitive to the information provided about other foreign substitutes. Implications of this finding are discussed. (author)

  14. Mitochondrial and nuclear genes-based phylogeography of Arvicanthis niloticus (Murinae and sub-Saharan open habitats pleistocene history.

    Directory of Open Access Journals (Sweden)

    Gauthier Dobigny

    Full Text Available A phylogeographic study was conducted on the Nile grass rat, Arvicanthis niloticus, a rodent species that is tightly associated with open grasslands from the Sudano-Sahelian regions. Using one mitochondrial (cytochrome b and one nuclear (intron 7 of Beta Fibrinogen gene, robust patterns were retrieved that clearly show that (i the species originated in East Africa concomitantly with expanding grasslands some 2 Ma, and (ii four parapatric and genetically well-defined lineages differentiated essentially from East to West following Pleistocene bioclimatic cycles. This strongly points towards allopatric genetic divergence within savannah refuges during humid episodes, then dispersal during arid ones; secondary contact zones would have then stabilized around geographic barriers, namely, Niger River and Lake Chad basins. Our results pertinently add to those obtained for several other African rodent as well as non-rodent species that inhabit forests, humid zones, savannahs and deserts, all studies that now allow one to depict a more comprehensive picture of the Pleistocene history of the continent south of the Sahara. In particular, although their precise location remains to be determined, at least three Pleistocene refuges are identified within the West and Central African savannah biome.

  15. Quantifying the invasiveness of species

    Directory of Open Access Journals (Sweden)

    Robert Colautti

    2014-04-01

    Full Text Available The success of invasive species has been explained by two contrasting but non-exclusive views: (i intrinsic factors make some species inherently good invaders; (ii species become invasive as a result of extrinsic ecological and genetic influences such as release from natural enemies, hybridization or other novel ecological and evolutionary interactions. These viewpoints are rarely distinguished but hinge on distinct mechanisms leading to different management scenarios. To improve tests of these hypotheses of invasion success we introduce a simple mathematical framework to quantify the invasiveness of species along two axes: (i interspecific differences in performance among native and introduced species within a region, and (ii intraspecific differences between populations of a species in its native and introduced ranges. Applying these equations to a sample dataset of occurrences of 1,416 plant species across Europe, Argentina, and South Africa, we found that many species are common in their native range but become rare following introduction; only a few introduced species become more common. Biogeographical factors limiting spread (e.g. biotic resistance, time of invasion therefore appear more common than those promoting invasion (e.g. enemy release. Invasiveness, as measured by occurrence data, is better explained by inter-specific variation in invasion potential than biogeographical changes in performance. We discuss how applying these comparisons to more detailed performance data would improve hypothesis testing in invasion biology and potentially lead to more efficient management strategies.

  16. Invasive species and biodiversity crises: testing the link in the late devonian.

    Directory of Open Access Journals (Sweden)

    Alycia L Stigall

    Full Text Available During the Late Devonian Biodiversity Crisis, the primary driver of biodiversity decline was the dramatic reduction in speciation rates, not elevated extinction rates; however, the causes of speciation decline have been previously unstudied. Speciation, the formation of new species from ancestral populations, occurs by two primary allopatric mechanisms: vicariance, where the ancestral population is passively divided into two large subpopulations that later diverge and form two daughter species, and dispersal, in which a small subset of the ancestral population actively migrates then diverges to form a new species. Studies of modern and fossil clades typically document speciation by vicariance in much higher frequencies than speciation by dispersal. To assess the mechanism behind Late Devonian speciation reduction, speciation rates were calculated within stratigraphically constrained species-level phylogenetic hypotheses for three representative clades and mode of speciation at cladogenetic events was assessed across four clades in three phyla: Arthropoda, Brachiopoda, and Mollusca. In all cases, Devonian taxa exhibited a congruent reduction in speciation rate between the Middle Devonian pre-crisis interval and the Late Devonian crisis interval. Furthermore, speciation via vicariance is almost entirely absent during the crisis interval; most episodes of speciation during this time were due to dispersal. The shutdown of speciation by vicariance during this interval was related to widespread interbasinal species invasions. The lack of Late Devonian vicariance is diametrically opposed to the pattern observed in other geologic intervals, which suggests the loss of vicariant speciation attributable to species invasions during the Late Devonian was a causal factor in the biodiversity crisis. Similarly, modern ecosystems, in which invasive species are rampant, may be expected to exhibit similar shutdown of speciation by vicariance as an outcome of the

  17. Invasive species and biodiversity crises: testing the link in the late devonian.

    Science.gov (United States)

    Stigall, Alycia L

    2010-12-29

    During the Late Devonian Biodiversity Crisis, the primary driver of biodiversity decline was the dramatic reduction in speciation rates, not elevated extinction rates; however, the causes of speciation decline have been previously unstudied. Speciation, the formation of new species from ancestral populations, occurs by two primary allopatric mechanisms: vicariance, where the ancestral population is passively divided into two large subpopulations that later diverge and form two daughter species, and dispersal, in which a small subset of the ancestral population actively migrates then diverges to form a new species. Studies of modern and fossil clades typically document speciation by vicariance in much higher frequencies than speciation by dispersal. To assess the mechanism behind Late Devonian speciation reduction, speciation rates were calculated within stratigraphically constrained species-level phylogenetic hypotheses for three representative clades and mode of speciation at cladogenetic events was assessed across four clades in three phyla: Arthropoda, Brachiopoda, and Mollusca. In all cases, Devonian taxa exhibited a congruent reduction in speciation rate between the Middle Devonian pre-crisis interval and the Late Devonian crisis interval. Furthermore, speciation via vicariance is almost entirely absent during the crisis interval; most episodes of speciation during this time were due to dispersal. The shutdown of speciation by vicariance during this interval was related to widespread interbasinal species invasions. The lack of Late Devonian vicariance is diametrically opposed to the pattern observed in other geologic intervals, which suggests the loss of vicariant speciation attributable to species invasions during the Late Devonian was a causal factor in the biodiversity crisis. Similarly, modern ecosystems, in which invasive species are rampant, may be expected to exhibit similar shutdown of speciation by vicariance as an outcome of the modern biodiversity

  18. Short Communication. Comparing flammability traits among fire-stricken (low elevation and non fire-stricken (high elevation conifer forest species of Europe: A test of the Mutch hypothesis

    Directory of Open Access Journals (Sweden)

    A. P. Dimitrakopoulos

    2013-04-01

    Full Text Available Aim of study. The flammability of the main coniferous forest species of Europe, divided into two groups according to their fire regime and altitudinal distribution, was tested in an effort to detect species-specific differences that may have an influence on community-wide fire regimes.Area of study. Conifer species comprising low- and high-elevation forests in Europe.Materials and Methods. The following conifer species were tested: low elevation; Pinus halepensis (Aleppo pine, Pinus brutia (Turkish pine, Pinus pinaster (maritime pine, Pinus pinea (stone pine and Cupressus sempervirens (cypress, high elevation (i.e., above 600 m a.s.l.; Pinus sylvestris (Scots pine, Abies alba (white fir, Picea excelsa (Norway spruce, Abies borissii regis (Macedonian fir and Pinus nigra (black pine. Flammability assessment (time-to-ignition and ignition temperature was conducted by an innovative ignition apparatus, heat content was measured with an IKA Adiabatic Bomb Calorimeter and ash content by heating 5 g of plant material in a muffle furnace at 650ºC for 1 h. Differences among species was statistically analysed by Duncan’s multiple comparison test.Main results. The results did not distinguish separate groups among traits between fire- and non-fire-stricken communities at the individual species level.Research highlights. Differences in fire regimes among low and high elevation conifer forests could be attributed either to differences in flammability of the plant communities as a whole (i.e., fuelbed or canopy properties vs. individual fuel properties or to other factors (climatic or anthropogenic.Key words: flammability; ignitability; heat content; ash content; conifer species; Mutch hypothesis.

  19. Species trees from consensus single nucleotide polymorphism (SNP) data: Testing phylogenetic approaches with simulated and empirical data.

    Science.gov (United States)

    Schmidt-Lebuhn, Alexander N; Aitken, Nicola C; Chuah, Aaron

    2017-11-01

    Datasets of hundreds or thousands of SNPs (Single Nucleotide Polymorphisms) from multiple individuals per species are increasingly used to study population structure, species delimitation and shallow phylogenetics. The principal software tool to infer species or population trees from SNP data is currently the BEAST template SNAPP which uses a Bayesian coalescent analysis. However, it is computationally extremely demanding and tolerates only small amounts of missing data. We used simulated and empirical SNPs from plants (Australian Craspedia, Asteraceae, and Pelargonium, Geraniaceae) to compare species trees produced (1) by SNAPP, (2) using SVD quartets, and (3) using Bayesian and parsimony analysis with several different approaches to summarising data from multiple samples into one set of traits per species. Our aims were to explore the impact of tree topology and missing data on the results, and to test which data summarising and analyses approaches would best approximate the results obtained from SNAPP for empirical data. SVD quartets retrieved the correct topology from simulated data, as did SNAPP except in the case of a very unbalanced phylogeny. Both methods failed to retrieve the correct topology when large amounts of data were missing. Bayesian analysis of species level summary data scoring the two alleles of each SNP as independent characters and parsimony analysis of data scoring each SNP as one character produced trees with branch length distributions closest to the true trees on which SNPs were simulated. For empirical data, Bayesian inference and Dollo parsimony analysis of data scored allele-wise produced phylogenies most congruent with the results of SNAPP. In the case of study groups divergent enough for missing data to be phylogenetically informative (because of additional mutations preventing amplification of genomic fragments or bioinformatic establishment of homology), scoring of SNP data as a presence/absence matrix irrespective of allele

  20. How to estimate the differential acceleration in a two-species atom interferometer to test the equivalence principle

    Energy Technology Data Exchange (ETDEWEB)

    Varoquaux, G; Nyman, R A; Geiger, R; Cheinet, P; Bouyer, P [Laboratoire Charles Fabry de l' Institut d' Optique, Campus Polytechnique, RD 128, 91127 Palaiseau (France); Landragin, A [LNE-SYRTE, UMR8630, UPMC, Observatoire de Paris, 61 avenue de l' Observatoire, 75014 Paris (France)], E-mail: philippe.bouyer@institutoptique.fr

    2009-11-15

    We propose a scheme for testing the weak equivalence principle (universality of free-fall (UFF)) using an atom-interferometric measurement of the local differential acceleration between two atomic species with a large mass ratio as test masses. An apparatus in free fall can be used to track atomic free-fall trajectories over large distances. We show how the differential acceleration can be extracted from the interferometric signal using Bayesian statistical estimation, even in the case of a large mass and laser wavelength difference. We show that this statistical estimation method does not suffer from acceleration noise of the platform and does not require repeatable experimental conditions. We specialize our discussion to a dual potassium/rubidium interferometer and extend our protocol with other atomic mixtures. Finally, we discuss the performance of the UFF test developed for the free-fall (zero-gravity) airplane in the ICE project (http://www.ice-space.fr)

  1. How to estimate the differential acceleration in a two-species atom interferometer to test the equivalence principle

    International Nuclear Information System (INIS)

    Varoquaux, G; Nyman, R A; Geiger, R; Cheinet, P; Bouyer, P; Landragin, A

    2009-01-01

    We propose a scheme for testing the weak equivalence principle (universality of free-fall (UFF)) using an atom-interferometric measurement of the local differential acceleration between two atomic species with a large mass ratio as test masses. An apparatus in free fall can be used to track atomic free-fall trajectories over large distances. We show how the differential acceleration can be extracted from the interferometric signal using Bayesian statistical estimation, even in the case of a large mass and laser wavelength difference. We show that this statistical estimation method does not suffer from acceleration noise of the platform and does not require repeatable experimental conditions. We specialize our discussion to a dual potassium/rubidium interferometer and extend our protocol with other atomic mixtures. Finally, we discuss the performance of the UFF test developed for the free-fall (zero-gravity) airplane in the ICE project (http://www.ice-space.fr).

  2. Testing the Role of Climate Change in Species Decline: Is the Eastern Quoll a Victim of a Change in the Weather?

    Directory of Open Access Journals (Sweden)

    Bronwyn A Fancourt

    Full Text Available To conserve a declining species we first need to diagnose the causes of decline. This is one of the most challenging tasks faced by conservation practitioners. In this study, we used temporally explicit species distribution models (SDMs to test whether shifting weather can explain the recent decline of a marsupial carnivore, the eastern quoll (Dasyurus viverrinus. We developed an SDM using weather variables matched to occurrence records of the eastern quoll over the last 60 years, and used the model to reconstruct variation through time in the distribution of climatically suitable range for the species. The weather model produced a meaningful prediction of the known distribution of the species. Abundance of quolls, indexed by transect counts, was positively related to the modelled area of suitable habitat between 1990 and 2004. In particular, a sharp decline in abundance from 2001 to 2003 coincided with a sustained period of unsuitable weather over much of the species' distribution. Since 2004, abundance has not recovered despite a return to suitable weather conditions, and abundance and area of suitable habitat have been uncorrelated. We suggest that fluctuations in weather account for the species' recent decline, but other unrelated factors have suppressed recovery.

  3. An analysis of species boundaries and biogeographic patterns in a cryptic species complex: the rotifer--Brachionus plicatilis.

    Science.gov (United States)

    Suatoni, Elizabeth; Vicario, Saverio; Rice, Sean; Snell, Terry; Caccone, Adalgisa

    2006-10-01

    Since the advent of molecular phylogenetics, there is increasing evidence that many small aquatic and marine invertebrates--once believed to be single, cosmopolitan species--are in fact cryptic species complexes. Although the application of the biological species concept is central to the identification of species boundaries in these cryptic complexes, tests of reproductive isolation do not frequently accompany phylogenetic studies. Because different species concepts generally identify different boundaries in cryptic complexes, studies that apply multiple species concepts are needed to gain a more detailed understanding of patterns of diversification in these taxa. Here we explore different methods of empirically delimiting species boundaries in the salt water rotifer Brachionus plicatilis by comparing reproductive data (i.e., the traditional biological species concept) to phylogenetic data (the genealogical species concept). Based on a high degree of molecular sequence divergence and largely concordant genetic patterns in COI and ITS1, the genealogical species hypothesis indicates the existence of at least 14 species--the highest estimate for the group thus far. A test of the genealogical species concept with biological crosses shows a fairly high level of concordance, depending on the degree of reproductive success used to draw boundaries. The convergence of species concepts in this group suggests that many of the species within the group may be old. Although the diversity of the group is higher than previously understood, geographic distributions remain broad. Efficient passive dispersal has resulted in global distributions for many species with some evidence of isolation by distance over large geographic scales. These patterns concur with expectations that micro-meiofauna (0.1-1mm) have biogeographies intermediate to microbial organisms and large vertebrates. Sympatry of genetically distant strains is common.

  4. Species-area relationships are controlled by species traits.

    Science.gov (United States)

    Franzén, Markus; Schweiger, Oliver; Betzholtz, Per-Eric

    2012-01-01

    The species-area relationship (SAR) is one of the most thoroughly investigated empirical relationships in ecology. Two theories have been proposed to explain SARs: classical island biogeography theory and niche theory. Classical island biogeography theory considers the processes of persistence, extinction, and colonization, whereas niche theory focuses on species requirements, such as habitat and resource use. Recent studies have called for the unification of these two theories to better explain the underlying mechanisms that generates SARs. In this context, species traits that can be related to each theory seem promising. Here we analyzed the SARs of butterfly and moth assemblages on islands differing in size and isolation. We tested whether species traits modify the SAR and the response to isolation. In addition to the expected overall effects on the area, traits related to each of the two theories increased the model fit, from 69% up to 90%. Steeper slopes have been shown to have a particularly higher sensitivity to area, which was indicated by species with restricted range (slope = 0.82), narrow dietary niche (slope= 0.59), low abundance (slope= 0.52), and low reproductive potential (slope = 0.51). We concluded that considering species traits by analyzing SARs yields considerable potential for unifying island biogeography theory and niche theory, and that the systematic and predictable effects observed when considering traits can help to guide conservation and management actions.

  5. Evaluating Hypotheses of Plant Species Invasions on Mediterranean Islands: Inverse Patterns between Alien and Endemic Species

    Directory of Open Access Journals (Sweden)

    Alexander Bjarnason

    2017-08-01

    Full Text Available Invasive alien species cause major changes to ecosystem functioning and patterns of biodiversity, and the main factors involved in invasion success remain contested. Using the Mediterranean island of Crete, Greece as a case study, we suggest a framework for analyzing spatial data of alien species distributions, based on environmental predictors, aiming to gain an understanding of their spatial patterns and spread. Mediterranean islands are under strong ecological pressure from invading species due to their restricted size and increased human impact. Four hypotheses of invasibility, the “propagule pressure hypothesis” (H1, “biotic resistance hypothesis vs. acceptance hypothesis” (H2, “disturbance-mediated hypothesis” (H3, and “environmental heterogeneity hypothesis” (H4 were tested. Using data from alien, native, and endemic vascular plant species, the propagule pressure, biotic resistance vs. acceptance, disturbance-mediated, and environmental heterogeneity hypotheses were tested with Generalized Additive Modeling (GAM of 39 models. Based on model selection, the optimal model includes the positive covariates of native species richness, the negative covariates of endemic species richness, and land area. Variance partitioning between the four hypotheses indicated that the biotic resistance vs. acceptance hypothesis explained the vast majority of the total variance. These results show that areas of high species richness have greater invasibility and support the acceptance hypothesis and “rich-get-richer” distribution of alien species. The negative correlation between alien and endemic species appears to be predominantly driven by altitude, with fewer alien and more endemic species at greater altitudes, and habitat richness. The negative relationship between alien and endemic species richness provides potential for understanding patterns of endemic and alien species on islands, contributing to more effective conservation

  6. Short communication: Identification of coagulase-negative staphylococcus species from goat milk with the API Staph identification test and with transfer RNA-intergenic spacer PCR combined with capillary electrophoresis.

    Science.gov (United States)

    Koop, G; De Visscher, A; Collar, C A; Bacon, D A C; Maga, E A; Murray, J D; Supré, K; De Vliegher, S; Haesebrouck, F; Rowe, J D; Nielen, M; van Werven, T

    2012-12-01

    Coagulase-negative staphylococci (CNS) are the most commonly isolated bacteria from goat milk, but they have often been identified with phenotypic methods, which may have resulted in misclassification. The aims of this paper were to assess the amount of misclassification of a phenotypic test for identifying CNS species from goat milk compared with transfer RNA intergenic spacer PCR (tDNA-PCR) followed by capillary electrophoresis, and to apply the tDNA-PCR technique on different capillary electrophoresis equipment. Milk samples were collected from 416 does in 5 Californian dairy goat herds on 3 occasions during lactation. In total, 219 CNS isolates were identified at the species level with tDNA-PCR and subjected to the API 20 Staph identification test kit (API Staph; bioMérieux, Durham, NC). If the same species was isolated multiple times from the same udder gland, only the first isolate was used for further analyses, resulting in 115 unique CNS isolates. According to the tDNA-PCR test, the most prevalent CNS species were Staphylococcus epidermidis, Staphylococcus caprae, and Staphylococcus simulans. Typeability with API staph was low (72%). Although the API Staph test was capable of identifying the majority of Staph. epidermidis and Staph. caprae isolates, sensitivity for identification of Staph. simulans was low. The true positive fraction was high for the 3 most prevalent species. It was concluded that the overall performance of API Staph in differentiating CNS species from goat milk was moderate to low, mainly because of the low typeability, and that genotypic methods such as tDNA-PCR are preferred. Copyright © 2012 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  7. Antifungal susceptibility testing of Candida species isolated from the immunocompromised patients admitted to ten university hospitals in Iran: comparison of colonizing and infecting isolates.

    Science.gov (United States)

    Badiee, Parisa; Badali, Hamid; Boekhout, Teun; Diba, Kambiz; Moghadam, Abdolkarim Ghadimi; Hossaini Nasab, Ali; Jafarian, Hadis; Mohammadi, Rasoul; Mirhendi, Hossein; Najafzadeh, Mohammad Javad; Shamsizadeh, Ahmad; Soltani, Jafar

    2017-11-21

    Antifungal susceptibility testing is a subject of interest in the field of medical mycology. The aim of the present study were the distributions and antifungal susceptibility patterns of various Candida species isolated from colonized and infected immunocompromised patients admitted to ten university hospitals in Iran. In totally, 846 Candida species were isolated from more than 4000 clinical samples and identified by the API 20 C AUX system. Antifungal susceptibility testing was performed by broth microdilution method according to CLSI. The most frequent Candida species isolated from all patients was Candida albicans (510/846). The epidemiological cutoff value and percentage of wild-type species for amphotericin B and fluconazole in Candida albicans, Candida tropicalis, Candida glabrata and Candida krusei were 0.5 μg/ml (95%) and 4 μg/ml (96%); 1 μg/ml (95%) and 8 μg/ml (95%); 0.5 μg/ml (99%) and 19 μg/ml (98%); and 4 μg/ml (95%) and 64 μg/ml (95%), respectively. The MIC90 and epidemiological cutoff values to posaconazole in Candida krusei were 0.5 μg/ml. There were significant differences between infecting and colonizing isolates of Candida tropicalis in MIC 90 values of amphotericin B, and isolates of Candida glabrata in values of amphotericin B, caspofungin, and voriconazole (P Candida species (colonizing and infecting isolates) in immunocompromised patients are not the same and acquired resistance was seen in some species.

  8. Developing and testing an Early Warning System for Non Indigenous Species and Ballast Water Management

    Science.gov (United States)

    Magaletti, Erika; Garaventa, Francesca; David, Matej; Castriota, Luca; Kraus, Romina; Luna, Gian Marco; Silvestri, Cecilia; Forte, Cosmo; Bastianini, Mauro; Falautano, Manuela; Maggio, Teresa; Rak, Giulietta; Gollasch, Stephan

    2018-03-01

    This paper describes the methodological approach used for the development of an Early Warning System (EWS) for Non Indigenous Species (NIS) and ballast water management and summarizes the results obtained. The specific goals of the EWS are firstly to warn vessels to prevent loading of ballast water when critical biological conditions occur in ports and surrounding areas i.e. mass development or blooms of Harmful Aquatic Organisms and Pathogens (HAOP). Secondly, to warn environmental and health authorities when NIS or pathogens are present in ports or surrounding areas to enable an early response and an implementation of remediation measures. The EWS is designed to be used for implementing various parallel obligations, by taking into consideration different legal scopes, associated information and decision-making needs. The EWS was elaborated, tested in the Adriatic Sea and illustrated by two case studies. Although the EWS was developed with an Adriatic Sea focus, it is presented in a format so that it may be used as a model when establishing similar systems in other locations. The role of the various actors is discussed and recommendations on further developments of the EWS are presented. It was concluded that the EWS is a suitable tool to reduce the spread of potentially harmful and ballast water mediated species.

  9. Cryptic species as a window into the paradigm shift of the species concept.

    Science.gov (United States)

    Fišer, Cene; Robinson, Christopher T; Malard, Florian

    2018-02-01

    The species concept is the cornerstone of biodiversity science, and any paradigm shift in the delimitation of species affects many research fields. Many biologists now are embracing a new "species" paradigm as separately evolving populations using different delimitation criteria. Individual criteria can emerge during different periods of speciation; some may never evolve. As such, a paradigm shift in the species concept relates to this inherent heterogeneity in the speciation process and species category-which is fundamentally overlooked in biodiversity research. Cryptic species fall within this paradigm shift: they are continuously being reported from diverse animal phyla but are poorly considered in current tests of ecological and evolutionary theory. The aim of this review is to integrate cryptic species in biodiversity science. In the first section, we address that the absence of morphological diversification is an evolutionary phenomenon, a "process" counterpart to the long-studied mechanisms of morphological diversification. In the next section regarding taxonomy, we show that molecular delimitation of cryptic species is heavily biased towards distance-based methods. We also stress the importance of formally naming of cryptic species for better integration into research fields that use species as units of analysis. Finally, we show that incorporating cryptic species leads to novel insights regarding biodiversity patterns and processes, including large-scale biodiversity assessments, geographic variation in species distribution and species coexistence. It is time for incorporating multicriteria species approaches aiming to understand speciation across space and taxa, thus allowing integration into biodiversity conservation while accommodating for species uncertainty. © 2018 John Wiley & Sons Ltd.

  10. [A clinical trial of neutron capture therapy for brain tumors

    International Nuclear Information System (INIS)

    Zamenhof, R.G.

    1990-01-01

    This document briefly describes recent advances in the author's laboratory. Topics described include neutron beam design, high- resolution autoradiography, boronated phenylalanine (BPA) distribution and survival studies in glioma bearing mice, computer- aided treatment planning, prompt gamma boron 10 analysis facility at MITI-II, non-rodent BPA toxicity studies, and preparations for clinical studies

  11. SURROGATE SPECIES IN ASSESSING CONTAMINANT RISK FOR ENDANGERED FISHES

    Science.gov (United States)

    Rainbow trout, fathead minnows, and sheepshead minnows were tested as surrogate species to assess contaminant risk for 17 endangered fishes and one toad species. Acute toxicity tests were conducted with carbaryl, copper, 4-nonylphenol, pentachlorophenol, and permethrin in accord...

  12. Antifungal susceptibility testing of Candida species isolated from the immunocompromised patients admitted to ten university hospitals in Iran: comparison of colonizing and infecting isolates

    Directory of Open Access Journals (Sweden)

    Parisa Badiee

    2017-11-01

    Full Text Available Abstract Background Antifungal susceptibility testing is a subject of interest in the field of medical mycology. The aim of the present study were the distributions and antifungal susceptibility patterns of various Candida species isolated from colonized and infected immunocompromised patients admitted to ten university hospitals in Iran. Methods In totally, 846 Candida species were isolated from more than 4000 clinical samples and identified by the API 20 C AUX system. Antifungal susceptibility testing was performed by broth microdilution method according to CLSI. Results The most frequent Candida species isolated from all patients was Candida albicans (510/846. The epidemiological cutoff value and percentage of wild-type species for amphotericin B and fluconazole in Candida albicans, Candida tropicalis, Candida glabrata and Candida krusei were 0.5 μg/ml (95% and 4 μg/ml (96%; 1 μg/ml (95% and 8 μg/ml (95%; 0.5 μg/ml (99% and 19 μg/ml (98%; and 4 μg/ml (95% and 64 μg/ml (95%, respectively. The MIC90 and epidemiological cutoff values to posaconazole in Candida krusei were 0.5 μg/ml. There were significant differences between infecting and colonizing isolates of Candida tropicalis in MIC 90 values of amphotericin B, and isolates of Candida glabrata in values of amphotericin B, caspofungin, and voriconazole (P < 0.05. Conclusions Our findings suggest that the susceptibility patterns of Candida species (colonizing and infecting isolates in immunocompromised patients are not the same and acquired resistance was seen in some species.

  13. Profiling of Leptospira interrogans, L. santarosai, L. meyeri and L. borgpetersenii by SE-AFLP, PFGE and susceptibility testing--a continuous attempt at species and serovar differentiation.

    Science.gov (United States)

    Moreno, Luisa Z; Miraglia, Fabiana; Lilenbaum, Walter; Neto, José S F; Freitas, Julio C; Morais, Zenaide M; Hartskeerl, Rudy A; da Costa, Barbara L P; Vasconcellos, Silvio A; Moreno, Andrea M

    2016-03-09

    Leptospirosis is a widespread systemic zoonosis, considered as reemerging in certain developing countries. Although the cross agglutinin absorption test is still considered the standard method for Leptospira identification, it presents several disadvantages. The aim of this study was to characterize Leptospira spp. isolated from various hosts by genotyping and broth microdilution susceptibility testing in an attempt to differentiate Leptospira species, serogroups and serovars. Forty-seven isolates were studied. They were previously serotyped, and species confirmation was performed by 16S rRNA sequencing. Single-enzyme amplified fragment length polymorphism (SE-AFLP) and pulsed-field gel electrophoresis (PFGE) analysis enabled the distinction of L. interrogans from L. santarosai, L. meyeri and L. borgpetersenii in two main clusters. Among L. interrogans, it was possible to differentiate into two new clusters the serogroup Icterohaemorrhagiae from the serogroups Canicola and Pomona. L. santarosai isolates presented higher genetic variation than the other species in both techniques. Interestingly, the minimum inhibitory concentration (MIC) cluster analysis also provided Leptospira serogroup differentiation. Further studies are necessary regarding serovar Bananal isolates, as they presented the highest MIC values for most of the antimicrobials tested. All studied techniques successfully distinguished Leptospira species and serogroups. Despite being library-dependent methods, these approaches are less labor intensive and more economically viable, particularly SE-AFLP, and can be implemented in most reference laboratories worldwide to enable faster Leptospira typing.

  14. Multi-species biofilm of Candida albicans and non-Candida albicans Candida species on acrylic substrate

    Directory of Open Access Journals (Sweden)

    Apurva K Pathak

    2012-02-01

    Full Text Available OBJECTIVE: In polymicrobial biofilms bacteria extensively interact with Candida species, but the interaction among the different species of the Candida is yet to be completely evaluated. In the present study, the difference in biofilm formation ability of clinical isolates of four species of Candida in both single-species and multi-species combinations on the surface of dental acrylic resin strips was evaluated. MATERIAL AND METHODS: The species of Candida, isolated from multiple species oral candidiasis of the neutropenic patients, were used for the experiment. Organisms were cultured on Sabouraud dextrose broth with 8% glucose (SDB. Biofilm production on the acrylic resins strips was determined by crystal violet assay. Student's t-test and ANOVA were used to compare in vitro biofilm formation for the individual species of Candida and its different multi-species combinations. RESULTS: In the present study, differences between the mean values of the biofilm-forming ability of individual species (C. glabrata>C. krusei>C. tropicalis>C. albicans and in its multi-species' combinations (the highest for C. albicans with C. glabrata and the lowest for all the four species combination were reported. CONCLUSIONS: The findings of this study showed that biofilm-forming ability was found greater for non-Candida albicans Candida species (NCAC than for C. albicans species with intra-species variation. Presence of C. albicans in multi-species biofilms increased, whereas; C. tropicalis decreased the biofilm production with all other NCAC species.

  15. Are ecosystem services stabilized by differences among species? A test using crop pollination.

    Science.gov (United States)

    Winfree, Rachael; Kremen, Claire

    2009-01-22

    Biological diversity could enhance ecosystem service provision by increasing the mean level of services provided, and/or by providing more consistent (stable) services over space and time. Ecological theory predicts that when an ecosystem service is provided by many species, it will be stabilized against disturbance by a variety of 'stabilizing mechanisms.' However, few studies have investigated whether stabilizing mechanisms occur in real landscapes affected by human disturbance. We used two datasets on crop pollination by wild native bees to screen for and differentiate among three stabilizing mechanisms: density compensation (negative co-variance among species' abundances); response diversity (differential response to environmental variables among species); and cross-scale resilience (response to the same environmental variable at different scales by different species). In both datasets, we found response diversity and cross-scale resilience, but not density compensation. We conclude that stabilizing mechanisms may contribute to the stability of pollination services in our study areas, emphasizing the insurance value of seemingly 'redundant' species. Furthermore, the absence of density compensation that we found at the landscape scale contrasts with findings of previous small-scale experimental and modelling work, suggesting that we should not assume that density compensation will stabilize ecosystem services in real landscapes.

  16. Different responses to reward comparisons by three primate species.

    Science.gov (United States)

    Freeman, Hani D; Sullivan, Jennifer; Hopper, Lydia M; Talbot, Catherine F; Holmes, Andrea N; Schultz-Darken, Nancy; Williams, Lawrence E; Brosnan, Sarah F

    2013-01-01

    Recently, much attention has been paid to the role of cooperative breeding in the evolution of behavior. In many measures, cooperative breeders are more prosocial than non-cooperatively breeding species, including being more likely to actively share food. This is hypothesized to be due to selective pressures specific to the interdependency characteristic of cooperatively breeding species. Given the high costs of finding a new mate, it has been proposed that cooperative breeders, unlike primates that cooperate in other contexts, should not respond negatively to unequal outcomes between themselves and their partner. However, in this context such pressures may extend beyond cooperative breeders to other species with pair-bonding and bi-parental care. Here we test the response of two New World primate species with different parental strategies to unequal outcomes in both individual and social contrast conditions. One species tested was a cooperative breeder (Callithrix spp.) and the second practiced bi-parental care (Aotus spp.). Additionally, to verify our procedure, we tested a third confamilial species that shows no such interdependence but does respond to individual (but not social) contrast (Saimiri spp.). We tested all three genera using an established inequity paradigm in which individuals in a pair took turns to gain rewards that sometimes differed from those of their partners. None of the three species tested responded negatively to inequitable outcomes in this experimental context. Importantly, the Saimiri spp responded to individual contrast, as in earlier studies, validating our procedure. When these data are considered in relation to previous studies investigating responses to inequity in primates, they indicate that one aspect of cooperative breeding, pair-bonding or bi-parental care, may influence the evolution of these behaviors. These results emphasize the need to study a variety of species to gain insight in to how decision-making may vary across

  17. Different responses to reward comparisons by three primate species.

    Directory of Open Access Journals (Sweden)

    Hani D Freeman

    Full Text Available Recently, much attention has been paid to the role of cooperative breeding in the evolution of behavior. In many measures, cooperative breeders are more prosocial than non-cooperatively breeding species, including being more likely to actively share food. This is hypothesized to be due to selective pressures specific to the interdependency characteristic of cooperatively breeding species. Given the high costs of finding a new mate, it has been proposed that cooperative breeders, unlike primates that cooperate in other contexts, should not respond negatively to unequal outcomes between themselves and their partner. However, in this context such pressures may extend beyond cooperative breeders to other species with pair-bonding and bi-parental care.Here we test the response of two New World primate species with different parental strategies to unequal outcomes in both individual and social contrast conditions. One species tested was a cooperative breeder (Callithrix spp. and the second practiced bi-parental care (Aotus spp.. Additionally, to verify our procedure, we tested a third confamilial species that shows no such interdependence but does respond to individual (but not social contrast (Saimiri spp.. We tested all three genera using an established inequity paradigm in which individuals in a pair took turns to gain rewards that sometimes differed from those of their partners.None of the three species tested responded negatively to inequitable outcomes in this experimental context. Importantly, the Saimiri spp responded to individual contrast, as in earlier studies, validating our procedure. When these data are considered in relation to previous studies investigating responses to inequity in primates, they indicate that one aspect of cooperative breeding, pair-bonding or bi-parental care, may influence the evolution of these behaviors. These results emphasize the need to study a variety of species to gain insight in to how decision-making may

  18. Assessing species boundaries using multilocus species delimitation in a morphologically conserved group of neotropical freshwater fishes, the Poecilia sphenops species complex (Poeciliidae.

    Directory of Open Access Journals (Sweden)

    Justin C Bagley

    importance of testing for hybridization versus incomplete lineage sorting, which aids inference of not only species limits but also evolutionary processes influencing genetic diversity.

  19. Copper toxicity to different field-collected cladoceran species: intra-and inter-species sensitivity

    International Nuclear Information System (INIS)

    Bossuyt, Bart T.A.; Janssen, Colin R.

    2005-01-01

    The acute copper sensitivity of 44 European freshwater cladocerans, from four families (Daphniidae, Bosminidae, Macrothricidae, Chydoridae) and 13 genera (Daphnia, Ctenodaphnia, Ceriodaphnia, Simocephalus, Scapholeberis, Bosmina, Acantholeberis, Alona, Acroperus, Chydorus, Eurycercus, Disparalona and Pleuroxus) were assayed. The 48-h EC 50 s of field-collected organisms tested in reconstituted standard laboratory water ranged from 5.3 to 70.6 μg Cu L -1 . Only among Ctenodaphnia were significant intra-species differences observed. Significant inter-species differences were noted among Alonina and Daphnia. Between all genera tested, a maximum of a 12-fold difference in copper sensitivity was noted. Most animals were more sensitive than a laboratory D. magna clone. A weak non-significant increasing trend was noted between mean cladoceran 48-h EC 50 and ambient copper concentration of the different aquatic systems, suggesting acclimation/adaptation in the field. A positive relationship was also observed between the 48-h EC 50 of the field-collected cladoceran species (without the Chydoridae family) and the size of the organisms. - Zooplankton living in natural waters are more sensitive to copper than laboratory animals

  20. Do intrinsically dominant and subordinate species exist? A test statistic for field data

    NARCIS (Netherlands)

    Olff, Han; Bakker, Jan P.

    . We propose a new method to obtain information about processes that structure plant communities. We analysed the relationship between the presence and dominance of species across a range of habitats. A simple regression model was used to describe this relationship for each species. Based on the

  1. Unidirectional hybrid male sterility from crosses between species A and species B of the taxon Anopheles (Cellia) culicifacies Giles.

    Science.gov (United States)

    Miles, S J

    1981-02-01

    Crosses between species A females and species B males of the taxon Anopheles culicifacies give F1 males with undeveloped testes, reduced vasa deferentia, and apparently normal accessory glands. F1 males from the reciprocal cross, and F1 hybrid females from both reciprocal crosses are fertile, though their fertility is less than that of either parental species

  2. A test of the nest sanitation hypothesis for the evolution of foreign egg rejection in an avian brood parasite rejecter host species.

    Science.gov (United States)

    Luro, Alec B; Hauber, Mark E

    2017-04-01

    Hosts of avian brood parasites have evolved diverse defenses to avoid the costs associated with raising brood parasite nestlings. In egg ejection, the host recognizes and removes foreign eggs laid in its nest. Nest sanitation, a behavior similar in motor pattern to egg ejection, has been proposed repeatedly as a potential pre-adaptation to egg ejection. Here, we separately placed blue 3D-printed, brown-headed cowbird (Molothrus ater) eggs known to elicit interindividual variation in ejection responses and semi-natural leaves into American robins' (Turdus migratorius) nests to test proximate predictions that (1) rejecter hosts should sanitize debris from nests more frequently and consistently than accepter hosts and (2) hosts that sanitize their nests of debris prior to the presentation of a foreign egg will be more likely to eject the foreign egg. Egg ejection responses were highly repeatable within individuals yet variable between them, but were not influenced by prior exposure to debris, nor related to sanitation tendencies as a whole, because nearly all individuals sanitized their nests. Additionally, we collected published data for eight different host species to test for a potential positive correlation between sanitation and egg ejection. We found no significant correlation between nest sanitation and egg ejection rates; however, our comparative analysis was limited to a sample size of 8, and we advise that more data from additional species are necessary to properly address interspecific tests of the pre-adaptation hypothesis. In lack of support for the nest sanitation hypothesis, our study suggests that, within individuals, foreign egg ejection is distinct from nest sanitation tendencies, and sanitation and foreign egg ejection may not correlate across species.

  3. Response of Microtermes mycophagus (Isoptera: Termitidae to twenty one wood species

    Directory of Open Access Journals (Sweden)

    Naeem Iqbal

    2015-08-01

    Full Text Available The responses of termite species to bait depend upon the quality of the food used in the stations. Woods are the most common food sources for termites but different termite species behave differently to different wood species and types. The knowledge of the preference status of different wood species to a termite species helps in effective monitoring and baiting program. The current study was carried out to evaluate the preference of 21 wood species to the termite, Microtermes mycophagus in the field by no-choice and choice feeding tests. The results indicated silk cotton tree and sacred fig woods as the most preferred wood species with mean mass losses of 71.21 ± 5.09% and 68.38 ± 7.27% in no-choice test and 95.02 ± 1.65% and 91.69 ± 2.07% in choice tests, respectively. White cedar was the least preferred wood species with mean mass losses of 7.49 ± 1.64% and 13.92 ± 1.89% in no choice and choice feeding tests, respectively. Based on present studies, sapwood of silk cotton tree and sacred fig may be used in effective monitoring and baiting program against M. mycophagus.

  4. Characterization of the nociceptin receptor (ORL-1) agonist, Ro64-6198, in tests of anxiety across multiple species.

    Science.gov (United States)

    Varty, G B; Hyde, L A; Hodgson, R A; Lu, S X; McCool, M F; Kazdoba, T M; Del Vecchio, R A; Guthrie, D H; Pond, A J; Grzelak, M E; Xu, X; Korfmacher, W A; Tulshian, D; Parker, E M; Higgins, G A

    2005-10-01

    Previous studies have demonstrated behaviors indicative of anxiolysis in rats pretreated with the nociceptin receptor (opioid receptor like-1, ORL-1) agonist, Ro64-6198. The aim of this study was to examine the effects of Ro64-6198 in anxiety models across three species: rat, guinea pig, and mouse. In addition, the receptor specificity of Ro64-6198 was studied, using the ORL-1 receptor antagonist, J-113397, and ORL-1 receptor knockout (KO) mice. Finally, neurological studies examined potential side effects of Ro64-6198 in the rat and mouse. Ro64-6198 (3-10 mg/kg) increased punished responding in a rat conditioned lick suppression test similarly to chlordiazepoxide (6 mg/kg). This effect of Ro64-6198 was attenuated by J-113397 (10 mg/kg), but not the mu opioid antagonist, naltrexone (3 mg/kg). In addition, Ro64-6198 (1-3 mg/kg) reduced isolation-induced vocalizations in rat and guinea pig pups. Ro64-6198 (3 mg/kg) increased the proportion of punished responding in a mouse Geller-Seifter test in wild-type (WT) but not ORL-1 KO mice, whereas diazepam (1-5.6 mg/kg) was effective in both genotypes. In rats, Ro64-6198 reduced locomotor activity (LMA) and body temperature and impaired rotarod, beam walking, and fixed-ratio (FR) performance at doses of 10-30 mg/kg, i.e., three to ten times higher than an anxiolytic dose. In WT mice, Ro64-6198 (3-10 mg/kg) reduced LMA and rotarod performance, body temperature, and FR responding, but these same measures were unaffected in ORL-1 KO mice. Haloperidol (0.3-3 mg/kg) reduced these measures to a similar extent in both genotypes. These studies confirm the potent, ORL-1 receptor-mediated, anxiolytic-like effects of Ro64-6198, extending the findings across three species. Ro64-6198 has target-based side effects, although the magnitude of these effects varies across species.

  5. A comparison of auditory brainstem responses across diving bird species

    Science.gov (United States)

    Crowell, Sara E.; Berlin, Alicia; Carr, Catherine E.; Olsen, Glenn H.; Therrien, Ronald E.; Yannuzzi, Sally E.; Ketten, Darlene R.

    2015-01-01

    There is little biological data available for diving birds because many live in hard-to-study, remote habitats. Only one species of diving bird, the black-footed penguin (Spheniscus demersus), has been studied in respect to auditory capabilities (Wever et al., Proc Natl Acad Sci USA 63:676–680, 1969). We, therefore, measured in-air auditory threshold in ten species of diving birds, using the auditory brainstem response (ABR). The average audiogram obtained for each species followed the U-shape typical of birds and many other animals. All species tested shared a common region of the greatest sensitivity, from 1000 to 3000 Hz, although audiograms differed significantly across species. Thresholds of all duck species tested were more similar to each other than to the two non-duck species tested. The red-throated loon (Gavia stellata) and northern gannet (Morus bassanus) exhibited the highest thresholds while the lowest thresholds belonged to the duck species, specifically the lesser scaup (Aythya affinis) and ruddy duck (Oxyura jamaicensis). Vocalization parameters were also measured for each species, and showed that with the exception of the common eider (Somateria mollisima), the peak frequency, i.e., frequency at the greatest intensity, of all species' vocalizations measured here fell between 1000 and 3000 Hz, matching the bandwidth of the most sensitive hearing range.

  6. Phytotoxic studies of medicinal plant species of Pakistan

    International Nuclear Information System (INIS)

    Gilani, S.A.; Adnan, M.; Kikuchi, A.; Fujii, Y.; Shinwari, Z.K.; Kazuo, N.; Watanabe, K.N.

    2010-01-01

    Allelopathic screening of 81 medicinal plant species, collected from North West Frontier Province (NWFP) Pakistan, was carried out to identify significantly higher allelopathic species for future phyto chemical analyses. For this purpose, sandwich method was used to test allelopathic potentials of leaf leachates of these plant species against lettuce seeds (Lactuca sativa L.). Two different concentrations of 10 mg and 50 mg of leaf leachates were used in the study. The radicle and hypocotyl growths were measured and compared with control treatments. It was observed that an endemic species Seriphidium kurramense, Andrachne cordifolia and Rhazya stricta were the stronger phyto toxic plants as compared to the other test species. Based on the current screening, three potential medicinal plants are recommended for future bioassay guided isolation of allelochemicals and for genetic diversity studies. It would also be interesting to see correlation between genetic markers and isolated allelochemicals. (author)

  7. How Does Temperature Impact Leaf Size and Shape in Four Woody Dicot Species? Testing the Assumptions of Leaf Physiognomy-Climate Models

    Science.gov (United States)

    McKee, M.; Royer, D. L.

    2017-12-01

    The physiognomy (size and shape) of fossilized leaves has been used to reconstruct the mean annual temperature of ancient environments. Colder temperatures often select for larger and more abundant leaf teeth—serrated edges on leaf margins—as well as a greater degree of leaf dissection. However, to be able to accurately predict paleotemperature from the morphology of fossilized leaves, leaves must be able to react quickly and in a predictable manner to changes in temperature. We examined the extent to which temperature affects leaf morphology in four tree species: Carpinus caroliniana, Acer negundo, Ilex opaca, and Ostrya virginiana. Saplings of these species were grown in two growth cabinets under contrasting temperatures (17 and 25 °C). Compared to the cool treatment, in the warm treatment Carpinus caroliniana leaves had significantly fewer leaf teeth and a lower ratio of total number of leaf teeth to internal perimeter; and Acer negundo leaves had a significantly lower feret diameter ratio (a measure of leaf dissection). In addition, a two-way ANOVA tested the influence of temperature and species on leaf physiognomy. This analysis revealed that all plants, regardless of species, tended to develop more highly dissected leaves with more leaf teeth in the cool treatment. Because the cabinets maintained equivalent moisture, humidity, and CO2 concentration between the two treatments, these results demonstrate that these species could rapidly adapt to changes in temperature. However, not all of the species reacted identically to temperature changes. For example, Acer negundo, Carpinus caroliniana, and Ostrya virginiana all had a higher number of total teeth in the cool treatment compared to the warm treatment, but the opposite was true for Ilex opaca. Our work questions a fundamental assumption common to all models predicting paleotemperature from the physiognomy of fossilized leaves: a given climate will inevitably select for the same leaf physiognomy

  8. Copper toxicity to different field-collected cladoceran species: intra-and inter-species sensitivity

    Energy Technology Data Exchange (ETDEWEB)

    Bossuyt, Bart T.A. [Laboratory of Environmental Toxicology and Aquatic Ecology, Ghent University, J. Plateaustraat 22, B-9000 Ghent (Belgium)]. E-mail: bart.bossuyt@ugent.be; Janssen, Colin R. [Laboratory of Environmental Toxicology and Aquatic Ecology, Ghent University, J. Plateaustraat 22, B-9000 Ghent (Belgium)

    2005-07-15

    The acute copper sensitivity of 44 European freshwater cladocerans, from four families (Daphniidae, Bosminidae, Macrothricidae, Chydoridae) and 13 genera (Daphnia, Ctenodaphnia, Ceriodaphnia, Simocephalus, Scapholeberis, Bosmina, Acantholeberis, Alona, Acroperus, Chydorus, Eurycercus, Disparalona and Pleuroxus) were assayed. The 48-h EC{sub 50}s of field-collected organisms tested in reconstituted standard laboratory water ranged from 5.3 to 70.6 {mu}g Cu L{sup -1}. Only among Ctenodaphnia were significant intra-species differences observed. Significant inter-species differences were noted among Alonina and Daphnia. Between all genera tested, a maximum of a 12-fold difference in copper sensitivity was noted. Most animals were more sensitive than a laboratory D. magna clone. A weak non-significant increasing trend was noted between mean cladoceran 48-h EC{sub 50} and ambient copper concentration of the different aquatic systems, suggesting acclimation/adaptation in the field. A positive relationship was also observed between the 48-h EC{sub 50} of the field-collected cladoceran species (without the Chydoridae family) and the size of the organisms. - Zooplankton living in natural waters are more sensitive to copper than laboratory animals.

  9. Campylobacter species in animal, food, and environmental sources, and relevant testing programs in Canada.

    Science.gov (United States)

    Huang, Hongsheng; Brooks, Brian W; Lowman, Ruff; Carrillo, Catherine D

    2015-10-01

    Campylobacter species, particularly thermophilic campylobacters, have emerged as a leading cause of human foodborne gastroenteritis worldwide, with Campylobacter jejuni, Campylobacter coli, and Campylobacter lari responsible for the majority of human infections. Although most cases of campylobacteriosis are self-limiting, campylobacteriosis represents a significant public health burden. Human illness caused by infection with campylobacters has been reported across Canada since the early 1970s. Many studies have shown that dietary sources, including food, particularly raw poultry and other meat products, raw milk, and contaminated water, have contributed to outbreaks of campylobacteriosis in Canada. Campylobacter spp. have also been detected in a wide range of animal and environmental sources, including water, in Canada. The purpose of this article is to review (i) the prevalence of Campylobacter spp. in animals, food, and the environment, and (ii) the relevant testing programs in Canada with a focus on the potential links between campylobacters and human health in Canada.

  10. USING TAXONOMIC REVISION DATA TO ESTIMATE THE GLOBAL SPECIES RICHNESS AND CHARACTERISTICS OF UNDESCRIBED SPECIES OF DIVING BEETLES (COLEOPTERA: DYTISCIDAE

    Directory of Open Access Journals (Sweden)

    Viktor Nilsson-Örtman

    2010-06-01

    Full Text Available Many methods used for estimating species richness are either difficult to use on poorly known taxa or require input data that are laborious and expensive to collect. In this paper we apply a method which takes advantage of the carefully conducted tests of how the described diversity compares to real species richness that are inherent in taxonomic revisions. We analyze the quantitative outcome from such revisions with respect to body size, zoogeographical region and phylogenetic relationship. The best fitting model is used to predict the diversity of unrevised groups if these would have been subject to as rigorous species level hypothesis-testing as the revised groups. The sensitivity of the predictive model to single observations is estimated by bootstrapping over resampled subsets of the original data. The Dytiscidae is with its 4080 described species (end of May 2009 the most diverse group of aquatic beetles and have a world-wide distribution. Extensive taxonomic work has been carried out on the family but still the number of described species increases exponentially in most zoogeographical regions making many commonly used methods of estimation difficult to apply. We provide independent species richness estimates of subsamples for which species richness estimates can be reached through extrapolation and compare these to the species richness estimates obtained through the method using revision data. We estimate there to be 5405 species of dytiscids, a 1.32-fold increase over the present number of described species. The undescribed diversity is likely to be biased towards species with small body size from tropical regions outside of Africa.

  11. Antifungal susceptibility testing of Candida species isolated from the immunocompromised patients admitted to ten university hospitals in Iran : comparison of colonizing and infecting isolates

    NARCIS (Netherlands)

    Badiee, Parisa; Badali, Hamid; Boekhout, Teun; Diba, Kambiz; Moghadam, Abdolkarim Ghadimi; Hossaini Nasab, Ali; Jafarian, Hadis; Mohammadi, Rasoul; Mirhendi, Hossein; Najafzadeh, Mohammad Javad; Shamsizadeh, Ahmad; Soltani, Jafar

    2017-01-01

    BACKGROUND: Antifungal susceptibility testing is a subject of interest in the field of medical mycology. The aim of the present study were the distributions and antifungal susceptibility patterns of various Candida species isolated from colonized and infected immunocompromised patients admitted to

  12. Development and validation of real-time PCR tests for the identification of four Spodoptera species: Spodoptera eridania, Spodoptera frugiperda, Spodoptera littoralis, and Spodoptera litura (Lepidoptera: Noctuidae).

    Science.gov (United States)

    Van de Vossenberg, B T L H; Van der Straten, M J

    2014-08-01

    The genus Spodoptera comprises 31 species, 4 of which are listed as quarantine pests for the European Union: Spodoptera eridania (Cramer), Spodoptera frugiperda (Smith), Spodoptera littoralis (Boisduval), and Spodoptera litura (F.). In international trade, the earlier life stages (eggs and larvae) are being intercepted at point of inspection most frequently, challenging the possibilities of morphological identification. To realize a rapid and reliable identification for all stages, we developed and validated four simplex real-time polymerase chain reaction identification tests based on the mitochondrial cytochrome b gene using dual-labeled hydrolysis probes. Method validation on dilutions of extracted DNA of the target organisms showed that low levels of template (up to 0.2-100 pg) can reliably be identified. No cross-reactivity was observed with 14 nontarget Spodoptera and 5 non-Spodoptera species in the specific Spodoptera tests. The tests showed to be repeatable, reproducible (both 100%), and robust. The new Spodoptera tests have proven to be suitable tools for routine identification of all life stages of S. eridania, S. frugiperda, S. littoralis, and S. litura.

  13. Changing drivers of species dominance during tropical forest succession

    NARCIS (Netherlands)

    Lohbeck, M.W.M.; Poorter, L.; Martinez-Ramos, M.; Rodriguez-Valázquez, J.; Breugel, van M.; Bongers, F.

    2014-01-01

    1. Deterministic theories predict that local communities assemble from a regional species pool based on niche differences, thus by plant functional adaptations. We tested whether functional traits can also explain patterns in species dominance among the suite of co-occurring species. 2. We predicted

  14. Above- and below-ground effects of plant diversity depend on species origin

    DEFF Research Database (Denmark)

    Kuebbing, Sara E.; Classen, Aimee Taylor; Sanders, Nate

    2015-01-01

    -interaction models to describe how species' interactions influenced diversity-productivity relationships. Communities with more species had higher total biomass than did monoculture communities, but native and nonnative communities diverged in root : shoot ratios and the mechanism responsible for increased......Although many plant communities are invaded by multiple nonnative species, we have limited information on how a species' origin affects ecosystem function. We tested how differences in species richness and origin affect productivity and seedling establishment. We created phylogenetically paired...... native and nonnative plant communities in a glasshouse experiment to test diversity-productivity relationships and responsible mechanisms (i.e. selection or complementarity effects). Additionally, we tested how productivity and associated mechanisms influenced seedling establishment. We used diversity...

  15. Multiplex real-time PCR assay for Legionella species.

    Science.gov (United States)

    Kim, Seung Min; Jeong, Yoojung; Sohn, Jang Wook; Kim, Min Ja

    2015-12-01

    Legionella pneumophila serogroup 1 (sg1) accounts for the majority of infections in humans, but other Legionella species are also associated with human disease. In this study, a new SYBR Green I-based multiplex real-time PCR assay in a single reaction was developed to allow the rapid detection and differentiation of Legionella species by targeting specific gene sequences. Candidate target genes were selected, and primer sets were designed by referring to comparative genomic hybridization data of Legionella species. The Legionella species-specific groES primer set successfully detected all 30 Legionella strains tested. The xcpX and rfbA primers specifically detected L. pneumophila sg1-15 and L. pneumophila sg1, respectively. In addition, this assay was validated by testing clinical samples and isolates. In conclusion, this novel multiplex real-time PCR assay might be a useful diagnostic tool for the rapid detection and differentiation of Legionella species in both clinical and epidemiological studies. Copyright © 2015 Elsevier Ltd. All rights reserved.

  16. Projecting future expansion of invasive species: comparing and improving methodologies for species distribution modeling.

    Science.gov (United States)

    Mainali, Kumar P; Warren, Dan L; Dhileepan, Kunjithapatham; McConnachie, Andrew; Strathie, Lorraine; Hassan, Gul; Karki, Debendra; Shrestha, Bharat B; Parmesan, Camille

    2015-12-01

    Modeling the distributions of species, especially of invasive species in non-native ranges, involves multiple challenges. Here, we developed some novel approaches to species distribution modeling aimed at reducing the influences of such challenges and improving the realism of projections. We estimated species-environment relationships for Parthenium hysterophorus L. (Asteraceae) with four modeling methods run with multiple scenarios of (i) sources of occurrences and geographically isolated background ranges for absences, (ii) approaches to drawing background (absence) points, and (iii) alternate sets of predictor variables. We further tested various quantitative metrics of model evaluation against biological insight. Model projections were very sensitive to the choice of training dataset. Model accuracy was much improved using a global dataset for model training, rather than restricting data input to the species' native range. AUC score was a poor metric for model evaluation and, if used alone, was not a useful criterion for assessing model performance. Projections away from the sampled space (i.e., into areas of potential future invasion) were very different depending on the modeling methods used, raising questions about the reliability of ensemble projections. Generalized linear models gave very unrealistic projections far away from the training region. Models that efficiently fit the dominant pattern, but exclude highly local patterns in the dataset and capture interactions as they appear in data (e.g., boosted regression trees), improved generalization of the models. Biological knowledge of the species and its distribution was important in refining choices about the best set of projections. A post hoc test conducted on a new Parthenium dataset from Nepal validated excellent predictive performance of our 'best' model. We showed that vast stretches of currently uninvaded geographic areas on multiple continents harbor highly suitable habitats for parthenium

  17. Using aquatic macroinvertebrate species traits to build test batteries for sediment toxicity assessment: accounting for the diversity of potential biological responses to toxicants.

