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Sample records for salamander genotypes impact

  1. Invasive Asian Earthworms Negatively Impact Keystone Terrestrial Salamanders.

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    Julie L Ziemba

    Full Text Available Asian pheretimoid earthworms (e.g. Amynthas and Metaphire spp. are invading North American forests and consuming the vital detrital layer that forest floor biota [including the keystone species Plethodon cinereus (Eastern Red-backed Salamander], rely on for protection, food, and habitat. Plethodon cinereus population declines have been associated with leaf litter loss following the invasion of several exotic earthworm species, but there have been few studies on the specific interactions between pheretimoid earthworms and P. cinereus. Since some species of large and active pheretimoids spatially overlap with salamanders beneath natural cover objects and in detritus, they may distinctively compound the negative consequences of earthworm-mediated resource degradation by physically disturbing important salamander activities (foraging, mating, and egg brooding. We predicted that earthworms would exclude salamanders from high quality microhabitat, reduce foraging efficiency, and negatively affect salamander fitness. In laboratory trials, salamanders used lower quality microhabitat and consumed fewer flies in the presence of earthworms. In a natural field experiment, conducted on salamander populations from "non-invaded" and "pheretimoid invaded" sites in Ohio, salamanders and earthworms shared cover objects ~60% less than expected. Earthworm abundance was negatively associated with juvenile and male salamander abundance, but had no relationship with female salamander abundance. There was no effect of pheretimoid invasion on salamander body condition. Juvenile and non-resident male salamanders do not hold stable territories centered beneath cover objects such as rocks or logs, which results in reduced access to prey, greater risk of desiccation, and dispersal pressure. Habitat degradation and physical exclusion of salamanders from cover objects may hinder juvenile and male salamander performance, ultimately reducing recruitment and salamander abundance

  2. Invasive Asian Earthworms Negatively Impact Keystone Terrestrial Salamanders.

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    Ziemba, Julie L; Hickerson, Cari-Ann M; Anthony, Carl D

    2016-01-01

    Asian pheretimoid earthworms (e.g. Amynthas and Metaphire spp.) are invading North American forests and consuming the vital detrital layer that forest floor biota [including the keystone species Plethodon cinereus (Eastern Red-backed Salamander)], rely on for protection, food, and habitat. Plethodon cinereus population declines have been associated with leaf litter loss following the invasion of several exotic earthworm species, but there have been few studies on the specific interactions between pheretimoid earthworms and P. cinereus. Since some species of large and active pheretimoids spatially overlap with salamanders beneath natural cover objects and in detritus, they may distinctively compound the negative consequences of earthworm-mediated resource degradation by physically disturbing important salamander activities (foraging, mating, and egg brooding). We predicted that earthworms would exclude salamanders from high quality microhabitat, reduce foraging efficiency, and negatively affect salamander fitness. In laboratory trials, salamanders used lower quality microhabitat and consumed fewer flies in the presence of earthworms. In a natural field experiment, conducted on salamander populations from "non-invaded" and "pheretimoid invaded" sites in Ohio, salamanders and earthworms shared cover objects ~60% less than expected. Earthworm abundance was negatively associated with juvenile and male salamander abundance, but had no relationship with female salamander abundance. There was no effect of pheretimoid invasion on salamander body condition. Juvenile and non-resident male salamanders do not hold stable territories centered beneath cover objects such as rocks or logs, which results in reduced access to prey, greater risk of desiccation, and dispersal pressure. Habitat degradation and physical exclusion of salamanders from cover objects may hinder juvenile and male salamander performance, ultimately reducing recruitment and salamander abundance following Asian

  3. Impact of valley fills on streamside salamanders in southern West Virginia

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    Wood, Petra Bohall; Williams, Jennifer M.

    2013-01-01

    Valley fills associated with mountaintop-removal mining bury stream headwaters and affect water quality and ecological function of reaches below fills. We quantified relative abundance of streamside salamanders in southern West Virginia during 2002 in three streams below valley fills (VFS) and in three reference streams (RS). We surveyed 36 10- × 2-m stream transects, once in summer and fall, paired by order and structure. Of 2,343 salamanders captured, 66.7% were from RS. Total salamanders (adults plus larvae) were more abundant in RS than VFS for first-order and second-order reaches. Adult salamanders had greater abundance in first-order reaches of RS than VFS. Larval salamanders were more abundant in second-order reaches of RS than VFS. No stream width or mesohabitat variables differed between VFS and RS. Only two cover variables differed. Silt cover, greater in VFS than RS first-order reaches, is a likely contributor to reduced abundance of salamanders in VFS. Second-order RS had more boulder cover than second-order VFS, which may have contributed to the higher total and larval salamander abundance in RS. Water chemistry assessments of our VFS and RS reported elevated levels of metal and ion concentrations in VFS, which can depress macroinvertebrate populations and likely affect salamander abundance. Valley fills appear to have significant negative effects on stream salamander abundance due to alterations in habitat structure, water quality and chemistry, and macroinvertebrate communities in streams below fills.

  4. The trophic role of a forest salamander: impacts on invertebrates, leaf litter retention, and the humification process

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    M. L. Best; H. H. Welsh

    2014-01-01

    Woodland (Plethodontid) salamanders are the most abundant vertebrates in North American forests, functioning as predators on invertebrates and prey for higher trophic levels. We investigated the role of Ensatina (Ensatina eschscholtzii) in regulating invertebrate numbers and leaf litter retention in a northern California forest. Our objective was...

  5. Effects of red-backed salamanders on ecosystem functions.

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    Daniel J Hocking

    Full Text Available Ecosystems provide a vast array of services for human societies, but understanding how various organisms contribute to the functions that maintain these services remains an important ecological challenge. Predators can affect ecosystem functions through a combination of top-down trophic cascades and bottom-up effects on nutrient dynamics. As the most abundant vertebrate predator in many eastern US forests, woodland salamanders (Plethodon spp. likely affect ecosystems functions. We examined the effects of red-backed salamanders (Plethodon cinereus on a variety of forest ecosystem functions using a combined approach of large-scale salamander removals (314-m(2 plots and small-scale enclosures (2 m(2 where we explicitly manipulated salamander density (0, 0.5, 1, 2, 4 m(-2. In these experiments, we measured the rates of litter and wood decomposition, potential nitrogen mineralization and nitrification rates, acorn germination, and foliar insect damage on red oak seedlings. Across both experimental venues, we found no significant effect of red-backed salamanders on any of the ecosystem functions. We also found no effect of salamanders on intraguild predator abundance (carabid beetles, centipedes, spiders. Our study adds to the already conflicting evidence on effects of red-backed salamander and other amphibians on terrestrial ecosystem functions. It appears likely that the impact of terrestrial amphibians on ecosystem functions is context dependent. Future research would benefit from explicitly examining terrestrial amphibian effects on ecosystem functions under a variety of environmental conditions and in different forest types.

  6. Effects of red-backed salamanders on ecosystem functions.

    Science.gov (United States)

    Hocking, Daniel J; Babbitt, Kimberly J

    2014-01-01

    Ecosystems provide a vast array of services for human societies, but understanding how various organisms contribute to the functions that maintain these services remains an important ecological challenge. Predators can affect ecosystem functions through a combination of top-down trophic cascades and bottom-up effects on nutrient dynamics. As the most abundant vertebrate predator in many eastern US forests, woodland salamanders (Plethodon spp.) likely affect ecosystems functions. We examined the effects of red-backed salamanders (Plethodon cinereus) on a variety of forest ecosystem functions using a combined approach of large-scale salamander removals (314-m(2) plots) and small-scale enclosures (2 m(2)) where we explicitly manipulated salamander density (0, 0.5, 1, 2, 4 m(-2)). In these experiments, we measured the rates of litter and wood decomposition, potential nitrogen mineralization and nitrification rates, acorn germination, and foliar insect damage on red oak seedlings. Across both experimental venues, we found no significant effect of red-backed salamanders on any of the ecosystem functions. We also found no effect of salamanders on intraguild predator abundance (carabid beetles, centipedes, spiders). Our study adds to the already conflicting evidence on effects of red-backed salamander and other amphibians on terrestrial ecosystem functions. It appears likely that the impact of terrestrial amphibians on ecosystem functions is context dependent. Future research would benefit from explicitly examining terrestrial amphibian effects on ecosystem functions under a variety of environmental conditions and in different forest types.

  7. Impact of inter-genotypic recombination and probe cross-reactivity on the performance of the Abbott RealTime HCV Genotype II assay for hepatitis C genotyping.

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    Sridhar, Siddharth; Yip, Cyril C Y; Chan, Jasper F W; To, Kelvin K W; Cheng, Vincent C C; Yuen, Kwok-Yung

    2018-05-01

    The Abbott RealTime HCV Genotype II assay (Abbott-RT-HCV assay) is a real-time PCR based genotyping method for hepatitis C virus (HCV). This study measured the impact of inter-genotypic recombination and probe cross-reactivity on the performance of the Abbott-RT-HCV assay. 517 samples were genotyped using the Abbott-RT-HCV assay over a one-year period, 34 (6.6%) were identified as HCV genotype 1 without further subtype designation raising the possibility of inaccurate genotyping. These samples were subjected to confirmatory sequencing. 27 of these 34 (79%) samples were genotype 1b while five (15%) were genotype 6. One HCV isolate was an inter-genotypic 1a/4o recombinant. This is a novel natural HCV recombinant that has never been reported. Inter-genotypic recombination and probe cross-reactivity can affect the accuracy of the Abbott-RT-HCV assay, both of which have significant implications on antiviral regimen choice. Confirmatory sequencing of ambiguous results is crucial for accurate genotyping. Copyright © 2018 Elsevier Inc. All rights reserved.

  8. Environmental and Anthropogenic Factors Influencing Salamanders in Riparian Forests: A Review

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    Hannah L. Clipp

    2014-11-01

    Full Text Available Salamanders and riparian forests are intimately interconnected. Salamanders are integral to ecosystem functions, contributing to vertebrate biomass and complex food webs in riparian forests. In turn, these forests are critical ecosystems that perform many environmental services, facilitate high biodiversity and species richness, and provide habitat to salamander populations. Due to the global decline of amphibians, it is important to understand, as thoroughly and holistically as possible, the roles of environmental parameters and the impact of human activities on salamander abundance and diversity in riparian forests. To determine the population responses of salamanders to a variety of environmental factors and anthropogenic activities, we conducted a review of published literature that compared salamander abundance and diversity, and then summarized and synthesized the data into general patterns. We identify stream quality, leaf litter and woody debris, riparian buffer width, and soil characteristics as major environmental factors influencing salamander populations in riparian forests, describe and explain salamander responses to those factors, and discuss the effects of anthropogenic activities such as timber harvest, prescribed fires, urbanization, road construction, and habitat fragmentation. This review can assist land and natural resource managers in anticipating the consequences of human activities and preparing strategic conservation plans.

  9. Data congruence, paedomorphosis and salamanders

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    Struck Torsten H

    2007-10-01

    Full Text Available Abstract Background The retention of ancestral juvenile characters by adult stages of descendants is called paedomorphosis. However, this process can mislead phylogenetic analyses based on morphological data, even in combination with molecular data, because the assessment if a character is primary absent or secondary lost is difficult. Thus, the detection of incongruence between morphological and molecular data is necessary to investigate the reliability of simultaneous analyses. Different methods have been proposed to detect data congruence or incongruence. Five of them (PABA, PBS, NDI, LILD, DRI are used herein to assess incongruence between morphological and molecular data in a case study addressing salamander phylogeny, which comprises several supposedly paedomorphic taxa. Therefore, previously published data sets were compiled herein. Furthermore, two strategies ameliorating effects of paedomorphosis on phylogenetic studies were tested herein using a statistical rigor. Additionally, efficiency of the different methods to assess incongruence was analyzed using this empirical data set. Finally, a test statistic is presented for all these methods except DRI. Results The addition of morphological data to molecular data results in both different positions of three of the four paedomorphic taxa and strong incongruence, but treating the morphological data using different strategies ameliorating the negative impact of paedomorphosis revokes these changes and minimizes the conflict. Of these strategies the strategy to just exclude paedomorphic character traits seem to be most beneficial. Of the three molecular partitions analyzed herein the RAG1 partition seems to be the most suitable to resolve deep salamander phylogeny. The rRNA and mtDNA partition are either too conserved or too variable, respectively. Of the different methods to detect incongruence, the NDI and PABA approaches are more conservative in the indication of incongruence than LILD and

  10. Woodland salamander responses to a shelterwood harvest-prescribed burn silvicultural treatment within Appalachian mixed-oak forests

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    Ford, W. Mark; Mahoney, Kathleen R.; Russell, Kevin R.; Rodrigue, Jane L.; Riddle, Jason D.; Schuler, Thomas M.; Adams, Mary Beth

    2015-01-01

    silvicultural treatment compared to previous research within the same study area that examined pre-harvest fire effects. However, because of the multi-faceted complexities of this specific silvicultural system, continued research is warranted that evaluates long-term, additive impacts on woodland salamanders within managed central Appalachian deciduous forests.

  11. Tiger salamanders' (Ambystoma tigrinum) response learning and usage of visual cues.

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    Kundey, Shannon M A; Millar, Roberto; McPherson, Justin; Gonzalez, Maya; Fitz, Aleyna; Allen, Chadbourne

    2016-05-01

    We explored tiger salamanders' (Ambystoma tigrinum) learning to execute a response within a maze as proximal visual cue conditions varied. In Experiment 1, salamanders learned to turn consistently in a T-maze for reinforcement before the maze was rotated. All learned the initial task and executed the trained turn during test, suggesting that they learned to demonstrate the reinforced response during training and continued to perform it during test. In a second experiment utilizing a similar procedure, two visual cues were placed consistently at the maze junction. Salamanders were reinforced for turning towards one cue. Cue placement was reversed during test. All learned the initial task, but executed the trained turn rather than turning towards the visual cue during test, evidencing response learning. In Experiment 3, we investigated whether a compound visual cue could control salamanders' behaviour when it was the only cue predictive of reinforcement in a cross-maze by varying start position and cue placement. All learned to turn in the direction indicated by the compound visual cue, indicating that visual cues can come to control their behaviour. Following training, testing revealed that salamanders attended to stimuli foreground over background features. Overall, these results suggest that salamanders learn to execute responses over learning to use visual cues but can use visual cues if required. Our success with this paradigm offers the potential in future studies to explore salamanders' cognition further, as well as to shed light on how features of the tiger salamanders' life history (e.g. hibernation and metamorphosis) impact cognition.

  12. IDH Mutations: Genotype-Phenotype Correlation and Prognostic Impact

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    Xiao-Wei Wang

    2014-01-01

    Full Text Available IDH1/2 mutation is the most frequent genomic alteration found in gliomas, affecting 40% of these tumors and is one of the earliest alterations occurring in gliomagenesis. We investigated a series of 1305 gliomas and showed that IDH mutation is almost constant in 1p19q codeleted tumors. We found that the distribution of IDH1R132H, IDH1nonR132H, and IDH2 mutations differed between astrocytic, mixed, and oligodendroglial tumors, with an overrepresentation of IDH2 mutations in oligodendroglial phenotype and an overrepresentation of IDH1nonR132H in astrocytic tumors. We stratified grade II and grade III gliomas according to the codeletion of 1p19q and IDH mutation to define three distinct prognostic subgroups: 1p19q and IDH mutated, IDH mutated—which contains mostly TP53 mutated tumors, and none of these alterations. We confirmed that IDH mutation with a hazard ratio = 0.358 is an independent prognostic factor of good outcome. These data refine current knowledge on IDH mutation prognostic impact and genotype-phenotype associations.

  13. Impact of irrigation intervals, nitrogen fertilizer levels and heritability on spineless performance in safflower genotypes

    International Nuclear Information System (INIS)

    Ragab, A.I.; Kassem, M.

    2003-01-01

    The present study was conducted to study the impact of irrigation intervals, nitrogen fertilizer levels on spineless percentages, meanwhile, heritability and genetic gain were determind for further selection for eight safflower genotype, during 1998/1999-1999/2000 seasons, at nuclear research center-inshas. Concerning irrigation intervals, results showed that spineless percentages of safflower genotypes were markedly increased with the increasing of irrigation intervals, this eans that increase of drought conditions leds to increase the spineless percentages in all the genotypes. Regarding nitrogen fertilizer levels, results exhibited that spineless percentages were increased with the increasing of nitrogen fertilizer levels for all the studied genotypes. Combined analysis of variance chowed highly significant effect for irrigation intervals, fertilizer levels, years and genotypes for spineles trait. The first order interaction, second order interaction and third order interaction were highly significant suggesting that spineless trait was affected the environmental factors

  14. Conservation assessment for the Siskiyou Mountains salamander and Scott Bar salamander in northern California.

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    Vinikour, W. S.; LaGory, K. E.; Adduci, J. J.; Environmental Science Division

    2006-10-20

    The purpose of this conservation assessment is to summarize existing knowledge regarding the biology and ecology of the Siskiyou Mountains salamander and Scott Bar salamander, identify threats to the two species, and identify conservation considerations to aid federal management for persistence of the species. The conservation assessment will serve as the basis for a conservation strategy for the species.

  15. Salt and genotype impact on plant physiology and root proteome variations in tomato.

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    Manaa, Arafet; Ben Ahmed, Hela; Valot, Benoît; Bouchet, Jean-Paul; Aschi-Smiti, Samira; Causse, Mathilde; Faurobert, Mireille

    2011-05-01

    To evaluate the genotypic variation of salt stress response in tomato, physiological analyses and a proteomic approach have been conducted in parallel on four contrasting tomato genotypes. After a 14 d period of salt stress in hydroponic conditions, the genotypes exhibited different responses in terms of plant growth, particularly root growth, foliar accumulation of Na(+), and foliar K/Na ratio. As a whole, Levovil appeared to be the most tolerant genotype while Cervil was the most sensitive one. Roma and Supermarmande exhibited intermediary behaviours. Among the 1300 protein spots reproducibly detected by two-dimensional electrophoresis, 90 exhibited significant abundance variations between samples and were submitted to mass spectrometry for identification. A common set of proteins (nine spots), up- or down-regulated by salt-stress whatever the genotype, was detected. But the impact of the tomato genotype on the proteome variations was much higher than the salt effect: 33 spots that were not variable with salt stress varied with the genotype. The remaining number of variable spots (48) exhibited combined effects of the genotype and the salt factors, putatively linked to the degrees of genotype tolerance. The carbon metabolism and energy-related proteins were mainly up-regulated by salt stress and exhibited most-tolerant versus most-sensitive abundance variations. Unexpectedly, some antioxidant and defence proteins were also down-regulated, while some proteins putatively involved in osmoprotectant synthesis and cell wall reinforcement were up-regulated by salt stress mainly in tolerant genotypes. The results showed the effect of 14 d stress on the tomato root proteome and underlined significant genotype differences, suggesting the importance of making use of genetic variability.

  16. Chloride equilibrium potential in salamander cones

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    Bryson Eric J

    2004-12-01

    Full Text Available Abstract Background GABAergic inhibition and effects of intracellular chloride ions on calcium channel activity have been proposed to regulate neurotransmission from photoreceptors. To assess the impact of these and other chloride-dependent mechanisms on release from cones, the chloride equilibrium potential (ECl was determined in red-sensitive, large single cones from the tiger salamander retinal slice. Results Whole cell recordings were done using gramicidin perforated patch techniques to maintain endogenous Cl- levels. Membrane potentials were corrected for liquid junction potentials. Cone resting potentials were found to average -46 mV. To measure ECl, we applied long depolarizing steps to activate the calcium-activated chloride current (ICl(Ca and then determined the reversal potential for the current component that was inhibited by the Cl- channel blocker, niflumic acid. With this method, ECl was found to average -46 mV. In a complementary approach, we used a Cl-sensitive dye, MEQ, to measure the Cl- flux produced by depolarization with elevated concentrations of K+. The membrane potentials produced by the various high K+ solutions were measured in separate current clamp experiments. Consistent with electrophysiological experiments, MEQ fluorescence measurements indicated that ECl was below -36 mV. Conclusions The results of this study indicate that ECl is close to the dark resting potential. This will minimize the impact of chloride-dependent presynaptic mechanisms in cone terminals involving GABAa receptors, glutamate transporters and ICl(Ca.

  17. The effect of waist twisting on walking speed of an amphibious salamander like robot

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    Yin, Xin-Yan; Jia, Li-Chao; Wang, Chen; Xie, Guang-Ming

    2016-06-01

    Amphibious salamanders often swing their waist to coordinate quadruped walking in order to improve their crawling speed. A robot with a swing waist joint, like an amphibious salamander, is used to mimic this locomotion. A control method is designed to allow the robot to maintain the rotational speed of its legs continuous and avoid impact between its legs and the ground. An analytical expression is established between the amplitude of the waist joint and the step length. Further, an optimization amplitude is obtained corresponding to the maximum stride. The simulation results based on automatic dynamic analysis of mechanical systems (ADAMS) and physical experiments verify the rationality and validity of this expression.

  18. Salamander occupancy in headwater stream networks

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    Grant, E.H.C.; Green, L.E.; Lowe, W.H.

    2009-01-01

    1. Stream ecosystems exhibit a highly consistent dendritic geometry in which linear habitat units intersect to create a hierarchical network of connected branches. 2. Ecological and life history traits of species living in streams, such as the potential for overland movement, may interact with this architecture to shape patterns of occupancy and response to disturbance. Specifically, large-scale habitat alteration that fragments stream networks and reduces connectivity may reduce the probability a stream is occupied by sensitive species, such as stream salamanders. 3. We collected habitat occupancy data on four species of stream salamanders in first-order (i.e. headwater) streams in undeveloped and urbanised regions of the eastern U.S.A. We then used an information-theoretic approach to test alternative models of salamander occupancy based on a priori predictions of the effects of network configuration, region and salamander life history. 4. Across all four species, we found that streams connected to other first-order streams had higher occupancy than those flowing directly into larger streams and rivers. For three of the four species, occupancy was lower in the urbanised region than in the undeveloped region. 5. These results demonstrate that the spatial configuration of stream networks within protected areas affects the occurrences of stream salamander species. We strongly encourage preservation of network connections between first-order streams in conservation planning and management decisions that may affect stream species.

  19. Evolution of gigantism in amphiumid salamanders.

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    Ronald M Bonett

    2009-05-01

    Full Text Available The Amphiumidae contains three species of elongate, permanently aquatic salamanders with four diminutive limbs that append one, two, or three toes. Two of the species, Amphiuma means and A. tridactylum, are among the largest salamanders in the world, reaching lengths of more than one meter, whereas the third species (A. pholeter, extinct amphiumids, and closely related salamander families are relatively small. Amphiuma means and A. tridactylum are widespread species and live in a wide range of lowland aquatic habitats on the Coastal Plain of the southeastern United States, whereas A. pholeter is restricted to very specialized organic muck habitats and is syntopic with A. means. Here we present analyses of sequences of mitochondrial and nuclear loci from across the distribution of the three taxa to assess lineage diversity, relationships, and relative timing of divergence in amphiumid salamanders. In addition we analyze the evolution of gigantism in the clade. Our analyses indicate three lineages that have diverged since the late Miocene, that correspond to the three currently recognized species, but the two gigantic species are not each other's closest relatives. Given that the most closely related salamander families and fossil amphiumids from the Upper Cretaceous and Paleocene are relatively small, our results suggest at least two extreme changes in body size within the Amphuimidae. Gigantic body size either evolved once as the ancestral condition of modern amphiumas, with a subsequent strong size reduction in A. pholeter, or gigantism independently evolved twice in the modern species, A. means and A. tridactylum. These patterns are concordant with differences in habitat breadth and range size among lineages, and have implications for reproductive isolation and diversification of amphiumid salamanders.

  20. Road deicing salt irreversibly disrupts osmoregulation of salamander egg clutches

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    Karraker, Nancy E.; Gibbs, James P.

    2011-01-01

    It has been postulated that road deicing salts are sufficiently diluted by spring rains to ameliorate any physiological impacts to amphibians breeding in wetlands near roads. We tested this conjecture by exposing clutches of the spotted salamander (Ambystoma maculatum) to three chloride concentrations (1 mg/L, 145 mg/L, 945 mg/L) for nine days, then transferred clutches to control water for nine days, and measured change in mass at three-day intervals. We measured mass change because water uptake by clutches reduces risks to embryos associated with freezing, predation, and disease. Clutches in controls sequestered water asymptotically. Those in the moderate concentrations lost 18% mass initially and regained 14% after transfer to control water. Clutches in high concentration lost 33% mass and then lost an additional 8% after transfer. Our results suggest that spring rains do not ameliorate the effects of deicing salts in wetlands with extremely high chloride concentrations. - Road deicing salts irreversibly disrupts osmoregulation of salamander egg clutches.

  1. Road deicing salt irreversibly disrupts osmoregulation of salamander egg clutches

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    Karraker, Nancy E., E-mail: karraker@hku.hk [Department of Environmental and Forest Biology, State University of New York, College of Environmental Science and Forestry, Syracuse, NY 13210 (United States); Gibbs, James P [Department of Environmental and Forest Biology, State University of New York, College of Environmental Science and Forestry, Syracuse, NY 13210 (United States)

    2011-03-15

    It has been postulated that road deicing salts are sufficiently diluted by spring rains to ameliorate any physiological impacts to amphibians breeding in wetlands near roads. We tested this conjecture by exposing clutches of the spotted salamander (Ambystoma maculatum) to three chloride concentrations (1 mg/L, 145 mg/L, 945 mg/L) for nine days, then transferred clutches to control water for nine days, and measured change in mass at three-day intervals. We measured mass change because water uptake by clutches reduces risks to embryos associated with freezing, predation, and disease. Clutches in controls sequestered water asymptotically. Those in the moderate concentrations lost 18% mass initially and regained 14% after transfer to control water. Clutches in high concentration lost 33% mass and then lost an additional 8% after transfer. Our results suggest that spring rains do not ameliorate the effects of deicing salts in wetlands with extremely high chloride concentrations. - Road deicing salts irreversibly disrupts osmoregulation of salamander egg clutches.

  2. Conservation genetics of the endangered Shenandoah salamander (Plethodon shenandoah, Plethodontidae)

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    Carpenter, D.W.; Jung, R.E.; Sites, J.W.

    2001-01-01

    The Shenandoah salamander (Plethodon shenandoah) is restricted to three isolated talus outcrops in Shenandoah National Park, VA, USA and has one of the smallest ranges of any tetrapod vertebrate. This species was listed as endangered under the US Endangered Species Act in 1989 over concern that direct competition with the red-backed salamander (Plethodon cinereus), successional habitat changes, and human impacts may cause its decline and possible extinction. We address two issues herein: (1) whether extensive introgression (through long-term hybridization) is present between the two species and threatens the survival of P. shenandoah, and (2) the level of population structure within P. shenandoah. We provide evidence from mtDNA haplotypes that shows no genetic differentiation among the three isolates of P. shenandoah, suggesting that their fragmentation is a geologically recent event, and/or that the isolates are still connected by occasional gene flow. There is also no evidence for extensive introgression of alleles in either direction between P. cinereus and P. shenandoah, which suggests that P. shenandoah may not be in danger of being genetically swamped out through hybridization with P. cinereus.

  3. Evaluating multi-level models to test occupancy state responses of Plethodontid salamanders

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    Kroll, Andrew J.; Garcia, Tiffany S.; Jones, Jay E.; Dugger, Catherine; Murden, Blake; Johnson, Josh; Peerman, Summer; Brintz, Ben; Rochelle, Michael

    2015-01-01

    Plethodontid salamanders are diverse and widely distributed taxa and play critical roles in ecosystem processes. Due to salamander use of structurally complex habitats, and because only a portion of a population is available for sampling, evaluation of sampling designs and estimators is critical to provide strong inference about Plethodontid ecology and responses to conservation and management activities. We conducted a simulation study to evaluate the effectiveness of multi-scale and hierarchical single-scale occupancy models in the context of a Before-After Control-Impact (BACI) experimental design with multiple levels of sampling. Also, we fit the hierarchical single-scale model to empirical data collected for Oregon slender and Ensatina salamanders across two years on 66 forest stands in the Cascade Range, Oregon, USA. All models were fit within a Bayesian framework. Estimator precision in both models improved with increasing numbers of primary and secondary sampling units, underscoring the potential gains accrued when adding secondary sampling units. Both models showed evidence of estimator bias at low detection probabilities and low sample sizes; this problem was particularly acute for the multi-scale model. Our results suggested that sufficient sample sizes at both the primary and secondary sampling levels could ameliorate this issue. Empirical data indicated Oregon slender salamander occupancy was associated strongly with the amount of coarse woody debris (posterior mean = 0.74; SD = 0.24); Ensatina occupancy was not associated with amount of coarse woody debris (posterior mean = -0.01; SD = 0.29). Our simulation results indicate that either model is suitable for use in an experimental study of Plethodontid salamanders provided that sample sizes are sufficiently large. However, hierarchical single-scale and multi-scale models describe different processes and estimate different parameters. As a result, we recommend careful consideration of study questions

  4. Evaluating Multi-Level Models to Test Occupancy State Responses of Plethodontid Salamanders.

    Directory of Open Access Journals (Sweden)

    Andrew J Kroll

    Full Text Available Plethodontid salamanders are diverse and widely distributed taxa and play critical roles in ecosystem processes. Due to salamander use of structurally complex habitats, and because only a portion of a population is available for sampling, evaluation of sampling designs and estimators is critical to provide strong inference about Plethodontid ecology and responses to conservation and management activities. We conducted a simulation study to evaluate the effectiveness of multi-scale and hierarchical single-scale occupancy models in the context of a Before-After Control-Impact (BACI experimental design with multiple levels of sampling. Also, we fit the hierarchical single-scale model to empirical data collected for Oregon slender and Ensatina salamanders across two years on 66 forest stands in the Cascade Range, Oregon, USA. All models were fit within a Bayesian framework. Estimator precision in both models improved with increasing numbers of primary and secondary sampling units, underscoring the potential gains accrued when adding secondary sampling units. Both models showed evidence of estimator bias at low detection probabilities and low sample sizes; this problem was particularly acute for the multi-scale model. Our results suggested that sufficient sample sizes at both the primary and secondary sampling levels could ameliorate this issue. Empirical data indicated Oregon slender salamander occupancy was associated strongly with the amount of coarse woody debris (posterior mean = 0.74; SD = 0.24; Ensatina occupancy was not associated with amount of coarse woody debris (posterior mean = -0.01; SD = 0.29. Our simulation results indicate that either model is suitable for use in an experimental study of Plethodontid salamanders provided that sample sizes are sufficiently large. However, hierarchical single-scale and multi-scale models describe different processes and estimate different parameters. As a result, we recommend careful consideration of

  5. Reproductive biology of Ambystoma salamanders in the southeastern United States

    Science.gov (United States)

    Glorioso, Brad M.; Waddle, J. Hardin; Hefner, J. M.

    2015-01-01

    Reproductive aspects of Ambystoma salamanders were investigated at sites in Louisiana (2010–12) and Mississippi (2013). Three species occurred at the Louisiana site, Spotted Salamander (A. maculatum), Marbled Salamander (A. opacum), and Mole Salamander (A. talpoideum), whereas only Spotted Salamanders were studied at the Mississippi site. A total of 162 and 71 egg masses of Spotted Salamanders were examined at the Louisiana and Mississippi sites, respectively. Significantly more Spotted Salamander eggs per egg mass were observed at the Mississippi site (x̄ = 78.2) than the Louisiana site (x̄ = 53.8; P < 0.001). The mean snout–vent length of female Spotted Salamanders at the Mississippi site (82.9 mm) was significantly larger than the Louisiana site (76.1 mm; P < 0.001). Opaque Spotted Salamander egg masses were not found at the Mississippi site, but accounted for 11% of examined egg masses at the Louisiana site. The mean number of eggs per egg mass at the Louisiana site did not differ between opaque (47.3) and clear (54.6) egg masses (P = 0.21). A total of 47 egg masses of the Mole Salamander were examined, with a mean number of 6.7 embryos per mass. Twenty-three individual nests of the Marbled Salamander were found either under or in decaying logs in the dry pond basins. There was no difference between the mean numbers of eggs per mass of attended nests (93.0) versus those that were discovered unattended (86.6; P = 0.67). Females tended to place their nests at intermediate heights within the pond basin.

  6. Effects of Buffering Key Habitat for Terrestrial Salamanders: Implications for the Management of the Federally Threatened Red Hills Salamander (Phaeognathus hubrichti and Other Imperiled Plethodontids

    Directory of Open Access Journals (Sweden)

    Joseph J. Apodaca

    2015-03-01

    Full Text Available Forestry practices are placing ever increasing emphasis on sustainability and the maintenance of ecological processes, biodiversity, and endangered species or populations. Balancing timber harvest and the management of imperiled species presents a particularly difficult challenge during this shift, as we often know very little about these species’ natural history and how and why silviculture practices affect their populations. Accordingly, investigation of and improvement on current management practices for threatened species is imperative. We investigated the effectiveness of habitat buffers as a management technique for the imperiled Red Hills salamander (Phaeognathus hubrichti by combining genetic, transect, and body-condition data. We found that populations where habitat buffers have been employed have higher genetic diversity and higher population densities, and individuals have better overall body condition. These results indicate that buffering the habitat of imperiled species can be an effective management tool for terrestrial salamanders. Additionally, they provide further evidence that leaving the habitat of imperiled salamanders unbuffered can have both immediate and long-term negative impacts on populations.

  7. Bromeliad Selection by Two Salamander Species in a Harsh Environment

    Science.gov (United States)

    Ruano-Fajardo, Gustavo; Rovito, Sean M.; Ladle, Richard J.

    2014-01-01

    Bromeliad phytotelmata are frequently used by several Neotropical amphibian taxa, possibly due to their high humidity, microclimatic stability, and role as a refuge from predators. Indeed, the ability of phytotelmata to buffer against adverse environmental conditions may be instrumental in allowing some amphibian species to survive during periods of environmental change or to colonize sub-optimal habitats. Association between bromeliad traits and salamanders has not been studied at a fine scale, despite the intimate association of many salamander species with bromeliads. Here, we identify microhabitat characteristics of epiphytic bromeliads used by two species of the Bolitoglossa morio group (B. morio and B. pacaya) in forest disturbed by volcanic activity in Guatemala. Specifically, we measured multiple variables for bromeliads (height and position in tree, phytotelma water temperature and pH, canopy cover, phytotelma size, leaf size, and tree diameter at breast height), as well as salamander size. We employed a DNA barcoding approach to identify salamanders. We found that B. morio and B. pacaya occurred in microsympatry in bromeliads and that phytotelmata size and temperature of bromeliad microhabitat were the most important factors associated with the presence of salamanders. Moreover, phytotelmata with higher pH contained larger salamanders, suggesting that larger salamanders or aggregated individuals might modify pH. These results show that bromeliad selection is nonrandom with respect to microhabitat characteristics, and provide insight into the relationship between salamanders and this unique arboreal environment. PMID:24892414

  8. Bromeliad selection by two salamander species in a harsh environment.

    Directory of Open Access Journals (Sweden)

    Gustavo Ruano-Fajardo

    Full Text Available Bromeliad phytotelmata are frequently used by several Neotropical amphibian taxa, possibly due to their high humidity, microclimatic stability, and role as a refuge from predators. Indeed, the ability of phytotelmata to buffer against adverse environmental conditions may be instrumental in allowing some amphibian species to survive during periods of environmental change or to colonize sub-optimal habitats. Association between bromeliad traits and salamanders has not been studied at a fine scale, despite the intimate association of many salamander species with bromeliads. Here, we identify microhabitat characteristics of epiphytic bromeliads used by two species of the Bolitoglossa morio group (B. morio and B. pacaya in forest disturbed by volcanic activity in Guatemala. Specifically, we measured multiple variables for bromeliads (height and position in tree, phytotelma water temperature and pH, canopy cover, phytotelma size, leaf size, and tree diameter at breast height, as well as salamander size. We employed a DNA barcoding approach to identify salamanders. We found that B. morio and B. pacaya occurred in microsympatry in bromeliads and that phytotelmata size and temperature of bromeliad microhabitat were the most important factors associated with the presence of salamanders. Moreover, phytotelmata with higher pH contained larger salamanders, suggesting that larger salamanders or aggregated individuals might modify pH. These results show that bromeliad selection is nonrandom with respect to microhabitat characteristics, and provide insight into the relationship between salamanders and this unique arboreal environment.

  9. Response of stream-breeding salamander larvae to sediment deposition in southern Appalachian (U.S.A.) headwater streams

    Science.gov (United States)

    S. Conner Keitzer; Reuben. Goforth

    2012-01-01

    Summary 1. Increased fine sediment deposition is a prevalent threat to stream biodiversity and has been shown to impact stream-breeding salamanders negatively. However, their complex life histories make it difficult to determine which stage is affected. 2. We conducted field experiments from 26 August to 11 September 2010 and 11 October to 11...

  10. Impact of Genotype on EPA and DHA Status and Responsiveness to Increased Intakes

    Directory of Open Access Journals (Sweden)

    Anne Marie Minihane

    2016-03-01

    Full Text Available At a population level, cardioprotective and cognitive actions of the fish oil (FO derived long-chain n-3 polyunsaturated fatty acids (LC n-3 PUFAs eicosapentaenoic acid (EPA and docosahexaenoic acid (DHA have been extensively demonstrated. In addition to dietary intake, which is limited for many individuals, EPA and DHA status is dependent on the efficiency of their biosynthesis from α-linolenic acid. Gender and common gene variants have been identified as influencing the rate-limiting desaturase and elongase enzymes. Response to a particular intake or status is also highly heterogeneous and likely influenced by genetic variants which impact on EPA and DHA metabolism and tissue partitioning, transcription factor activity, or physiological end-point regulation. Here, available literature relating genotype to tissue LC n-3 PUFA status and response to FO intervention is considered. It is concluded that the available evidence is relatively limited, with much of the variability unexplained, though APOE and FADS genotypes are emerging as being important. Although genotype × LC n-3 PUFA interactions have been described for a number of phenotypes, few have been confirmed in independent studies. A more comprehensive understanding of the genetic, physiological and behavioural modulators of EPA and DHA status and response to intervention is needed to allow refinement of current dietary LC n-3 PUFA recommendations and stratification of advice to “vulnerable” and responsive subgroups.

  11. Impact of 6-month frozen storage of cervical specimens in alkaline buffer conditions on human papillomavirus genotyping.

    Science.gov (United States)

    LaMere, Brandon J; Howell, Renee; Fetterman, Barbara; Shieh, Jen; Castle, Philip E

    2008-08-01

    The impact of 6-month storage of cervical specimens under alkaline conditions that occurs as the result of Hybrid Capture 2 testing on human papillomavirus (HPV) genotyping is not well documented. To examine this issue, 143 frozen hc2-positive specimens in specimen transport medium were selected at random from each of the following groups: specimens stored for 6 months, 4 months, and 2.5 months under alkaline pH (pH 12-13) and specimens stored 1 month at neutral pH (pH 6-7) as controls. Specimens were tested in a masked fashion for 20 HPV genotypes (HPV6, 11, 16, 18, 26, 31, 33, 35, 39, 45, 51, 52, 53, 56, 58, 59, 66, 68, 73, and 82) using a prototype, research-use-only GP5+/6+ L1 consensus PCR method and multiplex hybridization using Luminex xMAP for detection of specific HPV genotypes One control specimen had missing test results. There were no statistical differences in the number of HPV genotypes detected, number of carcinogenic HPV genotypes detected, or in the signal strength among HPV-positive results across groups. Six-month frozen storage of cervical specimens at alkaline pH had little impact on testing for HPV genotypes among hc2-positive women using this HPV genotyping method.

  12. Root phenotypic differences across a historical gradient of wheat genotypes alter soil rhizosphere communities and their impact on nitrogen cycling

    Science.gov (United States)

    Kallenbach, C.; Junaidi, D.; Fonte, S.; Byrne, P. F.; Wallenstein, M. D.

    2017-12-01

    Plants and soil microorganisms can exhibit coevolutionary relationships where, for example, in exchange for root carbon, rhizosphere microbes enhance plant fitness through improved plant nutrient availability. Organic agriculture relies heavily on these interactions to enhance crop nitrogen (N) availability. However, modern agriculture and breeding under high mineral N fertilization may have disrupted these interactions through alterations to belowground carbon inputs and associated impacts on the soil microbiome. As sustainability initiatives lead to a restoration of agricultural soil organic matter, modern crop cultivars may still be constrained by crop roots' ability to effectively support microbial-mediated N mineralization. We investigated how differences in root traits across a historical gradient of spring wheat genotypes influence the rhizosphere microbial community and effects on soil N and wheat yield. Five genotypes, representing wild (Wild), pre-Green Revolution (Old), and modern (Modern) wheat, were grown under greenhouse conditions in soils with and without compost to also compare genotype response to difference in native soil microbiomes and organic resource availability. We analyzed rhizosphere soils for microbial community composition, enzyme activities, inorganic N, and microbial biomass. Root length density, surface area, fine root volume and root:shoot ratio were higher in the Wild and Old genotype (Gypsum) compared to the two Modern genotypes (Psoil inorganic N, compared to Modern genotypes. However, under unamended soils, the microbial community and soil N were not affected by genotypes. We also relate how root traits and N cycling across genotypes correspond to microbial community composition. Our preliminary data suggest that the older wheat genotypes and their root traits are more effective at enhancing microbial N mineralization under organically managed soils. Thus, to optimize crop N availability from organic sources, breeding efforts

  13. Better than fish on land? Hearing across metamorphosis in salamanders

    DEFF Research Database (Denmark)

    Christensen, Christian Bech; Lauridsen, Henrik; Christensen-Dalsgaard, Jakob

    2015-01-01

    hearing in early tetrapods. Here, we combine imaging techniques with neurophysiological measurements to resolve how the change from aquatic larvae to terrestrial adult affects the ear morphology and sensory capabilities of salamanders. We show that air-induced pressure detection enhances underwater...... hearing sensitivity of salamanders at frequencies above 120 Hz, and that both terrestrial adults and fully aquatic juvenile salamanders can detect airborne sound. Collectively, these findings suggest that early atympanic tetrapods may have been pre-equipped to aerial hearing and are able to hear airborne...

  14. Ballistic tongue projection in a miniaturized salamander.

    Science.gov (United States)

    Deban, Stephen M; Bloom, Segall V

    2018-05-20

    Miniaturization of body size is often accompanied by peculiarities in morphology that can have functional consequences. We examined the feeding behavior and morphology of the miniaturized plethodontid salamander Thorius, one of the smallest vertebrates, to determine if its performance and biomechanics differ from those of its larger relatives. High-speed imaging and dynamics analysis of feeding at a range of temperatures show that tongue projection in Thorius macdougalli is ballistic and achieves accelerations of up to 600 G with low thermal sensitivity, indicating that tongue projection is powered by an elastic-recoil mechanism. Preceding ballistic projection is an unusual preparatory phase of tongue protrusion, which, like tongue retraction, shows lower performance and higher thermal sensitivity that are indicative of movement being powered directly by muscle shortening. The variability of tongue-projection kinematics and dynamics is comparable to larger ballistic-tongued plethodontids and reveals that Thorius is capable of modulating its tongue movements in response to prey distance. Morphological examination revealed that T. macdougalli possesses a reduced number of myofibers in the tongue muscles, a large projector muscle mass relative to tongue mass, and an unusual folding of the tongue skeleton, compared with larger relatives. Nonetheless, T. macdougalli retains the elaborated collagen aponeuroses in the projector muscle that store elastic energy and a tongue skeleton that is free of direct myofiber insertion, two features that appear to be essential for ballistic tongue projection in salamanders. © 2018 Wiley Periodicals, Inc.

  15. Comparing population patterns to processes: abundance and survival of a forest salamander following habitat degradation.

    Directory of Open Access Journals (Sweden)

    Clint R V Otto

    Full Text Available Habitat degradation resulting from anthropogenic activities poses immediate and prolonged threats to biodiversity, particularly among declining amphibians. Many studies infer amphibian response to habitat degradation by correlating patterns in species occupancy or abundance with environmental effects, often without regard to the demographic processes underlying these patterns. We evaluated how retention of vertical green trees (CANOPY and coarse woody debris (CWD influenced terrestrial salamander abundance and apparent survival in recently clearcut forests. Estimated abundance of unmarked salamanders was positively related to CANOPY (β Canopy  = 0.21 (0.02-1.19; 95% CI, but not CWD (β CWD  = 0.11 (-0.13-0.35 within 3,600 m2 sites, whereas estimated abundance of unmarked salamanders was not related to CANOPY (β Canopy  = -0.01 (-0.21-0.18 or CWD (β CWD  = -0.02 (-0.23-0.19 for 9 m2 enclosures. In contrast, apparent survival of marked salamanders within our enclosures over 1 month was positively influenced by both CANOPY and CWD retention (β Canopy  = 0.73 (0.27-1.19; 95% CI and β CWD  = 1.01 (0.53-1.50. Our results indicate that environmental correlates to abundance are scale dependent reflecting habitat selection processes and organism movements after a habitat disturbance event. Our study also provides a cautionary example of how scientific inference is conditional on the response variable(s, and scale(s of measure chosen by the investigator, which can have important implications for species conservation and management. Our research highlights the need for joint evaluation of population state variables, such as abundance, and population-level process, such as survival, when assessing anthropogenic impacts on forest biodiversity.

  16. Evolution of coprophagy and nutrient absorption in a Cave Salamander

    Directory of Open Access Journals (Sweden)

    Daphne Soares

    2017-11-01

    Full Text Available The transition from carnivory to omnivory is poorly understood. The ability to feed at more than one trophic level theoretically increases an animal’s fitness in a novel environment. Because of the absence of light and photosynthesis, most subterranean ecosystems are characterized by very few trophic levels, such that food scarcity is a challenge in many subterranean habitats. One strategy against starvation is to expand diet breadth. Grotto Salamanders (Eurycea spelaea (Stejneger, 1892 are known to ingest bat guano deliberately, challenging the general understanding that salamanders are strictly carnivorous. Here we tested the hypothesis that grotto salamanders have broadened their diet related to cave adaptation and found that, although coprophagous behavior is present, salamanders are unable to acquire sufficient nutrition from bat guano alone. Our results suggest that the coprophagic behavior has emerged prior to physiological or gut biome adaptations.

  17. Impact of enumeration method on diversity of Escherichia coli genotypes isolated from surface water.

    Science.gov (United States)

    Martin, E C; Gentry, T J

    2016-11-01

    There are numerous regulatory-approved Escherichia coli enumeration methods, but it is not known whether differences in media composition and incubation conditions impact the diversity of E. coli populations detected by these methods. A study was conducted to determine if three standard water quality assessments, Colilert ® , USEPA Method 1603, (modified mTEC) and USEPA Method 1604 (MI), detect different populations of E. coli. Samples were collected from six watersheds and analysed using the three enumeration approaches followed by E. coli isolation and genotyping. Results indicated that the three methods generally produced similar enumeration data across the sites, although there were some differences on a site-by-site basis. The Colilert ® method consistently generated the least diverse collection of E. coli genotypes as compared to modified mTEC and MI, with those two methods being roughly equal to each other. Although the three media assessed in this study were designed to enumerate E. coli, the differences in the media composition, incubation temperature, and growth platform appear to have a strong selective influence on the populations of E. coli isolated. This study suggests that standardized methods of enumeration and isolation may be warranted if researchers intend to obtain individual E. coli isolates for further characterization. This study characterized the impact of three USEPA-approved Escherichia coli enumeration methods on observed E. coli population diversity in surface water samples. Results indicated that these methods produced similar E. coli enumeration data but were more variable in the diversity of E. coli genotypes observed. Although the three methods enumerate the same species, differences in media composition, growth platform, and incubation temperature likely contribute to the selection of different cultivable populations of E. coli, and thus caution should be used when implementing these methods interchangeably for

  18. Terrestrial salamander abundance on reclaimed mountaintop removal mines

    Science.gov (United States)

    Wood, Petra Bohall; Williams, Jennifer M.

    2013-01-01

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

  19. 77 FR 36287 - Proposed Low-Effect Habitat Conservation Plan for the California Tiger Salamander, Calaveras...

    Science.gov (United States)

    2012-06-18

    ...-FXES11120800000F2-123-F2] Proposed Low-Effect Habitat Conservation Plan for the California Tiger Salamander... animal, the threatened Central California Distinct Population Segment of the California tiger salamander (tiger salamander). The applicant would implement a conservation program to minimize and mitigate the...

  20. Road deicing salt irreversibly disrupts osmoregulation of salamander egg clutches.

    Science.gov (United States)

    Karraker, Nancy E; Gibbs, James P

    2011-03-01

    It has been postulated that road deicing salts are sufficiently diluted by spring rains to ameliorate any physiological impacts to amphibians breeding in wetlands near roads. We tested this conjecture by exposing clutches of the spotted salamander (Ambystoma maculatum) to three chloride concentrations (1 mg/L, 145 mg/L, 945 mg/L) for nine days, then transferred clutches to control water for nine days, and measured change in mass at three-day intervals. We measured mass change because water uptake by clutches reduces risks to embryos associated with freezing, predation, and disease. Clutches in controls sequestered water asymptotically. Those in the moderate concentrations lost 18% mass initially and regained 14% after transfer to control water. Clutches in high concentration lost 33% mass and then lost an additional 8% after transfer. Our results suggest that spring rains do not ameliorate the effects of deicing salts in wetlands with extremely high chloride concentrations. Copyright © 2010 Elsevier Ltd. All rights reserved.

  1. Population Structure and Evolution after Speciation of the Hokkaido Salamander (Hynobius retardatus.

    Directory of Open Access Journals (Sweden)

    Masatoshi Matsunami

    Full Text Available The Hokkaido salamander (Hynobius retardatus is endemic to Hokkaido Island, Japan, and shows intriguing flexible phenotypic plasticity and regional morphological diversity. However, to date, allozymes and partial mitochondria DNA sequences have provided only an outline of its demographic histories and the pattern of its genetic diversification. To understand the finer details of the population structure of this species and its evolution since speciation, we genotyped five regional populations by using 12 recently developed microsatellite polymorphic markers. We found a clear population structure with low gene flow among the five populations, but a close genetic relationship between the Teshio and Kitami populations. Our demographic analysis suggested that Teshio and Erimo had the largest effective population sizes among the five populations. These findings regarding the population structure and demography of H. retardatus improve our understanding of the faunal phylogeography on Hokkaido Island and also provide fundamental genetic information that will be useful for future studies.

  2. Inhibition of Fungal Pathogens across Genotypes and Temperatures by Amphibian Skin Bacteria

    Directory of Open Access Journals (Sweden)

    Carly R. Muletz-Wolz

    2017-08-01

    Full Text Available Symbiotic bacteria may dampen the impacts of infectious diseases on hosts by inhibiting pathogen growth. However, our understanding of the generality of pathogen inhibition by different bacterial taxa across pathogen genotypes and environmental conditions is limited. Bacterial inhibitory properties are of particular interest for the amphibian-killing fungal pathogens (Batrachochytrium dendrobatidis and Batrachochytrium salamandrivorans, for which probiotic applications as conservation strategies have been proposed. We quantified the inhibition strength of five putatively B. dendrobatidis-inhibitory bacteria isolated from woodland salamander skin against six Batrachochytrium genotypes at two temperatures (12 and 18°C. We selected six genotypes from across the Batrachochytrium phylogeny: B. salamandrivorans, B. dendrobatidis-Brazil and four genotypes of the B. dendrobatidis Global Panzootic Lineage (GPL1: JEL647, JEL404; GPL2: SRS810, JEL423. We performed 96-well plate challenge assays in a full factorial design. We detected a Batrachochytrium genotype by temperature interaction on bacterial inhibition score for all bacteria, indicating that bacteria vary in ability to inhibit Batrachochytrium depending on pathogen genotype and temperature. Acinetobacter rhizosphaerae moderately inhibited B. salamandrivorans at both temperatures (μ = 46–53%, but not any B. dendrobatidis genotypes. Chryseobacterium sp. inhibited three Batrachochytrium genotypes at both temperatures (μ = 5–71%. Pseudomonas sp. strain 1 inhibited all Batrachochytrium genotypes at 12°C and four Batrachochytrium genotypes at 18°C (μ = 5–100%. Pseudomonas sp. strain 2 and Stenotrophomonas sp. moderately to strongly inhibited all six Batrachochytrium genotypes at both temperatures (μ = 57–100%. All bacteria consistently inhibited B. salamandrivorans. Using cluster analysis of inhibition scores, we found that more closely related Batrachochytrium genotypes grouped together

  3. Predicting the impact of selection for scrapie resistance on PRNP genotype frequencies in goats.

    Science.gov (United States)

    Sacchi, Paola; Rasero, Roberto; Ru, Giuseppe; Aiassa, Eleonora; Colussi, Silvia; Ingravalle, Francesco; Peletto, Simone; Perrotta, Maria Gabriella; Sartore, Stefano; Soglia, Dominga; Acutis, Pierluigi

    2018-03-06

    The European Union has implemented breeding programmes to increase scrapie resistance in sheep. A similar approach can be applied also in goats since the K222 allele provides a level of resistance equivalent to that of ARR in sheep. The European Food Safety Authority stated that breeding for resistance could be offered as an option for Member States to control classical scrapie in goats. We assessed the impact of different breeding strategies on PRNP genotype frequencies using a mathematical model that describes in detail the evolution of K222 in two goat breeds, Chamois Coloured and Saanen. Different patterns of age structure and replacement rate were modelled as factors affecting response to selection. Breeding for scrapie resistance can be implemented in goats, even though the initial K222 frequencies in these breeds are not particularly favourable and the rate at which the resistant animals increase, both breeding and slaughtered for meat production, is slow. If the goal is not to achieve the fixation of resistance allele, it is advisable to carry out selection only until a desired frequency of K222-carriers has been attained. Nucleus selection vs. selection on the overall populations is less expensive but takes longer to reach the desired output. The programme performed on the two goat breeds serves as a model of the response the selection could have in other breeds that show different initial frequencies and population structure. In this respect, the model has a general applicability.

  4. Impact of selective genotyping in the training population on accuracy and bias of genomic selection.

    Science.gov (United States)

    Zhao, Yusheng; Gowda, Manje; Longin, Friedrich H; Würschum, Tobias; Ranc, Nicolas; Reif, Jochen C

    2012-08-01

    Estimating marker effects based on routinely generated phenotypic data of breeding programs is a cost-effective strategy to implement genomic selection. Truncation selection in breeding populations, however, could have a strong impact on the accuracy to predict genomic breeding values. The main objective of our study was to investigate the influence of phenotypic selection on the accuracy and bias of genomic selection. We used experimental data of 788 testcross progenies from an elite maize breeding program. The testcross progenies were evaluated in unreplicated field trials in ten environments and fingerprinted with 857 SNP markers. Random regression best linear unbiased prediction method was used in combination with fivefold cross-validation based on genotypic sampling. We observed a substantial loss in the accuracy to predict genomic breeding values in unidirectional selected populations. In contrast, estimating marker effects based on bidirectional selected populations led to only a marginal decrease in the prediction accuracy of genomic breeding values. We concluded that bidirectional selection is a valuable approach to efficiently implement genomic selection in applied plant breeding programs.

  5. Ontogenetic evidence for the Paleozoic ancestry of salamanders.

    Science.gov (United States)

    Schoch, Rainer R; Carroll, Robert L

    2003-01-01

    The phylogenetic positions of frogs, salamanders, and caecilians have been difficult to establish. Data matrices based primarily on Paleozoic taxa support a monophyletic origin of all Lissamphibia but have resulted in widely divergent hypotheses of the nature of their common ancestor. Analysis that concentrates on the character states of the stem taxa of the extant orders, in contrast, suggests a polyphyletic origin from divergent Paleozoic clades. Comparison of patterns of larval development in Paleozoic and modern amphibians provides a means to test previous phylogenies based primarily on adult characteristics. This proves to be highly informative in the case of the origin of salamanders. Putative ancestors of salamanders are recognized from the Permo-Carboniferous boundary of Germany on the basis of ontogenetic changes observed in fossil remains of larval growth series. The entire developmental sequence from hatching to metamorphosis is revealed in an assemblage of over 600 specimens from a single locality, all belonging to the genus Apateon. Apateon forms the most speciose genus of the neotenic temnospondyl family Branchiosauridae. The sequence of ossification of individual bones and the changing configuration of the skull closely parallel those observed in the development of primitive living salamanders. These fossils provide a model of how derived features of the salamander skull may have evolved in the context of feeding specializations that appeared in early larval stages of members of the Branchiosauridae. Larvae of Apateon share many unique derived characters with salamanders of the families Hynobiidae, Salamandridae, and Ambystomatidae, which have not been recognized in any other group of Paleozoic amphibians.

  6. Reproductive biology of the Del Norte salamander (Plethodon elongatus).

    Science.gov (United States)

    Clara A. Wheeler; Hartwell H. Welsh Jr.; Lisa M. Ollivier

    2013-01-01

    We examined seasonal reproductive patterns of the Del Norte Salamander, Plethodon elongatus, in mixed conifer and hardwood forests of northwestern California and southwestern Oregon. Seasonal size differences in reproductive structures suggested that maximum spermatogenic activity occurred during the late summer, with spermatozoa transfer to the...

  7. Design tradeoffs in long-term research for stream salamanders

    Science.gov (United States)

    Brand, Adrianne B,; Grant, Evan H. Campbell

    2017-01-01

    Long-term research programs can benefit from early and periodic evaluation of their ability to meet stated objectives. In particular, consideration of the spatial allocation of effort is key. We sampled 4 species of stream salamanders intensively for 2 years (2010–2011) in the Chesapeake and Ohio Canal National Historical Park, Maryland, USA to evaluate alternative distributions of sampling locations within stream networks, and then evaluated via simulation the ability of multiple survey designs to detect declines in occupancy and to estimate dynamic parameters (colonization, extinction) over 5 years for 2 species. We expected that fine-scale microhabitat variables (e.g., cobble, detritus) would be the strongest determinants of occupancy for each of the 4 species; however, we found greater support for all species for models including variables describing position within the stream network, stream size, or stream microhabitat. A monitoring design focused on headwater sections had greater power to detect changes in occupancy and the dynamic parameters in each of 3 scenarios for the dusky salamander (Desmognathus fuscus) and red salamander (Pseudotriton ruber). Results for transect length were more variable, but across all species and scenarios, 25-m transects are most suitable as a balance between maximizing detection probability and describing colonization and extinction. These results inform sampling design and provide a general framework for setting appropriate goals, effort, and duration in the initial planning stages of research programs on stream salamanders in the eastern United States.

  8. Salamander blue-sensitive cones lost during metamorphosis.

    NARCIS (Netherlands)

    Chen, Y.; Znoiko, S.; Grip, W.J. de; Crouch, R.K.; Ma, J.X.

    2008-01-01

    The tiger salamander lives in shallow water with bright light in the aquatic phase, and in dim tunnels or caves in the terrestrial phase. In the aquatic phase, there are five types of photoreceptors--two types of rods and three types of cones. Our previous studies showed that the green rods and

  9. A Salamander Tale: Effective Exhibits and Attitude Change

    Science.gov (United States)

    Rollins, Jeffrey; Watson, Sunnie Lee

    2017-01-01

    Little information exists regarding intention behind the design and development of Extension outreach and educational exhibits. An evaluation of response to the exhibit "A Salamander Tale" indicates that the methods used to develop the exhibit resulted in an effective way to present information to an adult audience. Survey questions were…

  10. in Chinese giant salamander ( Andrias davidianus , Blanchard, 1871)

    African Journals Online (AJOL)

    A disease in farmed Chinese giant salamander (Andrias davidianus) was a common event, being an economically important threat for Chinese farms. Based on the clinical signs, epizootiology and pathogens belonging to the genus, Ranavirus was suspected as the possible etiology. Although in a cultured Chinese giant ...

  11. Overview of the status of the Cheat Mountain salamander

    Science.gov (United States)

    Thomas K. Pauley

    2010-01-01

    Plethodon nettingi, the Cheat Mountain salamander, is endemic to the high elevations of the Allegheny Mountains in eastern West Virginia. In 1938, N.B. Green named the species from specimens collected at Barton Knob, Randolph County, in honor of his friend and colleague Graham Netting.

  12. Seasonality and microhabitat selection in a forest-dwelling salamander

    Science.gov (United States)

    Basile, Marco; Romano, Antonio; Costa, Andrea; Posillico, Mario; Scinti Roger, Daniele; Crisci, Aldo; Raimondi, Ranieri; Altea, Tiziana; Garfì, Vittorio; Santopuoli, Giovanni; Marchetti, Marco; Salvidio, Sebastiano; De Cinti, Bruno; Matteucci, Giorgio

    2017-10-01

    Many small terrestrial vertebrates exhibit limited spatial movement and are considerably exposed to changes in local environmental variables. Among such vertebrates, amphibians at present experience a dramatic decline due to their limited resilience to environmental change. Since the local survival and abundance of amphibians is intrinsically related to the availability of shelters, conservation plans need to take microhabitat requirements into account. In order to gain insight into the terrestrial ecology of the spectacled salamander Salamandrina perspicillata and to identify appropriate forest management strategies, we investigated the salamander's seasonal variability in habitat use of trees as shelters in relation to tree features (size, buttresses, basal holes) and environmental variables in a beech forest in Italy. We used the occupancy approach to assess tree suitability on a non-conventional spatial scale. Our approach provides fine-grained parameters of microhabitat suitability and elucidates many aspects of the salamander's terrestrial ecology . Occupancy changed with the annual life cycle and was higher in autumn than in spring, when females were found closer to the stream in the study area. Salamanders showed a seasonal pattern regarding the trees they occupied and a clear preference for trees with a larger diameter and more burrows. With respect to forest management, we suggest maintaining a suitable number of trees with a trunk diameter exceeding 30 cm. A practice of selective logging along the banks of streams could help maintain an adequate quantity of the appropriate microhabitat. Furthermore, in areas with a presence of salamanders, a good forest management plan requires leaving an adequate buffer zone around streams, which should be wider in autumn than in spring.

  13. Serotonin Transporter Genotype (5HTTLPR) Moderates the Longitudinal Impact of Atypical Attachment on Externalizing Behavior.

    Science.gov (United States)

    Humphreys, Kathryn L; Zeanah, Charles H; Nelson, Charles A; Fox, Nathan A; Drury, Stacy S

    2015-01-01

    To test whether genotype of the serotonin transporter-linked polymorphic region (5HTTLPR) and atypical attachment interact to predict externalizing psychopathology prospectively in a sample of children with a history of early institutional care. Caregiver report of externalizing behavior at 54 months was examined in 105 children initially reared in institutional care and enrolled in the Bucharest Early Intervention Project, a randomized controlled trial of high quality foster care. 5HTTLPR genotype, attachment status at 42 months of age (typical [secure, avoidant, or ambivalent] or atypical [disorganized-controlling, insecure-other]), and their interaction were examined as predictors of externalizing behavior at age 54 months. 5HTTLPR genotype and atypical attachment at age 42 months interacted to predict externalizing behavior at age 54 months. Specifically, children with the s/s genotype with an atypical attachment had the highest externalizing scores. However, s/s children with a typical attachment demonstrated the lowest externalizing scores, even after controlling for intervention group status. There was no association between attachment status and externalizing behavior among children carrying at least 1 copy of the l allele. These findings indicate that genetic variation in the serotonergic system moderates the association between atypical attachment status and externalizing in young children. Our findings suggest that children, as a result of genetic variability in the serotonergic system, demonstrate differential sensitivity to the attachment relationship.

  14. Serotonin Transporter Genotype (5HTTLPR) Moderates the Longitudinal Impact of Atypical Attachment on Externalizing Behavior

    Science.gov (United States)

    Humphreys, Kathryn L.; Zeanah, Charles H.; Nelson, Charles A.; Fox, Nathan A.; Drury, Stacy S.

    2015-01-01

    Objective To test whether genotype of the serotonin transporter-linked polymorphic region (5HTTLPR) and atypical attachment interact to predict externalizing psychopathology prospectively in a sample of children with a history of early institutional care. Methods Caregiver report of externalizing behavior at 54 months was examined in 105 children initially reared in institutional care and enrolled in the Bucharest Early Intervention Project, a randomized controlled trial of high quality foster care. 5HTTLPR genotype, attachment status at 42 months of age (typical [secure, avoidant, or ambivalent] or atypical [disorganized-controlling, insecure-other]), as well as their interaction, were examined as predictors of externalizing behavior at age 54 months. Results 5HTTLPR genotype and atypical attachment at age 42 months interacted to predict externalizing behavior at age 54 months. Specifically, children with the s/s genotype with an atypical attachment had the highest externalizing scores. However, s/s children with a typical attachment demonstrated the lowest externalizing scores, even after controlling for intervention group status. There was no association between attachment status and externalizing behavior among children carrying at least one copy of the l allele. Discussion These findings indicate that genetic variation in the serotonergic system moderates the association between atypical attachment status and externalizing in young children. Our findings suggest that children, as a result of genetic variability in the serotonergic system, demonstrate differential sensitivity to the attachment relationship. PMID:25933228

  15. Impacts of irrigation and genotype on yield, protein, starch and oil contents in grain of maize inbred lines

    Directory of Open Access Journals (Sweden)

    Josipovic Marko

    2014-01-01

    Full Text Available Four inbred lines of maize (Os 438-95 = C1, Os 30-8 = C2, Os 6 = C3 and Os 1-44 =C4 were grown for 4-year period (2006-2009 in the stationary field experiment on Osijek eutric cambisol. Impact of irrigation, nitrogen fertilization and genotype were tested. Soil moisture was maintained by two irrigation rates from 60-100% and 80-100% of the field water capacity. Two steps of N (0, 100 and 200 kg N ha-1 were applied, while P and K fertilization was equal (500 kg/ha NPK 0:30:20. Eight maize genotypes (four inbred lines and four hybrids were grown on each basic plot of fertilization. The experiment was duplicated for maize - soybean rotation. The experiment was set by split-split plot method according to randomized block design in three replicates. The basic plot areas were 617.2 m2 (irrigation, 313.6 m2 (fertilization and 39.2 m2 (genotype. Selection of N non-fertilized treatment and four inbred lines were made for this study with aim of testing year (A irrigation (B and genotype (C effects under natural N-soil conditions. Average grain yield in level 1809 kg ha-1without N fertilization is indication of very high fertility of the soil. Differences of yield among the years were from 823 (2007 to 2450 (2006 kg ha-1. Excessive drought and high air-temperature stress is responsible for the low maize yield in 2007. Irrigation considerable affected on maize yields (4-year averages: 1500, 1809 and 2118 kg ha-1, for B1, B2 and B3, respectively. Differences of the 4-year average yields among the genotypes were from 1259 (C3 to 2765 (C1 kg ha-1. Differences of yield among the genotypes in the different years were also considerable because the lowest yield was for 71% (A1, 23% (A2, 63% (A3 and 40% (A4 lower in comparison to the highest yield. The genotype effects under different water supplies were less influencing factor because the high-yielding C1 had for 128%, 129% and 106% the higher yield compared to the low-yielding C3, for B1, B2 and B3, respectively

  16. Impact of osmotic stress on seedling growth observations, membrane characteristics and antioxidant defense system of different wheat genotypes

    Directory of Open Access Journals (Sweden)

    Bardees M. Mickky

    2017-03-01

    Full Text Available The objective of the present study was to find out a straightforward technique for screening the tolerance of ten wheat genotypes to two levels of osmotic stress at early seedling stage. Data revealed that polyethylene glycol-induced drought had general negative effect on seedling morphological characters indicated by plumule and radicle length, number of adventitious roots as well as seedling biomass and water content. Water deficit could also suppress membrane integrity by stimulating lipid peroxidation with marked increase in membrane leakage and subsequent decrease in its stability index. For all the addressed germination parameters and seedling membrane features, the impact of severe drought was more pronounced than that of moderate drought. Simultaneously, moderate stress could activate peroxidase, polyphenol oxidase and ascorbic peroxidase of the studied genotypes; but these enzymes were inhibited by severe stress. The activity of catalase, superoxide dismutase and glutathione reductase was conversely retarded by drought whether at moderate or severe level. More interestingly, a novel function “Stress Impact Index; SII” was introduced to rank the estimated morpho-physiological traits (SIItrait as well as the considered genotypes (SIIgenotype according to their sensitivity to stress. Values of SIItrait implied that germination parameters were generally affected by drought more intensively than membrane characteristics and finally came the antioxidant enzymes with the least degree of suppression when applying stress. Based on the magnitudes of SIIgenotype, Sids 13 seemed to be the most drought-tolerant wheat cultivar while Shandawel 1 could be the most sensitive one at their juvenile growth stage.

  17. Impact of HBV genotype and mutations on HBV DNA and qHBsAg levels in patients with HBeAg-negative chronic HBV infection.

    Science.gov (United States)

    Kuhnhenn, L; Jiang, B; Kubesch, A; Vermehren, J; Knop, V; Susser, S; Dietz, J; Carra, G; Finkelmeier, F; Grammatikos, G; Zeuzem, S; Sarrazin, C; Hildt, E; Peiffer, K-H

    2018-04-10

    HBV DNA and quantitative (q)HBsAg levels as prognostic markers for HBV-related disease are mostly validated in Asia and their significance in Western populations is uncertain. To analyse the impact of the HBV genotype and frequent mutations in precore (PC), basal core promoter (BCP) and preS on HBV DNA and qHBsAg levels. HBV DNA and qHBsAg serum levels of 465 patients with HBeAg-negative chronic HBV infection were correlated with the HBV genotype and mutations in PC, BCP and preS. For a detailed analysis of the molecular virology, genotype A2 genomes harbouring these mutations were analysed for replication efficacy and HBsAg release in cell culture. While no impact of the HBV genotype on HBV DNA levels was observed, qHBsAg levels differed up to 1.4 log among the genotypes (P HBV DNA levels (P HBV genome harbouring a preS deletion. In contrast, a perinuclear HBsAg accumulation was detected for the PC and BCP-variants, reflecting an impaired HBsAg release. qHBsAg serum levels depend on the HBV genotype and together with HBV DNA levels on frequent mutations in PC, BCP and preS in HBeAg-negative patients. qHBsAg cut-offs when used as prognostic markers require genotype-dependent validation. © 2018 John Wiley & Sons Ltd.

  18. Identification of conservation units of the hynobiid salamander Pachyhynobius shangchengensis.

    Science.gov (United States)

    Su, L-N; Zhao, Y-Y; Wu, X-M; Zhang, H-F; Li, X-C

    2015-08-19

    The evolutionary significant units (ESUs) of the salamander Pachyhynobius shangchengensis (Hynobiidae) in the Dabieshan mountains, southeastern China, were identified based on mitochondrial DNA data. We used methods for detecting cryptic species, such as the minimum spanning tree, the automatic barcode gap discovery, and the generalized mixed Yule-coalescent model; geographical partitioning was also used to identify the ESUs. A total of four ESUs were identified.

  19. Differentiated egg size of the cannibalistic salamander Hynobius retardatus

    OpenAIRE

    Michimae, Hirofumi

    2007-01-01

    Larvae of the salamander, Hynobius retardatus, are carnivorous, and even though there are two morphs, a typical morph and a broad-headed or “cannibal” morph, both are cannibalistic. They also sometimes eat other large prey, for example larvae of the frog, Rana pirica. In natural habitats, use of both conspecific and R. pirica larvae as food may contribute more strongly to high survival and substantially to fitness when larval densities are higher, because early-stage H. retardatus larvae some...

  20. Cannibalistic-morph Tiger Salamanders in unexpected ecological contexts

    Science.gov (United States)

    McLean, Kyle I.; Stockwell, Craig A.; Mushet, David M.

    2016-01-01

    Barred tiger salamanders [Ambystoma mavortium (Baird, 1850)] exhibit two trophic morphologies; a typical and a cannibalistic morph. Cannibalistic morphs, distinguished by enlarged vomerine teeth, wide heads, slender bodies, and cannibalistic tendencies, are often found where conspecifics occur at high density. During 2012 and 2013, 162 North Dakota wetlands and lakes were sampled for salamanders. Fifty-one contained A. mavortium populations; four of these contained cannibalistic morph individuals. Two populations with cannibalistic morphs occurred at sites with high abundances of conspecifics. However, the other two populations occurred at sites with unexpectedly low conspecific but high fathead minnow [Pimephales promelas (Rafinesque, 1820)] abundances. Further, no typical morphs were observed in either of these later two populations, contrasting with earlier research suggesting cannibalistic morphs only occur at low frequencies in salamander populations. Another anomaly of all four populations was the occurrence of cannibalistic morphs in permanent water sites, suggesting their presence was due to factors other than faster growth allowing them to occupy ephemeral habitats. Therefore, our findings suggest environmental factors inducing the cannibalistic morphism may be more complex than previously thought.

  1. Comparative and developmental patterns of amphibious auditory function in salamanders.

    Science.gov (United States)

    Zeyl, Jeffrey N; Johnston, Carol E

    2016-12-01

    Early amphibious tetrapods may have detected aquatic sound pressure using sound-induced lung vibrations, but their lack of tympanic middle ears would have restricted aerial sensitivity. Sharing these characteristics, salamanders could be models for the carryover of auditory function across an aquatic-terrestrial boundary without tympanic middle ears. We measured amphibious auditory evoked potential audiograms in five phylogenetically and ecologically distinct salamanders (Amphiuma means, Notophthalmus viridescens, Ambystoma talpoideum, Eurycea spp., and Plethodon glutinosus) and tested whether metamorphosis and terrestrial niche were linked to aerial sensitivity. Threshold differences between media varied between species. A. means' relative aerial sensitivity was greatest at 100 Hz and decreased with increasing frequency. In contrast, all other salamanders retained greater sensitivity up to 500 Hz, and in A. talpoideum and Eurycea, relative sensitivity at 500 Hz was higher than at 100 Hz. Aerial thresholds of terrestrial P. glutinosus above 200 Hz were similar to A. talpoideum and Eurycea, but lower than N. viridescens and A. means. Metamorphosis did not affect aerial sensitivity in N. viridescens or A. talpoideum. These results fail to support a hypothesis of terrestrial hearing specialization across ontogeny or phylogeny. We discuss methodological limitations to our amphibious comparisons and factors affecting variation in amphibious performance.

  2. Acid precipitation and reproductive success of Ambystoma salamanders

    Energy Technology Data Exchange (ETDEWEB)

    Pough, R H; Wilson, R E

    1976-01-01

    The two species of mole salamander that occur in the Ithaca, New York, region (Ambystoma maculatum and A. jeffersonianum) breed in temporary ponds that are formed by accumulation of melted snow and spring rains. Water in many of these pools during the breeding season is acid; pH values as low as 3.5 have been measured. In laboratory experiments A. maculatum tolerated pHs from 6 to 10 and had greatest hatching success at pH 7 to 9. Ambystoma Jeffersonianum tolerated pH 4 to 8 and was most successful at pH 5 to 6. Mortality rose abruptly beyond the tolerance limits. The pH optimum shifted upward with increasing temperature for A. jeffersonianum and downward for A. maculatum. Judging from our laboratory studies, the acidity measured in breeding ponds should cause mortality in A. maculatum and permit normal development in A. jeffersonianum. In a four-year study of a large acidic vernal pond, 938 adult A. maculatum produced 486 metamorphosed juveniles (0.52 juvenile/adult), while 686 adult A. jeffersonianum produced 2157 juveniles (3.14 juveniles/adult). Because the effects of acid precipitation on the salamanders' breeding ponds are cumulative from year to year, profound changes in the salamander populations can be anticipated.

  3. Acid precipitation and reproductive success of Ambystoma salamanders

    Energy Technology Data Exchange (ETDEWEB)

    Pough, F H; Wilson, R E

    1977-03-01

    The two species of mole salamander that occur in the Ithaca, New York, region (Ambystoma maculatum and A. jeffersonianum) breed in temporary ponds that are formed by accumulation of melted snow and spring rains. Water in many of these pools during the breeding season is acid; pH values as low as 3.5 have been measured. In laboratory experiments A. maculatum tolerated pHs from 6 to 10 and had greatest hatching success at pH 7 to 9. Ambystoma jeffersonianum tolerated pH 4 to 8 and was most successful at pH 5 to 6. Mortality rose abruptly beyond the tolerance limits. The pH optimum shifted upward with increasing temperature for A. jeffersonianum and downward for A. maculatum. Judging from our laboratory studies, the acidity measured in breeding ponds should cause mortality in A. maculatum and permit normal development in A. jeffersonianum. In a 4 yr study of a large, acidic vernal pond, 938 adult A. maculatum produced 486 metamorphosed juveniles (0.52 juvenile/adult), while 686 adult A. jeffersonianum produced 2157 juveniles (3.14 juveniles/adult). Because the effects of acid precipitation on the salamanders' breeding ponds are cumulative from year to year, profound changes in the salamander populations can be anticipated.

  4. Detection of an enigmatic plethodontid Salamander using Environmental DNA

    Science.gov (United States)

    Pierson, Todd W.; Mckee, Anna; Spear, Stephen F.; Maerz, John C.; Camp, Carlos D.; Glenn, Travis C.

    2016-01-01

    The isolation and identification of environmental DNA (eDNA) offers a non-invasive and efficient method for the detection of rare and secretive aquatic wildlife, and it is being widely integrated into inventory and monitoring efforts. The Patch-Nosed Salamander (Urspelerpes brucei) is a tiny, recently discovered species of plethodontid salamander known only from headwater streams in a small region of Georgia and South Carolina. Here, we present results of a quantitative PCR-based eDNA assay capable of detecting Urspelerpes in more than 75% of 33 samples from five confirmed streams. We deployed the method at 31 additional streams and located three previously undocumented populations of Urspelerpes. We compare the results of our eDNA assay with our attempt to use aquatic leaf litterbags for the rapid detection of Urspelerpes and demonstrate the relative efficacy of the eDNA assay. We suggest that eDNA offers great potential for use in detecting other aquatic and semi-aquatic plethodontid salamanders.

  5. Genotypic and Phenotypic Diversity of Cryptococcus gattii VGII Clinical Isolates and Its Impact on Virulence

    Directory of Open Access Journals (Sweden)

    Vanessa A. Barcellos

    2018-02-01

    Full Text Available The Cryptococcus gattii species complex harbors the main etiological agents of cryptococcosis in immunocompetent patients. C. gattii molecular type VGII predominates in the north and northeastern regions of Brazil, leading to high morbidity and mortality rates. C. gattii VGII isolates have a strong clinical relevance and phenotypic variations. These phenotypic variations among C. gattii species complex isolates suggest that some strains are more virulent than others, but little information is available related to the pathogenic properties of those strains. In this study, we analyzed some virulence determinants of C. gattii VGII strains (CG01, CG02, and CG03 isolated from patients in the state of Piauí, Brazil. The C. gattii R265 VGIIa strain, which was isolated from the Vancouver outbreak, differed from C. gattii CG01, CG02 and CG03 isolates (also classified as VGII when analyzed the capsular dimensions, melanin production, urease activity, as well as the glucuronoxylomannan (GXM secretion. Those differences directly reflected in their virulence potential. In addition, CG02 displayed higher virulence compared to R265 (VGIIa strain in a cryptococcal murine model of infection. Lastly, we examined the genotypic diversity of these strains through Multilocus Sequence Type (MLST and one new subtype was described for the CG02 isolate. This study confirms the presence and the phenotypic and genotypic diversity of highly virulent strains in the Northeast region of Brazil.

  6. Effects of microhabitat and land use on stream salamander abundance in the southwest Virginia coalfields

    Science.gov (United States)

    Sweeten, Sara E.; Ford, W. Mark

    2015-01-01

    Large-scale land uses such as residential wastewater discharge and coal mining practices, particularly surface coal extraction and associated valley fills, are of particular ecological concern in central Appalachia. Identification and quantification of both alterations across scales are a necessary first-step to mitigate negative consequences to biota. In central Appalachian headwater streams absent of fish, salamanders are the dominant, most abundant vertebrate predator providing a significant intermediate trophic role. Stream salamander species are considered to be sensitive to aquatic stressors and environmental alterations, and past research has shown linkages among microhabitat parameters, large-scale land use such as urbanization and logging with salamander abundances. However, little is known about these linkages in the coalfields of central Appalachia. In the summer of 2013, we visited 70 sites (sampled three times each) in the southwest Virginia coalfields to survey salamanders and quantify stream and riparian microhabitat parameters. Using an information-theoretic framework we compared the effects of microhabitat and large-scale land use on salamander abundances. Our findings indicate that dusky salamander (Desmognathus spp.) abundances are more correlated to microhabitat parameters such as canopy cover than to subwatershed land uses. Brook salamander (Eurycea spp.) abundances show strong negative associations to the suspended sediments and stream substrate embeddedness. Neither Desmognathus spp. nor Eurycea spp. abundances were influenced by water conductivity. These suggest protection or restoration of riparian habitats and erosion control is an important conservation component for maintaining stream salamanders in the mined landscapes of central Appalachia.

  7. Effects of mercury on behavior and performance of northern two-lined salamanders (Eurycea bislineata)

    International Nuclear Information System (INIS)

    Burke, John N.; Bergeron, Christine M.; Todd, Brian D.; Hopkins, William A.

    2010-01-01

    Mercury (Hg) causes a range of deleterious effects in wildlife, but little is known about its effects on amphibians. Our objective was to determine whether Hg affects performance and behavior in two-lined salamanders (Eurycea bislineata). We collected salamanders from Hg-contaminated and reference sites and assessed speed, responsiveness, and prey capture ability. Mercury concentrations were >17x higher in salamanders from the contaminated sites and were among the highest documented in amphibians. In the first, but not in the second, locomotion trial, we found a significant effect of Hg on speed and responsiveness. In the prey capture experiment, reference salamanders ate approximately twice as many prey items as the contaminated salamanders. Together, our results suggest that sublethal Hg concentrations may negatively affect salamanders by reducing their ability to successfully execute tasks critical to survival. Future work is warranted to determine whether Hg has other sublethal effects on salamanders and whether other amphibians are similarly affected. - Mercury contamination may alter behavior and performance in the northern two-lined salamander (Eurycea bislineata).

  8. Effects of mercury on behavior and performance of northern two-lined salamanders (Eurycea bislineata)

    Energy Technology Data Exchange (ETDEWEB)

    Burke, John N; Bergeron, Christine M; Todd, Brian D [Wildlife Ecotoxicology and Physiological Ecology Program, Department of Fisheries and Wildlife Sciences, Virginia Polytechnic Institute and State University, 100 Cheatham Hall, Blacksburg, VA 24061 (United States); Hopkins, William A., E-mail: hopkinsw@vt.ed [Wildlife Ecotoxicology and Physiological Ecology Program, Department of Fisheries and Wildlife Sciences, Virginia Polytechnic Institute and State University, 100 Cheatham Hall, Blacksburg, VA 24061 (United States)

    2010-12-15

    Mercury (Hg) causes a range of deleterious effects in wildlife, but little is known about its effects on amphibians. Our objective was to determine whether Hg affects performance and behavior in two-lined salamanders (Eurycea bislineata). We collected salamanders from Hg-contaminated and reference sites and assessed speed, responsiveness, and prey capture ability. Mercury concentrations were >17x higher in salamanders from the contaminated sites and were among the highest documented in amphibians. In the first, but not in the second, locomotion trial, we found a significant effect of Hg on speed and responsiveness. In the prey capture experiment, reference salamanders ate approximately twice as many prey items as the contaminated salamanders. Together, our results suggest that sublethal Hg concentrations may negatively affect salamanders by reducing their ability to successfully execute tasks critical to survival. Future work is warranted to determine whether Hg has other sublethal effects on salamanders and whether other amphibians are similarly affected. - Mercury contamination may alter behavior and performance in the northern two-lined salamander (Eurycea bislineata).

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

    Science.gov (United States)

    Richard M. DeGraaf; Mariko. Yamasaki

    1992-01-01

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

  10. Using a GIS model to assess terrestrial salamander response to alternative forest management plans

    Science.gov (United States)

    Eric J. Gustafson; Nathan L. Murphy; Thomas R. Crow

    2001-01-01

    A GIS model predicting the spatial distribution of terrestrial salamander abundance based on topography and forest age was developed using parameters derived from the literature. The model was tested by sampling salamander abundance across the full range of site conditions used in the model. A regression of the predictions of our GIS model against these sample data...

  11. Habitat relationships of eastern red-backed salamanders (Plethodon cinereus) in Appalachian agroforestry and grazing systems

    Science.gov (United States)

    Breanna L. Riedel; Kevin R. Russell; W. Mark Ford; Katherine P. O' Neill; Harry W. Godwin

    2008-01-01

    Woodland salamander responses to either traditional grazing or silvopasture systems are virtually unknown. An information-theoretic modelling approach was used to evaluate responses of red-backed salamanders (Plethodon cinereus) to silvopasture and meadow conversions in southern West Virginia. Searches of area-constrained plots and artificial...

  12. Effects of edge contrast on redback salamander distribution in even-aged northern hardwoods

    Science.gov (United States)

    Richard M. DeGraaf; Mariko. Yamasaki

    2002-01-01

    Terrestrial salamanders are sensitive to forest disturbance associated with even-aged management. We studied the distribution of redback salamanders (Plethodon cinereus) for 4 yr at edges between even-aged northern hardwood stands along three replicate transects in each of three edge contrast types: regeneration/mature, sapling/mature, and...

  13. Variable infection of stream salamanders in the southern Appalachians by the trematode Metagonimoides oregonensis (family: Heterophyidae)

    Science.gov (United States)

    Jennie A. Wyderko; Ernest F. Benfield; John C. Maerz; Kristen C. Cecala; Lisa K. Belden

    2015-01-01

    Many factors contribute to parasites varying in host specificity and distribution among potential hosts. Metagonimoides oregonensis is a digenetic trematode that uses stream-dwelling plethodontid salamanders as second intermediate hosts in the Eastern US. We completed a field survey to identify which stream salamander species, at a regional level, are most...

  14. Can the eastern red-backed salamander (Plethodon cinereus) persist in an acidified landscape?

    Science.gov (United States)

    Bondi, Cheryl A; Beier, Colin M.; Ducey, Peter K; Lawrence, Gregory B.; Bailey, Scott W.

    2016-01-01

    Hardwood forests of eastern North America have experienced decades of acidic deposition, leading to soil acidification where base cation supply was insufficient to neutralize acid inputs. Negative impacts of soil acidity on amphibians include disrupted embryonic development, lower growth rates, and habitat loss. However, some amphibians exhibit intraspecific variation in acid tolerance, suggesting the potential for local adaptation in areas where soils are naturally acidic. The eastern red-backed salamander (Plethodon cinereus) is a highly abundant top predator of the northern hardwood forest floor. Early research found that P. cinereus was sensitive to acidic soils, avoiding substrates with pH habitats. However, recent studies have documented P. cinereus populations in lower pH conditions than previously observed, suggesting some populations may persist in acidic conditions. Here, we evaluated relationships between organic horizon soil pH and P. cinereus abundance, adult health (body size and condition), and microhabitat selection, based on surveys of 34 hardwood forests in northeastern United States that encompass a regional soil pH gradient. We found no associations between soil pH and P. cinereus abundance or health, and observed that this salamander used substrates with pH similar to that available, suggesting that pH does not mediate their fine-scale distributions. The strongest negative predictor of P. cinereus abundance was the presence of dusky salamanders (Desmognathus spp.), which were most abundant in the western Adirondacks. Our results indicate that P. cinereus occupies a wider range of soil pH than has been previously thought, which has implications for their functional role in forest food webs and nutrient cycles in acid-impaired ecosystems. Tolerance of P. cinereus for more acidic habitats, including anthropogenically acidified forests, may be due to local adaptation in reproductively isolated populations and/or generalist

  15. Effects of atrazine on egg masses of the yellow-spotted salamander (Ambystoma maculatum) and its endosymbiotic alga (Oophila amblystomatis)

    International Nuclear Information System (INIS)

    Baxter, Leilan; Brain, Richard A.; Hosmer, Alan J.; Nema, Mohini; Müller, Kirsten M.; Solomon, Keith R.; Hanson, Mark L.

    2015-01-01

    Embryonic growth of the yellow-spotted salamander (Ambystoma maculatum) is enhanced by the presence of the green alga Oophila amblystomatis, in the egg capsule. To further assess potential impacts of herbicides on this relationship, A. maculatum egg masses were exposed to atrazine (0–338 μg/L) until hatching (up to 66 days). Exposure to atrazine reduced PSII yield of the symbiotic algae in a concentration-dependent manner, but did not significantly affect visible algal growth or any metrics associated with salamander development. Algal cells were also cultured in the laboratory for toxicity testing. In the 96-h growth inhibition test (0–680 μg/L), ECx values were generally greater than those reported for standard algal test species. Complete recovery of growth rates occurred within 96-h of transferring cells to untreated media. Overall, development of A. maculatum embryos was not affected by exposure to atrazine at concentrations and durations exceeding those found in the environment. - Highlights: • The yellow-spotted salamander produces eggs that are colonized by a symbiotic green alga. • We tested the sensitivity of this system to the herbicide atrazine. • Embryo development was not significantly affected by exposure at up to 300 μg/L. • The alga was isolated and 96-h growth tests were performed in the laboratory. • EC50s for Oophila sp. were >100 μg/L. - Development of Ambystoma maculatum embryos in egg masses was not impacted by exposure to atrazine at concentrations and durations exceeding those commonly found in the environment.