    Science.gov (United States)

    Ducrot, Virginie; Usseglio-Polatera, Philippe; Péry, T Alexandre R R; Mouthon, Jacques; Lafont, Michel; Roger, Marie-Claude; Garric, Jeanne; Férard, Jean-François

    2005-09-01

    An original species-selection method for the building of test batteries is presented. This method is based on the statistical analysis of the biological and ecological trait patterns of species. It has been applied to build a macroinvertebrate test battery for the assessment of sediment toxicity, which efficiently describes the diversity of benthic macroinvertebrate biological responses to toxicants in a large European lowland river. First, 109 potential representatives of benthic communities of European lowland rivers were selected from a list of 479 taxa, considering 11 biological traits accounting for the main routes of exposure to a sediment-bound toxicant and eight ecological traits providing an adequate description of habitat characteristics used by the taxa. Second, their biological and ecological trait patterns were compared using coinertia analysis. This comparison allowed the clustering of taxa into groups of organisms that exhibited similar life-history characteristics, physiological and behavioral features, and similar habitat use. Groups exhibited various sizes (7-35 taxa), taxonomic compositions, and biological and ecological features. Main differences among group characteristics concerned morphology, substrate preferendum and habitat utilization, nutritional features, maximal size, and life-history strategy. Third, the best representatives of the mean biological and ecological characteristics of each group were included in the test battery. The final selection was composed of Chironomus riparius (Insecta: Diptera), Branchiura sowerbyi (Oligochaeta: Tubificidae), Lumbriculus variegatus (Oligochaeta: Lumbriculidae), Valvata piscinalis (Gastropoda: Valvatidae), and Sericostoma personatum (Trichoptera: Sericostomatidae). This approach permitted the biological and ecological variety of the battery to be maximized. Because biological and ecological traits of taxa determine species sensitivity, such maximization should permit the battery to better account

  18. Evaluating species richness: biased ecological inference results from spatial heterogeneity in species detection probabilities

    Science.gov (United States)

    McNew, Lance B.; Handel, Colleen M.

    2015-01-01

    Accurate estimates of species richness are necessary to test predictions of ecological theory and evaluate biodiversity for conservation purposes. However, species richness is difficult to measure in the field because some species will almost always be overlooked due to their cryptic nature or the observer's failure to perceive their cues. Common measures of species richness that assume consistent observability across species are inviting because they may require only single counts of species at survey sites. Single-visit estimation methods ignore spatial and temporal variation in species detection probabilities related to survey or site conditions that may confound estimates of species richness. We used simulated and empirical data to evaluate the bias and precision of raw species counts, the limiting forms of jackknife and Chao estimators, and multi-species occupancy models when estimating species richness to evaluate whether the choice of estimator can affect inferences about the relationships between environmental conditions and community size under variable detection processes. Four simulated scenarios with realistic and variable detection processes were considered. Results of simulations indicated that (1) raw species counts were always biased low, (2) single-visit jackknife and Chao estimators were significantly biased regardless of detection process, (3) multispecies occupancy models were more precise and generally less biased than the jackknife and Chao estimators, and (4) spatial heterogeneity resulting from the effects of a site covariate on species detection probabilities had significant impacts on the inferred relationships between species richness and a spatially explicit environmental condition. For a real dataset of bird observations in northwestern Alaska, the four estimation methods produced different estimates of local species richness, which severely affected inferences about the effects of shrubs on local avian richness. Overall, our results

  19. Single-locus species delimitation: a test of the mixed Yule-coalescent model, with an empirical application to Philippine round-leaf bats.

    Science.gov (United States)

    Esselstyn, Jacob A; Evans, Ben J; Sedlock, Jodi L; Anwarali Khan, Faisal Ali; Heaney, Lawrence R

    2012-09-22

    Prospects for a comprehensive inventory of global biodiversity would be greatly improved by automating methods of species delimitation. The general mixed Yule-coalescent (GMYC) was recently proposed as a potential means of increasing the rate of biodiversity exploration. We tested this method with simulated data and applied it to a group of poorly known bats (Hipposideros) from the Philippines. We then used echolocation call characteristics to evaluate the plausibility of species boundaries suggested by GMYC. In our simulations, GMYC performed relatively well (errors in estimated species diversity less than 25%) when the product of the haploid effective population size (N(e)) and speciation rate (SR; per lineage per million years) was less than or equal to 10(5), while interspecific variation in N(e) was twofold or less. However, at higher but also biologically relevant values of N(e) × SR and when N(e) varied tenfold among species, performance was very poor. GMYC analyses of mitochondrial DNA sequences from Philippine Hipposideros suggest actual diversity may be approximately twice the current estimate, and available echolocation call data are mostly consistent with GMYC delimitations. In conclusion, we consider the GMYC model useful under some conditions, but additional information on N(e), SR and/or corroboration from independent character data are needed to allow meaningful interpretation of results.

  20. Effects of 'target' plant species body size on neighbourhood species richness and composition in old-field vegetation.

    Directory of Open Access Journals (Sweden)

    Brandon S Schamp

    Full Text Available Competition is generally regarded as an important force in organizing the structure of vegetation, and evidence from several experimental studies of species mixtures suggests that larger mature plant size elicits a competitive advantage. However, these findings are at odds with the fact that large and small plant species generally coexist, and relatively smaller species are more common in virtually all plant communities. Here, we use replicates of ten relatively large old-field plant species to explore the competitive impact of target individual size on their surrounding neighbourhoods compared to nearby neighbourhoods of the same size that are not centred by a large target individual. While target individuals of the largest of our test species, Centaurea jacea L., had a strong impact on neighbouring species, in general, target species size was a weak predictor of the number of other resident species growing within its immediate neighbourhood, as well as the number of resident species that were reproductive. Thus, the presence of a large competitor did not restrict the ability of neighbouring species to reproduce. Lastly, target species size did not have any impact on the species size structure of neighbouring species; i.e. they did not restrict smaller, supposedly poorer competitors, from growing and reproducing close by. Taken together, these results provide no support for a size-advantage in competition restricting local species richness or the ability of small species to coexist and successfully reproduce in the immediate neighbourhood of a large species.

  1. Failed sperm development as a reproductive isolating barrier between species.

    Science.gov (United States)

    Wünsch, Lisa K; Pfennig, Karin S

    2013-01-01

    Hybrid male sterility is a common reproductive isolating barrier between species. Yet, little is known about the actual developmental causes of this phenomenon, especially in naturally hybridizing species. We sought to evaluate the developmental causes of hybrid male sterility, using spadefoot toads as our study system. Plains spadefoot toads (Spea bombifrons) and Mexican spadefoot toads (S. multiplicata) hybridize where they co-occur in the southwestern USA. Hybrids are viable, but hybrid males suffer reduced fertility. We compared testes size and developmental stages of sperm cell maturation between hybrid males and males of each species. We found that testes of hybrid males did not differ in mean size from pure-species males. However, hybrids showed a greater range of within-individual variation in testes size than pure-species males. Moreover, although hybrids produced similar numbers of early stage sperm cells, hybrids produced significantly fewer mature spermatozoids than pure-species males. Interestingly, an introgressed individual produced numbers of live sperm comparable to pure-species males, but the majority of these sperm cells were abnormally shaped and non-motile. These results indicate that hybrid incompatibilities in late sperm development serve as a reproductive isolating barrier between species. The nature of this breakdown highlights the possibilities that hybrid males may vary in fertility and that fertility could possibly be recovered in introgressed males. © 2013 Wiley Periodicals, Inc.

  2. Structure-Based Design of an Iminoheterocyclic β-Site Amyloid Precursor Protein Cleaving Enzyme (BACE) Inhibitor that Lowers Central Aβ in Nonhuman Primates

    Energy Technology Data Exchange (ETDEWEB)

    Mandal, Mihirbaran; Wu, Yusheng; Misiaszek, Jeffrey; Li, Guoqing; Buevich, Alexei; Caldwell, John P.; Liu, Xiaoxiang; Mazzola, Robert D.; Orth, Peter; Strickland, Corey; Voigt, Johannes; Wang, Hongwu; Zhu, Zhaoning; Chen, Xia; Grzelak, Michael; Hyde, Lynn A.; Kuvelkar, Reshma; Leach, Prescott T.; Terracina, Giuseppe; Zhang, Lili; Zhang, Qi; Michener, Maria S.; Smith, Brad; Cox, Kathleen; Grotz, Diane; Favreau, Leonard; Mitra, Kaushik; Kazakevich, Irina; McKittrick, Brian A.; Greenlee, William; Kennedy, Matthew E.; Parker, Eric M.; Cumming, Jared N.; Stamford, Andrew W. (Merck)

    2016-04-14

    We describe successful efforts to optimize the in vivo profile and address off-target liabilities of a series of BACE1 inhibitors represented by 6 that embodies the recently validated fused pyrrolidine iminopyrimidinone scaffold. Employing structure-based design, truncation of the cyanophenyl group of 6 that binds in the S3 pocket of BACE1 followed by modification of the thienyl group in S1 was pursued. Optimization of the pyrimidine substituent that binds in the S2'–S2'' pocket of BACE1 remediated time-dependent CYP3A4 inhibition of earlier analogues in this series and imparted high BACE1 affinity. These efforts resulted in the discovery of difluorophenyl analogue 9 (MBi-4), which robustly lowered CSF and cortex Aβ40 in both rats and cynomolgus monkeys following a single oral dose. Compound 9 represents a unique molecular shape among BACE inhibitors reported to potently lower central Aβ in nonrodent preclinical species.

  3. RS-1 enhances CRISPR/Cas9- and TALEN-mediated knock-in efficiency.

    Science.gov (United States)

    Song, Jun; Yang, Dongshan; Xu, Jie; Zhu, Tianqing; Chen, Y Eugene; Zhang, Jifeng

    2016-01-28

    Zinc-finger nuclease, transcription activator-like effector nuclease and CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 (CRISPR-associated protein 9) are becoming major tools for genome editing. Importantly, knock-in in several non-rodent species has been finally achieved thanks to these customizable nucleases; yet the rates remain to be further improved. We hypothesize that inhibiting non-homologous end joining (NHEJ) or enhancing homology-directed repair (HDR) will improve the nuclease-mediated knock-in efficiency. Here we show that the in vitro application of an HDR enhancer, RS-1, increases the knock-in efficiency by two- to five-fold at different loci, whereas NHEJ inhibitor SCR7 has minimal effects. We then apply RS-1 for animal production and have achieved multifold improvement on the knock-in rates as well. Our work presents tools to nuclease-mediated knock-in animal production, and sheds light on improving gene-targeting efficiencies on pluripotent stem cells.

  4. Effects of fenbendazole on routine immune response parameters of BALB/c mice.

    Science.gov (United States)

    Cray, Carolyn; Villar, David; Zaias, Julia; Altman, Norman H

    2008-11-01

    Fenbendazole (FBZ) is an anthelmintic drug widely used to treat and prevent pinworm outbreaks in laboratory rodents. Although data in nonrodent species indicate possible effects of fenbendazole on the bone marrow and lymphocyte proliferation and function, little has been reported regarding possible effects on the rodent immune system. The purpose of the current study was to determine the effects of a therapeutic regimen of FBZ on immune parameters in BALB/c mice. Both 9-wk on-off and 5-wk continuous medicated feed protocols were assessed. No significant differences between normal and FBZ diet treated mice were observed in the following parameters: complete blood count, blood chemistry, quantitation of major T and B cell markers in spleen, quantitation of T cell markers in the thymus, spleen cell proliferation to T and B cell mitogens, bone marrow colony-forming cell assays, skin graft rejection, and primary and secondary humoral immune responses. These data indicate that FBZ treatment does not affect many standard broad measures of immune function.

  5. RS-1 enhances CRISPR/Cas9- and TALEN-mediated knock-in efficiency

    Science.gov (United States)

    Song, Jun; Yang, Dongshan; Xu, Jie; Zhu, Tianqing; Chen, Y. Eugene; Zhang, Jifeng

    2016-01-01

    Zinc-finger nuclease, transcription activator-like effector nuclease and CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 (CRISPR-associated protein 9) are becoming major tools for genome editing. Importantly, knock-in in several non-rodent species has been finally achieved thanks to these customizable nucleases; yet the rates remain to be further improved. We hypothesize that inhibiting non-homologous end joining (NHEJ) or enhancing homology-directed repair (HDR) will improve the nuclease-mediated knock-in efficiency. Here we show that the in vitro application of an HDR enhancer, RS-1, increases the knock-in efficiency by two- to five-fold at different loci, whereas NHEJ inhibitor SCR7 has minimal effects. We then apply RS-1 for animal production and have achieved multifold improvement on the knock-in rates as well. Our work presents tools to nuclease-mediated knock-in animal production, and sheds light on improving gene-targeting efficiencies on pluripotent stem cells. PMID:26817820

  6. A new Legionella species, Legionella feeleii species nova, causes Pontiac fever in an automobile plant.

    Science.gov (United States)

    Herwaldt, L A; Gorman, G W; McGrath, T; Toma, S; Brake, B; Hightower, A W; Jones, J; Reingold, A L; Boxer, P A; Tang, P W

    1984-03-01

    From 15 to 21 August 1981, Pontiac fever affected 317 automobile assembly plant workers. Results of serologic tests were negative for Mycoplasma, Chlamydia, respiratory tract viruses, and previously described legionellae. A gram-negative, rod-shaped organism (WO-44C) that did not grow on blood agar, required L-cysteine for growth, and contained large amounts of branched-chain fatty acids was isolated from a water-based coolant. The organism did not react with antisera against other legionellae, and on DNA hybridization the organism was less than 10% related to other Legionella species. Geometric mean titers found by indirect fluorescent antibody testing to WO-44C were significantly higher in ill employees than in controls (p = 0.0001). Attack rates by department decreased linearly with the department's distance from the implicated coolant system. The etiologic agent apparently was a new Legionella species; we propose the name Legionella feeleii species nova (AATC 35072). This is the first outbreak of nonpneumonic legionellosis in which the etiologic agent is not L. pneumophila, serogroup 1.

  7. A nuclear DNA-based species determination and DNA quantification assay for common poultry species.

    Science.gov (United States)

    Ng, J; Satkoski, J; Premasuthan, A; Kanthaswamy, S

    2014-12-01

    DNA testing for food authentication and quality control requires sensitive species-specific quantification of nuclear DNA from complex and unknown biological sources. We have developed a multiplex assay based on TaqMan® real-time quantitative PCR (qPCR) for species-specific detection and quantification of chicken (Gallus gallus), duck (Anas platyrhynchos), and turkey (Meleagris gallopavo) nuclear DNA. The multiplex assay is able to accurately detect very low quantities of species-specific DNA from single or multispecies sample mixtures; its minimum effective quantification range is 5 to 50 pg of starting DNA material. In addition to its use in food fraudulence cases, we have validated the assay using simulated forensic sample conditions to demonstrate its utility in forensic investigations. Despite treatment with potent inhibitors such as hematin and humic acid, and degradation of template DNA by DNase, the assay was still able to robustly detect and quantify DNA from each of the three poultry species in mixed samples. The efficient species determination and accurate DNA quantification will help reduce fraudulent food labeling and facilitate downstream DNA analysis for genetic identification and traceability.

  8. A transcontinental challenge--a test of DNA barcode performance for 1,541 species of Canadian Noctuoidea (Lepidoptera.

    Directory of Open Access Journals (Sweden)

    Reza Zahiri

    Full Text Available This study provides a first, comprehensive, diagnostic use of DNA barcodes for the Canadian fauna of noctuoids or "owlet" moths (Lepidoptera: Noctuoidea based on vouchered records for 1,541 species (99.1% species coverage, and more than 30,000 sequences. When viewed from a Canada-wide perspective, DNA barcodes unambiguously discriminate 90% of the noctuoid species recognized through prior taxonomic study, and resolution reaches 95.6% when considered at a provincial scale. Barcode sharing is concentrated in certain lineages with 54% of the cases involving 1.8% of the genera. Deep intraspecific divergence exists in 7.7% of the species, but further studies are required to clarify whether these cases reflect an overlooked species complex or phylogeographic variation in a single species. Non-native species possess higher Nearest-Neighbour (NN distances than native taxa, whereas generalist feeders have lower NN distances than those with more specialized feeding habits. We found high concordance between taxonomic names and sequence clusters delineated by the Barcode Index Number (BIN system with 1,082 species (70% assigned to a unique BIN. The cases of discordance involve both BIN mergers and BIN splits with 38 species falling into both categories, most likely reflecting bidirectional introgression. One fifth of the species are involved in a BIN merger reflecting the presence of 158 species sharing their barcode sequence with at least one other taxon, and 189 species with low, but diagnostic COI divergence. A very few cases (13 involved species whose members fell into both categories. Most of the remaining 140 species show a split into two or three BINs per species, while Virbia ferruginosa was divided into 16. The overall results confirm that DNA barcodes are effective for the identification of Canadian noctuoids. This study also affirms that BINs are a strong proxy for species, providing a pathway for a rapid, accurate estimation of animal diversity.

  9. Fuzzy species among recombinogenic bacteria

    Directory of Open Access Journals (Sweden)

    Fraser Christophe

    2005-03-01

    Full Text Available Abstract Background It is a matter of ongoing debate whether a universal species concept is possible for bacteria. Indeed, it is not clear whether closely related isolates of bacteria typically form discrete genotypic clusters that can be assigned as species. The most challenging test of whether species can be clearly delineated is provided by analysis of large populations of closely-related, highly recombinogenic, bacteria that colonise the same body site. We have used concatenated sequences of seven house-keeping loci from 770 strains of 11 named Neisseria species, and phylogenetic trees, to investigate whether genotypic clusters can be resolved among these recombinogenic bacteria and, if so, the extent to which they correspond to named species. Results Alleles at individual loci were widely distributed among the named species but this distorting effect of recombination was largely buffered by using concatenated sequences, which resolved clusters corresponding to the three species most numerous in the sample, N. meningitidis, N. lactamica and N. gonorrhoeae. A few isolates arose from the branch that separated N. meningitidis from N. lactamica leading us to describe these species as 'fuzzy'. Conclusion A multilocus approach using large samples of closely related isolates delineates species even in the highly recombinogenic human Neisseria where individual loci are inadequate for the task. This approach should be applied by taxonomists to large samples of other groups of closely-related bacteria, and especially to those where species delineation has historically been difficult, to determine whether genotypic clusters can be delineated, and to guide the definition of species.

  10. Cognitive differences between orang-utan species: a test of the cultural intelligence hypothesis.

    Science.gov (United States)

    Forss, Sofia I F; Willems, Erik; Call, Josep; van Schaik, Carel P

    2016-07-28

    Cultural species can - or even prefer to - learn their skills from conspecifics. According to the cultural intelligence hypothesis, selection on underlying mechanisms not only improves this social learning ability but also the asocial (individual) learning ability. Thus, species with systematically richer opportunities to socially acquire knowledge and skills should over time evolve to become more intelligent. We experimentally compared the problem-solving ability of Sumatran orang-utans (Pongo abelii), which are sociable in the wild, with that of the closely related, but more solitary Bornean orang-utans (P. pygmaeus), under the homogeneous environmental conditions provided by zoos. Our results revealed that Sumatrans showed superior innate problem-solving skills to Borneans, and also showed greater inhibition and a more cautious and less rough exploration style. This pattern is consistent with the cultural intelligence hypothesis, which predicts that the more sociable of two sister species experienced stronger selection on cognitive mechanisms underlying learning.

  11. Current distribution, habitat, and status of Category 2 candidate plant species on and near the U.S. Department of Energy's Nevada Test Site

    Energy Technology Data Exchange (ETDEWEB)

    Blomquist, Kevin W. [EG& G Energy Measurements, Gaithersburg, MD (United States); Lindemann, Tim A. [EG& G Energy Measurements, Gaithersburg, MD (United States); Lyon, Glen E. [EG& G Energy Measurements, Gaithersburg, MD (United States); Steen, Dan C. [EG& G Energy Measurements, Gaithersburg, MD (United States); Wills, Cathy A. [EG& G Energy Measurements, Gaithersburg, MD (United States); Flick, Sarah A. [EG& G Energy Measurements, Gaithersburg, MD (United States); Ostler, W. Kent [EG& G Energy Measurements, Gaithersburg, MD (United States)

    1995-12-31

    Results of surveys conducted between 1991 and 1995 were used to document the distribution and habitat of 11 Category 2 candidate plant species known to occur on or near the Nevada Test Site (NTS). Approximately 200 areas encompassing about 13,000 ha were surveyed. Distributions of all species except Frasera-pahutensis and Phaceliaparishii were increased, and the ranges of Camissonia megalantha, Galium hilendiae ssp. kingstonense, Penstemon albomarginatus, and Penstemon pahutensis were expanded. The status of each species was assessed based on current distribution population trends, and potential threats. Recommendations were made to reclassi& the following five species to Category 3C: Arctomecon merriamii, F. pahutensis, P. pahutensis, Phacelia beatleyae, and Phaceliaparishii. Two species, C. megalantha and Cymopterus ripIeyi var. saniculoides, were recommended for reclassification to Category 3B status. No recommendation was made to reclassify Astragalus funereus, G. hilendiae ssp. kingstonense, P. albomarginatus, or Penstemon fruticiformis var. amargosae from their current Category 2 status. Populations of these four species are not threatened on NTS, but the NTS populations represent only a.small portion of each species’ range and the potential threats of mining or grazing activities off NTS on these species was notassessed. Conservation measures recommended included the development of an NTS ecosystem conservation plan, continued conduct of preactivity and plant surveys on NTS, and protection of plant type localities on NTS.

  12. Species hybridization in the genus Pinus

    Science.gov (United States)

    Peter W. Garrett

    1979-01-01

    Results of a breeding program in which a large number of pine species were tested indicate that a number of species and hybrids may be useful in the northeastern United States. Austrian black pine x Japanese black pine and hybrids containing Japanese red pine all had good growth rates. While none of the soft pines grew faster than eastern white pine, a number of...

  13. Cross-species infection trials reveal cryptic parasite varieties and a putative polymorphism shared among host species.

    Science.gov (United States)

    Luijckx, Pepijn; Duneau, David; Andras, Jason P; Ebert, Dieter

    2014-02-01

    A parasite's host range can have important consequences for ecological and evolutionary processes but can be difficult to infer. Successful infection depends on the outcome of multiple steps and only some steps of the infection process may be critical in determining a parasites host range. To test this hypothesis, we investigated the host range of the bacterium Pasteuria ramosa, a Daphnia parasite, and determined the parasites success in different stages of the infection process. Multiple genotypes of Daphnia pulex, Daphnia longispina and Daphnia magna were tested with four Pasteuria genotypes using infection trials and an assay that determines the ability of the parasite to attach to the hosts esophagus. We find that attachment is not specific to host species but is specific to host genotype. This may suggest that alleles on the locus controlling attachment are shared among different host species that diverged 100 million year. However, in our trials, Pasteuria was never able to reproduce in nonnative host species, suggesting that Pasteuria infecting different host species are different varieties, each with a narrow host range. Our approach highlights the explanatory power of dissecting the steps of the infection process and resolves potentially conflicting reports on parasite host ranges. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

  14. Freshwater fishes in Greek lakes: Species richness and body size patterns

    Directory of Open Access Journals (Sweden)

    Anthi Oikonomou

    2015-11-01

    Full Text Available Freshwater ecosystems are widely recognised as hotspots of biodiversity and endemism; thus they are of great value for conservation biogeography. Amongst the taxa found in freshwater ecosystems, fish are the ideal biological model for testing biogeographical patterns and have often been used in large-scale ecological and biogeographical analyses. Lakes of Greece provide a unique opportunity to test biogeographical theories, however, biogeographical studies in Greece at broader, regional, scales, based on the distribution of freshwater species, species richness and endemism, are scarce. The aim of the current study is to test the effect of key environmental factors and spatial variables on species richness of lacustrine fishes and to test their effect on species’ size distributions. We assembled datasets of species richness and body size and environmental (predictor factors for 13 Greek lakes. Model selection procedures revealed that fish species richness increased with ecosystem area and decreased with altitude. In addition, our results showed that latitude per se is a good predictor of body size. Indeed, the mean size of lacustrine communities in the northern and southern lake ecosystems differed significantly. These patterns reflect the biogeographical history of these areas and highlight the crucial role connectivity plays in communities’ species composition.

  15. Análise da pele de três espécies de peixes: histologia, morfometria e testes de resistência Analysis of the skin of three fish species: histology, morphometry and resistance tests

    Directory of Open Access Journals (Sweden)

    Maria Luiza R. Souza

    2003-12-01

    Full Text Available O objetivo deste trabalho foi analisar a pele de três espécies de peixes (piavuçu Leporinus macrocephalus, pacu prata Mylossoma sp e piraputanga Brycon hilarii através de análise histologica e morfometrica e testes de resistência após o curtimento. Amostras de peles da região dorsal foram coletadas, fixadas em Bouin por 24 horas, incluídas em parafina, cortadas em 5 µm de espessura e coradas por Hematoxilina-eosina. Os cortes foram analisados pela microscopia de luz. Foi utilizado o dinamômetro EMIC para a análise físico-mecânica do couro em 10 amostras no sentido longitudinal a partir da região dorsal do peixe de cada espécie. A derme desses peixes possui um padrão estrutural comum aos teleósteos, porém a disposição e distribuição das fibras colágenas apresentaram-se diferentes entre as espécies analisadas. Através da análise morfométrica constatou-se que a espessura da derme da pele diferiu entre as três espécies. Não houve diferença no teste de resistência à tração no couro da piraputanga (16,88 N/mm² e piavuçu (18,50 N/mm². Os resultados para os couros destas duas espécies de peixes foram superiores ao pacu (11,83 N/mm². O valor de alongamento até a ruptura foi superior para piavuçu (52,83% e piraputanga (60,45%, não diferindo entre eles, porém foi inferior para o pacu (33,83%. O rasgamento progressivo foi maior no couro de pacu (36,51 N/mm. As peles das três espécies analisadas podem ser transformadas em couro para sua aplicação em diversos artefatos.This study was carried out to analyse the skin of three species of fish (piavuçu Leporinus macrocephalus, pacu prata Mylossoma sp e piraputanga Brycon hilarii through histological and morphometrical analysis and resistance tests after hardening. Skin samples from the dorsal region were taken and fixed in Bouin solution for 24 hours. They were embedded in paraffin, cut 5 µm thick and stained by Hematoxylin-eosin technique. The cuts were analyzed

  16. PREDICTING FIELD PERFORMANCE OF HERBACEOUS SPECIES FOR PHYTOREMEDIATION OF PERCHLORATE

    Science.gov (United States)

    Results of these short-term experiments coupled with ecological knowledge of the nine herbaceous plant species tested suggest that several species may by successful in on-site remediation of perchlorate. The two wetland species which appear to be most suitable for field experimen...

  17. The nature of plant species.

    Science.gov (United States)

    Rieseberg, Loren H; Wood, Troy E; Baack, Eric J

    2006-03-23

    Many botanists doubt the existence of plant species, viewing them as arbitrary constructs of the human mind, as opposed to discrete, objective entities that represent reproductively independent lineages or 'units of evolution'. However, the discreteness of plant species and their correspondence with reproductive communities have not been tested quantitatively, allowing zoologists to argue that botanists have been overly influenced by a few 'botanical horror stories', such as dandelions, blackberries and oaks. Here we analyse phenetic and/or crossing relationships in over 400 genera of plants and animals. We show that although discrete phenotypic clusters exist in most genera (> 80%), the correspondence of taxonomic species to these clusters is poor (< 60%) and no different between plants and animals. Lack of congruence is caused by polyploidy, asexual reproduction and over-differentiation by taxonomists, but not by contemporary hybridization. Nonetheless, crossability data indicate that 70% of taxonomic species and 75% of phenotypic clusters in plants correspond to reproductively independent lineages (as measured by postmating isolation), and thus represent biologically real entities. Contrary to conventional wisdom, plant species are more likely than animal species to represent reproductively independent lineages.

  18. Quantifying Species Diversity with a DNA Barcoding-Based Method: Tibetan Moth Species (Noctuidae) on the Qinghai-Tibetan Plateau

    Science.gov (United States)

    Jin, Qian; Han, Huilin; Hu, XiMin; Li, XinHai; Zhu, ChaoDong; Ho, Simon Y. W.; Ward, Robert D.; Zhang, Ai-bing

    2013-01-01

    With the ongoing loss of biodiversity, there is a great need for fast and effective ways to assess species richness and diversity: DNA barcoding provides a powerful new tool for this. We investigated this approach by focusing on the Tibetan plateau, which is one of the world's top biodiversity hotspots. There have been few studies of its invertebrates, although they constitute the vast majority of the region's diversity. Here we investigated species diversity of the lepidopteran family Noctuidae, across different environmental gradients, using measurements based on traditional morphology as well as on DNA barcoding. The COI barcode showed an average interspecific K2P distance of , which is about four times larger than the mean intraspecific distance (). Using six diversity indices, we did not detect any significant differences in estimated species diversity between measurements based on traditional morphology and on DNA barcoding. Furthermore, we found strong positive correlations between them, indicating that barcode-based measures of species diversity can serve as a good surrogate for morphology-based measures in most situations tested. Eastern communities were found to have significantly higher diversity than Western ones. Among 22 environmental factors tested, we found that three (precipitation of driest month, precipitation of driest quarter, and precipitation of coldest quarter) were significantly correlated with species diversity. Our results indicate that these factors could be the key ecological factors influencing the species diversity of the lepidopteran family Noctuidae on the Tibetan plateau. PMID:23741330

  19. Molecular and morphometric evidence for separate species of Uncinaria (Nematoda: Ancylostomatidae) in California sea lions and northern fur seals: hypothesis testing supplants verification.

    Science.gov (United States)

    Nadler, S A; Adams, B J; Lyons, E T; DeLong, R L; Melin, S R

    2000-10-01

    California sea lions (Zalophus californianus) and northern fur seals (Callorhinus ursinus) are each believed to host distinct hookworm species (Uncinaria spp.). However, a recent morphometric analysis suggested that a single species parasitizes multiple pinniped hosts, and that the observed differences are host-induced. To explore the systematics of these hookworms and test these competing hypotheses, we obtained nucleotide sequences of nuclear ribosomal DNA (D2/D3 28S, D18/D19 28S, and internal transcribed spacer [ITS] regions) from 20 individual hookworms parasitizing California sea lion and northern fur seal pups where their breeding grounds are sympatric. Five individuals from an allopatric population of California sea lions were also sampled for ITS-1 and D18/D19 28S sequences. The 28S D2/D3 sequences showed no diagnostic differences among hookworms sampled from individual sea lions and fur seals, whereas the 28S D18/D19 sequences had one derived (apomorphic) character demarcating hookworms from northern fur seals. ITS sequences were variable for 7 characters, with 4 derived (apomorphic) states in ITS-1 demarcating hookworms from California sea lions. Multivariate analysis of morphometric data also revealed significant differences between nematodes representing these 2 host-associated lineages. These results indicate that these hookworms represent 2 species that are not distributed indiscriminately between these host species, but instead exhibit host fidelity, evolving independently with each respective host species. This evolutionary approach to analyzing sequence data for species delimitation is contrasted with similarity-based methods that have been applied to numerous diagnostic studies of nematode parasites.

  20. Simultaneous presence of multiple Campylobacter species in dogs

    NARCIS (Netherlands)

    Koene, M.G.J.; Houwers, D.J.; Dijkstra, J.R.; Duim, B.; Wagenaar, J.A.

    2004-01-01

    The prevalence of coinfection of Campylobacter species in dogs was determined using four isolation methods. In 26% of the positive-testing stools, multiple Campylobacter species were identified. The use of multiple isolation methods as well as the time lapse between sampling and processing are

  1. Genetic diversity of Aspergillus species isolated from onychomycosis and Aspergillus hongkongensis sp. nov., with implications to antifungal susceptibility testing.

    Science.gov (United States)

    Tsang, Chi-Ching; Hui, Teresa W S; Lee, Kim-Chung; Chen, Jonathan H K; Ngan, Antonio H Y; Tam, Emily W T; Chan, Jasper F W; Wu, Andrea L; Cheung, Mei; Tse, Brian P H; Wu, Alan K L; Lai, Christopher K C; Tsang, Dominic N C; Que, Tak-Lun; Lam, Ching-Wan; Yuen, Kwok-Yung; Lau, Susanna K P; Woo, Patrick C Y

    2016-02-01

    Thirteen Aspergillus isolates recovered from nails of 13 patients (fingernails, n=2; toenails, n=11) with onychomycosis were characterized. Twelve strains were identified by multilocus sequencing as Aspergillus spp. (Aspergillus sydowii [n=4], Aspergillus welwitschiae [n=3], Aspergillus terreus [n=2], Aspergillus flavus [n=1], Aspergillus tubingensis [n=1], and Aspergillus unguis [n=1]). Isolates of A. terreus, A. flavus, and A. unguis were also identifiable by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The 13th isolate (HKU49(T)) possessed unique morphological characteristics different from other Aspergillus spp. Molecular characterization also unambiguously showed that HKU49(T) was distinct from other Aspergillus spp. We propose the novel species Aspergillus hongkongensis to describe this previously unknown fungus. Antifungal susceptibility testing showed most Aspergillus isolates had low MICs against itraconazole and voriconazole, but all Aspergillus isolates had high MICs against fluconazole. A diverse spectrum of Aspergillus species is associated with onychomycosis. Itraconazole and voriconazole are probably better drug options for Aspergillus onychomycosis. Copyright © 2016 Elsevier Inc. All rights reserved.

  2. Development and validation of OECD test guidelines on mollusc reproductive toxicity tests

    DEFF Research Database (Denmark)

    Lagadic, Laurent; Holbech, Henrik; hutchinson, tom

    the comparison of endpoints relevant for reproduction in invertebrates often shows a much higher sensitivity in molluscs vs. e.g. daphnids. The OECD test guideline programme has thus been extended to cover reproduction effects of chemicals in molluscs. Existing mollusc toxicity test protocols have been reviewed...... in an OECD Detailed Review Paper that identifies two relevant candidate species for developing freshwater tests: Potamopyrgus antipodarum and Lymnaea stagnalis. However, this review did not clarify which toxicity test design/conditions are the most appropriate for chemicals assessment. Therefore, a mollusc...... reproduction test guideline will be developed describing partial- and full- life-cycle test protocols in these species, so as to propose a balanced suite of apical mollusc toxicity tests applicable for the assessment of any type of chemical, including endocrine disruptors, as level 4 and 5 assays of the EDTA...

  3. Antimicrobial activity of some Ganoderma species from Nigeria.

    Science.gov (United States)

    Ofodile, L N; Uma, N U; Kokubun, T; Grayer, R J; Ogundipe, O T; Simmonds, M S J

    2005-04-01

    The crude n-hexane:diethyl ether, chloroform:acetone and methanol extracts of four species of Ganoderma (Ganoderma colossum (Fr.) C. F. Baker, G. resinaceum Boud., G. lucidum (cf.) (Curtis) P. Karst. and G. boninense (cf.) Pat.), from Nigeria, were tested for antimicrobial activity. The three solvent extracts of all the species of Ganoderma were active against Pseudomonas syringae and Bacillus subtilis, whereas none of the extracts were active against Cladosporium herbarum. Preliminary thin layer chromatography chemical tests on these extracts of Ganoderma showed that they contained compounds that stained blue-violet and blue or green when sprayed with anisaldehyde-sulphuric acid or Dragendorff, respectively. The profile of compounds in the extracts showed some variation among the four species. (c) 2005 John Wiley & Sons, Ltd.

  4. Cephalosporium maydis is a distinct species in the Gaeumannomyces-Harpophora species complex.

    Science.gov (United States)

    Saleh, Amgad A; Leslie, John F

    2004-01-01

    Cephalosporium maydis is an important plant pathogen whose phylogenetic position relative to other fungi has not been established clearly. We compared strains of C. maydis, strains from several other plant-pathogenic Cephalosporium spp. and several possible relatives within the Gaeumannomyces-Harpophora species complex, to which C. maydis has been suggested to belong based on previous preliminary DNA sequence analyses. DNA sequences of the nuclear genes encoding the rDNA ITS region, β-tubulin, histone H3, and MAT-2 support the hypothesis that C. maydis is a distinct taxon within the Gaeumannomyces-Harpophora species complex. Based on amplified fragment length polymorphism (AFLP) profiles, C. maydis also is distinct from the other tested species of Cephalosporium, Phialophora sensu lato and members of Gaeumannomyces-Harpophora species complex, which supports its classification as Harpophora maydis. Oligonucleotide primers for H. maydis were developed that can be used in a PCR diagnostic protocol to rapidly and reliably detect and identify this pathogen. These diagnostic PCR primers will aid the detection of H. maydis in diseased maize because this fungus can be difficult to detect and isolate, and the movement of authentic cultures may be limited by quarantine restrictions.

  5. Emergence of unusual species of enterococci causing infections, South India

    Directory of Open Access Journals (Sweden)

    Rao Sambasiva R

    2005-03-01

    Full Text Available Abstract Background Enterococci tend to be one of the leading causes of nosocomial infections, with E. faecalis and E. faecium accounting up to 90% of the clinical isolates. Nevertheless, the incidence of other species of enterococci from clinical sources shows an alarming increase with the properties of intrinsic resistance to several antibiotics including beta-lactams and glycopeptides. Thus proper identification of enterococci to species level is quintessential for management and prevention of these bacteria in any healthcare facility. Hence this work was undertaken to study the prevalence of unusual species of enterococci causing human infections, in a tertiary care hospital in South India. Methods The study was conducted in a tertiary care hospital in South India from July 2001 to June 2003. Isolates of enterococci were collected from various clinical specimens and speciated using extensive phenotypic and physiological tests. Antimicrobial susceptibility testing were performed and interpreted as per NCCLS guidelines. Whole cell protein (WCP fingerprinting of enterococci were done for species validation by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE and analyzed computationally. Results Our study showed the prevalence of unusual (non-faecalis and non-faecium enterococci and atypical (biochemical variant species of enterococci as 19% (46 isolates and 5% (12 isolates respectively. The 7 unusual species (46 isolates isolated and confirmed by phenotypic characterization includes: 15 E. gallinarum (6.2%, 10 E. avium (4.1%, 6 E. raffinosus (2.5%, 6 E. hirae (2.5%, 4 E. mundtii (1.7%, 3 E. casseliflavus-including the two atypical isolates (1.2% and 2 E. durans (0.8%. The 12 atypical enterococcal species (5% that showed aberrant sugar reactions in conventional phenotyping were confirmed as E. faecalis, E. faecium and E. casseliflavus respectively by WCP fingerprinting. The antimicrobial susceptibility testing depicted the

  6. Physilogical and Biochemical Responses of Avena species to ...

    African Journals Online (AJOL)

    mk

    2013-10-23

    Oct 23, 2013 ... Seven species of oat (Avena) were evaluated for their relative drought tolerance under soil moisture stress. The plant height, leaf area production and biomass yield reduced under soil moisture stress. Among the species tested, minimum reduction in height was recorded in Avena vaviloviana, Avena.

  7. Rapid lysostaphin test to differentiate Staphylococcus and Micrococcus species.

    Science.gov (United States)

    Geary, C; Stevens, M

    1986-01-01

    A rapid, simple lysostaphin lysis susceptibility test to differentiate the genera Staphylococcus and Micrococcus was evaluated. Of 181 strains from culture collections, 95 of 95 Staphylococcus strains were lysed, and 79 of 79 Micrococcus strains were not lysed. The seven Planococcus strains were resistant. Clinical isolates (890) were tested with lysostaphin and for the ability to produce acid from glycerol in the presence of erythromycin. Overall agreement between the methods was 99.2%. All clinical Micrococcus strains (43) were resistant to lysostaphin, and all clinical Staphylococcus strains (847) were susceptible. Seven of the Staphylococcus strains did not produce acid from glycerol in the presence of erythromycin. This lysostaphin test provides results in 2 h. It is easier to perform than previously described lysostaphin lysis methods. It is also more rapid and accurate than the glycerol-erythromycin test. PMID:3519667

  8. Modelling survival: exposure pattern, species sensitivity and uncertainty.

    Science.gov (United States)

    Ashauer, Roman; Albert, Carlo; Augustine, Starrlight; Cedergreen, Nina; Charles, Sandrine; Ducrot, Virginie; Focks, Andreas; Gabsi, Faten; Gergs, André; Goussen, Benoit; Jager, Tjalling; Kramer, Nynke I; Nyman, Anna-Maija; Poulsen, Veronique; Reichenberger, Stefan; Schäfer, Ralf B; Van den Brink, Paul J; Veltman, Karin; Vogel, Sören; Zimmer, Elke I; Preuss, Thomas G

    2016-07-06

    The General Unified Threshold model for Survival (GUTS) integrates previously published toxicokinetic-toxicodynamic models and estimates survival with explicitly defined assumptions. Importantly, GUTS accounts for time-variable exposure to the stressor. We performed three studies to test the ability of GUTS to predict survival of aquatic organisms across different pesticide exposure patterns, time scales and species. Firstly, using synthetic data, we identified experimental data requirements which allow for the estimation of all parameters of the GUTS proper model. Secondly, we assessed how well GUTS, calibrated with short-term survival data of Gammarus pulex exposed to four pesticides, can forecast effects of longer-term pulsed exposures. Thirdly, we tested the ability of GUTS to estimate 14-day median effect concentrations of malathion for a range of species and use these estimates to build species sensitivity distributions for different exposure patterns. We find that GUTS adequately predicts survival across exposure patterns that vary over time. When toxicity is assessed for time-variable concentrations species may differ in their responses depending on the exposure profile. This can result in different species sensitivity rankings and safe levels. The interplay of exposure pattern and species sensitivity deserves systematic investigation in order to better understand how organisms respond to stress, including humans.

  9. Animal models got you puzzled?: think pig.

    Science.gov (United States)

    Walters, Eric M; Agca, Yuksel; Ganjam, Venkataseshu; Evans, Tim

    2011-12-01

    Swine are an excellent large animal model for human health and disease because their size and physiology are similar to humans, in particular, with respect to the skin, heart, gastrointestinal tract, and kidneys. In addition, the pig has many emerging technologies that will only enhance the development of the pig as the nonrodent biomedical model of choice. © 2011 New York Academy of Sciences.

  10. DNA barcoding for species assignment: the case of Mediterranean marine fishes.

    Directory of Open Access Journals (Sweden)

    Monica Landi

    Full Text Available DNA barcoding enhances the prospects for species-level identifications globally using a standardized and authenticated DNA-based approach. Reference libraries comprising validated DNA barcodes (COI constitute robust datasets for testing query sequences, providing considerable utility to identify marine fish and other organisms. Here we test the feasibility of using DNA barcoding to assign species to tissue samples from fish collected in the central Mediterranean Sea, a major contributor to the European marine ichthyofaunal diversity.A dataset of 1278 DNA barcodes, representing 218 marine fish species, was used to test the utility of DNA barcodes to assign species from query sequences. We tested query sequences against 1 a reference library of ranked DNA barcodes from the neighbouring North East Atlantic, and 2 the public databases BOLD and GenBank. In the first case, a reference library comprising DNA barcodes with reliability grades for 146 fish species was used as diagnostic dataset to screen 486 query DNA sequences from fish specimens collected in the central basin of the Mediterranean Sea. Of all query sequences suitable for comparisons 98% were unambiguously confirmed through complete match with reference DNA barcodes. In the second case, it was possible to assign species to 83% (BOLD-IDS and 72% (GenBank of the sequences from the Mediterranean. Relatively high intraspecific genetic distances were found in 7 species (2.2%-18.74%, most of them of high commercial relevance, suggesting possible cryptic species.We emphasize the discriminatory power of COI barcodes and their application to cases requiring species level resolution starting from query sequences. Results highlight the value of public reference libraries of reliability grade-annotated DNA barcodes, to identify species from different geographical origins. The ability to assign species with high precision from DNA samples of disparate quality and origin has major utility in several

  11. Species associations in a species-rich subtropical forest were not well-explained by stochastic geometry of biodiversity.

    Science.gov (United States)

    Wang, Qinggang; Bao, Dachuan; Guo, Yili; Lu, Junmeng; Lu, Zhijun; Xu, Yaozhan; Zhang, Kuihan; Liu, Haibo; Meng, Hongjie; Jiang, Mingxi; Qiao, Xiujuan; Huang, Handong

    2014-01-01

    The stochastic dilution hypothesis has been proposed to explain species coexistence in species-rich communities. The relative importance of the stochastic dilution effects with respect to other effects such as competition and habitat filtering required to be tested. In this study, using data from a 25-ha species-rich subtropical forest plot with a strong topographic structure at Badagongshan in central China, we analyzed overall species associations and fine-scale species interactions between 2,550 species pairs. The result showed that: (1) the proportion of segregation in overall species association analysis at 2 m neighborhood in this plot followed the prediction of the stochastic dilution hypothesis that segregations should decrease with species richness but that at 10 m neighborhood was higher than the prediction. (2) The proportion of no association type was lower than the expectation of stochastic dilution hypothesis. (3) Fine-scale species interaction analyses using Heterogeneous Poisson processes as null models revealed a high proportion (47%) of significant species effects. However, the assumption of separation of scale of this method was not fully met in this plot with a strong fine-scale topographic structure. We also found that for species within the same families, fine-scale positive species interactions occurred more frequently and negative ones occurred less frequently than expected by chance. These results suggested effects of environmental filtering other than species interaction in this forest. (4) We also found that arbor species showed a much higher proportion of significant fine-scale species interactions (66%) than shrub species (18%). We concluded that the stochastic dilution hypothesis only be partly supported and environmental filtering left discernible spatial signals in the spatial associations between species in this species-rich subtropical forest with a strong topographic structure.

  12. Species associations in a species-rich subtropical forest were not well-explained by stochastic geometry of biodiversity.

    Directory of Open Access Journals (Sweden)

    Qinggang Wang

    Full Text Available The stochastic dilution hypothesis has been proposed to explain species coexistence in species-rich communities. The relative importance of the stochastic dilution effects with respect to other effects such as competition and habitat filtering required to be tested. In this study, using data from a 25-ha species-rich subtropical forest plot with a strong topographic structure at Badagongshan in central China, we analyzed overall species associations and fine-scale species interactions between 2,550 species pairs. The result showed that: (1 the proportion of segregation in overall species association analysis at 2 m neighborhood in this plot followed the prediction of the stochastic dilution hypothesis that segregations should decrease with species richness but that at 10 m neighborhood was higher than the prediction. (2 The proportion of no association type was lower than the expectation of stochastic dilution hypothesis. (3 Fine-scale species interaction analyses using Heterogeneous Poisson processes as null models revealed a high proportion (47% of significant species effects. However, the assumption of separation of scale of this method was not fully met in this plot with a strong fine-scale topographic structure. We also found that for species within the same families, fine-scale positive species interactions occurred more frequently and negative ones occurred less frequently than expected by chance. These results suggested effects of environmental filtering other than species interaction in this forest. (4 We also found that arbor species showed a much higher proportion of significant fine-scale species interactions (66% than shrub species (18%. We concluded that the stochastic dilution hypothesis only be partly supported and environmental filtering left discernible spatial signals in the spatial associations between species in this species-rich subtropical forest with a strong topographic structure.

  13. Toxoplasmosis in prey species and consequences for prevalence in feral cats: not all prey species are equal.

    Science.gov (United States)

    Afonso, E; Thulliez, P; Pontier, D; Gilot-Fromont, E

    2007-12-01

    Toxoplasma gondii is largely transmitted to definitive felid hosts through predation. Not all prey species represent identical risks of infection for cats because of differences in prey susceptibility, exposure and/or lifespan. Previously published studies have shown that prevalence in rodent and lagomorph species is positively correlated with body mass. We tested the hypothesis that different prey species have different infection risks by comparing infection dynamics of feral cats at 4 sites in the sub-Antarctic Kerguelen archipelago which differed in prey availability. Cats were trapped from 1994 to 2004 and anti-T. gondii IgG antibodies were detected using the modified agglutination test (> or =1:40). Overall seroprevalence was 51.09%. Antibody prevalence differed between sites, depending on diet and also on sex, after taking into account the effect of age. Males were more often infected than females and the difference between the sexes tended to be more pronounced in the site where more prey species were available. A difference in predation efficiency between male and female cats may explain this result. Overall, our results suggest that the composition of prey items in cat diet influences the risk of T. gondii infection. Prey compositon should therefore be considered important in any understanding of infection dynamics of T. gondii.

  14. Testing Nordmøre grids on the target and by-catch species of the commercial bottom trawl fishery in the Gulf of Cadiz

    Directory of Open Access Journals (Sweden)

    Mariángeles Gamaza

    2015-12-01

    Full Text Available Sorting grids have been tested worldwide in trawl fisheries. Here we report upon the first trials performed using Nordmøre sorting grids with four different bar spacings in the trawl fisheries of the Gulf of Cadiz targeting crustaceans as the main resource. A total of 288 valid hauls and 67 commercial species were caught. Escapement and escape size selectivity were evaluated for the most important target and by-catch species. A decrease in the percentage of biomass escape was recorded with increasing grid spacing for the two target species, deep-water rose shrimp (Parapenaeus longirostris and Norway lobster (Nephrops norvegicus, from 24% to 8% for the former and from 86 to 9% for the latter, with a 15-mm and 30-mm grid respectively. In general, high escape rates were found for most finfish and cephalopods. For hake (Merluccius merluccius, as the main by-catch species, the results showed an escape rate decreasing from 96% to 71% as the bar spacing increased. Our findings suggest the 30-mm grid would be effective for the deep-water crustacean trawlers but different mitigation measures will be required for other métiers in the multispecies trawl fishery of the Gulf of Cadiz.

  15. Endangered Species Day | Endangered Species Coalition

    Science.gov (United States)

    Annual Top 10 Report Protecting the Endangered Species Act Wildlife Voices Stand for Wolves Endangered Campaigns Wildlife Voices Protecting the Endangered Species Act Annual Top 10 Report Endangered Species Day Stand for Wolves Vanishing BOOK: A Wild Success The Endangered Species Act at 40 Endangered Species The

  16. OECD Guidelines for the Testing of Chemicals, Test No. 232: Collembolan Reproduction Test in Soil

    DEFF Research Database (Denmark)

    Krogh, Paul Henning; Scott-Fordsmand, Janeck James; Ahtianen, Jukka

    2009-01-01

    This Test Guideline is designed for assessing the effects of chemicals on the reproduction of collembolans in soil. The parthenogenetic Folsomia candida is the recommended species for use, but an alternative species such as sexually reproducing Folsomia fimetaria could also be used if they meet...... the validity criteria. This Guideline can be used for testing both water soluble and insoluble substances but it is not applicable to volatile ones. The Guideline aims to determine toxic effects of the test substance on adult mortality and reproductive output expressed as LCx and ECx respectively, or NOEC....../LOEC value. The number of treatment concentrations varies depending on endpoints to be determined. For a combined approach to examine both the NOEC/LOEC and ECx, eight concentrations in a geometric series with four replicates for each concentration as well as eight control replicates should be used. In each...

  17. Toxicity of fluoride to aquatic species and evaluation of toxicity modifying factors.

    Science.gov (United States)

    Pearcy, Krysta; Elphick, James; Burnett-Seidel, Charlene

    2015-07-01

    The present study was performed to investigate the toxicity of fluoride to a variety of freshwater aquatic organisms and to establish whether water quality variables contribute substantively to modifying its toxicity. Water hardness, chloride, and alkalinity were tested as possible toxicity modifying factors for fluoride using acute toxicity tests with Hyalella azteca and Oncorhynchus mykiss. Chloride appeared to be the major toxicity modifying factor for fluoride in these acute toxicity tests. The chronic toxicity of fluoride was evaluated with a variety of species, including 3 fish (Pimephales promelas, O. mykiss, and Salvelinus namaycush), 3 invertebrates (Ceriodaphnia dubia, H. azteca, and Chironomus dilutus), 1 plant (Lemna minor), and 1 alga (Pseudokirchneriella subcapitata). Hyalella azteca was the most sensitive species overall, and O. mykiss was the most sensitive species of fish. The role of chloride as a toxicity modifying factor was inconsistent between species in the chronic toxicity tests. © 2015 SETAC.

  18. Evaluation of the Thermo Scientific™ SureTect™ Listeria species Assay.

    Science.gov (United States)

    Cloke, Jonathan; Evans, Katharine; Crabtree, David; Hughes, Annette; Simpson, Helen; Holopainen, Jani; Wickstrand, Nina; Kauppinen, Mikko

    2014-03-01

    The Thermo Scientific™ SureTect™ Listeria species Assay is a new real-time PCR assay for the detection of all species of Listeria in food and environmental samples. This validation study was conducted using the AOAC Research Institute (RI) Performance Tested MethodsSM program to validate the SureTect Listeria species Assay in comparison to the reference method detailed in International Organization for Standardization 11290-1:1996 including amendment 1:2004 in a variety of foods plus plastic and stainless steel. The food matrixes validated were smoked salmon, processed cheese, fresh bagged spinach, cantaloupe, cooked prawns, cooked sliced turkey meat, cooked sliced ham, salami, pork frankfurters, and raw ground beef. All matrixes were tested by Thermo Fisher Scientific, Microbiology Division, Basingstoke, UK. In addition, three matrixes (pork frankfurters, fresh bagged spinach, and stainless steel surface samples) were analyzed independently as part of the AOAC-RI-controlled independent laboratory study by the University of Guelph, Canada. Using probability of detection statistical analysis, a significant difference in favour of the SureTect assay was demonstrated between the SureTect and reference method for high level spiked samples of pork frankfurters, smoked salmon, cooked prawns, stainless steel, and low-spiked samples of salami. For all other matrixes, no significant difference was seen between the two methods during the study. Inclusivity testing was conducted with 68 different isolates of Listeria species, all of which were detected by the SureTect Listeria species Assay. None of the 33 exclusivity isolates were detected by the SureTect Listeria species Assay. Ruggedness testing was conducted to evaluate the performance of the assay with specific method deviations outside of the recommended parameters open to variation, which demonstrated that the assay gave reliable performance. Accelerated stability testing was additionally conducted, validating the

  19. Quantifying species diversity with a DNA barcoding-based method: Tibetan moth species (Noctuidae on the Qinghai-Tibetan Plateau.

    Directory of Open Access Journals (Sweden)

    Qian Jin

    Full Text Available With the ongoing loss of biodiversity, there is a great need for fast and effective ways to assess species richness and diversity: DNA barcoding provides a powerful new tool for this. We investigated this approach by focusing on the Tibetan plateau, which is one of the world's top biodiversity hotspots. There have been few studies of its invertebrates, although they constitute the vast majority of the region's diversity. Here we investigated species diversity of the lepidopteran family Noctuidae, across different environmental gradients, using measurements based on traditional morphology as well as on DNA barcoding. The COI barcode showed an average interspecific K2P distance of 9.45±2.08%, which is about four times larger than the mean intraspecific distance (1.85±3.20%. Using six diversity indices, we did not detect any significant differences in estimated species diversity between measurements based on traditional morphology and on DNA barcoding. Furthermore, we found strong positive correlations between them, indicating that barcode-based measures of species diversity can serve as a good surrogate for morphology-based measures in most situations tested. Eastern communities were found to have significantly higher diversity than Western ones. Among 22 environmental factors tested, we found that three (precipitation of driest month, precipitation of driest quarter, and precipitation of coldest quarter were significantly correlated with species diversity. Our results indicate that these factors could be the key ecological factors influencing the species diversity of the lepidopteran family Noctuidae on the Tibetan plateau.

  20. Efficient distinction of invasive aquatic plant species from non-invasive related species using DNA barcoding.

    Science.gov (United States)

    Ghahramanzadeh, R; Esselink, G; Kodde, L P; Duistermaat, H; van Valkenburg, J L C H; Marashi, S H; Smulders, M J M; van de Wiel, C C M

    2013-01-01

    Biological invasions are regarded as threats to global biodiversity. Among invasive aliens, a number of plant species belonging to the genera Myriophyllum, Ludwigia and Cabomba, and to the Hydrocharitaceae family pose a particular ecological threat to water bodies. Therefore, one would try to prevent them from entering a country. However, many related species are commercially traded, and distinguishing invasive from non-invasive species based on morphology alone is often difficult for plants in a vegetative stage. In this regard, DNA barcoding could become a good alternative. In this study, 242 samples belonging to 26 species from 10 genera of aquatic plants were assessed using the chloroplast loci trnH-psbA, matK and rbcL. Despite testing a large number of primer sets and several PCR protocols, the matK locus could not be amplified or sequenced reliably and therefore was left out of the analysis. Using the other two loci, eight invasive species could be distinguished from their respective related species, a ninth one failed to produce sequences of sufficient quality. Based on the criteria of universal application, high sequence divergence and level of species discrimination, the trnH-psbA noncoding spacer was the best performing barcode in the aquatic plant species studied. Thus, DNA barcoding may be helpful with enforcing a ban on trade of such invasive species, such as is already in place in the Netherlands. This will become even more so once DNA barcoding would be turned into machinery routinely operable by a nonspecialist in botany and molecular genetics. © 2012 Blackwell Publishing Ltd.

  1. Endangered plant species of the Nevada Test Site, Ash Meadows, and Central-Southern Nevada

    International Nuclear Information System (INIS)

    Beatley, J.C.