  16. Impact of air pollution and genotype variability on DNA damage in Prague policemen

    Czech Academy of Sciences Publication Activity Database

    Novotná, Božena; Topinka, Jan; Solanský, I.; Chvátalová, Irena; Lněničková, Zdena; Šrám, Radim

    2007-01-01

    Roč. 172, - (2007), s. 37-47 ISSN 0378-4274 R&D Projects: GA MŽP SL/5/160/05 Institutional research plan: CEZ:AV0Z50390512 Keywords : oxidative DNA damage * comet assay * carcinogenic polycyclic aromatic hydrocarbons Subject RIV: DN - Health Impact of the Environment Quality Impact factor: 2.826, year: 2007

  17. Retrotransposon long interspersed nucleotide element-1 (LINE-1) is activated during salamander limb regeneration

    Science.gov (United States)

    Zhu, Wei; Kuo, Dwight; Nathanson, Jason; Satoh, Akira; Pao, Gerald M.; Yeo, Gene W.; Bryant, Susan V.; Voss, S. Randal; Gardiner, David M.; Hunter, Tony

    2012-01-01

    Salamanders possess an extraordinary capacity for tissue and organ regeneration when compared to mammals. In our effort to characterize the unique transcriptional fingerprint emerging during the early phase of salamander limb regeneration, we identified transcriptional activation of some germline-specific genes within the Mexican axolotl (Ambystoma mexicanum) that is indicative of cellular reprogramming of differentiated cells into a germline-like state. In this work, we focus on one of these genes, the long interspersed nucleotide element-1 (LINE-1) retrotransposon, which is usually active in germ cells and silent in most of the somatic tissues in other organisms. LINE-1 was found to be dramatically upregulated during regeneration. In addition, higher genomic LINE-1 content was also detected in the limb regenerate when compared to that before amputation indicating that LINE-1 retrotransposition is indeed active during regeneration. Active LINE-1 retrotransposition has been suggested to have a potentially deleterious impact on genomic integrity. Silencing of activated LINE-1 by small RNAs has been reported to be part of the machinery aiming to maintain genomic integrity. Indeed, we were able to identify putative LINE-1-related piRNAs in the limb blastema. Transposable element-related piRNAs have been identified frequently in the germline in other organisms. Thus, we present here a scenario in which a unique germline-like state is established during axolotl limb regeneration, and the re-activation of LINE-1 may serve as a marker for cellular dedifferentiation in the early-stage of limb regeneration. PMID:22913491

  18. Impact of hepatitis C virus genotype-4 eradication following direct acting antivirals on liver stiffness measurement

    Directory of Open Access Journals (Sweden)

    Tag-Adeen M

    2017-10-01

    Full Text Available Mohammed Tag-Adeen,1,2 Ahlam Mohamed Sabra,1 Yuko Akazawa,2 Ken Ohnita,2 Kazuhiko Nakao2 1Department of Internal Medicine, Qena School of Medicine, South Valley University, Qena, Egypt; 2Department of Gastroenterology and Hepatology, Nagasaki School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan Background: Liver fibrosis is the most important prognostic factor in chronic hepatitis C virus (HCV patients, and Egypt shows the highest worldwide HCV prevalence with genotype-4 predominance. The aim of this study was to investigate the degree of liver stiffness measurement (LSM improvement after successful HCV eradication.Patients and methods: The study included 84 chronic HCV Egyptian patients, and was conducted at Qena University Hospital from November 1, 2015 till October 31, 2016. LSM was obtained by FibroScan® before starting direct acting antiviral (DAA treatment and after achieving sustained virologic response-24 (SVR-24. Based on baseline LSM, patients were stratified into F0–F1, F2, F3 and F4 groups (METAVIR. LSM and laboratory data after achieving SVR-24 was compared with that before starting therapy in each fibrosis group (F0-F4, p-value <0.05 was statistically significant.Results: Following DAA treatment, 80 patients achieved SVR-24; of these, 50 were males (62.5%, mean age: 54.2±7.6 years, and mean body mass index: 28.6±2.2 kg/m2. Mean baseline LSM dropped from 15.6±10.8 to 12.1±8.7 kPa post-SVR; the maximum change of −5.8 occurred in F4 versus −2.79, −1.28 and +0.08 in F3, F2 and F0–F1 respectively (p<0.0001. At baseline, 41 patients were in the F4 group; only 16 (39% regressed to non-cirrhotic range (<12.5 kPa, while 25 (61% were still cirrhotic despite achieving SVR-24 (p<0.0001. Patients who achieved LSM improvement (n=64 have had significantly higher baseline aspartate transferase (AST and alanine transaminase (ALT. Also, those patients showed significant improvement in AST, AST/platelets ratio index

  19. Taxonomy Icon Data: Japanese giant salamander [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available Japanese giant salamander Andrias japonicus Chordata/Vertebrata/Amphibia Andrias_japonicus_L.png Andrias_jap...onicus_NL.png Andrias_japonicus_S.png Andrias_japonicus_NS.png http://biosciencedbc....jp/taxonomy_icon/icon.cgi?i=Andrias+japonicus&t=L http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Andrias+jap...onicus&t=NL http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Andrias+japonicus...&t=S http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Andrias+japonicus&t=NS ...

  20. Environmental influences on egg and clutch sizes in lentic- and lotic-breeding salamanders

    Directory of Open Access Journals (Sweden)

    Jon M. Davenport

    2010-12-01

    Full Text Available Recent research indicates that social and environmental factors influence egg and clutch sizes in amphibians. However, most of this work is based on the reproductively diverse order Anura (frogs and toads, whereas less research has been conducted on Caudata (salamanders and Gymnophiona (caecilians. Researchers have suggested that a relationship exists between social and environmental factors and egg and clutch sizes in salamanders, but studies controlling for phylogenetic context are lacking. We could not identify a sufficient number of comparisons for social influences on egg and clutch sizes; therefore, we focused on environmental influences for this study. Data on egg size, clutch size, environmental factors, and phylogenies for salamanders were assembled from the scientific literature. We used independent, pair-wise comparisons to investigate the association of larval salamander habitat and egg size and the association of larval salamander habitat with clutch sizes within a phylogenetic framework. There is a significant association between larval habitat and egg size; specifically, stream-breeding species produce larger eggs. There is no significant association between larval habitat and clutchsize. Our study confirms earlier reports that salamander egg size is associated with larval environments, but is the first to use phylogenetically independent contrasts to account for the lack of phylogenetic independence of the traits measured (egg size and clutch size associated with many of the diverse lineages. Our study shows that environmental selection pressure can be quite strong on one aspect of salamander reproduction—egg size.

  1. Telocytes in pancreas of the Chinese giant salamander (Andrias davidianus).

    Science.gov (United States)

    Zhang, Hui; Yu, Pengcheng; Zhong, Shengwei; Ge, Tingting; Peng, Shasha; Guo, Xiaoquan; Zhou, Zuohong

    2016-11-01

    Telocytes (TCs), novel interstitial cells, have been identified in various organs of many mammals. However, information about TCs of lower animals remains rare. Herein, pancreatic TCs of the Chinese giant salamanders (Andrias davidianus) were identified by CD34 immunohistochemistry (IHC) and transmission electron microscopy (TEM). The IHC micrographs revealed CD34 + TCs with long telopodes (Tps) that were located in the interstitium of the pancreas. CD34 + TCs/Tps were frequently observed between exocrine acinar cells and were close to blood vessels. The TEM micrographs also showed the existence of TCs in the interstitium of the pancreas. TCs had distinctive ultrastructural features, such as one to three very long and thin Tps with podoms and podomers, caveolae, dichotomous branching, neighbouring exosomes and vesicles. The Tps and exosomes were found in close proximity to exocrine acinar cells and α cells. It is suggested that TCs may play a role in the regeneration of acinar cells and α cells. In conclusion, our results demonstrated the presence of TCs in the pancreas of the Chinese giant salamander. This finding will assist us in a better understanding of TCs functions in the amphibian pancreas. © 2016 The Authors. Journal of Cellular and Molecular Medicine published by John Wiley & Sons Ltd and Foundation for Cellular and Molecular Medicine.

  2. Transcriptomic SNP discovery for custom genotyping arrays: impacts of sequence data, SNP calling method and genotyping technology on the probability of validation success.

    Science.gov (United States)

    Humble, Emily; Thorne, Michael A S; Forcada, Jaume; Hoffman, Joseph I

    2016-08-26

    Single nucleotide polymorphism (SNP) discovery is an important goal of many studies. However, the number of 'putative' SNPs discovered from a sequence resource may not provide a reliable indication of the number that will successfully validate with a given genotyping technology. For this it may be necessary to account for factors such as the method used for SNP discovery and the type of sequence data from which it originates, suitability of the SNP flanking sequences for probe design, and genomic context. To explore the relative importance of these and other factors, we used Illumina sequencing to augment an existing Roche 454 transcriptome assembly for the Antarctic fur seal (Arctocephalus gazella). We then mapped the raw Illumina reads to the new hybrid transcriptome using BWA and BOWTIE2 before calling SNPs with GATK. The resulting markers were pooled with two existing sets of SNPs called from the original 454 assembly using NEWBLER and SWAP454. Finally, we explored the extent to which SNPs discovered using these four methods overlapped and predicted the corresponding validation outcomes for both Illumina Infinium iSelect HD and Affymetrix Axiom arrays. Collating markers across all discovery methods resulted in a global list of 34,718 SNPs. However, concordance between the methods was surprisingly poor, with only 51.0 % of SNPs being discovered by more than one method and 13.5 % being called from both the 454 and Illumina datasets. Using a predictive modeling approach, we could also show that SNPs called from the Illumina data were on average more likely to successfully validate, as were SNPs called by more than one method. Above and beyond this pattern, predicted validation outcomes were also consistently better for Affymetrix Axiom arrays. Our results suggest that focusing on SNPs called by more than one method could potentially improve validation outcomes. They also highlight possible differences between alternative genotyping technologies that could be

  3. Slow Lives in the Fast Landscape: Conservation and Management of Plethodontid Salamanders in Production Forests of the United States

    Directory of Open Access Journals (Sweden)

    Jessica A. Homyack

    2014-11-01

    Full Text Available Intensively-managed forest (IMF ecosystems support environmental processes, retain biodiversity and reduce pressure to extract wood products from other forests, but may affect species, such as plethodontid salamanders, that are associated with closed canopies and possess limited vagility. We describe: (1 critical aspects of IMF ecosystems; (2 effectiveness of plethodontid salamanders as barometers of forest change; (3 two case studies of relationships between salamanders and coarse woody debris (CWD; and (4 research needs for effective management of salamanders in IMF ecosystems. Although plethodontid salamanders are sensitive to microclimate changes, their role as ecological indicators rarely have been evaluated quantitatively. Our case studies of CWD and salamanders in western and eastern forests demonstrated effects of species, region and spatial scale on the existence and strength of relationships between plethodontid species and a “critical” microhabitat variable. Oregon slender salamanders (Batrachoseps wrighti were more strongly associated with abundance of CWD in managed second growth forests than ensatina salamanders (Ensatina eschscholtzii. Similarly, CWD was not an important predictor of abundance of Appalachian salamanders in managed hardwood forest. Gaining knowledge of salamanders in IMF ecosystems is critical to reconciling ecological and economic objectives of intensive forest management, but faces challenges in design and implementation.

  4. Impact of QTL minor allele frequency on genomic evaluation using real genotype data and simulated phenotypes in Japanese Black cattle.

    Science.gov (United States)

    Uemoto, Yoshinobu; Sasaki, Shinji; Kojima, Takatoshi; Sugimoto, Yoshikazu; Watanabe, Toshio

    2015-11-19

    Genetic variance that is not captured by single nucleotide polymorphisms (SNPs) is due to imperfect linkage disequilibrium (LD) between SNPs and quantitative trait loci (QTLs), and the extent of LD between SNPs and QTLs depends on different minor allele frequencies (MAF) between them. To evaluate the impact of MAF of QTLs on genomic evaluation, we performed a simulation study using real cattle genotype data. In total, 1368 Japanese Black cattle and 592,034 SNPs (Illumina BovineHD BeadChip) were used. We simulated phenotypes using real genotypes under different scenarios, varying the MAF categories, QTL heritability, number of QTLs, and distribution of QTL effect. After generating true breeding values and phenotypes, QTL heritability was estimated and the prediction accuracy of genomic estimated breeding value (GEBV) was assessed under different SNP densities, prediction models, and population size by a reference-test validation design. The extent of LD between SNPs and QTLs in this population was higher in the QTLs with high MAF than in those with low MAF. The effect of MAF of QTLs depended on the genetic architecture, evaluation strategy, and population size in genomic evaluation. In genetic architecture, genomic evaluation was affected by the MAF of QTLs combined with the QTL heritability and the distribution of QTL effect. The number of QTL was not affected on genomic evaluation if the number of QTL was more than 50. In the evaluation strategy, we showed that different SNP densities and prediction models affect the heritability estimation and genomic prediction and that this depends on the MAF of QTLs. In addition, accurate QTL heritability and GEBV were obtained using denser SNP information and the prediction model accounted for the SNPs with low and high MAFs. In population size, a large sample size is needed to increase the accuracy of GEBV. The MAF of QTL had an impact on heritability estimation and prediction accuracy. Most genetic variance can be captured

  5. The Importance of Maintaining Upland Forest Habitat Surrounding Salamander Breeding Ponds: Case Study of the Eastern Tiger Salamander in New York, USA

    Directory of Open Access Journals (Sweden)

    Valorie Titus

    2014-12-01

    Full Text Available Most amphibians use both wetland and upland habitats, but the extent of their movement in forested habitats is poorly known. We used radiotelemetry to observe the movements of adult and juvenile eastern tiger salamanders over a 4-year period. Females tended to move farther from the breeding ponds into upland forested habitat than males, while the distance a juvenile moved appeared to be related to body size, with the largest individuals moving as far as the adult females. Individuals chose refugia in native pitch pine—oak forested habitat and avoided open fields, roads, and developed areas. We also observed a difference in potential predation pressures in relation to the distance an individual moved from the edge of the pond. Our results support delineating forested wetland buffer zones on a case-by-case basis to reduce the impacts of concentrated predation, to increase and protect the availability of pitch pine—oak forests near the breeding pond, and to focus primarily on the habitat needs of the adult females and larger juveniles, which in turn will encompass habitat needs of adult males and smaller juveniles.

  6. Metabolite Profiling of Barley Grains Subjected to Water Stress: To Explain the Genotypic Difference in Drought-Induced Impacts on Malting Quality

    Directory of Open Access Journals (Sweden)

    Xiaojian Wu

    2017-09-01

    Full Text Available Grain weight and protein content will be reduced and increased, respectively, when barley is subjected to water stress after anthesis, consequently deteriorating the malt quality. However, such adverse impact of water stress differs greatly among barley genotypes. In this study, two Tibetan wild barley accessions and two cultivated varieties differing in water stress tolerance were used to investigate the genotypic difference in metabolic profiles during grain-filling stage under drought condition. Totally, 71 differently accumulated metabolites were identified, including organic acids, amino acids/amines, and sugars/sugar alcohols. Their relative contents were significantly affected by water stress for all genotypes and differed distinctly between the wild and cultivated barleys. The principal component analysis of metabolites indicated that the Tibetan wild barley XZ147 possessed a unique response to water stress. When subjected to water stress, the wild barley XZ147 showed the most increase of β-amylase activity among the four genotypes, as a result of its higher lysine content, less indole-3-acetic acid (IAA biosynthesis, more stable H2O2 homeostasis, and more up-regulation of BMY1 gene. On the other hand, XZ147 had the most reduction of β-glucan content under water stress than the other genotypes, which could be explained by the faster grain filling process and the less expression of β-glucan synthase gene GSL7. All these results indicated a great potential for XZ147 in barley breeding for improving water stress tolerance.

  7. Finding the right coverage : The impact of coverage and sequence quality on single nucleotide polymorphism genotyping error rates

    NARCIS (Netherlands)

    Fountain, Emily D.; Pauli, Jonathan N.; Reid, Brendan N.; Palsboll, Per J.; Peery, M. Zachariah

    Restriction-enzyme-based sequencing methods enable the genotyping of thousands of single nucleotide polymorphism (SNP) loci in nonmodel organisms. However, in contrast to traditional genetic markers, genotyping error rates in SNPs derived from restriction-enzyme-based methods remain largely unknown.

  8. Impact of Chronic Hepatitis C Virus Genotype 1b Infection on Triglyceride Concentration in Serum Lipoprotein Fractions

    Directory of Open Access Journals (Sweden)

    Tomohisa Nagano

    2015-08-01

    Full Text Available Reduced low-density lipoprotein (LDL cholesterol level is a characteristic feature of dyslipidemia in chronic hepatitis C virus (HCV infection. However, abnormality in serum triglyceride (TG has not been fully investigated. To clarify the impact of HCV genotype 1b (G1b infection and advanced fibrosis on serum TG profiles, TG concentrations in lipoprotein fractions were examined in fasting sera from 185 subjects with active or cleared HCV infection by high-performance liquid chromatography. Serum lipoproteins were fractionated into four classes: chylomicron, very low-density lipoprotein (VLDL, LDL, and high-density lipoprotein (HDL. Then, the significance of HCV G1b infection on TG levels in each lipoprotein fraction was determined using multiple regression models. We found that active HCV G1b infection was positively associated with high HDL-TG levels and low VLDL-TG levels, independent of other factors included in the regression model. In VLDL sub-fractions, active HCV infection was only found to be associated with low levels of large VLDL-TG. Similarly, advanced liver fibrosis in chronic HCV G1b infection was associated with high levels of LDL-TG, HDL-TG, and small VLDL-TG, independent of other clinical factors. These findings indicate that active HCV G1b infection and advanced fibrosis are closely associated with abnormal serum TG profiles.

  9. Impact of HIV-1 subtype and antiretroviral therapy on protease and reverse transcriptase genotype: results of a global collaboration.

    Directory of Open Access Journals (Sweden)

    Rami Kantor

    2005-04-01

    Full Text Available The genetic differences among HIV-1 subtypes may be critical to clinical management and drug resistance surveillance as antiretroviral treatment is expanded to regions of the world where diverse non-subtype-B viruses predominate.To assess the impact of HIV-1 subtype and antiretroviral treatment on the distribution of mutations in protease and reverse transcriptase, a binomial response model using subtype and treatment as explanatory variables was used to analyze a large compiled dataset of non-subtype-B HIV-1 sequences. Non-subtype-B sequences from 3,686 persons with well characterized antiretroviral treatment histories were analyzed in comparison to subtype B sequences from 4,769 persons. The non-subtype-B sequences included 461 with subtype A, 1,185 with C, 331 with D, 245 with F, 293 with G, 513 with CRF01_AE, and 618 with CRF02_AG. Each of the 55 known subtype B drug-resistance mutations occurred in at least one non-B isolate, and 44 (80% of these mutations were significantly associated with antiretroviral treatment in at least one non-B subtype. Conversely, of 67 mutations found to be associated with antiretroviral therapy in at least one non-B subtype, 61 were also associated with antiretroviral therapy in subtype B isolates.Global surveillance and genotypic assessment of drug resistance should focus primarily on the known subtype B drug-resistance mutations.

  10. SPATIALLY AUTOCORRELATED DEMOGRAPHY AND INTERPOND MIGRATION IN THE CALIFORNIA TIGER SALAMANDER (AMBYSTOME CALIFORNIENSE)

    Science.gov (United States)

    We investigated the metapopulation structure of the California tiger salamander (Ambystoma californiense) using a combination of indirect and direct methods to evaluate two key requirements of modern metapopulation models: 1) that patches support somewhat independent populations ...

  11. Stoichiometry of excreta and excretion rates of a stream-dwelling plethodontid salamander

    Data.gov (United States)

    U.S. Environmental Protection Agency — Stoichiometry of excreta and excretion rates of a stream-dwelling plethodontid salamander in Cincinnati, OH, USA. This dataset is associated with the following...

  12. An annotated review of the Salamander types described in the Fauna Japonica

    NARCIS (Netherlands)

    Hoogmoed, M.S.

    1978-01-01

    The whereabouts of the salamander types described by Temminck & Schlegel in the Fauna Japonica (1838) are discussed and lectotypes are selected from the syntypes for the following nominal species : Salamandra naevia Temminck & Schlegel, S. unguiculata Temminck & Schlegel, S. subcristata Temminck &

  13. Egg predators of an endemic Italian salamander, Salamandrina perspicillata (Savi, 1821

    Directory of Open Access Journals (Sweden)

    Antonio Romano

    2008-05-01

    Full Text Available We report new aquatic predators feeding on Northern spectacled salamander eggs, Salamandrina perspicillata, an endemic Italian species. Eggs were preyed upon by the leech, Trocheta bykowskii, and the trichopteran larvae of Potamophylax cingulatus and Halesus appenninus.

  14. Larval salamanders and channel geomorphology are indicators of hydrologic permanence in forested headwater streams

    Science.gov (United States)

    Regulatory agencies need rapid indicators of hydrologic permanence for jurisdictional determinations of headwater streams. Our study objective was to assess the utility of larval salamander presence and assemblage structure and habitat variables for determining stream permanence ...

  15. Protective Immunity Induced by DNA Vaccination against Ranavirus Infection in Chinese Giant Salamander Andrias davidianus

    Directory of Open Access Journals (Sweden)

    Zhong-Yuan Chen

    2018-01-01

    Full Text Available Andrias davidianus ranavirus (ADRV is an emerging viral pathogen that causes severe systemic hemorrhagic disease in Chinese giant salamanders. There is an urgent need for developing an effective vaccine against this fatal disease. In this study, DNA vaccines containing the ADRV 2L gene (pcDNA-2L and the 58L gene (pcDNA-58L were respectively constructed, and their immune protective effects were evaluated in Chinese giant salamanders. In vitro and in vivo expression of the vaccine plasmids were confirmed in transfected cells and muscle tissues of vaccinated Chinese giant salamanders by using immunoblot analysis or RT-PCR. Following ADRV challenge, the Chinese giant salamanders vaccinated with pcDNA-2L showed a relative percent survival (RPS of 66.7%, which was significant higher than that in Chinese giant salamanders immunized with pcDNA-58L (RPS of 3.3%. Moreover, the specific antibody against ADRV was detected in Chinese giant salamanders vaccinated with pcDNA-2L at 14 and 21 days post-vaccination by indirect enzyme-linked immunosorbent assay (ELISA. Transcriptional analysis revealed that the expression levels of immune-related genes including type I interferon (IFN, myxovirus resistance (Mx, major histocompatibility complex class IA (MHC IA, and immunoglobulin M (IgM were strongly up-regulated after vaccination with pcDNA-2L. Furthermore, vaccination with pcDNA-2L significantly suppressed the virus replication, which was seen by a low viral load in the spleen of Chinese giant salamander survivals after ADRV challenge. These results indicated that pcDNA-2L could induce a significant innate immune response and an adaptive immune response involving both humoral and cell-mediated immunity that conferred effective protection against ADRV infection, and might be a potential vaccine candidate for controlling ADRV disease in Chinese giant salamanders.

  16. Diagnostic and molecular evaluation of three iridovirus-associated salamander mortality events

    Science.gov (United States)

    Docherty, D.E.; Meteyer, C.U.; Wang, Jingyuan; Mao, J.; Case, S.T.; Chinchar, V.G.

    2003-01-01

    In 1998 viruses were isolated from tiger salamander larvae (Ambystoma tigrinum diaboli and A. tigrinum melanostictum) involved in North Dakota and Utah (USA) mortality events and spotted salamander (A. maculatum) larvae in a third event in Maine (USA). Although sympatric caudates and anurans were present at all three sites only ambystomid larvae appeared to be affected. Mortality at the North Dakota site was in the thousands while at the Utah and Maine sites mortality was in the hundreds. Sick larvae were lethargic and slow moving. They swam in circles with obvious buoyancy problems and were unable to remain upright. On the ventral surface, near the gills and hind limbs, red spots or swollen areas were noted. Necropsy findings included: hemorrhages and ulceration of the skin, subcutaneous and intramuscular edema, swollen and pale livers with multifocal hemorrhage, and distended fluid-filled intestines with areas of hemorrhage. Light microscopy revealed intracytoplasmic inclusions, suggestive of a viral infection, in a variety of organs. Electron microscopy of ultra thin sections of the same tissues revealed iridovirus-like particles within the inclusions. These viruses were isolated from a variety of organs, indicating a systemic infection. Representative viral isolates from the three mortality events were characterized using molecular assays. Characterization confirmed that the viral isolates were iridoviruses and that the two tiger salamander isolates were similar and could be distinguished from the spotted salamander isolate. The spotted salamander isolate was similar to frog virus 3, the type species of the genus Ranavirus, while the tiger salamander isolates were not. These data indicate that different species of salamanders can become infected and die in association with different iridoviruses. Challenge assays are required to determine the fish and amphibian host range of these isolates and to assess the susceptibility of tiger and spotted salamanders to

  17. Ambient ultraviolet radiation causes mortality in salamander eggs

    International Nuclear Information System (INIS)

    Blaustein, A.R.; Edmond, B.; Kiesecker, J.M.

    1995-01-01

    Previous research has shown that amphibian species have differential sensitivity to ultraviolet-B (UV-B) radiation. In some anuran species, ambient levels of UV-B cause mortality in embryonic stages and hatching success is significantly reduced. Projected increases in UV-B may affect an increasing number of species. The adverse effects of UV-B may eventually be manifested at the population level and may ultimately contribute to population declines. Using field experiments, we investigated the effects of ambient UV-B on salamander (Ambystoma gracile) embryos developing at natural oviposition sites. We show that the hatching success of eggs of A. gracile shielded from UV-B is significantly higher than those not shielded from UV-B. 27 refs., 1 fig

  18. Deep divergences and extensive phylogeographic structure in a clade of lowland tropical salamanders

    Directory of Open Access Journals (Sweden)

    Rovito Sean M

    2012-12-01

    Full Text Available Abstract Background The complex geological history of Mesoamerica provides the opportunity to study the impact of multiple biogeographic barriers on population differentiation. We examine phylogeographic patterns in a clade of lowland salamanders (Bolitoglossa subgenus Nanotriton using two mitochondrial genes and one nuclear gene. We use several phylogeographic analyses to infer the history of this clade and test hypotheses regarding the geographic origin of species and location of genetic breaks within species. We compare our results to those for other taxa to determine if historical events impacted different species in a similar manner. Results Deep genetic divergence between species indicates that they are relatively old, and two of the three widespread species show strong phylogeographic structure. Comparison of mtDNA and nuclear gene trees shows no evidence of hybridization or introgression between species. Isolated populations of Bolitoglossa rufescens from Los Tuxtlas region constitute a separate lineage based on molecular data and morphology, and divergence between Los Tuxtlas and other areas appears to predate the arrival of B. rufescens in other areas west of the Isthmus of Tehuantepec. The Isthmus appears responsible for Pliocene vicariance within B. rufescens, as has been shown for other taxa. The Motagua-Polochic fault system does not appear to have caused population vicariance, unlike in other systems. Conclusions Species of Nanotriton have responded to some major geological events in the same manner as other taxa, particularly in the case of the Isthmus of Tehuantepec. The deep divergence of the Los Tuxtlas populations of B. rufescens from other populations highlights the contribution of this volcanic system to patterns of regional endemism, and morphological differences observed in the Los Tuxtlas populations suggests that they may represent an undescribed species of Bolitoglossa. The absence of phylogeographic structure in B

  19. Predicted Changes in Climatic Niche and Climate Refugia of Conservation Priority Salamander Species in the Northeastern United States

    Directory of Open Access Journals (Sweden)

    William B. Sutton

    2014-12-01

    Full Text Available Global climate change represents one of the most extensive and pervasive threats to wildlife populations. Amphibians, specifically salamanders, are particularly susceptible to the effects of changing climates due to their restrictive physiological requirements and low vagility; however, little is known about which landscapes and species are vulnerable to climate change. Our study objectives included, (1 evaluating species-specific predictions (based on 2050 climate projections and vulnerabilities to climate change and (2 using collective species responses to identify areas of climate refugia for conservation priority salamanders in the northeastern United States. All evaluated salamander species were projected to lose a portion of their climatic niche. Averaged projected losses ranged from 3%–100% for individual species, with the Cow Knob Salamander (Plethodon punctatus, Cheat Mountain Salamander (Plethodon nettingi, Shenandoah Mountain Salamander (Plethodon virginia, Mabee’s Salamander (Ambystoma mabeei, and Streamside Salamander (Ambystoma barbouri predicted to lose at least 97% of their landscape-scale climatic niche. The Western Allegheny Plateau was predicted to lose the greatest salamander climate refugia richness (i.e., number of species with a climatically-suitable niche in a landscape patch, whereas the Central Appalachians provided refugia for the greatest number of species during current and projected climate scenarios. Our results can be used to identify species and landscapes that are likely to be further affected by climate change and potentially resilient habitats that will provide consistent climatic conditions in the face of environmental change.

  20. Effects of host species and environment on the skin microbiome of Plethodontid salamanders

    Science.gov (United States)

    Muletz-Wolz, Carly R.; Yarwood, Stephanie A.; Grant, Evan H. Campbell; Fleischer, Robert C.; Lips, Karen R.

    2018-01-01

    The amphibian skin microbiome is recognized for its role in defence against pathogens, including the deadly fungal pathogen Batrachochytrium dendrobatidis (Bd). Yet, we have little understanding of evolutionary and ecological processes that structure these communities, especially for salamanders and closely related species. We investigated patterns in the distribution of bacterial communities on Plethodon salamander skin across host species and environments.Quantifying salamander skin microbiome structure contributes to our understanding of how host-associated bacteria are distributed across the landscape, among host species, and their putative relationship with disease.We characterized skin microbiome structure (alpha-diversity, beta-diversity and bacterial operational taxonomic unit [OTU] abundances) using 16S rRNA gene sequencing for co-occurring Plethodon salamander species (35 Plethodon cinereus, 17 Plethodon glutinosus, 10 Plethodon cylindraceus) at three localities to differentiate the effects of host species from environmental factors on the microbiome. We sampled the microbiome of P. cinereus along an elevational gradient (n = 50, 700–1,000 m a.s.l.) at one locality to determine whether elevation predicts microbiome structure. Finally, we quantified prevalence and abundance of putatively anti-Bd bacteria to determine if Bd-inhibitory bacteria are dominant microbiome members.Co-occurring salamanders had similar microbiome structure, but among sites salamanders had dissimilar microbiome structure for beta-diversity and abundance of 28 bacterial OTUs. We found that alpha-diversity increased with elevation, beta-diversity and the abundance of 17 bacterial OTUs changed with elevation (16 OTUs decreasing, 1 OTU increasing). We detected 11 putatively anti-Bd bacterial OTUs that were present on 90% of salamanders and made up an average relative abundance of 83% (SD ± 8.5) per salamander. All salamanders tested negative for Bd.We conclude that

  1. The impact of some physiomorphic characters of sugarcane genotypes on their resistance against sugarcane pyrilla, pyrilla perpusilla wlk. (lophopidae: homoptera)

    International Nuclear Information System (INIS)

    Rasul, A.; Hassan, M.; Suhail, A.; Sahi, S.T.

    2010-01-01

    Field trials were conducted in the Research Area, Directorate of Sugarcane, Ayub Agricultural Research Institute, Faisalabad to study he physio-morphic characters of sugarcane resistance to the sucking pest Pyrilla perpusilla. Twenty genotypes of sugarcane were tested for their resistance susceptibility against P. perpusilla, as a preliminary screening experiment, during 2006. Based on the population-density count, 3 genotypes, viz., HSF- 240, CPF-243 and S-2002-US-114 showing resistance responses, 3 genotypes viz. CPHS-35, S-2003-US-394 and S-2003-US-623 showing susceptible trends and 3 genotypes viz. S-2003-US-809, S-2002-US-140 and S- 2002-US-104 exerting intermediate trends against the pest under test were selected for the final screening trials during 2007.The genotype S-2003-US-623, was found to be comparatively susceptible; whereas, HSF-240, showed resistance responses. The leaf-width and cane length showed a positive and significant correlation whereas the leaf-spine density had a significant negative effect with pest-population. The Leaf-length and Cane-Diameter did not show a significant correlation with the pest population. (author)

  2. Current and historical drivers of landscape genetic structure differ in core and peripheral salamander populations.

    Directory of Open Access Journals (Sweden)

    Rachael Y Dudaniec

    Full Text Available With predicted decreases in genetic diversity and greater genetic differentiation at range peripheries relative to their cores, it can be difficult to distinguish between the roles of current disturbance versus historic processes in shaping contemporary genetic patterns. To address this problem, we test for differences in historic demography and landscape genetic structure of coastal giant salamanders (Dicamptodon tenebrosus in two core regions (Washington State, United States versus the species' northern peripheral region (British Columbia, Canada where the species is listed as threatened. Coalescent-based demographic simulations were consistent with a pattern of post-glacial range expansion, with both ancestral and current estimates of effective population size being much larger within the core region relative to the periphery. However, contrary to predictions of recent human-induced population decline in the less genetically diverse peripheral region, there was no genetic signature of population size change. Effects of current demographic processes on genetic structure were evident using a resistance-based landscape genetics approach. Among core populations, genetic structure was best explained by length of the growing season and isolation by resistance (i.e. a 'flat' landscape, but at the periphery, topography (slope and elevation had the greatest influence on genetic structure. Although reduced genetic variation at the range periphery of D. tenebrosus appears to be largely the result of biogeographical history rather than recent impacts, our analyses suggest that inherent landscape features act to alter dispersal pathways uniquely in different parts of the species' geographic range, with implications for habitat management.

  3. Genotypic and Functional Impact of HIV-1 Adaptation to Its Host Population during the North American Epidemic

    Science.gov (United States)

    Carlson, Jonathan M.; Chan, Benjamin; Chopera, Denis R.; Brumme, Chanson J.; Markle, Tristan J.; Martin, Eric; Shahid, Aniqa; Anmole, Gursev; Mwimanzi, Philip; Nassab, Pauline; Penney, Kali A.; Rahman, Manal A.; Milloy, M.-J.; Schechter, Martin T.; Markowitz, Martin; Carrington, Mary; Walker, Bruce D.; Wagner, Theresa; Buchbinder, Susan; Fuchs, Jonathan; Koblin, Beryl; Mayer, Kenneth H.; Harrigan, P. Richard; Brockman, Mark A.; Poon, Art F. Y.; Brumme, Zabrina L.

    2014-01-01

    HLA-restricted immune escape mutations that persist following HIV transmission could gradually spread through the viral population, thereby compromising host antiviral immunity as the epidemic progresses. To assess the extent and phenotypic impact of this phenomenon in an immunogenetically diverse population, we genotypically and functionally compared linked HLA and HIV (Gag/Nef) sequences from 358 historic (1979–1989) and 382 modern (2000–2011) specimens from four key cities in the North American epidemic (New York, Boston, San Francisco, Vancouver). Inferred HIV phylogenies were star-like, with approximately two-fold greater mean pairwise distances in modern versus historic sequences. The reconstructed epidemic ancestral (founder) HIV sequence was essentially identical to the North American subtype B consensus. Consistent with gradual diversification of a “consensus-like” founder virus, the median “background” frequencies of individual HLA-associated polymorphisms in HIV (in individuals lacking the restricting HLA[s]) were ∼2-fold higher in modern versus historic HIV sequences, though these remained notably low overall (e.g. in Gag, medians were 3.7% in the 2000s versus 2.0% in the 1980s). HIV polymorphisms exhibiting the greatest relative spread were those restricted by protective HLAs. Despite these increases, when HIV sequences were analyzed as a whole, their total average burden of polymorphisms that were “pre-adapted” to the average host HLA profile was only ∼2% greater in modern versus historic eras. Furthermore, HLA-associated polymorphisms identified in historic HIV sequences were consistent with those detectable today, with none identified that could explain the few HIV codons where the inferred epidemic ancestor differed from the modern consensus. Results are therefore consistent with slow HIV adaptation to HLA, but at a rate unlikely to yield imminent negative implications for cellular immunity, at least in North America

  4. Morphological variation in two genetically distinct groups of the golden-striped salamander, Chioglossa lusitanica (Amphibia: Urodela)

    NARCIS (Netherlands)

    Alexandrino, J.; Ferrand, N.; Arntzen, J.W.

    2005-01-01

    Morphometric and colour pattern variation in the endemic Iberian salamander Chioglossa lusitanica is concordant with the genetic differentiation of two groups of populations separated by the Mondego river in Portugal. Salamanders from the south have shorter digits than those from the north. Clinal

  5. 76 FR 55413 - Proposed Safe Harbor Agreement for California Red-legged Frog, California Tiger Salamander, Smith...

    Science.gov (United States)

    2011-09-07

    ...] Proposed Safe Harbor Agreement for California Red-legged Frog, California Tiger Salamander, Smith's Blue... endangered Smith's blue butterfly (Euphilotes enoptes smithi) under the Endangered Species Act of 1973, as..., California tiger salamander, Smith's blue butterfly, and Yadon's piperia on the property subject to the...

  6. Abundance of western red-backed salamanders (Plethodon vehiculum) in the Washington Coast Range after headwater stream-buffer manipulation

    Science.gov (United States)

    Randall J. Wilk; Jeffrey D. Ricklefs; Martin G. Raphael

    2014-01-01

    We evaluated the effect of forest riparian alternative tree buffer designs on Western Red-backed Salamanders (Plethodon vehiculum) along headwater stream banks in managed forests of the Washington Coast Range. We used pit trap live removals in early autumn to estimate relative abundances of surface-active salamanders before and after 3 levels of riparian buffer...

  7. Digits lost or gained? Evidence for pedal evolution in the dwarf salamander complex (Eurycea, Plethodontidae.

    Directory of Open Access Journals (Sweden)

    Trip Lamb

    Full Text Available Change in digit number, particularly digit loss, has occurred repeatedly over the evolutionary history of tetrapods. Although digit loss has been documented among distantly related species of salamanders, it is relatively uncommon in this amphibian order. For example, reduction from five to four toes appears to have evolved just three times in the morphologically and ecologically diverse family Plethodontidae. Here we report a molecular phylogenetic analysis for one of these four-toed lineages--the Eurycea quadridigitata complex (dwarf salamanders--emphasizing relationships to other species in the genus. A multilocus phylogeny reveals that dwarf salamanders are paraphyletic with respect to a complex of five-toed, paedomorphic Eurycea from the Edwards Plateau in Texas. We use this phylogeny to examine evolution of digit number within the dwarf-Edwards Plateau clade, testing contrasting hypotheses of digit loss (parallelism among dwarf salamanders versus digit gain (re-evolution in the Edwards Plateau complex. Bayes factors analysis provides statistical support for a five-toed common ancestor at the dwarf-Edwards node, favoring, slightly, the parallelism hypothesis for digit loss. More importantly, our phylogenetic results pinpoint a rare event in the pedal evolution of plethodontid salamanders.

  8. Stream water temperature limits occupancy of salamanders in mid-Atlantic protected areas

    Science.gov (United States)

    Grant, Evan H. Campbell; Wiewel, Amber N. M.; Rice, Karen C.

    2014-01-01

    Stream ecosystems are particularly sensitive to urbanization, and tolerance of water-quality parameters is likely important to population persistence of stream salamanders. Forecasted climate and landscape changes may lead to significant changes in stream flow, chemical composition, and temperatures in coming decades. Protected areas where landscape alterations are minimized will therefore become increasingly important for salamander populations. We surveyed 29 streams at three national parks in the highly urbanized greater metropolitan area of Washington, DC. We investigated relationships among water-quality variables and occupancy of three species of stream salamanders (Desmognathus fuscus, Eurycea bislineata, and Pseudotriton ruber). With the use of a set of site-occupancy models, and accounting for imperfect detection, we found that stream-water temperature limits salamander occupancy. There was substantial uncertainty about the effects of the other water-quality variables, although both specific conductance (SC) and pH were included in competitive models. Our estimates of occupancy suggest that temperature, SC, and pH have some importance in structuring stream salamander distribution.

  9. Anatomy, function, and evolution of jaw and hyobranchial muscles in cryptobranchoid salamander larvae.

    Science.gov (United States)

    Kleinteich, Thomas; Herzen, Julia; Beckmann, Felix; Matsui, Masafumi; Haas, Alexander

    2014-02-01

    Larval salamanders (Lissamphibia: Caudata) are known to be effective suction feeders in their aquatic environments, although they will eventually transform into terrestrial tongue feeding adults during metamorphosis. Early tetrapods may have had a similar biphasic life cycle and this makes larval salamanders a particularly interesting model to study the anatomy, function, development, and evolution of the feeding apparatus in terrestrial vertebrates. Here, we provide a description of the muscles that are involved in the feeding strike in salamander larvae of the Hynobiidae and compare them to larvae of the paedomorphic Cryptobranchidae. We provide a functional and evolutionary interpretation for the observed muscle characters. The cranial muscles in larvae from species of the Hynobiidae and Cryptobranchidae are generally very similar. Most notable are the differences in the presence of the m. hyomandibularis, a muscle that connects the hyobranchial apparatus with the lower jaw. We found this muscle only in Onychodactylus japonicus (Hynobiidae) but not in other hynobiid or cryptobranchid salamanders. Interestingly, the m. hyomandibularis in O. japonicus originates from the ceratobranchial I and not the ceratohyal, and thus exhibits what was previously assumed to be the derived condition. Finally, we applied a biomechanical model to simulate suction feeding in larval salamanders. We provide evidence that a flattened shape of the hyobranchial apparatus in its resting position is beneficial for a fast and successful suction feeding strike. Copyright © 2013 Wiley Periodicals, Inc.

  10. Apparent survival of the salamander Salamandra salamandra is low because of high migratory activity

    Directory of Open Access Journals (Sweden)

    Schaub Michael

    2007-09-01

    Full Text Available Abstract Background Understanding the demographic processes underlying population dynamics is a central theme in ecology. Populations decline if losses from the population (i.e., mortality and emigration exceed gains (i.e., recruitment and immigration. Amphibians are thought to exhibit little movement even though local populations often fluctuate dramatically and are likely to go exinct if there is no rescue effect through immigration from nearby populations. Terrestrial salamanders are generally portrayed as amphibians with low migratory activity. Our study uses demographic analysis as a key to unravel whether emigration or mortality is the main cause of "losses" from the population. In particular, we use the analysis to challenge the common belief that terrestrial salamanders show low migratory activity. Results The mark-recapture analysis of adult salamanders showed that monthly survival was high (> 90% without a seasonal pattern. These estimates, however, translate into rather low rates of local annual survival of only ~40% and suggest that emigration was important. The estimated probability of emigration was 49%. Conclusion Our analysis shows that terrestrial salamanders exhibit more migratory activity than commonly thought. This may be due either because the spatial extent of salamander populations is underestimated or because there is a substantial exchange of individuals between populations. Our current results are in line with several other studies that suggest high migratory activity in amphibians. In particular, many amphibian populations may be characterized by high proportions of transients and/or floaters.

  11. Impact of null genotypes of GSTT1 and GSTM1 with uterine leiomyoma risk in Iranian population.

    Science.gov (United States)

    Mostafavi, Salva Sadat; Ebrahimi, Ahmad; Sadat, Seyed Mehdi; Davari Tanha, Fatemeh; Aghasadeghi, Mohammad Reza; Bahramali, Golnaz; Abbasi Ranjbar, Parinaz; Sadeghifard, Vida; Javadi, Foozieh

    2016-04-01

    Few studies have investigated the role of the GSTM1 and GSTT1 genes in uterine leiomyoma. Therefore, in the current study the distribution of these genotypes in Iranian women and susceptibility to uterine leiomyoma was investigated. Blood samples of 50 patients with uterine leiomyoma and 50 healthy individual controls were collected in this cross-sectional study. Genomic DNA was extracted, and subsequently GSTM1 and GSTT1 null genotypes were detected by the Gap-polymerase chain reaction method. A total of 42% of patients appeared to lack GSTM1 enzyme activity due to the presence of an extended deletion (GSTM1 0/0 genotype), compared with 18% in a control group (odds ratio [OR], 3.56; 95% confidence interval [CI], 1.35-9.37; P leiomyoma and null GSTM1 and GSTT1 genotypes among Iranian patients. Our data support the involvement of GSTM1 and GSTT1 in uterine leiomyoma liability, and especially its role as a genetic factor in the occurrence of this disease. © 2016 Japan Society of Obstetrics and Gynecology.

  12. Serotonin transporter linked polymorphic region (5-HTTLPR) genotype moderates the longitudinal impact of early caregiving on externalizing behavior.

    Science.gov (United States)

    Brett, Zoë H; Humphreys, Kathryn L; Smyke, Anna T; Gleason, Mary Margaret; Nelson, Charles A; Zeanah, Charles H; Fox, Nathan A; Drury, Stacy S

    2015-02-01

    We examined caregiver report of externalizing behavior from 12 to 54 months of age in 102 children randomized to care as usual in institutions or to newly created high-quality foster care. At baseline no differences by group or genotype in externalizing were found. However, changes in externalizing from baseline to 42 months of age were moderated by the serotonin transporter linked polymorphic region genotype and intervention group, where the slope for short-short (S/S) individuals differed as a function of intervention group. The slope for individuals carrying the long allele did not significantly differ between groups. At 54 months of age, S/S children in the foster care group had the lowest levels of externalizing behavior, while children with the S/S genotype in the care as usual group demonstrated the highest rates of externalizing behavior. No intervention group differences were found in externalizing behavior among children who carried the long allele. These findings, within a randomized controlled trial of foster care compared to continued care as usual, indicate that the serotonin transporter linked polymorphic region genotype moderates the relation between early caregiving environments to predict externalizing behavior in children exposed to early institutional care in a manner most consistent with differential susceptibility.

  13. Batrachochytrium salamandrivorans is the predominant chytrid fungus in Vietnamese salamanders

    Science.gov (United States)

    Laking, Alexandra E.; Ngo, Hai Ngoc; Pasmans, Frank; Martel, An; Nguyen, Tao Thien

    2017-01-01

    The amphibian chytrid fungi, Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal), pose a major threat to amphibian biodiversity. Recent evidence suggests Southeast Asia as a potential cradle for both fungi, which likely resulted in widespread host-pathogen co-existence. We sampled 583 salamanders from 8 species across Vietnam in 55 locations for Bsal and Bd, determined scaled mass index as a proxy for fitness and collected environmental data. Bsal was found within 14 of the 55 habitats (2 of which it was detected in 2013), in 5 salamandrid species, with a prevalence of 2.92%. The globalized pandemic lineage of Bd was found within one pond on one species with a prevalence of 0.69%. Combined with a complete lack of correlation between infection and individual body condition and absence of indication of associated disease, this suggests low level pathogen endemism and Bsal and Bd co-existence with Vietnamese salamandrid populations. Bsal was more widespread than Bd, and occurs at temperatures higher than tolerated by the type strain, suggesting a wider thermal niche than currently known. Therefore, this study provides support for the hypothesis that these chytrid fungi may be endemic to Asia and that species within this region may act as a disease reservoir. PMID:28287614

  14. Status of some populations of Mexican salamanders (Amphibia: Plethodontidae

    Directory of Open Access Journals (Sweden)

    Gabriela Parra-Olea

    1999-06-01

    Full Text Available Populations of Mexican plethodontid salamanders have been surveyed non-systematically over the last 25 years. In light of many reports of disappearance of amphibians around the world, we checked for persistence of reported species at ten of these sites. All of the commoner species persist (we observed individuals representing a total of 30 species. While observed densities of many species of Mexican plethodontids are lower to much lower than was the case 20 to 25 years ago, evidence for recent extinctions, such as has been reported for amphibian taxa elsewhere, is equivocal or lacking. Habitat modification has contributed to difficulties in finding certain species.Poblaciones de varias especies de salamandras pletodóntidas en México han sido monitoreadas de manera no sistemática durante los últimos 25 años. Diez de éstas poblaciones fueran visitadas recientemente con el propósito de verificar la persistencia de las especies reportadas para dichas localidades. Nuestras observaciones confirman la persistencia local de más de 30 especies cuyo estatus era desconocido, aunque la frecuencia de observación de estas especies es en general menor que en fechas anteriores. Estas observaciones son particularmente relevantes dada la situación actual de preocupación por la disminución mundial de anfibios.

  15. Heterogeneous vesicles in mucous epithelial cells of posterior esophagus of Chinese giant salamander (Andrias davidianus

    Directory of Open Access Journals (Sweden)

    H. Zhang

    2015-08-01

    Full Text Available The Chinese giant salamander belongs to an old lineage of salamanders and endangered species. Many studies of breeding and disease regarding this amphibian had been implemented. However, the studies on the ultrastructure of this amphibian are rare. In this work, we provide a histological and ultrastructural investigation on posterior esophagus of Chinese giant salamander. The sections of amphibian esophagus were stained by hematoxylin & eosin (H&E. Moreover, the esophageal epithelium was observed by transmission electron microscopy (TEM. The results showed that esophageal epithelium was a single layer epithelium, which consisted of mucous cells and columnar cells. The esophageal glands were present in submucosa. The columnar cells were ciliated. According to the diverging ultrastructure of mucous vesicles, three types of mucous cells could be identified in the esophageal mucosa: i electron-lucent vesicles mucous cell (ELV-MC; ii electron-dense vesicles mucous cell (EDV-MC; and iii mixed vesicles mucous cell (MV-MC.

  16. Effects of acid precipitation on embryonic mortality of Ambystoma salamanders in the Connecticut Valley of Massachusetts

    Energy Technology Data Exchange (ETDEWEB)

    Cook, R P

    1983-01-01

    An investigation of increased embryonic mortality of the spotted salamander Ambystoma maculatum concomitant with breeding pond acidification from acid rainfall in the Connecticut Valley of Massachusetts analyzes the pH and chemistry of rain and pond water and monitored embryonic mortality in 1976 and 1977. Although acid rain continues to occur in the area and Ambystoma breeding ponds are acidic, the average pH of six ponds dropped from 5.62 to 5.10 during the study. Pond pH decreased up to 0.75 pH units following heavy rainfall. Despite this, embryonic mortality of spotted and Jefferson salamanders was low, and no significant correlation between pond pH and percent embryonic mortality was found. The size of present populations and the embryonic acid tolerance exhibited by the salamander indicate that acid rain has not had an effect in this location. 22 references, 2 figures, 4 tables.

  17. Mechanics of lung ventilation in a post-metamorphic salamander, Ambystoma Tigrinum.

    Science.gov (United States)

    Simons, R S; Bennett, W O; Brainerd, E L

    2000-03-01

    The mechanics of lung ventilation in frogs and aquatic salamanders has been well characterized, whereas lung ventilation in terrestrial-phase (post-metamorphic) salamanders has received little attention. We used electromyography (EMG), X-ray videography, standard videography and buccal and body cavity pressure measurements to characterize the ventilation mechanics of adult (post-metamorphic) tiger salamanders (Ambystoma tigrinum). Three results emerged: (i) under terrestrial conditions or when floating at the surface of the water, adult A. tigrinum breathed through their nares using a two-stroke buccal pump; (ii) in addition to this narial two-stroke pump, adult tiger salamanders also gulped air in through their mouths using a modified two-stroke buccal pump when in an aquatic environment; and (iii) exhalation in adult tiger salamanders is active during aquatic gulping breaths, whereas exhalation appears to be passive during terrestrial breathing at rest. Active exhalation in aquatic breaths is indicated by an increase in body cavity pressure during exhalation and associated EMG activity in the lateral hypaxial musculature, particularly the M. transversus abdominis. In terrestrial breathing, no EMG activity in the lateral hypaxial muscles is generally present, and body cavity pressure decreases during exhalation. In aquatic breaths, tidal volume is larger than in terrestrial breaths, and breathing frequency is much lower (approximately 1 breath 10 min(-)(1 )versus 4-6 breaths min(-)(1)). The use of hypaxial muscles to power active exhalation in the aquatic environment may result from the need for more complete exhalation and larger tidal volumes when breathing infrequently. This hypothesis is supported by previous findings that terrestrial frogs ventilate their lungs with small tidal volumes and exhale passively, whereas aquatic frogs and salamanders use large tidal volumes and and exhale actively.

  18. Desmanthus GENOTYPES

    Directory of Open Access Journals (Sweden)

    JOSÉ HENRIQUE DE ALBUQUERQUE RANGEL

    2015-01-01

    Full Text Available Desmanthus is a genus of forage legumes with potential to improve pastures and livestock produc-tion on clay soils of dry tropical and subtropical regions such as the existing in Brazil and Australia. Despite this patterns of natural or enforced after-ripening of Desmanthus seeds have not been well established. Four year old seed banks of nine Desmanthus genotypes at James Cook University were accessed for their patterns of seed softe-ning in response to a range of temperatures. Persistent seed banks were found to exist under all of the studied ge-notypes. The largest seeds banks were found in the genotypes CPI 78373 and CPI 78382 and the smallest in the genotypes CPI’s 37143, 67643, and 83563. An increase in the percentage of softened seeds was correlated with higher temperatures, in two patterns of response: in some accessions seeds were not significantly affected by tempe-ratures below 80º C; and in others, seeds become soft when temperature rose to as little as 60 ºC. At 80 °C the heat started to depress germination. High seed production of Desmanthus associated with dependence of seeds on eleva-ted temperatures to softening can be a very important strategy for plants to survive in dry tropical regions.

  19. Hindcasting Historical Breeding Conditions for an Endangered Salamander in Ephemeral Wetlands of the Southeastern USA: Implications of Climate Change.

    Directory of Open Access Journals (Sweden)

    Houston C Chandler

    Full Text Available The hydroperiod of ephemeral wetlands is often the most important characteristic determining amphibian breeding success, especially for species with long development times. In mesic and wet pine flatwoods of the southeastern United States, ephemeral wetlands were a common landscape feature. Reticulated flatwoods salamanders (Ambystoma bishopi, a federally endangered species, depend exclusively on ephemeral wetlands and require at least 11 weeks to successfully metamorphose into terrestrial adults. We empirically modeled hydroperiod of 17 A. bishopi breeding wetlands by combining downscaled historical climate-model data with a recent 9-year record (2006-2014 of observed water levels. Empirical models were subsequently used to reconstruct wetland hydrologic conditions from 1896-2014 using the downscaled historical climate datasets. Reconstructed hydroperiods for the 17 wetlands were highly variable through time but were frequently unfavorable for A. bishopi reproduction (e.g., only 61% of years, using a conservative estimate of development time [12 weeks], were conducive to larval development and metamorphosis. Using change-point analysis, we identified significant shifts in average hydroperiod over the last century in all 17 wetlands. Mean hydroperiods were shorter in recent years than at any other point since 1896, and thus less suitable for A. bishopi reproduction. We suggest that climate change will continue to impact the reproductive success of flatwoods salamanders and other ephemeral wetland breeders by reducing the number of years these wetlands have suitable hydroperiods. Consequently, we emphasize the importance of conservation and management for mitigating other forms of habitat degradation, especially maintenance of high quality breeding sites where reproduction can occur during appropriate environmental conditions.

  20. Survey of Pathogenic Chytrid Fungi (Batrachochytrium dendrobatidis and B. salamandrivorans) in Salamanders from Three Mountain Ranges in Europe and the Americas.

    Science.gov (United States)

    Parrott, Joshua Curtis; Shepack, Alexander; Burkart, David; LaBumbard, Brandon; Scimè, Patrick; Baruch, Ethan; Catenazzi, Alessandro

    2017-06-01

    Batrachochytrium salamandrivorans (Bsal) is a virulent fungal pathogen that infects salamanders. It is implicated in the recent collapse of several populations of fire salamanders in Europe. This pathogen seems much like that of its sister species, Batrachochytrium dendrobatidis (Bd), the agent responsible for anuran extinctions and extirpations worldwide, and is considered to be an emerging global threat to salamander communities. Bsal thrives at temperatures found in many mountainous regions rich in salamander species; because of this, we have screened specimens of salamanders representing 17 species inhabiting mountain ranges in three continents: The Smoky Mountains, the Swiss Alps, and the Peruvian Andes. We screened 509 salamanders, with 192 representing New World salamanders that were never tested for Bsal previously. Bsal was not detected, and Bd was mostly present at low prevalence except for one site in the Andes.

  1. The impact of short-term UV irradiation on grains of sensitive and tolerant cereal genotypes studied by EPR.

    Science.gov (United States)

    Kurdziel, Magdalena; Filek, Maria; Łabanowska, Maria

    2018-05-01

    UV irradiation has ionisation character and leads to the generation of reactive oxygen species (ROS). The destructive character of ROS was observed among others during interaction of cereal grains with ozone and was caused by changes in structures of biomolecules leading to the formation of stable organic radicals. That effect was more evident for stress sensitive genotypes. In this study we investigated the influence of UV irradiation on cereal grains originating from genotypes with different tolerance to oxidative stress. Grains and their parts (endosperm, embryo and seed coat) of barley, wheat and oat were subjected to short-term UV irradiation. It was found that UV caused the appearance of various kinds of reactive species (O 2 -• , H 2 O 2 ) and stable radicals (semiquinone, phenoxyl and carbon-centred). Simultaneously, lipid peroxidation occurred and the organic structure of Mn(II) and Fe(III) complexes become disturbed. UV irradiation causes damage of main biochemical structures of plant tissues, the effect is more significant in sensitive genotypes. In comparison with ozone treatment, UV irradiation leads to stronger destruction of biomolecules in grains and their parts. It is caused by the high energy of UV light, facilitating easier breakage of molecular bonds in biochemical compounds. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

  2. Decadal changes in phenology of peak abundance patterns of woodland pond salamanders in northern Wisconsin

    Science.gov (United States)

    Donner, Deahn M.; Ribic, Christine; Beck, Albert J.; Higgins, Dale; Eklund, Dan; Reinecke, Susan

    2015-01-01

    Woodland ponds are important landscape features that help sustain populations of amphibians that require this aquatic habitat for successful reproduction. Species abundance patterns often reflect site-specific differences in hydrology, physical characteristics, and surrounding vegetation. Large-scale processes such as changing land cover and environmental conditions are other potential drivers influencing amphibian populations in the Upper Midwest, but little information exists on the combined effects of these factors. We used Blue-spotted (Ambystoma laterale Hallowell) and Spotted Salamander (A. maculatum Shaw) monitoring data collected at the same woodland ponds thirteen years apart to determine if changing environmental conditions and vegetation cover in surrounding landscapes influenced salamander movement phenology and abundance. Four woodland ponds in northern Wisconsin were sampled for salamanders in April 1992-1994 and 2005-2007. While Blue-spotted Salamanders were more abundant than Spotted Salamanders in all ponds, there was no change in the numbers of either species over the years. However, peak numbers of Blue-spotted Salamanders occurred 11.7 days earlier (range: 9-14 days) in the 2000s compared to the 1990s; Spotted Salamanders occurred 9.5 days earlier (range: 3 - 13 days). Air and water temperatures (April 13- 24) increased, on average, 4.8°C and 3.7°C, respectively, between the decades regardless of pond. There were no discernible changes in canopy openness in surrounding forests between decades that would have warmed the water sooner (i.e., more light penetration). Our finding that salamander breeding phenology can vary by roughly 10 days in Wisconsin contributes to growing evidence that amphibian populations have responded to changing climate conditions by shifting life-cycle events. Managers can use this information to adjust monitoring programs and forest management activities in the surrounding landscape to avoid vulnerable amphibian

  3. Infection of spotted salamanders (Ambystoma maculatum) with Ichthyophonus-like organisms in Virginia.

    Science.gov (United States)

    Ware, Joy L; Viverette, Cathy; Kleopfer, John D; Pletcher, Leeanna; Massey, Davis; Wright, Anne

    2008-01-01

    Ichthyophonus-like organisms were found in two free-ranging adult spotted salamanders (Ambystoma maculatum) captured within two different vernal ponds in the Virginia Commonwealth University Rice Center for Environmental Life Sciences in Charles City County, Virginia. Histopathologic examination of necropsied specimens revealed large spores, often enclosed by granulomas. These enclosed spores resembled those caused by the fish pathogen Ichthyophonus hoeferi. One salamander displayed an externally visible large swelling beneath the jaws. The other lacked macroscopic abnormalities, but histologic sections of ventral muscle revealed early-stage Ichthyophonus-like organisms and minimal granulomatous reactions. This is the first report of Ichthyophonus-like infection of Ambystoma maculatum in Virginia.

  4. Antifungal Bacteria on Woodland Salamander Skin Exhibit High Taxonomic Diversity and Geographic Variability.

    Science.gov (United States)

    Muletz-Wolz, Carly R; DiRenzo, Graziella V; Yarwood, Stephanie A; Campbell Grant, Evan H; Fleischer, Robert C; Lips, Karen R

    2017-05-01

    Diverse bacteria inhabit amphibian skin; some of those bacteria inhibit growth of the fungal pathogen Batrachochytrium dendrobatidis Yet there has been no systematic survey of anti- B. dendrobatidis bacteria across localities, species, and elevations. This is important given geographic and taxonomic variations in amphibian susceptibility to B. dendrobatidis Our collection sites were at locations within the Appalachian Mountains where previous sampling had indicated low B. dendrobatidis prevalence. We determined the numbers and identities of anti- B. dendrobatidis bacteria on 61 Plethodon salamanders (37 P. cinereus , 15 P. glutinosus , 9 P. cylindraceus ) via culturing methods and 16S rRNA gene sequencing. We sampled co-occurring species at three localities and sampled P. cinereus along an elevational gradient (700 to 1,000 meters above sea level [masl]) at one locality. We identified 50 anti- B. dendrobatidis bacterial operational taxonomic units (OTUs) and found that the degree of B. dendrobatidis inhibition was not correlated with relatedness. Five anti- B. dendrobatidis bacterial strains occurred on multiple amphibian species at multiple localities, but none were shared among all species and localities. The prevalence of anti- B. dendrobatidis bacteria was higher at Shenandoah National Park (NP), VA, with 96% (25/26) of salamanders hosting at least one anti- B. dendrobatidis bacterial species compared to 50% (7/14) at Catoctin Mountain Park (MP), MD, and 38% (8/21) at Mt. Rogers National Recreation Area (NRA), VA. At the individual level, salamanders at Shenandoah NP had more anti- B. dendrobatidis bacteria per individual (μ = 3.3) than those at Catoctin MP (μ = 0.8) and at Mt. Rogers NRA (μ = 0.4). All salamanders tested negative for B. dendrobatidis Anti- B. dendrobatidis bacterial species are diverse in central Appalachian Plethodon salamanders, and their distribution varied geographically. The antifungal bacterial species that we identified may play a

  5. Molecular characterization and expression analysis of cathepsin C in Chinese giant salamander (Andrias davidianus after Aeromonas hydrophila infection

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    Zisheng Wang

    2018-03-01

    Full Text Available Background: Cathepsin C (CTSC (dipeptidyl peptidase I, DPPI, is a member of the papain superfamily of cysteine proteases and involves in a variety of host reactions. However, the information of CTST in Chinese giant salamander (Andrias davidianus, an amphibian species with important evolutionary position and economic values, remained unclear. Results: The full-length salamander CTSC cDNA contained a 96 bp of 5′-UTR, a 1392 bp of ORF encoding 463 amino acids, and a 95 bp of 3′-UTR. The salamander CTSC possessed several sequence features similar to other reported CTSCs such as a signal peptide, a propeptide and a mature peptide. The active site triad of Cys, His and Asn were also found existing in salamander CTSC. Salamander CTSC mRNA was constitutively expressed in all the examined tissues with significantly variant expression level. The highest expression of CTSC was in intestine, followed with stomach, spleen, lung and brain. Following Aeromonas hydrophila infection for 12 h, salamander CTSC was significantly up-regulated in several tissues including lung, spleen, brain, kidney, heart, stomach and skin. Conclusion: CTSC plays roles in the immune response to bacterial infection, which provided valuable information for further studying the functions of CTSC in salamander. Keywords: cDNA, CTSC, Dipeptidyl peptidase I, Gene expression, Hydrophila, Immune, Peptide, Sequence, Tissue

  6. Long bone histology of the stem salamander Kokartus honorarius (Amphibia: Caudata) from the Middle Jurassic of Kyrgyzstan.

    Science.gov (United States)

    Skutschas, Pavel; Stein, Koen

    2015-04-01

    Kokartus honorarius from the Middle Jurassic (Bathonian) of Kyrgyzstan is one of the oldest salamanders in the fossil record, characterized by a mixture of plesiomorphic morphological features and characters shared with crown-group salamanders. Here we present a detailed histological analysis of its long bones. The analysis of a growth series demonstrates a significant histological maturation during ontogeny, expressed by the progressive appearance of longitudinally oriented primary vascular canals, primary osteons, growth marks, remodelling features in primary bone tissues, as well as progressive resorption of the calcified cartilage, formation of endochondral bone and development of cartilaginous to bony trabeculae in the epiphyses. Apart from the presence of secondary osteons, the long bone histology of Kokartus is very similar to that of miniaturized temnospondyls, other Jurassic stem salamanders, miniaturized seymouriamorphs and modern crown-group salamanders. We propose that the presence of secondary osteons in Kokartus honorarius is a plesiomorphic feature, and the loss of secondary osteons in the long bones of crown-group salamanders as well as in those of miniaturized temnospondyls is the result of miniaturization processes. Hitherto, all stem salamander long bong histology (Kokartus, Marmorerpeton and 'salamander A') has been generally described as having paedomorphic features (i.e. the presence of Katschenko's Line and a layer of calcified cartilage), these taxa were thus most likely neotenic forms. The absence of clear lines of arrested growth and annuli in long bones of Kokartus honorarius suggests that the animals lived in an environment with stable local conditions. © 2015 Anatomical Society.

  7. A metagenomics-based approach to the top-down effect on the detritivore food web: a salamanders influence on fungal communities within a deciduous forest.

    Science.gov (United States)

    Walker, Donald M; Lawrence, Brandy R; Esterline, Dakota; Graham, Sean P; Edelbrock, Michael A; Wooten, Jessica A

    2014-11-01

    The flow of energy within an ecosystem can be considered either top-down, where predators influence consumers, or bottom-up, where producers influence consumers. Plethodon cinereus (Red-backed Salamander) is a terrestrial keystone predator who feeds on invertebrates within the ecosystem. We investigated the impact of the removal of P. cinereus on the detritivore food web in an upland deciduous forest in northwest Ohio, U.S.A. A total of eight aluminum enclosures, each containing a single P. cinereus under a small log, were constructed in the deciduous forest. On Day 1 of the experiment, four salamanders were evicted from four of the eight enclosures. Organic matter and soil were collected from the center of each enclosure at Day 1 and Day 21. From each sample, DNA was extracted, fungal-specific amplification performed, and 454 pyrosequencing was used to sequence the nuclear ribosomal internal transcribed spacer (ITS2) region and partial ribosomal large subunit (LSU). Changes in overall fungal community composition or species diversity were not statistically significant between treatments. Statistically significant shifts in the most abundant taxonomic groups of fungi were documented in presence but not absence enclosures. We concluded that P. cinereus does not affect the overall composition or diversity of fungal communities, but does have an impact on specific groups of fungi. This study used a metagenomics-based approach to investigate a missing link among a keystone predator, P. cinereus, invertebrates, and fungal communities, all of which are critical in the detritivore food web.

  8. Impact of weight-based ribavirin with peginterferon alfa-2b in African Americans with hepatitis C virus genotype 1.

    Science.gov (United States)

    Jacobson, Ira M; Brown, Robert S; McCone, Jonathan; Black, Martin; Albert, Clive; Dragutsky, Michael S; Siddiqui, Firdous A; Hargrave, Thomas; Kwo, Paul Y; Lambiase, Louis; Galler, Greg W; Araya, Victor; Freilich, Bradley; Harvey, Joann; Griffel, Louis H; Brass, Clifford A

    2007-10-01

    WIN-R (Weight-based dosing of pegINterferon alfa-2b and Ribavirin) was a multicenter, randomized, open-label, investigator-initiated trial involving 236 community and academic sites in the United States, comparing response to pegylated interferon (PEG-IFN) alfa-2b plus a flat or weight-based dose of ribavirin (RBV) in treatment-naive patients with chronic hepatitis C and compensated liver disease. Patients were randomized to receive PEG-IFN alfa-2b at 1.5 microg/kg/week plus flat-dose (800 mg/day) or weight-based-dose RBV (800 mg/day for weight 85-105 kg, or 1400 mg/day for >105- or =65 kg was the primary end point. Low SVR rates have been reported among African American individuals, in whom there is a preponderance of HCV genotype 1. This subanalysis of WIN-R was conducted to evaluate the efficacy of weight-based dosing among African American individuals with genotype 1 infection enrolled in the trial. Of 362 African American patients in the primary efficacy analysis, 188 received RBV flat dosing and 174 received weight-based dosing. SVR rates were higher (21% versus 10%; P = 0.0006) and relapse rates were lower (22% versus 30%) in the weight-based-dose group than in the flat-dose group. Safety and rates of drug discontinuation were similar between the 2 groups. Weight-based dosing of RBV is more effective than flat dosing in combination with PEG-IFN alfa-2b in African American individuals with HCV genotype 1. Even with weight-based dosing, response rates in African American individuals are lower than reported in other ethnic groups.

  9. Molecular mechanisms of extensive mitochondrial gene rearrangementin plethodontid salamanders

    Energy Technology Data Exchange (ETDEWEB)

    Mueller, Rachel Lockridge; Boore, Jeffrey L.

    2005-06-01

    Extensive gene rearrangement is reported in the mitochondrial genomes of lungless salamanders (Plethodontidae). In each genome with a novel gene order, there is evidence that the rearrangement was mediated by duplication of part of the mitochondrial genome, including the presence of both pseudogenes and additional, presumably functional, copies of duplicated genes. All rearrangement-mediating duplications include either the origin of light strand replication and the nearby tRNA genes or the regions flanking the origin of heavy strand replication. The latter regions comprise nad6, trnE, cob, trnT, an intergenic spacer between trnT and trnP and, in some genomes, trnP, the control region, trnF, rrnS, trnV, rrnL, trnL1, and nad1. In some cases, two copies of duplicated genes, presumptive regulatory regions, and/or sequences with no assignable function have been retained in the genome following the initial duplication; in other genomes, only one of the duplicated copies has been retained. Both tandem and non-tandem duplications are present in these genomes, suggesting different duplication mechanisms. In some of these mtDNAs, up to 25 percent of the total length is composed of tandem duplications of non-coding sequence that includes putative regulatory regions and/or pseudogenes of tRNAs and protein-coding genes along with otherwise unassignable sequences. These data indicate that imprecise initiation and termination of replication, slipped-strand mispairing, and intra-molecular recombination may all have played a role in generating repeats during the evolutionary history of plethodontid mitochondrial genomes.

  10. Methodological considerations for detection of terrestrial small-body salamander eDNA and implications for biodiversity conservation

    Science.gov (United States)

    Walker, Donald M.; Leys, Jacob E.; Dunham, Kelly E.; Oliver, Joshua C.; Schiller, Emily E.; Stephenson, Kelsey S.; Kimrey, John T.; Wooten, Jessica; Rogers, Mark W.

    2017-01-01

    Environmental DNA (eDNA) can be used as an assessment tool to detect populations of threatened species and provide fine-scale data required to make management decisions. The objectives of this project were to use quantitative PCR (qPCR) to: (i) detect spiked salamander DNA in soil, (ii) quantify eDNA degradation over time, (iii) determine detectability of salamander eDNA in a terrestrial environment using soil, faeces, and skin swabs, (iv) detect salamander eDNA in a mesocosm experiment. Salamander eDNA was positively detected in 100% of skin swabs and 66% of faecal samples and concentrations did not differ between the two sources. However, eDNA was not detected in soil samples collected from directly underneath wild-caught living salamanders. Salamander genomic DNA (gDNA) was detected in all qPCR reactions when spiked into soil at 10.0, 5.0, and 1.0 ng/g soil and spike concentration had a significant effect on detected concentrations. Only 33% of samples showed recoverable eDNA when spiked with 0.25 ng/g soil, which was the low end of eDNA detection. To determine the rate of eDNA degradation, gDNA (1 ng/g soil) was spiked into soil and quantified over seven days. Salamander eDNA concentrations decreased across days, but eDNA was still amplifiable at day 7. Salamander eDNA was detected in two of 182 mesocosm soil samples over 12 weeks (n = 52 control samples; n = 65 presence samples; n = 65 eviction samples). The discrepancy in detection success between experiments indicates the potential challenges for this method to be used as a monitoring technique for small-bodied wild terrestrial salamander populations.

  11. Geographic variation, genetic structure, and conservation unit designation in the Larch Mountain salamander (Plethodon larselli).

    Science.gov (United States)

    R. Steven Wagner; Mark P. Miller; Charles M. Crisafulli; Susan M. Haig

    2005-01-01

    The Larch Mountain salamander (Plethodon larselli Burns, 1954) is an endemic species in the Pacific northwestern United States facing threats related to habitat destruction. To facilitate development of conservation strategies, we used DNA sequences and RAPDs (random amplified polymorphic DNA) to examine differences among populations of this...

  12. Projected loss of a salamander diversity hotspot as a consequence of projected global climate change

    Science.gov (United States)

    Joseph R. Milanovich; William E. Peterman; Nathan P. Nibbelink; John C. Maerz

    2010-01-01

    Background: Significant shifts in climate are considered a threat to plants and animals with significant physiological limitations and limited dispersal abilities. The southern Appalachian Mountains are a global hotspot for plethodontid salamander diversity. Plethodontids are lungless ectotherms, so their ecology is strongly governed by temperature and precipitation....

  13. Cytogenetics of the Brazilian Bolitoglossa paraensis (Unterstein, 1930 salamanders (Caudata, Plethodontidae

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    Jéssica Barata da Silva

    2014-09-01

    Full Text Available Plethodontid salamanders of genus Bolitoglossa constitute the largest and most diverse group of salamanders, including around 20% of living caudate species. Recent studies have indicated the occurrence of five recognized species in the Brazilian Amazon Rainforest. We present here the first cytogenetic data of a Brazilian salamander, which may prove to be a useful by contribution to the cytotaxonomy of the genus. Specimens were collected near the "type" locality (Utinga, Belém, PA, Brazil. Chromosomal preparations from duodenal epithelial cells and testes were subjected to Giemsa staining, C-banding and DAPI/CMA3 fluorochrome staining. All specimens showed a karyotype with 13 bi-armed chromosome pairs (2n = 26. Nucleolar Organizer Regions, evidenced by CMA3, were located distally on the long arm of pair 7 (7q. DAPI+ heterochromatin was predominantly centromeric, with some small pericentromeric bands. Although the C-banding patterns of other Bolitoglossa species are so far unknown, cytogenetic studies conducted in other Plethodontid salamanders have demonstrated that pericentromeric heterochromatin is a useful cytological marker for identifying interspecific homeologies. Species diversification is usually accompanied by chromosomal changes. Therefore, the cytogenetic characterization of Bolitoglossa populations from the middle and western Brazilian Amazon Basin could identify differences which may lead to the identification of new species.

  14. Prevalence of Batrachochytrium dendrobatidis in a Nicaraguan, micro-endemic Neotropical salamander, Bolitoglossa mombachoensis

    NARCIS (Netherlands)

    Stark, Tariq; Laurijssens, Carlijn; Weterings, Martijn; Martel, An; Köhler, Gunther; Pasmans, Frank

    2017-01-01

    Amphibians are the most threatened terrestrial vertebrates on the planet and are iconic in the global biodiversity crisis. Their global decline caused by the fungal agent Batrachochytrium dendrobatidis (Bd) is well known. Declines of Mesoamerican salamanders of the family Plethodontidae, mainly

  15. Data from proteomic analysis of the skin of Chinese giant salamander (Andrias davidianus

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    Xiaofang Geng

    2015-06-01

    Full Text Available The Chinese giant salamander (Andrias davidianus, renowned as a living fossil, is the largest and longest-lived amphibian species in the world. Its skin is rich in collagens, and has developed mucous gland which could secrete a large amount of mucus under the scraping and electric stimulation. The molting is the degraded skin stratum corneum. To establish the functional skin proteome of Chinese giant salamander, two-dimensional gel electrophoresis (2DE and mass spectrometry (MS were applied to detect the composition and relative abundance of the proteins in the skin, mucus and molting. The determination of the general proteome in the skin can potentially serve as a foundation for future studies characterizing the skin proteomes from diseased salamander to provide molecular and mechanistic insights into various disease states and potential therapeutic interventions. Data presented here are also related to the research article “Proteomic analysis of the skin of Chinese giant salamander (Andrias davidianus” in the Journal of Proteomics [1].

  16. A new approach for surveying the Alpine Salamander (Salamandra atra in Austria

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    Ursula Reinthaler-Lottermoser

    2010-12-01

    Full Text Available The Alpine Salamander is a small pitch black amphibian which is endemic to the European Alps and the Dinarides. It is strictly protected according to the European FFH guidelines. Despite its central role in the alpine ecosystem our actual published record in Austria is small. In order to resolve this shortcoming our project explores its distribution in Austria. It uses a participatory and community based approach to gather data. Everybody can enter and look at Alpine Salamander observations on our website www.alpensalamander.eu. This approach also allows us to establish an “oral history” of Salamander observations in the past 50 years by conducting interviews in the local community. Since July 2009 the website and salamander report database are online. From the actual data (more than 5600 records we already obtained an overview about the present distribution and data quality. The data are an excellent basis for detailed scientific studies on these remarkable amphibians. With this new and highly interactive approach science and education are combined to initiate protection measures with the public.

  17. Exceptional soft tissues preservation in a mummified frog-eating Eocene salamander

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    Jérémy Tissier

    2017-10-01

    Full Text Available Fossils are almost always represented by hard tissues but we present here the exceptional case of a three-dimensionally preserved specimen that was ‘mummified’ (likely between 40 and 34 million years ago in a terrestrial karstic environment. This fossil is the incomplete body of a salamander, Phosphotriton sigei, whose skeleton and external morphology are well preserved, as revealed by phase-contrast synchrotron X-ray microtomography. In addition, internal structures composed of soft tissues preserved in three dimensions are now identified: a lung, the spinal cord, a lumbosacral plexus, the digestive tract, muscles and urogenital organs that may be cloacal glands. These are among the oldest known cases of three-dimensional preservation of these organs in vertebrates and shed light on the ecology of this salamander. Indeed, the digestive tract contains remains of a frog, which represents the only known case of an extinct salamander that fed on a frog, an extremely rare type of predation in extant salamanders. These new data improve our scarce knowledge on soft tissue anatomy of early urodeles and should prove useful for future biologists and palaeontologists working on urodele evolutionary biology. We also suggest that the presence of bat guano and carcasses represented a close source of phosphorus, favouring preservation of soft tissues. Bone microanatomy indicates that P. sigei was likely amphibious or terrestrial, and was probably not neotenic.

  18. A new species of salamander (Bolitoglossa: Plethodontidae from the Cordillera Oriental of the Colombian Andes

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    Andrés R. Acosta-Galvis

    2012-01-01

    Full Text Available Eight species of salamanders are recognized to Cordillera Oriental of Colombia. Here we describe a new species of the genus Bolitoglossa, named Bolitoglossa guaneae sp. nov. The highest number of species of this genus is found in the cloud forests located in the western flank of the Cordillera Oriental.

  19. Behavioral and Physiological Responses of Ozark Zigzag Salamanders to Stimuli from an Invasive Predator: The Armadillo

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    Adam L. Crane

    2012-01-01

    Full Text Available When new predators invade a habitat, either through range extensions or introductions, prey may be at a high risk because they do not recognize the predators as dangerous. The nine-banded armadillo (Dasypus novemcinctus has recently expanded its range in North America. Armadillos forage by searching soil and leaf litter, consuming invertebrates and small vertebrates, including salamanders. We tested whether Ozark zigzag salamanders (Plethodon angusticlavius from a population coexisting with armadillos for about 30 years exhibit antipredator behavior in the presence of armadillo chemical cues and whether they can discriminate between stimuli from armadillos and a nonpredatory sympatric mammal (white-tailed deer, Odocoileus virginianus. Salamanders appeared to recognize substrate cues from armadillos as a threat because they increased escape behaviors and oxygen consumption. When exposed to airborne cues from armadillos, salamanders also exhibited an antipredator response by spending more time in an inconspicuous posture. Additionally, individually consistent behaviors across treatments for some response variables suggest the potential for a behavioral syndrome in this species.

  20. The Dynamics of Two Hybrid Zones in Appalachian Salamanders of the Genus Plethodon

    Science.gov (United States)

    Nelson G. Hairston; R. Haven Wiley; Charles K. Smith; Kenneth A. Kneidel

    1992-01-01

    Two zones of intergradation between populations of Plethodon have been studied for 18 and 20 years, respectively. The data consist of systematic scores of colors, made at least twice annually. Near Heintooga Overlook in the Balsam Mountains (Great Smoky Mountains National Park), the salamanders' cheeks are gray. Proceeding north toward the...

  1. Macrohabitat models of occurrence for the threatened Cheat Mountain salamander, Plethodon nettingi

    Science.gov (United States)

    Lester O. Dillard; Kevin R. Russell; W. Mark Ford

    2008-01-01

    The federally threatened Cheat Mountain salamander (Plethodon nettingi; hereafter CMS) is known to occur at approximately 70 small, scattered sites in the Allegheny Mountains of eastern West Virginia. We used a comparative modeling approach to explain the landscape-level distribution and habitat relationships of CMS in relation to a suite of biotic...

  2. Exceptional soft tissues preservation in a mummified frog-eating Eocene salamander.

    Science.gov (United States)

    Tissier, Jérémy; Rage, Jean-Claude; Laurin, Michel

    2017-01-01

    Fossils are almost always represented by hard tissues but we present here the exceptional case of a three-dimensionally preserved specimen that was 'mummified' (likely between 40 and 34 million years ago) in a terrestrial karstic environment. This fossil is the incomplete body of a salamander, Phosphotriton sigei , whose skeleton and external morphology are well preserved, as revealed by phase-contrast synchrotron X-ray microtomography. In addition, internal structures composed of soft tissues preserved in three dimensions are now identified: a lung, the spinal cord, a lumbosacral plexus, the digestive tract, muscles and urogenital organs that may be cloacal glands. These are among the oldest known cases of three-dimensional preservation of these organs in vertebrates and shed light on the ecology of this salamander. Indeed, the digestive tract contains remains of a frog, which represents the only known case of an extinct salamander that fed on a frog, an extremely rare type of predation in extant salamanders. These new data improve our scarce knowledge on soft tissue anatomy of early urodeles and should prove useful for future biologists and palaeontologists working on urodele evolutionary biology. We also suggest that the presence of bat guano and carcasses represented a close source of phosphorus, favouring preservation of soft tissues. Bone microanatomy indicates that P. sigei was likely amphibious or terrestrial, and was probably not neotenic.

  3. Woodland salamanders as metrics of forest ecosystem recovery: a case study from California’s redwoods

    Science.gov (United States)

    Hart Welsh; Garth Hodgson

    2013-01-01

    Woodland (Plethodontid) salamanders occur in huge numbers in healthy forests in North America where the abundances of many species vary along successional gradients. Their high numbers and trophic role as predators on shredder and decomposer arthropods influence nutrient and carbon pathways at the leaf litter/soil interface. Their extreme niche conservatism and low...

  4. Microarray analysis of a salamander hopeful monster reveals transcriptional signatures of paedomorphic brain development

    Science.gov (United States)

    2010-01-01

    Background The Mexican axolotl (Ambystoma mexicanum) is considered a hopeful monster because it exhibits an adaptive and derived mode of development - paedomorphosis - that has evolved rapidly and independently among tiger salamanders. Unlike related tiger salamanders that undergo metamorphosis, axolotls retain larval morphological traits into adulthood and thus present an adult body plan that differs dramatically from the ancestral (metamorphic) form. The basis of paedomorphic development was investigated by comparing temporal patterns of gene transcription between axolotl and tiger salamander larvae (Ambystoma tigrinum tigrinum) that typically undergo a metamorphosis. Results Transcript abundances from whole brain and pituitary were estimated via microarray analysis on four different days post hatching (42, 56, 70, 84 dph) and regression modeling was used to independently identify genes that were differentially expressed as a function of time in both species. Collectively, more differentially expressed genes (DEGs) were identified as unique to the axolotl (n = 76) and tiger salamander (n = 292) than were identified as shared (n = 108). All but two of the shared DEGs exhibited the same temporal pattern of expression and the unique genes tended to show greater changes later in the larval period when tiger salamander larvae were undergoing anatomical metamorphosis. A second, complementary analysis that directly compared the expression of 1320 genes between the species identified 409 genes that differed as a function of species or the interaction between time and species. Of these 409 DEGs, 84% exhibited higher abundances in tiger salamander larvae at all sampling times. Conclusions Many of the unique tiger salamander transcriptional responses are probably associated with metamorphic biological processes. However, the axolotl also showed unique patterns of transcription early in development. In particular, the axolotl showed a genome-wide reduction in mRNA abundance

  5. Microarray analysis of a salamander hopeful monster reveals transcriptional signatures of paedomorphic brain development

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    Putta Srikrishna

    2010-06-01

    Full Text Available Abstract Background The Mexican axolotl (Ambystoma mexicanum is considered a hopeful monster because it exhibits an adaptive and derived mode of development - paedomorphosis - that has evolved rapidly and independently among tiger salamanders. Unlike related tiger salamanders that undergo metamorphosis, axolotls retain larval morphological traits into adulthood and thus present an adult body plan that differs dramatically from the ancestral (metamorphic form. The basis of paedomorphic development was investigated by comparing temporal patterns of gene transcription between axolotl and tiger salamander larvae (Ambystoma tigrinum tigrinum that typically undergo a metamorphosis. Results Transcript abundances from whole brain and pituitary were estimated via microarray analysis on four different days post hatching (42, 56, 70, 84 dph and regression modeling was used to independently identify genes that were differentially expressed as a function of time in both species. Collectively, more differentially expressed genes (DEGs were identified as unique to the axolotl (n = 76 and tiger salamander (n = 292 than were identified as shared (n = 108. All but two of the shared DEGs exhibited the same temporal pattern of expression and the unique genes tended to show greater changes later in the larval period when tiger salamander larvae were undergoing anatomical metamorphosis. A second, complementary analysis that directly compared the expression of 1320 genes between the species identified 409 genes that differed as a function of species or the interaction between time and species. Of these 409 DEGs, 84% exhibited higher abundances in tiger salamander larvae at all sampling times. Conclusions Many of the unique tiger salamander transcriptional responses are probably associated with metamorphic biological processes. However, the axolotl also showed unique patterns of transcription early in development. In particular, the axolotl showed a genome

  6. Skin Microbiomes of California Terrestrial Salamanders Are Influenced by Habitat More Than Host Phylogeny

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    Alicia K. Bird

    2018-03-01

    Full Text Available A multitude of microorganisms live on and within plant and animal hosts, yet the ecology and evolution of these microbial communities remains poorly understood in many taxa. This study examined the extent to which environmental factors and host taxonomic identity explain microbiome variation within two salamander genera, Ensatina and Batrachoseps, in the family Plethodontidae. In particular, we assessed whether microbiome differentiation paralleled host genetic distance at three levels of taxonomy: genus and high and low clade levels within Ensatina eschscholtzii. We predicted that more genetically related host populations would have more similar microbiomes than more distantly related host populations. We found that salamander microbiomes possess bacterial species that are most likely acquired from their surrounding soil environment, but the relative representation of those bacterial species is significantly different on the skin of salamanders compared to soil. We found differences in skin microbiome alpha diversity among Ensatina higher and lower clade groups, as well as differences between Ensatina and Batrachoseps. We also found that relative microbiome composition (beta diversity did vary between Ensatina lower clades, but differences were driven by only a few clades and not correlated to clade genetic distances. We conclude this difference was likely a result of Ensatina lower clades being associated with geographic location and habitat type, as salamander identity at higher taxonomic levels (genus and Ensatina higher clades was a weak predictor of microbiome composition. These results lead us to conclude that environmental factors are likely playing a more significant role in salamander cutaneous microbiome assemblages than host-specific traits.

  7. Low levels of LTR retrotransposon deletion by ectopic recombination in the gigantic genomes of salamanders.

    Science.gov (United States)

    Frahry, Matthew Blake; Sun, Cheng; Chong, Rebecca A; Mueller, Rachel Lockridge

    2015-02-01

    Across the tree of life, species vary dramatically in nuclear genome size. Mutations that add or remove sequences from genomes-insertions or deletions, or indels-are the ultimate source of this variation. Differences in the tempo and mode of insertion and deletion across taxa have been proposed to contribute to evolutionary diversity in genome size. Among vertebrates, most of the largest genomes are found within the salamanders, an amphibian clade with genome sizes ranging from ~14 to ~120 Gb. Salamander genomes have been shown to experience slower rates of DNA loss through small (i.e., genomes. However, no studies have addressed DNA loss from salamander genomes resulting from larger deletions. Here, we focus on one type of large deletion-ectopic-recombination-mediated removal of LTR retrotransposon sequences. In ectopic recombination, double-strand breaks are repaired using a "wrong" (i.e., ectopic, or non-allelic) template sequence-typically another locus of similar sequence. When breaks occur within the LTR portions of LTR retrotransposons, ectopic-recombination-mediated repair can produce deletions that remove the internal transposon sequence and the equivalent of one of the two LTR sequences. These deletions leave a signature in the genome-a solo LTR sequence. We compared levels of solo LTRs in the genomes of four salamander species with levels present in five vertebrates with smaller genomes. Our results demonstrate that salamanders have low levels of solo LTRs, suggesting that ectopic-recombination-mediated deletion of LTR retrotransposons occurs more slowly than in other vertebrates with smaller genomes.

  8. Multiple drivers, scales, and interactions influence southern Appalachian stream salamander occupancy

    Science.gov (United States)

    Cecala, Kristen K.; Maerz, John C.; Halstead, Brian J.; Frisch, John R.; Gragson, Ted L.; Hepinstall-Cymerman, Jeffrey; Leigh, David S.; Jackson, C. Rhett; Peterson, James T.; Pringle, Catherine M.