    1977-02-01

    A total of 15 vascular plant taxa, currently appearing on the Endangered Species list, occur in southern Nye County, Nevada, and/or adjacent Inyo County, California. It is the purpose of this report to record in detail the locations of the plant collections upon which the distributions are based, and other information relevant to their status as Endangered Species, and to recommend the areas to be designated critical habitats

  2. Endangered plant species of the Nevada Test Site, Ash Meadows, and Central-Southern Nevada

    Energy Technology Data Exchange (ETDEWEB)

    Beatley, J.C.

    1977-02-01

    A total of 15 vascular plant taxa, currently appearing on the Endangered Species list, occur in southern Nye County, Nevada, and/or adjacent Inyo County, California. It is the purpose of this report to record in detail the locations of the plant collections upon which the distributions are based, and other information relevant to their status as Endangered Species, and to recommend the areas to be designated critical habitats.

  3. DNA Barcoding for Species Identification of Insect Skins: A Test on Chironomidae (Diptera) Pupal Exuviae

    Science.gov (United States)

    Ekrem, Torbjørn; Stur, Elisabeth

    2017-01-01

    Abstract Chironomidae (Diptera) pupal exuviae samples are commonly used for biological monitoring of aquatic habitats. DNA barcoding has proved useful for species identification of chironomid life stages containing cellular tissue, but the barcoding success of chironomid pupal exuviae is unknown. We assessed whether standard DNA barcoding could be efficiently used for species identification of chironomid pupal exuviae when compared with morphological techniques and if there were differences in performance between temperate and tropical ecosystems, subfamilies, and tribes. PCR, sequence, and identification success differed significantly between geographic regions and taxonomic groups. For Norway, 27 out of 190 (14.2%) of pupal exuviae resulted in high-quality chironomid sequences that match species. For Costa Rica, 69 out of 190 (36.3%) Costa Rican pupal exuviae resulted in high-quality sequences, but none matched known species. Standard DNA barcoding of chironomid pupal exuviae had limited success in species identification of unknown specimens due to contaminations and lack of matching references in available barcode libraries, especially from Costa Rica. Therefore, we recommend future biodiversity studies that focus their efforts on understudied regions, to simultaneously use morphological and molecular identification techniques to identify all life stages of chironomids and populate the barcode reference library with identified sequences.

  4. Hide and go seek with temperature signals of Northeastern US Tree Species

    Science.gov (United States)

    Alexander, M. R.; Pederson, N.; Bishop, D. A.; Pearl, J. K.; Anchukaitis, K. J.

    2017-12-01

    Improving reconstructions of past climate is vital in providing long-term context for regional climate change. There have been only two published reconstructions of past temperatures in the northeastern U.S. (NEUS) since the 1980s, one based on Picea rubens, and one out in 2017 based upon Chamaecyparis thyoides (Atlantic white cedar; AWC). Because increased species diversity generally improves dendrohydroclimatic reconstructions and both Picea rubens and AWC have limitations as paleoproxies due to land-use and air pollution, we conducted a series of tests to ask, "Does species diversity improve reconstructions of temperature history in the northeastern United States?" The first two tests were performed on AWC and then a network of AWC and Picea rubens. Subsequent tests added groups of species or genera from a network of 230 tree-ring chronologies beginning with those having the strongest relation between warming temperatures and increased growth. PC1 of the AWC test represented 40% of the variance and showed a significant positive relation with winter temperature (r = 0.38). As additional species were included, the "winter temperature PC" accounted for less of the overall variance, ranging from 26% of the variance in test 2 to 5% by test 5. AWC is swamped by the hydroclimatic signal that dominates our network. Populations of species such as Fagus grandifolia, Fraxinus nigra, Juniperus virginiana, Liriodendron tulipifera, Pinus rigida, and Pinus strobus from our network loaded strongest with AWC on the winter temperature PC. Including multiple species accounted for almost 20% more variance in the winter temperature record than AWC alone. Although drought is a dominating influence of tree growth in this region, our results suggest that winter temperatures are recorded within NEUS tree rings. Increasing the species diversity of tree proxies has the potential for improving reconstruction of paleotemperatures in regions lacking latitudinal or altitudinal tree lines

  5. Environmental species sorting dominates forest-bird community assembly across scales

    DEFF Research Database (Denmark)

    Özkan, Korhan; Svenning, J.-C.; Jeppesen, Erik

    2013-01-01

    species richness and composition within the metacommunity. Second, we analysed species' abundance–occupancy relationship across the metacommunity and used null models to assess whether occupancy is determined by species' environmental niches. Third, we used generalized linear models to test for links...... between species' metacommunity-wide occupancy and their broader WP regional populations and assessed whether these links are consistent with environmental species sorting. There was strong environmental control on local species richness and composition patterns within the metacommunity, but non......-environmental spatial factors had also an important joint role. Null model analyses on randomized communities showed that species' occupancy across the metacommunity was strongly determined by species' environmental niches, with occupancy being related to niche position marginality. Species' metacommunity...

  6. Frost hardiness of tree species is independent of phenology and ...

    Indian Academy of Sciences (India)

    The differences in timing in bud burst between species have been interpreted as an adaptation to late frost events in spring. Thus, it has been suggested that the degree of frost susceptibility of leaves is species-specific and depends on the species' phenology and geographic distribution range. To test for relationships ...

  7. Bat Species Comparisons Based on External Morphology: A Test of Traditional versus Geometric Morphometric Approaches.

    Science.gov (United States)

    Schmieder, Daniela A; Benítez, Hugo A; Borissov, Ivailo M; Fruciano, Carmelo

    2015-01-01

    External morphology is commonly used to identify bats as well as to investigate flight and foraging behavior, typically relying on simple length and area measures or ratios. However, geometric morphometrics is increasingly used in the biological sciences to analyse variation in shape and discriminate among species and populations. Here we compare the ability of traditional versus geometric morphometric methods in discriminating between closely related bat species--in this case European horseshoe bats (Rhinolophidae, Chiroptera)--based on morphology of the wing, body and tail. In addition to comparing morphometric methods, we used geometric morphometrics to detect interspecies differences as shape changes. Geometric morphometrics yielded improved species discrimination relative to traditional methods. The predicted shape for the variation along the between group principal components revealed that the largest differences between species lay in the extent to which the wing reaches in the direction of the head. This strong trend in interspecific shape variation is associated with size, which we interpret as an evolutionary allometry pattern.

  8. Bat Species Comparisons Based on External Morphology: A Test of Traditional versus Geometric Morphometric Approaches.

    Directory of Open Access Journals (Sweden)

    Daniela A Schmieder

    Full Text Available External morphology is commonly used to identify bats as well as to investigate flight and foraging behavior, typically relying on simple length and area measures or ratios. However, geometric morphometrics is increasingly used in the biological sciences to analyse variation in shape and discriminate among species and populations. Here we compare the ability of traditional versus geometric morphometric methods in discriminating between closely related bat species--in this case European horseshoe bats (Rhinolophidae, Chiroptera--based on morphology of the wing, body and tail. In addition to comparing morphometric methods, we used geometric morphometrics to detect interspecies differences as shape changes. Geometric morphometrics yielded improved species discrimination relative to traditional methods. The predicted shape for the variation along the between group principal components revealed that the largest differences between species lay in the extent to which the wing reaches in the direction of the head. This strong trend in interspecific shape variation is associated with size, which we interpret as an evolutionary allometry pattern.

  9. Differences in susceptibility of five cladoceran species to two systemic insecticides, imidacloprid and fipronil.

    Science.gov (United States)

    Hayasaka, Daisuke; Korenaga, Tomoko; Suzuki, Kazutaka; Sánchez-Bayo, Francisco; Goka, Koichi

    2012-03-01

    Differences in susceptibility of five cladocerans to the neonicotinoid imidacloprid and the phenyl-pyrazole fipronil, which have been dominantly used in rice fields of Japan in recent years, were examined based on short-term (48-h), semi-static acute immobilization exposure tests. Additionally, we compared the species sensitivity distribution (SSD) patterns of both insecticides between two sets of species: the five tested cladocerans and all other aquatic organisms tested so far, using data from the ECOTOX database of U.S. Environmental Protection Agency (USEPA). The sensitivity of the test species to either imidacloprid or fipronil was consistent, spanning similar orders of magnitude (100 times). At the genus level, sensitivities to both insecticides were in the following descending order: Ceriodaphnia > Moina > Daphnia. A positive relationship was found between body lengths of each species and the acute toxicity (EC(50)) of the insecticides, in particular fipronil. Differences in SSD patterns of imidacloprid were found between the species groups compared, indicating that test cladocerans are much less susceptible than other aquatic species including amphibians, crustaceans, fish, insects, mollusks and worms. However, the SSD patterns for fipronil indicate no difference in sensitivity between cladocerans tested and other aquatic organisms despite the greater exposure, which overestimates the results, of our semi-static tests. From these results, Ceriodaphnia sp. should be considered as more sensitive bioindicators (instead of the standard Daphnia magna) for ecotoxicological assessments of aquatic ecosystems. In addition, we propose that ecotoxicity data associated with differences in susceptibility among species should be investigated whenever pesticides have different physicochemical properties and mode of action.

  10. TOXICITY OF PENTACHLOROPHENOL TO ENDANGERED AND SURROGATE FISH SPECIES

    Science.gov (United States)

    Water quality criteria (WQC) generally are based on the responses of easily cultured and tested surrogate species. Little is known about the relative sensitivity of surrogate and endangered species. The objective of this study was to compare acute and chronic (early life-stage) ...

  11. Bounding species distribution models

    Directory of Open Access Journals (Sweden)

    Thomas J. STOHLGREN, Catherine S. JARNEVICH, Wayne E. ESAIAS,Jeffrey T. MORISETTE

    2011-10-01

    Full Text Available Species distribution models are increasing in popularity for mapping suitable habitat for species of management concern. Many investigators now recognize that extrapolations of these models with geographic information systems (GIS might be sensitive to the environmental bounds of the data used in their development, yet there is no recommended best practice for “clamping” model extrapolations. We relied on two commonly used modeling approaches: classification and regression tree (CART and maximum entropy (Maxent models, and we tested a simple alteration of the model extrapolations, bounding extrapolations to the maximum and minimum values of primary environmental predictors, to provide a more realistic map of suitable habitat of hybridized Africanized honey bees in the southwestern United States. Findings suggest that multiple models of bounding, and the most conservative bounding of species distribution models, like those presented here, should probably replace the unbounded or loosely bounded techniques currently used [Current Zoology 57 (5: 642–647, 2011].

  12. Bounding Species Distribution Models

    Science.gov (United States)

    Stohlgren, Thomas J.; Jarnevich, Cahterine S.; Morisette, Jeffrey T.; Esaias, Wayne E.

    2011-01-01

    Species distribution models are increasing in popularity for mapping suitable habitat for species of management concern. Many investigators now recognize that extrapolations of these models with geographic information systems (GIS) might be sensitive to the environmental bounds of the data used in their development, yet there is no recommended best practice for "clamping" model extrapolations. We relied on two commonly used modeling approaches: classification and regression tree (CART) and maximum entropy (Maxent) models, and we tested a simple alteration of the model extrapolations, bounding extrapolations to the maximum and minimum values of primary environmental predictors, to provide a more realistic map of suitable habitat of hybridized Africanized honey bees in the southwestern United States. Findings suggest that multiple models of bounding, and the most conservative bounding of species distribution models, like those presented here, should probably replace the unbounded or loosely bounded techniques currently used [Current Zoology 57 (5): 642-647, 2011].

  13. A cross-species alignment tool (CAT)

    DEFF Research Database (Denmark)

    Li, Heng; Guan, Liang; Liu, Tao

    2007-01-01

    BACKGROUND: The main two sorts of automatic gene annotation frameworks are ab initio and alignment-based, the latter splitting into two sub-groups. The first group is used for intra-species alignments, among which are successful ones with high specificity and speed. The other group contains more...... sensitive methods which are usually applied in aligning inter-species sequences. RESULTS: Here we present a new algorithm called CAT (for Cross-species Alignment Tool). It is designed to align mRNA sequences to mammalian-sized genomes. CAT is implemented using C scripts and is freely available on the web...... at http://xat.sourceforge.net/. CONCLUSIONS: Examined from different angles, CAT outperforms other extant alignment tools. Tested against all available mouse-human and zebrafish-human orthologs, we demonstrate that CAT combines the specificity and speed of the best intra-species algorithms, like BLAT...

  14. Ecological impacts of invasive alien species along temperature gradients: testing the role of environmental matching.

    Science.gov (United States)

    Iacarella, Josephine C; Dick, Jaimie T A; Alexander, Mhairi E; Ricciardi, Anthony

    2015-04-01

    Invasive alien species (IAS) can cause substantive ecological impacts, and the role of temperature in mediating these impacts may become increasingly significant in a changing climate. Habitat conditions and physiological optima offer predictive information for IAS impacts in novel environments. Here, using meta-analysis and laboratory experiments, we tested the hypothesis that the impacts of IAS in the field are inversely correlated with the difference in their ambient and optimal temperatures. A meta-analysis of 29 studies of consumptive impacts of IAS in inland waters revealed that the impacts of fishes and crustaceans are higher at temperatures that more closely match their thermal growth optima. In particular, the maximum impact potential was constrained by increased differences between ambient and optimal temperatures, as indicated by the steeper slope of a quantile regression on the upper 25th percentile of impact data compared to that of a weighted linear regression on all data with measured variances. We complemented this study with an experimental analysis of the functional response (the relationship between predation rate and prey supply) of two invasive predators (freshwater mysid shrimp, Hemimysis anomala and Mysis diluviana) across. relevant temperature gradients; both of these species have previously been found to exert strong community-level impacts that are corroborated by their functional responses to different prey items. The functional response experiments showed that maximum feeding rates of H. anomala and M. diluviana have distinct peaks near their respective thermal optima. Although variation in impacts may be caused by numerous abiotic or biotic habitat characteristics, both our analyses point to temperature as a key mediator of IAS impact levels in inland waters and suggest that IAS management should prioritize habitats in the invaded range that more closely match the thermal optima of targeted invaders.

  15. Species interactions and plant polyploidy.

    Science.gov (United States)

    Segraves, Kari A; Anneberg, Thomas J

    2016-07-01

    Polyploidy is a common mode of speciation that can have far-reaching consequences for plant ecology and evolution. Because polyploidy can induce an array of phenotypic changes, there can be cascading effects on interactions with other species. These interactions, in turn, can have reciprocal effects on polyploid plants, potentially impacting their establishment and persistence. Although there is a wealth of information on the genetic and phenotypic effects of polyploidy, the study of species interactions in polyploid plants remains a comparatively young field. Here we reviewed the available evidence for how polyploidy may impact many types of species interactions that range from mutualism to antagonism. Specifically, we focused on three main questions: (1) Does polyploidy directly cause the formation of novel interactions not experienced by diploids, or does it create an opportunity for natural selection to then form novel interactions? (2) Does polyploidy cause consistent, predictable changes in species interactions vs. the evolution of idiosyncratic differences? (3) Does polyploidy lead to greater evolvability in species interactions? From the scarce evidence available, we found that novel interactions are rare but that polyploidy can induce changes in pollinator, herbivore, and pathogen interactions. Although further tests are needed, it is likely that selection following whole-genome duplication is important in all types of species interaction and that there are circumstances in which polyploidy can enhance the evolvability of interactions with other species. © 2016 Botanical Society of America.

  16. Molecular and morphological approaches for species delimitation and hybridization investigations of two Cichla species

    Directory of Open Access Journals (Sweden)

    Andrea A. F. Mourão

    Full Text Available ABSTRACT The hybridization is a widely-discussed issue in several studies with fish species. For some authors, hybridization may be related with diversification and speciation of several groups, or also with the extinction of populations or species. Difficulties to differentiate species and hybrids may be a problem to correctly apply a management of wild species, because hybrid lineages, especially the advanced ones, may resemble the parental species. The genus Cichla Bloch & Schneider, 1801 constitutes an interesting experimental model, considering that hybridization and taxonomic uncertainties hinder a correct identification. Considering these problems, in this study, we developed genetic methodologies and applied meristic and morphometric approaches in wild samples in order to identify species and for test a possible hybridization between Cichla kelberi Kullander & Ferreira, 2006 and Cichla piquiti Kullander & Ferreira, 2006. For this, C. kelberi, C. piquiti and potential hybrid ( carijó individuals were collected in Paraná and Tietê rivers (SP, Brazil. For meristic and morphometric methods, the individuals were analyzed using the statistical software Pcord 5:31, while for molecular methods, primers for PCR-multiplex were designed and enzyme for PCR-RFLP were selected, under the species-specific nucleotide. All results indicated that the carijó is not an interspecific hybrid, because it presented identical genetic pattern and morphology closed to C. piquiti. Thus, we propose that carijó is a C. piquiti morphotype. In addition, this study promotes a new molecular tool that could be used in future research, monitoring and management programs of the genus Cichla.

  17. Hichrom candida agar for identification of Candida species.

    Science.gov (United States)

    Baradkar, V P; Mathur, M; Kumar, S

    2010-01-01

    Chromogenic media are frequently used in direct and rapid identification of yeasts because different Candida species produce unique colors on these media. We used 60 isolates of Candida species including 30 C. albicans, 10 C. parapsilosis, 11 C. glabrata, five C. tropicalis, and four C. dubliniensis, isolated from various clinical specimens, to evaluate the performance of HiChrome Candida agar. These strains had been identified by germ tube test, morphology on cornmeal agar, chlamydospore formation on tobacco agar and sugar assimilation tests. The sensitivity and specificity results were: C. albicans (96.55 and 96.42%); C. parapsilosis (80 and 98.03%), C. glabrata (90.90 and 88.23%), C. tropicalis (100 and 100%) and C. dubliniensis (60 and 96.55%) respectively. HiChrom Candida agaris medium has been useful and capable of presumptive, rapid identification of Candida species within 48 hours.

  18. Consideration of species differences in developing novel molecules as cognition enhancers.

    Science.gov (United States)

    Young, Jared W; Jentsch, J David; Bussey, Timothy J; Wallace, Tanya L; Hutcheson, Daniel M

    2013-11-01

    The NIH-funded CNTRICS initiative has coordinated efforts to promote the vertical translation of novel procognitive molecules from testing in mice, rats and non-human primates, to clinical efficacy in patients with schizophrenia. CNTRICS highlighted improving construct validation of tasks across species to increase the likelihood that the translation of a candidate molecule to humans will be successful. Other aspects of cross-species behaviors remain important however. This review describes cognitive tasks utilized across species, providing examples of differences and similarities of innate behavior between species, as well as convergent construct and predictive validity. Tests of attention, olfactory discrimination, reversal learning, and paired associate learning are discussed. Moreover, information on the practical implication of species differences in drug development research is also provided. The issues covered here will aid in task development and utilization across species as well as reinforcing the positive role preclinical research can have in developing procognitive treatments for psychiatric disorders. Copyright © 2012 Elsevier Ltd. All rights reserved.

  19. Conserving the stage: climate change and the geophysical underpinnings of species diversity.

    Directory of Open Access Journals (Sweden)

    Mark G Anderson

    Full Text Available Conservationists have proposed methods for adapting to climate change that assume species distributions are primarily explained by climate variables. The key idea is to use the understanding of species-climate relationships to map corridors and to identify regions of faunal stability or high species turnover. An alternative approach is to adopt an evolutionary timescale and ask ultimately what factors control total diversity, so that over the long run the major drivers of total species richness can be protected. Within a single climatic region, the temperate area encompassing all of the Northeastern U.S. and Maritime Canada, we hypothesized that geologic factors may take precedence over climate in explaining diversity patterns. If geophysical diversity does drive regional diversity, then conserving geophysical settings may offer an approach to conservation that protects diversity under both current and future climates. Here we tested how well geology predicts the species diversity of 14 US states and three Canadian provinces, using a comprehensive new spatial dataset. Results of linear regressions of species diversity on all possible combinations of 23 geophysical and climatic variables indicated that four geophysical factors; the number of geological classes, latitude, elevation range and the amount of calcareous bedrock, predicted species diversity with certainty (adj. R(2 = 0.94. To confirm the species-geology relationships we ran an independent test using 18,700 location points for 885 rare species and found that 40% of the species were restricted to a single geology. Moreover, each geology class supported 5-95 endemic species and chi-square tests confirmed that calcareous bedrock and extreme elevations had significantly more rare species than expected by chance (P<0.0001, strongly corroborating the regression model. Our results suggest that protecting geophysical settings will conserve the stage for current and future biodiversity and may

  20. Role of genotype® mycobacterium common mycobacteria/additional species assay for rapid differentiation between Mycobacterium tuberculosis complex and different species of non-tuberculous mycobacteria

    Directory of Open Access Journals (Sweden)

    Amresh Kumar Singh

    2013-01-01

    Full Text Available Background: Mycobacterium tuberculosis complex (MTBC and non-tuberculous mycobacteria (NTM may or may not have same clinical presentations, but the treatment regimens are always different. Laboratory differentiation between MTBC and NTM by routine methods are time consuming and cumbersome to perform. We have evaluated the role of GenoType® Mycobacterium common mycobacteria/additional species (CM/AS assay for differentiation between MTBC and different species of NTM in clinical isolates from tuberculosis (TB cases. Materials and Methods: A total of 1080 clinical specimens were collected from January 2010 to June 2012. Diagnosis was performed by Ziehl-Neelsen staining followed by culture in BacT/ALERT 3D system (bioMerieux, France. A total of 219 culture positive clinical isolates (BacT/ALERT® MP cultures were selected for differentiation by p-nitrobenzoic acid (PNB sensitivity test as and BIO-LINE SD Ag MPT64 TB test considering as the gold standard test. Final identification and differentiation between MTBC and different species of NTM were further confirmed by GenoType® Mycobacterium CM/AS assay (Hain Lifescience, Nehren, Germany. Results: Out of 219 BacT/ALERT® MP culture positive isolates tested by PNB as 153 MTBC (69.9% and by GenoType® Mycobacterium CM/AS assay as 159 (72.6% MTBC and remaining 60 (27.4% were considered as NTM species. The GenoType® Mycobacterium CM/AS assay was proved 99.3% sensitive and 98.3% specific for rapid differentiation of MTBC and NTM. The most common NTM species were; Mycobacterium fortuitum 20 (33.3% among rapid growing mycobacteria and Mycobacterium intracellulare 11 (18.3% among slow growing mycobacteria. Conclusion: The GenoType® Mycobacterium assay makes rapid and accurate identification of NTM species as compared with different phenotypic and molecular diagnostic tool and helps in management of infections caused by different mycobacteria.

  1. Trait characteristics determine pyrethroid sensitivity in non-standard test species of freshwater macroinvertebrates – A reality check

    DEFF Research Database (Denmark)

    Wiberg-Larsen, Peter; Graeber, Daniel; Baattrup-Pedersen, Annette

    2016-01-01

    was recorded using automated video tracking. Most arthropod species showed mortality responses to the exposure concentrations (0.01-10 μg L(-1)), whereas nonarthropod species remained unaffected. LC50 varied by at least a factor of 1000 among arthropod species, even within the same family. This variation could...

  2. Invasive Species - A Threat to the Homeland?

    Science.gov (United States)

    2003-04-07

    species of weeds, diseases and organisms on both my farm and the surrounding woodlands. Some of these species include soybean cyst nematode, soybean aphid ...natural enemies in their new environment. Parasites, pathogens , or predators that would inhibit or limit their spread are few or non-existent. In...tested, and fielded to control the genetically modified organism. Serums would be less effective, and diagnosis of human pathogens could change and

  3. Germination of native understorey species for revegetation of New South Wales coal mines

    Energy Technology Data Exchange (ETDEWEB)

    Gillespie, M.J.; Bellairs, S.M.; Mulligan, D.R. [University of Queensland, St. Lucia, Qld. (Australia). Dept. of Agriculture and Centre for Mined Land Rehabilitation

    1997-06-01

    This project investigates the suitability of a range of native understorey species for rehabilitation at several coal mines in New South Wales. The germination of seeds from 69 species representing 12 families was tested under controlled laboratory conditions. Germination occurred in all but two of the species tested and 50% germination was exceeded by 29 species. Species of the Mimosaceae, Fabaceae and Proteaceae tended to have above average germination; however species representing other families had variable germination results. A pre-germination heat treatment applied to all of the Acacia species increased germination in some but not all species. Seeds of these understorey species which were used in this trial, are native to the New South Wales coal fields and available commercially or are relatively easy to collect. Glasshouse and field trials are now being undertaken to assess establishment and growth on mine soil, spoil and coal reject materials. 9 refs., 5 figs.

  4. Why abundant tropical tree species are phylogenetically old.

    Science.gov (United States)

    Wang, Shaopeng; Chen, Anping; Fang, Jingyun; Pacala, Stephen W

    2013-10-01

    Neutral models of species diversity predict patterns of abundance for communities in which all individuals are ecologically equivalent. These models were originally developed for Panamanian trees and successfully reproduce observed distributions of abundance. Neutral models also make macroevolutionary predictions that have rarely been evaluated or tested. Here we show that neutral models predict a humped or flat relationship between species age and population size. In contrast, ages and abundances of tree species in the Panamanian Canal watershed are found to be positively correlated, which falsifies the models. Speciation rates vary among phylogenetic lineages and are partially heritable from mother to daughter species. Variable speciation rates in an otherwise neutral model lead to a demographic advantage for species with low speciation rate. This demographic advantage results in a positive correlation between species age and abundance, as found in the Panamanian tropical forest community.

  5. Mapping National Plant Biodiversity Patterns in South Korea with the MARS Species Distribution Model.

    Directory of Open Access Journals (Sweden)

    Hyeyeong Choe

    Full Text Available Accurate information on the distribution of existing species is crucial to assess regional biodiversity. However, data inventories are insufficient in many areas. We examine the ability of Multivariate Adaptive Regression Splines (MARS multi-response species distribution model to overcome species' data limitations and portray plant species distribution patterns for 199 South Korean plant species. The study models species with two or more observations, examines their contribution to national patterns of species richness, provides a sensitivity analysis of different range threshold cutoff approaches for modeling species' ranges, and presents considerations for species modeling at fine spatial resolution. We ran MARS models for each species and tested four threshold methods to transform occurrence probabilities into presence or absence range maps. Modeled occurrence probabilities were extracted at each species' presence points, and the mean, median, and one standard deviation (SD calculated to define data-driven thresholds. A maximum sum of sensitivity and specificity threshold was also calculated, and the range maps from the four cutoffs were tested using independent plant survey data. The single SD values were the best threshold tested for minimizing omission errors and limiting species ranges to areas where the associated occurrence data were correctly classed. Eight individual species range maps for rare plant species were identified that are potentially affected by resampling predictor variables to fine spatial scales. We portray spatial patterns of high species richness by assessing the combined range maps from three classes of species: all species, endangered and endemic species, and range-size rarity of all species, which could be used in conservation planning for South Korea. The MARS model is promising for addressing the common problem of few species occurrence records. However, projected species ranges are highly dependent on the

  6. Feeding environment and other traits shape species' roles in marine food webs.

    Science.gov (United States)

    Cirtwill, Alyssa R; Eklöf, Anna

    2018-04-02

    Food webs and meso-scale motifs allow us to understand the structure of ecological communities and define species' roles within them. This species-level perspective on networks permits tests for relationships between species' traits and their patterns of direct and indirect interactions. Such relationships could allow us to predict food-web structure based on more easily obtained trait information. Here, we calculated the roles of species (as vectors of motif position frequencies) in six well-resolved marine food webs and identified the motif positions associated with the greatest variation in species' roles. We then tested whether the frequencies of these positions varied with species' traits. Despite the coarse-grained traits we used, our approach identified several strong associations between traits and motifs. Feeding environment was a key trait in our models and may shape species' roles by affecting encounter probabilities. Incorporating environment into future food-web models may improve predictions of an unknown network structure. © 2018 John Wiley & Sons Ltd/CNRS.

  7. The Pleurobemini (Bivalvia: Unionida) revisited: Molecular species delineation using a mitochondrial DNA gene reveals multiple conspecifics and undescribed species

    Science.gov (United States)

    Inoue, Kentaro; Hayes, David M.; Harris, John L.; Johnson, Nathan A.; Morrison, Cheryl L.; Eackles, Michael S.; King, Tim; Jones, Jess W.; Hallerman, Eric M.; Christian, Alan D.; Randklev, Charles R.

    2018-01-01

    The Pleurobemini (Bivalvia: Unionida) represent approximately one-third of freshwater mussel diversity in North America. Species identification within this group is challenging due to morphological convergence and phenotypic plasticity. Accurate species identification, including characterization of currently unrecognized taxa, is required to develop effective conservation strategies because many species in the group are imperiled. We examined 573 cox1 sequences from 110 currently recognized species (including 13 Fusconaia and 21 Pleurobema species) to understand phylogenetic relationships among pleurobemine species (mainly Fusconaia and Pleurobema) and to delineate species boundaries. The results of phylogenetic analyses showed no geographic structure within widespread species and illustrated a close relationship between Elliptio lanceolata and Parvaspina collina. Constraint tests supported monophyly of the genera Fusconaia and Pleurobema, including the subgenus P. (Sintoxia). Furthermore, results revealed multiple conspecifics, including P. hanleyianum and P. troschelianum, P. chattanoogaense and P. decisum, P. clava and P. oviforme, P. rubrum and P. sintoxia, F. askewi and F. lananensis, and F. cerina and F. flava. Species delimitation analyses identified three currently unrecognized taxa (two in Fusconaia and one in Pleurobema). Further investigation using additional genetic markers and other lines of evidence (e.g., morphology, life history, ecology) are necessary before any taxonomic changes are formalized.

  8. Isolation and Pathogenicity of Phytophthora Species from Poplar Plantations in Serbia

    Directory of Open Access Journals (Sweden)

    Ivan Milenković

    2018-06-01

    Full Text Available During a survey in three declining and three healthy poplar plantations in Serbia, six different Phytophthora species were obtained. Phytophthora plurivora was the most common, followed by P. pini, P. polonica, P. lacustris, P. cactorum, and P. gonapodyides. Pathogenicity of all isolated species to four-month and one-year-old cuttings of Populus hybrid clones I-214 and Pánnonia, respectively, was tested using both a soil infestation and stem inoculation test. Isolates of P. polonica, P. × cambivora, P. cryptogea, and P. × serendipita from other host plants were included as a comparison. In the soil infestation test, the most aggressive species to clone I-214 were P. plurivora, P. × serendipita, and P. pini. On clone Pánnonia, P. gonapodyides and P. pini were the most aggressive, both causing 100% mortality, followed by P. cactorum, P. × cambivora, and P. polonica. In the underbark inoculation test, the susceptibility of both poplar clones to the different Phytophthora species was largely similar, as in the soil infestation test, with the exception of P. polonica, which proved to be only weakly pathogenic to poplar bark. The most aggressive species to clone I-214 was P. pini, while on clone Pánnonia, the longest lesions and highest disease incidence were caused by P. gonapodyides. Phytophthora cactorum and P. plurivora were pathogenic to both clones, whereas P. × cambivora showed only weak pathogenicity. The implications of these findings and possible pathways of dispersion of the pathogens are discussed.

  9. Can temporal and spatial NDVI predict regional bird-species richness?

    Directory of Open Access Journals (Sweden)

    Sebastián Nieto

    2015-01-01

    Full Text Available Understanding the distribution of the species and its controls over biogeographic scales is still a major challenge in ecology. National Park Networks provide an opportunity to assess the relationship between ecosystem functioning and biodiversity in areas with low human impacts. We tested the productivity–biodiversity hypothesis which states that the number of species increases with the available energy, and the ​variability–biodiversity hypothesis which states that the number of species increases with the diversity of habitats. The available energy and habitat heterogeneity estimated by the normalized difference vegetation index (NDVI was shown as a good predictor of bird-species richness for a diverse set of biomes in previously published studies. However, there is not a universal relationship between NDVI and bird-species richness. Here we tested if the NDVI can predict bird species richness in areas with low human impact in Argentina. Using a dataset from the National Park Network of Argentina we found that the best predictor of bird species richness was the minimum value of NDVI per year which explained 75% of total variability. The inclusion of the spatial heterogeneity of NDVI improved the explanation power to 80%. Minimum NDVI was highly correlated with precipitation and winter temperature. Our analysis provides a tool for assessing bird-species richness at scales on which land-use planning practitioners make their decisions for Southern South America.

  10. Hichrom candida agar for identification of candida species

    Directory of Open Access Journals (Sweden)

    Baradkar V

    2010-01-01

    Full Text Available Chromogenic media are frequently used in direct and rapid identification of yeasts because different Candida species produce unique colors on these media. We used 60 isolates of Candida species including 30 C. albicans, 10 C. parapsilosis, 11 C. glabrata, five C. tropicalis, and four C. dubliniensis, isolated from various clinical specimens, to evaluate the performance of HiChrome Candida agar. These strains had been identified by germ tube test, morphology on cornmeal agar, chlamydospore formation on tobacco agar and sugar assimilation tests. The sensitivity and specificity results were: C. albicans (96.55 and 96.42%; C. parapsilosis (80 and 98.03%, C. glabrata (90.90 and 88.23%, C. tropicalis (100 and 100% and C. dubliniensis (60 and 96.55% respectively. HiChrom Candida agaris medium has been useful and capable of presumptive, rapid identification of Candida species within 48 hours.

  11. Brine shrimp bioassay: importance of correct taxonomic identification of Artemia (Anostraca) species.

    Science.gov (United States)

    Ruebhart, David R; Cock, Ian E; Shaw, Glen R

    2008-08-01

    Despite the common use of the brine shrimp bioassay in toxicology, there is confusion in the literature regarding citation of the correct taxonomic identity of the Artemia species used. The genus Artemia, once thought to be represented by a single species Artemia salina, is now known to be composed of several bisexual species as well as parthenogenetic populations. Artemia franciscana is the best studied of the Artemia species and is considered to represent the vast majority of studies in which Artemia is used as an experimental test organism. We found that in studies referring to the use of A. salina, the zoogeography of the cyst harvest site indicated that the species used was actually A. franciscana. Those performing bioassays with Artemia need to exercise diligence in assigning correct species identification, as the identity of the test organism is an important parameter in assuring the validity of the results of the assay.

  12. Using habitat suitability models to target invasive plant species surveys.

    Science.gov (United States)

    Crall, Alycia W; Jarnevich, Catherine S; Panke, Brendon; Young, Nick; Renz, Mark; Morisette, Jeffrey

    2013-01-01

    Managers need new tools for detecting the movement and spread of nonnative, invasive species. Habitat suitability models are a popular tool for mapping the potential distribution of current invaders, but the ability of these models to prioritize monitoring efforts has not been tested in the field. We tested the utility of an iterative sampling design (i.e., models based on field observations used to guide subsequent field data collection to improve the model), hypothesizing that model performance would increase when new data were gathered from targeted sampling using criteria based on the initial model results. We also tested the ability of habitat suitability models to predict the spread of invasive species, hypothesizing that models would accurately predict occurrences in the field, and that the use of targeted sampling would detect more species with less sampling effort than a nontargeted approach. We tested these hypotheses on two species at the state scale (Centaurea stoebe and Pastinaca sativa) in Wisconsin (USA), and one genus at the regional scale (Tamarix) in the western United States. These initial data were merged with environmental data at 30-m2 resolution for Wisconsin and 1-km2 resolution for the western United States to produce our first iteration models. We stratified these initial models to target field sampling and compared our models and success at detecting our species of interest to other surveys being conducted during the same field season (i.e., nontargeted sampling). Although more data did not always improve our models based on correct classification rate (CCR), sensitivity, specificity, kappa, or area under the curve (AUC), our models generated from targeted sampling data always performed better than models generated from nontargeted data. For Wisconsin species, the model described actual locations in the field fairly well (kappa = 0.51, 0.19, P guiding invasive species monitoring, and we support the use of an iterative sampling design for

  13. Use of tetrazolium (TTC, Germ's and greenhouse plant emergences methods for testing seed vigour of selected ornamental plant species

    Directory of Open Access Journals (Sweden)

    Roman Hołubowicz

    2013-12-01

    Full Text Available In the years 1996-1997 the experiments were carried out on methods to investigate seed vigour of tassel flower (Amaranthus caudatus L., sand pink (Dianthus chinensis L., babies' breath (Gypsophila elegans M.B., sweet pea (Lathyrus odorathus L., African marigold (Tagetes erecta L. and zinnia (Zinnia elegans Jasq.. The main goals of this research were to specify conditions for accelerated ageing (AA of the seeds of a few selected ornamental plant species and to choose the most appropriate methods for their seed vigour evaluation in the laboratory and greenhouse conditions. All used in the experiments seeds came from the commercial seed lots from Polish seed company. Evaluation was carried out on the seed samples with high and low vigour. The latter ones were received through subjecting the seed samples to AA, i.e. by placing them in 100% relative humidity (RH at 44°C, except African marigold-at 42°C, in the darkness and keeping them for 144, 88, 100, 48, 72 and 72 hours, respectively. The tested seed vigour estimated methods included the Germ's method, the 2,3,5-triphenyl tetrazoilum chloride (TTC method and the test of plant emergences in the greenhouse. The high vigour seeds samples were used as a check. The Germ's method was found to be useful to evaluate sand pink, babies' breath and African marigold seed vigour, whereas the TTC method was found to be suitable for vigour evaluation of sand pink, babies' breath and zinnia. At present stage of our knowledge about seed vigour, the plant emergences in the greenhouse method was found to be the best for evaluation of seed vigour of tassel flower, sand pink, babies' breath, sweet pea and zinnia. It is reasonable to combine a few methods of seed vigour evaluation for ornamental plant species.

  14. Assessing species saturation: conceptual and methodological challenges.

    Science.gov (United States)

    Olivares, Ingrid; Karger, Dirk N; Kessler, Michael

    2018-05-07

    Is there a maximum number of species that can coexist? Intuitively, we assume an upper limit to the number of species in a given assemblage, or that a lineage can produce, but defining and testing this limit has proven problematic. Herein, we first outline seven general challenges of studies on species saturation, most of which are independent of the actual method used to assess saturation. Among these are the challenge of defining saturation conceptually and operationally, the importance of setting an appropriate referential system, and the need to discriminate among patterns, processes and mechanisms. Second, we list and discuss the methodological approaches that have been used to study species saturation. These approaches vary in time and spatial scales, and in the variables and assumptions needed to assess saturation. We argue that assessing species saturation is possible, but that many studies conducted to date have conceptual and methodological flaws that prevent us from currently attaining a good idea of the occurrence of species saturation. © 2018 Cambridge Philosophical Society.

  15. Does temperature-mediated reproductive success drive the direction of species displacement in two invasive species of leafminer fly?

    Directory of Open Access Journals (Sweden)

    Haihong Wang

    Full Text Available Liriomyza sativae and L. trifolii (Diptera: Agromyzidae are two highly invasive species of leafmining flies, which have become established as pests of horticultural crops throughout the world. In certain regions where both species have been introduced, L. sativae has displaced L. trifolii, whereas the opposite has occurred in other regions. These opposing outcomes suggest that neither species is an inherently superior competitor. The regions where these displacements have been observed (southern China, Japan and western USA are climatically different. We determined whether temperature differentially affects the reproductive success of these species and therefore if climatic differences could affect the outcome of interspecific interactions where these species are sympatric. The results of life table parameters indicate that both species can develop successfully at all tested temperatures (20, 25, 31, 33°C. L. sativae had consistently higher fecundities at all temperatures, but L. trifolii developed to reproductive age faster. Age-stage specific survival rates were higher for L. sativae at low temperatures, but these were higher for L. trifolii at higher temperatures. We then compared the net reproductive rates (R0 for both species in pure and mixed cultures maintained at the same four constant temperatures. Both species had significantly lower net reproductive rates in mixed species cultures compared with their respective pure species cultures, indicating that both species are subject to intense interspecific competition. Net reproductive rates were significantly greater for L. sativae than for L. trifolii in mixed species groups at the lower temperatures, whereas the opposite occurred at the higher temperature. Therefore, interactions between the species are temperature dependent and small differences could shift the competitive balance between the species. These temperature mediated effects may contribute to the current ongoing displacement

  16. Formulated Beta-Cyfluthrin Shows Wide Divergence in Toxicity among Bird Species

    Directory of Open Access Journals (Sweden)

    Laura M. Addy-Orduna

    2011-01-01

    Full Text Available It is generally assumed that the toxicity of pyrethroid insecticides to birds is negligible, though few species have been tested. The oral acute toxicity of formulated beta-cyfluthrin was determined for canaries (Serinus sp., shiny cowbirds (Molothrus bonariensis, and eared doves (Zenaida auriculata. Single doses were administered to adults by gavage. Approximate lethal doses 50 (LD50 and their confidence intervals were determined by approximate D-optimal design. Canaries were found to be substantially more sensitive to formulated beta-cyfluthrin (LD50=(170±41 mg/kg than the other two species tested (LD50=(2234±544 mg/kg and LD50=(2271±433 mg/kg, resp.. The LD50 obtained for canaries was also considerably lower than typical toxicity values available in the literature for pyrethroids. This study emphasizes the need for testing a broader range of species with potentially toxic insecticides, using modern up and down test designs with minimal numbers of birds.

  17. Formulated Beta-Cyfluthrin Shows Wide Divergence in Toxicity among Bird Species.

    Science.gov (United States)

    Addy-Orduna, Laura M; Zaccagnini, María-Elena; Canavelli, Sonia B; Mineau, Pierre

    2011-01-01

    It is generally assumed that the toxicity of pyrethroid insecticides to birds is negligible, though few species have been tested. The oral acute toxicity of formulated beta-cyfluthrin was determined for canaries (Serinus sp.), shiny cowbirds (Molothrus bonariensis), and eared doves (Zenaida auriculata). Single doses were administered to adults by gavage. Approximate lethal doses 50 (LD(50)) and their confidence intervals were determined by approximate D-optimal design. Canaries were found to be substantially more sensitive to formulated beta-cyfluthrin (LD(50) = (170 ± 41) mg/kg) than the other two species tested (LD(50) = (2234 ± 544) mg/kg and LD(50) = (2271 ± 433) mg/kg, resp.). The LD(50) obtained for canaries was also considerably lower than typical toxicity values available in the literature for pyrethroids. This study emphasizes the need for testing a broader range of species with potentially toxic insecticides, using modern up and down test designs with minimal numbers of birds.

  18. Comparative toxicity of pentachlorophenol to three earthworm species in artificial soil

    Energy Technology Data Exchange (ETDEWEB)

    Fitzgerald, D.; Lanno, R.P.; Farwell, A.; Dixon, D.G. [Univ. of Waterloo, Ontario (Canada). Dept. of Biology

    1994-12-31

    Although methods for standardized toxicity tests with earthworms exist, many of the test parameters and conditions have not been validated in actual tests and with different species of worms. This study evaluated the toxicity of pentachlorophenol (PCP) to three species of earthworms, Lumbricus terrestris, Eisenia fetida, and Eudrilus eugeniae using various methods of data analysis and body residues. Tests were conducted in artificial soil for a period of 28 days or until an Acute Lethality Threshold (ALT) was reached. An intensive temporal sampling regime was applied to generate sufficient data for the accurate estimation of ALTs using both LC50/time and time-to-death/soil concentration methods of data analysis. L. terrestris was tested at 15 C, E. eugeniae at 24 C, and E. fetida at both temperatures. Total body residues of PCP were measured by GC following cryogenic separation of the lipid fraction of the worm. ALTs were significantly different between E. fetida and the two larger species of worms. No effect of temperature on the ALT for E. fetida was observed, although the time taken to reach the ALT increased at the lower temperature. The relationship of PCP residues at mortality will be discussed in terms of the effects of species, body size and temperature. Limitations of the artificial soil based upon growth curves of worms will also be examined.

  19. SpeciesGeoCoder: Fast Categorization of Species Occurrences for Analyses of Biodiversity, Biogeography, Ecology, and Evolution.

    Science.gov (United States)

    Töpel, Mats; Zizka, Alexander; Calió, Maria Fernanda; Scharn, Ruud; Silvestro, Daniele; Antonelli, Alexandre

    2017-03-01

    Understanding the patterns and processes underlying the uneven distribution of biodiversity across space constitutes a major scientific challenge in systematic biology and biogeography, which largely relies on effectively mapping and making sense of rapidly increasing species occurrence data. There is thus an urgent need for making the process of coding species into spatial units faster, automated, transparent, and reproducible. Here we present SpeciesGeoCoder, an open-source software package written in Python and R, that allows for easy coding of species into user-defined operational units. These units may be of any size and be purely spatial (i.e., polygons) such as countries and states, conservation areas, biomes, islands, biodiversity hotspots, and areas of endemism, but may also include elevation ranges. This flexibility allows scoring species into complex categories, such as those encountered in topographically and ecologically heterogeneous landscapes. In addition, SpeciesGeoCoder can be used to facilitate sorting and cleaning of occurrence data obtained from online databases, and for testing the impact of incorrect identification of specimens on the spatial coding of species. The various outputs of SpeciesGeoCoder include quantitative biodiversity statistics, global and local distribution maps, and files that can be used directly in many phylogeny-based applications for ancestral range reconstruction, investigations of biome evolution, and other comparative methods. Our simulations indicate that even datasets containing hundreds of millions of records can be analyzed in relatively short time using a standard computer. We exemplify the use of SpeciesGeoCoder by inferring the historical dispersal of birds across the Isthmus of Panama, showing that lowland species crossed the Isthmus about twice as frequently as montane species with a marked increase in the number of dispersals during the last 10 million years. [ancestral area reconstruction; biodiversity

  20. Ecological impacts of non-native species

    Science.gov (United States)

    Wilkinson, John W.

    2012-01-01

    Non-native species are considered one of the greatest threats to freshwater biodiversity worldwide (Drake et al. 1989; Allen and Flecker 1993; Dudgeon et al. 2005). Some of the first hypotheses proposed to explain global patterns of amphibian declines included the effects of non-native species (Barinaga 1990; Blaustein and Wake 1990; Wake and Morowitz 1991). Evidence for the impact of non-native species on amphibians stems (1) from correlative research that relates the distribution or abundance of a species to that of a putative non-native species, and (2) from experimental tests of the effects of a non-native species on survival, growth, development or behaviour of a target species (Kats and Ferrer 2003). Over the past two decades, research on the effects of non-native species on amphibians has mostly focused on introduced aquatic predators, particularly fish. Recent research has shifted to more complex ecological relationships such as influences of sub-lethal stressors (e.g. contaminants) on the effects of non-native species (Linder et al. 2003; Sih et al. 2004), non-native species as vectors of disease (Daszak et al. 2004; Garner et al. 2006), hybridization between non-natives and native congeners (Riley et al. 2003; Storfer et al. 2004), and the alteration of food-webs by non-native species (Nystrom et al. 2001). Other research has examined the interaction of non-native species in terms of facilitation (i.e. one non-native enabling another to become established or spread) or the synergistic effects of multiple non-native species on native amphibians, the so-called invasional meltdown hypothesis (Simerloff and Von Holle 1999). Although there is evidence that some non-native species may interact (Ricciardi 2001), there has yet to be convincing evidence that such interactions have led to an accelerated increase in the number of non-native species and cumulative impacts are still uncertain (Simberloff 2006). Applied research on the control, eradication, and

  1. Co-occurrence of Mycoplasma Species and Pigeon Herpesvirus-1 Infection in Racing Pigeons ( Columba livia).

    Science.gov (United States)

    Hellebuyck, Tom; Göbel, Stephan; Pasmans, Frank; Adriaensen, Connie; Martel, An

    2017-12-01

    Oropharyngeal swab samples were collected from 438 live racing pigeons ( Columba livia), with and without signs of respiratory disease, that were housed in 220 lofts in 3 provinces in the western part of the Netherlands. Polymerase chain reaction (PCR) was used to identify Mycoplasma species and pigeon herpesvirus-1 (PHV-1) from the samples. In 8.6% of the pigeon lofts tested, signs of respiratory disease were present in pigeons at sampling, and in 30.9% of the sampled pigeon lofts, respiratory signs were observed in pigeons during the 6-month period immediately before sampling. A total of 39.8% of tested pigeons (54.5% of tested lofts) were positive for Mycoplasma species, and 30.6% of tested pigeons (48.6% of tested lofts) were positive for PHV-1. In 15.8% of the tested pigeons (26.8% of tested pigeon lofts), coinfection by Mycoplasma species and PHV-1 was identified. The number of pigeon lofts having pigeons coinfected by Mycoplasma species and PHV-1 was higher than that where only one of the infections was identified. Neither the presence of Mycoplasma species, PHV-1, nor the co-occurrence of both infections was significantly associated with signs of respiratory disease.

  2. Production of sophorolipids biosurfactants by multiple species of the Starmerella (Candida) bombicola yeast clade

    Science.gov (United States)

    Sophorolipid production was tested for 26 strains representing 19 species of the Starmerella yeast clade, including S. bombicola and Candida apicola, which were previously reported to produce sophorolipids. Five of the 19 species tested showed significant production of sophorolipids: S. bombicola, ...

  3. The relationship between species diversity and genetic structure in the rare Picea chihuahuana tree species community, Mexico.

    Science.gov (United States)

    Simental-Rodríguez, Sergio Leonel; Quiñones-Pérez, Carmen Zulema; Moya, Daniel; Hernández-Tecles, Enrique; López-Sánchez, Carlos Antonio; Wehenkel, Christian

    2014-01-01

    Species diversity and genetic diversity, the most basic elements of biodiversity, have long been treated as separate topics, although populations evolve within a community context. Recent studies on community genetics and ecology have suggested that genetic diversity is not completely independent of species diversity. The Mexican Picea chihuahuana Martínez is an endemic species listed as "Endangered" on the Red List. Forty populations of Chihuahua spruce have been identified. This species is often associated with tree species of eight genera in gallery forests. This rare Picea chihuahuana tree community covers an area no more than 300 ha and has been subject of several studies involving different topics such as ecology, genetic structure and climate change. The overall aim of these studies was to obtain a dataset for developing management tools to help decision makers implement preservation and conservation strategies. However, this unique forest tree community may also represent an excellent subject for helping us to understand the interplay between ecological and evolutionary processes in determining community structure and dynamics. The AFLP technique and species composition data were used together to test the hypothesis that species diversity is related to the adaptive genetic structure of some dominant tree species (Picea chihuahuana, Pinus strobiformis, Pseudotsuga menziesii and Populus tremuloides) of the Picea chihuahuana tree community at fourteen locations. The Hill numbers were used as a diversity measure. The results revealed a significant correlation between tree species diversity and genetic structure in Populus tremuloides. Because the relationship between the two levels of diversity was found to be positive for the putative adaptive AFLP detected, genetic and species structures of the tree community were possibly simultaneously adapted to a combination of ecological or environmental factors. The present findings indicate that interactions between

  4. Behavioral choice across leech species: chacun à son goût.

    Science.gov (United States)

    Gaudry, Q; Ruiz, N; Huang, T; Kristan, W B; Kristan, W B

    2010-04-01

    At any one time, animals are simultaneously bombarded with many sensory stimuli, but they typically choose to respond to only a few of them. We used multidimensional analysis to determine the behavioral responses of six species of leeches to stimulation, as the responses are affected by species identity, diet, behavioral state and stimulus location. Our results show that each of the species tested while not feeding displayed remarkably similar behaviors in response to tactile stimulation of the surface of the body. When not feeding, stimulus location was the most reliable factor in determining behavioral response. While feeding, the three sanguivorous (bloodsucking) species tested ignored stimulation, whereas the three carnivorous leeches abandoned feeding in favor of locomotory responses, regardless of phylogenetic relationships. In the sanguivorous leeches, feeding abolished all mechanically elicited responses and mechanical stimulation in turn had no effect on feeding. We also show that the behavioral hierarchy of leeches was fixed and unchanging even in species that can consume both a carnivorous and a sanguivorous diet.

  5. A comparative approach using ecotoxicological methods from single-species bioassays to model ecosystems.

    Science.gov (United States)

    Haegerbaeumer, Arne; Höss, Sebastian; Ristau, Kai; Claus, Evelyn; Möhlenkamp, Christel; Heininger, Peter; Traunspurger, Walter

    2016-12-01

    Soft sediments are often hotspots of chemical contamination, and a thorough ecotoxicological assessment of this habitat can help to identify the causes of stress and to improve the health of the respective ecosystems. As an important component of the ecologically relevant meiobenthic fauna, nematodes can be used for sediment assessments, with various assay tools ranging from single-species toxicity tests to field studies. In the present study, microcosms containing sediment were used to investigate direct and indirect effects of zinc on natural nematode assemblages, and acute community toxicity tests considering only direct toxicity were conducted. The responses of the various freshwater nematode species in both approaches were compared with those of Caenorhabditis elegans, determined in standardized tests (ISO 10872). At a median lethal concentration (LC50) of 20 mg Zn/L, C. elegans represented the median susceptibility of 15 examined nematode species examined in the acute community toxicity tests. In the microcosms, Zn affected the nematodes dose-dependently, with changes in species composition first detected at 13 mg Zn/kg to 19 mg Zn/kg sediment dry weight. The observed species sensitivities in the microcosms corresponded better to field observations than to the results of the acute community toxicity tests. Environ Toxicol Chem 2016;35:2987-2997. © 2016 SETAC. © 2016 SETAC.

  6. Sensitivity to zinc of Mediterranean woody species important for restoration.

    Science.gov (United States)

    Disante, Karen B; Fuentes, David; Cortina, Jordi

    2010-04-15

    Heavy metals have increased in natural woodlands and shrublands over the last several decades as a consequence of anthropogenic activities. However, our knowledge of the effects of these elements on woody species is scarce. In this study, we examined the responses of six Mediterranean woody species to increasing levels of zinc in hydroponic culture and discussed the possible implications for the restoration of contaminated sites. The species used, Pinus pinea L., Pinus pinaster Ait., Pinus halepensis Mill., Tetraclinis articulata (Vahl) Mast., Rhamnus alaternus L. and Quercus suber L. represent a climatic gradient from dry sub-humid to semi-arid conditions. Zinc concentrations in shoots ranged from 53 microg g(-1) in Q. suber to 382 microg g(-1) in T. articulata and were well below the levels found in roots. Zinc inhibited root elongation and root biomass and changed the root length distribution per diameter class, but the magnitude of the effects was species-specific. Only P. halepensis and Q. suber showed toxicity symptoms in aboveground parts. Species more characteristic from xeric environments (T. articulata, R. alaternus and P. halepensis) were more sensitive to zinc than species from mesic environments (Q. suber, P. pinaster and P. pinea). According to the Zn responses and bioaccumulation, Q. suber P. pinea and P. halepensis are the best candidates for field trials to test the value of woody species to restore contaminated sites. None of the species tested seemed suitable for phytoremediation. Copyright 2010 Elsevier B.V. All rights reserved.

  7. Antimicrobial effect of probiotics on bacterial species from dental plaque.

    Science.gov (United States)

    Zambori, Csilla; Morvay, Attila Alexandru; Sala, Claudia; Licker, Monica; Gurban, Camelia; Tanasie, Gabriela; Tirziu, Emil

    2016-03-31

    The antimicrobial role of probiotic Lactobacillus casei subspecies casei DG (L. casei DG) and of the mix culture of probiotic Lactobacillus acidophilus LA-5 and Bifidobacterium BB-12 was tested on species of Staphylococcus, Streptococcus, Pasteurella, and Neisseria genera from supragingival sites from dogs with dental disease of different breed, age, sex, weight, and diet. The research was conducted on these four genera because of their importance in zoonotic infections after dog bites. Species from Staphylococcus, Streptococcus, Pasteurella, and Neisseria genera were isolated and identified. To test the antimicrobial efficacy of L. casei DG and the mixed culture of probiotic L. acidophilus LA-5 and Bifidobacterium bifidum BB-12 on the pathogenic species, the agar overlay method was used. L. casei DG had a bactericidal effect on all analyzed species isolated from Staphylococcus, Streptococcus, Pasteurella, and Neisseria genera after 24 hours of incubation. The mixed probiotic culture made up of L. acidophilus LA-5 and Bifidobacterium BB-12 species had no bactericidal effect on the species of Staphylococcus and Streptococcus genera, which were resistant. However, it had a bacteriostatic effect on several species of Pasteurella and Neisseria genera. This work highlights the antimicrobial potential of probiotics in vitro, demonstrating that the probiotic L. casei DG has a bactericidal effect on all analyzed species isolated from dental plaque and that the mix culture of probiotic L. acidophilus LA-5 and Bifidobacterium BB-12 has only a bacteriostatic effect.

  8. Testing the Effectiveness of Environmental Variables to Explain European Terrestrial Vertebrate Species Richness across Biogeographical Scales.

    Directory of Open Access Journals (Sweden)

    Maud Mouchet

    Full Text Available We compared the effectiveness of environmental variables, and in particular of land-use indicators, to explain species richness patterns across taxonomic groups and biogeographical scales (i.e. overall pan-Europe and ecoregions within pan-Europe. Using boosted regression trees that handle non-linear relationships, we compared the relative influence (as a measure of effectiveness of environmental variables related to climate, landscape (or habitat heterogeneity, land-use intensity or energy availability to explain European vertebrate species richness (birds, amphibians, and mammals at the continental and ecoregion scales. We found that dominant land cover and actual evapotranspiration that relate to energy availability were the main correlates of vertebrate species richness over Europe. At the ecoregion scale, we identified four distinct groups of ecoregions where species richness was essentially associated to (i seasonality of temperature, (ii actual evapotranspiration and/or mean annual temperature, (iii seasonality of precipitation, actual evapotranspiration and land cover and (iv and an even combination of the environmental variables. This typology of ecoregions remained valid for total vertebrate richness and the three vertebrate groups taken separately. Despite the overwhelming influence of land cover and actual evapotranspiration to explain vertebrate species richness patterns at European scale, the ranking of the main correlates of species richness varied between regions. Interestingly, landscape and land-use indicators did not stand out at the continental scale but their influence greatly increased in southern ecoregions, revealing the long-lasting human footprint on land-use-land-cover changes. Our study provides one of the first multi-scale descriptions of the variability in the ranking of correlates across several taxa.