    2018-01-01

    Understanding how factors that vary in spatial scale relate to population abundance is vital to forecasting species responses to environmental change. Stream and river ecosystems are inherently hierarchical, potentially resulting in organismal responses to fine‐scale changes in patch characteristics that are conditional on the watershed context. Here, we address how populations of two salamander species are affected by interactions among hierarchical processes operating at different scales within a rapidly changing landscape of the southern Appalachian Mountains. We modeled reach‐level occupancy of larval and adult black‐bellied salamanders (Desmognathus quadramaculatus) and larval Blue Ridge two‐lined salamanders (Eurycea wilderae) as a function of 17 different terrestrial and aquatic predictor variables that varied in spatial extent. We found that salamander occurrence varied widely among streams within fully forested catchments, but also exhibited species‐specific responses to changes in local conditions. While D. quadramaculatus declined predictably in relation to losses in forest cover, larval occupancy exhibited the strongest negative response to forest loss as well as decreases in elevation. Conversely, occupancy of E. wilderae was unassociated with watershed conditions, only responding negatively to higher proportions of fast‐flowing stream habitat types. Evaluation of hierarchical relationships demonstrated that most fine‐scale variables were closely correlated with broad watershed‐scale variables, suggesting that local reach‐scale factors have relatively smaller effects within the context of the larger landscape. Our results imply that effective management of southern Appalachian stream salamanders must first focus on the larger scale condition of watersheds before management of local‐scale conditions should proceed. Our findings confirm the results of some studies while refuting the results of others, which may indicate that

  9. Trial Protocol: Using genotype to tailor prescribing of nicotine replacement therapy: a randomised controlled trial assessing impact of communication upon adherence

    Directory of Open Access Journals (Sweden)

    Prevost A Toby

    2010-11-01

    Full Text Available Abstract Background The behavioural impact of pharmacogenomics is untested; informing smokers of genetic test results for responsiveness to smoking cessation medication may increase adherence to this medication. The objective of this trial is to estimate the impact upon adherence to nicotine replacement therapy (NRT of informing smokers that their oral dose of NRT has been tailored to a DNA analysis. Hypotheses to be tested are as follows: IAdherence to NRT is greater among smokers informed that their oral dose of NRT is tailored to an analysis of DNA (genotype, compared to one tailored to nicotine dependence questionnaire score (phenotype. II Amongst smokers who fail to quit at six months, motivation to make another quit attempt is lower when informed that their oral dose of NRT was tailored to genotype rather than phenotype. Methods/Design An open label, parallel groups randomised trial in which 630 adult smokers (smoking 10 or more cigarettes daily using National Health Service (NHS stop smoking services in primary care are randomly allocated to one of two groups: i. NRT oral dose tailored by DNA analysis (OPRM1 gene (genotype, or ii. NRT oral dose tailored by nicotine dependence questionnaire score (phenotype The primary outcome is proportion of prescribed NRT consumed in the first 28 days following an initial quit attempt, with the secondary outcome being motivation to make another quit attempt, amongst smokers not abstinent at six months. Other outcomes include adherence to NRT in the first seven days and biochemically validated smoking abstinence at six months. The primary outcome will be collected on 630 smokers allowing sufficient power to detect a 7.5% difference in mean proportion of NRT consumed using a two-tailed test at the 5% level of significance between groups. The proportion of all NRT consumed in the first four weeks of quitting will be compared between arms using an independent samples t-test and by estimating the 95

  10. The phenology of a rare salamander (Salamandra infraimmaculata in a population breeding under unpredictable ambient conditions: a 25 year study

    Directory of Open Access Journals (Sweden)

    Michael R. Warburg

    2007-11-01

    Full Text Available This is a long-term study (1974-1999 on the phenology of the rare, xeric- inhabiting salamander Salamandra infraimmaculata in a small isolated population during the breeding season near the breeding ponds on Mt. Carmel. This is a fringe area of the genus’ south-easternmost Palaearctic distribution. Salamanders were captured during the 25 year long study. The first years up to the 1980s the total number of salamanders increased but during the last years there seems to have been a decline. Although this could be a phase in normal population cyclic oscillations nevertheless when compared with long-term data on a European Salamandra it does not seem so. The interpretation of the species’ status is dependent on numbers of salamanders captured as well as on the duration of the study. These subjects are reviewed and discussed in this paper.

  11. 76 FR 44036 - Proposed Low-Effect Habitat Conservation Plan for the California Tiger Salamander, AT&T Portable...

    Science.gov (United States)

    2011-07-22

    ... developed portion of the AT&T facility on October 25 and 29, 2010. In addition, several salamander larvae... were rejected due to the presence of other Federally listed species, including vernal pool fairy shrimp...

  12. Vaccination with Recombinant Baculovirus Expressing Ranavirus Major Capsid Protein Induces Protective Immunity in Chinese Giant Salamander, Andrias davidianus

    Directory of Open Access Journals (Sweden)

    Xiaoyuan Zhou

    2017-07-01

    Full Text Available The Chinese giant salamander iridovirus (CGSIV, belonging to the genus Ranavirus in the family Iridoviridae, is the causative agent of an emerging infectious disease causing high mortality of more than 90% and economic losses in Chinese giant salamanders in China. In this study, a recombinant baculovirus-based vaccine expressing the CGSIV major capsid protein (MCP was developed and its protective immunity in Chinese giant salamanders was evaluated. The recombinant Autographa californica nucleopolyhedrosis virus (AcNPV, expressing CGSIV MCP, designated as AcNPV-MCP, was generated with the highest titers of 1 × 108 plaque forming units/mL (PFU/mL and confirmed by Western blot and indirect immunofluorescence (IIF assays. Western blot analysis revealed that the expressed MCP reacted with mouse anti-MCP monoclonal antibodies at the band of about 53 kDa. The results of IIF indicated that the MCP was expressed in the infected Spodoptera frugiperda 9 (Sf9 cells with the recombinant baculovirus, and the Chinese giant salamander muscle cells also transduced with the AcNPV-MCP. Immunization with the recombinant baculovirus of AcNPV-MCP elicited robust specific humoral immune responses detected by ELISA and neutralization assays and potent cellular immune responses in Chinese giant salamanders. Importantly, the effective immunization conferred highly protective immunity for Chinese giant salamanders against CGSIV challenge and produced a relative percent of survival rate of 84%. Thus, the recombinant baculovirus expressing CGSIV MCP can induce significant immune responses involving both humoral and cell-mediated immunity in Chinese giant salamanders and might represent a potential baculovirus based vaccine candidate for Chinese giant salamanders against CGSIV.

  13. BDNF Val 66 Met and 5-HTTLPR genotype moderate the impact of early psychosocial adversity on plasma brain-derived neurotrophic factor and depressive symptoms: a prospective study.

    Science.gov (United States)

    Buchmann, Arlette F; Hellweg, Rainer; Rietschel, Marcella; Treutlein, Jens; Witt, Stephanie H; Zimmermann, Ulrich S; Schmidt, Martin H; Esser, Günter; Banaschewski, Tobias; Laucht, Manfred; Deuschle, Michael

    2013-08-01

    Recent studies have emphasized an important role for neurotrophins, such as brain-derived neurotrophic factor (BDNF), in regulating the plasticity of neural circuits involved in the pathophysiology of stress-related diseases. The aim of the present study was to examine the interplay of the BDNF Val⁶⁶Met and the serotonin transporter promoter (5-HTTLPR) polymorphisms in moderating the impact of early-life adversity on BDNF plasma concentration and depressive symptoms. Participants were taken from an epidemiological cohort study following the long-term outcome of early risk factors from birth into young adulthood. In 259 individuals (119 males, 140 females), genotyped for the BDNF Val⁶⁶Met and the 5-HTTLPR polymorphisms, plasma BDNF was assessed at the age of 19 years. In addition, participants completed the Beck Depression Inventory (BDI). Early adversity was determined according to a family adversity index assessed at 3 months of age. Results indicated that individuals homozygous for both the BDNF Val and the 5-HTTLPR L allele showed significantly reduced BDNF levels following exposure to high adversity. In contrast, BDNF levels appeared to be unaffected by early psychosocial adversity in carriers of the BDNF Met or the 5-HTTLPR S allele. While the former group appeared to be most susceptible to depressive symptoms, the impact of early adversity was less pronounced in the latter group. This is the first preliminary evidence indicating that early-life adverse experiences may have lasting sequelae for plasma BDNF levels in humans, highlighting that the susceptibility to this effect is moderated by BDNF Val⁶⁶Met and 5-HTTLPR genotype. Copyright © 2013. Published by Elsevier B.V.

  14. Impact of the TCF7L2 genotype on risk of hypoglycaemia and glucagon secretion during hypoglycaemia

    DEFF Research Database (Denmark)

    Kristensen, Peter L; Pedersen-Bjergaard, Ulrik; Due-Andersen, Rikke

    2016-01-01

    hypoglycaemia and a higher frequency of severe hypoglycaemia (SH) in type 1 diabetes (T1DM). MATERIAL AND METHODS: This is a post hoc study of an earlier prospective observational study of SH and four mechanistic studies of physiological responses to hypoglycaemia. 269 patients with T1DM were followed in a one......-year observational study. A log-linear negative binomial model was applied with events of SH as dependent variable and TCF7L2 alleles as explanatory variable. In four experimental studies including 65 people, TCF7L2 genotyping was done and plasma glucagon concentration during experimental hypoglycaemia...... was determined. RESULTS: Incidences of SH were TT 0.54, TC 0.98 and CC 1.01 episodes per patient-year with no significant difference between groups. During experimental hypoglycaemia, the TCF7L2 polymorphism did not influence glucagon secretion. DISCUSSION: Patients with T1DM carrying the T allele of the TCF7L2...

  15. Hypervariable region 1 differentially impacts viability of hepatitis C virus strains of genotypes 1 to 6 and impairs virus neutralization

    DEFF Research Database (Denmark)

    Prentoe, Jannick; Jensen, Tanja B; Meuleman, Philip

    2011-01-01

    Hypervariable region 1 (HVR1) of hepatitis C virus (HCV) E2 envelope glycoprotein has been implicated in virus neutralization and persistence. We deleted HVR1 from JFH1-based HCV recombinants expressing Core/E1/E2/p7/NS2 of genotypes 1 to 6, previously found to grow efficiently in human hepatoma...... genetics studies revealed adaptive envelope mutations that rescued the infectivity of 1a(ΔHVR1), 1b(ΔHVR1), 2b(ΔHVR1), and 3a(ΔHVR1) recombinants. Thus, HVR1 might have distinct functional roles for different HCV isolates. Ultracentrifugation studies showed that deletion of HVR1 did not alter HCV RNA...... density distribution, whereas infectious particle density changed from a range of 1.0 to 1.1 g/ml to a single peak at ∼1.1 g/ml, suggesting that HVR1 was critical for low-density HCV particle infectivity. Using chronic-phase HCV patient sera, we found three distinct neutralization profiles...

  16. Hypervariable region 1 differentially impacts viability of hepatitis C virus strains of genotypes 1 to 6 and impairs virus neutralization

    DEFF Research Database (Denmark)

    Prentø, Jannick Cornelius; Jensen, Tanja Bertelsen; Meuleman, Philip

    2011-01-01

    Hypervariable region 1 (HVR1) of hepatitis C virus (HCV) E2 envelope glycoprotein has been implicated in virus neutralization and persistence. We deleted HVR1 from JFH1-based HCV recombinants expressing Core/E1/E2/p7/NS2 of genotypes 1 to 6, previously found to grow efficiently in human hepatoma...... genetics studies revealed adaptive envelope mutations that rescued the infectivity of 1a(¿HVR1), 1b(¿HVR1), 2b(¿HVR1), and 3a(¿HVR1) recombinants. Thus, HVR1 might have distinct functional roles for different HCV isolates. Ultracentrifugation studies showed that deletion of HVR1 did not alter HCV RNA...... density distribution, whereas infectious particle density changed from a range of 1.0 to 1.1 g/ml to a single peak at ~1.1 g/ml, suggesting that HVR1 was critical for low-density HCV particle infectivity. Using chronic-phase HCV patient sera, we found three distinct neutralization profiles...

  17. Impact of Health Care Exposure on Genotypic Antiseptic Tolerance in Staphylococcus aureus Infections in a Pediatric Population.

    Science.gov (United States)

    McNeil, J Chase; Hultén, Kristina G; Mason, Edward O; Kaplan, Sheldon L

    2017-07-01

    Staphylococcus aureus possessing either the smr gene or the qacA/B genes is associated with decreased susceptibility to chlorhexidine gluconate (CHG) and other antiseptics. Previous studies of antiseptic-tolerant staphylococci have focused largely on high-risk populations, and the exact role of health care exposure in the acquisition of these organisms is unclear. We sought to describe the risk factors and features of infection caused by antiseptic-tolerant S. aureus in a general pediatric population. Isolates were selected from an ongoing S. aureus surveillance study. Every third sequential isolate in the year 2014 was selected for inclusion. All isolates underwent PCR for the genes qacA/B and smr Medical records were reviewed. Five hundred six isolates were included in the study, with 377 (74.3%) being community acquired. One hundred (19.8%) isolates were smr positive and 79 (15.6%) qacA/B positive. In univariable analyses, the presence of either gene was associated with underlying medical conditions, nosocomial acquisition, recent hospitalization, central venous lines, and CHG exposure. In multivariable analyses, only differences between patients with chronic medical conditions (odds ratio [OR] = 1.72; 95% confidence interval [CI], 1.22 to 2.64) and nosocomial acquisition (OR = 2.48; 95% CI, 1.16 to 8.17) remained statistically significant. Among patients without risk factors, 27.9% had infection with an antiseptic-tolerant isolate. smr - or qacA/B -positive S. aureus isolates are common in children and are independently associated with nosocomial acquisition and underlying medical conditions. These findings imply a role for the health care environment in acquisition of these organisms. However, genotypic antiseptic tolerance was seen in >25% of healthy children with an S. aureus infection, indicating that these organism are prevalent in the community as well. Copyright © 2017 American Society for Microbiology.

  18. Distribution of the Sonora Tiger Salamander (Ambystoma mavortium stebbinsi) in Mexico

    Science.gov (United States)

    Hossack, Blake R.; Muths, Erin L.; Rorabaugh, James C.; Lemos Espinal, Julio A.; Sigafus, Brent H.; Chambert, Thierry A.; Carreon Arroyo, Gerardo; Hurtado Felix, David; Toyos Martinez, Daniel; Jones, Thomas R.

    2016-01-01

    The Sonoran Tiger Salamander (Ambystoma mavortium stebbinsi Lowe, 1954) was listed as federally endangered in the USA in 1997 (USFWS 1997). In the USA, the distribution of A. mavortium stebbinsi is limited to the San Rafael Valley (approximately 567 km2), between the Sierra San Antonio (called the Patagonia Mountains in Arizona) and Huachuca Mountains, and south of the Canelo Hills, Arizona (Fig. 1). The USA listing was triggered by loss of natural wetland habitats, threats from invasive predators, frequent die-offs from disease, introgression with the introduced Barred Tiger Salamander (A. mavortium mavortium), and small range and number of breeding sites that increases susceptibility to stochastic events (USFWS 1997). Small population sizes and limited gene flow have caused inbreeding, which may further reduce population viability and the potential for recovery (Jones et al. 1988; Storfer et al. 2014). 

  19. Climate-mediated competition in a high-elevation salamander community

    Science.gov (United States)

    Dallalio, Eric A.; Brand, Adrianne B,; Grant, Evan H. Campbell

    2017-01-01

    The distribution of the federally endangered Shenandoah Salamander (Plethodon shenandoah) is presumed to be limited by competition with the Red-backed Salamander (Plethodon cinereus). In particular, the current distribution of P. shenandoah is understood to be restricted to warmer and drier habitats because of interspecific interactions. These habitats may be particularly sensitive to climate change, though the influence of competition may also be affected by temperature and relative humidity. We investigated the response of P. shenandoah to competition with P. cinereus under four climate scenarios in 3-dimensional mesocosms. The results suggest that, although climate change may alleviate competitive pressure from P. cinereus, warmer temperatures may also significantly influence the persistence of the species across its known range.

  20. A little bit is better than nothing: the incomplete parthenogenesis of salamanders, frogs and fish

    Directory of Open Access Journals (Sweden)

    Schartl Manfred

    2010-08-01

    Full Text Available Abstract A re-examination of the mitochondrial genomes of unisexual salamander lineages, published in BMC Evolutionary Biology, shows them to be the oldest unisexual vertebrates known, having been around for 5 million years. This presents a challenge to the prediction that lack of genetic recombination is a fast track to extinction. See research article http://www.biomedcentral.com/1471-2148/10/238

  1. Efficacy of chemical disinfectants for the containment of the salamander chytrid fungus Batrachochytrium salamandrivorans

    OpenAIRE

    Van Rooij, Pascale; Pasmans, Frank; Coen, Yanaïka; Martel, An

    2017-01-01

    The recently emerged chytrid fungus Batrachochytrium salamandrivorans (Bsal) causes European salamander declines. Proper hygiene protocols including disinfection procedures are crucial to prevent disease transmission. Here, the efficacy of chemical disinfectants in killing Bsal was evaluated. At all tested conditions, Biocidal (R), Chloramine-T (R), Dettol medical (R), Disolol (R), ethanol, F10 (R), Hibiscrub (R), potassium permanganate, Safe4 (R), sodium hypochlorite, and Virkon S (R), were ...

  2. Effect of thermal acclimation on locomotor energetics and locomotor performance in a lungless salamander, Desmognathus ochrophaeus.

    Science.gov (United States)

    Feder, M E

    1986-03-01

    To determine the effects of thermal acclimation upon locomotor performance and the rate of oxygen consumption (MO2) during activity, small (less than 3 g), lungless salamanders, Desmognathus ochrophaeus Cope, were acclimated to three temperatures (5, 13 and 21 degrees C) and exercised at various controlled speeds within an exercise wheel while their MO2 was measured. MO2 increased with speed at low speeds (less than 14 cm min-1). Although animals could sustain greater speeds, MO2 did not increase further. These small, exclusively skin-breathing salamanders could increase their MO2 9-11 times during exercise and could sustain nearly half of the oxygen flux expected across a similar surface area of the mammalian lung. However, their maximum aerobic speed was remarkably slow (14 cm min-1) and their net cost of transport remarkably large (15-17 ml O2 g-1 km-1). Thermal acclimation affected MO2 during activity, the maximum sustainable speed and locomotor stamina in different ways. During exercise at 13 degrees C, cold-acclimated animals had a significantly greater MO2 than warm-acclimated animals, but did not differ in stamina or the maximum sustainable speed. During exercise at 21 degrees C, cold acclimation did not affect the MO2 significantly, but it decreased the stamina and increased the rate of lactate accumulation. Thus, these results suggest that thermal acclimation of the MO2 is not tightly coupled to thermal acclimation of locomotor performance in salamanders.

  3. Unexpected rarity of the pathogen Batrachochytrium dendrobatidis in Appalachian Plethodon Salamanders: 1957-2011.

    Directory of Open Access Journals (Sweden)

    Carly Muletz

    Full Text Available Widespread population declines in terrestrial Plethodon salamanders occurred by the 1980s throughout the Appalachian Mountains, the center of global salamander diversity, with no evident recovery. We tested the hypothesis that the historic introduction and spread of the pathogenic fungus Batrachochytrium dendrobatidis (Bd into the eastern US was followed by Plethodon population declines. We expected to detect elevated prevalence of Bd prior to population declines as observed for Central American plethodontids. We tested 1,498 Plethodon salamanders of 12 species (892 museum specimens, 606 wild individuals for the presence of Bd, and tested 94 of those for Batrachochytrium salamandrivorans (Bs and for ranavirus. Field samples were collected in 2011 from 48 field sites across a 767 km transect. Historic samples from museum specimens were collected at five sites with the greatest number and longest duration of collection (1957-987, four of which were sampled in the field in 2011. None of the museum specimens were positive for Bd, but four P. cinereus from field surveys were positive. The overall Bd prevalence from 1957-2011 for 12 Plethodon species sampled across a 757 km transect was 0.2% (95% CI 0.1-0.7%. All 94 samples were negative for Bs and ranavirus. We conclude that known amphibian pathogens are unlikely causes for declines in these Plethodon populations. Furthermore, these exceptionally low levels of Bd, in a region known to harbor Bd, may indicate that Plethodon specific traits limit Bd infection.

  4. Data set for transcriptome analysis of the Chinese giant salamander (Andrias davidianus

    Directory of Open Access Journals (Sweden)

    Xuemei Jiang

    2016-03-01

    Full Text Available The Chinese giant salamander (Andrias davidianus occupies a seat at the phylogenetic and species evolution process, which makes it an invaluable model for genetics; however, the genetic information and gene sequences about the Chinese giant salamander in public databases are scanty. Hence, we aimed to perform transcriptome analysis with the help of high-throughput sequencing. In this data, 61,317,940 raw reads were acquired from Chinese giant salamander mRNA using Illumina paired-end sequencing platform. After de novo assembly, a total of 72,072 unigenes were gained, in which 33,834 (46.95% and 29,479 (40.91% transcripts exhibited homology to sequences in the Nr database and Swiss-Prot database, (E-value <10−5, respectively. In the obtained unigenes, 18,019 (25% transcripts were assigned with at least one Gene Ontology term, of which 1218 (6.8% transcripts were assigned to immune system processes. In addition, a total of 17,572 assembled sequences were assigned into 241 predicted KEGG metabolic pathways. Among these, 2552 (14.5% transcripts were assigned to the immune system relevant pathway and 5 transcripts were identified as potential antimicrobial peptides (AMPs. Keywords: Andrias davidianus, Transcriptome

  5. Genic regions of a large salamander genome contain long introns and novel genes

    Directory of Open Access Journals (Sweden)

    Bryant Susan V

    2009-01-01

    Full Text Available Abstract Background The basis of genome size variation remains an outstanding question because DNA sequence data are lacking for organisms with large genomes. Sixteen BAC clones from the Mexican axolotl (Ambystoma mexicanum: c-value = 32 × 109 bp were isolated and sequenced to characterize the structure of genic regions. Results Annotation of genes within BACs showed that axolotl introns are on average 10× longer than orthologous vertebrate introns and they are predicted to contain more functional elements, including miRNAs and snoRNAs. Loci were discovered within BACs for two novel EST transcripts that are differentially expressed during spinal cord regeneration and skin metamorphosis. Unexpectedly, a third novel gene was also discovered while manually annotating BACs. Analysis of human-axolotl protein-coding sequences suggests there are 2% more lineage specific genes in the axolotl genome than the human genome, but the great majority (86% of genes between axolotl and human are predicted to be 1:1 orthologs. Considering that axolotl genes are on average 5× larger than human genes, the genic component of the salamander genome is estimated to be incredibly large, approximately 2.8 gigabases! Conclusion This study shows that a large salamander genome has a correspondingly large genic component, primarily because genes have incredibly long introns. These intronic sequences may harbor novel coding and non-coding sequences that regulate biological processes that are unique to salamanders.

  6. Phylogeography of Sardinian cave salamanders (genus Hydromantes) is mainly determined by geomorphology.

    Science.gov (United States)

    Chiari, Ylenia; van der Meijden, Arie; Mucedda, Mauro; Lourenço, João M; Hochkirch, Axel; Veith, Michael

    2012-01-01

    Detecting the factors that determine the interruption of gene flow between populations is key to understanding how speciation occurs. In this context, caves are an excellent system for studying processes of colonization, differentiation and speciation, since they represent discrete geographical units often with known geological histories. Here, we asked whether discontinuous calcareous areas and cave systems represent major barriers to gene flow within and among the five species of Sardinian cave salamanders (genus Hydromantes) and whether intraspecific genetic structure parallels geographic distance within and among caves. We generated mitochondrial cytochrome b gene sequences from 184 individuals representing 48 populations, and used a Bayesian phylogeographic approach to infer possible areas of cladogenesis for these species and reconstruct historical and current dispersal routes among distinct populations. Our results show deep genetic divergence within and among all Sardinian cave salamander species, which can mostly be attributed to the effects of mountains and discontinuities in major calcareous areas and cave systems acting as barriers to gene flow. While these salamander species can also occur outside caves, our results indicate that there is a very poor dispersal of these species between separate cave systems.

  7. Effects of microhabitat and large-scale land use on stream salamander occupancy in the coalfields of Central Appalachia

    Science.gov (United States)

    Sweeten, Sara E.; Ford, W. Mark

    2016-01-01

    Large-scale coal mining practices, particularly surface coal extraction and associated valley fills as well as residential wastewater discharge, are of ecological concern for aquatic systems in central Appalachia. Identifying and quantifying alterations to ecosystems along a gradient of spatial scales is a necessary first-step to aid in mitigation of negative consequences to aquatic biota. In central Appalachian headwater streams, apart from fish, salamanders are the most abundant vertebrate predator that provide a significant intermediate trophic role linking aquatic and terrestrial food webs. Stream salamander species are considered to be sensitive to aquatic stressors and environmental alterations, as past research has shown linkages among microhabitat parameters, large-scale land use such as urbanization and logging, and salamander abundances. However, there is little information examining these relationships between environmental conditions and salamander occupancy in the coalfields of central Appalachia. In the summer of 2013, 70 sites (sampled two to three times each) in the southwest Virginia coalfields were visited to collect salamanders and quantify stream and riparian microhabitat parameters. Using an information-theoretic framework, effects of microhabitat and large-scale land use on stream salamander occupancy were compared. The findings indicate that Desmognathus spp. occupancy rates are more correlated to microhabitat parameters such as canopy cover than to large-scale land uses. However, Eurycea spp. occupancy rates had a strong association with large-scale land uses, particularly recent mining and forest cover within the watershed. These findings suggest that protection of riparian habitats is an important consideration for maintaining aquatic systems in central Appalachia. If this is not possible, restoration riparian areas should follow guidelines using quick-growing tree species that are native to Appalachian riparian areas. These types of trees

  8. Salamander chytrid fungus (Batrachochytrium salamandrivorans) in the United States—Developing research, monitoring, and management strategies

    Science.gov (United States)

    Grant, Evan H. Campbell; Muths, Erin L.; Katz, Rachel A.; Canessa, Stefano; Adams, Michael J.; Ballard, Jennifer R.; Berger, Lee; Briggs, Cheryl J.; Coleman, Jeremy; Gray, Matthew J.; Harris, M. Camille; Harris, Reid N.; Hossack, Blake R.; Huyvaert, Kathryn P.; Kolby, Jonathan E.; Lips, Karen R.; Lovich, Robert E.; McCallum, Hamish I.; Mendelson, Joseph R.; Nanjappa, Priya; Olson, Deanna H.; Powers, Jenny G.; Richgels, Katherine L. D.; Russell, Robin E.; Schmidt, Benedikt R.; Spitzen-van der Sluijs, Annemarieke; Watry, Mary Kay; Woodhams, Douglas C.; White, C. LeAnn

    2016-01-20

    The recently (2013) identified pathogenic chytrid fungus, Batrachochytrium salamandrivorans (Bsal), poses a severe threat to the distribution and abundance of salamanders within the United States and Europe. Development of a response strategy for the potential, and likely, invasion of Bsal into the United States is crucial to protect global salamander biodiversity. A formal working group, led by Amphibian Research and Monitoring Initiative (ARMI) scientists from the U.S. Geological Survey (USGS) Patuxent Wildlife Research Center, Fort Collins Science Center, and Forest and Rangeland Ecosystem Science Center, was held at the USGS Powell Center for Analysis and Synthesis in Fort Collins, Colorado, United States from June 23 to June 25, 2015, to identify crucial Bsal research and monitoring needs that could inform conservation and management strategies for salamanders in the United States. Key findings of the workshop included the following: (1) the introduction of Bsal into the United States is highly probable, if not inevitable, thus requiring development of immediate short-term and long-term intervention strategies to prevent Bsal establishment and biodiversity decline; (2) management actions targeted towards pathogen containment may be ineffective in reducing the long-term spread of Bsal throughout the United States; and (3) early detection of Bsal through surveillance at key amphibian import locations, among high-risk wild populations, and through analysis of archived samples is necessary for developing management responses. Top research priorities during the preinvasion stage included the following: (1) deployment of qualified diagnostic methods for Bsal and establishment of standardized laboratory practices, (2) assessment of susceptibility for amphibian hosts (including anurans), and (3) development and evaluation of short- and long-term pathogen intervention and management strategies. Several outcomes were achieved during the workshop, including development

  9. Transcriptional and phylogenetic analysis of five complete ambystomatid salamander mitochondrial genomes.

    Science.gov (United States)

    Samuels, Amy K; Weisrock, David W; Smith, Jeramiah J; France, Katherine J; Walker, John A; Putta, Srikrishna; Voss, S Randal

    2005-04-11

    We report on a study that extended mitochondrial transcript information from a recent EST project to obtain complete mitochondrial genome sequence for 5 tiger salamander complex species (Ambystoma mexicanum, A. t. tigrinum, A. andersoni, A. californiense, and A. dumerilii). We describe, for the first time, aspects of mitochondrial transcription in a representative amphibian, and then use complete mitochondrial sequence data to examine salamander phylogeny at both deep and shallow levels of evolutionary divergence. The available mitochondrial ESTs for A. mexicanum (N=2481) and A. t. tigrinum (N=1205) provided 92% and 87% coverage of the mitochondrial genome, respectively. Complete mitochondrial sequences for all species were rapidly obtained by using long distance PCR and DNA sequencing. A number of genome structural characteristics (base pair length, base composition, gene number, gene boundaries, codon usage) were highly similar among all species and to other distantly related salamanders. Overall, mitochondrial transcription in Ambystoma approximated the pattern observed in other vertebrates. We inferred from the mapping of ESTs onto mtDNA that transcription occurs from both heavy and light strand promoters and continues around the entire length of the mtDNA, followed by post-transcriptional processing. However, the observation of many short transcripts corresponding to rRNA genes indicates that transcription may often terminate prematurely to bias transcription of rRNA genes; indeed an rRNA transcription termination signal sequence was observed immediately following the 16S rRNA gene. Phylogenetic analyses of salamander family relationships consistently grouped Ambystomatidae in a clade containing Cryptobranchidae and Hynobiidae, to the exclusion of Salamandridae. This robust result suggests a novel alternative hypothesis because previous studies have consistently identified Ambystomatidae and Salamandridae as closely related taxa. Phylogenetic analyses of tiger

  10. Physical condition, sex, and age-class of eastern red-backed salamanders (Plethodon cinereus) in forested and open habitats of West Virginia, USA

    Science.gov (United States)

    Breanna L. Riedel; Kevin R. Russell; W. Mark Ford

    2012-01-01

    Nonforested habitats such as open fields and pastures have been considered unsuitable for desiccation-prone woodland salamanders such as the Eastern Red-backed Salamander (Plethodon cinereus). Recent research has suggested that Plethodon cinereus may not only disperse across but also reside within open habitats including fields,...

  11. Efficacy of riparian buffers in mitigating local populations declines and the effects of even-aged timber harvest on larval salamanders

    Science.gov (United States)

    William E Peterman; Raymond D. Semlitch

    2009-01-01

    Headwater streams are an important and prevalent feature of the eastern North American landscape.These streams provide a wealth of ecosystem services and support tremendous biological diversity, which is predominated by salamanders in the Appalachian region. Salamanders are ubiquitous throughout the region, contributing a significant...

  12. Toxicological responses of red-backed salamanders (Plethodon cinereus) to subchronic soil exposures of 2,4-dinitrotoluene

    International Nuclear Information System (INIS)

    Johnson, Mark S.; Suski, Jamie; Bazar, Matthew A.

    2007-01-01

    Dinitrotoluenes are used as propellants and in explosives by the military and as such have been found at relatively high concentrations in the soil. To determine whether concentrations of 2,4-dinitrotoluene (2,4-DNT) in soil are toxic to amphibians, 100 red-backed salamanders (Plethodon cinereus) were exposed to either 1500, 800, 200, 75 or 0 mg 2,4-DNT/kg soil for 28 days and evaluated for indicators of toxicity. Concentrations of 2,4-DNT were less than targets and varied with time. Most salamanders exposed to concentrations exceeding 1050 mg/kg died or were moribund within the first week. Salamanders exposed to soil concentrations exceeding 345 mg/kg lost >6% of their body mass though no mortality occurred. Overt effects included a reduction in feed consumption and an increase in bucco-pharyngeal oscillations in salamanders. These results suggest that only high soil concentrations of 2,4-DNT have the potential to cause overtly toxic effects in terrestrial salamanders. - Exposures of 2,4-dinitrotoluene in soil exceeding 345 mg/kg causes toxicity to P. cinereus

  13. Historical dominance of low-severity fire in dry and wet mixed-conifer forest habitats of the endangered terrestrial Jemez Mountains salamander (Plethodon neomexicanus)

    Science.gov (United States)

    Margolis, Ellis; Malevich, Steven B.

    2016-01-01

    Anthropogenic alteration of ecosystem processes confounds forest management and conservation of rare, declining species. Restoration of forest structure and fire hazard reduction are central goals of forest management policy in the western United States, but restoration priorities and treatments have become increasingly contentious. Numerous studies have documented changes in fire regimes, forest stand structure and species composition following a century of fire exclusion in dry, frequent-fire forests of the western U.S. (e.g., ponderosa pine and dry mixed-conifer). In contrast, wet mixed-conifer forests are thought to have historically burned infrequently with mixed- or high-severity fire—resulting in reduced impacts from fire exclusion and low restoration need—but data are limited. In this study we quantified the current forest habitat of the federally endangered, terrestrial Jemez Mountains salamander (Plethodon neomexicanus) and compared it to dendroecological reconstructions of historical habitat (e.g., stand structure and composition), and fire regime parameters along a gradient from upper ponderosa pine to wet mixed-conifer forests. We found that current fire-free intervals in Jemez Mountains salamander habitat (116–165 years) are significantly longer than historical intervals, even in wet mixed-conifer forests. Historical mean fire intervals ranged from 10 to 42 years along the forest gradient. Low-severity fires were historically dominant across all forest types (92 of 102 fires). Although some mixed- or highseverity fire historically occurred at 67% of the plots over the last four centuries, complete mortality within 1.0 ha plots was rare, and asynchronous within and among sites. Climate was an important driver of temporal variability in fire severity, such that mixed- and high-severity fires were associated with more extreme drought than low-severity fires. Tree density in dry conifer forests historically ranged from open (90 trees/ha) to

  14. The INCA trial (Impact of NOD2 genotype-guided antibiotic prevention on survival in patients with liver Cirrhosis and Ascites): study protocol for a randomized controlled trial.

    Science.gov (United States)

    Casper, Markus; Mengel, Martin; Fuhrmann, Christine; Herrmann, Eva; Appenrodt, Beate; Schiedermaier, Peter; Reichert, Matthias; Bruns, Tony; Engelmann, Cornelius; Grünhage, Frank; Lammert, Frank

    2015-03-08

    Patients with liver cirrhosis have a highly elevated risk of developing bacterial infections that significantly decrease survival rates. One of the most relevant infections is spontaneous bacterial peritonitis (SBP). Recently, NOD2 germline variants were found to be potential predictors of the development of infectious complications and mortality in patients with cirrhosis. The aim of the INCA (Impact of NOD2 genotype-guided antibiotic prevention on survival in patients with liver Cirrhosis and Ascites) trial is to investigate whether survival of this genetically defined high-risk group of patients with cirrhosis defined by the presence of NOD2 variants is improved by primary antibiotic prophylaxis of SBP. The INCA trial is a double-blind, placebo-controlled clinical trial with two parallel treatment arms (arm 1: norfloxacin 400 mg once daily; arm 2: placebo once daily; 12-month treatment and observational period). Balanced randomization of 186 eligible patients with stratification for the protein content of the ascites (INCA trial is first in the field of hepatology aimed at rapidly transferring and validating information on individual genetic risk into clinical decision algorithms. German Clinical Trials Register DRKS00005616 . Registered 22 January 2014. EU Clinical Trials Register EudraCT 2013-001626-26 . Registered 26 January 2015.

  15. Impact Of Thermotherapy And Chlorothalonil On Plantlets Production Of Some Genotypes Of Cassava Manihot Esculenta Crantz Produce In Benin

    Directory of Open Access Journals (Sweden)

    J.A.

    2017-01-01

    Full Text Available Cassava Manihot esculenta is a starchy root plant of great economic importance in sub-Saharan Africa and particularly in Benin. Its production is confronted to virus diseases which cause a considerable losses of yield. This work aims to determine the impact of thermotherapy and chlorothalonil in the production of cassava material of plantation. Cuttings of four varieties RB89509 BEN86052 9102319 92B0057 are cultivated under two conditions of thermotherapy and a control under greenhouse during 4 weeks. These different conditions are a closed drying oven with 16 hours photoperiod at 40 C the day and 36C the night a drying oven Binder with photoperiod of 12 hours at 38C the day and 28C the night and the control carried out under the conditions of the greenhouse. The media used was Murashige and Skoog MS added with various amounts of chlorothalonil 0.6 gl and 2gl and control without chlorothalonil. Both techniques of thermotherapy eliminate the virus symptoms of cassava at the rate of 0 seedling infected in thermotherapy against 16 seedlings in natural condition. The technique of closed drying oven significantly favors the production of nodes at 5 level p0.000 and shoots p0.02 on the other hand Binder drying oven has no significant effect on the production of shoots p0.68. The chlorothalonil had a positive effect on in vitro infestations elimination of cassava p0.05 but influenced the growth and development of cassava explants by reducing of nodes production p0.01 without a lethal effect on the plantlets until the dose of 2gl.

  16. Informing recovery in a human-transformed landscape: Drought-mediated coexistence alters population trends of an imperiled salamander and invasive predators

    Science.gov (United States)

    Hossack, Blake R.; Honeycutt, Richard; Sigafus, Brent H.; Muths, Erin L.; Crawford, Catherine L.; Jones, Thomas R.; Sorensen, Jeff A.; Rorabaugh, James C.; Chambert, Thierry

    2017-01-01

    Understanding the additive or interactive threats of habitat transformation and invasive species is critical for conservation, especially where climate change is expected to increase the severity or frequency of drought. In the arid southwestern USA, this combination of stressors has caused widespread declines of native aquatic and semi-aquatic species. Achieving resilience to drought and other effects of climate change may depend upon continued management, so understanding the combined effects of stressors is important. We used Bayesian hierarchical models fitted with 10-years of pond-based monitoring surveys for the federally-endangered Sonoran Tiger Salamander (Ambystoma mavortium stebbinsi) and invasive predators (fishes and American Bullfrogs, Lithobates catesbeianus) that threaten native species. We estimated trends in occupancy of salamanders and invasive predators while accounting for hydrological dynamics of ponds, then used a two-species interaction model to directly estimate how invasive predators affected salamander occupancy. We also tested a conceptual model that predicted that drought, by limiting the distribution of invasive predators, could ultimately benefit native species. Even though occupancy of invasive predators was stationary and their presence in a pond reduced the probability of salamander presence by 23%, occupancy of Sonoran Tiger Salamanders increased, annually, by 2.2%. Occupancy of salamanders and invasive predators both declined dramatically following the 5th consecutive year of drought. Salamander occupancy recovered quickly after return to non-drought conditions, while occupancy of invasive predators remained suppressed. Models that incorporated three time-lagged periods (1 to 4 years) of local moisture conditions confirmed that salamanders and invasive predators responded differently to drought, reflecting how life-history strategies shape responses to disturbances. The positive 10-year trend in salamander occupancy and their

  17. Decoding noises in HIV computational genotyping.

    Science.gov (United States)

    Jia, MingRui; Shaw, Timothy; Zhang, Xing; Liu, Dong; Shen, Ye; Ezeamama, Amara E; Yang, Chunfu; Zhang, Ming

    2017-11-01

    Lack of a consistent and reliable genotyping system can critically impede HIV genomic research on pathogenesis, fitness, virulence, drug resistance, and genomic-based healthcare and treatment. At present, mis-genotyping, i.e., background noises in molecular genotyping, and its impact on epidemic surveillance is unknown. For the first time, we present a comprehensive assessment of HIV genotyping quality. HIV sequence data were retrieved from worldwide published records, and subjected to a systematic genotyping assessment pipeline. Results showed that mis-genotyped cases occurred at 4.6% globally, with some regional and high-risk population heterogeneities. Results also revealed a consistent mis-genotyping pattern in gp120 in all studied populations except the group of men who have sex with men. Our study also suggests novel virus diversities in the mis-genotyped cases. Finally, this study reemphasizes the importance of implementing a standardized genotyping pipeline to avoid genotyping disparity and to advance our understanding of virus evolution in various epidemiological settings. Copyright © 2017 Elsevier Inc. All rights reserved.

  18. Cave exploitation by an usual epigean species: a review on the current knowledge on fire salamander breeding in cave

    Directory of Open Access Journals (Sweden)

    Raoul Manenti

    2017-11-01

    Full Text Available The fire salamander (Salamandra salamandra is a relatively common epigean amphibian, widely distributed throughout Europe, which usually gives birth to aquatic larvae. Even if epigean streams represent the most common places in which the species breeds, in some countries caves with underground waters are also used. To improve our understanding of the habitat features allowing successful breeding of salamanders in underground sites, we combined an exhaustive review of the available literature, especially the grey one, with direct observations performed from 2008 to 2017 in several natural and artificial caves of Lombardy, Liguria and Tuscany (Italy, Ariège and Provence (France. We provide a synthesis of published and unpublished caves in which the fire salamander breeding has been observed, along with a synthesis of the investigated ecological, behavioural and morphological traits. The use of underground sites is reported in several published papers and appears to be a common phenomenon not limited to single karst areas. The absence of predators, the relative stability of the aquatic habitats and the possibility to exploit new ecological resources are environmental factors that favour the breeding of the fire salamander. Our synthesis suggests that breeding of fire salamanders in caves is not a random event, but a widespread phenomenon that may be linked to specific biogeographical factors. Further insights may be obtained by performing genetic analyses on both cave and epigean populations, and considering larger landscape scales for ecological studies as well. Gene flow between salamanders that breed in caves and in streams probably occurs, but on the other hand, assortative mating might limit it, thus allowing the conservation of local adaptations driving successful cave colonisation.

  19. In search of critically endangered species: the current situation of two tiny salamander species in the Neotropical mountains of Mexico.

    Directory of Open Access Journals (Sweden)

    Adriana Sandoval-Comte

    Full Text Available Worldwide, one in every three species of amphibian is endangered, 39 species have gone extinct in the last 500 years and another 130 species are suspected to have gone extinct in recent decades. Of the amphibians, salamanders have the highest portion of their species in one of the risk categories, even higher than the frogs. To date there have been few studies that have used recent field data to examine the status of populations of endangered salamanders. In this study we evaluate the current situation of two tiny salamanders, Parvimolge townsendi and Thorius pennatulus, both of which are distributed at intermediate elevations in the mountains of the northern Neotropics and are considered to be critically endangered; the first has been proposed as possibly extinct. By carrying out exhaustive surveys in both historical and potentially suitable sites for these two species, we evaluated their abundance and the characteristics of their habitats, and we estimated their potential geographic distribution. We visited 22 sites, investing 672 person-hours of sampling effort in the surveys, and found 201 P. townsendi salamanders in 11 sites and only 13 T. pennatulus salamanders in 5 sites. Both species were preferentially found in cloud forest fragments that were well conserved or only moderately transformed, and some of the salamanders were found in shade coffee plantations. The potential distribution area of both species is markedly fragmented and we estimate that it has decreased by more than 48%. The results of this study highlight the importance of carrying out exhaustive, systematic field surveys to obtain accurate information about the current situation of critically endangered species, and help us better understand the crisis that amphibians are facing worldwide.

  20. In search of critically endangered species: the current situation of two tiny salamander species in the Neotropical mountains of Mexico.

    Science.gov (United States)

    Sandoval-Comte, Adriana; Pineda, Eduardo; Aguilar-López, José L

    2012-01-01

    Worldwide, one in every three species of amphibian is endangered, 39 species have gone extinct in the last 500 years and another 130 species are suspected to have gone extinct in recent decades. Of the amphibians, salamanders have the highest portion of their species in one of the risk categories, even higher than the frogs. To date there have been few studies that have used recent field data to examine the status of populations of endangered salamanders. In this study we evaluate the current situation of two tiny salamanders, Parvimolge townsendi and Thorius pennatulus, both of which are distributed at intermediate elevations in the mountains of the northern Neotropics and are considered to be critically endangered; the first has been proposed as possibly extinct. By carrying out exhaustive surveys in both historical and potentially suitable sites for these two species, we evaluated their abundance and the characteristics of their habitats, and we estimated their potential geographic distribution. We visited 22 sites, investing 672 person-hours of sampling effort in the surveys, and found 201 P. townsendi salamanders in 11 sites and only 13 T. pennatulus salamanders in 5 sites. Both species were preferentially found in cloud forest fragments that were well conserved or only moderately transformed, and some of the salamanders were found in shade coffee plantations. The potential distribution area of both species is markedly fragmented and we estimate that it has decreased by more than 48%. The results of this study highlight the importance of carrying out exhaustive, systematic field surveys to obtain accurate information about the current situation of critically endangered species, and help us better understand the crisis that amphibians are facing worldwide.

  1. Propulsive forces of mudskipper fins and salamander limbs during terrestrial locomotion: implications for the invasion of land.

    Science.gov (United States)

    Kawano, Sandy M; Blob, Richard W

    2013-08-01

    The invasion of land was a pivotal event in vertebrate evolution that was associated with major appendicular modifications. Although fossils indicate that the evolution of fundamentally limb-like appendages likely occurred in aquatic environments, the functional consequences of using early digited limbs, rather than fins, for terrestrial propulsion have had little empirical investigation. Paleontological and experimental analyses both have led to the proposal of an early origin of "hind limb-driven" locomotion among tetrapods or their ancestors. However, the retention of a pectoral appendage that had already developed terrestrial adaptations has been proposed for some taxa, and few data are available from extant functional models that can provide a foundation for evaluating the relative contributions of pectoral and pelvic appendages to terrestrial support among early stem tetrapods. To examine these aspects of vertebrate locomotor evolution during the invasion of land, we measured three-dimensional ground reaction forces (GRFs) produced by isolated pectoral fins of mudskipper fishes (Periophthalmus barbarus) during terrestrial crutching, and compared these to isolated walking footfalls by the forelimbs and hind limbs of tiger salamanders (Ambystoma tigrinum), a species with subequally-sized limbs that facilitate comparisons to early tetrapods. Pectoral appendages of salamanders and mudskippers exhibited numerous differences in GRFs. Compared with salamander forelimbs, isolated fins of mudskippers bear lower vertical magnitudes of GRFs (as a proportion of body weight), and had GRFs that were oriented more medially. Comparing the salamanders' forelimbs and hind limbs, although the peak net GRF occurs later in stance for the forelimb, both limbs experience nearly identical mediolateral and vertical components of GRF, suggesting comparable contributions to support. Thus, forelimbs could also have played a significant locomotor role among basal tetrapods that had limbs

  2. Dose rate estimation of the Tohoku hynobiid salamander, Hynobius lichenatus, in Fukushima.

    Science.gov (United States)

    Fuma, Shoichi; Ihara, Sadao; Kawaguchi, Isao; Ishikawa, Takahiro; Watanabe, Yoshito; Kubota, Yoshihisa; Sato, Youji; Takahashi, Hiroyuki; Aono, Tatsuo; Ishii, Nobuyoshi; Soeda, Haruhi; Matsui, Kumi; Une, Yumi; Minamiya, Yukio; Yoshida, Satoshi

    2015-05-01

    The radiological risks to the Tohoku hynobiid salamanders (class Amphibia), Hynobius lichenatus due to the Fukushima Dai-ichi Nuclear Power Plant accident were assessed in Fukushima Prefecture, including evacuation areas. Aquatic egg clutches (n = 1 for each sampling date and site; n = 4 in total), overwintering larvae (n = 1-5 for each sampling date and site; n = 17 in total), and terrestrial juveniles or adults (n = 1 or 3 for each sampling date and site; n = 12 in total) of H. lichenatus were collected from the end of April 2011 to April 2013. Environmental media such as litter (n = 1-5 for each sampling date and site; n = 30 in total), soil (n = 1-8 for each sampling date and site; n = 31 in total), water (n = 1 for each sampling date and site; n = 17 in total), and sediment (n = 1 for each sampling date and site; n = 17 in total) were also collected. Activity concentrations of (134)Cs + (137)Cs were 1.9-2800, 0.13-320, and 0.51-220 kBq (dry kg) (-1) in the litter, soil, and sediment samples, respectively, and were 0.31-220 and <0.29-40 kBq (wet kg)(-1) in the adult and larval salamanders, respectively. External and internal absorbed dose rates to H. lichenatus were calculated from these activity concentration data, using the ERICA Assessment Tool methodology. External dose rates were also measured in situ with glass dosimeters. There was agreement within a factor of 2 between the calculated and measured external dose rates. In the most severely contaminated habitat of this salamander, a northern part of Abukuma Mountains, the highest total dose rates were estimated to be 50 and 15 μGy h(-1) for the adults and overwintering larvae, respectively. Growth and survival of H. lichenatus was not affected at a dose rate of up to 490 μGy h(-1) in the previous laboratory chronic gamma-irradiation experiment, and thus growth and survival of this salamander would not be affected, even in the most severely contaminated habitat in Fukushima Prefecture. However, further

  3. The impact of IL28B genotype on the gene expression profile of patients with chronic hepatitis C treated with pegylated interferon alpha and ribavirin

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    Younossi Zobair M

    2012-02-01

    Full Text Available Abstract Background Recent studies of CH-C patients have demonstrated a strong association between IL28B CC genotype and sustained virologic response (SVR after PEG-IFN/RBV treatment. We aimed to assess whether IL28B alleles rs12979860 genotype influences gene expression in response to PEG-IFN/RBV in CH-C patients. Methods Clinical data and gene expression data were available for 56 patients treated with PEG-IFN/RBV. Whole blood was used to determine IL28B genotypes. Differential expression of 153 human genes was assessed for each treatment time point (Days: 0, 1, 7, 28, 56 and was correlated with IL28B genotype (IL28B C/C or non-C/C over the course of the PEG-IFN/RBV treatment. Genes with statistically significant changes in their expression at each time point were used as an input for pathway analysis using KEGG Pathway Painter (KPP. Pathways were ranked based on number of gene involved separately per each study cohort. Results The most striking difference between the response patterns of patients with IL28B C/C and T* genotypes during treatment, across all pathways, is a sustained pattern of treatment-induced gene expression in patients carrying IL28B C/C. In the case of IL28B T* genotype, pre-activation of genes, the lack of sustained pattern of gene expression or a combination of both were observed. This observation could potentially provide an explanation for the lower rate of SVR observed in these patients. Additionally, when the lists of IL28B genotype-specific genes which were differentially expressed in patients without SVR were compared at their baseline, IRF2 and SOCS1 genes were down-regulated regardless of patients' IL28B genotype. Furthermore, our data suggest that CH-C patients who do not have the SOCS1 gene silenced have a better chance of achieving SVR. Our observations suggest that the action of SOCS1 is independent of IL28B genotype. Conclusions IL28B CC genotype patients with CH-C show a sustained treatment-induced gene

  4. The impact of IL28B genotype on the gene expression profile of patients with chronic hepatitis C treated with pegylated interferon alpha and ribavirin.

    Science.gov (United States)

    Younossi, Zobair M; Birerdinc, Aybike; Estep, Mike; Stepanova, Maria; Afendy, Arian; Baranova, Ancha

    2012-02-07

    Recent studies of CH-C patients have demonstrated a strong association between IL28B CC genotype and sustained virologic response (SVR) after PEG-IFN/RBV treatment. We aimed to assess whether IL28B alleles rs12979860 genotype influences gene expression in response to PEG-IFN/RBV in CH-C patients. Clinical data and gene expression data were available for 56 patients treated with PEG-IFN/RBV. Whole blood was used to determine IL28B genotypes. Differential expression of 153 human genes was assessed for each treatment time point (Days: 0, 1, 7, 28, 56) and was correlated with IL28B genotype (IL28B C/C or non-C/C) over the course of the PEG-IFN/RBV treatment. Genes with statistically significant changes in their expression at each time point were used as an input for pathway analysis using KEGG Pathway Painter (KPP). Pathways were ranked based on number of gene involved separately per each study cohort. The most striking difference between the response patterns of patients with IL28B C/C and T* genotypes during treatment, across all pathways, is a sustained pattern of treatment-induced gene expression in patients carrying IL28B C/C. In the case of IL28B T* genotype, pre-activation of genes, the lack of sustained pattern of gene expression or a combination of both were observed. This observation could potentially provide an explanation for the lower rate of SVR observed in these patients. Additionally, when the lists of IL28B genotype-specific genes which were differentially expressed in patients without SVR were compared at their baseline, IRF2 and SOCS1 genes were down-regulated regardless of patients' IL28B genotype. Furthermore, our data suggest that CH-C patients who do not have the SOCS1 gene silenced have a better chance of achieving SVR. Our observations suggest that the action of SOCS1 is independent of IL28B genotype. IL28B CC genotype patients with CH-C show a sustained treatment-induced gene expression profile which is not seen in non-CC genotype patients

  5. Modelling cross-scale relationships between climate, hydrology, and individual animals: Generating scenarios for stream salamanders

    Directory of Open Access Journals (Sweden)

    Philippe eGirard

    2015-07-01

    Full Text Available Hybrid modelling provides a unique opportunity to study cross-scale relationships in environmental systems by linking together models of global, regional, landscape, and local-scale processes, yet the approach is rarely applied to address conservation and management questions. Here, we demonstrate how a hybrid modelling approach can be used to assess the effect of cross-scale interactions on the survival of the Allegheny Mountain Dusky Salamander (Desmognathus ochrophaeus in response to changes in temperature and water availability induced by climate change at the northern limits of its distribution. To do so, we combine regional climate modelling with a landscape-scale integrated surface-groundwater flow model and an individual-based model of stream salamanders. On average, climate scenarios depict a warmer and wetter environment for the 2050 horizon. The increase in average annual temperature and extended hydrological activity time series in the future, combined with a better synchronization with the salamanders’ reproduction period, result in a significant increase in the long-term population viability of the salamanders. This indicates that climate change may not necessarily limit the survivability of small, stream-dwelling animals in headwater basins located in cold and humid regions. This new knowledge suggests that habitat conservation initiatives for amphibians with large latitudinal distributions in Eastern North America should be prioritized at the northern limits of their ranges to facilitate species migration and persistence in the face of climate change. This example demonstrates how hybrid models can serve as powerful tools for informing management and conservation decisions.

  6. Mechanics of lung ventilation in a large aquatic salamander, siren lacertina

    Science.gov (United States)

    Brainerd; j

    1998-06-01

    Lung ventilation in Siren lacertina was studied using X-ray video, measurements of body cavity pressure and electromyography of hypaxial muscles. S. lacertina utilizes a two-stroke buccal pump in which mixing of expired and inspired gas is minimized by partial expansion of the buccal cavity during exhalation and then full expansion after exhalation is complete. Mixing is further reduced by the use of one or two accessory inspirations after the first, mixed-gas cycle. Exhalation occurs in two phases: a passive phase in which hydrostatic pressure and possibly lung elasticity force air out of the lungs, and an active phase in which contraction of the transverse abdominis (TA) muscle increases body cavity pressure and forces most of the remaining air out. In electromyograms of the lateral hypaxial musculature, the TA became active 200-400 ms before the rise in body cavity pressure, and activity ceased at peak pressure. The TA was not active during inspiration, and no consistent activity during breathing was noted in the external oblique, internal oblique and rectus abdominis muscles. The finding that the TA is the primary expiratory muscle in S. lacertina agrees with findings in a previous study of another salamander, Necturus maculosus. Together, these results indicate that the use of the TA for exhalation is a primitive character for salamanders and support the hypothesis that the breathing mechanism of salamanders represents an intermediate step in evolution between a buccal pump, in which only head muscles are used for ventilation, and an aspiration pump, in which axial muscles are used for both exhalation and inhalation.

  7. Vapour pressure deficit during growth has little impact on genotypic differences of transpiration efficiency at leaf and whole-plant level: an example from Populus nigra L.

    Science.gov (United States)

    Rasheed, Fahad; Dreyer, Erwin; Richard, Béatrice; Brignolas, Franck; Brendel, Oliver; Le Thiec, Didier

    2015-04-01

    Poplar genotypes differ in transpiration efficiency (TE) at leaf and whole-plant level under similar conditions. We tested whether atmospheric vapour pressure deficit (VPD) affected TE to the same extent across genotypes. Six Populus nigra genotypes were grown under two VPD. We recorded (1) (13)C content in soluble sugars; (2) (18)O enrichment in leaf water; (3) leaf-level gas exchange; and (4) whole-plant biomass accumulation and water use. Whole-plant and intrinsic leaf TE and (13)C content in soluble sugars differed significantly among genotypes. Stomatal conductance contributed more to these differences than net CO2 assimilation rate. VPD increased water use and reduced whole-plant TE. It increased intrinsic leaf-level TE due to a decline in stomatal conductance. It also promoted higher (18)O enrichment in leaf water. VPD had no genotype-specific effect. We detected a deviation in the relationship between (13)C in leaf sugars and (13)C predicted from gas exchange and the standard discrimination model. This may be partly due to genotypic differences in mesophyll conductance, and to its lack of sensitivity to VPD. Leaf-level (13)C discrimination was a powerful predictor of the genetic variability of whole-plant TE irrespective of VPD during growth. © 2014 John Wiley & Sons Ltd.

  8. Impact of obesity on the bioavailability of peginterferon-α2a and ribavirin and treatment outcome for chronic hepatitis C genotype 2 or 3.

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    Åsa Alsiö

    Full Text Available BACKGROUND AND AIMS: Having a body mass index above or equal to 30 kg/m(2 in conjunction with chronic hepatitis C virus infection is associated with non-responsiveness to treatment with interferon and ribavirin, but details regarding the mechanisms whereby obesity reduces the efficacy of therapy remain unclear. METHODS: This study evaluated impact of obesity on outcome as well as interferon and ribavirin concentrations following standard-of-care fixed dosing with peginterferon-α2a 180 µg once weekly and ribavirin 800 mg daily among 303 HCV genotype 2/3-infected patients enrolled in the per-protocol analysis of a recently completed phase III trial (NORDynamIC. RESULTS: Patients with BMI ≥30 kg/m(2 showed poorer outcome following 24 weeks of therapy (SVR 62% vs. 89% for BMI ≥30 vs. <30; P = 0.006 along with significantly higher steatosis grade (P = 0.002, HOMA-IR (P<0.0001, triglyceride levels (P = 0.0002, and baseline viral load (P = 0.028. Obesity was also significantly associated with lower plasma interferon concentrations on days 3, 7, and 29 (P = 0.02, P = 0.0017, and P<0.0001, respectively and lower plasma ribavirin concentrations day 29 (P = 0.025, and lower concentration of interferon in turn was associated with a poorer first phase reduction in HCV RNA (P<0.0001. In multivariate analysis, ribavirin concentrations week 12, interferon concentrations day 29, and baseline HCV RNA levels were independent predictors of achieving SVR among patients treated for 24 weeks (n = 140. CONCLUSIONS: Reduced bioavailability of interferon and ribavirin along with higher baseline viral load are dominant risk factors for treatment failure in obese patients with chronic hepatitis C.

  9. Role of habitat complexity in predator-prey dynamics between an introduced fish and larval Long-toed Salamanders (Ambystoma macrodactylum)

    Science.gov (United States)

    Kenison, Erin K; Litt, Andrea R.; Pilliod, David S.; McMahon, Tom E

    2016-01-01

    Predation by nonnative fishes has reduced abundance and increased extinction risk for amphibian populations worldwide. Although rare, fish and palatable amphibians have been observed to coexist where aquatic vegetation and structural complexity provide suitable refugia. We examined whether larval long-toed salamanders (Ambystoma macrodactylum Baird, 1849) increased use of vegetation cover in lakes with trout and whether adding vegetation structure could reduce predation risk and nonconsumptive effects (NCEs), such as reductions in body size and delayed metamorphosis. We compared use of vegetation cover by larval salamanders in lakes with and without trout and conducted a field experiment to investigate the influence of added vegetation structure on salamander body morphology and life history. The probability of catching salamanders in traps in lakes with trout was positively correlated with the proportion of submerged vegetation and surface cover. Growth rates of salamanders in enclosures with trout cues decreased as much as 85% and the probability of metamorphosis decreased by 56%. We did not find evidence that adding vegetation reduced NCEs in experimental enclosures, but salamanders in lakes with trout utilized more highly-vegetated areas which suggests that adding vegetation structure at the scale of the whole lake may facilitate coexistence between salamanders and introduced trout.

  10. Predator cannibalism can intensify negative impacts on heterospecific prey.

    Science.gov (United States)

    Takatsu, Kunio; Kishida, Osamu

    2015-07-01

    Although natural populations consist of individuals with different traits, and the degree of phenotypic variation varies among populations, the impact of phenotypic variation on ecological interactions has received little attention, because traditional approaches to community ecology assume homogeneity of individuals within a population. Stage structure, which is a common way of generating size and developmental variation within predator populations, can drive cannibalistic interactions, which can affect the strength of predatory effects on the predator's heterospecific prey. Studies have shown that predator cannibalism weakens predatory effects on heterospecific prey by reducing the size of the predator population and by inducing less feeding activity of noncannibal predators. We predict, however, that predator cannibalism, by promoting rapid growth of the cannibals, can also intensify predation pressure on heterospecific prey, because large predators have large resource requirements and may utilize a wider variety of prey species. To test this hypothesis, we conducted an experiment in which we created carnivorous salamander (Hynobius retardatus) populations with different stage structures by manipulating the salamander's hatch timing (i.e., populations with large or small variation in the timing of hatching), and explored the resultant impacts on the abundance, behavior, morphology, and life history of the salamander's large heterospecific prey, Rana pirica frog tadpoles. Cannibalism was rare in salamander populations having small hatch-timing variation, but was frequent in those having large hatch-timing variation. Thus, giant salamander cannibals occurred only in the latter. We clearly showed that salamander giants exerted strong predation pressure on frog tadpoles, which induced large behavioral and morphological defenses in the tadpoles and caused them to metamorphose late at large size. Hence, predator cannibalism arising from large variation in the timing

  11. Estimating occurrence and detection probabilities for stream-breeding salamanders in the Gulf Coastal Plain

    Science.gov (United States)

    Lamb, Jennifer Y.; Waddle, J. Hardin; Qualls, Carl P.

    2017-01-01

    Large gaps exist in our knowledge of the ecology of stream-breeding plethodontid salamanders in the Gulf Coastal Plain. Data describing where these salamanders are likely to occur along environmental gradients, as well as their likelihood of detection, are important for the prevention and management of amphibian declines. We used presence/absence data from leaf litter bag surveys and a hierarchical Bayesian multispecies single-season occupancy model to estimate the occurrence of five species of plethodontids across reaches in headwater streams in the Gulf Coastal Plain. Average detection probabilities were high (range = 0.432–0.942) and unaffected by sampling covariates specific to the use of litter bags (i.e., bag submergence, sampling season, in-stream cover). Estimates of occurrence probabilities differed substantially between species (range = 0.092–0.703) and were influenced by the size of the upstream drainage area and by the maximum proportion of the reach that dried. The effects of these two factors were not equivalent across species. Our results demonstrate that hierarchical multispecies models successfully estimate occurrence parameters for both rare and common stream-breeding plethodontids. The resulting models clarify how species are distributed within stream networks, and they provide baseline values that will be useful in evaluating the conservation statuses of plethodontid species within lotic systems in the Gulf Coastal Plain.

  12. Computer-assisted photo identification outperforms visible implant elastomers in an endangered salamander, Eurycea tonkawae.

    Directory of Open Access Journals (Sweden)

    Nathan F Bendik

    Full Text Available Despite recognition that nearly one-third of the 6300 amphibian species are threatened with extinction, our understanding of the general ecology and population status of many amphibians is relatively poor. A widely-used method for monitoring amphibians involves injecting captured individuals with unique combinations of colored visible implant elastomer (VIE. We compared VIE identification to a less-invasive method - computer-assisted photographic identification (photoID - in endangered Jollyville Plateau salamanders (Eurycea tonkawae, a species with a known range limited to eight stream drainages in central Texas. We based photoID on the unique pigmentation patterns on the dorsal head region of 1215 individual salamanders using identification software Wild-ID. We compared the performance of photoID methods to VIEs using both 'high-quality' and 'low-quality' images, which were taken using two different camera types and technologies. For high-quality images, the photoID method had a false rejection rate of 0.76% compared to 1.90% for VIEs. Using a comparable dataset of lower-quality images, the false rejection rate was much higher (15.9%. Photo matching scores were negatively correlated with time between captures, suggesting that evolving natural marks could increase misidentification rates in longer term capture-recapture studies. Our study demonstrates the utility of large-scale capture-recapture using photo identification methods for Eurycea and other species with stable natural marks that can be reliably photographed.

  13. Cutaneous mastocytomas in the neotenic caudate amphibians Ambystoma mexicanum (axolotl) and Ambystoma tigrinun (tiger salamander)

    Science.gov (United States)

    Harshbarger, J.C.; Chang, S.C.; DeLanney, L.E.; Rose, F.L.; Green, D.E.

    1999-01-01

    Spontaneous mastocytomas studied in 18 axolotls (Ambystoma mexicanum) and six tiger salamanders (Ambystoma tigrinum) were gray-white, uni- to multilobular cutaneous protrusions from 2mm to 2cm in diameter. Tumors were moderately cellular unencapsulated masses that usually infiltrated the dermis and hypodermis with the destruction of intervening tissues. Some tumors were invading superficial bundles of the underlying skeletal muscle. Tumors consisted of mitotically active cells derived from a single lineage but showing a range of differentiation. Immature cells had nearly smooth to lightly cleft or folded basophilic nuclei bordered by a band of cytoplasm with few cytoplasmic processes and containing a few small uniform eccentric granules. Mature cells had basophilic nuclei with deep clefts or folds and abundant eosinophilic cytoplasm with multiple long intertwining cytoplasmic extensions packed with metachromatic granules. The axolotls were old individuals from an inbred laboratory colony. The tiger salamanders were wild animals from a single polluted pond. They could have been old and inbred. Both groups were neotenic. These are the first mastocytomas discovered in cold-blooded animals.

  14. Identification of Mutant Genes and Introgressed Tiger Salamander DNA in the Laboratory Axolotl, Ambystoma mexicanum.

    Science.gov (United States)

    Woodcock, M Ryan; Vaughn-Wolfe, Jennifer; Elias, Alexandra; Kump, D Kevin; Kendall, Katharina Denise; Timoshevskaya, Nataliya; Timoshevskiy, Vladimir; Perry, Dustin W; Smith, Jeramiah J; Spiewak, Jessica E; Parichy, David M; Voss, S Randal

    2017-01-31

    The molecular genetic toolkit of the Mexican axolotl, a classic model organism, has matured to the point where it is now possible to identify genes for mutant phenotypes. We used a positional cloning-candidate gene approach to identify molecular bases for two historic axolotl pigment phenotypes: white and albino. White (d/d) mutants have defects in pigment cell morphogenesis and differentiation, whereas albino (a/a) mutants lack melanin. We identified in white mutants a transcriptional defect in endothelin 3 (edn3), encoding a peptide factor that promotes pigment cell migration and differentiation in other vertebrates. Transgenic restoration of Edn3 expression rescued the homozygous white mutant phenotype. We mapped the albino locus to tyrosinase (tyr) and identified polymorphisms shared between the albino allele (tyr a ) and tyr alleles in a Minnesota population of tiger salamanders from which the albino trait was introgressed. tyr a has a 142 bp deletion and similar engineered alleles recapitulated the albino phenotype. Finally, we show that historical introgression of tyr a significantly altered genomic composition of the laboratory axolotl, yielding a distinct, hybrid strain of ambystomatid salamander. Our results demonstrate the feasibility of identifying genes for traits in the laboratory Mexican axolotl.

  15. Conservation genetics of extremely isolated urban populations of the northern dusky salamander (Desmognathus fuscus in New York City

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    Jason Munshi-South

    2013-04-01

    Full Text Available Urbanization is a major cause of amphibian decline. Stream-dwelling plethodontid salamanders are particularly susceptible to urbanization due to declining water quality and hydrological changes, but few studies have examined these taxa in cities. The northern dusky salamander (Desmognathus fuscus was once common in the New York City metropolitan area, but has substantially declined throughout the region in recent decades. We used five tetranucleotide microsatellite loci to examine population differentiation, genetic variation, and bottlenecks among five remnant urban populations of dusky salamanders in NYC. These genetic measures provide information on isolation, prevalence of inbreeding, long-term prospects for population persistence, and potential for evolutionary responses to future environmental change. All populations were genetically differentiated from each other, and the most isolated populations in Manhattan have maintained very little genetic variation (i.e. <20% heterozygosity. A majority of the populations also exhibited evidence of genetic bottlenecks. These findings contrast with published estimates of high genetic variation within and lack of structure between populations of other desmognathine salamanders sampled over similar or larger spatial scales. Declines in genetic variation likely resulted from population extirpations and the degradation of stream and terrestrial paths for dispersal in NYC. Loss of genetic variability in populations isolated by human development may be an underappreciated cause and/or consequence of the decline of this species in urbanized areas of the northeast USA.

  16. Impact of Harvesting Time and Length of Cold Storage Period On Physiological and Quality Traits of Four Quince Genotypes (Cydonia Oblonga Mill.

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    Tatari Maryam

    2017-06-01

    Full Text Available The investigation was conducted to determine the best harvesting time and the storage period of some quince cultivars and promising genotypes from the collection of quince germplasm in the Horticultural Research Station of Isfahan, Iran. For this study, fruits of ‘Vidoja’ and ‘Isfahan’ cultivars as well as promising genotypes PH2 and NB4 were harvested on 6, 14 and 21 October 2015 and 2016 and then stored at 0 ± 1 °C with 90 ± 5% R.H. for five months. Weight loss, firmness, total soluble solids (TSS, titrable acids (TA, taste index, pectin, total phenols, and percent of decay and surface browning of fruits were measured immediately after harvest and one-month intervals after storage in a factorial experiment based on a completely randomized design with three replications and 10 fruits per each replication. The results showed that ‘Isfahan’ cultivar had the highest TSS (18.83%, total phenols and weight loss. The least weight loss was observed in the ‘Vidoja’ cultivar. NB4 genotype showed the least taste index and pectin, while the most pectin and firmness was related to PH2 genotype. Generally, the delay in harvesting and prolongation of storage led to increasing of TSS and weight loss and declining of firmness and phenols, TA, and pectins. Until the third month of storage, there was no surface browning. Browning symptoms were observed from the fourth month of storage and increased in the fifth month up to 1.72%. Generally, the best harvesting time for ‘Vidoja’ was 185 days and for the rest of the genotypes, it was 193 days after full bloom. Fruit storage for four months in cold is advisable for these cultivars and genotypes.

  17. Impact of IL28B-Related Single Nucleotide Polymorphisms on Liver Histopathology in Chronic Hepatitis C Genotype 2 and 3

    DEFF Research Database (Denmark)

    Rembeck, Karolina; Alsiö, Asa; Christensen, Peer Brehm

    2012-01-01

    Recently, several genome-wide association studies have revealed that single nucleotide polymorphisms (SNPs) in proximity to IL28B predict spontaneous clearance of HCV infection as well as outcome following peginterferon and ribavirin therapy among HCV genotype 1 infected patients. The present stu...

  18. A Europe-wide experiment for assessing the impact of genotype-environment interactions on the vitality and performance of honey bee colonies

    DEFF Research Database (Denmark)

    Costa, Cecilia; Büchler, Ralph; Berg, Stefan

    2012-01-01

    An international experiment to estimate the importance of genotype-environment interactions on vitality and performance of honey bees and on colony losses was run between July 2009 and March 2012. Altogether 621 bee colonies, involving 16 different genetic origins of European honey bees, were...

  19. Chlorophyll fluorescence is a rigorous, high throughput tool to analyze the impacts of genotype, species, and stress on plant and ecosystem productivity

    Science.gov (United States)

    Ewers, B. E.; Pleban, J. R.; Aston, T.; Beverly, D.; Speckman, H. N.; Hosseini, A.; Bretfeld, M.; Edwards, C.; Yarkhunova, Y.; Weinig, C.; Mackay, D. S.

    2017-12-01

    Abiotic and biotic stresses reduce plant productivity, yet high-throughput characterization of plant responses across genotypes, species and stress conditions are limited by both instrumentation and data analysis techniques. Recent developments in chlorophyll a fluorescence measurement at leaf to landscape scales could improve our predictive understanding of plants response to stressors. We analyzed the interaction of species and stress across two crop types, five gymnosperm and two angiosperm tree species from boreal and montane forests, grasses, forbs and shrubs from sagebrush steppe, and 30 tree species from seasonally wet tropical forest. We also analyzed chlorophyll fluorescence and gas exchange data from twelve Brassica rapa crop accessions and 120 recombinant inbred lines to investigate phenotypic responses to drought. These data represent more than 10,000 measurements of fluorescence and allow us to answer two questions 1) are the measurements from high-throughput, hand held and drone-mounted instruments quantitatively similar to lower throughput camera and gas exchange mounted instruments and 2) do the measurements find differences in genotypic, species and environmental stress on plants? We found through regression that the high and low throughput instruments agreed across both individual chlorophyll fluorescence components and calculated ratios and were not different from a 1:1 relationship with correlation greater than 0.9. We used hierarchical Bayesian modeling to test the second question. We found a linear relationship between the fluorescence-derived quantum yield of PSII and the quantum yield of CO2 assimilation from gas-exchange, with a slope of ca. 0.1 indicating that the efficiency of the entire photosynthetic process was about 10% of PSII across genotypes, species and drought stress. Posterior estimates of quantum yield revealed that drought-treatment, genotype and species differences were preserved when accounting for measurement uncertainty

  20. Plethodontid salamander mitochondrial genomics: A parsimonyevaluation of character conflict and implications for historicalbiogeography

    Energy Technology Data Exchange (ETDEWEB)

    Macey, J. Robert

    2005-01-19

    A new parsimony analysis of 27 complete mitochondrial genomic sequences is conducted to investigate the phylogenetic relationships of plethodontid salamanders. This analysis focuses on the amount of character conflict between phylogenetic trees recovered from newly conducted parsimony searches and the Bayesian and maximum likelihood topology reported by Mueller et al. (2004, PNAS, 101, 13820-13825). Strong support for Hemidactylium as the sister taxon to all other plethodontids is recovered from parsimony analyses. Plotting area relationships on the most parsimonious phylogenetic tree suggests that eastern North America is the origin of the family Plethodontidae supporting the ''Out of Appalachia'' hypothesis. A new taxonomy that recognizes clades recovered from phylogenetic analyses is proposed.

  1. Randomized Trial Evaluating the Impact of Ribavirin Mono-Therapy and Double Dosing on Viral Kinetics, Ribavirin Pharmacokinetics and Anemia in Hepatitis C Virus Genotype 1 Infection

    DEFF Research Database (Denmark)

    Waldenström, Jesper; Westin, Johan; Nyström, Kristina

    2016-01-01

    In this pilot study (RibaC), 58 hepatitis C virus (HCV) genotype 1 infected treatment-naïve patients were randomized to (i) 2 weeks ribavirin double dosing concomitant with pegylated interferon-α (pegIFN-α), (ii) 4 weeks ribavirin mono-therapy prior to adding pegIFN-α, or (iii) standard-of-care (......In this pilot study (RibaC), 58 hepatitis C virus (HCV) genotype 1 infected treatment-naïve patients were randomized to (i) 2 weeks ribavirin double dosing concomitant with pegylated interferon-α (pegIFN-α), (ii) 4 weeks ribavirin mono-therapy prior to adding pegIFN-α, or (iii) standard......, by day 14, double dosing entailed a greater hemoglobin decline as compared to SOC (2.2 vs. 1.4 g/dL; P = 0.03). Conclusion: Ribavirin down-regulates IP-10, and may have an anti-viral effect differently regulated across IL28B genotypes....

  2. Hepatitis B virus genotypes circulating in Brazil: molecular characterization of genotype F isolates

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    Virgolino Helaine A

    2007-11-01

    Full Text Available Abstract Background Hepatitis B virus (HBV isolates have been classified in eight genotypes, A to H, which exhibit distinct geographical distributions. Genotypes A, D and F are predominant in Brazil, a country formed by a miscegenated population, where the proportion of individuals from Caucasian, Amerindian and African origins varies by region. Genotype F, which is the most divergent, is considered indigenous to the Americas. A systematic molecular characterization of HBV isolates from different parts of the world would be invaluable in establishing HBV evolutionary origins and dispersion patterns. A large-scale study is needed to map the region-by-region distribution of the HBV genotypes in Brazil. Results Genotyping by PCR-RFLP of 303 HBV isolates from HBsAg-positive blood donors showed that at least two of the three genotypes, A, D, and F, co-circulate in each of the five geographic regions of Brazil. No other genotypes were identified. Overall, genotype A was most prevalent (48.5%, and most of these isolates were classified as subgenotype A1 (138/153; 90.2%. Genotype D was the most common genotype in the South (84.2% and Central (47.6% regions. The prevalence of genotype F was low (13% countrywide. Nucleotide sequencing of the S gene and a phylogenetic analysis of 32 HBV genotype F isolates showed that a great majority (28/32; 87.5% belonged to subgenotype F2, cluster II. The deduced serotype of 31 of 32 F isolates was adw4. The remaining isolate showed a leucine-to-isoleucine substitution at position 127. Conclusion The presence of genotypes A, D and F, and the absence of other genotypes in a large cohort of HBV infected individuals may reflect the ethnic origins of the Brazilian population. The high prevalence of isolates from subgenotype A1 (of African origin indicates that the African influx during the colonial slavery period had a major impact on the circulation of HBV genotype A currently found in Brazil. Although most genotype F

  3. Habitat adaptation rather than genetic distance correlates with female preference in fire salamanders (Salamandra salamandra

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    Weitere Markus

    2009-06-01

    Full Text Available Abstract Background Although some mechanisms of habitat adaptation of conspecific populations have been recently elucidated, the evolution of female preference has rarely been addressed as a force driving habitat adaptation in natural settings. Habitat adaptation of fire salamanders (Salamandra salamandra, as found in Middle Europe (Germany, can be framed in an explicit phylogeographic framework that allows for the evolution of habitat adaptation between distinct populations to be traced. Typically, females of S. salamandra only deposit their larvae in small permanent streams. However, some populations of the western post-glacial recolonization lineage use small temporary ponds as larval habitats. Pond larvae display several habitat-specific adaptations that are absent in stream-adapted larvae. We conducted mate preference tests with females from three distinct German populations in order to determine the influence of habitat adaptation versus neutral genetic distance on female mate choice. Two populations that we tested belong to the western post-glacial recolonization group, but are adapted to either stream or pond habitats. The third population is adapted to streams but represents the eastern recolonization lineage. Results Despite large genetic distances with FST values around 0.5, the stream-adapted females preferred males from the same habitat type regardless of genetic distance. Conversely, pond-adapted females did not prefer males from their own population when compared to stream-adapted individuals of either lineage. Conclusion A comparative analysis of our data showed that habitat adaptation rather than neutral genetic distance correlates with female preference in these salamanders, and that habitat-dependent female preference of a specific pond-reproducing population may have been lost during adaptation to the novel environmental conditions of ponds.

  4. From biomedicine to natural history research: EST resources for ambystomatid salamanders

    Directory of Open Access Journals (Sweden)

    Bryant Susan V

    2004-08-01

    Full Text Available Abstract Background Establishing genomic resources for closely related species will provide comparative insights that are crucial for understanding diversity and variability at multiple levels of biological organization. We developed ESTs for Mexican axolotl (Ambystoma mexicanum and Eastern tiger salamander (A. tigrinum tigrinum, species with deep and diverse research histories. Results Approximately 40,000 quality cDNA sequences were isolated for these species from various tissues, including regenerating limb and tail. These sequences and an existing set of 16,030 cDNA sequences for A. mexicanum were processed to yield 35,413 and 20,599 high quality ESTs for A. mexicanum and A. t. tigrinum, respectively. Because the A. t. tigrinum ESTs were obtained primarily from a normalized library, an approximately equal number of contigs were obtained for each species, with 21,091 unique contigs identified overall. The 10,592 contigs that showed significant similarity to sequences from the human RefSeq database reflected a diverse array of molecular functions and biological processes, with many corresponding to genes expressed during spinal cord injury in rat and fin regeneration in zebrafish. To demonstrate the utility of these EST resources, we searched databases to identify probes for regeneration research, characterized intra- and interspecific nucleotide polymorphism, saturated a human – Ambystoma synteny group with marker loci, and extended PCR primer sets designed for A. mexicanum / A. t. tigrinum orthologues to a related tiger salamander species. Conclusions Our study highlights the value of developing resources in traditional model systems where the likelihood of information transfer to multiple, closely related taxa is high, thus simultaneously enabling both laboratory and natural history research.

  5. From biomedicine to natural history research: EST resources for ambystomatid salamanders

    Science.gov (United States)

    Putta, Srikrishna; Smith, Jeramiah J; Walker, John A; Rondet, Mathieu; Weisrock, David W; Monaghan, James; Samuels, Amy K; Kump, Kevin; King, David C; Maness, Nicholas J; Habermann, Bianca; Tanaka, Elly; Bryant, Susan V; Gardiner, David M; Parichy, David M; Voss, S Randal

    2004-01-01

    Background Establishing genomic resources for closely related species will provide comparative insights that are crucial for understanding diversity and variability at multiple levels of biological organization. We developed ESTs for Mexican axolotl (Ambystoma mexicanum) and Eastern tiger salamander (A. tigrinum tigrinum), species with deep and diverse research histories. Results Approximately 40,000 quality cDNA sequences were isolated for these species from various tissues, including regenerating limb and tail. These sequences and an existing set of 16,030 cDNA sequences for A. mexicanum were processed to yield 35,413 and 20,599 high quality ESTs for A. mexicanum and A. t. tigrinum, respectively. Because the A. t. tigrinum ESTs were obtained primarily from a normalized library, an approximately equal number of contigs were obtained for each species, with 21,091 unique contigs identified overall. The 10,592 contigs that showed significant similarity to sequences from the human RefSeq database reflected a diverse array of molecular functions and biological processes, with many corresponding to genes expressed during spinal cord injury in rat and fin regeneration in zebrafish. To demonstrate the utility of these EST resources, we searched databases to identify probes for regeneration research, characterized intra- and interspecific nucleotide polymorphism, saturated a human – Ambystoma synteny group with marker loci, and extended PCR primer sets designed for A. mexicanum / A. t. tigrinum orthologues to a related tiger salamander species. Conclusions Our study highlights the value of developing resources in traditional model systems where the likelihood of information transfer to multiple, closely related taxa is high, thus simultaneously enabling both laboratory and natural history research. PMID:15310388

  6. Effects of metamorphosis on the aquatic escape response of the two-lined salamander (Eurycea bislineata).

    Science.gov (United States)

    Azizi, Emanuel; Landberg, Tobias

    2002-03-01

    Although numerous studies have described the escape kinematics of fishes, little is known about the aquatic escape responses of salamanders. We compare the escape kinematics of larval and adult Eurycea bislineata, the two-lined salamander, to examine the effects of metamorphosis on aquatic escape performance. We hypothesize that shape changes associated with resorption of the larval tail fin at metamorphosis will affect aquatic locomotor performance. Escape responses were recorded using high-speed video, and the effects of life stage and total length on escape kinematics were analyzed statistically using analysis of covariance. Our results show that both larval and adult E. bislineata use a two-stage escape response (similar to the C-starts of fishes) that consists of a preparatory (stage 1) and a propulsive (stage 2) stroke. The duration of both kinematic stages and the distance traveled during stage 2 increased with total length. Both larval and adult E. bislineata had final escape trajectories that were directed away from the stimulus. The main kinematic difference between larvae and adults is that adults exhibit significantly greater maximum curvature during stage 1. Total escape duration and the distance traveled during stage 2 did not differ significantly between larvae and adults. Despite the significantly lower tail aspect ratio of adults, we found no significant decrease in the overall escape performance of adult E. bislineata. Our results suggest that adults may compensate for the decrease in tail aspect ratio by increasing their maximum curvature. These findings do not support the hypothesis that larvae exhibit better locomotor performance than adults as a result of stronger selective pressures on early life stages.

  7. The Impact of Five VDR Polymorphisms on Multiple Sclerosis Risk and Progression: a Case-Control and Genotype-Phenotype Study.

    Science.gov (United States)

    Křenek, Pavel; Benešová, Yvonne; Bienertová-Vašků, Julie; Vašků, Anna

    2018-04-01

    Vitamin D receptor polymorphisms have been the target of many studies focusing on multiple sclerosis. However, previously reported results have been inconclusive. The objective of this study was to investigate the association between five vitamin D receptor polymorphisms (EcoRV, FokI, ApaI, TaqI, and BsmI) and multiple sclerosis susceptibility and its course. The study was carried out as a case-control and genotype-phenotype study, consisted of 296 Czech multiple sclerosis patients and 135 healthy controls. Genotyping was carried out using polymerase chain reaction and restriction analysis. In multiple sclerosis men, allele and/or genotype distributions differed in EcoRV, TaqI, BsmI, and ApaI polymorphisms as compared to controls (EcoRV, p a = 0.02; Taq, p g = 0.02, p a = 0.02; BsmI, p g = 0.02, p a = 0.04; ApaI, p g = 0.008, p a = 0.005). In multiple sclerosis women, differences in the frequency of alleles and genotypes were found to be significant in ApaI (controls vs multiple sclerosis women: p g = 0.01, p a = 0.05). Conclusive results were observed between multiple sclerosis women in the case of EcoRV [differences in Expanded Disability Status Scale (p = 0.05); CT genotype was found to increase the risk of primary progressive multiple sclerosis 5.5 times (CT vs CC+TT p corr = 0.01, sensitivity 0.833, specificity 0.525, power test 0.823)] and FokI [borderline difference in Multiple Sclerosis Severity Score (p = 0.05)]. Our results indicate that the distribution of investigated vitamin D receptor polymorphisms is a risk factor for multiple sclerosis susceptibility and progression in the Czech population. The association between disease risk and polymorphisms was found to be stronger in men. The association of disease progression with polymorphisms was observed only in women.

  8. Effects of pH on embryo tolerance and adult behavior in the tiger salamander, Ambystoma tigrinum tigrinum

    Energy Technology Data Exchange (ETDEWEB)

    Whiteman, H H; Howard, R D; Whitten, K A [Purdue Univ., Lafayette, IN (United States). Dept. of Biological Sciences

    1995-08-01

    Adult discrimination ability and embryo performance was examined under different pH conditions in the eastern tiger salamander. Individuals from three populations were collected in habitats that differed naturally in pH. Two pH treatments were used to determine adult pH discrimination ability, and eight pH treatments to evaluate embryo performance. Results suggested that the pH of the source-population habitat could influence breeding-habitat discrimination by adults. Decreasing pH produced similar patterns of lethal and sublethal effects on embryos from the three populations, with reduced performance at low pH. The pH at which 50% mortality occurs was estimated at 4.2, suggesting that tiger salamanders were relatively acid tolerant. The study suggested that adult behavior patterns could influence the success of population reintroductions to previously acidified areas. 78 refs., 2 tabs., 4 figs.

  9. Transcriptomic analysis of endangered Chinese salamander: identification of immune, sex and reproduction-related genes and genetic markers.

    Directory of Open Access Journals (Sweden)

    Rongbo Che

    Full Text Available The Chinese salamander (Hynobius chinensis, an endangered amphibian species of salamander endemic to China, has attracted much attention because of its value of studying paleontology evolutionary history and decreasing population size. Despite increasing interest in the Hynobius chinensis genome, genomic resources for the species are still very limited. A comprehensive transcriptome of Hynobius chinensis, which will provide a resource for genome annotation, candidate genes identification and molecular marker development should be generated to supplement it.We performed a de novo assembly of Hynobius chinensis transcriptome by Illumina sequencing. A total of 148,510 nonredundant unigenes with an average length of approximately 580 bp were obtained. In all, 60,388 (40.66% unigenes showed homologous matches in at least one database and 33,537 (22.58% unigenes were annotated by all four databases. In total, 41,553 unigenes were categorized into 62 sub-categories by BLAST2GO search, and 19,468 transcripts were assigned to 140 KEGG pathways. A large number of unigenes involved in immune system, local adaptation, reproduction and sex determination were identified, as well as 31,982 simple sequence repeats (SSRs and 460,923 putative single nucleotide polymorphisms (SNPs.This dataset represents the first transcriptome analysis of the Chinese salamander (Hynobius chinensis, an endangered species, to be also the first time of hynobiidae. The transcriptome will provide valuable resource for further research in discovery of new genes, protection of population, adaptive evolution and survey of various pathways, as well as development of molecule markers in Chinese salamander; and reference information for closely related species.

  10. Sensory feedback plays a significant role in generating walking gait and in gait transition in salamanders: A simulation study

    Directory of Open Access Journals (Sweden)

    Nalin eHarischandra

    2011-11-01

    Full Text Available Here, we use a three-dimensional, neuro-musculo-mechanical model of a salamander with realistic physical parameters in order to investigate the role of sensory feedback in gait generation and transition. Activation of limb and axial muscles were driven by neural output patterns obtained from a central pattern generator (CPG which is composed of simulated spiking neurons with adaptation. The CPG consists of a body CPG and four limb CPGs that are interconnected via synapses both ipsilateraly and contralaterally. We use the model both with and without sensory modulation and for different combinations of ipsilateral and contralateral coupling between the limb CPGs. We found that the proprioceptive sensory inputs are essential in obtaining a coordinated walking gait. The sensory feedback includes the signals coming from the stretch receptor like intraspinal neurons located in the girdle regions and the limb stretch receptors residing in the hip and scapula regions of the salamander. On the other hand, coordinated motor output patterns for the trotting gait were obtainable without the sensory inputs. We found that the gait transition from walking to trotting can be induced by increased activity of the descending drive coming from the mesencephalic locomotor region (MLR and is helped by the sensory inputs at the hip and scapula regions detecting the late stance phase. More neurophysiological experiments are required to identify the precise type of mechanoreceptors in the salamander and the neural mechanisms mediating the sensory modulation.