  9. Global variation in woodpecker species richness shaped by tree availability

    DEFF Research Database (Denmark)

    Ilsoe, Sigrid Kistrup; Kissling, W. Daniel; Fjeldsa, Jon

    2017-01-01

    . Location: Global. Methods: We used spatial and non-spatial regressions to test for relationships between broad-scale woodpecker species richness and predictor variables describing current and deep-time availability of trees, current climate, Quaternary climate change, human impact, topographical...... a negative indirect effect on woodpecker species richness. Main conclusions: Global species richness of woodpeckers is primarily shaped by current tree cover and precipitation, reflecting a strong biotic association between woodpeckers and trees. Human influence can have a negative effect on woodpecker....... As an example, woodpeckers (Picidae) are closely associated with trees and woody habitats because of multiple morphological and ecological specializations. In this study, we test whether this strong biotic association causes woodpecker diversity to be closely linked to tree availability at a global scale...

  10. Cytogenetic studies in some species of Bromus L., section Genea ...

    Indian Academy of Sciences (India)

    Unknown

    test performed between chromosome number and relative chiasmata values in Bromus species also did not show a significant correlation. Sticky chromosomes. Sticky chromosomes were observed from early stages of prophase and continued to the final stages of meiosis in. Table 1. Meiotic characters in Bromus species ...

  11. The toxicity of sulfolane and DIPA from sour gas plants to aquatic species

    International Nuclear Information System (INIS)

    Lintott, D.R.; Goudey, J.S.; Wilson, J.; Swanson, S.; Drury, C.

    1997-01-01

    The ecological effects of sulfolane and diisopropanolamine (DIPA), which are used to remove sulfur compounds from natural gas, were studied to establish risk-based cleanup criteria and to evaluate effective remedial measures. Toxicity tests were conducted on both the parent compounds and the thermal and biological degradation products. Toxicity testing focused on aquatic species because surface outlets, such as creeks, were found to be the major pathways for the water soluble DIPA and sulfolane chemicals. Sulfolane proved to be relatively non-toxic to aquatic species, with the exception of bacteria. DIPA was relatively toxic to algae at pH found in ground and surface waters. Aqueous and methanol reclaimer bottom extracts from five different gas plant sites were also tested using modified acute toxicity screening tests with different species. The reclaimer bottoms were found to be highly toxic to all species tested. DIPA and sulfolane did not entirely account for the toxicity of the reclaimer bottoms. Inorganic salts and metals present in reclaimer bottoms were found not to contribute to toxicity directly. The same was true for DIPA and sulfolane degradation products. 3 refs., 7 tabs., 8 figs

  12. The toxicity of sulfolane and DIPA from sour gas plants to aquatic species

    Energy Technology Data Exchange (ETDEWEB)

    Lintott, D.R.; Goudey, J.S. [HydroQual Consultants, Inc., Calgary, AB (Canada); Wilson, J.; Swanson, S. [Golder Associates, Calgary, AB (Canada); Drury, C. [Shell Canada Ltd., Calgary, AB (Canada). Calgary Research Centre

    1997-12-31

    The ecological effects of sulfolane and diisopropanolamine (DIPA), which are used to remove sulfur compounds from natural gas, were studied to establish risk-based cleanup criteria and to evaluate effective remedial measures. Toxicity tests were conducted on both the parent compounds and the thermal and biological degradation products. Toxicity testing focused on aquatic species because surface outlets, such as creeks, were found to be the major pathways for the water soluble DIPA and sulfolane chemicals. Sulfolane proved to be relatively non-toxic to aquatic species, with the exception of bacteria. DIPA was relatively toxic to algae at pH found in ground and surface waters. Aqueous and methanol reclaimer bottom extracts from five different gas plant sites were also tested using modified acute toxicity screening tests with different species. The reclaimer bottoms were found to be highly toxic to all species tested. DIPA and sulfolane did not entirely account for the toxicity of the reclaimer bottoms. Inorganic salts and metals present in reclaimer bottoms were found not to contribute to toxicity directly. The same was true for DIPA and sulfolane degradation products. 3 refs., 7 tabs., 8 figs.

  13. Effect of species rarity on the accuracy of species distribution models for reptiles and amphibians in southern California

    Science.gov (United States)

    Franklin, J.; Wejnert, K.E.; Hathaway, S.A.; Rochester, C.J.; Fisher, R.N.

    2009-01-01

    Aim: Several studies have found that more accurate predictive models of species' occurrences can be developed for rarer species; however, one recent study found the relationship between range size and model performance to be an artefact of sample prevalence, that is, the proportion of presence versus absence observations in the data used to train the model. We examined the effect of model type, species rarity class, species' survey frequency, detectability and manipulated sample prevalence on the accuracy of distribution models developed for 30 reptile and amphibian species. Location: Coastal southern California, USA. Methods: Classification trees, generalized additive models and generalized linear models were developed using species presence and absence data from 420 locations. Model performance was measured using sensitivity, specificity and the area under the curve (AUC) of the receiver-operating characteristic (ROC) plot based on twofold cross-validation, or on bootstrapping. Predictors included climate, terrain, soil and vegetation variables. Species were assigned to rarity classes by experts. The data were sampled to generate subsets with varying ratios of presences and absences to test for the effect of sample prevalence. Join count statistics were used to characterize spatial dependence in the prediction errors. Results: Species in classes with higher rarity were more accurately predicted than common species, and this effect was independent of sample prevalence. Although positive spatial autocorrelation remained in the prediction errors, it was weaker than was observed in the species occurrence data. The differences in accuracy among model types were slight. Main conclusions: Using a variety of modelling methods, more accurate species distribution models were developed for rarer than for more common species. This was presumably because it is difficult to discriminate suitable from unsuitable habitat for habitat generalists, and not as an artefact of the

  14. Novel and highly informative Capsicum SSR markers and their cross-species transferability.

    Science.gov (United States)

    Buso, G S C; Reis, A M M; Amaral, Z P S; Ferreira, M E

    2016-09-23

    This study was undertaken primarily to develop new simple sequence repeat (SSR) markers for Capsicum. As part of this project aimed at broadening the use of molecular tools in Capsicum breeding, two genomic libraries enriched for AG/TC repeat sequences were constructed for Capsicum annuum. A total of 475 DNA clones were sequenced from both libraries and 144 SSR markers were tested on cultivated and wild species of Capsicum. Forty-five SSR markers were randomly selected to genotype a panel of 48 accessions of the Capsicum germplasm bank. The number of alleles per locus ranged from 2 to 11, with an average of 6 alleles. The polymorphism information content was on average 0.60, ranging from 0.20 to 0.83. The cross-species transferability to seven cultivated and wild Capsicum species was tested with a set of 91 SSR markers. We found that a high proportion of the loci produced amplicons in all species tested. C. frutescens had the highest number of transferable markers, whereas the wild species had the lowest. Our results indicate that the new markers can be readily used in genetic analyses of Capsicum.

  15. 136-147 Enclosures to Enhance Woody Species Diversity in The ...

    African Journals Online (AJOL)

    *Corresponding author. E-mail: ... population structure in exclosure, and obstructed population structure in open area, showed favorable ... survival rate of planted species. ..... ANOVA test was employed to test the significance of ...... of Norway.

  16. Nutritional ecology of the formosan subterranean termite (Isoptera: Rhinotermitidae): feeding response to commercial wood species.

    Science.gov (United States)

    Morales-Ramos, J A; Rojas, M G

    2001-04-01

    The feeding preferences of the Formosan subterranean termite, Coptotermes formosanus Shiraki, were tested in three separate experiments on 28 different wood species. Experiment 1 was a multiple-choice test designed to test relative preferences among 24 wood species commercially available in New Orleans, LA. Experiment 2 was a similar study designed to test relative preferences among 21 wood species shown or reported to be unpalatable to the Formosan subterranean termite. Experiment 3 was a no-choice test to examine the feeding deterrence of the 10 least preferred wood species. Preference was determined by consumption rates. Birch (Betula alleghaniensis Britton), red gum (Liquidambar styraciflua L.), Parana pine [Araucaria angustifolia (Bert.) 1, sugar maple (Acer saccharum Marsh.), pecan (Carya illinoensis Wangenh.), and northern red oak (Quercus rubra L.) were the most preferred species by C. formosanus in order of consumption rate. All of these species were significantly more preferred than southern yellow pine (Pinus taeda L.), widely used for monitoring. Sinker cypress [ = old growth bald cypress, Taxodium distichum (L.)], western red cedar (Thuja plicata Donn), Alaskan yellow cedar (Chamaecyparis nootkatensis D. Don), eastern red cedar (Juniperus virginiana L.), sassafras [Sassafras albidum (Nutt.)], Spanish cedar (Cedrella odorata L.), Honduras mahogany (Swietenia macrophyla King), Indian rosewood (Dalbergia latifolia Roxb.), Honduras rosewood (D. stevensonii Standl.), and morado (Machaerium sp.) induced significant feeding deterrence and mortality to C. formosanus. The last eight species produced 100% mortality after 3 mo.

  17. Integrative taxonomy and preliminary assessment of species limits in the Liolaemus walkeri complex (Squamata, Liolaemidae with descriptions of three new species from Peru

    Directory of Open Access Journals (Sweden)

    Cesar Aguilar

    2013-12-01

    Full Text Available Species delimitation studies based on integrative taxonomic approaches have received considerable attention in the last few years, and have provided the strongest hypotheses of species boundaries. We used three lines of evidence (molecular, morphological, and niche envelopes to test for species boundaries in Peruvian populations of the Liolaemus walkeri complex. Our results show that different lines of evidence and analyses are congruent in different combinations, for unambiguous delimitation of three lineages that were “hidden” within known species, and now deserve species status. Our phylogenetic analysis shows that L. walkeri, L. tacnae and the three new species are strongly separated from other species assigned to the alticolor-bibronii group. Few conventional morphological characters distinguish the new species from closely related taxa and this highlights the need to integrate other sources of data to erect strong hypothesis of species limits. A taxonomic key for known Peruvian species of the subgenus Lioalemus is provided.

  18. Cross-species amplification of microsatellites in genera ...

    Indian Academy of Sciences (India)

    species in Chinese freshwater polyculture system. Accord- ing to several recent ... cephala transcriptome database were chosen to test their utility for ..... 2012BAD26B00) and Fundamental Research Funds for the Central. Universities (no.

  19. Phylogenetic Molecular Species Delimitations Unravel Potential New Species in the Pest Genus Spodoptera Guenée, 1852 (Lepidoptera, Noctuidae)

    Science.gov (United States)

    Dumas, Pascaline; Barbut, Jérôme; Le Ru, Bruno; Silvain, Jean-François; Clamens, Anne-Laure; d’Alençon, Emmanuelle; Kergoat, Gael J.

    2015-01-01

    Nowadays molecular species delimitation methods promote the identification of species boundaries within complex taxonomic groups by adopting innovative species concepts and theories (e.g. branching patterns, coalescence). As some of them can efficiently deal with large single-locus datasets, they could speed up the process of species discovery compared to more time consuming molecular methods, and benefit from the existence of large public datasets; these methods can also particularly favour scientific research and actions dealing with threatened or economically important taxa. In this study we aim to investigate and clarify the status of economically important moths species belonging to the genus Spodoptera (Lepidoptera, Noctuidae), a complex group in which previous phylogenetic analyses and integrative approaches already suggested the possible occurrence of cryptic species and taxonomic ambiguities. In this work, the effectiveness of innovative (and faster) species delimitation approaches to infer putative species boundaries has been successfully tested in Spodoptera, by processing the most comprehensive dataset (in terms of number of species and specimens) ever achieved; results are congruent and reliable, irrespective of the set of parameters and phylogenetic models applied. Our analyses confirm the existence of three potential new species clusters (for S. exigua (Hübner, 1808), S. frugiperda (J.E. Smith, 1797) and S. mauritia (Boisduval, 1833)) and support the synonymy of S. marima (Schaus, 1904) with S. ornithogalli (Guenée, 1852). They also highlight the ambiguity of the status of S. cosmiodes (Walker, 1858) and S. descoinsi Lalanne-Cassou & Silvain, 1994. This case study highlights the interest of molecular species delimitation methods as valuable tools for species discovery and to emphasize taxonomic ambiguities. PMID:25853412

  20. Phylogenetic molecular species delimitations unravel potential new species in the pest genus Spodoptera Guenée, 1852 (Lepidoptera, Noctuidae.

    Directory of Open Access Journals (Sweden)

    Pascaline Dumas

    Full Text Available Nowadays molecular species delimitation methods promote the identification of species boundaries within complex taxonomic groups by adopting innovative species concepts and theories (e.g. branching patterns, coalescence. As some of them can efficiently deal with large single-locus datasets, they could speed up the process of species discovery compared to more time consuming molecular methods, and benefit from the existence of large public datasets; these methods can also particularly favour scientific research and actions dealing with threatened or economically important taxa. In this study we aim to investigate and clarify the status of economically important moths species belonging to the genus Spodoptera (Lepidoptera, Noctuidae, a complex group in which previous phylogenetic analyses and integrative approaches already suggested the possible occurrence of cryptic species and taxonomic ambiguities. In this work, the effectiveness of innovative (and faster species delimitation approaches to infer putative species boundaries has been successfully tested in Spodoptera, by processing the most comprehensive dataset (in terms of number of species and specimens ever achieved; results are congruent and reliable, irrespective of the set of parameters and phylogenetic models applied. Our analyses confirm the existence of three potential new species clusters (for S. exigua (Hübner, 1808, S. frugiperda (J.E. Smith, 1797 and S. mauritia (Boisduval, 1833 and support the synonymy of S. marima (Schaus, 1904 with S. ornithogalli (Guenée, 1852. They also highlight the ambiguity of the status of S. cosmiodes (Walker, 1858 and S. descoinsi Lalanne-Cassou & Silvain, 1994. This case study highlights the interest of molecular species delimitation methods as valuable tools for species discovery and to emphasize taxonomic ambiguities.

  1. Use of abundance of one species as a surrogate for abundance of others

    Science.gov (United States)

    Samuel A. Cushman; Kevin S. McKelvey; Barry R. Noon; Kevin McGarigal

    2010-01-01

    Indicator species concepts have a long history in conservation biology. Arguments in favor of these approaches generally stress expediency and assume efficacy. We tested the premise that the abundance patterns of one species can be used to infer those of other species. Our data consisted of 72,495 bird observations on 55 species across 1046 plots distributed across 30...

  2. Microsatellite primers for a species of South African everlasting daisy (Helichrysum odoratissimum; Gnaphalieae, Asteraceae).

    Science.gov (United States)

    Glennon, Kelsey L; Cron, Glynis V

    2016-05-01

    Microsatellites were developed for the widespread Helichrysum odoratissimum (Asteraceae) to estimate gene flow across diploid populations and to test if gene flow occurs among other closely related lineages within this genus. Ten primer pairs were developed and tested using populations across South Africa; however, only seven primer pairs were polymorphic for the target species. The seven polymorphic primers amplified di- and trinucleotide repeats with up to 16 alleles per locus among 125 diploid individuals used for analyses. These markers can be used to estimate gene flow among populations of known ploidy level of H. odoratissimum to test evolutionary hypotheses. Furthermore, these markers amplify successfully in other Helichrysum species, including the other three taxonomic Group 4 species, and therefore can be used to inform taxonomic work on these species.

  3. Evaluation of Volatile Species in Green Monopropellant Project

    Science.gov (United States)

    Greene, Benjamin

    2015-01-01

    NASA is interested in green monopropellants to replace hydrazine in reaction control systems (RCSs). Some current NASA programs require reduced vapor pressure and low toxicity monopropellant (green) and superior performance (specific impulse and density) formulations. Earlier vapor phase studies of a candidate green monopropellant at the NASA White Sands Test Facility (WSTF) showed the presence of a volatile species that warranted further investigation. The purpose of this study was to further characterize the volatile species and to evaluate it. The evaluation was with respect to whether the volatile species was an impurity or how it is formed, and to use that information to examine whether its presence as an impurity can be eliminated during formulation. The evaluation also considered whether formation of the volatile impurity could be prevented while not compromising the propellant. To reduce variables associated with evaluation of the propellant formulation as a whole, a precursor to one of the individual components in the propellant formulation was subjected to a NASA Standard 6001B Flammability, Off-gassing, and Compatibility Requirements and Test Procedures "Determination of Off-gassed Products (Test 7)". Testing took place in the NASA WSTF Molecular Desorption and Analysis Laboratory. One gram of the precursor was placed in a flask within a specimen container. After thermal conditioning for 72 +/- 1 h at 50 +/- 3 deg C (122 +/- 5 deg F), the atmosphere inside the specimen container was analyzed for off-gassed compounds by cryotrap gas chromatography-mass spectrometry (GC-MS) and fixed sample loop GC-flame ionization detection (GC-FID). The specimen container used was glass to minimize potential catalytic surfaces. The identification of compounds was difficult due to the complexity of the vapor phase concentrations and overlapping chromatographic peaks and mass spectra. However, eleven compounds were specifically identified and five compounds or classes of

  4. Antifungal susceptibility testing of Aspergillus species complex in the Clinical Laboratory: how to do it, when to do it, and how to interpret it

    Directory of Open Access Journals (Sweden)

    Esther Manso

    2014-12-01

    Full Text Available The emergence of drug resistance in fungal pathogens has a profound impact on human health given limited number of antifungal drugs. Antifungal resistance in Aspergillus spp. infection can be encountered in the antifungal drug-exposed patient due to selection of intrinsically resistant species or isolates with acquired resistance belonging to species that are normally susceptible. Resistance to triazoles is not common in Aspergillus spp., however, triazole resistance in A. fumigatus appears to be increasing in several European countries in recent years and can be clinically relevant. The Clinical and Laboratory Standards Institute and European Committee on Antimicrobial Susceptibility Testing have developed breakpoints and epidemiological cutoff values that are now established for Aspergillus spp. Clinical microbiology laboratories will be employed commercial susceptibility assays, rather than reference broth microdilution methods and comparative studies are particularly important.

  5. The Pleurobemini (Bivalvia: Unionida) revisited: Molecular species delineation using a mitochondrial DNA gene reveals multiple conspecifics and undescribed species

    Science.gov (United States)

    Inoue, Kentaro; Hayes, David M.; Harris, John L.; Johnson, Nathan A.; Morrison, Cheryl L.; Eackles, Michael S.; King, Tim; Jones, Jess W.; Hallerman, Eric M.; Christian, Alan D.; Randklev, Charles R.

    2018-01-01

    The Pleurobemini (Bivalvia: Unionida) represent approximately one-third of freshwater mussel diversity in North America. Species identification within this group is challenging due to morphological convergence and phenotypic plasticity. Accurate species identification, including characterisation of currently unrecognised taxa, is required to develop effective conservation strategies because many species in the group are imperiled. We examined 575 cox1 sequences from 110 currently recognised species (including 13 Fusconaia and 21 Pleurobema species) to understand phylogenetic relationships among pleurobemine species (mainly Fusconaia and Pleurobema) and to delineate species boundaries. The results of phylogenetic analyses showed no geographic structure within widespread species and illustrated a close relationship between Elliptio lanceolata and Parvaspina collina. Constraint tests supported monophyly of the genera Fusconaia and Pleurobema, including the subgenus P. (Sintoxia). Furthermore, results revealed multiple conspecifics, including P. hanleyianum and P. troschelianum, P. chattanoogaense and P. decisum, P. clava and P. oviforme, P. rubrum and P. sintoxia, F. askewi and F. lananensis, and F. cerina and F. flava. Species delimitation analyses identified three currently unrecognised taxa (two in Fusconaia and one in Pleurobema). Further investigation using additional genetic markers and other lines of evidence (e.g. morphology, life history, ecology) are necessary before any taxonomic changes are formalised.

  6. Mannheimia Species Associated with Ovine Mastitis▿

    OpenAIRE

    Omaleki, Lida; Barber, Stuart R.; Allen, Joanne L.; Browning, Glenn F.

    2010-01-01

    Mannheimia glucosida, M. haemolytica, and M. ruminalis were isolated from cases of acute mastitis in ewes. M. glucosida was found to be a common cause of clinical mastitis in sheep. Selected phenotypic tests in addition to genotyping were needed to definitively identify Mannheimia species causing ovine mastitis.

  7. The loci recommended as universal barcodes for plants on the basis of floristic studies may not work with congeneric species as exemplified by DNA barcoding of Dendrobium species

    Directory of Open Access Journals (Sweden)

    Singh Hemant

    2012-01-01

    Full Text Available Abstract Background Based on the testing of several loci, predominantly against floristic backgrounds, individual or different combinations of loci have been suggested as possible universal DNA barcodes for plants. The present investigation was undertaken to check the applicability of the recommended locus/loci for congeneric species with Dendrobium species as an illustrative example. Results Six loci, matK, rbcL, rpoB, rpoC1, trnH-psbA spacer from the chloroplast genome and ITS, from the nuclear genome, were compared for their amplification, sequencing and species discrimination success rates among multiple accessions of 36 Dendrobium species. The trnH-psbA spacer could not be considered for analysis as good quality sequences were not obtained with its forward primer. Among the tested loci, ITS, recommended by some as a possible barcode for plants, provided 100% species identification. Another locus, matK, also recommended as a universal barcode for plants, resolved 80.56% species. ITS remained the best even when sequences of investigated loci of additional Dendrobium species available on the NCBI GenBank (93, 33, 20, 18 and 17 of ITS, matK, rbcL, rpoB and rpoC1, respectively were also considered for calculating the percent species resolution capabilities. The species discrimination of various combinations of the loci was also compared based on the 36 investigated species and additional 16 for which sequences of all the five loci were available on GenBank. Two-locus combination of matK+rbcL recommended by the Plant Working Group of Consortium for Barcoding of Life (CBOL could discriminate 86.11% of 36 species. The species discriminating ability of this barcode was reduced to 80.77% when additional sequences available on NCBI were included in the analysis. Among the recommended combinations, the barcode based on three loci - matK, rpoB and rpoC1- resolved maximum number of species. Conclusions Any recommended barcode based on the loci tested so

  8. The loci recommended as universal barcodes for plants on the basis of floristic studies may not work with congeneric species as exemplified by DNA barcoding of Dendrobium species.

    Science.gov (United States)

    Singh, Hemant Kumar; Parveen, Iffat; Raghuvanshi, Saurabh; Babbar, Shashi B

    2012-01-19

    Based on the testing of several loci, predominantly against floristic backgrounds, individual or different combinations of loci have been suggested as possible universal DNA barcodes for plants. The present investigation was undertaken to check the applicability of the recommended locus/loci for congeneric species with Dendrobium species as an illustrative example. Six loci, matK, rbcL, rpoB, rpoC1, trnH-psbA spacer from the chloroplast genome and ITS, from the nuclear genome, were compared for their amplification, sequencing and species discrimination success rates among multiple accessions of 36 Dendrobium species. The trnH-psbA spacer could not be considered for analysis as good quality sequences were not obtained with its forward primer. Among the tested loci, ITS, recommended by some as a possible barcode for plants, provided 100% species identification. Another locus, matK, also recommended as a universal barcode for plants, resolved 80.56% species. ITS remained the best even when sequences of investigated loci of additional Dendrobium species available on the NCBI GenBank (93, 33, 20, 18 and 17 of ITS, matK, rbcL, rpoB and rpoC1, respectively) were also considered for calculating the percent species resolution capabilities. The species discrimination of various combinations of the loci was also compared based on the 36 investigated species and additional 16 for which sequences of all the five loci were available on GenBank. Two-locus combination of matK+rbcL recommended by the Plant Working Group of Consortium for Barcoding of Life (CBOL) could discriminate 86.11% of 36 species. The species discriminating ability of this barcode was reduced to 80.77% when additional sequences available on NCBI were included in the analysis. Among the recommended combinations, the barcode based on three loci - matK, rpoB and rpoC1- resolved maximum number of species. Any recommended barcode based on the loci tested so far, is not likely to provide 100% species identification

  9. Molecular traceability of the species origin of meats using multiplex ...

    African Journals Online (AJOL)

    The objective of this study was the designing of a fast and reliable multiplex polymerase chain reaction (PCR) identification system for testing the pure and mixed species origin of meat samples. For conducting this research, different primers were designed for each species according to the conserved region of mitochondrial ...

  10. Measuring β-diversity with species abundance data.

    Science.gov (United States)

    Barwell, Louise J; Isaac, Nick J B; Kunin, William E

    2015-07-01

    In 2003, 24 presence-absence β-diversity metrics were reviewed and a number of trade-offs and redundancies identified. We present a parallel investigation into the performance of abundance-based metrics of β-diversity. β-diversity is a multi-faceted concept, central to spatial ecology. There are multiple metrics available to quantify it: the choice of metric is an important decision. We test 16 conceptual properties and two sampling properties of a β-diversity metric: metrics should be 1) independent of α-diversity and 2) cumulative along a gradient of species turnover. Similarity should be 3) probabilistic when assemblages are independently and identically distributed. Metrics should have 4) a minimum of zero and increase monotonically with the degree of 5) species turnover, 6) decoupling of species ranks and 7) evenness differences. However, complete species turnover should always generate greater values of β than extreme 8) rank shifts or 9) evenness differences. Metrics should 10) have a fixed upper limit, 11) symmetry (βA,B  = βB,A ), 12) double-zero asymmetry for double absences and double presences and 13) not decrease in a series of nested assemblages. Additionally, metrics should be independent of 14) species replication 15) the units of abundance and 16) differences in total abundance between sampling units. When samples are used to infer β-diversity, metrics should be 1) independent of sample sizes and 2) independent of unequal sample sizes. We test 29 metrics for these properties and five 'personality' properties. Thirteen metrics were outperformed or equalled across all conceptual and sampling properties. Differences in sensitivity to species' abundance lead to a performance trade-off between sample size bias and the ability to detect turnover among rare species. In general, abundance-based metrics are substantially less biased in the face of undersampling, although the presence-absence metric, βsim , performed well overall. Only

  11. Are range-size distributions consistent with species-level heritability?

    DEFF Research Database (Denmark)

    Borregaard, Michael Krabbe; Gotelli, Nicholas; Rahbek, Carsten

    2012-01-01

    The concept of species-level heritability is widely contested. Because it is most likely to apply to emergent, species-level traits, one of the central discussions has focused on the potential heritability of geographic range size. However, a central argument against range-size heritability has...... been that it is not compatible with the observed shape of present-day species range-size distributions (SRDs), a claim that has never been tested. To assess this claim, we used forward simulation of range-size evolution in clades with varying degrees of range-size heritability, and compared the output...

  12. Selecting a Conservation Surrogate Species for Small Fragmented Habitats Using Ecological Niche Modelling

    Directory of Open Access Journals (Sweden)

    K. Anne-Isola Nekaris

    2015-01-01

    Full Text Available Flagship species are traditionally large, charismatic animals used to rally conservation efforts. Accepted flagship definitions suggest they need only fulfil a strategic role, unlike umbrella species that are used to shelter cohabitant taxa. The criteria used to select both flagship and umbrella species may not stand up in the face of dramatic forest loss, where remaining fragments may only contain species that do not suit either set of criteria. The Cinderella species concept covers aesthetically pleasing and overlooked species that fulfil the criteria of flagships or umbrellas. Such species are also more likely to occur in fragmented habitats. We tested Cinderella criteria on mammals in the fragmented forests of the Sri Lankan Wet Zone. We selected taxa that fulfilled both strategic and ecological roles. We created a shortlist of ten species, and from a survey of local perceptions highlighted two finalists. We tested these for umbrella characteristics against the original shortlist, utilizing Maximum Entropy (MaxEnt modelling, and analysed distribution overlap using ArcGIS. The criteria highlighted Loris tardigradus tardigradus and Prionailurus viverrinus as finalists, with the former having highest flagship potential. We suggest Cinderella species can be effective conservation surrogates especially in habitats where traditional flagship species have been extirpated.

  13. Hichrom candida agar for identification of candida species

    OpenAIRE

    Baradkar V; Mathur M; Kumar S

    2010-01-01

    Chromogenic media are frequently used in direct and rapid identification of yeasts because different Candida species produce unique colors on these media. We used 60 isolates of Candida species including 30 C. albicans, 10 C. parapsilosis, 11 C. glabrata, five C. tropicalis, and four C. dubliniensis, isolated from various clinical specimens, to evaluate the performance of HiChrome Candida agar. These strains had been identified by germ tube test, morphology on cornmeal agar, chlamydospore for...

  14. Prevalence of Campylobacter species in wild birds of South Korea.

    Science.gov (United States)

    Kwon, Yong-Kuk; Oh, Jae-Young; Jeong, Ok-Mi; Moon, Oun-Kyoung; Kang, Min-Su; Jung, Byeong-Yeal; An, Byung-Ki; Youn, So-Youn; Kim, Hye-Ryoung; Jang, Il; Lee, Hee-Soo

    2017-10-01

    Campylobacter species cause human gastrointestinal infections worldwide. They commonly inhabit intestines of avian species including wild birds. They might play a role in the spread of infections to humans and other bird species. The prevalence of Campylobacter species in 2164 faecal samples of wild birds (representing 71 species and 28 families) captured across the Korean peninsula was evaluated in this study. The overall prevalence was 15.3% (332/2164). Bird species belonging to the family Charadriidae had the highest isolation rate (30.0%), followed by those belonging to the families Ardeidae (26.4%), Turdidae (21.9%), and Anatidae (15.3%). The prevalence of Campylobacter spp. differed significantly according to migratory habit. Stopover birds were the most commonly infected (19.0%), followed by winter migratory (16.7%) and summer migratory birds (12.3%). However, indigenous birds showed very low prevalence (2.7%). Antimicrobial susceptibility tests were performed for 213 isolates. Results showed that Campylobacter jejuni isolates (n = 169) exhibited resistance to nalidixic acid (5.3%), ciprofloxacin (3.0%), and tetracycline (1.8%), while Campylobacter lari (n = 1) displayed resistance to nalidixic acid and ciprofloxacin. However, all Campylobacter coli isolates (n = 20) were susceptible to all antimicrobials tested. This is the first report on the prevalence of Campylobacter species in wild birds that seasonally or indigenously inhabit the Korean peninsula. Our results indicate that the overall prevalence of Campylobacter in wild birds is moderate. Therefore, birds might serve as significant reservoirs for Campylobacter pathogens.

  15. Effects of Solutol (Kolliphor) and cremophor in polyethylene glycol 400 vehicle formulations in Sprague-Dawley rats and beagle dogs.

    Science.gov (United States)

    Stokes, Alan H; Kemp, Daniel C; Faiola, Brenda; Jordan, Holly L; Merrill, Christine L; Hailey, James R; Brown, Randy E; Bailey, David W

    2013-01-01

    When conventional vehicles (eg, methylcellulose and water) impart inadequate physical, chemical, and/or biological properties for proper toxicological assessment of test article formulations, nonconventional vehicles may be considered. Often toxicity data for nonconventional vehicle formulations are limited. Studies were conducted to collect toxicity data from a rodent and a non-rodent species given 2 nonconventional vehicles, Solutol HS15/polyethylene glycol (PEG) 400 and Cremophor RH40/PEG 400, with differing formulations and dose volumes (10 mL/kg for rats; 2 or 5 mL/kg for dogs). In rats, both vehicles caused increase in kidney weights (males only) and decrease in thymic weights (males only) without concurrent microscopic findings; altered urine electrolytes, minimally decreased serum electrolytes (males only), and increased serum total cholesterol (females only) were also present. The Cremophor formulation was also associated with increased serum urea (males only) and urine phosphorus: creatinine. For rats given the Solutol formulation, both genders had decreased urine glucose parameters and males had increased urine volume. In dogs, loose/watery feces and emesis were present given either vehicle, and mucus-cell hyperplasia of the ileum was present given the Solutol formulation. Increased red blood cell mass and decreased urine volume in dogs given 30% Solutol/70% PEG 400 (5 mL/kg/d) were likely due to subclinical dehydration and hemoconcentration. For the Cremophor formulations, dose volume-dependent increased incidence of minimal subepithelial gastric hemorrhage was noted in dogs, and dogs given 5 mL/kg/d showed increased serum urea nitrogen. Overall, regardless of the formulation or dose volume, neither vehicle produced overt toxicity in either species, but the Solutol formulation produced fewer effects in rats. Generally, lower dose volumes minimized the severity and/or incidence of findings.

  16. Relating tree growth to rainfall in Bolivian rain forests: a test for six species using tree ring analysis.

    Science.gov (United States)

    Brienen, Roel J W; Zuidema, Pieter A

    2005-11-01

    Many tropical regions show one distinct dry season. Often, this seasonality induces cambial dormancy of trees, particularly if these belong to deciduous species. This will often lead to the formation of annual rings. The aim of this study was to determine whether tree species in the Bolivian Amazon region form annual rings and to study the influence of the total amount and seasonal distribution of rainfall on diameter growth. Ring widths were measured on stem discs of a total of 154 trees belonging to six rain forest species. By correlating ring width and monthly rainfall data we proved the annual character of the tree rings for four of our study species. For two other species the annual character was proved by counting rings on trees of known age and by radiocarbon dating. The results of the climate-growth analysis show a positive relationship between tree growth and rainfall in certain periods of the year, indicating that rainfall plays a major role in tree growth. Three species showed a strong relationship with rainfall at the beginning of the rainy season, while one species is most sensitive to the rainfall at the end of the previous growing season. These results clearly demonstrate that tree ring analysis can be successfully applied in the tropics and that it is a promising method for various research disciplines.

  17. Upscaling species richness and abundances in tropical forests.

    Science.gov (United States)

    Tovo, Anna; Suweis, Samir; Formentin, Marco; Favretti, Marco; Volkov, Igor; Banavar, Jayanth R; Azaele, Sandro; Maritan, Amos

    2017-10-01

    The quantification of tropical tree biodiversity worldwide remains an open and challenging problem. More than two-fifths of the number of worldwide trees can be found either in tropical or in subtropical forests, but only ≈0.000067% of species identities are known. We introduce an analytical framework that provides robust and accurate estimates of species richness and abundances in biodiversity-rich ecosystems, as confirmed by tests performed on both in silico-generated and real forests. Our analysis shows that the approach outperforms other methods. In particular, we find that upscaling methods based on the log-series species distribution systematically overestimate the number of species and abundances of the rare species. We finally apply our new framework on 15 empirical tropical forest plots and quantify the minimum percentage cover that should be sampled to achieve a given average confidence interval in the upscaled estimate of biodiversity. Our theoretical framework confirms that the forests studied are comprised of a large number of rare or hyper-rare species. This is a signature of critical-like behavior of species-rich ecosystems and can provide a buffer against extinction.

  18. Reproductive interference explains persistence of aggression between species.

    Science.gov (United States)

    Drury, Jonathan P; Okamoto, Kenichi W; Anderson, Christopher N; Grether, Gregory F

    2015-04-07

    Interspecific territoriality occurs when individuals of different species fight over space, and may arise spontaneously when populations of closely related territorial species first come into contact. But defence of space is costly, and unless the benefits of excluding heterospecifics exceed the costs, natural selection should favour divergence in competitor recognition until the species no longer interact aggressively. Ordinarily males of different species do not compete for mates, but when males cannot distinguish females of sympatric species, females may effectively become a shared resource. We model how reproductive interference caused by undiscriminating males can prevent interspecific divergence, or even cause convergence, in traits used to recognize competitors. We then test the model in a genus of visually orienting insects and show that, as predicted by the model, differences between species pairs in the level of reproductive interference, which is causally related to species differences in female coloration, are strongly predictive of the current level of interspecific aggression. Interspecific reproductive interference is very common and we discuss how it may account for the persistence of interspecific aggression in many taxonomic groups. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

  19. Microsatellite Loci for Orthophytum ophiuroides (Bromelioideae, Bromeliaceae Species Adapted to Neotropical Rock Outcrops

    Directory of Open Access Journals (Sweden)

    Felipe Aoki-Gonçalves

    2014-03-01

    Full Text Available Premise of the study: Microsatellite primers were developed for Orthophytum ophiuroides, a rupicolous bromeliad species endemic to neotropical rocky fields. These microsatellite loci will be used to investigate population differentiation and species cohesion in such fragmented environments. The loci were tested for cross-amplification in related bromeliad species. Methods and Results: Eleven polymorphic microsatellite markers were isolated and characterized from an enriched library of O. ophiuroides. The loci were tested on 42 individuals from two populations of this species. The number of alleles per locus ranged from three to nine and the expected and observed heterozygosities ranged from 0.167 to 0.870 and from 0.369 to 0.958, respectively. Seven loci successfully amplified in other related bromeliad species. Conclusions: Our results suggest that the microsatellite loci developed here will be useful to assess genetic diversity and gene flow in O. ophiuroides for the investigation of population differentiation and species cohesion in neotropical mountainous habitats.

  20. Evaluation of the Thermo Scientific™ SureTect™ Salmonella species Assay.

    Science.gov (United States)

    Cloke, Jonathan; Clark, Dorn; Radcliff, Roy; Leon-Velarde, Carlos; Larson, Nathan; Dave, Keron; Evans, Katharine; Crabtree, David; Hughes, Annette; Simpson, Helen; Holopainen, Jani; Wickstrand, Nina; Kauppinen, Mikko

    2014-03-01

    The Thermo Scientific™ SureTect™ Salmonella species Assay is a new real-time PCR assay for the detection of Salmonellae in food and environmental samples. This validation study was conducted using the AOAC Research Institute (RI) Performance Tested MethodsSM program to validate the SureTect Salmonella species Assay in comparison to the reference method detailed in International Organization for Standardization 6579:2002 in a variety of food matrixes, namely, raw ground beef, raw chicken breast, raw ground pork, fresh bagged lettuce, pork frankfurters, nonfat dried milk powder, cooked peeled shrimp, pasteurized liquid whole egg, ready-to-eat meal containing beef, and stainless steel surface samples. With the exception of liquid whole egg and fresh bagged lettuce, which were tested in-house, all matrixes were tested by Marshfield Food Safety, Marshfield, WI, on behalf of Thermo Fisher Scientific. In addition, three matrixes (pork frankfurters, lettuce, and stainless steel surface samples) were analyzed independently as part of the AOAC-RI-controlled laboratory study by the University of Guelph, Canada. No significant difference by probability of detection or McNemars Chi-squared statistical analysis was found between the candidate or reference methods for any of the food matrixes or environmental surface samples tested during the validation study. Inclusivity and exclusivity testing was conducted with 117 and 36 isolates, respectively, which demonstrated that the SureTect Salmonella species Assay was able to detect all the major groups of Salmonella enterica subspecies enterica (e.g., Typhimurium) and the less common subspecies of S. enterica (e.g., arizoniae) and the rarely encountered S. bongori. None of the exclusivity isolates analyzed were detected by the SureTect Salmonella species Assay. Ruggedness testing was conducted to evaluate the performance of the assay with specific method deviations outside of the recommended parameters open to variation

  1. Umbrellas can work under water: Using threatened species as indicator and management surrogates can improve coastal conservation

    Science.gov (United States)

    Gilby, Ben L.; Olds, Andrew D.; Connolly, Rod M.; Yabsley, Nicholas A.; Maxwell, Paul S.; Tibbetts, Ian R.; Schoeman, David S.; Schlacher, Thomas A.

    2017-12-01

    Species surrogates, the use of particular species to index habitat condition or to represent ecological assemblages are commonly identified in many ecosystems, but are less tested, and therefore less employed in estuaries. Estuaries provide important ecosystem goods (e.g. harvestable species) and services (e.g. carbon processing, coastal armouring), but require protection from multiple human activities, meaning that finding surrogates for estuarine condition or faunal assemblages is a significant knowledge gap. In this study, we test the efficacy of the threatened estuary ray Hemitrygon fluviorum, as a suitable indicator of ecosystem condition and management umbrella surrogate species for conservation prioritisation and monitoring purposes within estuaries. We surveyed fish assemblages and ray presence at ten sites within each of 22 estuaries in southeast Queensland, Australia, using one hour deployments of baited video arrays. We then tested for correlations between ray presence, a series of environmental variables considered important to ecosystem management within estuaries (i.e. testing rays as indicator species), and the co-occurring fish species (i.e. testing rays as umbrella species). Estuary rays function as both umbrella species and ecological indicators of habitat status in subtropical Australian estuaries. As umbrellas, ray occurrence concords with elevated species richness. As ecological indicators, ray distribution concords with habitats of good water quality (especially low turbidity) and more natural vegetation remaining in the catchment. These results highlight the potential for other threatened aquatic vertebrates that are both readily detectable and that are reliable proxies for ecosystems status to be become useful management tools in estuaries. The protection of such large, threatened species in coastal seascapes allows managers to address multiple targets for conservation, especially; (1) protecting species of conservation concern; (2

  2. In vitro evaluation of single- and multi-strain probiotics: Inter-species inhibition between probiotic strains, and inhibition of pathogens.

    Science.gov (United States)

    Chapman, C M C; Gibson, G R; Rowland, I

    2012-08-01

    Many studies comparing the effects of single- and multi-strain probiotics on pathogen inhibition compare treatments with different concentrations. They also do not examine the possibility of inhibition between probiotic strains with a mixture. We tested the ability of 14 single-species probiotics to inhibit each other using a cross-streak assay, and agar spot test. We then tested the ability of 15 single-species probiotics and 5 probiotic mixtures to inhibit Clostridium difficile, Escherichia coli and S. typhimurium, using the agar spot test. Testing was done with mixtures created in two ways: one group contained component species incubated together, the other group of mixtures was made using component species which had been incubated separately, equalised to equal optical density, and then mixed in equal volumes. Inhibition was observed for all combinations of probiotics, suggesting that when used as such there may be inhibition between probiotics, potentially reducing efficacy of the mixture. Significant inter-species variation was seen against each pathogen. When single species were tested against mixtures, the multi-species preparations displayed significantly (p probiotic species will inhibit each other when incubated together in vitro, in many cases a probiotic mixture was more effective at inhibiting pathogens than its component species when tested at approximately equal concentrations of biomass. This suggests that using a probiotic mixture might be more effective at reducing gastrointestinal infections, and that creating a mixture using species with different effects against different pathogens may have a broader spectrum of action that a single provided by a single strain. Copyright © 2012 Elsevier Ltd. All rights reserved.

  3. Behavior of sulfur species in steam generator conditions of PWRs - towards an update of the secondary side corrosion cracking model based on laboratory tests in sulfate environments

    International Nuclear Information System (INIS)

    Mansour, C.; Legras, L.; Catalette, H.; Lefevre, G.; Fedoroff, M.; Pavageau, E.-M.

    2007-01-01

    Secondary side corrosion cracking affects Mill Annealed Alloy 600 steam generator (SG) tubes of PWRs in flow restricted areas where pollutants, such as sulfate, can concentrate and form various aggressive local environments. The 'sulfate model', based on laboratory tests in sulfate environments, was developed to predict the degradation of SG tubes. Such prediction is aimed to be done after having evaluated the chemistry in the flow restricted areas where the degradation occurs. For such purpose, a better knowledge of the behavior of sulfur species in SG conditions is needed. After a brief description of the sulfate model, this paper focuses on the latest experimental results that have been obtained : sorption of sulfur species over magnetite in SG temperature conditions, thermodynamical calculations as well as transmission electron microscopy and X-ray photoelectron spectroscopy observations of magnetite after sorption and C-Ring specimens tested in sulfate environments. Then, all these results are discussed in order to contribute to a better understanding of the secondary side corrosion cracking of SG tubes. (author)

  4. Environmental species sorting dominates forest-bird community assembly across scales.

    Science.gov (United States)

    Özkan, Korhan; Svenning, Jens-Christian; Jeppesen, Erik

    2013-01-01

    Environmental species sorting and dispersal are seen as key factors in community assembly, but their relative importance and scale dependence remain uncertain, as the extent to which communities are consistently assembled throughout their biomes. To address these issues, we analysed bird metacommunity structure in a 1200-km(2) forested landscape (Istranca Forests) in Turkish Thrace at the margin of the Western Palaearctic (WP) temperate-forest biome. First, we used spatial regressions and Mantel tests to assess the relative importance of environmental and spatial factors as drivers of local species richness and composition within the metacommunity. Second, we analysed species' abundance-occupancy relationship across the metacommunity and used null models to assess whether occupancy is determined by species' environmental niches. Third, we used generalized linear models to test for links between species' metacommunity-wide occupancy and their broader WP regional populations and assessed whether these links are consistent with environmental species sorting. There was strong environmental control on local species richness and composition patterns within the metacommunity, but non-environmental spatial factors had also an important joint role. Null model analyses on randomized communities showed that species' occupancy across the metacommunity was strongly determined by species' environmental niches, with occupancy being related to niche position marginality. Species' metacommunity-wide occupancy correlated with their local abundance as well as with their range size and total abundance for the whole WP, suggesting that the same assembly mechanisms act consistently across local to regional scales. A species specialization index that was estimated by bird species' habitat use across France, incorporating both niche position and breadth, was significantly related to species' occupancy and abundance at both metacommunity and WP regional scales. Hence, the same niche

  5. Codivergence and multiple host species use by fig wasp populations of the Ficus pollination mutualism

    Directory of Open Access Journals (Sweden)

    McLeish Michael J

    2012-01-01

    Full Text Available Abstract Background The interaction between insects and plants takes myriad forms in the generation of spectacular diversity. In this association a species host range is fundamental and often measured using an estimate of phylogenetic concordance between species. Pollinating fig wasps display extreme host species specificity, but the intraspecific variation in empirical accounts of host affiliation has previously been underestimated. In this investigation, lineage delimitation and codiversification tests are used to generate and discuss hypotheses elucidating on pollinating fig wasp associations with Ficus. Results Statistical parsimony and AMOVA revealed deep divergences at the COI locus within several pollinating fig wasp species that persist on the same host Ficus species. Changes in branching patterns estimated using the generalized mixed Yule coalescent test indicated lineage duplication on the same Ficus species. Conversely, Elisabethiella and Alfonsiella fig wasp species are able to reproduce on multiple, but closely related host fig species. Tree reconciliation tests indicate significant codiversification as well as significant incongruence between fig wasp and Ficus phylogenies. Conclusions The findings demonstrate more relaxed pollinating fig wasp host specificity than previously appreciated. Evolutionarily conservative host associations have been tempered by horizontal transfer and lineage duplication among closely related Ficus species. Independent and asynchronistic diversification of pollinating fig wasps is best explained by a combination of both sympatric and allopatric models of speciation. Pollinator host preference constraints permit reproduction on closely related Ficus species, but uncertainty of the frequency and duration of these associations requires better resolution.

  6. Evolutionary relationships between Rhynchosporium lolii sp. nov. and other Rhynchosporium species on grasses.

    Directory of Open Access Journals (Sweden)

    Kevin M King

    Full Text Available The fungal genus Rhynchosporium (causative agent of leaf blotch contains several host-specialised species, including R. commune (colonising barley and brome-grass, R. agropyri (couch-grass, R. secalis (rye and triticale and the more distantly related R. orthosporum (cocksfoot. This study used molecular fingerprinting, multilocus DNA sequence data, conidial morphology, host range tests and scanning electron microscopy to investigate the relationship between Rhynchosporium species on ryegrasses, both economically important forage grasses and common wild grasses in many cereal growing areas, and other plant species. Two different types of Rhynchosporium were found on ryegrasses in the UK. Firstly, there were isolates of R. commune that were pathogenic to both barley and Italian ryegrass. Secondly, there were isolates of a new species, here named R. lolii, that were pathogenic only to ryegrass species. R. lolii was most closely related to R. orthosporum, but exhibited clear molecular, morphological and host range differences. The species was estimated to have diverged from R. orthosporum ca. 5735 years before the present. The colonisation strategy of all of the different Rhynchosporium species involved extensive hyphal growth in the sub-cuticular regions of the leaves. Finally, new species-specific PCR diagnostic tests were developed that could distinguish between these five closely related Rhynchosporium species.

  7. Molecular detection of salmonella species from selected vegetables ...

    African Journals Online (AJOL)

    Molecular detection of salmonella species from selected vegetables sold in a north-central ... African Journal of Clinical and Experimental Microbiology ... of the pure isolates testing positive as being pathogenic after biochemical analysis.

  8. Antimicrobial properties of poriferan species from Indian waters

    Digital Repository Service at National Institute of Oceanography (India)

    Mokashe, S.S.; Tulaskar, A.S.; Venkat, K.; Wagh, A.B.

    Poriferan species belonging to Class Demospongiae were collected from the rocky intertidal pools of Ratnagiri (Maharashtra, India) and extracted with methanol. The methanol extracts were tested for antimicrobial activity against six fouling...

  9. Immunodiagnosis of Echinococcus Infections: Confirmatory Testing and Species Differentiation by a New Commercial Western Blot

    Science.gov (United States)

    Liance, Martine; Janin, Veronique; Bresson-Hadni, Solange; Vuitton, Dominique-Angele; Houin, Rene; Piarroux, Renaud

    2000-01-01

    The Echinococcus Western Blot IgG (LDBIO Diagnostics, Lyon, France), using a whole larval antigen from Echinococcus multilocularis, was evaluated for serodiagnosis and differentiation between two human parasitic infections of worldwide importance: cystic echinococcosis, due to Echinococcus granulosus, and alveolar echinococcosis, due to E. multilocularis. Fifty and 61 serum samples from patients with cystic and alveolar echinococcosis, respectively, were used for assessing diagnostic sensitivity. The sensitivity of the assay was compared with those of screening tests used for these applications. Sera used for assessing cross-reactivities were from 154 patients with other diseases, either parasitic or not. The assay allowed the detection of serum immunoglobulin G antibodies in 97% of Echinococcus-infected patients. It had a higher sensitivity than screening assays for the detection for each echinococcosis. The assay allowed us to correctly distinguish between E. granulosus- and E. multilocularis-infected patients in 76% of cases. It did not allow us to distinguish active from inactive forms of both echinococcoses. The occurrence of cross-reactivities with neurocysticercosis indicates the necessity for retesting sera with species-specific antigens, for rare patients with neurologic disorders. This study shows the usefulness of the commercially available Echinococcus Western Blot IgG for the serological confirmation of human echinococcosis. PMID:11015390

  10. Testing DNA barcodes in closely related species of Curcuma (Zingiberaceae) from Myanmar and China.

    Science.gov (United States)

    Chen, Juan; Zhao, Jietang; Erickson, David L; Xia, Nianhe; Kress, W John

    2015-03-01

    The genus Curcuma L. is commonly used as spices, medicines, dyes and ornamentals. Owing to its economic significance and lack of clear-cut morphological differences between species, this genus is an ideal case for developing DNA barcodes. In this study, four chloroplast DNA regions (matK, rbcL, trnH-psbA and trnL-F) and one nuclear region (ITS2) were generated for 44 Curcuma species and five species from closely related genera, represented by 96 samples. PCR amplification success rate, intra- and inter-specific genetic distance variation and the correct identification percentage were taken into account to assess candidate barcode regions. PCR and sequence success rate were high in matK (89.7%), rbcL (100%), trnH-psbA (100%), trnL-F (95.7%) and ITS2 (82.6%) regions. The results further showed that four candidate chloroplast barcoding regions (matK, rbcL, trnH-psbA and trnL-F) yield no barcode gaps, indicating that the genus Curcuma represents a challenging group for DNA barcoding. The ITS2 region presented large interspecific variation and provided the highest correct identification rates (46.7%) based on BLASTClust method among the five regions. However, the ITS2 only provided 7.9% based on NJ tree method. An increase in discriminatory power needs the development of more variable markers. © 2014 John Wiley & Sons Ltd.

  11. Holographic nondestructive testing in bone biomechanics

    Science.gov (United States)

    Silvennoinen, Raimo V. J.; Nygren, Kaarlo; Karna, Markku

    1992-08-01

    Holographic nondestructive testing (HNDT) is used to investigate the complex structures of bones of various shapes and sizes subjected to forces. During the course of the present study three antlered deer skulls of different species were investigated, and significant species- specific differences were observed. The HNDT method was also used to verify the advanced healing of an osteosynthetized sheep jawbone. Radioulnar bones of normal and orphaned moose calves were subjected to the bending test. Different bending dynamics were observed.

  12. Quantitative Adverse Outcome Pathways and their Utility to Ecological Risk Assessments of Endangered Species

    Science.gov (United States)

    Ecological risk assessments of endangered species are often hampered by a lack of knowledge about the sensitivity of endangered species to chemicals of concern. However, traditional in vivo toxicity testing of endangered species is often not possible for practical and ethical rea...

  13. Prevalence of different Malassezia species in pityriasis versicolor in central India.

    Science.gov (United States)

    Chaudhary, Rahul; Singh, Sanjay; Banerjee, Tuhina; Tilak, Ragini

    2010-01-01

    In the last 10 years, different studies have shown interesting geographical variations in the prevalence of different Malassezia species in pityriasis versicolor. Identification of Malassezia species isolated from patients with pityriasis versicolor. In 100 patients with pityriasis versicolor, Malassezia species were identified by culture in Sabouraud's dextrose agar containing cycloheximide with olive oil overlay and modified Dixon agar and by doing biochemical tests (catalase reaction, assimilation of glycine, and Tween utilisation tests). In 10 patients, 10% KOH smear was negative, while in 90 patients the smear showed characteristic "spaghetti and meatball" appearance. Of these 90 cases, growth was obtained on modified Dixon's agar in 87 cases. Fifty of the isolates (57.5%) were M. globosa, 15 (17.2%) were M. sympodialis, seven (8.0%) were suspected M. sympodialis, 6 (6.9%) each of the isolates were M. furfur and M. obtusa, and three (3.4%) isolates were M. restricta. M. globosa was the most common species, followed by M. sympodialis, M. furfur, M. obtusa, and M. restricta.

  14. Can a Single Amphibian Species Be a Good Biodiversity Indicator?

    Directory of Open Access Journals (Sweden)

    David Sewell

    2009-11-01

    Full Text Available Although amphibians have been widely promoted as indicators of biodiversity and environmental change, rigorous tests are lacking. Here key indicator criteria are distilled from published papers, and a species that has been promoted as a bioindicator, the great crested newt, is tested against them. Although a link was established between the presence of great crested newts and aquatic plant diversity, this was not repeated with the diversity of macroinvertebrates. Equally, amphibians do not meet many of the published criteria of bioindicators. Our research suggests that a suite of indicators, rather than a single species, will usually be required.

  15. Photoreactivation of UV-irradiated Legionella pneumophila and other Legionella species

    International Nuclear Information System (INIS)

    Knudson, G.B.

    1985-01-01

    Shortwave UV light was assessed as a feasible modality for the control of Legionnaires disease bacterium in water. The results of this study show that Legionella pneumophila and six other Legionella species are very sensitive to low doses of UV. However, all Legionella species tested effectively countered the germicidal effect of UV when subsequently exposed to photoreactivating light

  16. Testing the priority-of-access model in a seasonally breeding primate species

    OpenAIRE

    Dubuc, Constance; Muniz, Laura; Heistermann, Michael; Engelhardt, Antje; Widdig, Anja

    2011-01-01

    In mammals, when females are clumped in space, male access to receptive females is usually determined by a dominance hierarchy based on fighting ability. In polygynandrous primates, as opposed to most mammalian species, the strength of the relationship between male social status and reproductive success varies greatly. It has been proposed that the degree to which paternity is determined by male rank decreases with increasing female reproductive synchrony. The priority-of-access model (PoA) p...

  17. Characterization of Aspergillus species based on fatty acid profiles.

    Science.gov (United States)

    Fraga, Marcelo E; Santana, Djalva Maria N; Gatti, Mario Jorge; Direito, Gloria Maria; Cavaglieri, Lilia R; Rosa, Carlos Alberto R

    2008-09-01

    Cellular fatty acid (FA) composition was utilized as a taxonomic tool to discriminate between different Aspergillus species. Several of the tested species had the same FA composition and different relative FA concentrations. The most important FAs were palmitic acid (C16:0), estearic acid (C18:0), oleic acid (C18:1) and linoleic acid (C18:2), which represented 95% of Aspergillus FAs. Multivariate data analysis demonstrated that FA analysis is a useful tool for differentiating species belonging to genus Aspergillus. All the species analyzed showed significantly FA acid profiles (p < 0.001). Furthermore, it will be possible to distinguish among Aspergillus spp. in the Flavi Section. FA composition can serve as a useful tool for the identification of filamentous fungi.