  11. Microarray analysis identifies keratin loci as sensitive biomarkers for thyroid hormone disruption in the salamander Ambystoma mexicanum.

    Science.gov (United States)

    Page, Robert B; Monaghan, James R; Samuels, Amy K; Smith, Jeramiah J; Beachy, Christopher K; Voss, S Randal

    2007-02-01

    Ambystomatid salamanders offer several advantages for endocrine disruption research, including genomic and bioinformatics resources, an accessible laboratory model (Ambystoma mexicanum), and natural lineages that are broadly distributed among North American habitats. We used microarray analysis to measure the relative abundance of transcripts isolated from A. mexicanum epidermis (skin) after exogenous application of thyroid hormone (TH). Only one gene had a >2-fold change in transcript abundance after 2 days of TH treatment. However, hundreds of genes showed significantly different transcript levels at days 12 and 28 in comparison to day 0. A list of 123 TH-responsive genes was identified using statistical, BLAST, and fold level criteria. Cluster analysis identified two groups of genes with similar transcription patterns: up-regulated versus down-regulated. Most notably, several keratins exhibited dramatic (1000 fold) increases or decreases in transcript abundance. Keratin gene expression changes coincided with morphological remodeling of epithelial tissues. This suggests that keratin loci can be developed as sensitive biomarkers to assay temporal disruptions of larval-to-adult gene expression programs. Our study has identified the first collection of loci that are regulated during TH-induced metamorphosis in a salamander, thus setting the stage for future investigations of TH disruption in the Mexican axolotl and other salamanders of the genus Ambystoma.

  12. Osteological Variation among Extreme Morphological Forms in the Mexican Salamander Genus Chiropterotriton (Amphibia: Plethodontidae: Morphological Evolution And Homoplasy.

    Directory of Open Access Journals (Sweden)

    David M Darda

    Full Text Available Osteological variation is recorded among and within four of the most distinctive species of the Mexican salamander genus Chiropterotriton. Analysis of the data is consistent with the monophyletic status of the genus and documents previously unrecorded intraspecific and interspecific variation. Most of the recorded variation involves qualitative and quantitative proportional differences, but four fixed differences constitute autapomorphic states that affirm and diagnose some species (C. dimidiatus, C. magnipes. Osteological variation in 15 characters is analyzed with respect to predictions generated from four hypotheses: 1 phylogeny, 2 adaptation to specific habitats (the four species include cave-dwelling, terrestrial, and arboreal forms, 3 size-free shape, and 4 size. High levels of intraspecific variation suggest that the characters studied are not subject to rigid functional constraints in salamanders, regardless of size. The pattern predicted by the hypothesis based on size differences seen among these four Chiropterotriton species matches most closely the observed pattern of relative skull robustness. Since size change and heterochrony are often associated in plethodontid evolution, it is likely that changes in developmental timing play a role in the morphological transitions among these morphologically diverse taxa. Webbed feet, miniaturization, body shape, and an unusual tarsal arrangement are morphologies exhibited in species of Chiropterotrition that are shown to be homoplastic with other clades of tropical plethodontids. Although extensive homoplasy in salamanders might be seen as a roadblock to unraveling phylogenetic hypotheses, the homologous developmental systems that appear to underlie such homoplasy may reveal common and consistent evolutionary processes at work.

  13. APOE Genotyping, Cardiovascular Disease

    Science.gov (United States)

    ... Resources For Health Professionals Subscribe Search APOE Genotyping, Cardiovascular Disease Send Us Your Feedback Choose Topic At a ... help understand the role of genetic factors in cardiovascular disease . However, the testing is sometimes used in clinical ...

  14. Radiosensitivity of fingermillet genotypes

    Energy Technology Data Exchange (ETDEWEB)

    Raveendran, T S; Nagarajan, C; Appadurai, R; Prasad, M N; Sundaresan, N [Tamil Nadu Agricultural Univ., Coimbatore (India)

    1984-07-01

    Varietal differences in radiosensitivity were observed in a study involving 4 genotypes of fingermillet (Eleusine coracana (Linn.) Gaertn.) subjected to gamma-irradiation. Harder seeds were found to tolerate a higher dose of the mutagen.

  15. Effects of chronic γ-irradiation on growth and survival of the Tohoku hynobiid salamander, Hynobius lichenatus

    Energy Technology Data Exchange (ETDEWEB)

    Fuma, Shoichi [Project for Environmental Dynamics and Radiation Effects, Fukushima Project Headquarters, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555 Japan (Japan); Une, Yumi [Laboratory of Veterinary Pathology, School of Veterinary Medicine, Azabu University, 1-17-71 Fuchinobe, Sagamihara, Kanagawa 252-5201 (Japan); Ihara, Sadao [Hokkaido University of Education Kushiro Campus, 1-15-55 Shiroyama, Kushiro, Hokkaido 085-8580 Japan (Japan); Matsui, Kumi [Laboratory of Veterinary Physiology 1, School of Veterinary Medicine, Azabu University, 1-17-71 Fuchinobe, Sagamihara, Kanagawa 252-5201 (Japan); Kudo, Tomoo; Tokiwa, Toshihiro [Laboratory of Veterinary Pathology, School of Veterinary Medicine, Azabu University, 1-17-71 Fuchinobe, Sagamihara, Kanagawa 252-5201 (Japan); Kubota, Yoshihisa; Soeda, Haruhi [Project for Environmental Dynamics and Radiation Effects, Fukushima Project Headquarters, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555 Japan (Japan); Ishikawa, Takahiro [Department of Technical Support and Development, Research, Development and Support Centre, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555 Japan (Japan); Doi, Kazutaka [Project for Human Health, Fukushima Project Headquarters, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555 Japan (Japan); Watanabe, Yoshito; Yoshida, Satoshi [Project for Environmental Dynamics and Radiation Effects, Fukushima Project Headquarters, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555 Japan (Japan)

    2014-09-15

    The Tohoku hynobiid salamanders, Hynobius lichenatus, were chronically irradiated with γ-rays from embryonic to juvenile stages for 450 days. At 490 μGy h{sup −1} or lower dose rates, growth and survival were not significantly affected by irradiation, and any morphological aberrations and histological damages were not observed. At 4600 μGy h{sup −1}, growth was severely inhibited, and all the individuals died mostly at the juvenile stage. Chronic LD{sub 50} was 42 Gy as a total dose. In the liver, the number of hematopoietic cells was significantly reduced in the living juveniles, and these cells disappeared in the dead juveniles. In the spleen, mature lymphocytes were depleted in the living larvae, and almost all the heamtopoietic cells disappeared in the dead juveniles. These results suggest that this salamander died due to acute radiation syndrome, i.e., hematopoietic damage and subsequent sepsis caused by immune depression. The death would be also attributed to skin damage inducing infection. At 18,000 μGy h{sup −1}, morphological aberrations and severe growth inhibition were observed. All the individuals died at the larval stage due to a multiple organ failure. Chronic LD{sub 50} was 28 Gy as a total dose. Assuming that chronic LD{sub 50} was 42 Gy at lower dose rates than 4600 μGy h{sup −1}, a chronic median lethal dose rate could be estimated to be <340 μGy h{sup −1} for the whole life (>14 years). These results suggest that, among guidance dose rates, i.e., 4–400 μGy h{sup −1}, proposed by various organisations and research programmes for protection of amphibians and taxonomic groups or ecosystems including amphibians, most of them would protect this salamander but the highest value may not on the whole life scale. - Highlights: • The salamanders, Hynobius lichenatus, were chronically γ-irradiated for 450 days. • At 490 μGy h{sup −1} or lower, irradiation did not significantly affect growth and survival. • All the individuals

  16. Phylogenetic analysis of Common Garter Snake (Thamnophis sirtalis) stomach contents detects cryptic range of a secretive salamander (Ensatina eschscholtzii oregonensis) Herpetological Conservation and Biology 5(3):395–402

    Science.gov (United States)

    Sean B. Reilly; Andrew D Gottsho; Justin M. Garwood; Bryan. Jennings

    2010-01-01

    Given the current global amphibian decline, it is crucial to obtain accurate and current information regarding species distributions. Secretive amphibians such as plethodontid salamanders can be difficult to detect in many cases, especially in remote, high elevation areas. We used molecular phylogenetic analyses to identify three partially digested salamanders palped...

  17. Predictive and prognostic impact of TP53 mutations and MDM2 promoter genotype in primary breast cancer patients treated with epirubicin or paclitaxel.

    Directory of Open Access Journals (Sweden)

    Ranjan Chrisanthar

    Full Text Available BACKGROUND: TP53 mutations have been associated with resistance to anthracyclines but not to taxanes in breast cancer patients. The MDM2 promoter single nucleotide polymorphism (SNP T309G increases MDM2 activity and may reduce wild-type p53 protein activity. Here, we explored the predictive and prognostic value of TP53 and CHEK2 mutation status together with MDM2 SNP309 genotype in stage III breast cancer patients receiving paclitaxel or epirubicin monotherapy. EXPERIMENTAL DESIGN: Each patient was randomly assigned to treatment with epirubicin 90 mg/m(2 (n = 109 or paclitaxel 200 mg/m(2 (n = 114 every 3rd week as monotherapy for 4-6 cycles. Patients obtaining a suboptimal response on first-line treatment requiring further chemotherapy received the opposite regimen. Time from last patient inclusion to follow-up censoring was 69 months. Each patient had snap-frozen tumor tissue specimens collected prior to commencing chemotherapy. PRINCIPAL FINDINGS: While TP53 and CHEK2 mutations predicted resistance to epirubicin, MDM2 status did not. Neither TP53/CHEK2 mutations nor MDM2 status was associated with paclitaxel response. Remarkably, TP53 mutations (p = 0.007 but also MDM2 309TG/GG genotype status (p = 0.012 were associated with a poor disease-specific survival among patients having paclitaxel but not patients having epirubicin first-line. The effect of MDM2 status was observed among individuals harbouring wild-type TP53 (p = 0.039 but not among individuals with TP53 mutated tumors (p>0.5. CONCLUSION: TP53 and CHEK2 mutations were associated with lack of response to epirubicin monotherapy. In contrast, TP53 mutations and MDM2 309G allele status conferred poor disease-specific survival among patients treated with primary paclitaxel but not epirubicin monotherapy.

  18. Cryptosporidium Pig Genotype II in Immunocompetent Man

    Czech Academy of Sciences Publication Activity Database

    Kváč, Martin; Květoňová, Dana; Sak, Bohumil; Ditrich, Oleg

    2009-01-01

    Roč. 15, č. 6 (2009), s. 982-983 ISSN 1080-6040 R&D Projects: GA ČR GP523/07/P117 Institutional research plan: CEZ:AV0Z60220518 Keywords : immunocompetent patients * cryptosporidiosis * Cryptosporidium pig genotype II Subject RIV: GJ - Animal Vermins ; Diseases , Veterinary Medicine Impact factor: 6.794, year: 2009

  19. Efficiency and response of conilon coffee genotypes to nitrogen supply

    African Journals Online (AJOL)

    The objective of the study was to differentiate genotypes with higher efficiency and responsiveness to nitrogen supply, to understand how the nitrogen supply can impact the dry matter allocation and the accumulation of this nutrient in the different plant compartments of genotypes of conilon coffee, cultivated under ...

  20. Recovery of bimodal locomotion in the spinal-transected salamander, Pleurodeles waltlii.

    Science.gov (United States)

    Chevallier, Stéphanie; Landry, Marc; Nagy, Frédéric; Cabelguen, Jean-Marie

    2004-10-01

    Electromyographic (EMG) analysis was used to provide an assessment of the recovery of locomotion in spinal-transected adult salamanders (Pleurodeles waltlii). EMG recordings were performed during swimming and overground stepping in the same animal before and at various times (up to 500 days) after a mid-trunk spinalization. Two-three weeks after spinalization, locomotor EMG activity was limited to the forelimbs and the body rostral to the transection. Thereafter, there was a return of the locomotor EMG activity at progressively more caudal levels below the transection. The animals reached stable locomotor patterns 3-4 months post-transection. Several locomotor parameters (cycle duration, burst duration, burst proportion, intersegmental phase lag, interlimb coupling) measured at various recovery times after spinalization were compared with those in intact animals. These comparisons revealed transient and long-term alterations in the locomotor parameters both above and below the transection site. These alterations were much more pronounced for swimming than for stepping and revealed differences in adaptive plasticity between the two locomotor networks. Recovered locomotor activity was immediately abolished by retransection at the site of the original spinalization, suggesting that the spinal cord caudal to the transection was reinnervated by descending brain and/or propriospinal axons, and that this regeneration contributed to the restoration of locomotor activity. Anatomical studies conducted in parallel further demonstrated that some of the regenerated axons came from glutamatergic and serotoninergic immunoreactive cells within the reticular formation.

  1. Biology of tiny animals: three new species of minute salamanders (Plethodontidae: Thorius from Oaxaca, Mexico

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    Gabriela Parra-Olea

    2016-11-01

    Full Text Available We describe three new species of minute salamanders, genus Thorius, from the Sierra Madre del Sur of Oaxaca, Mexico. Until now only a single species, T. minutissimus, has been reported from this region, although molecular data have long shown extensive genetic differentiation among geographically disjunct populations. Adult Thorius pinicola sp. nov., T. longicaudus sp. nov., and T. tlaxiacus sp. nov. are larger than T. minutissimus and possess elliptical rather than oval nostrils; T. pinicola and T. longicaudus also have longer tails. All three new species occur west of the range of T. minutissimus, which has the easternmost distribution of any member of the genus. The new species are distinguished from each other and from other named Thorius in Oaxaca by a combination of adult body size, external morphology and osteology, and by protein characters (allozymes and differences in DNA sequences. In addition, we redescribe T. minutissimus and a related species, T. narisovalis, to further clarify the taxonomic status of Oaxacan populations and to facilitate future studies of the remaining genetically differentiated Thorius that cannot be satisfactorily assigned to any named species. Populations of all five species considered here appear to have declined dramatically over the last one or two decades and live specimens are difficult to find in nature. Thorius may be the most endangered genus of amphibians in the world. All species may go extinct before the end of this century.

  2. Sequencing and de novo transcriptome assembly of the Chinese giant salamander (Andrias davidianus

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    Yong Huang

    2017-06-01

    Full Text Available Next-generation technologies for determination of genomics and transcriptomics composition have a wide range of applications. Andrias davidianus, has become an endangered amphibian species of salamander endemic in China. However, there is a lack of the molecular information. In this study, we obtained the RNA-Seq data from a pool of A. davidianus tissue including spleen, liver, muscle, kidney, skin, testis, gut and heart using Illumina HiSeq 2500 platform. A total of 15,398,997,600 bp were obtained, corresponding to 102,659,984 raw reads. A total of 102,659,984 reads were filtered after removing low-quality reads and trimming the adapter sequences. The Trinity program was used to de novo assemble 132,912 unigenes with an average length of 690 bp and N50 of 1263 bp. Unigenes were annotated through number of databases. These transcriptomic data of A. davidianus should open the door to molecular evolution studies based on the entire transcriptome or targeted genes of interest to sequence. The raw data in this study can be available in NCBI SRA database with accession number of SRP099564.

  3. Male pheromone protein components activate female vomeronasal neurons in the salamander Plethodon shermani

    Directory of Open Access Journals (Sweden)

    Feldhoff Pamela W

    2006-03-01

    Full Text Available Abstract Background The mental gland pheromone of male Plethodon salamanders contains two main protein components: a 22 kDa protein named Plethodon Receptivity Factor (PRF and a 7 kDa protein named Plethodon Modulating Factor (PMF, respectively. Each protein component individually has opposing effects on female courtship behavior, with PRF shortening and PMF lengthening courtship. In this study, we test the hypothesis that PRF or PMF individually activate vomeronasal neurons. The agmatine-uptake technique was used to visualize chemosensory neurons that were activated by each protein component individually. Results Vomeronasal neurons exposed to agmatine in saline did not demonstrate significant labeling. However, a population of vomeronasal neurons was labeled following exposure to either PRF or PMF. When expressed as a percent of control level labeled cells, PRF labeled more neurons than did PMF. These percentages for PRF and PMF, added together, parallel the percentage of labeled vomeronasal neurons when females are exposed to the whole pheromone. Conclusion This study suggests that two specific populations of female vomeronasal neurons are responsible for responding to each of the two components of the male pheromone mixture. These two neural populations, therefore, could express different receptors which, in turn, transmit different information to the brain, thus accounting for the different female behavior elicited by each pheromone component.

  4. Olfactory effects of a hypervariable multicomponent pheromone in the red-legged salamander, Plethodon shermani.

    Directory of Open Access Journals (Sweden)

    Damien B Wilburn

    Full Text Available Chemical communication via chemosensory signaling is an essential process for promoting and modifying reproductive behavior in many species. During courtship in plethodontid salamanders, males deliver a mixture of non-volatile proteinaceous pheromones that activate chemosensory neurons in the vomeronasal epithelium (VNE and increase female receptivity. One component of this mixture, Plethodontid Modulating Factor (PMF, is a hypervariable pheromone expressed as more than 30 unique isoforms that differ between individual males-likely driven by co-evolution with female receptors to promote gene duplication and positive selection of the PMF gene complex. Courtship trials with females receiving different PMF isoform mixtures had variable effects on female mating receptivity, with only the most complex mixtures increasing receptivity, such that we believe that sufficient isoform diversity allows males to improve their reproductive success with any female in the mating population. The aim of this study was to test the effects of isoform variability on VNE neuron activation using the agmatine uptake assay. All isoform mixtures activated a similar number of neurons (>200% over background except for a single purified PMF isoform (+17%. These data further support the hypothesis that PMF isoforms act synergistically in order to regulate female receptivity, and different putative mechanisms are discussed.

  5. Transcriptome analysis of the Chinese giant salamander (Andrias davidianus using RNA-sequencing

    Directory of Open Access Journals (Sweden)

    Yong Huang

    2017-12-01

    Full Text Available The Chinese giant salamander (Andrias davidianus is an economically important animal on academic value. However, the genomic information of this species has been less studied. In our study, the transcripts of A. davidianus were obtained by RNA-seq to conduct a transcriptomic analysis. In total 132,912 unigenes were generated with an average length of 690 bp and N50 of 1263 bp by de novo assembly using Trinity software. Using a sequence similarity search against the nine public databases (CDD, KOG, NR, NT, PFAM, Swiss-prot, TrEMBL, GO and KEGG databases, a total of 24,049, 18,406, 36,711, 15,858, 20,500, 27,515, 36,705, 28,879 and 10,958 unigenes were annotated in databases, respectively. Of these, 6323 unigenes were annotated in all database and 39,672 unigenes were annotated in at least one database. Blasted with KEGG pathway, 10,958 unigenes were annotated, and it was divided into 343 categories according to different pathways. In addition, we also identified 29,790 SSRs. This study provided a valuable resource for understanding transcriptomic information of A. davidianus and laid a foundation for further research on functional gene cloning, genomics, genetic diversity analysis and molecular marker exploitation in A. davidianus.

  6. Temporal response of the tiger salamander (Ambystoma tigrinum to 3,000 years of climatic variation

    Directory of Open Access Journals (Sweden)

    Long Webb

    2005-09-01

    Full Text Available Abstract Background Amphibians are sensitive indicators of environmental conditions and show measurable responses, such as changes in phenology, abundance and range limits to local changes in precipitation and temperature regimes. Amphibians offer unique opportunities to study the important ecological and evolutionary implications of responses in life history characteristics to climatic change. We analyzed a late-Holocene fossil record of the Tiger Salamander (Ambystoma tigrinum for evidence of population-level changes in body size and paedomorphosis to climatic change over the last 3000 years. Results We found a significant difference in body size index between paedomorphic and metamorphic individuals during the time interval dominated by the Medieval Warm Period. There is a consistent ratio of paedomorphic to metamorphic specimens through the entire 3000 years, demonstrating that not all life history characteristics of the population were significantly altered by changes in climate on this timescale. Conclusion The fossil record of Ambystoma tigrinum we used spans an ecologically relevant timescale appropriate for understanding population and community response to projected climatic change. The population-level responses we documented are concordant with expectations based on modern environmental studies, and yield insight into population-level patterns across hundreds of generations, especially the independence of different life history characteristics. These conclusions lead us to offer general predictions about the future response of this species based on likely scenarios of climatic warming in the Rocky Mountain region.

  7. Wetland and microhabitat use by nesting four-toed salamanders in Maine

    Science.gov (United States)

    Chalmers, R.J.; Loftin, C.S.

    2006-01-01

    Little is known of Four-Toed Salamander (Hemidactylium scutatum) habitat use, despite the species' extensive range and elevated conservation status. We investigated species-habitat relationships that predict H. scutatum nesting presence in Maine at wetland and microhabitat scales by comparing microhabitats with and without nests. We created logistic regression models, selected models with AIC, and evaluated models with reserve data. Wetlands with nests were best predicted by shoreline microhabitat of Sphagnum spp., wood substrate, water flow, blue-joint reed grass (Calamagrostis canadensis), meadowsweet (Spiraea alba), steeplebush (Spiraea tomentosa), sensitive fern (Onoclea sensibilis), and absence of sheep laurel (Kalmia angustifolia) or deciduous forest canopy. Within occupied wetlands, shoreline microhabitat where nests occurred was best distinguished from available, unoccupied shoreline microhabitat by steeper shore, greater near-shore and basin water depth, deeper nesting vegetation, presence of moss spp. and winterberry (Ilex verticillata), and a negative association with S. alba, leatherleaf (Chamaedaphne calyculata), and K. angustifolia. These models of wetland and microhabitat use by H. scutatum may assist ecologists and managers in detecting and conserving this species. Copyright 2006 Society for the Study of Amphibians and Reptiles.

  8. Gonadotropin-Releasing Hormone Modulates Vomeronasal Neuron Response to Male Salamander Pheromone

    Directory of Open Access Journals (Sweden)

    Celeste R. Wirsig-Wiechmann

    2012-01-01

    Full Text Available Electrophysiological studies have shown that gonadotropin-releasing hormone (GnRH modifies chemosensory neurons responses to odors. We have previously demonstrated that male Plethodon shermani pheromone stimulates vomeronasal neurons in the female conspecific. In the present study we used agmatine uptake as a relative measure of the effects of GnRH on this pheromone-induced neural activation of vomeronasal neurons. Whole male pheromone extract containing 3 millimolar agmatine with or without 10 micromolar GnRH was applied to the nasolabial groove of female salamanders for 45 minutes. Immunocytochemical procedures were conducted to visualize and quantify relative agmatine uptake as measured by labeling density of activated vomeronasal neurons. The relative number of labeled neurons did not differ between the two groups: pheromone alone or pheromone-GnRH. However, vomeronasal neurons exposed to pheromone-GnRH collectively demonstrated higher labeling intensity, as a percentage above background (75% as compared with neurons exposed to pheromone alone (63%, P < 0.018. Since the labeling intensity of agmatine within neurons signifies the relative activity levels of the neurons, these results suggest that GnRH increases the response of female vomeronasal neurons to male pheromone.

  9. Efficacy of chemical disinfectants for the containment of the salamander chytrid fungus Batrachochytrium salamandrivorans.

    Science.gov (United States)

    Van Rooij, Pascale; Pasmans, Frank; Coen, Yanaika; Martel, An

    2017-01-01

    The recently emerged chytrid fungus Batrachochytrium salamandrivorans (Bsal) causes European salamander declines. Proper hygiene protocols including disinfection procedures are crucial to prevent disease transmission. Here, the efficacy of chemical disinfectants in killing Bsal was evaluated. At all tested conditions, Biocidal®, Chloramine-T®, Dettol medical®, Disolol®, ethanol, F10®, Hibiscrub®, potassium permanganate, Safe4®, sodium hypochlorite, and Virkon S®, were effective at killing Bsal. Concentrations of 5% sodium chloride or lower, 0.01% peracetic acid and 0.001-1% copper sulphate were inactive against Bsal. None of the conditions tested for hydrogen peroxide affected Bsal viability, while it did kill Batrachochytrium dendrobatidis (Bd). For Bsal, enzymatic breakdown of hydrogen peroxide by catalases and specific morphological features (clustering of sporangia, development of new sporangia within the original sporangium), were identified as fungal factors altering susceptibility to several of the disinfectants tested. Based on the in vitro results we recommend 1% Virkon S®, 4% sodium hypochlorite and 70% ethanol for disinfecting equipment in the field, lab or captive setting, with a minimal contact time of 5 minutes for 1% Virkon S® and 1 minute for the latter disinfectants. These conditions not only efficiently target Bsal, but also Bd and Ranavirus.

  10. Efficacy of chemical disinfectants for the containment of the salamander chytrid fungus Batrachochytrium salamandrivorans.

    Directory of Open Access Journals (Sweden)

    Pascale Van Rooij

    Full Text Available The recently emerged chytrid fungus Batrachochytrium salamandrivorans (Bsal causes European salamander declines. Proper hygiene protocols including disinfection procedures are crucial to prevent disease transmission. Here, the efficacy of chemical disinfectants in killing Bsal was evaluated. At all tested conditions, Biocidal®, Chloramine-T®, Dettol medical®, Disolol®, ethanol, F10®, Hibiscrub®, potassium permanganate, Safe4®, sodium hypochlorite, and Virkon S®, were effective at killing Bsal. Concentrations of 5% sodium chloride or lower, 0.01% peracetic acid and 0.001-1% copper sulphate were inactive against Bsal. None of the conditions tested for hydrogen peroxide affected Bsal viability, while it did kill Batrachochytrium dendrobatidis (Bd. For Bsal, enzymatic breakdown of hydrogen peroxide by catalases and specific morphological features (clustering of sporangia, development of new sporangia within the original sporangium, were identified as fungal factors altering susceptibility to several of the disinfectants tested. Based on the in vitro results we recommend 1% Virkon S®, 4% sodium hypochlorite and 70% ethanol for disinfecting equipment in the field, lab or captive setting, with a minimal contact time of 5 minutes for 1% Virkon S® and 1 minute for the latter disinfectants. These conditions not only efficiently target Bsal, but also Bd and Ranavirus.

  11. Extinction debt as a driver of amphibian declines: An example with imperiled flatwoods salamanders

    Science.gov (United States)

    Semiltsch, Raymond D; Walls, Susan; Barichivich, William J.; O'Donnell, Katherine

    2017-01-01

    A comprehensive view of population declines and their underlying causes is necessary to reverse species loss. Historically, in many cases, a narrow view may have allowed species declines to continue, virtually undetected, for long periods of time (perhaps even decades). We suggest that extinction debt is likely responsible for numerous (perhaps most) amphibian declines and that this perspective should be incorporated into the structure of amphibian research and management. Extinction debt, originally proposed to explain changes in species richness following environmental disturbance, also may refer to the proportion of populations of an individual species that is expected to eventually be lost because of habitat change. A conservation framework to address extinction debt focuses research on threats at the individual, population, and metapopulation levels. This approach will help enhance, restore, and protect specific processes and habitats at the proper scale by directing management to the most vulnerable level and stage of a species. We illustrate this approach using Flatwoods Salamanders, Ambystoma cingulatumand Ambystoma bishopi, which occurred historically throughout the Coastal Plain of the southeastern United States but have experienced a greater than 85% loss of populations in recent years. Reversal of these losses is possible only if conservation and recovery efforts encompass individual, population, and metapopulation levels. We illustrate our framework by outlining actions that could be taken at each of these levels to help guide conservation and management of amphibians with complex life cycles and provide options for how to prioritize conservation actions in the face of logistical and budgetary shortfalls.

  12. Morphological homoplasy, life history evolution, and historical biogeography of plethodontid salamanders inferred from complete mitochondrial genomes

    Energy Technology Data Exchange (ETDEWEB)

    Mueller, Rachel Lockridge; Macey, J. Robert; Jaekel, Martin; Wake, David B.; Boore, Jeffrey L.

    2004-08-01

    The evolutionary history of the largest salamander family (Plethodontidae) is characterized by extreme morphological homoplasy. Analysis of the mechanisms generating such homoplasy requires an independent, molecular phylogeny. To this end, we sequenced 24 complete mitochondrial genomes (22 plethodontids and two outgroup taxa), added data for three species from GenBank, and performed partitioned and unpartitioned Bayesian, ML, and MP phylogenetic analyses. We explored four dataset partitioning strategies to account for evolutionary process heterogeneity among genes and codon positions, all of which yielded increased model likelihoods and decreased numbers of supported nodes in the topologies (PP > 0.95) relative to the unpartitioned analysis. Our phylogenetic analyses yielded congruent trees that contrast with the traditional morphology-based taxonomy; the monophyly of three out of four major groups is rejected. Reanalysis of current hypotheses in light of these new evolutionary relationships suggests that (1) a larval life history stage re-evolved from a direct-developing ancestor multiple times, (2) there is no phylogenetic support for the ''Out of Appalachia'' hypothesis of plethodontid origins, and (3) novel scenarios must be reconstructed for the convergent evolution of projectile tongues, reduction in toe number, and specialization for defensive tail loss. Some of these novel scenarios imply morphological transformation series that proceed in the opposite direction than was previously thought. In addition, they suggest surprising evolutionary lability in traits previously interpreted to be conservative.

  13. Welcome to the neighbourhood: interspecific genotype by genotype interactions in Solidago influence above- and belowground biomass and associated communities.

    Science.gov (United States)

    Genung, Mark A; Bailey, Joseph K; Schweitzer, Jennifer A

    2012-01-01

    Intra- and interspecific plant-plant interactions are fundamental to patterns of community assembly and to the mixture effects observed in biodiversity studies. Although much research has been conducted at the species level, very little is understood about how genetic variation within and among interacting species may drive these processes. Using clones of both Solidago altissima and Solidago gigantea, we found that genotypic variation in a plant's neighbours affected both above- and belowground plant traits, and that genotype by genotype interactions between neighbouring plants impacted associated pollinator communities. The traits for which focal plant genotypic variation explained the most variation varied by plant species, whereas neighbour genotypic variation explained the most variation in coarse root biomass. Our results provide new insight into genotypic and species diversity effects in plant-neighbour interactions, the extended consequences of diversity effects, and the potential for evolution in response to competitive or to facilitative plant-neighbour interactions. © 2011 Blackwell Publishing Ltd/CNRS.

  14. Fostering Children’s Connection to Nature Through Authentic Situations: The Case of Saving Salamanders at School

    Directory of Open Access Journals (Sweden)

    Stephan Barthel

    2018-06-01

    Full Text Available The aim of this paper is to explore how children learn to form new relationships with nature. It draws on a longitudinal case study of children participating in a stewardship project involving the conservation of salamanders during the school day in Stockholm, Sweden. The qualitative method includes two waves of data collection: when a group of 10-year-old children participated in the project (2015 and 2 years after they participated (2017. We conducted 49 interviews with children as well as using participant observations and questionnaires. We found indications that children developed sympathy for salamanders and increased concern and care for nature, and that such relationships persisted 2 years after participation. Our rich qualitative data suggest that whole situations of sufficient unpredictability triggering free exploration of the area, direct sensory contact and significant experiences of interacting with a species were important for children’s development of affective relationships with the salamander species and with nature in an open-ended sense. Saving the lives of trapped animals enabled direct sensory interaction, feedback, increased understanding, and development of new skills for dynamically exploring further ways of saving species in an interactive process experienced as deeply meaningful, enjoyable and connecting. The behavioral setting instilled a sense of pride and commitment, and the high degree of responsibility given to the children while exploring the habitat during authentic situations enriched children’s enjoyment. The study has implications for the design of education programs that aim to connect children with nature and for a child-sensitive urban policy that supports authentic nature situations in close spatial proximity to preschools and schools.

  15. A preliminary investigation into genotype x environment interaction ...

    African Journals Online (AJOL)

    uvp

    2014-08-24

    Aug 24, 2014 ... Genotype x environment interaction (G x E) in dairy cattle is a contentious ... environments, if it exists, with a negative impact on genetic response ..... interaction for Holstein milk yield in Colombia, Mexico and Puerto Rico.

  16. Genomic sequence of a ranavirus (family Iridoviridae) associated with salamander mortalities in North America

    Energy Technology Data Exchange (ETDEWEB)

    Jancovich, James K; Jinghe, Mao; Chinchar, V Gregory; Wyatt, Christopher; Case, Steven T; Kumar, Sudhir; Valente, Graziela; Subramanian, Sankar; Davidson, Elizabeth W; Collins, James P; Jacobs, Bertram L

    2003-11-10

    Disease is among the suspected causes of amphibian population declines, and an iridovirus and a chytrid fungus are the primary pathogens associated with amphibian mortalities. Ambystoma tigrinum virus (ATV) and a closely related strain, Regina ranavirus (RRV), are implicated in salamander die-offs in Arizona and Canada, respectively. We report the complete sequence of the ATV genome and partial sequence of the RRV genome. Sequence analysis of the ATV/RRV genomes showed marked similarity to other ranaviruses, including tiger frog virus (TFV) and frog virus 3 (FV3), the type virus of the genus Ranavirus (family Iridoviridae), as well as more distant relationships to lymphocystis disease virus, Chilo iridescent virus, and infectious spleen and kidney necrosis virus. Putative open reading frames (ORFs) in the ATV sequence identified 24 genes that appear to control virus replication and block antiviral responses. In addition, >50 other putative genes, homologous to ORFs in other iridoviral genomes but of unknown function, were also identified. Sequence comparison performed by dot plot analysis between ATV and itself revealed a conserved 14-bp palindromic repeat within most intragenic regions. Dot plot analysis of ATV vs RRV sequences identified several polymorphisms between the two isolates. Finally, a comparison of ATV and TFV genomic sequences identified genomic rearrangements consistent with the high recombination frequency of iridoviruses. Given the adverse effects that ranavirus infections have on amphibian and fish populations, ATV/RRV sequence information will allow the design of better diagnostic probes for identifying ranavirus infections and extend our understanding of molecular events in ranavirus-infected cells.

  17. Ontogenetic convergence and evolution of foot morphology in European cave salamanders (Family: Plethodontidae

    Directory of Open Access Journals (Sweden)

    Nistri Annamaria

    2010-07-01

    Full Text Available Abstract Background A major goal in evolutionary biology is to understand the evolution of phenotypic diversity. Both natural and sexual selection play a large role in generating phenotypic adaptations, with biomechanical requirements and developmental mechanisms mediating patterns of phenotypic evolution. For many traits, the relative importance of selective and developmental components remains understudied. Results We investigated ontogenetic trajectories of foot morphology in the eight species of European plethodontid cave salamander to test the hypothesis that adult foot morphology was adapted for climbing. Using geometric morphometrics and other approaches, we found that developmental patterns in five species displayed little morphological change during growth (isometry, where the extensive interdigital webbing in adults was best explained as the retention of the juvenile morphological state. By contrast, three species exhibited significant allometry, with an increase in interdigital webbing during growth. Phylogenetic analyses revealed that multiple evolutionary transitions between isometry and allometry of foot webbing have occurred in this lineage. Allometric parameters of foot growth were most similar to those of a tropical species previously shown to be adapted for climbing. Finally, interspecific variation in adult foot morphology was significantly reduced as compared to variation among juveniles, indicating that ontogenetic convergence had resulted in a common adult foot morphology across species. Conclusions The results presented here provide evidence of a complex history of phenotypic evolution in this clade. The common adult phenotype exhibited among species reveals that selection plays an important part in generating patterns of foot diversity in the group. However, developmental trajectories arriving at this common morphology are distinct; with some species displaying developmental stasis (isometry, while others show an increase

  18. Understanding positional cues in salamander limb regeneration: implications for optimizing cell-based regenerative therapies

    Directory of Open Access Journals (Sweden)

    Catherine D. McCusker

    2014-06-01

    Full Text Available Regenerative medicine has reached the point where we are performing clinical trials with stem-cell-derived cell populations in an effort to treat numerous human pathologies. However, many of these efforts have been challenged by the inability of the engrafted populations to properly integrate into the host environment to make a functional biological unit. It is apparent that we must understand the basic biology of tissue integration in order to apply these principles to the development of regenerative therapies in humans. Studying tissue integration in model organisms, where the process of integration between the newly regenerated tissues and the ‘old’ existing structures can be observed and manipulated, can provide valuable insights. Embryonic and adult cells have a memory of their original position, and this positional information can modify surrounding tissues and drive the formation of new structures. In this Review, we discuss the positional interactions that control the ability of grafted cells to integrate into existing tissues during the process of salamander limb regeneration, and discuss how these insights could explain the integration defects observed in current cell-based regenerative therapies. Additionally, we describe potential molecular tools that can be used to manipulate the positional information in grafted cell populations, and to promote the communication of positional cues in the host environment to facilitate the integration of engrafted cells. Lastly, we explain how studying positional information in current cell-based therapies and in regenerating limbs could provide key insights to improve the integration of cell-based regenerative therapies in the future.

  19. Genomic sequence of a ranavirus (family Iridoviridae) associated with salamander mortalities in North America

    International Nuclear Information System (INIS)

    Jancovich, James K.; Mao Jinghe; Chinchar, V. Gregory; Wyatt, Christopher; Case, Steven T.; Kumar, Sudhir; Valente, Graziela; Subramanian, Sankar; Davidson, Elizabeth W.; Collins, James P.; Jacobs, Bertram L.

    2003-01-01

    Disease is among the suspected causes of amphibian population declines, and an iridovirus and a chytrid fungus are the primary pathogens associated with amphibian mortalities. Ambystoma tigrinum virus (ATV) and a closely related strain, Regina ranavirus (RRV), are implicated in salamander die-offs in Arizona and Canada, respectively. We report the complete sequence of the ATV genome and partial sequence of the RRV genome. Sequence analysis of the ATV/RRV genomes showed marked similarity to other ranaviruses, including tiger frog virus (TFV) and frog virus 3 (FV3), the type virus of the genus Ranavirus (family Iridoviridae), as well as more distant relationships to lymphocystis disease virus, Chilo iridescent virus, and infectious spleen and kidney necrosis virus. Putative open reading frames (ORFs) in the ATV sequence identified 24 genes that appear to control virus replication and block antiviral responses. In addition, >50 other putative genes, homologous to ORFs in other iridoviral genomes but of unknown function, were also identified. Sequence comparison performed by dot plot analysis between ATV and itself revealed a conserved 14-bp palindromic repeat within most intragenic regions. Dot plot analysis of ATV vs RRV sequences identified several polymorphisms between the two isolates. Finally, a comparison of ATV and TFV genomic sequences identified genomic rearrangements consistent with the high recombination frequency of iridoviruses. Given the adverse effects that ranavirus infections have on amphibian and fish populations, ATV/RRV sequence information will allow the design of better diagnostic probes for identifying ranavirus infections and extend our understanding of molecular events in ranavirus-infected cells

  20. A 3D musculo-mechanical model of the salamander for the study of different gaits and modes of locomotion

    Directory of Open Access Journals (Sweden)

    Nalin eHarischandra

    2010-12-01

    Full Text Available Computer simulation has been used to investigate several aspectsof locomotion in salamanders. Here we introduce a three-dimensionalforward dynamics mechanical model of a salamander, with physicallyrealistic weight and size parameters. Movements of the four limbs and ofthe trunk and tail are generated by sets of linearly modeled skeletalmuscles. In this study, activation of these muscles were driven byprescribed neural output patterns. The model was successfully used tomimic locomotion on level ground and in water. We compare thewalking gait where a wave of activity in the axial muscles travelsbetween the girdles, with the trotting gait in simulations usingthe musculo-mechanical model. In a separate experiment, the model is usedto compare different strategies for turning while stepping; either bybending the trunk or by using side-stepping in the front legs. We foundthat for turning, the use of side-stepping alone or in combination withtrunk bending, was more effective than the use of trunk bending alone. Weconclude that the musculo-mechanical model described here together with aproper neural controller is useful for neuro-physiological experiments insilico.

  1. Nutritional and medicinal characteristics of Chinese giant salamander (Andrias davidianus for applications in healthcare industry by artificial cultivation: A review

    Directory of Open Access Journals (Sweden)

    Dong He

    2018-03-01

    Full Text Available Andrias davidianus, i. e. Chinese giant salamander (CGS, is one of the largest and oldest amphibians existing in the world and is also one of the valuable biological resources of China. Wild CGS has been threatened with extinction in the past decades due to over capturing, deterioration of natural environment, the slow breeding and growth of the wild species in nature. However, in the past twenty years, with the breakthrough and progress of artificial breeding technology by artificial insemination, the number of artificially cultivated CGS has increased rapidly. Artificially cultivated CGS can either be released to the CGS living environment to increase the population in nature or legally applied in food and medicinal industry as a feedstock due to the unique nutritional and medicinal values of CGS as recorded historically. In this review, the nutritional components, bioactive components and medicinal activities of the artificially cultivated CGS will be summarized. The mucus, skin, meat and bone of CGS contain many different bioactive substances thereby having various medicinal activities including anti-aging, anti-fatigue, anti-tumor, therapy of burn and anti-infection and other physiological functions. This paper will further discuss the potential applications of the artificially cultivated CGS in healthcare industry and prospects of future technological development. Keywords: Andrias davidianus, Artificial breeding, Chinese giant salamander, Functional foods, Medicinal activity, Natural resource protection, Nutrition

  2. Tongue and taste organ development in the ontogeny of direct-developing salamander Plethodon cinereus (Lissamphibia: Plethodontidae).

    Science.gov (United States)

    Budzik, Karolina A; Żuwała, Krystyna; Kerney, Ryan

    2016-07-01

    The latest research on direct developing caecilian and anuran species indicate presence of only one generation of taste organs during their ontogeny. This is distinct from indirect developing batrachians studied thus far, which possess taste buds in larvae and anatomically distinct taste discs in metamorphs. This study is a description of the tongue and taste organ morphology and development in direct developing salamander Plethodon cinereus (Plethodontidae) using histology and electron microscopy techniques. The results reveal two distinct stages tongue morphology (primary and secondary), similar to metamorphic urodeles, although only one stage of taste organ morphology. Taste disc sensory zones emerge on the surface of the oropharyngeal epithelium by the end of embryonic development, which coincides with maturation of the soft tongue. Taste organs occur in the epithelium of the tongue pad (where they are situated on the dermal papillae), the palate and the inner surface of the mandible and the maxilla. Plethodon cinereus embryos only possess taste disc type taste organs. Similar to the direct developing anuran Eleutherodactylus coqui (Eleutherodactylidae), these salamanders do not recapitulate larval taste bud morphology as an embryo. The lack of taste bud formation is probably a broadly distributed feature characteristic to direct developing batrachians. J. Morphol. 277:906-915, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  3. Diet of larval Ambystoma rivulare (Caudata: Ambystomatidae, a threatened salamander from the Volcán Nevado de Toluca, Mexico

    Directory of Open Access Journals (Sweden)

    Julio A. Lemos-Espinal

    2015-06-01

    Full Text Available Several species of salamander in the genus Ambystoma occur in the mountains surrounding Mexico City and are considered at risk of extinction. However, little is known about their ecology and natural history. The Toluca Stream Siredon (Ambystoma rivulare is classified as “Data Deficient” by the IUCN, and considered “Threatened” under Mexican law. From October 2013 to September 2014, we examined the diet of larval A. rivulare from a stream on the Volcán Nevado de Toluca in Mexico to provide insight into the suitability of the habitat to support this population of salamanders. Ostracods accounted for approximately 90% of all prey items consumed by larval A. rivulare. The number of ostracods found in stomachs increased with individual body size, but the proportion of ostracods in stomachs did not vary with body size. Nematodes were observed in approximately one third of the stomachs we examined. The diversity of prey in the diet of A. rivulare in the stream we studied is low and dominated by a single prey taxon, ostracods. Our results suggest that if environmental conditions in the stream change such that ostracods are negatively affected then the long-term persistence of this population of A. rivulare might be in jeopardy.

  4. Developing landscape habitat models for rare amphibians with small geographic ranges: a case study of Siskiyou Mountains salamanders in the western USA

    Science.gov (United States)

    Nobuya Suzuki; Deanna H. Olson; Edward C. Reilly

    2007-01-01

    To advance the development of conservation planning for rare species with small geographic ranges, we determined habitat associations of Siskiyou Mountains salamanders (Plethodon stormi) and developed habitat suitability models at fine (10 ha), medium (40 ha), and broad (202 ha) spatial scales using available geographic information systems data and...

  5. 3D bite modeling and feeding mechanics of the largest living amphibian, the Chinese giant salamander Andrias davidianus (Amphibia:Urodela.