  18. Detection and differentiation of the six Brucella species by polymerase chain reaction.

    Science.gov (United States)

    Sifuentes-Rincón, A M; Revol, A; Barrera-Saldaña, H A

    1997-11-01

    Brucelosis is a severe acute febrile disease caused by bacteria of the genus Brucella. Its current diagnosis is based on clinical observations that may be complemented by serology and microbiological culture tests; however, the former is limited in sensitivity and specificity, the latter is time consuming. To improve brucelosis diagnosis we developed a test which is specific and sensitive and is capable of differentiating the six species of Brucella. Four primers were designed from B. abortus sequences at the well-conserved Omp2 locus that are able to amplify the DNAs of all six species of Brucella. Our test detected all six species of Brucella. Their differentiation resulted directly from differences in the amplification patterns or was achieved indirectly using a RFLP present in one of the PCR products. The sensitivity and specificity of the new test were then determined; it was applied successfully in confirming the diagnosis of a patient whose clinical history and serology indicated infection with Brucella. The results make possible the use of a PCR test for Brucella detection and differentiation without relying on the measurement of the antibodies or microorganism culture. Our first results showed that the PCR test can confirm the presence of Brucella in blood samples of infected patients.

  19. Plant Size as Determinant of Species Richness of Herbivores, Natural Enemies and Pollinators across 21 Brassicaceae Species.

    Directory of Open Access Journals (Sweden)

    Hella Schlinkert

    Full Text Available Large plants are often more conspicuous and more attractive for associated animals than small plants, e.g. due to their wider range of resources. Therefore, plant size can positively affect species richness of associated animals, as shown for single groups of herbivores, but studies usually consider intraspecific size differences of plants in unstandardised environments. As comprehensive tests of interspecific plant size differences under standardised conditions are missing so far, we investigated effects of plant size on species richness of all associated arthropods using a common garden experiment with 21 Brassicaceae species covering a broad interspecific plant size gradient from 10 to 130 cm height. We recorded plant associated ecto- and endophagous herbivores, their natural enemies and pollinators on and in each aboveground plant organ, i.e. flowers, fruits, leaves and stems. Plant size (measured as height from the ground, the number of different plant organ entities and their biomass were assessed. Increasing plant size led to increased species richness of associated herbivores, natural enemies and pollinating insects. This pattern was found for ectophagous and endophagous herbivores, their natural enemies, as well as for herbivores associated with leaves and fruits and their natural enemies, independently of the additional positive effects of resource availability (i.e. organ biomass or number of entities and, regarding natural enemies, herbivore species richness. We found a lower R2 for pollinators compared to herbivores and natural enemies, probably caused by the high importance of flower characteristics for pollinator species richness besides plant size. Overall, the increase in plant height from 10 to 130 cm led to a 2.7-fold increase in predicted total arthropod species richness. In conclusion, plant size is a comprehensive driver of species richness of the plant associated arthropods, including pollinators, herbivores and their

  20. Widespread correlations between climatic niche evolution and species diversification in birds.

    Science.gov (United States)

    Cooney, Christopher R; Seddon, Nathalie; Tobias, Joseph A

    2016-07-01

    The adaptability of species' climatic niches can influence the dynamics of colonization and gene flow across climatic gradients, potentially increasing the likelihood of speciation or reducing extinction in the face of environmental change. However, previous comparative studies have tested these ideas using geographically, taxonomically and ecologically restricted samples, yielding mixed results, and thus the processes linking climatic niche evolution with diversification remain poorly understood. Focusing on birds, the largest and most widespread class of terrestrial vertebrates, we test whether variation in species diversification among clades is correlated with rates of climatic niche evolution and the extent to which these patterns are modified by underlying gradients in biogeography and species' ecology. We quantified climatic niches, latitudinal distribution and ecological traits for 7657 (˜75%) bird species based on geographical range polygons and then used Bayesian phylogenetic analyses to test whether niche evolution was related to species richness and rates of diversification across genus- and family-level clades. We found that the rate of climatic niche evolution has a positive linear relationship with both species richness and diversification rate at two different taxonomic levels (genus and family). Furthermore, this positive association between labile climatic niches and diversification was detected regardless of variation in clade latitude or key ecological traits. Our findings suggest either that rapid adaptation to unoccupied areas of climatic niche space promotes avian diversification, or that diversification promotes adaptation. Either way, we propose that climatic niche evolution is a fundamental process regulating the link between climate and biodiversity at global scales, irrespective of the geographical and ecological context of speciation and extinction. © 2016 The Authors. Journal of Animal Ecology © 2016 British Ecological Society.

  1. Hydraulic lift and tolerance to salinity of semiarid species: consequences for species interactions.

    Science.gov (United States)

    Armas, Cristina; Padilla, Francisco M; Pugnaire, Francisco I; Jackson, Robert B

    2010-01-01

    The different abilities of plant species to use ephemeral or permanent water sources strongly affect physiological performance and species coexistence in water-limited ecosystems. In addition to withstanding drought, plants in coastal habitats often have to withstand highly saline soils, an additional ecological stress. Here we tested whether observed competitive abilities and C-water relations of two interacting shrub species from an arid coastal system were more related to differences in root architecture or salinity tolerance. We explored water sources of interacting Juniperus phoenicea Guss. and Pistacia lentiscus L. plants by conducting physiology measurements, including water relations, CO2 exchange, photochemical efficiency, sap osmolality, and water and C isotopes. We also conducted parallel soil analyses that included electrical conductivity, humidity, and water isotopes. During drought, Pistacia shrubs relied primarily on permanent salty groundwater, while isolated Juniperus plants took up the scarce and relatively fresh water stored in upper soil layers. As drought progressed further, the physiological activity of Juniperus plants nearly stopped while Pistacia plants were only slightly affected. Juniperus plants growing with Pistacia had stem-water isotopes that matched Pistacia, unlike values for isolated Juniperus plants. This result suggests that Pistacia shrubs supplied water to nearby Juniperus plants through hydraulic lift. This lifted water, however, did not appear to benefit Juniperus plants, as their physiological performance with co-occurring Pistacia plants was poor, including lower water potentials and rates of photosynthesis than isolated plants. Juniperus was more salt sensitive than Pistacia, which withstood salinity levels similar to that of groundwater. Overall, the different abilities of the two species to use salty water appear to drive the outcome of their interaction, resulting in asymmetric competition where Juniperus is negatively

  2. Endangered Species

    Science.gov (United States)

    EPA's Endangered Species Protection Program helps promote recovery of listed species. The ESPP determines if pesticide use in a geographic area may affect any listed species. Find needed limits on pesticide use in Endangered Species Protection Bulletins.

  3. Species collapse via hybridization in Darwin's tree finches.

    Science.gov (United States)

    Kleindorfer, Sonia; O'Connor, Jody A; Dudaniec, Rachael Y; Myers, Steven A; Robertson, Jeremy; Sulloway, Frank J

    2014-03-01

    Species hybridization can lead to fitness costs, species collapse, and novel evolutionary trajectories in changing environments. Hybridization is predicted to be more common when environmental conditions change rapidly. Here, we test patterns of hybridization in three sympatric tree finch species (small tree finch Camarhynchus parvulus, medium tree finch Camarhynchus pauper, and large tree finch: Camarhynchus psittacula) that are currently recognized on Floreana Island, Galápagos Archipelago. Genetic analysis of microsatellite data from contemporary samples showed two genetic populations and one hybrid cluster in both 2005 and 2010; hybrid individuals were derived from genetic population 1 (small morph) and genetic population 2 (large morph). Females of the large and rare species were more likely to pair with males of the small common species. Finch populations differed in morphology in 1852-1906 compared with 2005/2010. An unsupervised clustering method showed (a) support for three morphological clusters in the historical tree finch sample (1852-1906), which is consistent with current species recognition; (b) support for two or three morphological clusters in 2005 with some (19%) hybridization; and (c) support for just two morphological clusters in 2010 with frequent (41%) hybridization. We discuss these findings in relation to species demarcations of Camarhynchus tree finches on Floreana Island.

  4. Seasonality effect on the allelopathy of cerrado species

    Directory of Open Access Journals (Sweden)

    AB Gatti

    Full Text Available The Brazilian cerrado presents strong climate seasonality. During the dry season, plants may be exposed to stressful situations, such as a soil surface water deficit, that stimulate their chemical defenses. However, the seasonality effect on the production of allelopathic compounds of cerrado plant species is poorly understood. In this study, the phytotoxic activities of common native cerrado plants were evaluated during rainy and dry seasons. Crude leaves extracts (10% concentration: weight/volume, with dry leaves and distilled water from eleven species were tested on lettuce and sesame germination. The negative effects on germination percentages, rates and informational entropies of the target species were higher when submitted to plant extracts from the dry season, where the germination rate was the most sensible parameter. The higher sensibility of lettuce and the germination rate parameter showed this difference. Only two exceptions had higher effects for rainy season extracts; one species showed higher negative effects on germination informational entropy of lettuce and another species on the germination rate of sesame. Thus, increases in the allelopathic activity were seen in the majority of the studied cerrado plant species during the dry season. These distinct responses to stressful situations in a complex environment such as the Brazilian cerrado may support the establishment and survival of some species.

  5. Development of a species-specific coproantigen ELISA for human Taenia solium taeniasis.

    Science.gov (United States)

    Guezala, Maria-Claudia; Rodriguez, Silvia; Zamora, Humberto; Garcia, Hector H; Gonzalez, Armando E; Tembo, Alice; Allan, James C; Craig, Philip S

    2009-09-01

    Taenia solium causes human neurocysticercosis and is endemic in underdeveloped countries where backyard pig keeping is common. Microscopic fecal diagnostic methods for human T. solium taeniasis are not very sensitive, and Taenia saginata and Taenia solium eggs are indistinguishable under the light microscope. Coproantigen (CoAg) ELISA methods are very sensitive, but currently only genus (Taenia) specific. This paper describes the development of a highly species-specific coproantigen ELISA test to detect T. solium intestinal taeniasis. Sensitivity was maintained using a capture antibody of rabbit IgG against T. solium adult whole worm somatic extract, whereas species specificity was achieved by utilization of an enzyme-conjugated rabbit IgG against T. solium adult excretory-secretory (ES) antigen. A known panel of positive and negative human fecal samples was tested with this hybrid sandwich ELISA. The ELISA test gave 100% specificity and 96.4% sensitivity for T. solium tapeworm carriers (N = 28), with a J index of 0.96. This simple ELISA incorporating anti-adult somatic and anti-adult ES antibodies provides the first potentially species-specific coproantigen test for human T. solium taeniasis.

  6. DNA-based species detection capabilities using laser transmission spectroscopy.

    Science.gov (United States)

    Mahon, A R; Barnes, M A; Li, F; Egan, S P; Tanner, C E; Ruggiero, S T; Feder, J L; Lodge, D M

    2013-01-06

    Early detection of invasive species is critical for effective biocontrol to mitigate potential ecological and economic damage. Laser transmission spectroscopy (LTS) is a powerful solution offering real-time, DNA-based species detection in the field. LTS can measure the size, shape and number of nanoparticles in a solution and was used here to detect size shifts resulting from hybridization of the polymerase chain reaction product to nanoparticles functionalized with species-specific oligonucleotide probes or with the species-specific oligonucleotide probes alone. We carried out a series of DNA detection experiments using the invasive freshwater quagga mussel (Dreissena bugensis) to evaluate the capability of the LTS platform for invasive species detection. Specifically, we tested LTS sensitivity to (i) DNA concentrations of a single target species, (ii) the presence of a target species within a mixed sample of other closely related species, (iii) species-specific functionalized nanoparticles versus species-specific oligonucleotide probes alone, and (iv) amplified DNA fragments versus unamplified genomic DNA. We demonstrate that LTS is a highly sensitive technique for rapid target species detection, with detection limits in the picomolar range, capable of successful identification in multispecies samples containing target and non-target species DNA. These results indicate that the LTS DNA detection platform will be useful for field application of target species. Additionally, we find that LTS detection is effective with species-specific oligonucleotide tags alone or when they are attached to polystyrene nanobeads and with both amplified and unamplified DNA, indicating that the technique may also have versatility for broader applications.

  7. Prevalence of Candida species in the buccal cavity of diabetic and non-diabetic individuals in and around Pondicherry.

    Science.gov (United States)

    Lydia Rajakumari, M; Saravana Kumari, P

    2016-12-01

    The aim of the present study was to determine the prevalence of Candida in the buccal cavity of diabetic and non-diabetic individuals in and around Pondicherry, India and to analyse the antifungal susceptibility profile of the selected isolates. A total of 400 buccal samples, 200 each from diabetic and non-diabetic healthy individuals were included in the study. Sabouraud's dextrose agar was used for isolation of Candida species. Identification was performed through microscopy, germ tube test, sugar fermentation test, sugar assimilation test and by using Hichrome agar. Distinct and phenotypically representative colonies were selected and subjected to ITS analysis. In vitro antifungal susceptibility testing for the isolated Candida species was performed using E-test. Results revealed that the prevalence of Candida species in diabetic individuals was higher when compared with non-diabetic healthy individuals. The most predominantly isolated species in diabetic and non-diabetic individuals from buccal cavity was Candida albicans. C. tropicalis was predominant among the non-albicans Candida isolated from both diabetic and non-diabetic individuals. Among denture wearers C. glabrata was predominant. In vitro antifungal susceptibility testing shows that ketoconazole, fluconazole and itraconazole were effective against the isolated Candida species. The rate of candidal carriage in diabetic individuals is higher. Different species of Candida are present in the oral cavity of diabetic individuals. There may be a positive correlation between glycemic control and candidal colonization. In vitro antifungal susceptibility testing of Candia species are required for proper management and treatment of candidal infections. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

  8. Biodegradation of 2,4-dinitrotoluene by different plant species.

    Science.gov (United States)

    Podlipná, Radka; Pospíšilová, Blanka; Vaněk, Tomáš

    2015-02-01

    Over the past century, rapid growth of population, mining and industrialization significantly contributed to extensive soil, air and water contamination. The 2,4-dinitrotoluene (2,4-DNT), used mostly as explosive, belongs to the hazardous xenobiotics. Soils and waters contaminated with 2,4-DNT may be cleaned by phytoremediation using suitable plant species. The ability of crop plants (hemp, flax, sunflower and mustard) to germinate and grow on soils contaminated with 2,4-DNT was compared. Stimulation of their growth was found at 0.252 mg/g 2,4-DNT. The lethal concentration for the growth for these species was around 1 mg/g. In hydropony, the above mentioned species were able to survive 200 mg/l 2,4-DNT, the concentration close to maximal solubility of 2,4-DNT in water. Metabolism of 2,4-DNT was tested using suspension culture of soapwort and reed. The degradation products 2-aminonitrotoluene and 4-aminonitrotoluene were found both in the medium and in the acetone extract of plant cells. The test showed that the toxicity of these metabolites was higher than the toxicity of the parent compound, but 2,4-diaminotoluene, the product of next reduction step, was less toxic in the concentration range tested (0-200 mg/l). Copyright © 2014. Published by Elsevier Inc.

  9. Applying species-energy theory to conservation: A case study for North American birds

    Science.gov (United States)

    Linda Bowers Phillips; Andrew J. Hansen; Curtis H. Flather; Jim Robinson-Cox

    2010-01-01

    Ecosystem energy is now recognized as a primary correlate and potential driver of global patterns of species richness. The increasingly well-tested species-energy relationship is now ripe for application to conservation, and recent advances in satellite technology make this more feasible. While the correlates for the species-energy relationship have been addressed many...

  10. Mollusc reproductive toxicity tests - Development and validation of test guidelines

    DEFF Research Database (Denmark)

    Ducrot, Virginie; Holbech, Henrik; Kinnberg, Karin Lund

    . Draft standard operating procedures (SOPs) have been designed based upon literature and expert knowledge from project partners. Pre-validation studies have been implemented to validate the proposed test conditions and identify issues in performing the SOPs and analyzing test results. Pre-validation work......The Organisation for Economic Cooperation and Development is promoting the development and validation of mollusc toxicity tests within its test guidelines programme, eventually aiming for the standardization of mollusc apical toxicity tests. Through collaborative work between academia, industry...... and stakeholders, this study aims to develop innovative partial life-cycle tests on the reproduction of the freshwater gastropods Potamopyrgus antipodarum and Lymnaea stagnalis, which are relevant candidate species for the standardization of mollusc apical toxicity tests assessing reprotoxic effects of chemicals...

  11. Site Release Report for C-Well Pipeline, UE-25 Large Rocks Test Site, and 29 GSF Test Pits

    International Nuclear Information System (INIS)

    K.E. Rasmuson

    2002-01-01

    The U.S. Department of Energy has implemented a program to reclaim lands disturbed by site characterization at Yucca Mountain. Long term goals of the program are to re-establish processes on disturbed sites that will lead to self-sustaining plant communities. The Biological Opinion for Yucca Mountain Site Characterization Studies required that the U.S. Department of Energy develop a Reclamation Standards and Monitoring Plan to evaluate the success of reclamation efforts. According to the Reclamation Standards and Monitoring Plan, reclaimed sites will be monitored periodically, remediated if necessary, and eventually compared to an appropriate reference area to determine whether reclamation goals have been achieved and the site can be released from further monitoring. Plant cover, density, and species richness (success parameters) on reclaimed sites are compared to 60 percent of the values (success criteria) for the same parameters on the reference area. Small sites (less than 0.1 ha) are evaluated for release using qualitative methods while large sites (greater than 0.1 ha) are evaluated using quantitative methods. In the summer of 2000, 31 small sites reclaimed in 1993 and 1994 were evaluated for reclamation success and potential release from further monitoring. Plant density, cover, and species richness were estimated on the C-Well Pipeline, UE-25 Large Rocks test site, and 29 ground surface facility test pits. Evidence of erosion, reproduction and natural recruitment, exotic species abundance, and animal use (key attributes) also were recorded for each site and used in success evaluations. The C-Well Pipeline and ground surface facility test pits were located in a ''Larrea tridentata - Ephedra nevadensis'' vegetation association while the UE-25 Large Rocks test site was located in an area dominated by ''Coleogyne ramosissima and Ephedra nevadensis''. Reference areas in the same vegetation associations with similar slope and aspect were chosen for comparison to

  12. Site Release Reports for C-Well Pipeline, UE-25 Large Rocks Test Site, and 29 GSF Test Pits

    Energy Technology Data Exchange (ETDEWEB)

    K.E. Rasmuson

    2002-04-02

    The U.S. Department of Energy has implemented a program to reclaim lands disturbed by site characterization at Yucca Mountain. Long term goals of the program are to re-establish processes on disturbed sites that will lead to self-sustaining plant communities. The Biological Opinion for Yucca Mountain Site Characterization Studies required that the U.S. Department of Energy develop a Reclamation Standards and Monitoring Plan to evaluate the success of reclamation efforts. According to the Reclamation Standards and Monitoring Plan, reclaimed sites will be monitored periodically, remediated if necessary, and eventually compared to an appropriate reference area to determine whether reclamation goals have been achieved and the site can be released from further monitoring. Plant cover, density, and species richness (success parameters) on reclaimed sites are compared to 60 percent of the values (success criteria) for the same parameters on the reference area. Small sites (less than 0.1 ha) are evaluated for release using qualitative methods while large sites (greater than 0.1 ha) are evaluated using quantitative methods. In the summer of 2000, 31 small sites reclaimed in 1993 and 1994 were evaluated for reclamation success and potential release from further monitoring. Plant density, cover, and species richness were estimated on the C-Well Pipeline, UE-25 Large Rocks test site, and 29 ground surface facility test pits. Evidence of erosion, reproduction and natural recruitment, exotic species abundance, and animal use (key attributes) also were recorded for each site and used in success evaluations. The C-Well Pipeline and ground surface facility test pits were located in a ''Larrea tridentata - Ephedra nevadensis'' vegetation association while the UE-25 Large Rocks test site was located in an area dominated by ''Coleogyne ramosissima and Ephedra nevadensis''. Reference areas in the same vegetation associations with similar slope

  13. Toxicological Response of Poecilia reticulata, Hyla species and ...

    African Journals Online (AJOL)

    PROF HORSFALL

    response of Poecilia reticulata, Hyla and Culex species was investigated using acute and chronic toxicity tests. ... responses over a 28 day period. .... sample. A control with only de-chlorinated tap water ..... landfills using luminescent bacteria.

  14. Identification of different bacterial species in biofilms using confocal Raman microscopy

    Science.gov (United States)

    Beier, Brooke D.; Quivey, Robert G.; Berger, Andrew J.

    2010-11-01

    Confocal Raman microspectroscopy is used to discriminate between different species of bacteria grown in biofilms. Tests are performed using two bacterial species, Streptococcus sanguinis and Streptococcus mutans, which are major components of oral plaque and of particular interest due to their association with healthy and cariogenic plaque, respectively. Dehydrated biofilms of these species are studied as a simplified model of dental plaque. A prediction model based on principal component analysis and logistic regression is calibrated using pure biofilms of each species and validated on pure biofilms grown months later, achieving 96% accuracy in prospective classification. When biofilms of the two species are partially mixed together, Raman-based identifications are achieved within ~2 μm of the boundaries between species with 97% accuracy. This combination of spatial resolution and predication accuracy should be suitable for forming images of species distributions within intact two-species biofilms.

  15. Bacillus subtilis Protects Public Goods by Extending Kin Discrimination to Closely Related Species.

    Science.gov (United States)

    Lyons, Nicholas A; Kolter, Roberto

    2017-07-05

    Kin discrimination systems are found in numerous communal contexts like multicellularity and are theorized to prevent exploitation of cooperative behaviors. The kin discrimination system in Bacillus subtilis differs from most other such systems because it excludes nonkin cells rather than including kin cells. Because nonkin are the target of the system, B. subtilis can potentially distinguish degrees of nonkin relatedness, not just kin versus nonkin. We examined this by testing a large strain collection of diverse Bacillus species against B. subtilis in different multicellular contexts. The effects of kin discrimination extend to nearby species, as the other subtilis clade species were treated with the same antagonism as nonkin. Species in the less-related pumilus clade started to display varied phenotypes but were mostly still discriminated against, while cereus clade members and beyond were no longer subject to kin discrimination. Seeking a reason why other species are perceived as antagonistic nonkin, we tested the ability of B. subtilis to steal communally produced surfactant from these species. We found that the species treated as nonkin were the only ones that made a surfactant that B. subtilis could utilize and that nonkin antagonism prevented such stealing when the two strains were mixed. The nonkin exclusion kin discrimination method thus allows effective protection of the cooperative behaviors prevalent in multicellularity while still permitting interactions with more distant species that are not a threat. IMPORTANCE Multicellular systems like bacterial biofilms and swarms rely on cooperative behaviors that could be undermined by exploitative invaders. Discriminating kin from nonkin is one way to help guard against such exploitation but has thus far been examined only intraspecifically, so the phylogenetic range of this important trait is unknown. We tested whether Bacillus subtilis treats other species as nonkin by testing a single strain against a

  16. Novel PCR Assays Complement Laser Biosensor-Based Method and Facilitate Listeria Species Detection from Food

    Directory of Open Access Journals (Sweden)

    Kwang-Pyo Kim

    2015-09-01

    Full Text Available The goal of this study was to develop the Listeria species-specific PCR assays based on a house-keeping gene (lmo1634 encoding alcohol acetaldehyde dehydrogenase (Aad, previously designated as Listeria adhesion protein (LAP, and compare results with a label-free light scattering sensor, BARDOT (bacterial rapid detection using optical scattering technology. PCR primer sets targeting the lap genes from the species of Listeria sensu stricto were designed and tested with 47 Listeria and 8 non-Listeria strains. The resulting PCR primer sets detected either all species of Listeria sensu stricto or individual L. innocua, L. ivanovii and L. seeligeri, L. welshimeri, and L. marthii without producing any amplified products from other bacteria tested. The PCR assays with Listeria sensu stricto-specific primers also successfully detected all species of Listeria sensu stricto and/or Listeria innocua from mixed culture-inoculated food samples, and each bacterium in food was verified by using the light scattering sensor that generated unique scatter signature for each species of Listeria tested. The PCR assays based on the house-keeping gene aad (lap can be used for detection of either all species of Listeria sensu stricto or certain individual Listeria species in a mixture from food with a detection limit of about 104 CFU/mL.

  17. Interspecific competition between alien and native congeneric species

    Science.gov (United States)

    Garcia-Serrano, H.; Sans, F. X.; Escarré, J.

    2007-01-01

    A good way to check hypotheses explaining the invasion of ecosystems by exotic plants is to compare alien and native congeneric species. To test the hypothesis that invasive alien plants are more competitive than natives, we designed a replacement series experiment to evaluate interspecific competition between three Senecio species representing the same bushy life form: two alien species ( S. inaequidens and S. pterophorus, both from South Africa) and a native species from the south-east of the Iberian Peninsula and Maghreb ( S. malacitanus). While S. inaequidens is widespread throughout western Europe and is expanding towards the south of Spanish-French border, the geographical distribution of the recently introduced S. pterophorus is still limited to north-eastern Spain. Plants from each species were grown in pure and in mixed cultures with one of their congeners, and water availability was manipulated to evaluate the effects of water stress on competitive abilities. Our results show that the alien S. inaequidens is the most competitive species for all water conditions. The native S. malacitanus is more competitive that the alien S. pterophorus in water stress conditions, but this situation is reversed when water availability is not limiting.

  18. Identification of cytosolic peroxisome proliferator binding protein as a member of the heat shock protein HSP70 family.

    Science.gov (United States)

    Alvares, K; Carrillo, A; Yuan, P M; Kawano, H; Morimoto, R I; Reddy, J K

    1990-01-01

    Clofibrate and many of its structural analogues induce proliferation of peroxisomes in the hepatic parenchymal cells of rodents and certain nonrodent species including primates. This induction is tissue specific, occurring mainly in the liver parenchymal cells and to a lesser extent in the kidney cortical epithelium. The induction of peroxisomes is associated with a predictable pleiotropic response, characterized by hepatomegaly, and increased activities and mRNA levels of certain peroxisomal enzymes. Using affinity chromatography, we had previously isolated a protein that binds to clofibric acid. We now show that this protein is homologous with the heat shock protein HSP70 family by analysis of amino acid sequences of isolated peptides from trypsin-treated clofibric acid binding protein and by cross-reactivity with a monoclonal antibody raised against the conserved region of the 70-kDa heat shock proteins. The clofibric acid-Sepharose column could bind HSP70 proteins isolated from various species, which could then be eluted with either clofibric acid or ATP. Conversely, when a rat liver cytosol containing multiple members of the HSP70 family was passed through an ATP-agarose column, and eluted with clofibric acid, only P72 (HSC70) was eluted. These results suggest that clofibric acid, a peroxisome proliferator, preferentially interacts with P72 at or near the ATP binding site. Images PMID:2371272

  19. Assessing Environmental Impact on Aquatic Macrophyte Species ...

    African Journals Online (AJOL)

    Impact of environmental variables on distribution and composition of aquatic macrophyte community in a tropical river was assessed for one year (March 2009 to February 2010). Hypothesis tested was that the spatial variation in environmental variables on the river's longitudinal gradient affects macrophyte species ...

  20. CLIMBING BEHAVIOUR IN THREE AFRICAN RODENT SPECIES ...

    African Journals Online (AJOL)

    These two species, but more no~ ably TIUlllomy8 ... covered by thin wire mesh. Three branches, two with rough bark and the third barkless, were ... Animals were tested during the dark phase of a reversed photoperiod (09hOO-17hOO of the.

  1. Molecular identification and in-vitro antifungal susceptibility testing of Candida species isolated from patients with onychomycosis

    Directory of Open Access Journals (Sweden)

    Keyvan Pakshir

    2015-03-01

    Full Text Available Background and Purpose: Candida species are the most opportunistic fungi affecting the nails and resulting in onychomycosis. In this study, we identified and evaluated in-vitro susceptibility of the recovered isolates against fluconazole (FLC, voriconazole (VRC, and clotrimazole (CLT using the Clinical and Laboratory Standards Institute (CLSI M27-A3 document. Materials and Methods: From patients with either clinically or mycologically proven onychomycosis, 97 isolates comprising of seven Candida species were isolated, which were identified by both conventional and molecular techniques such as polymerase chain reaction-restriction fragment length polymorphism. In addition, Candida dubliniensis was confirmed by restriction endonuclease analysis. Antifungal susceptibility of each isolate against the three azoles applied in this study was determined using the CLSI microdilution reference method M27-A3. Results: Candida parapsilosis (C. parapsilosis was the most frequently isolated species (n=44, followed by C. albicans (n=23, C. tropicalis (n=13, C. glabrata (n=7, C. krusei (n=6, C. guilliermondii (n=3, and C. dubliniensis (n=1. All the isolates were susceptible to CLT. VRC had lower minimum inhibitory concentration (MIC values for the isolates compared to FLC. Geometric mean MIC values of VRC, FLC, and CLT for C. parapsilosis isolates were 0.07 µg/ml, 0.8 µg/ml, and 0.35 µg/ml, respectively. Collectively, all species exhibited greater susceptibility to VRC in comparison to C. albicans (P≤0.001. Conclusion: This study showed that non-albicans Candida species were the most common etiologic agents of non-dermatophyte onychomycosis. The major antifungal agents used in clinics to empirically treat yeast onychomycosis are FLC and CLT. Our data suggested that CLT is a better choice for the treatment of Candida onychomycosis, especially in drug resistant cases.

  2. Characterization and susceptibility patterns of clinically important Enterococcus species in eastern Nepal.

    Science.gov (United States)

    Acharya, A; Khanal, A; Kanungo, R; Mohapatra, T

    2007-12-01

    Life threatening infections caused by enterococcus species with multidrug resistance has emerged as a threat to medical care in the present era. This study was conducted to characterize enterococcus species isolated from different clinical samples and to detect the pattern of susceptibility to some of the commonly used antibiotics in B.P Koirala Institute of Health Sciences (BPKIHS), a tertiary care hospital in eastern Nepal. Clinical samples submitted to the microbiology unit of Central Laboratory Service (CLS) for culture and sensitivity during March 2002 - February 2003 was analyzed. Enterococcus species were identified by colony characteristics, gram staining and relevant biochemical tests. Antibiotic susceptibility test was done by the Kirby Bauer disc diffusion technique. Of 50 Enterococcus species isolated, E. faecalis was the predominant isolate (48.0%) followed by E. faecium (32.0%) and E. avium (20.0%). Eighty-eight percent of E. faecalis showed sensitivity to cephotaxime and 87.0% to vancomycin. Multiple drug resistance was observed most commonly in E. faecium. Seventeen percent of E. faecium were resistant to vancomycin and 63.0% to ciprofloxacin and 44.0% to ampicillin. On the contrary E. avium rarely showed resistance to the antimicrobials tested including vancomycin. Enterococcal infections are common nowadays specially in hospitalized patients. Inappropriate use of antibiotics in clinical practice and poultry should be discouraged to prevent the emergence of multidrug resistant species.

  3. Disjunct populations of European vascular plant species keep the same climatic niches

    DEFF Research Database (Denmark)

    Wasof, Safaa; Lenoir, Jonathan; Aarrestad, Per Arild

    2015-01-01

    separated for thousands of years. Location: European Alps and Fennoscandia. Methods: Of the studied pool of 888 terrestrial vascular plant species occurring in both the Alps and Fennoscandia, we used two complementary approaches to test and quantify climatic-niche shifts for 31 species having strictly......Aim: Previous research on how climatic niches vary across species ranges has focused on a limited number of species, mostly invasive, and has not, to date, been very conclusive. Here we assess the degree of niche conservatism between distant populations of native alpine plant species that have been...... to be largely valid for arctic-alpine plants....

  4. Microsatellite primers for a species of South African everlasting daisy (Helichrysum odoratissimum; Gnaphalieae, Asteraceae)1

    Science.gov (United States)

    Glennon, Kelsey L.; Cron, Glynis V.

    2016-01-01

    Premise of the study: Microsatellites were developed for the widespread Helichrysum odoratissimum (Asteraceae) to estimate gene flow across diploid populations and to test if gene flow occurs among other closely related lineages within this genus. Methods and Results: Ten primer pairs were developed and tested using populations across South Africa; however, only seven primer pairs were polymorphic for the target species. The seven polymorphic primers amplified di- and trinucleotide repeats with up to 16 alleles per locus among 125 diploid individuals used for analyses. Conclusions: These markers can be used to estimate gene flow among populations of known ploidy level of H. odoratissimum to test evolutionary hypotheses. Furthermore, these markers amplify successfully in other Helichrysum species, including the other three taxonomic Group 4 species, and therefore can be used to inform taxonomic work on these species. PMID:27213125

  5. Germination and early plant development of ten plant species ...

    Science.gov (United States)

    Ten agronomic plant species were exposed to different concentrations of nano titanium dioxide (nTiO2) or nano cerium oxide (nCeO2) (0, 250, 500 and 1000 mg/L) to examine potential effects on germination and early seedling development. We modified a standard test protocol developed for soluble chemicals (OPPTS 850.4200) to determine if such an approach might be useful for screening engineered nanomaterials (ENMs) and whether there were differences in response across a range of commercially important plant species to two common metal oxide ENMs. Eight of 10 species responded to nTiO2, and 5 species responded to nCeO2. Overall, it appeared that early root growth may be a more sensitive indicator of potential effects from ENM exposure than germination. The observed effects did not always relate to the exposure concentration, indicating that mass-based concentration may not fully explain developmental effects of these two ENMs. The results suggest that nTiO2 and nCeO2 have different effects on early plant growth of agronomic species, which may alter the timing of specific developmental events during their life cycle. In addition, standard germination tests, which are commonly used for toxicity screening of new materials, may not detect the subtle but potentially more important changes associated with early growth and development in terrestrial plants. Engineered nanoparticles (ENMs) have been recognized as valuable components of new technologies and are current

  6. Species integrity enhanced by a predation cost to hybrids in the wild

    DEFF Research Database (Denmark)

    Nilsson, P. A.; Hulthén, Kaj; Chapman, Ben B.

    2017-01-01

    Species integrity can be challenged, and even eroded, if closely related species can hybridize and produce fertile offspring of comparable fitness to that of parental species. The maintenance of newly diverged or closely related species therefore hinges on the establishment and effectiveness of pre...... barrier to gene flow in the wild. Cyprinid fishes commonly produce fertile, viable hybrid offspring and therefore make excellent study organisms to investigate ecological costs to hybrids. We electronically tagged two freshwater cyprinid fish species (roach Rutilus rutilus and bream Abramis brama...... to directly test for a predation cost to hybrids in the wild. Hybrid individuals were found significantly more susceptible to cormorant predation than individuals from either parental species. Such ecological selection against hybrids contributes to species integrity, and can enhance species diversification....

  7. Competition, predation and species responses to environmental change

    Energy Technology Data Exchange (ETDEWEB)

    Jiang, Lin; Kulczychi, A. [Rutgers Univ., Cook College, Dept. of Ecology, Evolution and Natural Resources, New Brunswick, NJ (United States)

    2004-08-01

    Despite much effort over the past decade on the ecological consequences of global warming, ecologists still have little understanding of the importance of interspecific interactions in species responses to environmental change. Models predict that predation should mitigate species responses to environmental change, and that interspecific competition should aggravate species responses to environmental change. To test this prediction, we studied how predation and competition affected the responses of two ciliates, Colpidiumstriatum and Parameciumtetraurelia, to temperature change in laboratory microcosms. We found that neither predation nor competition altered the responses of Colpidiumstratum to temperature change, and that competition but not predation altered the responses of Paramecium tetraurelia to temperature change. Asymmetric interactions and temperature-dependent interactions may have contributed to the disparity between model predictions and experimental results. Our results suggest that models ignoring inherent complexities in ecological communities may be inadequate in forecasting species responses to environmental change. (au)

  8. Genetic diversity and differentiation in reef-building Millepora species, as revealed by cross-species amplification of fifteen novel microsatellite loci

    Directory of Open Access Journals (Sweden)

    Caroline E. Dubé

    2017-02-01

    Full Text Available Quantifying the genetic diversity in natural populations is crucial to address ecological and evolutionary questions. Despite recent advances in whole-genome sequencing, microsatellite markers have remained one of the most powerful tools for a myriad of population genetic approaches. Here, we used the 454 sequencing technique to develop microsatellite loci in the fire coral Millepora platyphylla, an important reef-builder of Indo-Pacific reefs. We tested the cross-species amplification of these loci in five other species of the genus Millepora and analysed its success in correlation with the genetic distances between species using mitochondrial 16S sequences. We succeeded in discovering fifteen microsatellite loci in our target species M. platyphylla, among which twelve were polymorphic with 2–13 alleles and a mean observed heterozygosity of 0.411. Cross-species amplification in the five other Millepora species revealed a high probability of amplification success (71% and polymorphism (59% of the loci. Our results show no evidence of decreased heterozygosity with increasing genetic distance. However, only one locus enabled measures of genetic diversity in the Caribbean species M. complanata due to high proportions of null alleles for most of the microsatellites. This result indicates that our novel markers may only be useful for the Indo-Pacific species of Millepora. Measures of genetic diversity revealed significant linkage disequilibrium, moderate levels of observed heterozygosity (0.323–0.496 and heterozygote deficiencies for the Indo-Pacific species. The accessibility to new polymorphic microsatellite markers for hydrozoan Millepora species creates new opportunities for future research on processes driving the complexity of their colonisation success on many Indo-Pacific reefs.

  9. Combinatorial Cis-regulation in Saccharomyces Species

    Directory of Open Access Journals (Sweden)

    Aaron T. Spivak

    2016-03-01

    Full Text Available Transcriptional control of gene expression requires interactions between the cis-regulatory elements (CREs controlling gene promoters. We developed a sensitive computational method to identify CRE combinations with conserved spacing that does not require genome alignments. When applied to seven sensu stricto and sensu lato Saccharomyces species, 80% of the predicted interactions displayed some evidence of combinatorial transcriptional behavior in several existing datasets including: (1 chromatin immunoprecipitation data for colocalization of transcription factors, (2 gene expression data for coexpression of predicted regulatory targets, and (3 gene ontology databases for common pathway membership of predicted regulatory targets. We tested several predicted CRE interactions with chromatin immunoprecipitation experiments in a wild-type strain and strains in which a predicted cofactor was deleted. Our experiments confirmed that transcription factor (TF occupancy at the promoters of the CRE combination target genes depends on the predicted cofactor while occupancy of other promoters is independent of the predicted cofactor. Our method has the additional advantage of identifying regulatory differences between species. By analyzing the S. cerevisiae and S. bayanus genomes, we identified differences in combinatorial cis-regulation between the species and showed that the predicted changes in gene regulation explain several of the species-specific differences seen in gene expression datasets. In some instances, the same CRE combinations appear to regulate genes involved in distinct biological processes in the two different species. The results of this research demonstrate that (1 combinatorial cis-regulation can be inferred by multi-genome analysis and (2 combinatorial cis-regulation can explain differences in gene expression between species.

  10. Ecological risk assessment of organic waste amendments using the species sensitivity distribution from a soil organisms test battery

    International Nuclear Information System (INIS)

    Domene, Xavier; Ramirez, Wilson; Mattana, Stefania; Alcaniz, Josep Maria; Andres, Pilar

    2008-01-01

    Safe amendment rates (the predicted no-effect concentration or PNEC) of seven organic wastes were estimated from the species sensitivity distribution of a battery of soil biota tests and compared with different realistic amendment scenarios (different predicted environmental concentrations or PEC). None of the wastes was expected to exert noxious effects on soil biota if applied according either to the usual maximum amendment rates in Europe or phosphorus demands of crops (below 2 tonnes DM ha -1 ). However, some of the wastes might be problematic if applied according to nitrogen demands of crops (above 2 tonnes DM ha -1 ). Ammonium content and organic matter stability of the studied wastes are the most influential determinants of the maximum amendment rates derived in this study, but not pollutant burden. This finding indicates the need to stabilize wastes prior to their reuse in soils in order to avoid short-term impacts on soil communities. - Ecological risk assessment of organic waste amendments

  11. Preliminary assessment of terrestrial microalgae isolated from lichens as testing species for environmental monitoring: lichen phycobionts present high sensitivity to environmental micropollutants.

    Science.gov (United States)

    Domínguez-Morueco, N; Moreno, H; Barreno, E; Catalá, M

    2014-01-01

    Bioassays constitute a tool for pollution analysis providing a holistic approach and high-quality indication of the toxicity. Microbioassays allow evaluating the toxicity of many samples, implying lower costs and enabling routine monitoring and pollution control. But tests conducted so far are limited to the use of a small number of taxa. Lichens are excellent bioindicators of pollution with great ecological significance. Studies show that the phycobiont is more sensitive to pollutants than the mycobiont. Phycobiont have features such as adaptation to anhydrobiosis and relatively rapid growth in vitro, making them suitable for microbioassays. Our aim is to determine the sensitivity of phycobionts to the pharmaceutical micropollutants carbamazepine and diclofenac as a preliminary step for the development of a toxicity microbioassay based on phycobionts. Optical dispersion and chlorophyll autofluorescence were used as endpoints of toxicity on two algal species showing that suspensions present cyclic and taxon specific patterns of aggregation. Trebouxia TR9 suspensions present a very high grade of aggregation while Asterochloris erici cells do not. Both micropollutants alter optical properties of the suspensions of both species. No significant alteration of chlorophyll autofluorescence by carbamazepine is observed. A. erici chlorophyll autofluorescence is extremely sensitive to diclofenac but the effect is not dependent on the drug concentration or on the time of exposure. Differently, TR9 only shows punctual chlorophyll alterations. Fluctuations in optical dispersion may indicate changes in the population structure of the species, including reproductive strategy. A. erici seems more sensitive to micropollutants, is better characterized and is available from commercial collections. © 2013 Published by Elsevier Inc.

  12. The nuclear question: rethinking species importance in multi-species animal groups.

    Science.gov (United States)

    Srinivasan, Umesh; Raza, Rashid Hasnain; Quader, Suhel

    2010-09-01

    1. Animals group for various benefits, and may form either simple single-species groups, or more complex multi-species associations. Multi-species groups are thought to provide anti-predator and foraging benefits to participant individuals. 2. Despite detailed studies on multi-species animal groups, the importance of species in group initiation and maintenance is still rated qualitatively as 'nuclear' (maintaining groups) or 'attendant' (species following nuclear species) based on species-specific traits. This overly simplifies and limits understanding of inherently complex associations, and is biologically unrealistic, because species roles in multi-species groups are: (i) likely to be context-specific and not simply a fixed species property, and (ii) much more variable than this dichotomy indicates. 3. We propose a new view of species importance (measured as number of inter-species associations), along a continuum from 'most nuclear' to 'least nuclear'. Using mixed-species bird flocks from a tropical rainforest in India as an example, we derive inter-species association measures from randomizations on bird species abundance data (which takes into account species 'availability') and data on 86 mixed-species flocks from two different flock types. Our results show that the number and average strength of inter-species associations covary positively, and we argue that species with many, strong associations are the most nuclear. 4. From our data, group size and foraging method are ecological and behavioural traits of species that best explain nuclearity in mixed-species bird flocks. Parallels have been observed in multi-species fish shoals, in which group size and foraging method, as well as diet, have been shown to correlate with nuclearity. Further, the context in which multi-species groups occur, in conjunction with species-specific traits, influences the role played by a species in a multi-species group, and this highlights the importance of extrinsic factors in

  13. Can species-specific prey responses to chemical cues explain prey susceptibility to predation?

    Science.gov (United States)

    Šmejkal, Marek; Ricard, Daniel; Sajdlová, Zuzana; Čech, Martin; Vejřík, Lukáš; Blabolil, Petr; Vejříková, Ivana; Prchalová, Marie; Vašek, Mojmír; Souza, Allan T; Brönmark, Christer; Peterka, Jiří

    2018-05-01

    The perception of danger represents an essential ability of prey for gaining an informational advantage over their natural enemies. Especially in complex environments or at night, animals strongly rely on chemoreception to avoid predators. The ability to recognize danger by chemical cues and subsequent adaptive responses to predation threats should generally increase prey survival. Recent findings suggest that European catfish ( Silurus glanis ) introduction induce changes in fish community and we tested whether the direction of change can be attributed to differences in chemical cue perception. We tested behavioral response to chemical cues using three species of freshwater fish common in European water: rudd ( Scardinius erythrophthalmus ), roach ( Rutilus rutilus ), and perch ( Perca fluviatilis ). Further, we conducted a prey selectivity experiment to evaluate the prey preferences of the European catfish. Roach exhibited the strongest reaction to chemical cues, rudd decreased use of refuge and perch did not alter any behavior in the experiment. These findings suggest that chemical cue perception might be behind community data change and we encourage collecting more community data of tested prey species before and after European catfish introduction to test the hypothesis. We conclude that used prey species can be used as a model species to verify whether chemical cue perception enhances prey survival.

  14. Reciprocal effects of litter from exotic and congeneric native plant species via soil nutrients.

    Directory of Open Access Journals (Sweden)

    Annelein Meisner

    Full Text Available Invasive exotic plant species are often expected to benefit exclusively from legacy effects of their litter inputs on soil processes and nutrient availability. However, there are relatively few experimental tests determining how litter of exotic plants affects their own growth conditions compared to congeneric native plant species. Here, we test how the legacy of litter from three exotic plant species affects their own performance in comparison to their congeneric natives that co-occur in the invaded habitat. We also analyzed litter effects on soil processes. In all three comparisons, soil with litter from exotic plant species had the highest respiration rates. In two out of the three exotic-native species comparisons, soil with litter from exotic plant species had higher inorganic nitrogen concentrations than their native congener, which was likely due to higher initial litter quality of the exotics. When litter from an exotic plant species had a positive effect on itself, it also had a positive effect on its native congener. We conclude that exotic plant species develop a legacy effect in soil from the invaded range through their litter inputs. This litter legacy effect results in altered soil processes that can promote both the exotic plant species and their native congener.

  15. Rickettsia species in fleas collected from small mammals in Slovakia.

    Science.gov (United States)

    Špitalská, Eva; Boldiš, Vojtech; Mošanský, Ladislav; Sparagano, Olivier; Stanko, Michal

    2015-11-01

    Epidemiological and epizootiological studies of Rickettsia felis and other Rickettsia spp. are very important, because their natural cycle has not yet been established completely. In total, 315 fleas (Siphonaptera) of 11 species of Ceratophyllidae, Hystrichopsyllidae and Leptopsyllidae families were tested for the presence of Rickettsia species and Coxiella burnetii with conventional and specific quantitative real-time PCR assays. Fleas were collected from five rodent hosts (Myodes glareolus, Apodemus flavicollis, Apodemus agrarius, Microtus subterraneus, Microtus arvalis) and three shrew species (Sorex araneus, Neomys fodiens, Crocidura suaveolens) captured in Eastern and Southern Slovakia. Overall, Rickettsia spp. was found in 10.8% (34/315) of the tested fleas of Ctenophthalmus agyrtes, Ctenophthalmus solutus, Ctenophthalmus uncinatus and Nosopsyllus fasciatus species. Infected fleas were coming from A. flavicollis, A. agrarius, and M. glareolus captured in Eastern Slovakia. C. burnetii was not found in any fleas. R. felis, Rickettsia helvetica, unidentified Rickettsia, and rickettsial endosymbionts were identified in fleas infesting small mammals in the Košice region, Eastern Slovakia. This study is the first report of R. felis infection in C. solutus male flea collected from A. agrarius in Slovakia.

  16. Native species that can replace exotic species in landscaping

    Directory of Open Access Journals (Sweden)

    Elisabeth Regina Tempel Stumpf

    2015-08-01

    Full Text Available Beyond aesthetics, the contemporary landscaping intends to provide other benefits for humans and environment, especially related to the environmental quality of urban spaces and conservation of the species. A trend in this direction is the reduction in the use of exotic plants in their designs, since, over time, they can become agents of replacement of native flora, as it has occurred in Rio Grande do Sul with many species introduced by settlers. However, the use of exotic species is unjustifiable, because the flora diversity of the Bioma Pampa offers many native species with appropriate features to the ornamental use. The commercial cultivation and the implantation of native species in landscaped areas constitute innovations for plant nurseries and landscapers and can provide a positive reduction in extractivism, contributing to dissemination, exploitation and preservation of native flora, and also decrease the impact of chemical products on environment. So, this work intends to identify native species of Bioma Pampa with features and uses similar to the most used exotic species at Brazilian landscaping. The species were selected from consulting books about native plants of Bioma Pampa and plants used at Brazilian landscaping, considering the similarity on habit and architecture, as well as characteristics of leafs, flowers and/or fruits and environmental conditions of occurrence and cultivation. There were identified 34 native species able to properly replace exotic species commonly used. The results show that many native species of Bioma Pampa have interesting ornamental features to landscape gardening, allowing them to replace exotic species that are traditionally cultivated.

  17. Use of Occupancy Models to Evaluate Expert Knowledge-based Species-Habitat Relationships

    Directory of Open Access Journals (Sweden)

    Monica N. Iglecia

    2012-12-01

    Full Text Available Expert knowledge-based species-habitat relationships are used extensively to guide conservation planning, particularly when data are scarce. Purported relationships describe the initial state of knowledge, but are rarely tested. We assessed support in the data for suitability rankings of vegetation types based on expert knowledge for three terrestrial avian species in the South Atlantic Coastal Plain of the United States. Experts used published studies, natural history, survey data, and field experience to rank vegetation types as optimal, suitable, and marginal. We used single-season occupancy models, coupled with land cover and Breeding Bird Survey data, to examine the hypothesis that patterns of occupancy conformed to species-habitat suitability rankings purported by experts. Purported habitat suitability was validated for two of three species. As predicted for the Eastern Wood-Pewee (Contopus virens and Brown-headed Nuthatch (Sitta pusilla, occupancy was strongly influenced by vegetation types classified as "optimal habitat" by the species suitability rankings for nuthatches and wood-pewees. Contrary to predictions, Red-headed Woodpecker (Melanerpes erythrocephalus models that included vegetation types as covariates received similar support by the data as models without vegetation types. For all three species, occupancy was also related to sampling latitude. Our results suggest that covariates representing other habitat requirements might be necessary to model occurrence of generalist species like the woodpecker. The modeling approach described herein provides a means to test expert knowledge-based species-habitat relationships, and hence, help guide conservation planning.

  18. Malassezia Species and Pityriasis Versicolor

    Directory of Open Access Journals (Sweden)

    Gulin Rodoplu

    2016-01-01

    Full Text Available Malassezia species are found in part of the normal human cutaneous commensal flora, however it has been known for many years that the Malassezia yeasts are associated with a number of different human diseases ranging from pityriasis versicolor to seborrhoeic dermatitis. In addition, since the 1980s, they have been reported as causing opportunistic systemic infections. The taxonomy of Malassezia spp. has recently been modified to include 13 obligatorily lipophilic species, plus one non-obligatorily lipophilic species, which only rarely colonizes human hosts and currently the genus consist 14 species as M. furfur, M. pachydermatis, M. sympodialis, M. globosa, M. obtusa, M. slooffiae, M. restricta, M. dermatis, M. japonica, M. nana, M. yamatoensis, M. caprae, M. equina, M. cuniculi. Fastidious growth requirements of Malassezia yeasts defied the initial attempts to culture these organisms and their true identification and the relationship between different species only became apparent with the application of modern molecular techniques. The causative fungus is seen especially in such seborrheic areas as the scalp, face, trunk and upper back. Under the influence of various exogenous or endogenous predisposing factors, these yeasts change from the blastospore form to the mycelial form and become pathogenic. Diagnosis of pityriasis versicolor which is caused by Malassezia species is generally easy and lies on the basis of its clinical appearance and can be confirmed by mycological examination. The diagnosisis is mainly based on direct examination with potassium hydroxide (KOH and demonstration that represents pseudohyphae and blastoconidia as the typical %u201Cspaghetti and meatballs%u201D pattern. Characteristic features of the genus Malassezia include a distinctive morphology and an affinity for lipids in culture. Culture is necessary to recover the infecting strain, especially for epidemiologic purposes and also to test its antifungal susceptibility

  19. Reconciliation with non-binary species trees.

    Science.gov (United States)

    Vernot, Benjamin; Stolzer, Maureen; Goldman, Aiton; Durand, Dannie

    2008-10-01

    Reconciliation extracts information from the topological incongruence between gene and species trees to infer duplications and losses in the history of a gene family. The inferred duplication-loss histories provide valuable information for a broad range of biological applications, including ortholog identification, estimating gene duplication times, and rooting and correcting gene trees. While reconciliation for binary trees is a tractable and well studied problem, there are no algorithms for reconciliation with non-binary species trees. Yet a striking proportion of species trees are non-binary. For example, 64% of branch points in the NCBI taxonomy have three or more children. When applied to non-binary species trees, current algorithms overestimate the number of duplications because they cannot distinguish between duplication and incomplete lineage sorting. We present the first algorithms for reconciling binary gene trees with non-binary species trees under a duplication-loss parsimony model. Our algorithms utilize an efficient mapping from gene to species trees to infer the minimum number of duplications in O(|V(G) | x (k(S) + h(S))) time, where |V(G)| is the number of nodes in the gene tree, h(S) is the height of the species tree and k(S) is the size of its largest polytomy. We present a dynamic programming algorithm which also minimizes the total number of losses. Although this algorithm is exponential in the size of the largest polytomy, it performs well in practice for polytomies with outdegree of 12 or less. We also present a heuristic which estimates the minimal number of losses in polynomial time. In empirical tests, this algorithm finds an optimal loss history 99% of the time. Our algorithms have been implemented in NOTUNG, a robust, production quality, tree-fitting program, which provides a graphical user interface for exploratory analysis and also supports automated, high-throughput analysis of large data sets.

  20. ConSpeciFix: Classifying prokaryotic species based on gene flow.

    Science.gov (United States)

    Bobay, Louis-Marie; Ellis, Brian Shin-Hua; Ochman, Howard

    2018-05-16

    Classification of prokaryotic species is usually based on sequence similarity thresholds, which are easy to apply but lack a biologically-relevant foundation. Here, we present ConSpeciFix, a program that classifies prokaryotes into species using criteria set forth by the Biological Species Concept, thereby unifying species definition in all domains of life. ConSpeciFix's webserver is freely available at www.conspecifix.com. The local version of the program can be freely downloaded from https://github.com/Bobay-Ochman/ConSpeciFix. ConSpeciFix is written in Python 2.7 and requires the following dependencies: Usearch, MCL, MAFFT and RAxML. ljbobay@uncg.edu.

  1. Prevalence of different Malassezia species in pityriasis versicolor in central India

    Directory of Open Access Journals (Sweden)

    Chaudhary Rahul

    2010-01-01

    Full Text Available Background: In the last 10 years, different studies have shown interesting geographical variations in the prevalence of different Malassezia species in pityriasis versicolor. Aim: Identification of Malassezia species isolated from patients with pityriasis versicolor. Methods: In 100 patients with pityriasis versicolor, Malassezia species were identified by culture in Sabouraud′s dextrose agar containing cycloheximide with olive oil overlay and modified Dixon agar and by doing biochemical tests (catalase reaction, assimilation of glycine, and Tween utilisation tests. Results: In 10 patients, 10% KOH smear was negative, while in 90 patients the smear showed characteristic "spaghetti and meatball" appearance. Of these 90 cases, growth was obtained on modified Dixon′s agar in 87 cases. Fifty of the isolates (57.5% were M. globosa, 15 (17.2% were M. sympodialis, seven (8.0% were suspected M. sympodialis, 6 (6.9% each of the isolates were M. furfur and M. obtusa, and three (3.4% isolates were M. restricta. Conclusion: M. globosa was the most common species, followed by M. sympodialis, M. furfur, M. obtusa, and M. restricta.

  2. Novel and cross-species microsatellite markers for parentage analysis in Sanderling

    NARCIS (Netherlands)

    Luttikhuizen, P.C.; Bol, A.; Witte, H.; van Bleijswijk, J.; Haddrath, O.; Baker, A.J.; Piersma, T.; Reneerkens, J.; Piersma, T.

    2011-01-01

    We isolated and tested six novel microsatellite loci in Sanderling (Calidris alba) from Greenland for paternity analyses. In addition, we tested 11 already published microsatellite markers which were originally developed for the congeneric species, the Pectoral Sandpiper (C. melanotos). All loci

  3. Fever in the test tube--towards a human(e) pyrogen test.

    Science.gov (United States)

    Schindler, Stephanie; Fennrich, Stefan; Crameri, Reto; Jungi, Thomas W; Montag, Thomas; Hartung, Thomas

    2007-01-01

    The human whole blood IL-1 test exploits the reaction of monocytes/macrophages for the detection of pyrogens: human whole blood taken from healthy volunteers is incubated in the presence of the test sample in any form, be it a solution, a powder or even solid material. Pyrogenic contaminations initiate the release of the "endogenous pyrogen" Interleukin-1beta determined by ELISA after incubation. In order to understand any differences between the pyrogenic activity in this test and the existing live rabbit test (species differences versus aberrant response of the particular blood sample), the rabbit whole blood test was developed. This approach could also help to avoid the use of putatively infectious human blood for pyrogen testing in vitro.

  4. Testing DNA barcode performance in 1000 species of European lepidoptera: large geographic distances have small genetic impacts.

    Science.gov (United States)

    Huemer, Peter; Mutanen, Marko; Sefc, Kristina M; Hebert, Paul D N

    2014-01-01

    This study examines the performance of DNA barcodes (mt cytochrome c oxidase 1 gene) in the identification of 1004 species of Lepidoptera shared by two localities (Finland, Austria) that are 1600 km apart. Maximum intraspecific distances for the pooled data were less than 2% for 880 species (87.6%), while deeper divergence was detected in 124 species. Despite such variation, the overall DNA barcode library possessed diagnostic COI sequences for 98.8% of the taxa. Because a reference library based on Finnish specimens was highly effective in identifying specimens from Austria, we conclude that barcode libraries based on regional sampling can often be effective for a much larger area. Moreover, dispersal ability (poor, good) and distribution patterns (disjunct, fragmented, continuous, migratory) had little impact on levels of intraspecific geographic divergence. Furthermore, the present study revealed that, despite the intensity of past taxonomic work on European Lepidoptera, nearly 20% of the species shared by Austria and Finland require further work to clarify their status. Particularly discordant BIN (Barcode Index Number) cases should be checked to ascertain possible explanatory factors such as incorrect taxonomy, hybridization, introgression, and Wolbachia infections.

  5. Testing DNA barcode performance in 1000 species of European lepidoptera: large geographic distances have small genetic impacts.

    Directory of Open Access Journals (Sweden)

    Peter Huemer

    Full Text Available This study examines the performance of DNA barcodes (mt cytochrome c oxidase 1 gene in the identification of 1004 species of Lepidoptera shared by two localities (Finland, Austria that are 1600 km apart. Maximum intraspecific distances for the pooled data were less than 2% for 880 species (87.6%, while deeper divergence was detected in 124 species. Despite such variation, the overall DNA barcode library possessed diagnostic COI sequences for 98.8% of the taxa. Because a reference library based on Finnish specimens was highly effective in identifying specimens from Austria, we conclude that barcode libraries based on regional sampling can often be effective for a much larger area. Moreover, dispersal ability (poor, good and distribution patterns (disjunct, fragmented, continuous, migratory had little impact on levels of intraspecific geographic divergence. Furthermore, the present study revealed that, despite the intensity of past taxonomic work on European Lepidoptera, nearly 20% of the species shared by Austria and Finland require further work to clarify their status. Particularly discordant BIN (Barcode Index Number cases should be checked to ascertain possible explanatory factors such as incorrect taxonomy, hybridization, introgression, and Wolbachia infections.

  6. Diagnostic value of nested-PCR for identification of Malassezia species in dandruff

    Science.gov (United States)

    Jusuf, N. K.; Nasution, T. A.; Ullyana, S.

    2018-03-01

    Dandruff or pityriasis simplex is a condition of abnormal occurrence of formation of yellowish white scales from the scalp. Many factors play a role in the pathogenesis of dandruff, i.e.colonization of Malassezia species. Examination of Malassezia species previously done by culture as the gold standard. However, there are various difficulties in doing the culture. Identification method with anested-polymerase chain reaction (nested-PCR) is expected to provide quickly and easily detected. This study aimedto determine the diagnostic value of nested-PCR in the identification of Malassezia species in dandruff. From 21 subjects, scales from the scalp were taken and sent to the laboratory for nested-PCR identification. Statistical analysis of diagnostic test carried out to determine sensitivity, specificity, positive predictive value, and negative predictive value. The results showed nested-PCR detected 10 sample (47.6%) positive for Malassezia species consist of M. sympodialis (23.8%); M. slooffiae (9.5%); M. furfur (4.8%); M. globosa and M. furfur (4.8%); and M. restricta and M. sympodialis (4.8%). Detection of Malassezia species by nested-PCR has 100% in sensitivity whereas the specificity was 55%. Nested-PCR test has high sensitivity. Therefore nested-PCR may be considered for a faster and simpler alternative examination in identification for Malassezia species in dandruff.

  7. Identification and characterization of pathogenic Pestalotiopsis species to pecan tree in Brazil

    Directory of Open Access Journals (Sweden)

    Marília Lazarotto

    2014-06-01

    Full Text Available The objective of this work was to characterize and cluster isolates of Pestalotiopsis species and to identify those that are pathogenic to pecan, based on morphological and molecular characters. Pestalotiopsis spp. isolates were identified by sequencing the internal transcribed spacer (ITS and β?tubulin regions. Identification methods were compared to indicate the key morphological characters for species characterization. Thirteen isolates were used for the pathogenicity tests. Morphological characterization was performed using the following variables: mycelial growth rate, sporulation, colony pigmentation, and conidial length and width. Ten pathogenic isolates were identified, three as -tubulin regions. Identification methods were compared to indicate the key morphological characters for species characterization. Thirteen isolates were used for the pathogenicity tests. Morphological characterization was performed using the following variables: mycelial growth rate, sporulation, colony pigmentation, and conidial length and width. Ten pathogenic isolates were identified, three as Pestalotiopsis clavispora and three as P. cocculi. The other isolates remained as an undefined species. The morphological characters were efficient for an initial separation of the isolates, which were grouped according to differences at species level, mainly colony diameter, which was identified as an important morphological describer. Beta-tubulin gene sequencing was less informative than the ITS region sequencing for species identification.

  8. Species identification of Candida isolated from clinical specimens in a tertiary care hospital

    Directory of Open Access Journals (Sweden)

    lsmet Nigar

    2016-07-01

    Full Text Available Background: Candida species are responsible for various clinical manifestations from mucocutaneous overgrowth to blood stream infections especially in immunocompromized situations. Although C. albicans is the most prevalent species, high incidence of non-albicans Candida species with antifungal resistance are emerging which is posing a serious threat to the patients care.Objective: This study aimed to isolate and identify different species of Candida from different clinical specimens. Methods: A total of 100 different clinical specimens were studied of which 35 were oral swab, 28 were high vaginal swab, 15 were urine, 14 were nail, 04 were bronchoalveolar lavage and peritoneal fluid were 04. Among 100 clinical specimens, Candida isolates were identified in 64 specimens. Isolation of Candida species was done by primary culture in SDA. Subsequent identification of species were performed by germ tube test, subculture in chromo­genic agar medium and carbohydrate assimilation test with commonly used twelve sugars.Results: Out of 64 isolated Candida species, Candida albicans were 51.56% and the non-albicans Candida species were 48.44%. The most prevalent Candida species was C. albicans 33 (51.53% followed by C. tropicalis 17 (26.56%. C. glabrata 4 (6.25%, C. parapsilo­sis 4 (6.25%, C. krusei 3 (4.68% and C. guilliermondii 2 (3.2%. One of the isolated Candida species was unidentified.Conclusion: Though Candida albicans was found as the most common species, but non-albicans Candida species are appearing as emerging pathogens as well. Exposure to chemotherapy appeared to be the commonest predisposing factor for Candida infection followed by indwelling urinary catheter in situ for prolong period.

  9. Antimicrobial resistence of Shigella species isolated during 2004 and 2005 from selected sites in Zimbabwe.

    Science.gov (United States)

    Ndlovu, N; Tarupiwa, A; Mudzori, J T

    2006-01-01

    To determine the predominant serotype and antibiotic sensitivity pattern of Shigella isolates during 2004 and 2005 in Zimbabwe. Cross sectional study. National Microbiology Reference Laboratory (NMRL), Harare, Zimbabwe. 259 clinical isolates of Shigella species isolated during 2004 and 2005 in Zimbabwe were studied. These samples had been referred to the NMRL for further testing. Serotype and antibiotic sensitivity pattern of Shigella species. Of the 259 clinical isolates of Shigella tested the following species were serotyped; 141 (54.4%) were S. flexneri; 70 (27%) S. sonnei; 38 (14.7%) S. dysenteriae and 10 (3.9%) S. boydii. About 4% of all Shigella isolates tested showed full sensitivity to commonly used antibiotics, 20.8% were resistant to one antibiotic only while 75.3% were resistant to at least two antibiotics. The most common resistance among Shigella species was to cotrimoxazole (89%), tetracycline (73%), ampicillin (49%) and chloramphenicol (41%). High susceptibility among Shigella species was observed to nalidixic acid (86%), ciprofloxacin (99%) and ceftazidine (99%). There was a low drug resistance of Shigella species to nalidixic acid, a drug of choice in Zimbabwe, except among Shigella dysenteriae type 1 strains. Continuous monitoring of the susceptibility patterns of Shigella species is important in order to detect the emergence of drug resistance and to update guidelines for antibiotic treatment in shigellosis.

  10. Estimating Effects of Species Interactions on Populations of Endangered Species.

    Science.gov (United States)

    Roth, Tobias; Bühler, Christoph; Amrhein, Valentin

    2016-04-01

    Global change causes community composition to change considerably through time, with ever-new combinations of interacting species. To study the consequences of newly established species interactions, one available source of data could be observational surveys from biodiversity monitoring. However, approaches using observational data would need to account for niche differences between species and for imperfect detection of individuals. To estimate population sizes of interacting species, we extended N-mixture models that were developed to estimate true population sizes in single species. Simulations revealed that our model is able to disentangle direct effects of dominant on subordinate species from indirect effects of dominant species on detection probability of subordinate species. For illustration, we applied our model to data from a Swiss amphibian monitoring program and showed that sizes of expanding water frog populations were negatively related to population sizes of endangered yellow-bellied toads and common midwife toads and partly of natterjack toads. Unlike other studies that analyzed presence and absence of species, our model suggests that the spread of water frogs in Central Europe is one of the reasons for the decline of endangered toad species. Thus, studying population impacts of dominant species on population sizes of endangered species using data from biodiversity monitoring programs should help to inform conservation policy and to decide whether competing species should be subject to population management.

  11. Hydrothermal Disintegration and Extraction of Different Microalgae Species

    Directory of Open Access Journals (Sweden)

    Michael Kröger

    2018-02-01

    Full Text Available For the disintegration and extraction of microalgae to produce lipids and biofuels, a novel processing technology was investigated. The utilization of a hydrothermal treatment was tested on four different microalgae species (Scenedesmus rubescens, Chlorella vulgaris, Nannochloropsis oculata and Arthorspira platensis (Spirulina to determine whether it has an advantage in comparison to other disintegration methods for lipid extraction. It was shown, that hydrothermal treatment is a reasonable opportunity to utilize microalgae without drying and increase the lipid yield of an algae extraction process. For three of the four microalgae species, the extraction yield with a prior hydrothermal treatment elevated the lipid yield up to six times in comparison to direct extraction. Only Scenedesmus rubescens showed a different behaviour. Reason can be found in the different cell wall of the species. The investigation of the differences in cell wall composition of the used species indicate that the existence of algaenan as a cell wall compound plays a major role in stability.

  12. Detection of molecular markers by comparative sequence analysis of enzymes from mycobacteria species

    International Nuclear Information System (INIS)

    Asad, S.; Hussain, M.; Siddiqua, A.; Ain, Q.U.

    2014-01-01

    Mycobacterial species are one of the most important pathogens and among these members of non-tuberculous mycobacteria (NTM) and mycobacterial tuberculousis complex (MTC) are the causative agent of a relatively milder form of Tuberculosis. Traditional methods for identification of these groups of pathogens are time consuming, lack specificity and sensitivity and furthermore lead to the misidentification due to high similarity index. Therefore, more rapid, specific and cost-effective methods are required for the accurate identification of Mycobacterium species in routine diagnostics. In our study, we identified molecular markers in order to differentiate closely related cousin species of genus Mycobacterium including M. bovis, M. avium, M. leprae and M. tuberculosis. The nucleotide sequences of selected unique markers, i.e., enzymes (used previously in various biochemical tests for the identification of M. species) were selected and their ORFs were retrieved and selected functional proteins of respective biosynthetic pathways were compared in-silico. Result suggested that the variations in nucleotide sequences of the selected enzymes can be directly used for M. species discrimination in one step PCR test. We believe that the in-silico identification and storage of these distinctive characteristics of individual M. species will help in more precise recognition of pathogenic strains and hence specie specific targeted therapy. (author)

  13. Evolution of species diversity in the genus Chamaecostus (Costaceae): molecular phylogenetics and morphometric approaches

    OpenAIRE

    Andre, Thiago; Specht, Chelsea; Salzman, Shayla; Palma-Silva, Clarisse [UNESP; Wendt, Tania

    2015-01-01

    While most species within the genus Chamaecostus (Costaceae) are well defined, the broad geographic range and long list of synonyms associated with Chamaecostus subsessilis led us to believe there may be some cryptic species within the complex. We thus investigate the phylogenetic relationships of species in the Chamaecostus lineage and specifically test the monophyly and diversity of the Chamaecostus subsessilis species complex from a population perspective by analyzing molecular sequence da...

  14. Enzyme sequence similarity improves the reaction alignment method for cross-species pathway comparison

    Energy Technology Data Exchange (ETDEWEB)

    Ovacik, Meric A. [Chemical and Biochemical Engineering Department, Rutgers University, Piscataway, NJ 08854 (United States); Androulakis, Ioannis P., E-mail: yannis@rci.rutgers.edu [Chemical and Biochemical Engineering Department, Rutgers University, Piscataway, NJ 08854 (United States); Biomedical Engineering Department, Rutgers University, Piscataway, NJ 08854 (United States)

    2013-09-15

    Pathway-based information has become an important source of information for both establishing evolutionary relationships and understanding the mode of action of a chemical or pharmaceutical among species. Cross-species comparison of pathways can address two broad questions: comparison in order to inform evolutionary relationships and to extrapolate species differences used in a number of different applications including drug and toxicity testing. Cross-species comparison of metabolic pathways is complex as there are multiple features of a pathway that can be modeled and compared. Among the various methods that have been proposed, reaction alignment has emerged as the most successful at predicting phylogenetic relationships based on NCBI taxonomy. We propose an improvement of the reaction alignment method by accounting for sequence similarity in addition to reaction alignment method. Using nine species, including human and some model organisms and test species, we evaluate the standard and improved comparison methods by analyzing glycolysis and citrate cycle pathways conservation. In addition, we demonstrate how organism comparison can be conducted by accounting for the cumulative information retrieved from nine pathways in central metabolism as well as a more complete study involving 36 pathways common in all nine species. Our results indicate that reaction alignment with enzyme sequence similarity results in a more accurate representation of pathway specific cross-species similarities and differences based on NCBI taxonomy.

  15. Enzyme sequence similarity improves the reaction alignment method for cross-species pathway comparison

    International Nuclear Information System (INIS)

    Ovacik, Meric A.; Androulakis, Ioannis P.

    2013-01-01

    Pathway-based information has become an important source of information for both establishing evolutionary relationships and understanding the mode of action of a chemical or pharmaceutical among species. Cross-species comparison of pathways can address two broad questions: comparison in order to inform evolutionary relationships and to extrapolate species differences used in a number of different applications including drug and toxicity testing. Cross-species comparison of metabolic pathways is complex as there are multiple features of a pathway that can be modeled and compared. Among the various methods that have been proposed, reaction alignment has emerged as the most successful at predicting phylogenetic relationships based on NCBI taxonomy. We propose an improvement of the reaction alignment method by accounting for sequence similarity in addition to reaction alignment method. Using nine species, including human and some model organisms and test species, we evaluate the standard and improved comparison methods by analyzing glycolysis and citrate cycle pathways conservation. In addition, we demonstrate how organism comparison can be conducted by accounting for the cumulative information retrieved from nine pathways in central metabolism as well as a more complete study involving 36 pathways common in all nine species. Our results indicate that reaction alignment with enzyme sequence similarity results in a more accurate representation of pathway specific cross-species similarities and differences based on NCBI taxonomy

  16. Validation of microsatellite multiplexes for parentage analysis and species discrimination in two hybridizing species of coral reef fish (Plectropomus spp., Serranidae)

    KAUST Repository

    Harrison, H.B.

    2014-04-24

    Microsatellites are often considered ideal markers to investigate ecological processes in animal populations. They are regularly used as genetic barcodes to identify species, individuals, and infer familial relationships. However, such applications are highly sensitive the number and diversity of microsatellite markers, which are also prone to error. Here, we propose a novel framework to assess the suitability of microsatellite datasets for parentage analysis and species discrimination in two closely related species of coral reef fish, Plectropomus leopardus and P. maculatus (Serranidae). Coral trout are important fisheries species throughout the Indo-Pacific region and have been shown to hybridize in parts of the Great Barrier Reef, Australia. We first describe the development of 25 microsatellite loci and their integration to three multiplex PCRs that co-amplify in both species. Using simulations, we demonstrate that the complete suite of markers provides appropriate power to discriminate between species, detect hybrid individuals, and resolve parent-offspring relationships in natural populations, with over 99.6% accuracy in parent-offspring assignments. The markers were also tested on seven additional species within the Plectropomus genus with polymorphism in 28-96% of loci. The multiplex PCRs developed here provide a reliable and cost-effective strategy to investigate evolutionary and ecological dynamics and will be broadly applicable in studies of wild populations and aquaculture brood stocks for these closely related fish species. 2014 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.

  17. Validation of microsatellite multiplexes for parentage analysis and species discrimination in two hybridizing species of coral reef fish (Plectropomus spp., Serranidae)

    KAUST Repository

    Harrison, H.B.; Feldheim, K.A.; Jones, G.P.; Ma, K.; Mansour, H.; Perumal, S.; Williamson, D.H.; Berumen, Michael L.

    2014-01-01

    Microsatellites are often considered ideal markers to investigate ecological processes in animal populations. They are regularly used as genetic barcodes to identify species, individuals, and infer familial relationships. However, such applications are highly sensitive the number and diversity of microsatellite markers, which are also prone to error. Here, we propose a novel framework to assess the suitability of microsatellite datasets for parentage analysis and species discrimination in two closely related species of coral reef fish, Plectropomus leopardus and P. maculatus (Serranidae). Coral trout are important fisheries species throughout the Indo-Pacific region and have been shown to hybridize in parts of the Great Barrier Reef, Australia. We first describe the development of 25 microsatellite loci and their integration to three multiplex PCRs that co-amplify in both species. Using simulations, we demonstrate that the complete suite of markers provides appropriate power to discriminate between species, detect hybrid individuals, and resolve parent-offspring relationships in natural populations, with over 99.6% accuracy in parent-offspring assignments. The markers were also tested on seven additional species within the Plectropomus genus with polymorphism in 28-96% of loci. The multiplex PCRs developed here provide a reliable and cost-effective strategy to investigate evolutionary and ecological dynamics and will be broadly applicable in studies of wild populations and aquaculture brood stocks for these closely related fish species. 2014 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.

  18. Susceptibility of Staphylococcus species and subspecies to teicoplanin.

    Science.gov (United States)

    Bannerman, T L; Wadiak, D L; Kloos, W E

    1991-01-01

    Twenty-four Staphylococcus species and their subspecies were examined for their susceptibilities to teicoplanin by disk diffusion (30-micrograms disk) and agar dilution for the determination of MICs. Moderately susceptible and resistant clinical strains were further tested for their susceptibilities to oxacillin and vancomycin. Teicoplanin resistance was not observed in the reference strains of the various Staphylococcus species isolated from healthy volunteers or animals. However, the novobiocin-resistant species Staphylococcus saprophyticus, Staphylococcus cohnii, Staphylococcus xylosus, Staphylococcus arlettae, Staphylococcus kloosii, and Staphylococcus gallinarum were less susceptible to teicoplanin (MIC, 2 to 8 micrograms/ml) than most of the novobiocin-susceptible species were (MIC, 0.5 to 4 micrograms/ml). Clinical isolates of coagulase-negative species were generally less susceptible to teicoplanin than were reference strains. Seven percent of the Staphylococcus epidermidis clinical strains were moderately susceptible (MIC, 16 micrograms/ml) to teicoplanin. Of these strains, 70% were oxacillin resistant. For Staphylococcus haemolyticus strains, 11% were resistant (MIC, greater than 16 micrograms/ml) and 21% were moderately susceptible to teicoplanin. Of these strains, 95% were oxacillin resistant, No strains of S. epidermidis or S. haemolyticus were intermediate or resistant to vancomycin. Teicoplanin appears to be less active in vitro against oxacillin-resistant S. haemolyticus. However, teicoplanin is an effective antimicrobial agent against many Staphylococcus species. PMID:1835340

  19. Ecological impacts of non-native species: Chapter 2

    Science.gov (United States)

    Pilliod, David S.; Griffiths, R.A.; Kuzmin, S.L.; Heatwole, Harold; Wilkinson, John W.

    2012-01-01

    Non-native species are considered one of the greatest threats to freshwater biodiversity worldwide (Drake et al. 1989; Allen and Flecker 1993; Dudgeon et al. 2005). Some of the first hypotheses proposed to explain global patterns of amphibian declines included the effects of non-native species (Barinaga 1990; Blaustein and Wake 1990; Wake and Morowitz 1991). Evidence for the impact of non-native species on amphibians stems (1) from correlative research that relates the distribution or abundance of a species to that of a putative non-native species, and (2) from experimental tests of the effects of a non-native species on survival, growth, development or behaviour of a target species (Kats and Ferrer 2003). Over the past two decades, research on the effects of non-native species on amphibians has mostly focused on introduced aquatic predators, particularly fish. Recent research has shifted to more complex ecological relationships such as influences of sub-lethal stressors (e.g. contaminants) on the effects of non-native species (Linder et al. 2003; Sih et al. 2004), non-native species as vectors of disease (Daszak et al. 2004; Garner et al. 2006), hybridization between non-natives and native congeners (Riley et al. 2003; Storfer et al. 2004), and the alteration of food-webs by non-native species (Nystrom et al. 2001). Other research has examined the interaction of non-native species in terms of facilitation (i.e. one non-native enabling another to become established or spread) or the synergistic effects of multiple non-native species on native amphibians, the so-called invasional meltdown hypothesis (Simerloff and Von Holle 1999). Although there is evidence that some non-native species may interact (Ricciardi 2001), there has yet to be convincing evidence that such interactions have led to an accelerated increase in the number of non-native species and cumulative impacts are still uncertain (Simberloff 2006). Applied research on the control, eradication, and

  20. DNA endoreplication level in endosperm during seed development in three monocotyledonous species

    Directory of Open Access Journals (Sweden)

    Kazimierz Marciniak

    2014-01-01

    Full Text Available The DNA content after the Feulgen reaction in the endosperm of three monocotyledonous plant species (Asparagus officinalis, Muscari comosom, Haemanthus kurharinae differing in their 2C DNA content, was cytophotometrically measured. During endosperm development 1-6 endoreplication cycles take place, depending on the species. Differences in nuclear DNA endoreplication dynamics in the tested species are similar to those occurring in root parenchyma, but the endoreplication level in the endosperm is higher.

  1. Intra-and-Inter Species Biomass Prediction in a Plantation Forest: Testing the Utility of High Spatial Resolution Spaceborne Multispectral RapidEye Sensor and Advanced Machine Learning Algorithms

    Directory of Open Access Journals (Sweden)

    Timothy Dube

    2014-08-01

    Full Text Available The quantification of aboveground biomass using remote sensing is critical for better understanding the role of forests in carbon sequestration and for informed sustainable management. Although remote sensing techniques have been proven useful in assessing forest biomass in general, more is required to investigate their capabilities in predicting intra-and-inter species biomass which are mainly characterised by non-linear relationships. In this study, we tested two machine learning algorithms, Stochastic Gradient Boosting (SGB and Random Forest (RF regression trees to predict intra-and-inter species biomass using high resolution RapidEye reflectance bands as well as the derived vegetation indices in a commercial plantation. The results showed that the SGB algorithm yielded the best performance for intra-and-inter species biomass prediction; using all the predictor variables as well as based on the most important selected variables. For example using the most important variables the algorithm produced an R2 of 0.80 and RMSE of 16.93 t·ha−1 for E. grandis; R2 of 0.79, RMSE of 17.27 t·ha−1 for P. taeda and R2 of 0.61, RMSE of 43.39 t·ha−1 for the combined species data sets. Comparatively, RF yielded plausible results only for E. dunii (R2 of 0.79; RMSE of 7.18 t·ha−1. We demonstrated that although the two statistical methods were able to predict biomass accurately, RF produced weaker results as compared to SGB when applied to combined species dataset. The result underscores the relevance of stochastic models in predicting biomass drawn from different species and genera using the new generation high resolution RapidEye sensor with strategically positioned bands.

  2. Comparative toxicity of a brominated flame retardant (tetrabromobisphenol A) on microalgae with single and multi-species bioassays.

    Science.gov (United States)

    Debenest, Timothée; Petit, Anne-Nöelle; Gagné, François; Kohli, Mohan; Nguyen, Nien; Blaise, Christian

    2011-09-01

    The potential threat of emerging chemicals to the aquatic flora is a major issue. The purpose of the study was to develop a multispecies microalgae test in order to determine the impact of species interactions on the cytoxicity of an emergent toxic contaminant: the tetrabromobisphenol A (TBBPA). Single and multi-species tests were thus performed to study the effects of this flame retardant on two microalgae (Pseudokirchneriella subcapitata and Nitzschia palea) commonly observed in freshwater. A synthetic medium was designed to allow the growth of both species. The algae were exposed to 1.8, 4.8, 9.2, 12.9 and 16.5 μM of TBBPA for 72 h. After staining with fluorescein diacetate (FDA), viable cells of each alga species were analyzed by flow cytometry based on chlorophyll autofluorescence and intracellular esterase activity. Density and abundance of viable cells were assessed to follow the population growth and the cell viability. In TBBPA treated samples, the growth of the two microalgae was significantly inhibited at the three highest concentrations (9.2, 12.9 and 16.5 μM) in the two tests. At the end of the experiment (t=72 h), the cell viability was also significantly smaller at these concentrations. The decreases of growth rate and viable cell abundance in TBBPA treated populations of N. palea were significantly higher in multi-species test in comparison with the single-species test. No significant differences were noticed between the two tests for P. subcapitata populations exposed to TBBPA. Crown Copyright © 2011. Published by Elsevier Ltd. All rights reserved.

  3. Species delimitation in the Stenocereus griseus (Cactaceae) species complex reveals a new species, S. huastecorum.

    Science.gov (United States)

    Alvarado-Sizzo, Hernán; Casas, Alejandro; Parra, Fabiola; Arreola-Nava, Hilda Julieta; Terrazas, Teresa; Sánchez, Cristian

    2018-01-01

    The Stenocereus griseus species complex (SGSC) has long been considered taxonomically challenging because the number of taxa belonging to the complex and their geographical boundaries remain poorly understood. Bayesian clustering and genetic distance-based methods were used based on nine microsatellite loci in 377 individuals of three main putative species of the complex. The resulting genetic clusters were assessed for ecological niche divergence and areolar morphology, particularly spination patterns. We based our species boundaries on concordance between genetic, ecological, and morphological data, and were able to resolve four species, three of them corresponding to S. pruinosus from central Mexico, S. laevigatus from southern Mexico, and S. griseus from northern South America. A fourth species, previously considered to be S. griseus and commonly misidentified as S. pruinosus in northern Mexico showed significant genetic, ecological, and morphological differentiation suggesting that it should be considered a new species, S. huastecorum, which we describe here. We show that population genetic analyses, ecological niche modeling, and morphological studies are complementary approaches for delimiting species in taxonomically challenging plant groups such as the SGSC.

  4. Species delimitation in the Stenocereus griseus (Cactaceae species complex reveals a new species, S. huastecorum.

    Directory of Open Access Journals (Sweden)

    Hernán Alvarado-Sizzo

    Full Text Available The Stenocereus griseus species complex (SGSC has long been considered taxonomically challenging because the number of taxa belonging to the complex and their geographical boundaries remain poorly understood. Bayesian clustering and genetic distance-based methods were used based on nine microsatellite loci in 377 individuals of three main putative species of the complex. The resulting genetic clusters were assessed for ecological niche divergence and areolar morphology, particularly spination patterns. We based our species boundaries on concordance between genetic, ecological, and morphological data, and were able to resolve four species, three of them corresponding to S. pruinosus from central Mexico, S. laevigatus from southern Mexico, and S. griseus from northern South America. A fourth species, previously considered to be S. griseus and commonly misidentified as S. pruinosus in northern Mexico showed significant genetic, ecological, and morphological differentiation suggesting that it should be considered a new species, S. huastecorum, which we describe here. We show that population genetic analyses, ecological niche modeling, and morphological studies are complementary approaches for delimiting species in taxonomically challenging plant groups such as the SGSC.

  5. Differential phenotyping of Brucella species using a newly developed semi-automated metabolic system

    Directory of Open Access Journals (Sweden)

    Appel Bernd

    2010-10-01

    Full Text Available Abstract Background A commercial biotyping system (Taxa Profile™, Merlin Diagnostika testing the metabolization of various substrates by bacteria was used to determine if a set of phenotypic features will allow the identification of members of the genus Brucella and their differentiation into species and biovars. Results A total of 191 different amines, amides, amino acids, other organic acids and heterocyclic and aromatic substrates (Taxa Profile™ A, 191 different mono-, di-, tri- and polysaccharides and sugar derivates (Taxa Profile™ C and 95 amino peptidase- and protease-reactions, 76 glycosidase-, phosphatase- and other esterase-reactions, and 17 classic reactions (Taxa Profile™ E were tested with the 23 reference strains representing the currently known species and biovars of Brucella and a collection of 60 field isolates. Based on specific and stable reactions a 96-well "Brucella identification and typing" plate (Micronaut™ was designed and re-tested in 113 Brucella isolates and a couple of closely related bacteria. Brucella species and biovars revealed characteristic metabolic profiles and each strain showed an individual pattern. Due to their typical metabolic profiles a differentiation of Brucella isolates to the species level could be achieved. The separation of B. canis from B. suis bv 3, however, failed. At the biovar level, B. abortus bv 4, 5, 7 and B. suis bv 1-5 could be discriminated with a specificity of 100%. B. melitensis isolates clustered in a very homogenous group and could not be resolved according to their assigned biovars. Conclusions The comprehensive testing of metabolic activity allows cluster analysis within the genus Brucella. The biotyping system developed for the identification of Brucella and differentiation of its species and biovars may replace or at least complement time-consuming tube testing especially in case of atypical strains. An easy to handle identification software facilitates the

  6. Recognition of root exudates by seeds of broomrape (Orobanche and Phelipanche) species

    Science.gov (United States)

    Fernández-Aparicio, M.; Flores, F.; Rubiales, D.

    2009-01-01

    Background and Aims The long co-existence of broomrapes and their hosts within the same environment has culminated in a strong adaptation and effective parasitism. As a first step of specialization in the parasitic process, seed receptors of parasitic plant species vary in their ability to recognize compounds released by their hosts. This work aims to investigate potential patterns for the reception requirements needed to activate germination within Orobanche and Phelipanche species. Methods Induction of the germination of seeds of nine Orobanche and Pheliphanche species by root exudates of 41 plant species was studied and subjected to biplot multivariate analysis. Key Results A high level of specialization in root exudate recognition was found in Orobanche densiflora, O. gracilis and O. hederae, which germinated almost exclusively in contact with root exudates from the plants they infect in nature. At the opposite extreme, Phelipanche aegyptiaca, P. ramosa and O. minor were highly generalist, germinating when in contact with the root exudates of most plant species. Orobanche crenata, O. cumana and O. foetida showed intermediate behaviour. Conclusions A universal germination stimulant for all broomrape species has not being identified to date. The synthetic stimulant GR24 is active against most of the weedy broomrape species, but fails with the non-weedy species tested in this study and with the very recent weedy species O. foetida. In addition, germination behaviour of broomrape species depends on the crop plant tested. Weedy broomrapes with a broad host spectrum respond better to the different exudates released by a wide range of crops and wild species than do non-weedy broomrapes, which have a narrow host spectrum and are more restricted to their host range. Root exudates of many plant species were active in stimulating germination of seeds of Orobanche and Phelipanche species for which they are not described as hosts, representing interesting examples of

  7. An evaluation of sequence tagged microsatellite site markers for genetic analysis within Citrus and related species.

    Science.gov (United States)

    Kijas, J M; Fowler, J C; Thomas, M R

    1995-04-01

    Microsatellites, also called sequence tagged microsatellite sites (STMSs), have become important markers for genome analysis but are currently little studied in plants. To assess the value of STMSs for analysis within the Citrus plant species, two example STMSs were isolated from an intergeneric cross between rangpur lime (Citrus x limonia Osbeck) and trifoliate orange (Poncirus trifoliata (L.) Raf.). Unique flanking primers were constructed for polymerase chain reaction amplification both within the test cross and across a broad range of citrus and related species. Both loci showed length variation between test cross parents with alleles segregating in a Mendelian fashion to progeny. Amplification across species showed the STMS flanking primers to be conserved in every genome tested. The traits of polymorphism, inheritance, and conservation across species mean that STMS markers are ideal for genome mapping within Citrus, which contains high levels of genetic variability.

  8. Taper and volume equations for selected Appalachian hardwood species

    Science.gov (United States)

    A. Jeff Martin

    1981-01-01

    Coefficients for five taper/volume models are developed for 18 Appalachian hardwood species. Each model can be used to estimate diameter at any point on the bole, height to any preselected diameter, and cubic-foot volume between any two points on the bole. The resulting equations were tested on six sets of independent data and an evaluation of these tests is included,...

  9. Using mitochondrial and ribosomal DNA sequences to test the taxonomic validity of Clinostomum complanatum Rudolphi, 1814 in fish-eating birds and freshwater fishes in Mexico, with the description of a new species.

    Science.gov (United States)

    Sereno-Uribe, Ana L; Pinacho-Pinacho, Carlos D; García-Varela, Martín; de León, Gerardo Pérez-Ponce

    2013-08-01

    The taxonomic history and species composition of the genus Clinostomum has been unstable. Two species, Clinostomum complanatum Rudolphi, 1814 and Clinostomum marginatum Rudolphi, 1819, have been particularly problematic and its validity has been disputed for nearly 200 years. In this paper, we have made use of an integrative taxonomy approach, and we used, in first instance, DNA sequences of two genes (cox1 and ITS) to test the validity of C. complanatum, a species apparently widely distributed in Mexico and to link the metacercariae and adult forms of the recognized species of Clinostomum. Combining molecular data with morphology, host association, and geographical distribution, we searched for the potential existence of undescribed species. A new species of Clinostomum is described based on adults found in the mouthy cavity of three species of fish-eating birds as well as in metacercariae found in freshwater and estuarine fishes. A few morphological characteristics distinguish the new species from other congeners even though reciprocal monophyly in a phylogenetic tree based on maximum-likelihood and Bayesian analysis, genetic divergence, and a multivariate analysis of variance and a principal component analysis of 18 morphometric traits for adults and metacercariae demonstrates the validity of the new species. Based on our results, it seems that C. complanatum is not currently distributed in Mexico, although this requires further verification with a more thoroughful sampling in other areas of the country, but it is plausible to support the hypothesis that C. marginatum is the American form, as previously suggested by other authors.

  10. Chemical, Bioactive, and Antioxidant Potential of Twenty Wild Culinary Mushroom Species

    Science.gov (United States)

    Sharma, S. K.; Gautam, N.

    2015-01-01

    The chemical, bioactive, and antioxidant potential of twenty wild culinary mushroom species being consumed by the people of northern Himalayan regions has been evaluated for the first time in the present study. Nutrients analyzed include protein, crude fat, fibres, carbohydrates, and monosaccharides. Besides, preliminary study on the detection of toxic compounds was done on these species. Bioactive compounds evaluated are fatty acids, amino acids, tocopherol content, carotenoids (β-carotene, lycopene), flavonoids, ascorbic acid, and anthocyanidins. Fruitbodies extract of all the species was tested for different types of antioxidant assays. Although differences were observed in the net values of individual species all the species were found to be rich in protein, and carbohydrates and low in fat. Glucose was found to be the major monosaccharide. Predominance of UFA (65–70%) over SFA (30–35%) was observed in all the species with considerable amounts of other bioactive compounds. All the species showed higher effectiveness for antioxidant capacities. PMID:26199938

  11. Chemical, Bioactive, and Antioxidant Potential of Twenty Wild Culinary Mushroom Species

    Directory of Open Access Journals (Sweden)

    S. K. Sharma

    2015-01-01

    Full Text Available The chemical, bioactive, and antioxidant potential of twenty wild culinary mushroom species being consumed by the people of northern Himalayan regions has been evaluated for the first time in the present study. Nutrients analyzed include protein, crude fat, fibres, carbohydrates, and monosaccharides. Besides, preliminary study on the detection of toxic compounds was done on these species. Bioactive compounds evaluated are fatty acids, amino acids, tocopherol content, carotenoids (β-carotene, lycopene, flavonoids, ascorbic acid, and anthocyanidins. Fruitbodies extract of all the species was tested for different types of antioxidant assays. Although differences were observed in the net values of individual species all the species were found to be rich in protein, and carbohydrates and low in fat. Glucose was found to be the major monosaccharide. Predominance of UFA (65–70% over SFA (30–35% was observed in all the species with considerable amounts of other bioactive compounds. All the species showed higher effectiveness for antioxidant capacities.

  12. Chemical, Bioactive, and Antioxidant Potential of Twenty Wild Culinary Mushroom Species.

    Science.gov (United States)

    Sharma, S K; Gautam, N

    2015-01-01

    The chemical, bioactive, and antioxidant potential of twenty wild culinary mushroom species being consumed by the people of northern Himalayan regions has been evaluated for the first time in the present study. Nutrients analyzed include protein, crude fat, fibres, carbohydrates, and monosaccharides. Besides, preliminary study on the detection of toxic compounds was done on these species. Bioactive compounds evaluated are fatty acids, amino acids, tocopherol content, carotenoids (β-carotene, lycopene), flavonoids, ascorbic acid, and anthocyanidins. Fruitbodies extract of all the species was tested for different types of antioxidant assays. Although differences were observed in the net values of individual species all the species were found to be rich in protein, and carbohydrates and low in fat. Glucose was found to be the major monosaccharide. Predominance of UFA (65-70%) over SFA (30-35%) was observed in all the species with considerable amounts of other bioactive compounds. All the species showed higher effectiveness for antioxidant capacities.

  13. Mycobacterium bovis infections in domesticated non-bovine mammalian species. Part 2: A review of diagnostic methods.

    Science.gov (United States)

    Broughan, J M; Crawshaw, T R; Downs, S H; Brewer, J; Clifton-Hadley, R S

    2013-11-01

    Despite the large host range of Mycobacterium bovis, ante-mortem diagnostic tests for the infection mostly lack sensitivity/specificity and/or remain unvalidated in non-bovine species. The epidemiology and importance of M. bovis infection in these species are discussed in the first part of this two-part review. This second part focuses on the diagnostic options available to identify infected species such as sheep, goats, dogs, cats, and camelids, and highlights the significant challenges posed, both in establishing estimates of disease prevalence and in controlling infections in these species, in the absence of fully validated tests. Crown Copyright © 2013. Published by Elsevier Ltd. All rights reserved.

  14. Natamycin and Azithromycin are Synergistic in vitro against Ocular Pathogenic Aspergillus flavus species complex and Fusarium solani species complex Isolates.

    Science.gov (United States)

    Guo, Haoyi; Zhou, Lutan; He, Yi; Gao, Chuanwen; Han, Lei; Xu, Yan

    2018-05-07

    The interaction of natamycin-azithromycin combination against 60 ocular fungal isolates was tested in vitro The combination produced 100% synergistic interactions when natamycin added azithromycin at 20, 40, 50 μg/ml against Aspergillus flavus species complex (AFSC) isolates and added azithromycin at 50 μg/ml against Fusarium solani species complex isolates. The combination with 50 μg/ml azithromycin enhanced natamycin's effect against AFSC isolates by reducing natamycin MICs from MIC 90 64μg/ml to MIC 90 0.031μg/ml. No antagonism was observed. Copyright © 2018 American Society for Microbiology.

  15. Save Our Species: Protecting Endangered Species from Pesticides.

    Science.gov (United States)

    Environmental Protection Agency, Washington, DC.

    This full-size poster profiles 11 wildlife species that are endangered. Color illustrations of animals and plants are accompanied by narrative describing their habitats and reasons for endangerment. The reverse side of the poster contains information on the Endangered Species Act, why protecting endangered and threatened species is important, how…

  16. Antibiotics sensitivity profile of proteus species associated with ...

    African Journals Online (AJOL)

    Antibiotics sensitivity profile of proteus species associated with specific infections at University of Ilorin Teaching Hospital, Ilorin. ... Results of the antimicrobial sensitivity testing showed that Imipenem and Piperacillin antibiotics were the most effective against Proteus sppwith each having 100%, followed by Ceftazidime ...

  17. Amplified-fragment length polymorphism fingerprinting of Mycoplasma species

    DEFF Research Database (Denmark)

    Kokotovic, Branko; Friis, N.F.; Jensen, J.S.

    1999-01-01

    Amplified-fragment length polymorphism (AFLP) is a whole-genome fingerprinting method based on selective amplification of restriction fragments. The potential of the method for the characterization of mycoplasmas was investigated in a total of 50 strains of human and animal origin, including...... Mycoplasma genitalium (n = 11), Mycoplasma pneumoniae (n = 5), Mycoplasma hominis (n = 5), Mycoplasma hyopneunmoniae (n = 9), Myco plasma flocculare (n = 5), Mycoplasma hyosynoviae (n = 10), and Mycoplasma dispar (n = 5), AFLP templates were prepared by the digestion of mycoplasmal DNA with BglII and Mfe...... to discriminate the analyzed strains at species and intraspecies levels as well, Each of the tested Mycoplasma species developed a banding pattern entirely different from those obtained from other species under analysis, Subtle intraspecies genomic differences were detected among strains of all of the Mycoplasma...

  18. Species coexistence: macroevolutionary relationships and the contingency of historical interactions.

    Science.gov (United States)

    Germain, Rachel M; Weir, Jason T; Gilbert, Benjamin

    2016-03-30

    Evolutionary biologists since Darwin have hypothesized that closely related species compete more intensely and are therefore less likely to coexist. However, recent theory posits that species diverge in two ways: either through the evolution of 'stabilizing differences' that promote coexistence by causing individuals to compete more strongly with conspecifics than individuals of other species, or through the evolution of 'fitness differences' that cause species to differ in competitive ability and lead to exclusion of the weaker competitor. We tested macroevolutionary patterns of divergence by competing pairs of annual plant species that differ in their phylogenetic relationships, and in whether they have historically occurred in the same region or different regions (sympatric versus allopatric occurrence). For sympatrically occurring species pairs, stabilizing differences rapidly increased with phylogenetic distance. However, fitness differences also increased with phylogenetic distance, resulting in coexistence outcomes that were unpredictable based on phylogenetic relationships. For allopatric species, stabilizing differences showed no trend with phylogenetic distance, whereas fitness differences increased, causing coexistence to become less likely among distant relatives. Our results illustrate the role of species' historical interactions in shaping how phylogenetic relationships structure competitive dynamics, and offer an explanation for the evolution of invasion potential of non-native species. © 2016 The Author(s).

  19. The role of CVS (and FIA) data and genetic tests in assessing species vulnerability to invasive pests and changing climate

    Science.gov (United States)

    R.A. Sniezko; H.E. Lintz

    2017-01-01

    United States tree species and their associated ecosystems, managed forests, and urban plantings are increasingly vulnerable to non-native invasive pathogens and insects as well as effects associated with a changing climate. Some species, such as whitebark pine (Pinus albicaulis), have been proposed for listing under the Endangered Species Act. To...

  20. Accumulation of elements by edible mushroom species II. A comparison of aluminium, barium and nutritional element contents.

    Science.gov (United States)

    Mleczek, Mirosław; Siwulski, Marek; Stuper-Szablewska, Kinga; Sobieralski, Krzysztof; Magdziak, Zuzanna; Goliński, Piotr

    2013-01-01

    The aim of the study was to compare accumulation efficiency of Al, Ba and nutritional elements (Ca, Fe, K, Mg, Mn, Na) exhibited by six edible mushrooms collected in particular regions of Poland during the last 20 years. The studied mushroom species were Boletus edulis, Cantharellus cibarius, Lactarius deliciosus, Leccinum aurantiacum, Suillus luteus and Xerocomus badius. The highest and the lowest concentrations of the elements in tested mushroom species were 11 - 410, 34 - 337, 16785 - 34600, 140 - 607, 12 - 75 and 16 - 143 mg kg(-1)d.m., respectively. The highest average concentrations of Al, Mg and Mn were observed in Suillus luteus fruiting bodies, while for Ba, Ca, K and Na it was in Lactarius deliciosus. BCF >1 was found for K and Mg in all tested mushroom species and additionally for the highest Ca and Na concentrations of all tested mushroom species except for C. cibarius and S. luteus, respectively. For the other tested elements (Al, Ba, Fe and Mn) BCF values < 1 were recorded.

  1. Assessing the effects of fluoxetine on Physa acuta (Gastropoda, Pulmonata) and Chironomus riparius (Insecta, Diptera) using a two-species water-sediment test

    Energy Technology Data Exchange (ETDEWEB)

    Sanchez-Argueello, Paloma [Laboratory for Ecotoxicology, Department of the Environment, INIA, Crta, A Coruna km 7, 28040 Madrid (Spain)], E-mail: arguello@inia.es; Fernandez, Carlos; Tarazona, Jose V. [Laboratory for Ecotoxicology, Department of the Environment, INIA, Crta, A Coruna km 7, 28040 Madrid (Spain)

    2009-03-01

    Fluoxetine has been tested in a two-species water-sediment system, which allowed a two-generation study with Chironomus riparius and a partial life-cycle with the freshwater snail Physa acuta to be performed at the same time. The design considered the continuous application of fluoxetine to overlaying water for nominal concentrations of 31.25, 62.5, 125 and 250 {mu}g/L. A fifth treatment (87.5 {mu}g/L) level consisted of pulse applications once a week. Measures of water and sediment concentrations were determined once a week and at the end of experiment (day 44), respectively. The fate study demonstrated that water dissipation can be explained by partitioning of fluoxetine to sediment. At the end of experiment, the percentage of detected fluoxetine was up to 10-fold higher in sediment than in overlaying water. The employed two-species test allowed distinguishing, in the same exposure conditions, effects due to waterborne exposure together ingestion at the sediment surface (freshwater grazing snail P. acuta) and exposure by burrowing activities (sediment-dwelling insect larvae C. riparius). The effect assessment showed a stimulation of P. acuta reproduction at lower concentrations (31.25 and 62.5 {mu}g/L), while the opposite effect was observed at the highest treatment (250 {mu}g/L). Additional studies should be conducted to establish if the statistically significant differences observed in F0 sex ratio at the 62.5 {mu}g/L and F1 adult emergence at 31.25 {mu}g/L of C. riparius have a toxicological significance. This study showed that fluoxetine can affect reproduction of freshwater molluscs. The results of the present study may contribute to knowledge on ecotoxicology of pharmaceuticals, about which little data is available. The possible consequences and implications for targeting the environmental risk assessment of fluoxetine are discussed.

  2. Assessing the effects of fluoxetine on Physa acuta (Gastropoda, Pulmonata) and Chironomus riparius (Insecta, Diptera) using a two-species water-sediment test

    International Nuclear Information System (INIS)

    Sanchez-Argueello, Paloma; Fernandez, Carlos; Tarazona, Jose V.

    2009-01-01

    Fluoxetine has been tested in a two-species water-sediment system, which allowed a two-generation study with Chironomus riparius and a partial life-cycle with the freshwater snail Physa acuta to be performed at the same time. The design considered the continuous application of fluoxetine to overlaying water for nominal concentrations of 31.25, 62.5, 125 and 250 μg/L. A fifth treatment (87.5 μg/L) level consisted of pulse applications once a week. Measures of water and sediment concentrations were determined once a week and at the end of experiment (day 44), respectively. The fate study demonstrated that water dissipation can be explained by partitioning of fluoxetine to sediment. At the end of experiment, the percentage of detected fluoxetine was up to 10-fold higher in sediment than in overlaying water. The employed two-species test allowed distinguishing, in the same exposure conditions, effects due to waterborne exposure together ingestion at the sediment surface (freshwater grazing snail P. acuta) and exposure by burrowing activities (sediment-dwelling insect larvae C. riparius). The effect assessment showed a stimulation of P. acuta reproduction at lower concentrations (31.25 and 62.5 μg/L), while the opposite effect was observed at the highest treatment (250 μg/L). Additional studies should be conducted to establish if the statistically significant differences observed in F0 sex ratio at the 62.5 μg/L and F1 adult emergence at 31.25 μg/L of C. riparius have a toxicological significance. This study showed that fluoxetine can affect reproduction of freshwater molluscs. The results of the present study may contribute to knowledge on ecotoxicology of pharmaceuticals, about which little data is available. The possible consequences and implications for targeting the environmental risk assessment of fluoxetine are discussed

  3. Subsocial behaviour and brood adoption in mixed-species colonies of two theridiid spiders

    DEFF Research Database (Denmark)

    Grinsted, Lena; Agnarsson, Ingi; Bilde, Trine

    2012-01-01

    , aggression and cooperation through behavioural experiments and examine the potential for adoption of foreign brood. Morphological and genetic analyses confirmed that colonies consisted of two related species Chikunia nigra (O.P. Cambridge, 1880) new combination (previously Chrysso nigra) and a yet...... as in territorial, colonial spiders. Mixed species spider colonies, involving closely related species, have rarely been documented. We examined social interactions in newly discovered mixed-species colonies of theridiid spiders on Bali, Indonesia. Our aim was to test the degree of intra- and interspecific tolerance...

  4. Subsocial behaviour and brood adoption in mixed-species colonies of two theridiid spiders

    DEFF Research Database (Denmark)

    Grinsted, Lena; Agnarsson, Ingi; Bilde, Trine

    2012-01-01

    Cooperation and group living often evolves through kin selection. However, associations between unrelated organisms, such as different species, can evolve if both parties benefit from the interaction. Group living is rare in spiders, but occurs in cooperative, permanently social spiders, as well...... as in territorial, colonial spiders. Mixed species spider colonies, involving closely related species, have rarely been documented. We examined social interactions in newly discovered mixed-species colonies of theridiid spiders on Bali, Indonesia. Our aim was to test the degree of intra- and interspecific tolerance...

  5. Species specific anaesthetics for fish anaesthesia and euthanasia.

    Science.gov (United States)

    Readman, Gareth D; Owen, Stewart F; Knowles, Toby G; Murrell, Joanna C

    2017-08-02

    There is a need to ensure that the care and welfare for fish maintained in the laboratory are to the highest standards. This extends to the use of anaesthetics for both scientific study, humane killing and euthanasia at end of life. An anaesthetic should not induce negative behaviours and fish should not seek to avoid the anaesthetic. Surprisingly little information is available to facilitate a humane choice of anaesthetic agent for fish despite over 100 years of use and the millions of fish currently held in thousands of laboratories worldwide. Using a chemotaxic choice chamber we found different species specific behavioural responses among four closely related fish species commonly held in the laboratory, exposed to three widely used anaesthetic agents. As previously found for zebrafish (Danio rerio), the use of MS-222 and benzocaine also appears to induce avoidance behaviours in medaka (Oryzias latipes); but etomidate could provide an alternative choice. Carp (Cyprinus carpio), although closely related to zebrafish showed avoidance behaviours to etomidate, but not benzocaine or MS-222; and rainbow trout (Oncorhynchus mykiss) showed no avoidance to the three agents tested. We were unable to ascertain avoidance responses in fathead minnows (Pimephales promelas) and suggest different test paradigms are required for that species.

  6. Phycoremediation of Tannery Wastewater Using Microalgae Scenedesmus Species.

    Science.gov (United States)

    Ajayan, Kayil Veedu; Selvaraju, Muthusamy; Unnikannan, Pachikaran; Sruthi, Palliyath

    2015-01-01

    A number of microalgae species are efficient in removing toxicants from wastewater. Many of these potential species are a promising, eco-friendly, and sustainable option for tertiary wastewater treatment with a possible advantage of improving the economics of microalgae cultivation for biofuel production. The present study deals with the phycoremediation of tannery wastewater (TWW) using Scenedesmus sp. isolated from a local habitat. The test species was grown in TWW under laboratory conditions and harvested on the 12th day. The results revealed that the algal biomass during the growth period not only reduced the pollution load of heavy metals (Cr-81.2-96%, Cu-73.2-98%, Pb-75-98% and Zn-65-98%) but also the nutrients (NO3 >44.3% and PO4 >95%). Fourier Transform Infrared (FTIR) spectrums of Scenedesmus sp. biomass revealed the involvement of hydroxyl amino, carboxylic and carbonyl groups. The scanning electron micrograph (SEM) and Energy Dispersive X-ray Spectroscopic analysis (EDS) revealed the surface texture, morphology and element distribution of the biosorbent. Furthermore, the wastewater generated during wet-blue tanning process can support dense population of Scenedesmus sp., making it a potential growth medium for biomass production of the test alga for phycoremediation of toxicants in tannery wastewaters.

  7. An exactly solvable coarse-grained model for species diversity

    Science.gov (United States)

    Suweis, Samir; Rinaldo, Andrea; Maritan, Amos

    2012-07-01

    We present novel analytical results concerning ecosystem species diversity that stem from a proposed coarse-grained neutral model based on birth-death processes. The relevance of the problem lies in the urgency for understanding and synthesizing both theoretical results from ecological neutral theory and empirical evidence on species diversity preservation. The neutral model of biodiversity deals with ecosystems at the same trophic level, where per capita vital rates are assumed to be species independent. Closed-form analytical solutions for the neutral theory are obtained within a coarse-grained model, where the only input is the species persistence time distribution. Our results pertain to: the probability distribution function of the number of species in the ecosystem, both in transient and in stationary states; the n-point connected time correlation function; and the survival probability, defined as the distribution of time spans to local extinction for a species randomly sampled from the community. Analytical predictions are also tested on empirical data from an estuarine fish ecosystem. We find that emerging properties of the ecosystem are very robust and do not depend on specific details of the model, with implications for biodiversity and conservation biology.

  8. An exactly solvable coarse-grained model for species diversity

    International Nuclear Information System (INIS)

    Suweis, Samir; Maritan, Amos; Rinaldo, Andrea

    2012-01-01

    We present novel analytical results concerning ecosystem species diversity that stem from a proposed coarse-grained neutral model based on birth–death processes. The relevance of the problem lies in the urgency for understanding and synthesizing both theoretical results from ecological neutral theory and empirical evidence on species diversity preservation. The neutral model of biodiversity deals with ecosystems at the same trophic level, where per capita vital rates are assumed to be species independent. Closed-form analytical solutions for the neutral theory are obtained within a coarse-grained model, where the only input is the species persistence time distribution. Our results pertain to: the probability distribution function of the number of species in the ecosystem, both in transient and in stationary states; the n-point connected time correlation function; and the survival probability, defined as the distribution of time spans to local extinction for a species randomly sampled from the community. Analytical predictions are also tested on empirical data from an estuarine fish ecosystem. We find that emerging properties of the ecosystem are very robust and do not depend on specific details of the model, with implications for biodiversity and conservation biology. (paper)

  9. Candida Albicans and Non-Albicans Species as Etiological Agent of Vaginitis in Pregnant and Non-Pregnant Women

    Directory of Open Access Journals (Sweden)

    Mirela Babić

    2010-02-01

    Full Text Available Pregnancy represents a risk factor in the occurrence of vaginal candidosis. The objectives of our study were: to make determination of the microscopic findings of vaginal swab, frequency of Candida species in the culture of pregnant women and patients who are not pregnant, determine the Candida species in all cultures, and to determine the frequency and differences in the frequency of C. albicans and other non-albicans species. In one year study performed during 2006 year, we tested patients of Gynaecology and Obstetrics clinic of the Clinical Centre in Sarajevo and Gynaecology department of the General hospital in Sarajevo. 447 woman included in the study were separated in two groups: 203 pregnant (in the last trimester of pregnancy, and 244 non-pregnant woman in period of fertility. Each vaginal swab was examined microscopically. The yeast, number of colonies, and the species of Candida were determined on Sabouraud dextrose agar with presence of antibiotics. For determination of Candida species, we used germ tube test for detection of C. albicans, and cultivation on the selective medium and assimilation tests for detection of non-albicans species. The results indicated positive microscopic findings in the test group (40,9%, as well as greater number of positive cultures (46,8%. The most commonly detected species for both groups was C. albicans (test group 40.9% and control group 23,0%. The most commonly detected non-albicans species for the test group were C. glabrata (4,2 % and C. krusei (3,2%, and for the control group were C. glabrata (3,2% and C. parapsilosis (3,2%. The microscopic findings correlated with the number of colonies in positive cultures. In the test group, we found an increased number of yeasts (64,3%, and the pseudopyphae and blastopores by microscopic examination as an indication of infection. In the control group, we found a small number of yeasts (64,6%, in the form of blastopores, as an indication of the candida

  10. Does enemy damage vary across the range of exotic plant species? Evidence from two coastal dune plant species in eastern Australia.

    Science.gov (United States)

    Tabassum, Samiya; Leishman, Michelle R

    2018-02-01

    Release from natural enemies is often cited as a key factor for understanding the success of invasive plant species in novel environments. However, with time invasive species will accumulate native enemies in their invaded range, with factors such as spread distance from the site of introduction, climate and leaf-level traits potentially affecting enemy acquisition rates. However, the influence of such factors is difficult to assess without examining enemy attack across the entire species' range. We tested the significance of factors associated with range expansion (distance from source population and maximum population density), climatic variables (annual temperature and rainfall) and leaf-level traits [specific leaf area (SLA) and foliar nitrogen concentration] in explaining variation in enemy damage across multiple populations of two coastal invasive plants (Gladiolus gueinzii Kunze and Hydrocotyle bonariensis Lam.) along their entire introduced distribution in eastern Australia. We found that for H. bonariensis, amount of foliar damage increased with distance from source population. In contrast, for G. gueinzii, probability and amount of foliar damage decreased with decreasing temperature and increasing rainfall, respectively. Our results show that patterns of enemy attack across species' ranges are complex and cannot be generalised between species or even range edges.

  11. Real-Time RT-PCR for the Detection of Lyssavirus Species

    Directory of Open Access Journals (Sweden)

    A. Deubelbeiss

    2014-01-01

    Full Text Available The causative agents of rabies are single-stranded, negative-sense RNA viruses in the genus Lyssavirus of Rhabdoviridae, consisting of twelve classified and three as yet unclassified species including classical rabies virus (RABV. Highly neurotropic RABV causes rapidly progressive encephalomyelitis with nearly invariable fatal outcome. Rapid and reliable diagnosis of rabies is highly relevant for public and veterinary health. Due to growing variety of the genus Lyssavirus observed, the development of suitable molecular assays for diagnosis and differentiation is challenging. This work focused on the establishment of a suitable real-time RT-PCR technique for rabies diagnosis as a complement to fluorescent antibody test and rabies tissue culture infection test as gold standard for diagnosis and confirmation. The real-time RT-PCR was adapted with the goal to detect the whole spectrum of lyssavirus species, for nine of which synthesized DNA fragments were used. For the detection of species, seven probes were developed. Serial dilutions of the rabies virus strain CVS-11 showed a 100-fold higher sensitivity of real-time PCR compared to heminested RT-PCR. Using a panel of thirty-one lyssaviruses representing four species, the suitability of the protocol could be shown. Phylogenetic analysis of the sequences obtained by heminested PCR allowed correct classification of all viruses used.

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

    Science.gov (United States)

    J. Firn; J.L. Moore; A.S. MacDougall; E.T. Borer; E.W. Seabloom; J. HilleRisLambers; S. Harpole; E.E. Cleland; C.S. Brown; J.M.H. Knops; S.M. Prober; D.A. Pyke; K.A. Farrell; J.D. Bakker; L.R. O’Halloran; P.B. Adler; S.L. Collins; C.M. D’Antonio; M.J. Crawley; E.M. Wolkovich; K.J. La Pierre; B.A. Melbourne; Y. Hautier; J.W. Morgan; A.D.B. Leakey; A.D. Kay; R.L. McCulley; K.F. Davies; C.J. Stevens; C.J. Chu

    2011-01-01

    Many ecosystems worldwide are dominated by introduced plant species, leading to loss of biodiversity and ecosystem function. A common but rarely tested assumption is that these plants are more abundant in introduced vs. native communities, because ecological or evolutionary-based shifts in populations underlie invasion success. Here, data for 26 herbaceous species at...

  13. Effect of holothurian and zoanthid extracts on growth of some bacterial and diatom species

    Digital Repository Service at National Institute of Oceanography (India)

    Gonsalves, C.

    The antifouling properties of the extracts from two zoanthids, viz. Zoanthus sp, Protopalythoa sp and one holothurian species, viz. Holothuria leucospilota occurring in the coastal waters off Goa were tested against 5 bacteria and 2 diatom species...

  14. Bikini Atoll coral biodiversity resilience five decades after nuclear testing

    International Nuclear Information System (INIS)

    Richards, Zoe T.; Beger, Maria; Pinca, Silvia; Wallace, Carden C.

    2008-01-01

    Five decades after a series of nuclear tests began, we provide evidence that 70% of the Bikini Atoll zooxanthellate coral assemblage is resilient to large-scale anthropogenic disturbance. Species composition in 2002 was assessed and compared to that seen prior to nuclear testing. A total of 183 scleractinian coral species was recorded, compared to 126 species recorded in the previous study (excluding synonomies, 148 including synonomies). We found that 42 coral species may be locally extinct at Bikini. Fourteen of these losses may be pseudo-losses due to inconsistent taxonomy between the two studies or insufficient sampling in the second study, however 28 species appear to represent genuine losses. Of these losses, 16 species are obligate lagoonal specialists and 12 have wider habitat compatibility. Twelve species are recorded from Bikini for the first time. We suggest the highly diverse Rongelap Atoll to the east of Bikini may have contributed larval propagules to facilitate the partial resilience of coral biodiversity in the absence of additional anthropogenic threats

  15. Bikini Atoll coral biodiversity resilience five decades after nuclear testing

    Energy Technology Data Exchange (ETDEWEB)

    Richards, Zoe T. [Museum of Tropical Queensland, Flinders St, Townsville, QLD 4810 (Australia) and Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811 (Australia) and School of Marine and Tropical Biology, James Cook University, Townsville QLD 4811 (Australia); NRAS - Marshall Islands: Natural Resource Assessment Surveys (Australia)], E-mail: zoe.richards@jcu.edu.au; Beger, Maria [Ecology Centre and Commonwealth Research Facility for Applied Environmental Decision Analysis, University of Queensland, St Lucia, QLD 4072 (Australia); NRAS - Marshall Islands: Natural Resource Assessment Surveys (Australia); Pinca, Silvia [College of the Marshall Islands, Majuro, Marshall Islands, NRAS - Marshall Islands: Natural Resource Assessment Surveys (Australia); Wallace, Carden C. [Museum of Tropical Queensland, Flinders St, Townsville, QLD 4810 (Australia)

    2008-03-15

    Five decades after a series of nuclear tests began, we provide evidence that 70% of the Bikini Atoll zooxanthellate coral assemblage is resilient to large-scale anthropogenic disturbance. Species composition in 2002 was assessed and compared to that seen prior to nuclear testing. A total of 183 scleractinian coral species was recorded, compared to 126 species recorded in the previous study (excluding synonomies, 148 including synonomies). We found that 42 coral species may be locally extinct at Bikini. Fourteen of these losses may be pseudo-losses due to inconsistent taxonomy between the two studies or insufficient sampling in the second study, however 28 species appear to represent genuine losses. Of these losses, 16 species are obligate lagoonal specialists and 12 have wider habitat compatibility. Twelve species are recorded from Bikini for the first time. We suggest the highly diverse Rongelap Atoll to the east of Bikini may have contributed larval propagules to facilitate the partial resilience of coral biodiversity in the absence of additional anthropogenic threats.

  16. Bacillus subtilis Protects Public Goods by Extending Kin Discrimination to Closely Related Species

    Directory of Open Access Journals (Sweden)

    Nicholas A. Lyons

    2017-07-01

    Full Text Available Kin discrimination systems are found in numerous communal contexts like multicellularity and are theorized to prevent exploitation of cooperative behaviors. The kin discrimination system in Bacillus subtilis differs from most other such systems because it excludes nonkin cells rather than including kin cells. Because nonkin are the target of the system, B. subtilis can potentially distinguish degrees of nonkin relatedness, not just kin versus nonkin. We examined this by testing a large strain collection of diverse Bacillus species against B. subtilis in different multicellular contexts. The effects of kin discrimination extend to nearby species, as the other subtilis clade species were treated with the same antagonism as nonkin. Species in the less-related pumilus clade started to display varied phenotypes but were mostly still discriminated against, while cereus clade members and beyond were no longer subject to kin discrimination. Seeking a reason why other species are perceived as antagonistic nonkin, we tested the ability of B. subtilis to steal communally produced surfactant from these species. We found that the species treated as nonkin were the only ones that made a surfactant that B. subtilis could utilize and that nonkin antagonism prevented such stealing when the two strains were mixed. The nonkin exclusion kin discrimination method thus allows effective protection of the cooperative behaviors prevalent in multicellularity while still permitting interactions with more distant species that are not a threat.

  17. Species choice, provenance and species trials among native Brazilian species

    Energy Technology Data Exchange (ETDEWEB)

    Drumond, M A

    1982-01-01

    Six papers from the conference are presented. Drumond, M.A., Potential of species native to the semi-arid tropics, 766-781, (Refs. 18), reports on Anadenanthera macrocarpa, Mimosa species, Schinopsis brasiliensis, Spondias tuberosa, Ziziphus joazeiro, Cnidoscolus phyllacanthus, Bursera leptophleos (leptophloeos), Tabebuia impetiginosa, Astronium urundeuva, and Mimosa caesalpinia. Monteiro, R.F.R., Speltz, R.M., Gurgel, J.T. do A.; Silvicultural performance of 24 provenances of Araucaria angustifolia in Parana, 814-824, (Refs. 8). Pires, C.L. da S., Kalil Filho, A.N., Rosa, P.R.F. da, Parente, P.R., Zanatto, A.C.S.; Provenance trials of Cordia alliodora in the State of Sao Paulo, 988-995, (Refs. 9). Nogueira, J.C.B., Siqueira, A.C.M.F., Garrido, M.A.O., Gurgel Garrido, L.M. do A., Rosa, P.R.F., Moraes, J.L. de, Zandarin, M.A., Gurgel Filho, O.A., Trials of some native species in various regions of the State of Sao Paulo, 1051-1063, (Refs. 9) describes Centrolobium tomentosum, Peltophorum dubium, Tabebuia vellosoi, Cariniana legalis, and Balfourodendron riedelianum. Batista, M.P., Borges, J.F., Franco, M.A.B.; Early growth of a native species in comparison with exotics in northeastern Para, Brazil, 1105-1110, (Refs. 3). Jacaranda copaia is compared with Gmelina arborea, Pinus caribaea various hondurensis, Eucalyptus deglupta, and E. urophylla. Lima, P.C.F., Souza, S.M. de, Drumond, M.A.; Trials of native forest species at Petrolina, Pernambuco, 1139-1148, (Refs. 8), deals with Anadenanthera macrocarpa, Piptadenia obliqua, Pithecellobium foliolosum, Astronium urundeuva, Schinopsis brasiliensis, Cassia excelsa, Caesalpinia pyramidalis, Parkia platycephala, Pseudobombax simplicifolium, Tabebuia impetiginosa, Caesalpinia ferrea, and Aspidosperma pyrifolium. 18 references.

  18. Modification of species-based differential evolution for multimodal optimization

    Science.gov (United States)

    Idrus, Said Iskandar Al; Syahputra, Hermawan; Firdaus, Muliawan

    2015-12-01

    At this time optimization has an important role in various fields as well as between other operational research, industry, finance and management. Optimization problem is the problem of maximizing or minimizing a function of one variable or many variables, which include unimodal and multimodal functions. Differential Evolution (DE), is a random search technique using vectors as an alternative solution in the search for the optimum. To localize all local maximum and minimum on multimodal function, this function can be divided into several domain of fitness using niching method. Species-based niching method is one of method that build sub-populations or species in the domain functions. This paper describes the modification of species-based previously to reduce the computational complexity and run more efficiently. The results of the test functions show species-based modifications able to locate all the local optima in once run the program.

  19. Survival and development of Lymantria monacha (Lepidoptera: Lymantriidae) on North American and introduced Eurasian tree species.

    Science.gov (United States)

    Keena, M A

    2003-02-01

    Lymantria monacha (L.) (Lepidoptera: Lymantriidae), the nun moth, is a Eurasian pest of conifers that has potential for accidental introduction into North America. To project the potential host range of this insect if introduced into North America, survival and development of L. monacha on 26 North American and eight introduced Eurasian tree species were examined. Seven conifer species (Abies concolor, Picea abies, P. glauca, P. pungens, Pinus sylvestris with male cones, P. menziesii variety glance, and Tsuga canadensis) and six broadleaf species (Betula populifolia, Malus x domestica, Prunus serotiaa, Quercus lobata, Q. rubra, and Q. velutina) were suitable for L. monacha survival and development. Eleven of the host species tested were rated as intermediate in suitability, four conifer species (Larix occidentalis, P. nigra, P. ponderosa, P. strobus, and Pseudotsuga menziesii variety menziesii) and six broadleaf species (Carpinus caroliniana, Carya ovata, Fagus grandifolia, Populus grandidentata, Q. alba, and Tilia cordata) and the remaining 10 species tested were rated as poor (Acer rubrum, A. platanoidies, A. saccharum, F. americana, Juniperus virginiana, Larix kaempferi, Liriodendron tulipfera, Morus alba, P. taeda, and P. deltoides). The phenological state of the trees had a major impact on establishment, survival, and development of L. monacha on many of the tree species tested. Several of the deciduous tree species that are suitable for L. monacha also are suitable for L. dispar (L.) and L. mathura Moore. Establishment of L. monacha in North America would be catastrophic because of the large number of economically important tree species on which it can survive and develop, and the ability of mated females to fly and colonize new areas.

  20. Ballast Water Treatment Test Facility

    Data.gov (United States)

    Federal Laboratory Consortium — FUNCTION: Provides functionality for the full-scale testing and controlled simulation of ship ballasting operations for assessment of aquatic nuisance species (ANS)...

  1. Chronic Co-species Housing Mice and Rats Increased the Competitiveness of Male Mice.

    Science.gov (United States)

    Liu, Ying-Juan; Li, Lai-Fu; Zhang, Yao-Hua; Guo, Hui-Fen; Xia, Min; Zhang, Meng-Wei; Jing, Xiao-Yuan; Zhang, Jing-Hua; Zhang, Jian-Xu

    2017-03-01

    Rats are predators of mice in nature. Nevertheless, it is a common practice to house mice and rats in a same room in some laboratories. In this study, we investigated the behavioral and physiological responsively of mice in long-term co-species housing conditions. Twenty-four male mice were randomly assigned to their original raising room (control) or a rat room (co-species-housed) for more than 6 weeks. In the open-field and light-dark box tests, the behaviors of the co-species-housed mice and controls were not different. In a 2-choice test of paired urine odors [rabbit urine (as a novel odor) vs. rat urine, cat urine (as a natural predator-scent) vs. rabbit urine, and cat urine vs. rat urine], the co-species-housed mice were more ready to investigate the rat urine odor compared with the controls and may have adapted to it. In an encounter test, the rat-room-exposed mice exhibited increased aggression levels, and their urines were more attractive to females. Correspondingly, the levels of major urinary proteins were increased in the co-species-housed mouse urine, along with some volatile pheromones. The serum testosterone levels were also enhanced in the co-species-housed mice, whereas the corticosterone levels were not different. The norepinephrine, dopamine, and 5-HT levels in the right hippocampus and striatum were not different between the 2. Our findings indicate that chronic co-species housing results in adaptation in male mice; furthermore, it appears that long-term rat-odor stimuli enhance the competitiveness of mice, which suggests that appropriate predator-odor stimuli may be important to the fitness of prey animals. © The Author 2017. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  2. Weather, not climate, defines distributions of vagile bird species.

    Directory of Open Access Journals (Sweden)

    April E Reside

    Full Text Available BACKGROUND: Accurate predictions of species distributions are essential for climate change impact assessments. However the standard practice of using long-term climate averages to train species distribution models might mute important temporal patterns of species distribution. The benefit of using temporally explicit weather and distribution data has not been assessed. We hypothesized that short-term weather associated with the time a species was recorded should be superior to long-term climate measures for predicting distributions of mobile species. METHODOLOGY: We tested our hypothesis by generating distribution models for 157 bird species found in Australian tropical savannas (ATS using modelling algorithm Maxent. The variable weather of the ATS supports a bird assemblage with variable movement patterns and a high incidence of nomadism. We developed "weather" models by relating climatic variables (mean temperature, rainfall, rainfall seasonality and temperature seasonality from the three month, six month and one year period preceding each bird record over a 58 year period (1950-2008. These weather models were compared against models built using long-term (30 year averages of the same climatic variables. CONCLUSIONS: Weather models consistently achieved higher model scores than climate models, particularly for wide-ranging, nomadic and desert species. Climate models predicted larger range areas for species, whereas weather models quantified fluctuations in habitat suitability across months, seasons and years. Models based on long-term climate averages over-estimate availability of suitable habitat and species' climatic tolerances, masking species potential vulnerability to climate change. Our results demonstrate that dynamic approaches to distribution modelling, such as incorporating organism-appropriate temporal scales, improves understanding of species distributions.

  3. Discriminant WSRC for Large-Scale Plant Species Recognition

    Directory of Open Access Journals (Sweden)

    Shanwen Zhang

    2017-01-01

    Full Text Available In sparse representation based classification (SRC and weighted SRC (WSRC, it is time-consuming to solve the global sparse representation problem. A discriminant WSRC (DWSRC is proposed for large-scale plant species recognition, including two stages. Firstly, several subdictionaries are constructed by dividing the dataset into several similar classes, and a subdictionary is chosen by the maximum similarity between the test sample and the typical sample of each similar class. Secondly, the weighted sparse representation of the test image is calculated with respect to the chosen subdictionary, and then the leaf category is assigned through the minimum reconstruction error. Different from the traditional SRC and its improved approaches, we sparsely represent the test sample on a subdictionary whose base elements are the training samples of the selected similar class, instead of using the generic overcomplete dictionary on the entire training samples. Thus, the complexity to solving the sparse representation problem is reduced. Moreover, DWSRC is adapted to newly added leaf species without rebuilding the dictionary. Experimental results on the ICL plant leaf database show that the method has low computational complexity and high recognition rate and can be clearly interpreted.

  4. Molecular identification, antifungal susceptibility profile, and biofilm formation of clinical and environmental Rhodotorula species isolates.

    Science.gov (United States)

    Nunes, Jorge Meneses; Bizerra, Fernando César; Ferreira, Renata Carmona E; Colombo, Arnaldo Lopes

    2013-01-01

    Rhodotorula species are emergent fungal pathogens capable of causing invasive infections, primarily fungemia. They are particularly problematic in immunosuppressed patients when using a central venous catheter. In this study, we evaluated the species distribution of 51 clinical and 8 environmental Rhodotorula species isolates using the ID32C system and internal transcribed spacer (ITS) sequencing. Antifungal susceptibility testing and biofilm formation capability using a crystal violet staining assay were performed. Using ITS sequencing as the gold standard, the clinical isolates were identified as follows: 44 R. mucilaginosa isolates, 2 R. glutinis isolates, 2 R. minuta isolates, 2 R. dairenensis isolates, and 1 Rhodosporidium fluviale isolate. The environmental isolates included 7 R. mucilaginosa isolates and 1 R. slooffiae isolate. Using the ID32C system, along with a nitrate assimilation test, only 90.3% of the isolates tested were correctly identified. In the biofilm formation assay, R. mucilaginosa and R. minuta exhibited greater biofilm formation ability compared to the other Rhodotorula species; the clinical isolates of R. mucilaginosa showed greater biofilm formation compared to the environmental isolates (P = 0.04). Amphotericin B showed good in vitro activity (MIC ≤ 1 μg/ml) against planktonic cells, whereas voriconazole and posaconazole showed poor activity (MIC(50)/MIC(90), 2/4 μg/ml). Caspofungin and fluconazole MICs were consistently high for all isolates tested (≥64 μg/ml and ≥ 4 μg/ml, respectively). In this study, we emphasized the importance of molecular methods to correctly identify Rhodotorula species isolates and non-R. mucilaginosa species in particular. The antifungal susceptibility profile reinforces amphotericin B as the antifungal drug of choice for the treatment of Rhodotorula infections. To our knowledge, this is the first study evaluating putative differences in the ability of biofilm formation among different Rhodotorula

  5. Geographical range and local abundance of tree species in China.

    Directory of Open Access Journals (Sweden)

    Haibao Ren

    Full Text Available Most studies on the geographical distribution of species have utilized a few well-known taxa in Europe and North America, with little research in China and its wide range of climate and forest types. We assembled large datasets to quantify the geographic ranges of tree species in China and to test several biogeographic hypotheses: 1 whether locally abundant species tend to be geographically widespread; 2 whether species are more abundant towards their range-centers; and 3 how abundances are correlated between sites. Local abundances of 651 species were derived from four tree plots of 20-25 ha where all individuals ≥1 cm in stem diameter were mapped and identified taxonomically. Range sizes of these species across China were then estimated from over 460,000 geo-referenced records; a Bayesian approach was used, allowing careful measures of error of each range estimate. The log-transformed range sizes had a bell-shaped distribution with a median of 703,000 km(2, and >90% of 651 species had ranges >10(5 km(2. There was no relationship between local abundance and range size, and no evidence for species being more abundant towards their range-centers. Finally, species' abundances were positively correlated between sites. The widespread nature of most tree species in China suggests few are vulnerable to global extinction, and there is no indication of the double-peril that would result if rare species also had narrow ranges.

  6. Fouling Bryozoa from some Alexandria harbours, EGYPT. (I Erect species

    Directory of Open Access Journals (Sweden)

    KH.M. ABDEL-SALAM

    2008-05-01

    Full Text Available The fouling erect Bryozoa settled on polystyrene test panels immersed half a meter deep in the water of Abu Qir Harbour, the Eastern Harbour and El-Dekheila Harbour were studied. The present study yields 5 species of erect bryozoa. These areAmathia pruvoti, Zoobotryon verticillatum, Bowerbankia gracilis,Bugula neritina and Bugula stolonifera. The first three ones pertain to 3 genera of the family Vesiculariidae belonging to suborder the Stolonifera; while the other two species affiliate to the genus Bugula belonging to the family Bugulidae of suborder Anasca. The present record of Amathia pruvoti is the first from the Egyptian Mediterranean waters. A re-description, supplied with full structural illustrations of the recorded species is given. Moreover, the temporal and spatial distributions of the species recorded are encountered.

  7. Comparative toxicity of imidacloprid and thiacloprid to different species of soil invertebrates.

    Science.gov (United States)

    de Lima E Silva, Cláudia; Brennan, Nicola; Brouwer, Jitske M; Commandeur, Daniël; Verweij, Rudo A; van Gestel, Cornelis A M

    2017-05-01

    Neonicotinoid insecticides have come under increasing scrutiny for their impact on non-target organisms, especially pollinators. The current scientific literature is mainly focused on the impact of these insecticides on pollinators and some aquatic insects, leaving a knowledge gap concerning soil invertebrates. This study aimed at filling this gap, by determining the toxicity of imidacloprid and thiacloprid to five species of soil invertebrates: earthworms (Eisenia andrei), enchytraeids (Enchytraeus crypticus), Collembola (Folsomia candida), oribatid mites (Oppia nitens) and isopods (Porcellio scaber). Tests focused on survival and reproduction or growth, after 3-5 weeks exposure in natural LUFA 2.2 standard soil. Imidacloprid was more toxic than thiacloprid for all species tested. F. candida and E. andrei were the most sensitive species, with LC 50 s of 0.20-0.62 and 0.77 mg/kg dry soil for imidacloprid and 2.7-3.9 and 7.1 mg/kg dry soil for thiacloprid. EC 50 s for effects on the reproduction of F. candida and E. andrei were 0.097-0.30 and 0.39 mg/kg dry soil for imidacloprid and 1.7-2.4 and 0.44 mg/kg dry soil for thiacloprid. The least sensitive species were O. nitens and P. scaber. Enchytraeids were a factor of 5-40 less sensitive than the taxonomically related earthworm, depending on the endpoint considered. Although not all the species showed high sensitivity to the neonicotinoids tested, these results raise awareness about the effects these insecticides can have on non-target soil invertebrates.

  8. Feeding behavior and trophic interaction of three shark species in the Galapagos Marine Reserve

    Directory of Open Access Journals (Sweden)

    Diego Páez-Rosas

    2018-05-01

    Full Text Available There is great concern about the future of sharks in Ecuador because of the lack of biological knowledge of most species that inhabit the region. This paper analyzes the feeding behavior of the pelagic thresher shark (Alopias pelagicus, the blue shark (Prionace glauca and the silky shark (Carcharhinus falciformis through the use of stable isotopes of carbon and nitrogen (δ13C and δ15N, with the aim of determining the degree of interaction between these species in the Galapagos Marine Reserve. No interspecific differences were found in use of oceanic vs. inshore feeding areas (δ13C: Kruskal–Wallis test, p = 0.09. The position in the hierarchy of the food web where A. pelagicus feeds differed from that of the other species (δ15N: Kruskal–Wallis test, p = 0.01. There were no significant differences in δ13C and δ15N values between males and females of the three species (Student’s t-test, p > 0.05, which suggests that both sexes have a similar feeding behavior. A specialist strategy was observed in P. glauca (trophic niche breadth TNB = 0.69, while the other species were found to be generalist (A. pelagicus TNB = 1.50 and C. falciformis TNB = 1.09. The estimated trophic level (TL varied between the three species. C. falciformis occupied the highest trophic level (TL = 4.4, making it a quaternary predator in the region. The results of this study coincide with the identified behavior in these predators in other areas of the tropical Pacific (Colombia and Mexico, and suggest a pelagic foraging strategy with differential consumption of prey between the three species. These ecological aspects can provide timely information when implementing in conservation measures for these shark species in the Tropical Pacific and Galapagos Marine Reserve.

  9. Feeding behavior and trophic interaction of three shark species in the Galapagos Marine Reserve.

    Science.gov (United States)

    Páez-Rosas, Diego; Insuasti-Zarate, Paul; Riofrío-Lazo, Marjorie; Galván-Magaña, Felipe

    2018-01-01

    There is great concern about the future of sharks in Ecuador because of the lack of biological knowledge of most species that inhabit the region. This paper analyzes the feeding behavior of the pelagic thresher shark ( Alopias pelagicus ), the blue shark ( Prionace glauca ) and the silky shark ( Carcharhinus falciformis ) through the use of stable isotopes of carbon and nitrogen ( δ 13 C and δ 15 N), with the aim of determining the degree of interaction between these species in the Galapagos Marine Reserve. No interspecific differences were found in use of oceanic vs. inshore feeding areas ( δ 13 C: Kruskal-Wallis test, p = 0.09). The position in the hierarchy of the food web where A. pelagicus feeds differed from that of the other species ( δ 15 N: Kruskal-Wallis test, p = 0.01). There were no significant differences in δ 13 C and δ 15 N values between males and females of the three species (Student's t -test, p  > 0.05), which suggests that both sexes have a similar feeding behavior. A specialist strategy was observed in P. glauca (trophic niche breadth TNB = 0.69), while the other species were found to be generalist ( A. pelagicus TNB = 1.50 and C. falciformis TNB = 1.09). The estimated trophic level (TL) varied between the three species. C. falciformis occupied the highest trophic level (TL = 4.4), making it a quaternary predator in the region. The results of this study coincide with the identified behavior in these predators in other areas of the tropical Pacific (Colombia and Mexico), and suggest a pelagic foraging strategy with differential consumption of prey between the three species. These ecological aspects can provide timely information when implementing in conservation measures for these shark species in the Tropical Pacific and Galapagos Marine Reserve.

  10. Predictive value of species sensitivity distributions for effects of herbicides in freshwater ecosystems

    NARCIS (Netherlands)

    Brink, van den P.J.; Blake, N.; Brock, T.C.M.; Maltby, L.

    2006-01-01

    In this article we present a review of the laboratory and field toxicity of herbicides to aquatic ecosystems. Single-species acute toxicity data and ( micro) mesocosm data were collated for nine herbicides. These data were used to investigate the importance of test species selection in constructing

  11. Development of a suitable test method for evaluating the toxicity of contaminated soils to earthworms in Canada

    Energy Technology Data Exchange (ETDEWEB)

    Stephenson, G.L. [Univ. of Guelph, Ontario (Canada); Scroggins, R. [Environment Canada, Gloucester, Ontario (Canada). Method Development and Application Section

    1995-12-31

    Environment Canada has embarked on a five year program to develop, standardize, and validate a battery of soil toxicity tests which can be used to assess the relative toxicity of contaminants in soils to terrestrial organisms. These tests must be applicable to soil conditions typically found in Canadian environments and the test species must be representative of the species of soil invertebrates or plants inhabiting soil ecosystems in Canada. One of the toxicity tests being developed is designed to assess the toxicity of contaminated soils to earthworms. Five of the potential test species belong to the Lumbricidae family and include the Canadian worm (Allobophora calignosa/Aporrectodea tuberculate), the European bark worm (Dendrodtilus rubidus (rubida)), the pink soil worm (Eisenia rosea), the red marsh worm (Lumbricus rubellus), and the Canadian night crawler or dew worm (Lumbricus terrestris). The sixth species, the white pot worm (Enchytraeus albidus), belongs to the Enchytraeidae family. Further assessment reduced the number of representative species to three. Most earthworm test methods have been developed to assess the toxicity of chemically-spiked artificial soils to Eisenia fetida or E. andrei. Test methods have also been developed to assess the relative toxicity of contaminated soils from hazardous waste sites. Comparative acute toxicity data for three species of earthworm exposed to a hydrocarbon contamination will be presented. Comparative toxicity data for the same three species of earthworm will also be presented using test procedures and conditions that have been modified to accommodate biological differences among the species of earthworm. Recommendations regarding test design, methods, and conditions optimal for each test species will be summarized and discussed with respect to the precision of test results.

  12. Acute toxicity prediction to threatened and endangered species using Interspecies Correlation Estimation (ICE) models

    Science.gov (United States)

    Evaluating contaminant sensitivity of threatened and endangered (listed) species and protectiveness of chemical regulations often depends on toxicity data for commonly tested surrogate species. The U.S. EPA’s Internet application Web-ICE is a suite of Interspecies Correlati...

  13. Biofluorescence as a survey tool for cryptic marine species.

    Science.gov (United States)

    De Brauwer, Maarten; Hobbs, Jean-Paul A; Ambo-Rappe, Rohani; Jompa, Jamaluddin; Harvey, Euan S; McIlwain, Jennifer L

    2017-10-06

    As ecosystems come under increasing anthropogenic pressure, rare species face the highest risk of extinction. Paradoxically, data necessary to evaluate the conservation status of rare species are often lacking because of the challenges of detecting species with low abundance. One group of fishes subject to this undersampling bias are those with cryptic body patterns. Twenty-one percent of cryptic fish species assessed for their extinction risk (International Union for Conservation of Nature [IUCN]) are data deficient. We developed a nondestructive method for surveying cryptically patterned marine fishes based on the presence of biofluorescence (underwater biofluorescence census, UBC). Blue LED torches were used to investigate how widespread biofluorescence was in cryptic reef fishes in the Coral Triangle region. The effectiveness of UBC to generate abundance data was tested on a data-deficient pygmy seahorse species (Hippocampus bargibanti) and compared with data obtained from standard underwater visual census (UVC) surveys. We recorded 95 reef fish species displaying biofluorescence, 73 of which had not been previously described as biofluorescent. Of those fish with cryptic patterns, 87% were biofluorescent compared with 9% for noncryptic fishes. The probability of species displaying biofluorescence was 70.9 times greater for cryptic species than for noncryptic species. Almost twice the number of H. bargibanti was counted using the UBC compared with UVC. For 2 triplefin species (Ucla xenogrammus, Enneapterygius tutuilae), the abundance detected with UBC was triple that detected with UVC. The UBC method was effective at finding cryptic species that would otherwise be difficult to detect and thus will reduce interobserver variability inherent to UVC surveys. Biofluorescence is ubiquitous in cryptic fishes, making this method applicable across a wide range of species. Data collected using UBC could be used with multiple IUCN criteria to assess the extinction risk of

  14. Prevalence of Rickettsia species in Dermacentor variabilis ticks from Ontario, Canada.

    Science.gov (United States)

    Wood, Heidi; Dillon, Liz; Patel, Samir N; Ralevski, Filip

    2016-07-01

    Relatively little is known about the prevalence of rickettsial species in Dermacentor ticks in eastern Canada. In this study, Dermacentor ticks from the province of Ontario, Canada, were tested for the presence of spotted fever group rickettsial (SFGR) species, Coxiella burnetii and Francisella tularensis. Rickettsia rickettsii was not detected in any ticks tested, but R. montanensis was detected at a prevalence of 2.2% in D. variabilis (17/778). Two other SFGR species, R. parkeri and Candidatus R. andeanae, were detected individually in 2 Amblyomma maculatum ticks. Rickettsia peacockii, a non-pathogenic endosymbiont, was detected in two D. andersonii ticks. Given the highly abundant nature of D. variabilis, surveillance for human pathogens in this species of tick has important public health implications, but the lack of detection of known human pathogens indicates a low risk of infection via this tick species in Ontario. However, the detection of R. parkeri in an adventive A. maculatum tick indicates that health care providers should be aware of the possibility of spotted fever rickettsioses in individuals with a history of travel outside of Ontario and symptoms compatible with a spotted fever rickettsiosis. Coxiella burnetii and Francisella tularensis, human pathogens also potentially transmitted by D. variabilis, were not detected in a subset of the ticks. Copyright © 2016 Elsevier GmbH. All rights reserved.

  15. Mechanosensing of stem bending and its interspecific variability in five neotropical rainforest species.

    Science.gov (United States)

    Coutand, Catherine; Chevolot, Malia; Lacointe, André; Rowe, Nick; Scotti, Ivan

    2010-02-01

    In rain forests, sapling survival is highly dependent on the regulation of trunk slenderness (height/diameter ratio): shade-intolerant species have to grow in height as fast as possible to reach the canopy but also have to withstand mechanical loadings (wind and their own weight) to avoid buckling. Recent studies suggest that mechanosensing is essential to control tree dimensions and stability-related morphogenesis. Differences in species slenderness have been observed among rainforest trees; the present study thus investigates whether species with different slenderness and growth habits exhibit differences in mechanosensitivity. Recent studies have led to a model of mechanosensing (sum-of-strains model) that predicts a quantitative relationship between the applied sum of longitudinal strains and the plant's responses in the case of a single bending. Saplings of five different neotropical species (Eperua falcata, E. grandiflora, Tachigali melinonii, Symphonia globulifera and Bauhinia guianensis) were subjected to a regimen of controlled mechanical loading phases (bending) alternating with still phases over a period of 2 months. Mechanical loading was controlled in terms of strains and the five species were subjected to the same range of sum of strains. The application of the sum-of-strain model led to a dose-response curve for each species. Dose-response curves were then compared between tested species. The model of mechanosensing (sum-of-strain model) applied in the case of multiple bending as long as the bending frequency was low. A comparison of dose-response curves for each species demonstrated differences in the stimulus threshold, suggesting two groups of responses among the species. Interestingly, the liana species B. guianensis exhibited a higher threshold than other Leguminosae species tested. This study provides a conceptual framework to study variability in plant mechanosensing and demonstrated interspecific variability in mechanosensing.

  16. Actin expression in some Platyhelminthe species.

    Science.gov (United States)

    Fagotti, A; Panara, F; Di Rosa, I; Simoncelli, F; Gabbiani, G; Pascolini, R

    1994-10-01

    Actin expression in some Platyhelminthe species was demonstrated by western-blotting and immunocytochemical analysis using two distinct anti-actin antibodies: the anti-total actin that reacts against all actin isoforms of higher vertebrates and the anti-alpha SM-1 that recognizes the alpha-smooth muscle (alpha SM) isotype of endothermic vertebrates (Skalli et al., 1986). Western-blotting experiments showed that all species tested, including some free-living Platyhelminthes (Tricladida and Rhabdocoela) and the parasitic Fasciola hepatica, were stained by anti-total actin antibody while only Dugesidae and Dendrocoelidae showed a positive immunoreactivity against anti-alpha SM-1. These results were confirmed by cytochemical immunolocalization using both avidin biotin conjugated peroxidase reaction on paraffin sections, and immunogold staining on Lowicryl 4KM embedded specimens. Our findings may contribute to the understanding of Platyhelminthes phylogeny.

  17. Dietary specialization is linked to reduced species durations in North American fossil canids

    Science.gov (United States)

    Balisi, Mairin; Casey, Corinna; Van Valkenburgh, Blaire

    2018-04-01

    How traits influence species persistence is a fundamental question in ecology, evolution and palaeontology. We test the relationship between dietary traits and both species duration and locality coverage over 40 million years in North American canids, a clade with considerable ecomorphological disparity and a dense fossil record. Because ecomorphological generalization-broad resource use-may enable species to withstand disturbance, we predicted that canids of average size and mesocarnivory would exhibit longer durations and wider distributions than specialized larger or smaller species. Second, because locality coverage might reflect dispersal ability and/or survivability in a range of habitats, we predicted that high coverage would correspond with longer durations. We find a nonlinear relationship between species duration and degree of carnivory: species at either end of the carnivory spectrum tend to have shorter durations than mesocarnivores. Locality coverage shows no relationship with size, diet or duration. To test whether generalization (medium size, mesocarnivory) corresponds to an adaptive optimum, we fit trait evolution models to previously generated canid phylogenies. Our analyses identify no single optimum in size or diet. Instead, the primary model of size evolution is a classic Cope's Rule increase over time, while dietary evolution does not conform to a single model.

  18. Do black-furred animals compensate for high solar absorption with smaller hairs? A test with a polymorphic squirrel species

    Directory of Open Access Journals (Sweden)

    Melanie A. FRATTO, Andrew K. DAVIS

    2011-12-01

    Full Text Available In polymorphic mammalian species that display multiple color forms, those with dark, or melanic pelage would be prone to overheating, especially if they live in warm climates, because their fur absorbs solar energy at a higher rate. However, experimental studies indicate that certain physical properties of fur of dark individuals appear to prevent, or minimize heat stress, although it is not clear what properties do so. Here, we tested the possibility that black-furred individuals simply have shorter or thinner hair fibers, which would create a lighter (in terms of weight coat or one that allows greater air flow for evaporative coo- ling. We examined museum specimens of eastern fox squirrels Sciurus niger, a species native to the United States and one that displays brown, grey or all-black pelage color, and used image analysis procedures to quantify hairs from the dorsal surface and tail. From examination of 43 specimens (19 brown, 9 black and 15 grey, and 1,720 hairs, we found no significant difference in hair lengths across color morphs, but significant differences in hair fiber widths. Black squirrels had thinner body hairs than other forms (7% thinner, but thicker tail hairs (9% thicker than the others. Given that the dorsal surface would be directly exposed to solar radiation, we interpret this to be an adaptation to prevent heat stress during the day. The thicker tail hairs may be an adaptation for nighttime thermoregulation, since squirrels sleep with their tails wrapped around their bodies. These results add to a growing literature body of the functional significance of mammalian pelage [Current Zoology 57 (6: 731–736, 2011].

  19. Photosynthetic response to globally increasing CO2 of co-occurring temperate seagrass species

    DEFF Research Database (Denmark)

    Borum, Jens; Pedersen, Ole; Kotula, Lukasz

    2016-01-01

    Photosynthesis of most seagrass species seems to be limited by present concentrations of dissolved inorganic carbon (DIC). Therefore, the ongoing increase in atmospheric CO2 could enhance seagrass photosynthesis and internal O2 supply, and potentially change species competition through differential...... responses to increasing CO2 availability among species. We used short-term photosynthetic responses of nine seagrass species from the south-west of Australia to test species-specific responses to enhanced CO2 and changes in HCO3 -. Net photosynthesis of all species except Zostera polychlamys were limited...... at pre-industrial compared to saturating CO2 levels at light saturation, suggesting that enhanced CO2 availability will enhance seagrass performance. Seven out of the nine species were efficient HCO3 - users through acidification of diffusive boundary layers, production of extracellular carbonic...

  20. Terrestrial animals as invasive species and as species at risk from invasions

    Science.gov (United States)

    Deborah M. Finch; Dean Pearson; Joseph Wunderle; Wayne Arendt

    2010-01-01

    Including terrestrial animal species in the invasive species strategy plan is an important step in invasive species management. Invasions by nonindigenous species threaten nearly 50 percent of imperiled native species in the United States and are the Nation's second leading cause of species endangerment. Invasion and conversion of native habitats by exotic species...

  1. Phytotoxic potential of celtis australis L. (family ulmaceae) against four crop species

    International Nuclear Information System (INIS)

    Ahmad, I.; Hussain, F.

    2014-01-01

    Bioassays were conducted to test the phytotoxic potential of Celtis australis against Trifolium alexandrinum, Brassica campestris, Triticum aestivum and Lactuca sativa under laboratory condition. Aqueous extracts from twigs and leaves were obtained by soaking 5 and 10g plant material in 100 ml distilled water for 24 and 48hr durations. Aqueous extracts significantly delayed/retarded the germination and reduced the plumule and radicle growth of all the four test species. Generally, extracts soaked for 48h especially 10 gm/100ml were inhibitory than 24h extracts of 5 or 10gm material. Extracts from twigs were inhibitory to germination of wheat while same extracts inhibited the plumule growth of B. campestris. Radicle growth of T. alexandrinum was inhibited more by twig extracts. Hot water extracts from twigs were less inhibitory than leaf extracts. Litter and mulch also significantly delayed the seed germination and retarded the overall growth of seedlings of all test species. The number and length of seminal roots of T. aestivum was suppressed by all aqueous extracts, added litter and mulch. The inhibitory response depended upon the test species, concentration, soaking duration and physiological parameters. The results suggested that Celtis australis has strong phytotoxic potential. (author)

  2. Do laboratory species protect endangered species? Interspecies variation in responses to 17β-estradiol, a model endocrine active compound

    Science.gov (United States)

    Jorgenson, Zachary G.; Buhl, Kevin J.; Bartell, Stephen E.; Schoenfuss, Heiko L.

    2015-01-01

    Although the effects of estrogens on model laboratory species are well documented, their utility as surrogates for other species, including those listed as endangered, are less clear. Traditionally, conservation policies are evaluated based on model organism responses but are intended to protect all species in an environment. We tested the hypothesis that the endangered Rio Grande silvery minnow (Hybognathus amarus) is more vulnerable to endocrine disruption—as assessed through its larval predator-escape performance, survival, juvenile sex ratios, and whole-body vitellogenin concentration—than the commonly used toxicological model species fathead minnow (Pimephales promelas) and the bluegill sunfish (Lepomis macrochirus). Fish were exposed concurrently for 21 days to the model endocrine active compound (EAC) 17ß-estradiol (E2) at 10 ng E2/L and 30 ng E2/L in a flow-through system using reconstituted water that simulated the physicochemical conditions of the Middle Rio Grande in New Mexico, USA. No significant differences were observed between the fathead and silvery minnow in larval predator-escape response or juvenile sex ratio. Rio Grande silvery minnow survival decreased significantly at day 14 compared with the other two species; by day 21, both cyprinid species (silvery minnow and fathead minnow) exhibited a significant decrease in survival compared with bluegill sunfish, a member of the family Centrarchidae. Male Rio Grande silvery minnow showed a significant increase in whole-body vitellogenin concentration in the 10 ng/L treatment, whereas fathead minnow and bluegill sunfish showed no significant increases in vitellogenin concentrations across treatments. Our study showed response differences to estrogen exposures between the two cyprinid species and further divergence in responses between the families Cyprinidae and Centrarchidae. These results suggest that commonly used laboratory model organisms may be less sensitive to EACs than the endangered

  3. Do laboratory species protect endangered species? Interspecies variation in responses to 17β-estradiol, a model endocrine active compound.

    Science.gov (United States)

    Jorgenson, Z G; Buhl, K; Bartell, S E; Schoenfuss, H L

    2015-01-01

    Although the effects of estrogens on model laboratory species are well documented, their utility as surrogates for other species, including those listed as endangered, are less clear. Traditionally, conservation policies are evaluated based on model organism responses but are intended to protect all species in an environment. We tested the hypothesis that the endangered Rio Grande silvery minnow (Hybognathus amarus) is more vulnerable to endocrine disruption-as assessed through its larval predator-escape performance, survival, juvenile sex ratios, and whole-body vitellogenin concentration-than the commonly used toxicological model species fathead minnow (Pimephales promelas) and the bluegill sunfish (Lepomis macrochirus). Fish were exposed concurrently for 21 days to the model endocrine active compound (EAC) 17ß-estradiol (E2) at 10 ng E2/L and 30 ng E2/L in a flow-through system using reconstituted water that simulated the physicochemical conditions of the Middle Rio Grande in New Mexico, USA. No significant differences were observed between the fathead and silvery minnow in larval predator-escape response or juvenile sex ratio. Rio Grande silvery minnow survival decreased significantly at day 14 compared with the other two species; by day 21, both cyprinid species (silvery minnow and fathead minnow) exhibited a significant decrease in survival compared with bluegill sunfish, a member of the family Centrarchidae. Male Rio Grande silvery minnow showed a significant increase in whole-body vitellogenin concentration in the 10 ng/L treatment, whereas fathead minnow and bluegill sunfish showed no significant increases in vitellogenin concentrations across treatments. Our study showed response differences to estrogen exposures between the two cyprinid species and further divergence in responses between the families Cyprinidae and Centrarchidae. These results suggest that commonly used laboratory model organisms may be less sensitive to EACs than the endangered Rio

  4. A MULTIVARIATE APPROACH TO ANALYSE NATIVE FOREST TREE SPECIE SEEDS

    Directory of Open Access Journals (Sweden)

    Alessandro Dal Col Lúcio

    2006-03-01

    Full Text Available This work grouped, by species, the most similar seed tree, using the variables observed in exotic forest species of theBrazilian flora of seeds collected in the Forest Research and Soil Conservation Center of Santa Maria, Rio Grande do Sul, analyzedfrom January, 1997, to march, 2003. For the cluster analysis, all the species that possessed four or more analyses per lot wereanalyzed by the hierarchical Clustering method, of the standardized Euclidian medium distance, being also a principal componentanalysis technique for reducing the number of variables. The species Callistemon speciosus, Cassia fistula, Eucalyptus grandis,Eucalyptus robusta, Eucalyptus saligna, Eucalyptus tereticornis, Delonix regia, Jacaranda mimosaefolia e Pinus elliottii presentedmore than four analyses per lot, in which the third and fourth main components explained 80% of the total variation. The clusteranalysis was efficient in the separation of the groups of all tested species, as well as the method of the main components.

  5. Rare species contribute disproportionately to the functional structure of species assemblages.

    Science.gov (United States)

    Leitão, Rafael P; Zuanon, Jansen; Villéger, Sébastien; Williams, Stephen E; Baraloto, Christopher; Fortunel, Claire; Mendonça, Fernando P; Mouillot, David

    2016-04-13

    There is broad consensus that the diversity of functional traits within species assemblages drives several ecological processes. It is also widely recognized that rare species are the first to become extinct following human-induced disturbances. Surprisingly, however, the functional importance of rare species is still poorly understood, particularly in tropical species-rich assemblages where the majority of species are rare, and the rate of species extinction can be high. Here, we investigated the consequences of local and regional extinctions on the functional structure of species assemblages. We used three extensive datasets (stream fish from the Brazilian Amazon, rainforest trees from French Guiana, and birds from the Australian Wet Tropics) and built an integrative measure of species rarity versus commonness, combining local abundance, geographical range, and habitat breadth. Using different scenarios of species loss, we found a disproportionate impact of rare species extinction for the three groups, with significant reductions in levels of functional richness, specialization, and originality of assemblages, which may severely undermine the integrity of ecological processes. The whole breadth of functional abilities within species assemblages, which is disproportionately supported by rare species, is certainly critical in maintaining ecosystems particularly under the ongoing rapid environmental transitions. © 2016 The Author(s).

  6. Bioavailability and ecotoxicity of arsenic species in solution culture and soil system: implications to remediation.

    Science.gov (United States)

    Bolan, Nanthi; Mahimairaja, Santiago; Kunhikrishnan, Anitha; Seshadri, Balaji; Thangarajan, Ramya

    2015-06-01

    In this work, bioavailability and ecotoxicity of arsenite (As(III)) and arsenate (As(V)) species were compared between solution culture and soil system. Firstly, the adsorption of As(III) and As(V) was compared using a number of non-allophanic and allophanic soils. Secondly, the bioavailability and ecotoxicity were examined using germination, phytoavailability, earthworm, and soil microbial activity tests. Both As-spiked soils and As-contaminated sheep dip soils were used to test bioavailability and ecotoxicity. The sheep dip soil which contained predominantly As(V) species was subject to flooding to reduce As(V) to As(III) and then used along with the control treatment soil to compare the bioavailability between As species. Adsorption of As(V) was much higher than that of As(III), and the difference in adsorption between these two species was more pronounced in the allophanic than non-allophanic soils. In the solution culture, there was no significant difference in bioavailability and ecotoxicity, as measured by germination and phytoavailability tests, between these two As species. Whereas in the As-spiked soils, the bioavailability and ecotoxicity were higher for As(III) than As(V), and the difference was more pronounced in the allophanic than non-allophanic soils. Bioavailability of As increased with the flooding of the sheep dip soils which may be attributed to the reduction of As(V) to As(III) species. The results in this study have demonstrated that while in solution, the bioavailability and ecotoxicity do not vary between As(III) and As(V), in soils, the latter species is less bioavailable than the former species because As(V) is more strongly retained than As(III). Since the bioavailability and ecotoxicity of As depend on the nature of As species present in the environment, risk-based remediation approach should aim at controlling the dynamics of As transformation.

  7. Plant species diversity as a driver of early succession in abandoned fields: a multi-site approach.

    Science.gov (United States)

    Van der Putten, W H; Mortimer, S R; Hedlund, K; Van Dijk, C; Brown, V K; Lepä, J; Rodriguez-Barrueco, C; Roy, J; Diaz Len, T A; Gormsen, D; Korthals, G W; Lavorel, S; Regina, I Santa; Smilauer, P

    2000-07-01

    Succession is one of the most studied processes in ecology and succession theory provides strong predictability. However, few attempts have been made to influence the course of succession thereby testing the hypothesis that passing through one stage is essential before entering the next one. At each stage of succession ecosystem processes may be affected by the diversity of species present, but there is little empirical evidence showing that plant species diversity may affect succession. On ex-arable land, a major constraint of vegetation succession is the dominance of perennial early-successional (arable weed) species. Our aim was to change the initial vegetation succession by the direct sowing of later-successional plant species. The hypothesis was tested that a diverse plant species mixture would be more successful in weed suppression than species-poor mixtures. In order to provide a robust test including a wide range of environmental conditions and plant species, experiments were carried out at five sites across Europe. At each site, an identical experiment was set up, albeit that the plant species composition of the sown mixtures differed from site to site. Results of the 2-year study showed that diverse plant species mixtures were more effective at reducing the number of natural colonisers (mainly weeds from the seed bank) than the average low-diversity treatment. However, the effect of the low-diversity treatment depended on the composition of the species mixture. Thus, the effect of enhanced species diversity strongly depended on the species composition of the low-diversity treatments used for comparison. The effects of high-diversity plant species mixtures on weed suppression differed between sites. Low-productivity sites gave the weakest response to the diversity treatments. These differences among sites did not change the general pattern. The present results have implications for understanding biological invasions. It has been hypothesised that alien

  8. Do non-native plant species affect the shape of productivity-diversity relationships?

    Science.gov (United States)

    Drake, J.M.; Cleland, E.E.; Horner-Devine, M. C.; Fleishman, E.; Bowles, C.; Smith, M.D.; Carney, K.; Emery, S.; Gramling, J.; Vandermast, D.B.; Grace, J.B.

    2008-01-01

    The relationship between ecosystem processes and species richness is an active area of research and speculation. Both theoretical and experimental studies have been conducted in numerous ecosystems. One finding of these studies is that the shape of the relationship between productivity and species richness varies considerably among ecosystems and at different spatial scales, though little is known about the relative importance of physical and biological mechanisms causing this variation. Moreover, despite widespread concern about changes in species' global distributions, it remains unclear if and how such large-scale changes may affect this relationship. We present a new conceptual model of how invasive species might modulate relationships between primary production and species richness. We tested this model using long-term data on relationships between aboveground net primary production and species richness in six North American terrestrial ecosystems. We show that primary production and abundance of non-native species are both significant predictors of species richness, though we fail to detect effects of invasion extent on the shapes of the relationship between species richness and primary production.

  9. The terminator "toy" chemistry test: a simple tool to assess errors in transport schemes

    Directory of Open Access Journals (Sweden)

    P. H. Lauritzen

    2015-05-01

    Full Text Available This test extends the evaluation of transport schemes from prescribed advection of inert scalars to reactive species. The test consists of transporting two interacting chemical species in the Nair and Lauritzen 2-D idealized flow field. The sources and sinks for these two species are given by a simple, but non-linear, "toy" chemistry that represents combination (X + X → X2 and dissociation (X2 → X + X. This chemistry mimics photolysis-driven conditions near the solar terminator, where strong gradients in the spatial distribution of the species develop near its edge. Despite the large spatial variations in each species, the weighted sum XT = X + 2X2 should always be preserved at spatial scales at which molecular diffusion is excluded. The terminator test demonstrates how well the advection–transport scheme preserves linear correlations. Chemistry–transport (physics–dynamics coupling can also be studied with this test. Examples of the consequences of this test are shown for illustration.

  10. Enhanced passive bat rabies surveillance in indigenous bat species from Germany--a retrospective study.

    Directory of Open Access Journals (Sweden)

    Juliane Schatz

    2014-05-01

    Full Text Available In Germany, rabies in bats is a notifiable zoonotic disease, which is caused by European bat lyssaviruses type 1 and 2 (EBLV-1 and 2, and the recently discovered new lyssavirus species Bokeloh bat lyssavirus (BBLV. As the understanding of bat rabies in insectivorous bat species is limited, in addition to routine bat rabies diagnosis, an enhanced passive surveillance study, i.e. the retrospective investigation of dead bats that had not been tested for rabies, was initiated in 1998 to study the distribution, abundance and epidemiology of lyssavirus infections in bats from Germany. A total number of 5478 individuals representing 21 bat species within two families were included in this study. The Noctule bat (Nyctalus noctula and the Common pipistrelle (Pipistrellus pipistrellus represented the most specimens submitted. Of all investigated bats, 1.17% tested positive for lyssaviruses using the fluorescent antibody test (FAT. The vast majority of positive cases was identified as EBLV-1, predominately associated with the Serotine bat (Eptesicus serotinus. However, rabies cases in other species, i.e. Nathusius' pipistrelle bat (Pipistrellus nathusii, P. pipistrellus and Brown long-eared bat (Plecotus auritus were also characterized as EBLV-1. In contrast, EBLV-2 was isolated from three Daubenton's bats (Myotis daubentonii. These three cases contribute significantly to the understanding of EBLV-2 infections in Germany as only one case had been reported prior to this study. This enhanced passive surveillance indicated that besides known reservoir species, further bat species are affected by lyssavirus infections. Given the increasing diversity of lyssaviruses and bats as reservoir host species worldwide, lyssavirus positive specimens, i.e. both bat and virus need to be confirmed by molecular techniques.

  11. Enhanced Passive Bat Rabies Surveillance in Indigenous Bat Species from Germany - A Retrospective Study

    Science.gov (United States)

    Auer, Ernst; Goharriz, Hooman; Harbusch, Christine; Johnson, Nicholas; Kaipf, Ingrid; Mettenleiter, Thomas Christoph; Mühldorfer, Kristin; Mühle, Ralf-Udo; Ohlendorf, Bernd; Pott-Dörfer, Bärbel; Prüger, Julia; Ali, Hanan Sheikh; Stiefel, Dagmar; Teubner, Jens; Ulrich, Rainer Günter; Wibbelt, Gudrun; Müller, Thomas

    2014-01-01

    In Germany, rabies in bats is a notifiable zoonotic disease, which is caused by European bat lyssaviruses type 1 and 2 (EBLV-1 and 2), and the recently discovered new lyssavirus species Bokeloh bat lyssavirus (BBLV). As the understanding of bat rabies in insectivorous bat species is limited, in addition to routine bat rabies diagnosis, an enhanced passive surveillance study, i.e. the retrospective investigation of dead bats that had not been tested for rabies, was initiated in 1998 to study the distribution, abundance and epidemiology of lyssavirus infections in bats from Germany. A total number of 5478 individuals representing 21 bat species within two families were included in this study. The Noctule bat (Nyctalus noctula) and the Common pipistrelle (Pipistrellus pipistrellus) represented the most specimens submitted. Of all investigated bats, 1.17% tested positive for lyssaviruses using the fluorescent antibody test (FAT). The vast majority of positive cases was identified as EBLV-1, predominately associated with the Serotine bat (Eptesicus serotinus). However, rabies cases in other species, i.e. Nathusius' pipistrelle bat (Pipistrellus nathusii), P. pipistrellus and Brown long-eared bat (Plecotus auritus) were also characterized as EBLV-1. In contrast, EBLV-2 was isolated from three Daubenton's bats (Myotis daubentonii). These three cases contribute significantly to the understanding of EBLV-2 infections in Germany as only one case had been reported prior to this study. This enhanced passive surveillance indicated that besides known reservoir species, further bat species are affected by lyssavirus infections. Given the increasing diversity of lyssaviruses and bats as reservoir host species worldwide, lyssavirus positive specimens, i.e. both bat and virus need to be confirmed by molecular techniques. PMID:24784117

  12. Effect of glyphosate on growth of four freshwater species of phytoplankton: a microplate bioassay.

    Science.gov (United States)

    Vendrell, E; Ferraz, D Gómez de Barreda; Sabater, C; Carrasco, J M

    2009-05-01

    The acute toxicity of glyphosate herbicide was tested on the four species of freshwater phytoplankton, Scenedesmus acutus, Scenedesmus subspicatus, Chlorella vulgaris and Chlorella saccharophila. Herbicide concentrations eliciting a 50% growth reduction over 72 h (EC(50)) ranged from 24.5 to 41.7 mg L(-1), whilst a 10% growth inhibition is achieved by herbicide concentrations ranging from 1.6 to 3.0 mg L(-1), difficult to find neither in paddy fields (it is not used in rice) nor in the lake of the Albufera Natural Park. Chorella species are less sensitive to the herbicide than Scenedesmus species. It can be concluded that glyphosate has a low potential risk for the tested organisms.

  13. Searsia species with affinity to the N-methyl-d-aspartic acid (NMDA) receptor

    DEFF Research Database (Denmark)

    Jäger, Anna; Knap, D.M.; Nielsen, Birgitte

    2012-01-01

    Species of Searsia are used in traditional medicine to treat epilepsy. Previous studies on S. dentata and S. pyroides have shown that this is likely mediated via the N-methyl-d-aspartic acid (NMDA) receptor. Ethanolic extracts of leaves of six Searsia species were tested in a binding assay...

  14. Incorporating evolutionary insights to improve ecotoxicology for freshwater species

    Science.gov (United States)

    Brady, Steven P.; Richardson, Jonathan L.; Kunz, Bethany K.

    2017-01-01

    Ecotoxicological studies have provided extensive insights into the lethal and sublethal effects of environmental contaminants. These insights are critical for environmental regulatory frameworks, which rely on knowledge of toxicity for developing policies to manage contaminants. While varied approaches have been applied to ecotoxicological questions, perspectives related to the evolutionary history of focal species or populations have received little consideration. Here, we evaluate chloride toxicity from the perspectives of both macroevolution and contemporary evolution. First, by mapping chloride toxicity values derived from the literature onto a phylogeny of macroinvertebrates, fish, and amphibians, we tested whether macroevolutionary relationships across species and taxa are predictive of chloride tolerance. Next, we conducted chloride exposure tests for two amphibian species to assess whether potential contemporary evolutionary change associated with environmental chloride contamination influences chloride tolerance across local populations. We show that explicitly evaluating both macroevolution and contemporary evolution can provide important and even qualitatively different insights from those obtained via traditional ecotoxicological studies. While macroevolutionary perspectives can help forecast toxicological end points for species with untested sensitivities, contemporary evolutionary perspectives demonstrate the need to consider the environmental context of exposed populations when measuring toxicity. Accounting for divergence among populations of interest can provide more accurate and relevant information related to the sensitivity of populations that may be evolving in response to selection from contaminant exposure. Our data show that approaches accounting for and specifically examining variation among natural populations should become standard practice in ecotoxicology.

  15. Antioxidant, Antimicrobial and Antiproliferative Activities of Five Lichen Species

    Directory of Open Access Journals (Sweden)

    Snežana Marković

    2011-08-01

    Full Text Available The antioxidative, antimicrobial and antiproliferative potentials of the methanol extracts of the lichen species Parmelia sulcata, Flavoparmelia caperata, Evernia prunastri, Hypogymnia physodes and Cladonia foliacea were evaluated. The total phenolic content of the tested extracts varied from 78.12 to 141.59 mg of gallic acid equivalent (GA/g of extract and the total flavonoid content from 20.14 to 44.43 mg of rutin equivalent (Ru/g of extract. The antioxidant capacities of the lichen extracts were determined by 2,2-diphenyl-1-picrylhydrazyl (DPPH radicals scavenging. Hypogymnia physodes with the highest phenolic content showed the strongest DPPH radical scavenging effect. Further, the antimicrobial potential of the lichen extracts was determined by a microdilution method on 29 microorganisms, including 15 strains of bacteria, 10 species of filamentous fungi and 4 yeast species. A high antimicrobial activity of all the tested extracts was observed with more potent inhibitory effects on the growth of Gram (+ bacteria. The highest antimicrobial activity among lichens was demonstrated by Hypogymnia physodes and Cladonia foliacea. Finally, the antiproliferative activity of the lichen extracts was explored on the colon cancer adenocarcinoma cell line HCT-116 by MTT (3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide viability assay and acridine orange/ethidium bromide staining. The methanol extracts of Hypogymnia physodes and Cladonia foliacea showed a better cytotoxic activity than the other extracts. All lichen species showed the ability to induce apoptosis of HCT-116 cells.

  16. Antioxidant, Antimicrobial and Antiproliferative Activities of Five Lichen Species

    Science.gov (United States)

    Mitrović, Tatjana; Stamenković, Slaviša; Cvetković, Vladimir; Tošić, Svetlana; Stanković, Milan; Radojević, Ivana; Stefanović, Olgica; Čomić, Ljiljana; Đačić, Dragana; Ćurčić, Milena; Marković, Snežana

    2011-01-01

    The antioxidative, antimicrobial and antiproliferative potentials of the methanol extracts of the lichen species Parmelia sulcata, Flavoparmelia caperata, Evernia prunastri, Hypogymnia physodes and Cladonia foliacea were evaluated. The total phenolic content of the tested extracts varied from 78.12 to 141.59 mg of gallic acid equivalent (GA)/g of extract and the total flavonoid content from 20.14 to 44.43 mg of rutin equivalent (Ru)/g of extract. The antioxidant capacities of the lichen extracts were determined by 2,2-diphenyl-1-picrylhydrazyl (DPPH) radicals scavenging. Hypogymnia physodes with the highest phenolic content showed the strongest DPPH radical scavenging effect. Further, the antimicrobial potential of the lichen extracts was determined by a microdilution method on 29 microorganisms, including 15 strains of bacteria, 10 species of filamentous fungi and 4 yeast species. A high antimicrobial activity of all the tested extracts was observed with more potent inhibitory effects on the growth of Gram (+) bacteria. The highest antimicrobial activity among lichens was demonstrated by Hypogymnia physodes and Cladonia foliacea. Finally, the antiproliferative activity of the lichen extracts was explored on the colon cancer adenocarcinoma cell line HCT-116 by MTT (3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide) viability assay and acridine orange/ethidium bromide staining. The methanol extracts of Hypogymnia physodes and Cladonia foliacea showed a better cytotoxic activity than the other extracts. All lichen species showed the ability to induce apoptosis of HCT-116 cells. PMID:21954369

  17. Molecular identification of python species: development and validation of a novel assay for forensic investigations.

    Science.gov (United States)

    Ciavaglia, Sherryn A; Tobe, Shanan S; Donnellan, Stephen C; Henry, Julianne M; Linacre, Adrian M T

    2015-05-01

    Python snake species are often encountered in illegal activities and the question of species identity can be pertinent to such criminal investigations. Morphological identification of species of pythons can be confounded by many issues and molecular examination by DNA analysis can provide an alternative and objective means of identification. Our paper reports on the development and validation of a PCR primer pair that amplifies a segment of the mitochondrial cytochrome b gene that has been suggested previously as a good candidate locus for differentiating python species. We used this DNA region to perform species identification of pythons, even when the template DNA was of poor quality, as might be the case with forensic evidentiary items. Validation tests are presented to demonstrate the characteristics of the assay. Tests involved the cross-species amplification of this marker in non-target species, minimum amount of DNA template required, effects of degradation on product amplification and a blind trial to simulate a casework scenario that provided 100% correct identity. Our results demonstrate that this assay performs reliably and robustly on pythons and can be applied directly to forensic investigations where the presence of a species of python is in question. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  18. The role of web sharing, species recognition and host-plant defence in interspecific competition between two herbivorous mite species.

    Science.gov (United States)

    Sato, Yukie; Alba, Juan M; Egas, Martijn; Sabelis, Maurice W

    2016-11-01

    When competing with indigenous species, invasive species face a problem, because they typically start with a few colonizers. Evidently, some species succeeded, begging an answer to the question how they invade. Here, we investigate how the invasive spider mite Tetranychus evansi interacts with the indigenous species T. urticae when sharing the solanaceous host plant tomato: do they choose to live together or to avoid each other's colonies? Both species spin protective, silken webs on the leaf surfaces, under which they live in groups of con- and possibly heterospecifics. In Spain, T. evansi invaded the non-crop field where native Tetranychus species including T. urticae dominated. Moreover, T. evansi outcompetes T. urticae when released together on a tomato plant. However, molecular plant studies suggest that T. urticae benefits from the local down-regulation of tomato plant defences by T. evansi, whereas T. evansi suffers from the induction of these defences by T. urticae. Therefore, we hypothesize that T. evansi avoids leaves infested with T. urticae whereas T. urticae prefers leaves infested by T. evansi. Using wild-type tomato and a mutant lacking jasmonate-mediated anti-herbivore defences, we tested the hypothesis and found that T. evansi avoided sharing webs with T. urticae in favour of a web with conspecifics, whereas T. urticae more frequently chose to share webs with T. evansi than with conspecifics. Also, T. evansi shows higher aggregation on a tomato plant than T. urticae, irrespective of whether the mites occur on the plant together or not.

  19. Spatial Downscaling of Alien Species Presences Using Machine Learning

    Directory of Open Access Journals (Sweden)

    Ioannis N. Daliakopoulos

    2017-07-01

    Full Text Available Spatially explicit assessments of alien species environmental and socio-economic impacts, and subsequent management interventions for their mitigation, require large scale, high-resolution data on species presence distribution. However, these data are often unavailable. This paper presents a method that relies on Random Forest (RF models to distribute alien species presence counts at a finer resolution grid, thus achieving spatial downscaling. A bootstrapping scheme is designed to account for sub-setting uncertainty, and subsets are used to train a sufficiently large number of RF models. RF results are processed to estimate variable importance and model performance. The method is tested with an ~8 × 8 km2 grid containing floral alien species presence and several potentially exploratory indices of climatic, habitat, land use, and soil property covariates for the Mediterranean island of Crete, Greece. Alien species presence is aggregated at 16 × 16 km2 and used as a predictor of presence at the original resolution, thus simulating spatial downscaling. Uncertainty assessment of the spatial downscaling of alien species' occurrences was also performed and true/false presences and absences were quantified. The approach is promising for downscaling alien species datasets of larger spatial scale but coarse resolution, where the underlying environmental information is available at a finer resolution. Furthermore, the RF architecture allows for tuning toward operationally optimal sensitivity and specificity, thus providing a decision support tool for designing a resource efficient alien species census.

  20. Core-satellite species hypothesis and native versus exotic species in secondary succession

    Science.gov (United States)

    Martinez, Kelsey A.; Gibson, David J.; Middleton, Beth A.

    2015-01-01

    A number of hypotheses exist to explain species’ distributions in a landscape, but these hypotheses are not frequently utilized to explain the differences in native and exotic species distributions. The core-satellite species (CSS) hypothesis predicts species occupancy will be bimodally distributed, i.e., many species will be common and many species will be rare, but does not explicitly consider exotic species distributions. The parallel dynamics (PD) hypothesis predicts that regional occurrence patterns of exotic species will be similar to native species. Together, the CSS and PD hypotheses may increase our understanding of exotic species’ distribution relative to natives. We selected an old field undergoing secondary succession to study the CSS and PD hypotheses in conjunction with each other. The ratio of exotic to native species (richness and abundance) was observed through 17 years of secondary succession. We predicted species would be bimodally distributed and that exotic:native species ratios would remain steady or decrease through time under frequent disturbance. In contrast to the CSS and PD hypotheses, native species occupancies were not bimodally distributed at the site, but exotic species were. The exotic:native species ratios for both richness (E:Nrichness) and abundance (E:Ncover) generally decreased or remained constant throughout supporting the PD hypothesis. Our results suggest exotic species exhibit metapopulation structure in old field landscapes, but that metapopulation structures of native species are disrupted, perhaps because these species are dispersal limited in the fragmented landscape.

  1. Applicability of the EN ISO 11290-1 standard method for Listeria monocytogenes detection in presence of new Listeria species.

    Science.gov (United States)

    Barre, Léna; Angelidis, Apostolos S; Boussaid, Djouher; Brasseur, Emilie Decourseulles; Manso, Eléonore; Gnanou Besse, Nathalie

    2016-12-05

    During the past six years, new species of the genus Listeria have been isolated from foods and other environmental niches worldwide. The Standard method EN ISO 11290-1 that is currently under revision will include in its scope all Listeria species in addition to L. monocytogenes. The objective of this project was to evaluate the ability of the Standard EN ISO 11290-1 method to detect and identify the newly discovered Listeria spp., and to assess potential over-growth effects of the new species in mixed cultures with L. monocytogenes during each step of the enrichment process. This objective was addressed by the generation of necessary data on the behavior of the new species during the pre-enrichment and the enrichment steps of the reference method as well as data on their phenotypic characteristics on rich and selective media used for isolation and identification. Most of the new Listeria species developed well on selective agar media for Listeria, however the recovery of some species was difficult due to poor growth in Half Fraser and Fraser broth. Good results (consistently positive) were obtained for confirmation at the genus level via the catalase test, the Gram test and the blueish appearance test on non-selective medium, but not with the VP test, as most of the new species yielded a negative result. In the light of results obtained in co-culture experiments and inhibition tests, and considering the growth rates in Half Fraser and Fraser broths, the new species do not seem to interfere with the detection of L. monocytogenes. Copyright © 2016 Elsevier B.V. All rights reserved.

  2. A multiplex PCR method for the identification of commercially important salmon and trout species (Oncorhynchus and Salmo) in North America.

    Science.gov (United States)

    Rasmussen Hellberg, Rosalee S; Morrissey, Michael T; Hanner, Robert H

    2010-09-01

    The purpose of this study was to develop a species-specific multiplex polymerase chain reaction (PCR) method that allows for the detection of salmon species substitution on the commercial market. Species-specific primers and TaqMan® probes were developed based on a comprehensive collection of mitochondrial 5' cytochrome c oxidase subunit I (COI) deoxyribonucleic acid (DNA) "barcode" sequences. Primers and probes were combined into multiplex assays and tested for specificity against 112 reference samples representing 25 species. Sensitivity and linearity tests were conducted using 10-fold serial dilutions of target DNA (single-species samples) and DNA admixtures containing the target species at levels of 10%, 1.0%, and 0.1% mixed with a secondary species. The specificity tests showed positive signals for the target DNA in both real-time and conventional PCR systems. Nonspecific amplification in both systems was minimal; however, false positives were detected at low levels (1.2% to 8.3%) in conventional PCR. Detection levels were similar for admixtures and single-species samples based on a 30 PCR cycle cut-off, with limits of 0.25 to 2.5 ng (1% to 10%) in conventional PCR and 0.05 to 5.0 ng (0.1% to 10%) in real-time PCR. A small-scale test with food samples showed promising results, with species identification possible even in heavily processed food items. Overall, this study presents a rapid, specific, and sensitive method for salmon species identification that can be applied to mixed-species and heavily processed samples in either conventional or real-time PCR formats. This study provides a newly developed method for salmon and trout species identification that will assist both industry and regulatory agencies in the detection and prevention of species substitution. This multiplex PCR method allows for rapid, high-throughput species identification even in heavily processed and mixed-species samples. An inter-laboratory study is currently being carried out to

  3. Two-species occupancy modeling accounting for species misidentification and nondetection

    Science.gov (United States)

    Chambert, Thierry; Grant, Evan H. Campbell; Miller, David A. W.; Nichols, James; Mulder, Kevin P.; Brand, Adrianne B,

    2018-01-01

    1. In occupancy studies, species misidentification can lead to false positive detections, which can cause severe estimator biases. Currently, all models that account for false positive errors only consider omnibus sources of false detections and are limited to single species occupancy. 2. However, false detections for a given species often occur because of the misidentification with another, closely-related species. To exploit this explicit source of false positive detection error, we develop a two-species occupancy model that accounts for misidentifications between two species of interest. As with other false positive models, identifiability is greatly improved by the availability of unambiguous detections at a subset of site-occasions. Here, we consider the case where some of the field observations can be confirmed using laboratory or other independent identification methods (“confirmatory data”). 3. We performed three simulation studies to (1) assess the model’s performance under various realistic scenarios, (2) investigate the influence of the proportion of confirmatory data on estimator accuracy, and (3) compare the performance of this two-species model with that of the single-species false positive model. The model shows good performance under all scenarios, even when only small proportions of detections are confirmed (e.g., 5%). It also clearly outperforms the single-species model.

  4. Incorporating Context Dependency of Species Interactions in Species Distribution Models.

    Science.gov (United States)

    Lany, Nina K; Zarnetske, Phoebe L; Gouhier, Tarik C; Menge, Bruce A

    2017-07-01

    Species distribution models typically use correlative approaches that characterize the species-environment relationship using occurrence or abundance data for a single species. However, species distributions are determined by both abiotic conditions and biotic interactions with other species in the community. Therefore, climate change is expected to impact species through direct effects on their physiology and indirect effects propagated through their resources, predators, competitors, or mutualists. Furthermore, the sign and strength of species interactions can change according to abiotic conditions, resulting in context-dependent species interactions that may change across space or with climate change. Here, we incorporated the context dependency of species interactions into a dynamic species distribution model. We developed a multi-species model that uses a time-series of observational survey data to evaluate how abiotic conditions and species interactions affect the dynamics of three rocky intertidal species. The model further distinguishes between the direct effects of abiotic conditions on abundance and the indirect effects propagated through interactions with other species. We apply the model to keystone predation by the sea star Pisaster ochraceus on the mussel Mytilus californianus and the barnacle Balanus glandula in the rocky intertidal zone of the Pacific coast, USA. Our method indicated that biotic interactions between P. ochraceus and B. glandula affected B. glandula dynamics across >1000 km of coastline. Consistent with patterns from keystone predation, the growth rate of B. glandula varied according to the abundance of P. ochraceus in the previous year. The data and the model did not indicate that the strength of keystone predation by P. ochraceus varied with a mean annual upwelling index. Balanus glandula cover increased following years with high phytoplankton abundance measured as mean annual chlorophyll-a. M. californianus exhibited the same

  5. Life history affects how species experience succession in pen shell metacommunities.

    Science.gov (United States)

    Munguia, Pablo

    2014-04-01

    In nature, very few species are common and broadly distributed. Most species are rare and occupy few sites; this pattern is ubiquitous across habitats and taxa. In spatially structured communities (metacommunities), regional distribution and local abundance may change as the relative effects of within-habitat processes (e.g., species interactions) and among-habitat processes (e.g., dispersal) may vary through succession. A field experiment with the marine benthic inhabitants of pen shells (Atrina rigida) tested how common and rare species respond to succession and metacommunity size. I followed community development through time and partitioned species into sessile and motile based on their natural history. Rare species drive diversity patterns and are influenced by metacommunity size: there are strong abundance-distribution differences between common and rare species in large metacommunities, but motile species show lower rates of change than sessile species. In small metacommunities both common and rare species have similar changes through time; the dichotomous distinction of common and rare species is not present. Edge effects in metacommunities affect species' changes in distribution and abundance. In large metacommunities diversity is higher in edge habitats relative to small metacommunities during early succession. However, edge effects benefit motile species over time in small metacommunities showing a rapid increase in diversity. Individual mobility is sensitive to regional community size and allows individuals to sort among different communities. In contrast, sessile species do not show this edge effect. Metacommunity theory is a useful framework for understanding spatially structured communities, but the natural history of coexisting species cannot be ignored.

  6. Panoramic view of the occurrence of Yersinia species other than Y. pestis in Brazil

    Directory of Open Access Journals (Sweden)

    J. P. Falcão

    2009-01-01

    Full Text Available

    Data on the occurrence of Yersinia species. other than Y. pestis in Brazil are presented. Over the past 40 years, 767 Yersinia strains have been identified and typed by the National Reference Center on Yersinia spp. Other than Y. pestis, using the classical biochemical tests for species characterization. The strains were further classified into biotypes, serotypes and phagetypes when pertinent. These tests led to the identification of Yersinia cultures belonging to the species Y. enterocolitica, Y. pseudotuberculosis, Y. intermedia, Y. frederiksenii and Y. kristensenii. Six isolates could not be classified in any of the known Yersinia species and for this reason were defined as Non-typable (NT. The bio-sero-phagetypes of these strains were diverse. The following species of Yersinia were not identified among the Brazilian strains by the classical phenotypic or biochemical tests: Y. aldovae, Y. rhodei, Y. mollaretti, Y. bercovieri and Y. ruckeri. The Yersinia strains were isolated from clinical material taken from sick and/or healthy humans and animals, from various types of food and from the environment, by investigators of various Institutions localized in different cities and regions of Brazil. Keywords: Yersinia spp.; occurrence; Brazil

  7. Allelochemical Control of Non-Indigenous Invasive Plant Species Affecting Military Testing and Training Activities

    Science.gov (United States)

    2010-10-01

    exhibit resistance to flavonoids in knapweed root exudates and may serve as candidate species for management efforts. Because legumes form symbiotic...metabolite-related transcript, as this enzyme represents the first enzymatic step in the flavonoid synthesis pathway which contributes isoflavones...anthocyanins, condensed tannins and other secondary metabolic compounds in plants (La Camera et al. 2004; Treutter 2005; Winkel-Shirley 2001). Flavonoids

  8. Architecture of 53 rain forest tree species differing in adult stature and shade tolerance

    NARCIS (Netherlands)

    Poorter, L.; Bongers, F.J.J.M.; Sterck, F.J.; Wöll, H.

    2003-01-01

    Tree architecture determines a tree's light capture, stability, and efficiency of crown growth. The hypothesis that light demand and adult stature of tree species within a community, independently of each other, determine species' architectural traits was tested by comparing 53 Liberian rain forest

  9. A Multi-species Bait for Chagas Disease Vectors

    Science.gov (United States)

    Mota, Theo; Vitta, Ana C. R.; Lorenzo-Figueiras, Alicia N.; Barezani, Carla P.; Zani, Carlos L.; Lazzari, Claudio R.; Diotaiuti, Liléia; Jeffares, Lynne; Bohman, Björn; Lorenzo, Marcelo G.

    2014-01-01

    Background Triatomine bugs are the insect vectors of Trypanosoma cruzi, the etiological agent of Chagas disease. These insects are known to aggregate inside shelters during daylight hours and it has been demonstrated that within shelters, the aggregation is induced by volatiles emitted from bug feces. These signals promote inter-species aggregation among most species studied, but the chemical composition is unknown. Methodology/Principal Findings In the present work, feces from larvae of the three species were obtained and volatile compounds were identified by solid phase microextraction-gas chromatography-mass spectrometry (SPME-GC-MS). We identified five compounds, all present in feces of all of the three species: Triatoma infestans, Panstrongylus megistus and Triatoma brasiliensis. These substances were tested for attractivity and ability to recruit insects into shelters. Behaviorally active doses of the five substances were obtained for all three triatomine species. The bugs were significantly attracted to shelters baited with blends of 160 ng or 1.6 µg of each substance. Conclusions/Significance Common compounds were found in the feces of vectors of Chagas disease that actively recruited insects into shelters, which suggests that this blend of compounds could be used for the development of baits for early detection of reinfestation with triatomine bugs. PMID:24587457

  10. The effects of model and data complexity on predictions from species distributions models

    DEFF Research Database (Denmark)

    García-Callejas, David; Bastos, Miguel

    2016-01-01

    How complex does a model need to be to provide useful predictions is a matter of continuous debate across environmental sciences. In the species distributions modelling literature, studies have demonstrated that more complex models tend to provide better fits. However, studies have also shown...... that predictive performance does not always increase with complexity. Testing of species distributions models is challenging because independent data for testing are often lacking, but a more general problem is that model complexity has never been formally described in such studies. Here, we systematically...

  11. Automated cognitive testing of monkeys in social groups yields results comparable to individual laboratory-based testing.

    Science.gov (United States)

    Gazes, Regina Paxton; Brown, Emily Kathryn; Basile, Benjamin M; Hampton, Robert R

    2013-05-01

    Cognitive abilities likely evolved in response to specific environmental and social challenges and are therefore expected to be specialized for the life history of each species. Specialized cognitive abilities may be most readily engaged under conditions that approximate the natural environment of the species being studied. While naturalistic environments might therefore have advantages over laboratory settings for cognitive research, it is difficult to conduct certain types of cognitive tests in these settings. We implemented methods for automated cognitive testing of monkeys (Macaca mulatta) in large social groups (Field station) and compared the performance to that of laboratory-housed monkeys (Laboratory). The Field station animals shared access to four touch-screen computers in a large naturalistic social group. Each Field station subject had an RFID chip implanted in each arm for computerized identification and individualized assignment of cognitive tests. The Laboratory group was housed and tested in a typical laboratory setting, with individual access to testing computers in their home cages. Monkeys in both groups voluntarily participated at their own pace for food rewards. We evaluated performance in two visual psychophysics tests, a perceptual classification test, a transitive inference test, and a delayed matching-to-sample memory test. Despite the differences in housing, social environment, age, and sex, monkeys in the two groups performed similarly in all tests. Semi-free ranging monkeys living in complex social environments are therefore viable subjects for cognitive testing designed to take advantage of the unique affordances of naturalistic testing environments.

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

    Science.gov (United States)

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

    2011-01-01

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

  13. Using Bioassays and Species Sensitivity Distributions to Assess Herbicide Toxicity towards Benthic Diatoms

    Science.gov (United States)

    Larras, Floriane; Bouchez, Agnès; Rimet, Frédéric; Montuelle, Bernard

    2012-01-01

    Although benthic diatoms are widely used in ecological studies of aquatic systems, there is still a dearth of data concerning species sensitivities towards several contaminants. Within the same community, different species may respond differently depending on their physiological and ecological characteristics. This lack of knowledge makes specific appropriate risk assessment impossible. To find out whether species sensitivity distribution (SSD) could be used to estimate the risk of herbicide toxicity for diatoms, we need to know whether their sensitivity depends on their physiological and ecological characteristics. We carried out single-species bioassays on 11 diatom species exposed to 8 herbicides. Dose-responses relationships were used to extrapolate the Effective Concentration 5 (EC5) and the Effective Concentration 50 (EC50) for each exposure. These data were used to fit a SSD curve for each herbicide, and to determine the Hazardous concentration 5 (HC5) and 50 (HC50). Our results revealed a high level of variability of the sensitivity in the set of species tested. For photosystem-II inhibitor (PSII) herbicides, diatoms species displayed a typical grouping of sensitivity levels consistent with their trophic mode and their ecological guild. N-heterotroph and “motile” guild species were more tolerant of PSII inhibitors, while N-autotroph and “low profile” guild species were more sensitive. Comprehensive SSD curves were obtained for 5 herbicides, but not for sulfonylurea herbicides or for dimetachlor, which had toxicity levels that were below the range of concentration tested. The SSD curves provided the following ranking of toxicity: diuron> terbutryn> isoproturon> atrazine> metolachlor. The HC that affected 5% of the species revealed that, even at the usual environmental concentrations of herbicides, diatom assemblages could be affected, especially by isoproturon, terbutryn, and diuron. PMID:22952981

  14. Using bioassays and species sensitivity distributions to assess herbicide toxicity towards benthic diatoms.

    Directory of Open Access Journals (Sweden)

    Floriane Larras

    Full Text Available Although benthic diatoms are widely used in ecological studies of aquatic systems, there is still a dearth of data concerning species sensitivities towards several contaminants. Within the same community, different species may respond differently depending on their physiological and ecological characteristics. This lack of knowledge makes specific appropriate risk assessment impossible. To find out whether species sensitivity distribution (SSD could be used to estimate the risk of herbicide toxicity for diatoms, we need to know whether their sensitivity depends on their physiological and ecological characteristics. We carried out single-species bioassays on 11 diatom species exposed to 8 herbicides. Dose-responses relationships were used to extrapolate the Effective Concentration 5 (EC(5 and the Effective Concentration 50 (EC(50 for each exposure. These data were used to fit a SSD curve for each herbicide, and to determine the Hazardous concentration 5 (HC(5 and 50 (HC(50. Our results revealed a high level of variability of the sensitivity in the set of species tested. For photosystem-II inhibitor (PSII herbicides, diatoms species displayed a typical grouping of sensitivity levels consistent with their trophic mode and their ecological guild. N-heterotroph and "motile" guild species were more tolerant of PSII inhibitors, while N-autotroph and "low profile" guild species were more sensitive. Comprehensive SSD curves were obtained for 5 herbicides, but not for sulfonylurea herbicides or for dimetachlor, which had toxicity levels that were below the range of concentration tested. The SSD curves provided the following ranking of toxicity: diuron> terbutryn> isoproturon> atrazine> metolachlor. The HC that affected 5% of the species revealed that, even at the usual environmental concentrations of herbicides, diatom assemblages could be affected, especially by isoproturon, terbutryn, and diuron.

  15. Freshwater algae of the Nevada Test Site

    International Nuclear Information System (INIS)

    Taylor, W.D.; Giles, K.R.

    1979-06-01

    Fifty-two species of freshwater algae were identified in samples collected from the eight known natural springs of the Nevada Test Site. Although several species were widespread, 29 species were site specific. Diatoms provided the greatest variety of species at each spring. Three-fifths of all algal species encountered were diatoms. Well-developed mats of filamentous green algae (Chlorophyta) were common in many of the water tanks associated with the springs and accounted for most of the algal biomass. Major nutrients were adequate, if not abundant, in most spring waters - growth being limited primarily by light and physical habitat. There was some evidence of cesium-137 bioconcentration by algae at several of the springs

  16. Differences in species richness patterns between unicellular and multicellular organisms.

    Science.gov (United States)

    Hillebrand, Helmut; Watermann, Frank; Karez, Rolf; Berninger, Ulrike-G

    2001-01-01

    For unicellular organisms, a lack of effects of local species richness on ecosystem function has been proposed due to their locally high species richness and their ubiquitous distribution. High dispersal ability and high individual numbers may enable unicellular taxa to occur everywhere. Using our own and published data sets on uni- and multicellular organisms, we conducted thorough statistical analyses to test whether (1) unicellular taxa show higher relative local species richness compared to multicellular taxa, (2) unicellular taxa show lower slopes of the species:area relationships and species:individuals relationships, and (3) the species composition of unicellular taxa is less influenced by geographic distance compared to multicellular taxa. We found higher local species richness compared to the global species pool for unicellular organisms than for metazoan taxa. The difference was significant if global species richness was conservatively estimated but not if extrapolated, and therefore higher richness estimates were used. Both microalgae and protozoans showed lower slopes between species richness and sample size (area or individuals) compared to macrozoobenthos, also indicating higher local species richness for unicellular taxa. The similarity of species composition of both benthic diatoms and ciliates decreased with increasing geographic distance. This indicated restricted dispersal ability of protists and the absence of ubiquity. However, a steeper slope between similarity and distance was found for polychaetes and corals, suggesting a stronger effect of distance on the dispersal of metazoans compared to unicellular taxa. In conclusion, we found partly different species richness patterns among uni- and multicellular eukaryotes, but no strict ubiquity of unicellular taxa. Therefore, the effect of local unicellular species richness on ecosystem function has to be reanalyzed. Macroecological patterns suggested for multicellular organisms may differ in

  17. Predictive acute toxicity tests with pesticides.

    Science.gov (United States)

    Brown, V K

    1983-01-01

    By definition pesticides are biocidal products and this implies a probability that pesticides may be acutely toxic to species other than the designated target species. The ways in which pesticides are manufactured, formulated, packaged, distributed and used necessitates a potential for the exposure of non-target species although the technology exists to minimize adventitious exposure. The occurrence of deliberate exposure of non-target species due to the misuse of pesticides is known to happen. The array of predictive acute toxicity tests carried out on pesticides and involving the use of laboratory animals can be justified as providing data on which hazard assessment can be based. This paper addresses the justification and rationale of this statement.

  18. Development of a Species-specific PCR Assay for Three Xanthomonas Species, Causing Bulb and Flower Diseases, Based on Their Genome Sequences

    Directory of Open Access Journals (Sweden)

    Chang-Gi Back

    2015-09-01

    Full Text Available In this study, we developed a species-specific PCR assay for rapid and accurate detection of three Xanthomonas species, X. axonopodis pv. poinsettiicola (XAP, X. hyacinthi (XH and X. campestris pv. zantedeschiae (XCZ, based on their draft genome sequences. XAP, XH and XCZ genomes consist of single chromosomes that contain 5,221, 4,395 and 7,986 protein coding genes, respectively. Species-specific primers were designed from variable regions of the draft genome sequence data and assessed by a PCR-based detection method. These primers were also tested for specificity against 17 allied Xanthomonas species as well as against the host DNA and the microbial community of the host surface. Three primer sets were found to be very specific and no amplification product was obtained with the host DNA and the microbial community of the host surface. In addition, a detection limit of 1 pg/μl per PCR reaction was detected when these primer sets were used to amplify corresponding bacterial DNAs. Therefore, these primer sets and the developed species-specific PCR assay represent a valuable, sensitive, and rapid diagnostic tool that can be used to detect three specific pathogens at early stages of infection and may help control diseases.

  19. Natural selection constrains neutral diversity across a wide range of species.

    Science.gov (United States)

    Corbett-Detig, Russell B; Hartl, Daniel L; Sackton, Timothy B

    2015-04-01

    The neutral theory of molecular evolution predicts that the amount of neutral polymorphisms within a species will increase proportionally with the census population size (Nc). However, this prediction has not been borne out in practice: while the range of Nc spans many orders of magnitude, levels of genetic diversity within species fall in a comparatively narrow range. Although theoretical arguments have invoked the increased efficacy of natural selection in larger populations to explain this discrepancy, few direct empirical tests of this hypothesis have been conducted. In this work, we provide a direct test of this hypothesis using population genomic data from a wide range of taxonomically diverse species. To do this, we relied on the fact that the impact of natural selection on linked neutral diversity depends on the local recombinational environment. In regions of relatively low recombination, selected variants affect more neutral sites through linkage, and the resulting correlation between recombination and polymorphism allows a quantitative assessment of the magnitude of the impact of selection on linked neutral diversity. By comparing whole genome polymorphism data and genetic maps using a coalescent modeling framework, we estimate the degree to which natural selection reduces linked neutral diversity for 40 species of obligately sexual eukaryotes. We then show that the magnitude of the impact of natural selection is positively correlated with Nc, based on body size and species range as proxies for census population size. These results demonstrate that natural selection removes more variation at linked neutral sites in species with large Nc than those with small Nc and provides direct empirical evidence that natural selection constrains levels of neutral genetic diversity across many species. This implies that natural selection may provide an explanation for this longstanding paradox of population genetics.

  20. Generic reclassification and species boundaries in the rediscovered freshwater mussel ‘Quadrula’ mitchelli (Simpson in Dall, 1896)

    Science.gov (United States)

    Pfeiffer, John M.; Johnson, Nathan A.; Randklev, Charles R.; Howells, Robert G.; Williams, James D.

    2016-01-01

    The Central Texas endemic freshwater mussel, Quadrula mitchelli (Simpson in Dall, 1896), had been presumed extinct until relict populations were recently rediscovered. To help guide ongoing and future conservation efforts focused on Q. mitchelli we set out to resolve several uncertainties regarding its evolutionary history, specifically its unknown generic position and untested species boundaries. We designed a molecular matrix consisting of two loci (cytochrome c oxidase subunit I and internal transcribed spacer I) and 57 terminal taxa to test the generic position of Q. mitchelli using Bayesian inference and maximum likelihood phylogenetic reconstruction. We also employed two Bayesian species validation methods to test five a priori species models (i.e. hypotheses of species delimitation). Our study is the first to test the generic position of Q.mitchelli and we found robust support for its inclusion in the genusFusconaia. Accordingly, we introduce the binomial, Fusconaia mitchelli comb. nov., to accurately represent the systematic position of the species. We resolved F. mitchelli individuals in two well supported and divergent clades that were generally distinguished as distinct species using Bayesian species validation methods, although alternative hypotheses of species delineation were also supported. Despite strong evidence of genetic isolation within F. mitchelli, we do not advocate for species-level status of the two clades as they are allopatrically distributed and no morphological, behavioral, or ecological characters are known to distinguish them. These results are discussed in the context of the systematics, distribution, and conservation ofF. mitchelli.

  1. Agroforestry Species Switchboard

    DEFF Research Database (Denmark)

    Kindt, R.; John, I.; Ordonez, J.

    2016-01-01

    The current version of the Agroforestry Species Switchboard documents the presence of a total of 26,135 plant species (33,813 species including synonyms) across 19 web-based databases. When available, hyperlinks to information on the selected species in particular databases are provided. In total...

  2. Identification of fine-leaved species of genus Festuca by molecular methods

    International Nuclear Information System (INIS)

    Stukonis, V.; Armoniene, R.; Kemesyte, V.

    2015-01-01

    Festuca (L.) is a taxonomically complex genus of family Poaceae. The fine-leaved species of fescue are well adapted to grow in sandy and dry habitats, therefore, they can be used for establishment of lawns of minimal maintenance as well as recultivations of damaged soils. Breeding for the new varieties to meet these purposes requires reliable methods for identification of the species. The discrimination of fine-leaved fescue species based on morphological features is rather difficult, therefore reliable molecular marker would greatly facilitate it and eliminate the need to wait till floral organs are fully formed. Seven fine-leaved species of genus Festuca collected in Lithuania, namely, F. ovina, F. trachyphylla, F. polesica, F. psammophila, F. sabulosa, F. pseudovina and F. wolgensis were investigated at the Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry. The ISSR markers, seed storage proteins and isozymes were tested for their ability to distinguish between the fine-leaved species of the genus Festuca. Seed storage protein and ISSR fingerprint profiles could be used to distinguish between fine-leaved species of Festuca, except for closely related F. sabulosa and F. polesica species. Isozyme fingerprints did not contain sufficient number of species specific bands and were not feasible to discriminate between species. (author)

  3. Pest species diversity enhances control of spider mites and whiteflies by a generalist phytoseiid predator

    NARCIS (Netherlands)

    Messelink, G.J.; Maanen, van R.; Holstein-Saj, van R.; Sabelis, M.W.; Janssen, A.

    2010-01-01

    To test the hypothesis that pest species diversity enhances biological pest control with generalist predators, we studied the dynamics of three major pest species on greenhouse cucumber: Western flower thrips, Frankliniella occidentalis (Pergande), greenhouse whitefly, Trialeurodes vaporariorum

  4. Antibiotic susceptibility of enterobacteriaceae species isolated from mastitic milk in Algeria

    Directory of Open Access Journals (Sweden)

    R Saidi

    2014-12-01

    Conclusions: We conclude that Enterobacteriaceae species from bovine milk presented significantly distinct antimicrobial resistance profiles, evaluated by phenotypic test, which has implications for treatment and management decisions.

  5. Standardization of a two-step real-time polymerase chain reaction based method for species-specific detection of medically important Aspergillus species.

    Science.gov (United States)

    Das, P; Pandey, P; Harishankar, A; Chandy, M; Bhattacharya, S; Chakrabarti, A

    2017-01-01

    Standardization of Aspergillus polymerase chain reaction (PCR) poses two technical challenges (a) standardization of DNA extraction, (b) optimization of PCR against various medically important Aspergillus species. Many cases of aspergillosis go undiagnosed because of relative insensitivity of conventional diagnostic methods such as microscopy, culture or antigen detection. The present study is an attempt to standardize real-time PCR assay for rapid sensitive and specific detection of Aspergillus DNA in EDTA whole blood. Three nucleic acid extraction protocols were compared and a two-step real-time PCR assay was developed and validated following the recommendations of the European Aspergillus PCR Initiative in our setup. In the first PCR step (pan-Aspergillus PCR), the target was 28S rDNA gene, whereas in the second step, species specific PCR the targets were beta-tubulin (for Aspergillus fumigatus, Aspergillus flavus, Aspergillus terreus), gene and calmodulin gene (for Aspergillus niger). Species specific identification of four medically important Aspergillus species, namely, A. fumigatus, A. flavus, A. niger and A. terreus were achieved by this PCR. Specificity of the PCR was tested against 34 different DNA source including bacteria, virus, yeast, other Aspergillus sp., other fungal species and for human DNA and had no false-positive reactions. The analytical sensitivity of the PCR was found to be 102 CFU/ml. The present protocol of two-step real-time PCR assays for genus- and species-specific identification for commonly isolated species in whole blood for diagnosis of invasive Aspergillus infections offers a rapid, sensitive and specific assay option and requires clinical validation at multiple centers.

  6. Photosynthesis and Calcification by Emiliania huxleyi (Prymnesiophyceae) as a Function of Inorganic Carbon Species

    NARCIS (Netherlands)

    Buitenhuis, Erik T.; Baar, Hein J.W. de; Veldhuis, Marcel J.W.

    1999-01-01

    To test the possibility of inorganic carbon limitation of the marine unicellular alga Emiliania huxleyi (Lohmann) Hay and Mohler, its carbon acquisition was measured as a function of the different chemical species of inorganic carbon present in the medium. Because these different species are

  7. Characterization of Candida species isolated from cases of lower respiratory tract infection.

    Science.gov (United States)

    Jha, B J; Dey, S; Tamang, M D; Joshy, M E; Shivananda, P G; Brahmadatan, K N

    2006-01-01

    (1) To identify and characterize the Candida species isolates from lower respiratory tract infection. (2) to determine the rate of isolation of Candida species from sputum samples. This study was carried out in the Department of Microbiology, Manipal Teaching Hospital, Pokhara, Nepal from June 2002 to January 2003. A total of 462 sputum samples were collected from patients suspected lower respiratory tract infection. The samples were processed as Gram staining to find out the suitability of the specimen, cultured on Sabouraud's Dextrose Agar (SDA) and also on blood agar and chocolate agar to identify the potential lower respiratory tract pathogens. For the identification of Candida, sputum samples were processed for Gram stain, culture, germ tube test, production of chlamydospore, sugar fermentation and assimilation test. For the identification of bacteria, Gram stain, culture, and biochemical tests were performed by standardized procedure. Out of 462 samples, 246 (53.24%) samples grew potential pathogens of lower respiratory tract. Among them Haemophilus influenzae 61(24.79%) and Streptococcus pneumoniae 57 (23.17%) were the predominant bacterial pathogens. Candida species were isolated from 30 samples (12.2%). The majority of Candida species amongst the Candida isolates were Candida albicans 21(70%) followed by Candida tropicalis 4(13.33%). Candida krusei 3(10%), Candida parapsilosis 1(3.33%) and Candida stellatoidea 1(3.33%). The highest rate of isolation of Candida was between the age of 71 and 80. Candida isolation from sputum samples is important as found in the present study in which Candida species were the third most common pathogen isolated from patients with lower respiratory tract infection.

  8. Phytotoxic Activity and Chemical Composition of Aqueous Volatile Fractions from Eucalyptus Species

    Science.gov (United States)

    Zhang, Jinbiao; An, Min; Wu, Hanwen; Liu, De Li; Stanton, Rex

    2014-01-01

    The essential oils from four Eucalyptus species (E. spathulata, E. salubris, E. brockwayii and E. dundasii) have been previously confirmed to have stronger inhibitory effects on germination and seedling growth of silverleaf nightshade (Solanum elaeagnifolium Cav.). The aqueous volatile fractions (AVFs) were the water soluble volatile fractions produced together with the essential oils (water insoluble fractions) during the steam distillation process. The aim of this study was to further assess the phytotoxicity of AVFs from the four Eucalyptus species and their chemical composition. The fresh leaves of the four Eucalyptus species were used for the extraction of AVFs. The AVFs were tested for their phytotoxic effects on the perennial weed, silverleaf nightshade under laboratory conditions. The chemical compositions of the AVFs were determined by gas chromatograph–mass spectrometry (GC-MS). Our results showed that the AVFs had strong inhibition on the germination and seedling growth of silverleaf nightshade. The inhibition index increased with the increasing concentrations of AVFs. The inhibitory effects of the AVFs varied between different Eucalyptus species. The AVF from E. salubris demonstrated the highest inhibitory activity on the weed tested, with complete inhibition on germination and seedling growth at a concentration of 75%. The GC-MS analysis revealed that 1,8-cineole, isopentyl isovalerate, isomenthol, pinocarvone, trans-pinocarveol, alpha-terpineol and globulol were the main compounds in the AVFs. These results indicated that all AVFs tested had differential inhibition on the germination and seedling growth of silverleaf nightshade, which could be due to the joint effects of compounds present in the AVFs as these compounds were present in different quantities and ratio between Eucalyptus species. PMID:24681490

  9. Phytotoxic activity and chemical composition of aqueous volatile fractions from Eucalyptus species.

    Directory of Open Access Journals (Sweden)

    Jinbiao Zhang

    Full Text Available The essential oils from four Eucalyptus species (E. spathulata, E. salubris, E. brockwayii and E. dundasii have been previously confirmed to have stronger inhibitory effects on germination and seedling growth of silverleaf nightshade (Solanum elaeagnifolium Cav.. The aqueous volatile fractions (AVFs were the water soluble volatile fractions produced together with the essential oils (water insoluble fractions during the steam distillation process. The aim of this study was to further assess the phytotoxicity of AVFs from the four Eucalyptus species and their chemical composition. The fresh leaves of the four Eucalyptus species were used for the extraction of AVFs. The AVFs were tested for their phytotoxic effects on the perennial weed, silverleaf nightshade under laboratory conditions. The chemical compositions of the AVFs were determined by gas chromatograph-mass spectrometry (GC-MS. Our results showed that the AVFs had strong inhibition on the germination and seedling growth of silverleaf nightshade. The inhibition index increased with the increasing concentrations of AVFs. The inhibitory effects of the AVFs varied between different Eucalyptus species. The AVF from E. salubris demonstrated the highest inhibitory activity on the weed tested, with complete inhibition on germination and seedling growth at a concentration of 75%. The GC-MS analysis revealed that 1,8-cineole, isopentyl isovalerate, isomenthol, pinocarvone, trans-pinocarveol, alpha-terpineol and globulol were the main compounds in the AVFs. These results indicated that all AVFs tested had differential inhibition on the germination and seedling growth of silverleaf nightshade, which could be due to the joint effects of compounds present in the AVFs as these compounds were present in different quantities and ratio between Eucalyptus species.

  10. Identification of Chlamydiae and Mycoplasma species in ruminants with ocular infections.

    Science.gov (United States)

    Gupta, S; Chahota, R; Bhardwaj, B; Malik, P; Verma, S; Sharma, M

    2015-02-01

    Infectious keratoconjunctivitis (IKC) is a highly contagious ocular inflammatory condition, which is often reported in domestic small and large ruminants. Multiple infectious aetiologies are reported to be involved, but information about the role of certain fastidious bacterial pathogens such as chlamydiae and mycoplasmas is limited in India. Hence, this study was performed to determine the role of these pathogens and their identification by molecular approach. A total of 53 samples from 31 ovine, 14 caprine and eight bovine having clinical symptoms were collected and tested using species-specific PCR tests for chlamydiae and mycoplasmas followed by nucleotide sequence analysis. The results showed 77.41, 14.29 and 25% samples were chlamydiae positive in ovine, caprine and bovine, respectively, whereas 41.93, 14.29 and 37.5% prevalence of mycoplasma infection was detected in ovine, caprine and bovines, respectively. Chlamydophila abortus, Chlamydophila psittaci, Mycoplasma arginini and Mycoplasma hyorhinis were detected from tested samples. To the best of our knowledge, this is the first time these species are identified in IKC cases from India. Coinfection of both chlamydial and mycoplasmal species was detected in eight IKC cases of ovine which suggest synergistic roles played by both chlamydiae and mycoplasma in IKC samples. © 2014 The Society for Applied Microbiology.

  11. Revisiting Darwin's hypothesis: Does greater intraspecific variability increase species' ecological breadth?

    Science.gov (United States)

    Sides, Colby B; Enquist, Brian J; Ebersole, James J; Smith, Marielle N; Henderson, Amanda N; Sloat, Lindsey L

    2014-01-01

    Darwin first proposed that species with larger ecological breadth have greater phenotypic variation. We tested this hypothesis by comparing intraspecific variation in specific leaf area (SLA) to species' local elevational range and by assessing how external (abiotic) filters may influence observed differences in ecological breadth among species. Understanding the patterns of individual variation within and between populations will help evaluate differing hypotheses for structuring of communities and distribution of species. We selected 21 species with varying elevational ranges and compared the coefficient of variation of SLA for each species against its local elevational range. We examined the influence of external filters on local trait composition by determining if intraspecific changes in SLA with elevation have the same direction and similar rates of change as the change in community mean SLA value. In support of Darwin's hypothesis, we found a positive relationship between species' coefficient of variation for SLA with species' local elevational range. Intraspecific changes in SLA had the same sign, but generally lower magnitude than the community mean SLA. The results indicate that wide-ranging species are indeed characterized by greater intraspecific variation and that species' phenotypes shift along environmental gradients in the same direction as the community phenotypes. However, across species, the rate of intraspecific trait change, reflecting plastic and/or adaptive changes across populations, is limited and prevents species from adjusting to environmental gradients as quickly as interspecific changes resulting from community assembly.

  12. Aspergillus fumigatus-Related Species in Clinical Practice.

    Science.gov (United States)

    Lamoth, Frédéric

    2016-01-01

    Aspergillus fumigatus is the main etiologic agent of invasive aspergillosis (IA). Other Aspergillus species belonging to the section Fumigati (A. fumigatus complex) may occasionally be the cause of IA. These strains are often misidentified, as they cannot be distinguished from A. fumigatus by conventional morphological analysis and sequencing methods. This lack of recognition may have important consequences as these A. fumigatus-related species often display some level of intrinsic resistance to azoles and other antifungal drugs. A. lentulus, A. udagawae, A. viridinutans, and A. thermomutatus (Neosartorya pseudofischeri) have been associated with refractory cases of IA. Microbiologists should be able to suspect the presence of these cryptic species behind a putative A. fumigatus isolate on the basis of some simple characteristics, such as defect in sporulation and/or unusual antifungal susceptibility profile. However, definitive species identification requires specific sequencing analyses of the beta-tubulin or calmodulin genes, which are not available in most laboratories. Multiplex PCR assays or matrix-assisted laser desorption ionization - time-of-flight mass spectrometry (MALDI-TOF MS) gave promising results for rapid and accurate distinction between A. fumigatus and other Aspergillus spp. of the section Fumigati in clinical practice. Improved diagnostic procedures and antifungal susceptibility testing may be helpful for the early detection and management of these particular IA cases.

  13. Immunological detection of Fusarium species in cornmeal.

    Science.gov (United States)

    Iyer, M S; Cousin, M A

    2003-03-01

    An indirect enzyme-linked immunosorbent assay (ELISA) was developed to detect Fusarium species in foods. Antibodies to proteins extracted from the mycelia of Fusarium graminearum and Fusarium moniliforme (verticillioides) were produced in New Zealand white rabbits. These antibodies detected 13 Fusarium species in addition to the producer strains. Levels of Fusarium semitectum and Fusarium tricinctum strains were below the detection threshold. The specificity of the assay was tested against 70 molds and yeasts belonging to 23 genera. One strain of Monascus species and one strain of Phoma exigua were detected; however, these two molds are not common contaminants of cereal grains or foods and should not interfere with the assay. The indirect ELISA's detection limits for F. graminearum and F. moniliforme were 0.1 and 1 microg of mold mycelium per ml of a cornmeal mixture, respectively. When spores of each mold were added individually to cornmeal mixtures (at ca. 10 spores per g) and incubated at 25 degrees C, these spores were detected by the indirect ELISA when they reached levels of 10(2) to 10(3) CFU/ml after 24 to 36 h. The indirect ELISA developed here shows promise for the detection of Fusarium species in grains or foods.

  14. VEGETATIVE MORPHOLOGY FOR SPECIES IDENTIFICATION OF TROPICAL TREES: FAMILY DISTRIBUTION

    Directory of Open Access Journals (Sweden)

    Peter Hargreaves

    2006-03-01

    Full Text Available Tree specimens from the ESAL herbarium of the Universidade Federal de Lavras, Minas Gerais, Brazil, were describedby vegetative characteristics using CARipé, a Microsoft Access database application specially developed for this study. Only onespecimen per species was usually described. Thus, 2 observers described 567 herbarium species as a base to test methods ofidentification as part of a larger study. The present work formed part of that study and provides information on the distribution of22 vegetative characters among 16 families having 10 or more species described. The characters are discussed. The study foundmarked differences, even discontinuities, of distributions of characters between those families. Therefore it should be possible toincorporate phylogenetic relationships into the identification process.

  15. Bar-HRM for Authentication of Plant-Based Medicines: Evaluation of Three Medicinal Products Derived from Acanthaceae Species.

    Science.gov (United States)

    Osathanunkul, Maslin; Madesis, Panagiotis; de Boer, Hugo

    2015-01-01

    Medicinal plants are used as a popular alternative to synthetic drugs, both in developed and developing countries. The economic importance of the herbal and natural supplement industry is increasing every year. As the herbal industry grows, consumer safety is one issue that cannot be overlooked. Herbal products in Thai local markets are commonly sold without packaging or labels. Plant powders are stored in large bags or boxes, and therefore buying local herbal products poses a high risk of acquiring counterfeited, substituted and/or adulterated products. Due to these issues, a reliable method to authenticate products is needed. Here DNA barcoding was used in combination with High Resolution Melting analysis (Bar-HRM) to authenticate three medicinal Acanthaceae species (Acanthus ebracteatus, Andrographis paniculata and Rhinacanthus nasutus) commonly used in Thailand. The rbcL barcode was selected for use in primers design for HRM analysis to produce standard melting profiles of the selected species. Melting data from the HRM assay using the designed rbcL primers showed that the three chosen species could be distinguished from each other. HRM curves of all fifteen test samples indicated that three of tested products did not contain the indicated species. Two closely related species (A. paniculata and R. nasutus), which have a high level of morphological similarity, were interchanged with one another in three tested products. Incorrect information on packaging and labels of the tested herbal products was the cause of the results shown here. Morphological similarity among the species of interest also hindered the collection process. The Bar-HRM method developed here proved useful in aiding in the identification and authentication of herbal species in processed samples. In the future, species authentication through Bar-HRM could be used to promote consumer trust, as well as raising the quality of herbal products.

  16. RAPD-PCR analysis of some species of Euphorbia grown in ...

    African Journals Online (AJOL)

    family ^____^

    2013-12-04

    Dec 4, 2013 ... Molecular analysis was performed by using nine random markers in random amplified polymorphic DNA ..... plant species. Genetic variations were tested in normal ... A Ph.D. thesis, College of Science- Baghdad University.

  17. Novel intron markers to study the phylogeny of closely related mammalian species

    Directory of Open Access Journals (Sweden)

    Castresana Jose

    2010-11-01

    Full Text Available Abstract Background Multilocus phylogenies can be used to infer the species tree of a group of closely related species. In species trees, the nodes represent the actual separation between species, thus providing essential information about their evolutionary history. In addition, multilocus phylogenies can help in analyses of species delimitation, gene flow and genetic differentiation within species. However, few adequate markers are available for such studies. Results In order to develop nuclear markers that can be useful in multilocus studies of mammals, we analyzed the mammalian genomes of human, chimpanzee, macaque, dog and cow. Rodents were excluded due to their unusual genomic features. Introns were extracted from the mammalian genomes because of their greater genetic variability and ease of amplification from the flanking exons. To an initial set of more than 10,000 one-to-one orthologous introns we applied several filters to select introns that belong to single-copy genes, show neutral evolutionary rates and have an adequate length for their amplification. This analysis led to a final list of 224 intron markers randomly distributed along the genome. To experimentally test their validity, we amplified twelve of these introns in a panel of six mammalian species. The result was that seven of these introns gave rise to a PCR band of the expected size in all species. In addition, we sequenced these bands and analyzed the accumulation of substitutions in these introns in five pairs of closely related species. The results showed that the estimated genetic distances in the five species pairs was quite variable among introns and that this divergence cannot be directly predicted from the overall intron divergence in mammals. Conclusions We have designed a new set of 224 nuclear introns with optimal features for the phylogeny of closely related mammalian species. A large proportion of the introns tested experimentally showed a perfect amplification

  18. Larvicidal potential of Cyathea species against Culex quinquefasciatus

    Directory of Open Access Journals (Sweden)

    Johnson Marimuthu alias Antonysamy

    2017-05-01

    Full Text Available Resistance to insecticides has persuaded researchers to find new methods to control Culex quinquefasciatus proliferation. Plants may be a source of alternative agents for mosquito control due to ever-growing insecticide resistance in mosquito vectors and environmental imbalance caused by synthetic insecticides. The present study was intended to study the larvicidal activity of selected Cyathea species against the filarial vector Culex quinquefasciatus. Larvicidal potential of different extracts were evaluated and larval mortality were recorded. The larvae were more sensitive to ethanolic extracts of studied three Cyathea species when compared to other extracts. Acetone, chloroform and petroleum ether extracts were considered to be less effective. The LC50 values of different extracts ranged from 320.72 to 657.03 µg/ml. The results exhibited that the tested three Cyathea species showed concentration dependent potential larvicidal effects and also provide an indication of possible bioactive properties.

  19. Intraspecific Variation in Armillaria Species from Shrubs and Trees in Northwestern Spain

    OpenAIRE

    O. Aguín; J.P. Mansilla; M.J. Sainz

    2004-01-01

    Until recently, the identification of Armillaria species relied upon morphological characteristics and mating tests, but now molecular techniques based on polymorphisms in the IGS region of the fungal rDNA are more commonly used, since these are more rapid and reliable. Differences found in RFLP patterns identifying Armillaria species have suggested the existence of intraspecific variation. In this work, 185 Armillaria isolates from different plant species (including fruit trees, ...

  20. Ring species as demonstrations of the continuum of species formation

    DEFF Research Database (Denmark)

    Pereira, Ricardo José Do Nascimento; Wake, David B.

    2015-01-01

    In the mid-20th century, Ernst Mayr (1942) and Theodosius Dobzhansky (1958) championed the significance of 'circular overlaps' or 'ring species' as the perfect demonstration of the gradual nature of species formation. As an ancestral species expands its range, wrapping around a geographic barrier......? What conditions favour their formation? Modelling studies have attempted to address these knowledge gaps by estimating the biological parameters that result in stable ring species (Martins et al. 2013), and determining the necessary topographic parameters of the barriers encircled (Monahan et al. 2012......). However, any generalization is undermined by a major limitation: only a handful of ring species are known to exist in nature. In addition, many of them have been broken into multiple species presumed to be evolving independently, usually obscuring the evolutionary dynamics that generate diversity. A paper...