    Directory of Open Access Journals (Sweden)

    Josep Fortuny

    Full Text Available Biting is an integral feature of the feeding mechanism for aquatic and terrestrial salamanders to capture, fix or immobilize elusive or struggling prey. However, little information is available on how it works and the functional implications of this biting system in amphibians although such approaches might be essential to understand feeding systems performed by early tetrapods. Herein, the skull biomechanics of the Chinese giant salamander, Andrias davidianus is investigated using 3D finite element analysis. The results reveal that the prey contact position is crucial for the structural performance of the skull, which is probably related to the lack of a bony bridge between the posterior end of the maxilla and the anterior quadrato-squamosal region. Giant salamanders perform asymmetrical strikes. These strikes are unusual and specialized behavior but might indeed be beneficial in such sit-and-wait or ambush-predators to capture laterally approaching prey. However, once captured by an asymmetrical strike, large, elusive and struggling prey have to be brought to the anterior jaw region to be subdued by a strong bite. Given their basal position within extant salamanders and their "conservative" morphology, cryptobranchids may be useful models to reconstruct the feeding ecology and biomechanics of different members of early tetrapods and amphibians, with similar osteological and myological constraints.

  6. The influence of a water current on the larval deposition pattern of females of a diverging fire salamander population (Salamandra salamandra)

    NARCIS (Netherlands)

    Krause, E.T.; Caspers, B.A.

    2015-01-01

    Fire salamanders are amphibians that exhibit a highly specific reproductive mode termed ovo-viviparity. The eggs develop inside their mothers, and the females give birth to fully developed larvae. The larvae in our study area cluster in two distinct genetic groups that can be linked directly to the

  7. Pseudo-immunolabelling with the avidin-biotin-peroxidase complex (ABC) due to the presence of endogenous biotin in retinal Müller cells of goldfish and salamander

    NARCIS (Netherlands)

    Bhattacharjee, J.; Nunes Cardozo, B.; Kamphuis, W.; Kamermans, M.; Vrensen, G. F.

    1997-01-01

    Immunodetection techniques are dependent on enzyme-protein conjugates for the visualisation of antigen-antibody complexes. One of the most widely used is the avidin-biotin-peroxidase complex (ABC) method. The present study demonstrates that direct treatment of goldfish and salamander retinal

  8. Site-level habitat models for the endemic, threatened Cheat Mountain salamander (Plethodon nettingi): the importance of geophysical and biotic attributes for predicting occurrence

    Science.gov (United States)

    Lester O. Dillard; Kevin R. Russell; W. Mark Ford

    2008-01-01

    The federally threatened Cheat Mountain salamander (Plethodon nettingi; hereafter CMS) is known to occur in approximately 70 small, scattered populations in the Allegheny Mountains of eastern West Virginia, USA. Current conservation and management efforts on federal, state, and private lands involving CMS largely rely on small scale, largely...

  9. Molecular phylogenetic reconstruction of the endemic Asian salamander family Hynobiidae (Amphibia, Caudata).

    Science.gov (United States)

    Weisrock, David W; Macey, J Robert; Matsui, Masafumi; Mulcahy, Daniel G; Papenfuss, Theodore J

    2013-01-01

    The salamander family Hynobiidae contains over 50 species and has been the subject of a number of molecular phylogenetic investigations aimed at reconstructing branches across the entire family. In general, studies using the greatest amount of sequence data have used reduced taxon sampling, while the study with the greatest taxon sampling has used a limited sequence data set. Here, we provide insights into the phylogenetic history of the Hynobiidae using both dense taxon sampling and a large mitochondrial DNA sequence data set. We report exclusive new mitochondrial DNA data of 2566 aligned bases (with 151 excluded sites, of included sites 1157 are variable with 957 parsimony informative). This is sampled from two genic regions encoding a 12S-16S region (the 3' end of 12S rRNA, tRNA(VAI), and the 5' end of 16S rRNA), and a ND2-COI region (ND2, tRNA(Trp), tRNA(Ala), tRNA(Asn), the origin for light strand replication--O(L), tRNA(Cys), tRNAT(Tyr), and the 5' end of COI). Analyses using parsimony, Bayesian, and maximum likelihood optimality criteria produce similar phylogenetic trees, with discordant branches generally receiving low levels of branch support. Monophyly of the Hynobiidae is strongly supported across all analyses, as is the sister relationship and deep divergence between the genus Onychodactylus with all remaining hynobiids. Within this latter grouping our phylogenetic results identify six clades that are relatively divergent from one another, but for which there is minimal support for their phylogenetic placement. This includes the genus Batrachuperus, the genus Hynobius, the genus Pachyhynobius, the genus Salamandrella, a clade containing the genera Ranodon and Paradactylodon, and a clade containing the genera Liua and Pseudohynobius. This latter clade receives low bootstrap support in the parsimony analysis, but is consistent across all three analytical methods. Our results also clarify a number of well-supported relationships within the larger

  10. Recombinant nAG (a Salamander-Derived Protein Decreases the Formation of Hypertrophic Scarring in the Rabbit Ear Model

    Directory of Open Access Journals (Sweden)

    Mohammad M. Al-Qattan

    2014-01-01

    Full Text Available nAG (newt-Anterrior Gradient protein is the key mediator of regrowth of amputated limbs in salamanders. In a previous work in our lab, a new nAG gene (suitable for humans was designed and cloned. The cloned vector was transfected into primary human fibroblasts. The expression of nAG in human primary fibroblasts was found to suppress collagen expression. The current study shows that local injection of recombinant nAG reduces scar hypertrophy in the rabbit ear model. This is associated with lower scar elevation index (SEI, lower levels of collagen I & III, higher levels of MMP1, and a higher degree of scar maturation in experimental wounds compared to controls.

  11. Hatching success in salamanders and chorus frogs at two sites in Colorado, USA: Effects of acidic deposition and climate

    Science.gov (United States)

    Muths, E.; Campbell, D.H.; Corn, P.S.

    2003-01-01

    The snowpack in the vicinity of the Mount Zirkel Wilderness Area is among the most acidic in the western United States. We analyzed water chemistry and examined hatching success in tiger salamanders and chorus frogs at ponds there and at nearby Rabbit Ears Pass (Dumont) to determine whether acid deposition affects amphibians or their breeding habitats at these potentially sensitive locations. We found a wide range of acid neutralizing capacity among ponds within sites; the minimum pH recorded during the experiment was 5.4 at one of 12 ponds with all others at pH ??? 5.7. At Dumont, hatching success for chorus frogs was greater in ponds with low acid neutralizing capacity; however, lowest pHs were >5.8. At current levels of acid deposition, weather and pond characteristics are likely more important than acidity in influencing hatching success in amphibian larvae at these sites.

  12. Molecular detection of vertebrates in stream water: a demonstration using Rocky Mountain tailed frogs and Idaho giant salamanders.

    Science.gov (United States)

    Goldberg, Caren S; Pilliod, David S; Arkle, Robert S; Waits, Lisette P

    2011-01-01

    Stream ecosystems harbor many secretive and imperiled species, and studies of vertebrates in these systems face the challenges of relatively low detection rates and high costs. Environmental DNA (eDNA) has recently been confirmed as a sensitive and efficient tool for documenting aquatic vertebrates in wetlands and in a large river and canal system. However, it was unclear whether this tool could be used to detect low-density vertebrates in fast-moving streams where shed cells may travel rapidly away from their source. To evaluate the potential utility of eDNA techniques in stream systems, we designed targeted primers to amplify a short, species-specific DNA fragment for two secretive stream amphibian species in the northwestern region of the United States (Rocky Mountain tailed frogs, Ascaphus montanus, and Idaho giant salamanders, Dicamptodon aterrimus). We tested three DNA extraction and five PCR protocols to determine whether we could detect eDNA of these species in filtered water samples from five streams with varying densities of these species in central Idaho, USA. We successfully amplified and sequenced the targeted DNA regions for both species from stream water filter samples. We detected Idaho giant salamanders in all samples and Rocky Mountain tailed frogs in four of five streams and found some indication that these species are more difficult to detect using eDNA in early spring than in early fall. While the sensitivity of this method across taxa remains to be determined, the use of eDNA could revolutionize surveys for rare and invasive stream species. With this study, the utility of eDNA techniques for detecting aquatic vertebrates has been demonstrated across the majority of freshwater systems, setting the stage for an innovative transformation in approaches for aquatic research.

  13. Molecular detection of vertebrates in stream water: a demonstration using Rocky Mountain tailed frogs and Idaho giant salamanders.

    Directory of Open Access Journals (Sweden)

    Caren S Goldberg

    Full Text Available Stream ecosystems harbor many secretive and imperiled species, and studies of vertebrates in these systems face the challenges of relatively low detection rates and high costs. Environmental DNA (eDNA has recently been confirmed as a sensitive and efficient tool for documenting aquatic vertebrates in wetlands and in a large river and canal system. However, it was unclear whether this tool could be used to detect low-density vertebrates in fast-moving streams where shed cells may travel rapidly away from their source. To evaluate the potential utility of eDNA techniques in stream systems, we designed targeted primers to amplify a short, species-specific DNA fragment for two secretive stream amphibian species in the northwestern region of the United States (Rocky Mountain tailed frogs, Ascaphus montanus, and Idaho giant salamanders, Dicamptodon aterrimus. We tested three DNA extraction and five PCR protocols to determine whether we could detect eDNA of these species in filtered water samples from five streams with varying densities of these species in central Idaho, USA. We successfully amplified and sequenced the targeted DNA regions for both species from stream water filter samples. We detected Idaho giant salamanders in all samples and Rocky Mountain tailed frogs in four of five streams and found some indication that these species are more difficult to detect using eDNA in early spring than in early fall. While the sensitivity of this method across taxa remains to be determined, the use of eDNA could revolutionize surveys for rare and invasive stream species. With this study, the utility of eDNA techniques for detecting aquatic vertebrates has been demonstrated across the majority of freshwater systems, setting the stage for an innovative transformation in approaches for aquatic research.

  14. Histological and MS spectrometric analyses of the modified tissue of bulgy form tadpoles induced by salamander predation

    Directory of Open Access Journals (Sweden)

    Tsukasa Mori

    2012-02-01

    The rapid induction of a defensive morphology by a prey species in face of a predation risk is an intriguing in ecological context; however, the physiological mechanisms that underlie this phenotypic plasticity remain uncertain. Here we investigated the phenotypic changes shown by Rana pirica tadpoles in response to a predation threat by larvae of the salamander Hynobius retardatus. One such response is the bulgy morph phenotype, a relatively rapid swelling in size by the tadpoles that begins within 4 days and reaches a maximum at 8 to 10 days. We found that although the total volume of bodily fluid increased significantly (P<0.01 in bulgy morph tadpoles, osmotic pressure was maintained at the same level as control tadpoles by a significant increase (P<0.01 in Na and Cl ion concentrations. In our previous report, we identified a novel frog gene named pirica that affects the waterproofing of the skin membrane in tadpoles. Our results support the hypothesis that predator-induced expression of pirica on the skin membrane causes retention of absorbed water. Midline sections of bulgy morph tadpoles showed the presence of swollen connective tissue beneath the skin that was sparsely composed of cells containing hyaluronic acid. Mass spectrographic (LC-MS/MS analysis identified histone H3 and 14-3-3 zeta as the most abundant constituents in the liquid aspirated from the connective tissue of bulgy tadpoles. Immunohistochemistry using antibodies against these proteins showed the presence of non-chromatin associated histone H3 in the swollen connective tissue. Histones and 14-3-3 proteins are also involved in antimicrobial activity and secretion of antibacterial proteins, respectively. Bulgy tadpoles have a larger surface area than controls, and their skin often has bite wounds inflicted by the larval salamanders. Thus, formation of the bulgy morph may also require and be supported by activation of innate immune systems.

  15. Parallel habitat acclimatization is realized by the expression of different genes in two closely related salamander species (genus Salamandra).

    Science.gov (United States)

    Goedbloed, D J; Czypionka, T; Altmüller, J; Rodriguez, A; Küpfer, E; Segev, O; Blaustein, L; Templeton, A R; Nolte, A W; Steinfartz, S

    2017-12-01

    The utilization of similar habitats by different species provides an ideal opportunity to identify genes underlying adaptation and acclimatization. Here, we analysed the gene expression of two closely related salamander species: Salamandra salamandra in Central Europe and Salamandra infraimmaculata in the Near East. These species inhabit similar habitat types: 'temporary ponds' and 'permanent streams' during larval development. We developed two species-specific gene expression microarrays, each targeting over 12 000 transcripts, including an overlapping subset of 8331 orthologues. Gene expression was examined for systematic differences between temporary ponds and permanent streams in larvae from both salamander species to establish gene sets and functions associated with these two habitat types. Only 20 orthologues were associated with a habitat in both species, but these orthologues did not show parallel expression patterns across species more than expected by chance. Functional annotation of a set of 106 genes with the highest effect size for a habitat suggested four putative gene function categories associated with a habitat in both species: cell proliferation, neural development, oxygen responses and muscle capacity. Among these high effect size genes was a single orthologue (14-3-3 protein zeta/YWHAZ) that was downregulated in temporary ponds in both species. The emergence of four gene function categories combined with a lack of parallel expression of orthologues (except 14-3-3 protein zeta) suggests that parallel habitat adaptation or acclimatization by larvae from S. salamandra and S. infraimmaculata to temporary ponds and permanent streams is mainly realized by different genes with a converging functionality.

  16. Common genotypes of hepatitis B virus

    International Nuclear Information System (INIS)

    Idrees, M.; Khan, S.; Riazuddin, S.

    2004-01-01

    Objective: To find out the frequency of common genotypes of hepatitis-B virus (HBV). Subjects and Methods: HBV genotypes were determined in 112 HBV DNA positive sera by a simple and precise molecular genotyping system base on PCR using type-specific primers for the determination of genotypes of HBV A through H. Results: Four genotypes (A,B,C and D) out of total eight reported genotypes so far were identified. Genotypes A, B and C were predominant. HBV genotype C was the most predominant in this collection, appearing in 46 samples (41.7%). However, the genotypes of a total of 5 (4.46%) samples could not be determined with the present genotyping system. Mixed genotypes were seen in 8(7.14% HBV) isolates. Five of these were infected with genotypes A/D whereas two were with genotypes C/D. One patient was infected with 4 genotypes (A/B/C/D). Genotype A (68%) was predominant in Sindh genotype C was most predominant in North West Frontier Province (NWFP) (68.96) whereas genotype C and B were dominant in Punjab (39.65% and 25.86% respectively). Conclusion: All the four common genotypes of HBV found worldwide (A,B,C and D) were isolated. Genotype C is the predominant Genotypes B and C are predominant in Punjab and N.W.F.P. whereas genotype A is predominant in Sindh. (author)

  17. Applications of linking PBPK and PD models to predict the impact of genotypic variability, formulation differences, differences in target binding capacity and target site drug concentrations on drug responses and variability.

    Directory of Open Access Journals (Sweden)

    Manoranjenni eChetty

    2014-11-01

    Full Text Available This study aimed to demonstrate the added value of integrating prior in vitro data and knowledge-rich physiologically based pharmacokinetic (PBPK models with pharmacodynamics (PD models. Four distinct applications that were developed and tested are presented here. PBPK models were developed for metoprolol using different CYP2D6 genotypes based on in vitro data. Application of the models for prediction of phenotypic differences in the pharmacokinetics (PK and PD compared favourably with clinical data, demonstrating that these differences can be predicted prior to the availability of such data from clinical trials. In the second case, PK and PD data for an immediate release formulation of nifedipine together with in vitro dissolution data for a controlled release formulation (CR were used to predict the PK and PD of the CR. This approach can be useful to pharmaceutical scientists during formulation development. The operational model of agonism was used in the third application to describe the hypnotic effects of triazolam, and this was successfully extrapolated to zolpidem by changing only the drug related parameters from in vitro experiments. This PBPK modelling approach can be useful to developmental scientists who which to compare several drug candidates in the same therapeutic class. Finally, differences in QTc prolongation due to quinidine in Caucasian and Korean females were successfully predicted by the model using free heart concentrations as an input to the PD models. This PBPK linked PD model was used to demonstrate a higher sensitivity to free heart concentrations of quinidine in Caucasian females, thereby providing a mechanistic understanding of a clinical observation. In general, permutations of certain conditions which potentially change PK and hence PD may not be amenable to the conduct of clinical studies but linking PBPK with PD provides an alternative method of investigating the potential impact of PK changes on PD.

  18. Applications of linking PBPK and PD models to predict the impact of genotypic variability, formulation differences, differences in target binding capacity and target site drug concentrations on drug responses and variability.

    Science.gov (United States)

    Chetty, Manoranjenni; Rose, Rachel H; Abduljalil, Khaled; Patel, Nikunjkumar; Lu, Gaohua; Cain, Theresa; Jamei, Masoud; Rostami-Hodjegan, Amin

    2014-01-01

    This study aimed to demonstrate the added value of integrating prior in vitro data and knowledge-rich physiologically based pharmacokinetic (PBPK) models with pharmacodynamics (PDs) models. Four distinct applications that were developed and tested are presented here. PBPK models were developed for metoprolol using different CYP2D6 genotypes based on in vitro data. Application of the models for prediction of phenotypic differences in the pharmacokinetics (PKs) and PD compared favorably with clinical data, demonstrating that these differences can be predicted prior to the availability of such data from clinical trials. In the second case, PK and PD data for an immediate release formulation of nifedipine together with in vitro dissolution data for a controlled release (CR) formulation were used to predict the PK and PD of the CR. This approach can be useful to pharmaceutical scientists during formulation development. The operational model of agonism was used in the third application to describe the hypnotic effects of triazolam, and this was successfully extrapolated to zolpidem by changing only the drug related parameters from in vitro experiments. This PBPK modeling approach can be useful to developmental scientists who which to compare several drug candidates in the same therapeutic class. Finally, differences in QTc prolongation due to quinidine in Caucasian and Korean females were successfully predicted by the model using free heart concentrations as an input to the PD models. This PBPK linked PD model was used to demonstrate a higher sensitivity to free heart concentrations of quinidine in Caucasian females, thereby providing a mechanistic understanding of a clinical observation. In general, permutations of certain conditions which potentially change PK and hence PD may not be amenable to the conduct of clinical studies but linking PBPK with PD provides an alternative method of investigating the potential impact of PK changes on PD.

  19. The Extent of mRNA Editing Is Limited in Chicken Liver and Adipose, but Impacted by Tissular Context, Genotype, Age, and Feeding as Exemplified with a Conserved Edited Site in COG3

    Directory of Open Access Journals (Sweden)

    Pierre-François Roux

    2016-02-01

    Full Text Available RNA editing is a posttranscriptional process leading to differences between genomic DNA and transcript sequences, potentially enhancing transcriptome diversity. With recent advances in high-throughput sequencing, many efforts have been made to describe mRNA editing at the transcriptome scale, especially in mammals, yielding contradictory conclusions regarding the extent of this phenomenon. We show, by detailed description of the 25 studies focusing so far on mRNA editing at the whole-transcriptome scale, that systematic sequencing artifacts are considered in most studies whereas biological replication is often neglected and multi-alignment not properly evaluated, which ultimately impairs the legitimacy of results. We recently developed a rigorous strategy to identify mRNA editing using mRNA and genomic DNA sequencing, taking into account sequencing and mapping artifacts, and biological replicates. We applied this method to screen for mRNA editing in liver and white adipose tissue from eight chickens and confirm the small extent of mRNA recoding in this species. Among the 25 unique edited sites identified, three events were previously described in mammals, attesting that this phenomenon is conserved throughout evolution. Deeper investigations on five sites revealed the impact of tissular context, genotype, age, feeding conditions, and sex on mRNA editing levels. More specifically, this analysis highlighted that the editing level at the site located on COG3 was strongly regulated by four of these factors. By comprehensively characterizing the mRNA editing landscape in chickens, our results highlight how this phenomenon is limited and suggest regulation of editing levels by various genetic and environmental factors.

  20. HBV genotypic variability in Cuba.

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    Carmen L Loureiro

    Full Text Available The genetic diversity of HBV in human population is often a reflection of its genetic admixture. The aim of this study was to explore the genotypic diversity of HBV in Cuba. The S genomic region of Cuban HBV isolates was sequenced and for selected isolates the complete genome or precore-core sequence was analyzed. The most frequent genotype was A (167/250, 67%, mainly A2 (149, 60% but also A1 and one A4. A total of 77 isolates were classified as genotype D (31%, with co-circulation of several subgenotypes (56 D4, 2 D1, 5 D2, 7 D3/6 and 7 D7. Three isolates belonged to genotype E, two to H and one to B3. Complete genome sequence analysis of selected isolates confirmed the phylogenetic analysis performed with the S region. Mutations or polymorphisms in precore region were more common among genotype D compared to genotype A isolates. The HBV genotypic distribution in this Caribbean island correlates with the Y lineage genetic background of the population, where a European and African origin prevails. HBV genotypes E, B3 and H isolates might represent more recent introductions.

  1. HBV Genotypic Variability in Cuba

    Science.gov (United States)

    Loureiro, Carmen L.; Aguilar, Julio C.; Aguiar, Jorge; Muzio, Verena; Pentón, Eduardo; Garcia, Daymir; Guillen, Gerardo; Pujol, Flor H.

    2015-01-01

    The genetic diversity of HBV in human population is often a reflection of its genetic admixture. The aim of this study was to explore the genotypic diversity of HBV in Cuba. The S genomic region of Cuban HBV isolates was sequenced and for selected isolates the complete genome or precore-core sequence was analyzed. The most frequent genotype was A (167/250, 67%), mainly A2 (149, 60%) but also A1 and one A4. A total of 77 isolates were classified as genotype D (31%), with co-circulation of several subgenotypes (56 D4, 2 D1, 5 D2, 7 D3/6 and 7 D7). Three isolates belonged to genotype E, two to H and one to B3. Complete genome sequence analysis of selected isolates confirmed the phylogenetic analysis performed with the S region. Mutations or polymorphisms in precore region were more common among genotype D compared to genotype A isolates. The HBV genotypic distribution in this Caribbean island correlates with the Y lineage genetic background of the population, where a European and African origin prevails. HBV genotypes E, B3 and H isolates might represent more recent introductions. PMID:25742179

  2. A review of the biology and conservation of the Cope's giant salamander Dicamptodon copei Nussbaum, 1970 (Amphibia: Caudata: Dicamptodontidae) in the Pacific northwestern region of the USA

    Science.gov (United States)

    Alex D. Foster; Deanna H. Olson; Lawrence L.C. Jones

    2015-01-01

    The Cope’s Giant Salamander Dicamptodon copei is a stream dwelling amphibian reliant on cool streams, native to forested areas primarily west of the crest of the Cascade Range in the Pacific Northwest region, USA. Unlike other members of the genus, adult D. copei are most often found in a paedomorphic form, and rarely transforms to a terrestrial stage. As a result,...

  3. Solution structure and phylogenetics of Prod1, a member of the three-finger protein superfamily implicated in salamander limb regeneration.

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    Acely Garza-Garcia

    Full Text Available BACKGROUND: Following the amputation of a limb, newts and salamanders have the capability to regenerate the lost tissues via a complex process that takes place at the site of injury. Initially these cells undergo dedifferentiation to a state competent to regenerate the missing limb structures. Crucially, dedifferentiated cells have memory of their level of origin along the proximodistal (PD axis of the limb, a property known as positional identity. Notophthalmus viridescens Prod1 is a cell-surface molecule of the three-finger protein (TFP superfamily involved in the specification of newt limb PD identity. The TFP superfamily is a highly diverse group of metazoan proteins that includes snake venom toxins, mammalian transmembrane receptors and miscellaneous signaling molecules. METHODOLOGY/PRINCIPAL FINDINGS: With the aim of identifying potential orthologs of Prod1, we have solved its 3D structure and compared it to other known TFPs using phylogenetic techniques. The analysis shows that TFP 3D structures group in different categories according to function. Prod1 clusters with other cell surface protein TFP domains including the complement regulator CD59 and the C-terminal domain of urokinase-type plasminogen activator. To infer orthology, a structure-based multiple sequence alignment of representative TFP family members was built and analyzed by phylogenetic methods. Prod1 has been proposed to be the salamander CD59 but our analysis fails to support this association. Prod1 is not a good match for any of the TFP families present in mammals and this result was further supported by the identification of the putative orthologs of both CD59 and N. viridescens Prod1 in sequence data for the salamander Ambystoma tigrinum. CONCLUSIONS/SIGNIFICANCE: The available data suggest that Prod1, and thereby its role in encoding PD identity, is restricted to salamanders. The lack of comparable limb-regenerative capability in other adult vertebrates could be

  4. Growth, survival, longevity, and population size of the Big Mouth Cave salamander (Gyrinophilus palleucus necturoides) from the type locality in Grundy County, Tennessee, USA

    Science.gov (United States)

    Niemiller, Matthew L.; Glorioso, Brad M.; Fenolio, Dante B.; Reynolds, R. Graham; Taylor, Steven J.; Miller, Brian T.

    2016-01-01

    Salamander species that live entirely in subterranean habitats have evolved adaptations that allow them to cope with perpetual darkness and limited energy resources. We conducted a 26-month mark–recapture study to better understand the individual growth and demography of a population of the Big Mouth Cave Salamander (Gyrinophilus palleucus necturoides). We employed a growth model to estimate growth rates, age at sexual maturity, and longevity, and an open population model to estimate population size, density, detectability, and survival rates. Furthermore, we examined cover use and evidence of potential predation. Individuals probably reach sexual maturity in 3–5 years and live at least nine years. Survival rates were generally high (>75%) but declined during the study. More than 30% of captured salamanders had regenerating tails or tail damage, which presumably represent predation attempts by conspecifics or crayfishes. Most salamanders (>90%) were found under cover (e.g., rocks, trash, decaying plant material). Based on 11 surveys during the study, population size estimates ranged from 21 to 104 individuals in the ca. 710 m2 study area. Previous surveys indicated that this population experienced a significant decline from the early 1970s through the 1990s, perhaps related to silvicultural and agricultural practices. However, our data suggest that this population has either recovered or stabilized during the past 20 years. Differences in relative abundance between early surveys and our survey could be associated with differences in survey methods or sampling conditions rather than an increase in population size. Regardless, our study demonstrates that this population is larger than previously thought and is in no immediate risk of extirpation, though it does appear to exhibit higher rates of predation than expected for a species believed to be an apex predator of subterranean food webs.

  5. New species of salamander (Caudata: Plethodontidae: Cryptotriton) from Quebrada Cataguana, Francisco Morazán, Honduras, with comments on the taxonomic status of Cryptotriton wakei.

    Science.gov (United States)

    Mccranie, James R; Rovito, Sean M

    2014-05-09

    We describe a new species of the plethodontid salamander genus Cryptotriton from Honduras after comparing morphological, molecular, and osteological data from the holotype to that of the other nominal forms of the genus. The new species differs from all of the known species of Cryptotriton in at least one character from all three datasets. We also suggest placing C. wakei in the synonymy of C. nasalis after examining the morphological and osteological characters of the single known specimen of C. wakei.

  6. Fire salamander (Salamandra salamandra in Larzac plateau: low occurrence, pond-breeding and cohabitation of larvae with paedomorphic palmate newts (Lissotriton helveticus

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    Mathieu Denoël

    2014-06-01

    Full Text Available Alternative reproductive strategies are widespread in caudate amphibians. Among them, fire salamanders (Salamandra salamandra usually rely on streams to give birth to aquatic larvae but also use ponds, whereas palmate newt larvae (Lissotriton helveticus typically metamorphose into terrestrial juveniles, but can also reproduce in retaining their gills, a process known as paedomorphosis. Here we report repeated observations of an unusual case of coexistence of these two alternative traits in the same pond (Larzac, France. The prevalence of fire salamanders in Southern Larzac was very low (pond occupancy: 0.36%. The observed abundance of fire salamander larvae and paedomorphic newts was also low in the studied pond. On one hand, the rarity of this coexistence pattern may suggest that habitat characteristics may not be optimal or that competition or predation processes might be operating. However, these hypotheses remain to be tested. On the other hand, as this is the only known case of breeding in Southern Larzac, it could be considered to be at a high risk of extirpation.

  7. What are the consequences of combining nuclear and mitochondrial data for phylogenetic analysis? Lessons from Plethodon salamanders and 13 other vertebrate clades

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    Wiens John J

    2011-10-01

    Full Text Available Abstract Background The use of mitochondrial DNA data in phylogenetics is controversial, yet studies that combine mitochondrial and nuclear DNA data (mtDNA and nucDNA to estimate phylogeny are common, especially in vertebrates. Surprisingly, the consequences of combining these data types are largely unexplored, and many fundamental questions remain unaddressed in the literature. For example, how much do trees from mtDNA and nucDNA differ? How are topological conflicts between these data types typically resolved in the combined-data tree? What determines whether a node will be resolved in favor of mtDNA or nucDNA, and are there any generalities that can be made regarding resolution of mtDNA-nucDNA conflicts in combined-data trees? Here, we address these and related questions using new and published nucDNA and mtDNA data for Plethodon salamanders and published data from 13 other vertebrate clades (including fish, frogs, lizards, birds, turtles, and mammals. Results We find widespread discordance between trees from mtDNA and nucDNA (30-70% of nodes disagree per clade, but this discordance is typically not strongly supported. Despite often having larger numbers of variable characters, mtDNA data do not typically dominate combined-data analyses, and combined-data trees often share more nodes with trees from nucDNA alone. There is no relationship between the proportion of nodes shared between combined-data and mtDNA trees and relative numbers of variable characters or levels of homoplasy in the mtDNA and nucDNA data sets. Congruence between trees from mtDNA and nucDNA is higher on branches that are longer and deeper in the combined-data tree, but whether a conflicting node will be resolved in favor mtDNA or nucDNA is unrelated to branch length. Conflicts that are resolved in favor of nucDNA tend to occur at deeper nodes in the combined-data tree. In contrast to these overall trends, we find that Plethodon have an unusually large number of strongly

  8. Echinococcus granulosus genotypes in Iran

    Science.gov (United States)

    Sharafi, Seyedeh Maryam; Rostami-Nejad, Mohammad; Moazeni, Mohammad; Yousefi, Morteza; Saneie, Behnam; Hosseini-Safa, Ahmad

    2014-01-01

    Hydatidosis, caused by Echinococcus granulosus is one of the most important zoonotic diseases, throughout most parts of the world. Hydatidosis is endemic in Iran and responsible for approximately 1% of admission to surgical wards. There are extensive genetic variations within E. granulosus and 10 different genotypes (G1–G10) within this parasite have been reported. Identification of strains is important for improvement of control and prevention of the disease. No new review article presented the situation of Echinococcus granulosus genotypes in Iran in the recent years; therefore in this paper we reviewed the different studies regarding Echinococcus granulosus genotypes in Iran. PMID:24834298

  9. Despite Buffers, Experimental Forest Clearcuts Impact Amphibian Body Size and Biomass.

    Science.gov (United States)

    Veysey Powell, Jessica S; Babbitt, Kimberly J

    2015-01-01

    Forest buffers are a primary tool used to protect wetland-dependent wildlife. Though implemented widely, buffer efficacy is untested for most amphibian species. Consequently, it remains unclear whether buffers are sufficient for maintaining amphibian populations and if so, how wide buffers should be. We present evidence from a six-year, landscape-scale experiment testing the impacts of clearcutting, buffer width, and hydroperiod on body size and condition and biomass of breeding adults for two amphibian species at 11 vernal pools in the northeastern United States. We randomly assigned treatments (i.e., reference, 100m buffer, 30m buffer) across pools, clearcut to create buffers, and captured all spotted salamanders and wood frogs. Clearcuts strongly and negatively impacted size, condition, and biomass, but wider buffers mitigated effect magnitude and duration. Among recaptured individuals, for example, 30m-treatment salamanders were predicted to be about 9.5 mm shorter than, while 100m-treatment salamanders did not differ in length from, reference-treatment salamanders. Similarly, among recaptured frogs, mean length in the 30m treatment was predicted to decrease by about 1 mm/year, while in the 100m and reference treatments, length was time-invariant. Some, but not all, metrics recovered with time. For example, female new-captured and recaptured salamanders were predicted, respectively and on average, to weigh 4.5 and 7 g less in the 30m versus reference treatment right after the cut. While recaptured-female mass was predicted to recover by 9.5 years post-cut, new-captured-female mass did not recover. Hydroperiod was an important mediator: in the 100m treatment, cutting predominately affected pools that were stressed hydrologically. Overall, salamanders and female frogs were impacted more than male frogs. Our results highlight the importance of individualized metrics like body size, which can reveal sublethal effects and illuminate mechanisms by which habitat

  10. Despite Buffers, Experimental Forest Clearcuts Impact Amphibian Body Size and Biomass.

    Directory of Open Access Journals (Sweden)

    Jessica S Veysey Powell

    Full Text Available Forest buffers are a primary tool used to protect wetland-dependent wildlife. Though implemented widely, buffer efficacy is untested for most amphibian species. Consequently, it remains unclear whether buffers are sufficient for maintaining amphibian populations and if so, how wide buffers should be. We present evidence from a six-year, landscape-scale experiment testing the impacts of clearcutting, buffer width, and hydroperiod on body size and condition and biomass of breeding adults for two amphibian species at 11 vernal pools in the northeastern United States. We randomly assigned treatments (i.e., reference, 100m buffer, 30m buffer across pools, clearcut to create buffers, and captured all spotted salamanders and wood frogs. Clearcuts strongly and negatively impacted size, condition, and biomass, but wider buffers mitigated effect magnitude and duration. Among recaptured individuals, for example, 30m-treatment salamanders were predicted to be about 9.5 mm shorter than, while 100m-treatment salamanders did not differ in length from, reference-treatment salamanders. Similarly, among recaptured frogs, mean length in the 30m treatment was predicted to decrease by about 1 mm/year, while in the 100m and reference treatments, length was time-invariant. Some, but not all, metrics recovered with time. For example, female new-captured and recaptured salamanders were predicted, respectively and on average, to weigh 4.5 and 7 g less in the 30m versus reference treatment right after the cut. While recaptured-female mass was predicted to recover by 9.5 years post-cut, new-captured-female mass did not recover. Hydroperiod was an important mediator: in the 100m treatment, cutting predominately affected pools that were stressed hydrologically. Overall, salamanders and female frogs were impacted more than male frogs. Our results highlight the importance of individualized metrics like body size, which can reveal sublethal effects and illuminate mechanisms by

  11. Translation of Genotype to Phenotype by a Hierarchy of Cell Subsystems

    OpenAIRE

    Yu, Michael Ku; Kramer, Michael; Dutkowski, Janusz; Srivas, Rohith; Licon, Katherine; Kreisberg, Jason F.; Ng, Cherie T.; Krogan, Nevan; Sharan, Roded; Ideker, Trey

    2016-01-01

    Summary Accurately translating genotype to phenotype requires accounting for the functional impact of genetic variation at many biological scales. Here we present a strategy for genotype-phenotype reasoning based on existing knowledge of cellular subsystems. These subsystems and their hierarchical organization are defined by the Gene Ontology or a complementary ontology inferred directly from previously published datasets. Guided by the ontology?s hierarchical structure, we organize genotype ...

  12. The potential of different lime tree (Tilia spp genotypes for phytoextraction of heavy metals

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    Šijačić-Nikolić Mirjana

    2012-01-01

    Full Text Available The research of heavy metals contents (Pb, Mn, Zn, Ni, Fe in soil in the area of the National Park „Fruška gora”, along the highway M21 shows lower values for manganese, zinc and iron than the maximum allowed quantity prescribed by law. For nickel and lead it shows higher values than maximum allowed quantity. The heavy metals contents in leaves of lime tree in 12 analyzed genotypes are far below average values in accordance with ECCE with all genotypes except genotype 7 for lead and genotypes 7 and 8 for iron. The results of analysis of variance components show that out of four components (locality, genotype, locality x genotype and error only the interaction between locality and genotype does not contribute to variance. The contents of Pb, Mn, Fe and Zn in leaves is primarily influenced by genotype while Ni contents may be considered a consequence of locality. The selection of genotypes which is able to uptake greater quantities of heavy metals than other genotypes may serve as a solid basis for phytoextraction of heavy metals as a technology by which heavy metals, metalloids and radionuclides are extracted from environment through usage of suitable species and plant genotypes able to uptake and accumulate the given pollutants in parts of plant tissue. [Projekat Ministarstva nauke Republike Srbije, br. 43007: Studying climate change and its influence on the environment: Impacts, adaptation and mitigation

  13. Transforming microbial genotyping: a robotic pipeline for genotyping bacterial strains.

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    Brian O'Farrell

    Full Text Available Microbial genotyping increasingly deals with large numbers of samples, and data are commonly evaluated by unstructured approaches, such as spread-sheets. The efficiency, reliability and throughput of genotyping would benefit from the automation of manual manipulations within the context of sophisticated data storage. We developed a medium- throughput genotyping pipeline for MultiLocus Sequence Typing (MLST of bacterial pathogens. This pipeline was implemented through a combination of four automated liquid handling systems, a Laboratory Information Management System (LIMS consisting of a variety of dedicated commercial operating systems and programs, including a Sample Management System, plus numerous Python scripts. All tubes and microwell racks were bar-coded and their locations and status were recorded in the LIMS. We also created a hierarchical set of items that could be used to represent bacterial species, their products and experiments. The LIMS allowed reliable, semi-automated, traceable bacterial genotyping from initial single colony isolation and sub-cultivation through DNA extraction and normalization to PCRs, sequencing and MLST sequence trace evaluation. We also describe robotic sequencing to facilitate cherrypicking of sequence dropouts. This pipeline is user-friendly, with a throughput of 96 strains within 10 working days at a total cost of 200,000 items were processed by two to three people. Our sophisticated automated pipeline can be implemented by a small microbiology group without extensive external support, and provides a general framework for semi-automated bacterial genotyping of large numbers of samples at low cost.

  14. The effects of simulated solar UVB radiation on early developmental stages of the Northwestern Salamander (Ambystoma gracile) from three lakes

    Science.gov (United States)

    Calfee, Robin D.; Little, Edward E.; Pearl, Christopher A.; Hoffman, Robert L.

    2010-01-01

    Solar ultraviolet radiation (UV) has received much attention as a factor that could play a role in amphibian population declines. UV can be hazardous to some amphibians, but the resultant effects depend on a variety of environmental and behavioral factors. In this study, the potential effects of UV on the Northwestern Salamander, Ambystoma gracile, from three lakes were assessed in the laboratory using a solar simulator. We measured the survival of embryos and the survival and growth of larvae exposed to four UV treatments in controlled laboratory studies, the UV absorbance of egg jelly, oviposition depths in the lakes, and UV absorbance in water samples from the three lakes. Hatching success of embryos decreased in the higher UV treatments as compared to the control treatments, and growth of surviving larvae was significantly reduced in the higher UVB irradiance treatments. The egg jelly exhibited a small peak of absorbance within the UVB range (290–320 nm). The magnitude of UV absorbance differed among egg jellies from the three lakes. Oviposition depths at the three sites averaged 1.10 m below the water surface. Approximately 66% of surface UVB radiation was attenuated at 10-cm depth in all three lakes. Results of this study indicate that larvae may be sensitive to UVB exposure under laboratory conditions; however, in field conditions the depths of egg deposition in the lakes, absorbance of UV radiation by the water column, and the potential for behavioral adjustments may mitigate severe effects of UV radiation.

  15. Bayesian salamanders: analysing the demography of an underground population of the European plethodontid Speleomantes strinatii with state-space modelling

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    Salvidio Sebastiano

    2010-02-01

    Full Text Available Abstract Background It has been suggested that Plethodontid salamanders are excellent candidates for indicating ecosystem health. However, detailed, long-term data sets of their populations are rare, limiting our understanding of the demographic processes underlying their population fluctuations. Here we present a demographic analysis based on a 1996 - 2008 data set on an underground population of Speleomantes strinatii (Aellen in NW Italy. We utilised a Bayesian state-space approach allowing us to parameterise a stage-structured Lefkovitch model. We used all the available population data from annual temporary removal experiments to provide us with the baseline data on the numbers of juveniles, subadults and adult males and females present at any given time. Results Sampling the posterior chains of the converged state-space model gives us the likelihood distributions of the state-specific demographic rates and the associated uncertainty of these estimates. Analysing the resulting parameterised Lefkovitch matrices shows that the population growth is very close to 1, and that at population equilibrium we expect half of the individuals present to be adults of reproductive age which is what we also observe in the data. Elasticity analysis shows that adult survival is the key determinant for population growth. Conclusion This analysis demonstrates how an understanding of population demography can be gained from structured population data even in a case where following marked individuals over their whole lifespan is not practical.

  16. Temperature and ontogenetic effects on color change in the larval salamander species Ambystoma barbouri and Ambystoma texanum

    Energy Technology Data Exchange (ETDEWEB)

    Garcia, T S; Straus, R; Sih, A [Univ. of Kentucky, Dept. of Biological Sciences, Lexington, Kentucky (United States)

    2003-04-01

    Temperature has been shown to affect body color in several species of amphibians. The interaction between color and temperature may also change over larval ontogeny, perhaps because of age-related or seasonal changes in selection pressures on color. We quantified the effects of temperature on the color of the salamander sister species Ambystoma barbouri and Ambystoma texanum over larval ontogeny. We found that early-stage larvae responded to cold temperatures with a dark color relative to that of the warm temperature response. Both species then exhibited an ontogenetic shift in larval color, with larvae becoming lighter with age. Interestingly, older larvae showed decreased plasticity in color change to temperature when compared with younger stages. Older A. texanum larvae exhibited a reversal in the direction of color change, with cold temperatures inducing a lighter color relative to warm temperatures. We suggest that the overall pattern of color change (a plastic color response to temperature for young larvae, a progressive lightening of larvae over development, and an apparent loss of color plasticity to temperature over ontogeny) can be plausibly explained by seasonal changes in environmental factors (temperature, ultraviolet radiation) selecting for body color. (author)

  17. Movement, demographics, and occupancy dynamics of a federally-threatened salamander: evaluating the adequacy of critical habitat

    Directory of Open Access Journals (Sweden)

    Nathan F. Bendik

    2016-03-01

    Full Text Available Critical habitat for many species is often limited to occupied localities. For rare and cryptic species, or those lacking sufficient data, occupied habitats may go unrecognized, potentially hindering species recovery. Proposed critical habitat for the aquatic Jollyville Plateau salamander (Eurycea tonkawae and two sister species were delineated based on the assumption that surface habitat is restricted to springs and excludes intervening stream reaches. To test this assumption, we performed two studies to understand aspects of individual, population, and metapopulation ecology of E. tonkawae. First, we examined movement and population demographics using capture-recapture along a spring-influenced stream reach. We then extended our investigation of stream habitat use with a study of occupancy and habitat dynamics in multiple headwater streams. Indications of extensive stream channel use based on capture-recapture results included frequent movements of >15 m, and high juvenile abundance downstream of the spring. Initial occupancy of E. tonkawae was associated with shallow depths, maidenhair fern presence and low temperature variation (indicative of groundwater influence, although many occupied sites were far from known springs. Additionally, previously dry sites were three times more likely to be colonized than wet sites. Our results indicate extensive use of stream habitats, including intermittent ones, by E. tonkawae. These areas may be important for maintaining population connectivity or even as primary habitat patches. Restricting critical habitat to occupied sites will result in a mismatch with actual habitat use, particularly when assumptions of habitat use are untested, thus limiting the potential for recovery.

  18. Initial characterization of the large genome of the salamander Ambystoma mexicanum using shotgun and laser capture chromosome sequencing.

    Science.gov (United States)

    Keinath, Melissa C; Timoshevskiy, Vladimir A; Timoshevskaya, Nataliya Y; Tsonis, Panagiotis A; Voss, S Randal; Smith, Jeramiah J

    2015-11-10

    Vertebrates exhibit substantial diversity in genome size, and some of the largest genomes exist in species that uniquely inform diverse areas of basic and biomedical research. For example, the salamander Ambystoma mexicanum (the Mexican axolotl) is a model organism for studies of regeneration, development and genome evolution, yet its genome is ~10× larger than the human genome. As part of a hierarchical approach toward improving genome resources for the species, we generated 600 Gb of shotgun sequence data and developed methods for sequencing individual laser-captured chromosomes. Based on these data, we estimate that the A. mexicanum genome is ~32 Gb. Notably, as much as 19 Gb of the A. mexicanum genome can potentially be considered single copy, which presumably reflects the evolutionary diversification of mobile elements that accumulated during an ancient episode of genome expansion. Chromosome-targeted sequencing permitted the development of assemblies within the constraints of modern computational platforms, allowed us to place 2062 genes on the two smallest A. mexicanum chromosomes and resolves key events in the history of vertebrate genome evolution. Our analyses show that the capture and sequencing of individual chromosomes is likely to provide valuable information for the systematic sequencing, assembly and scaffolding of large genomes.

  19. Sixty-Five Million Years of Change in Temperature and Topography Explain Evolutionary History in Eastern North American Plethodontid Salamanders.

    Science.gov (United States)

    Barnes, Richard; Clark, Adam Thomas

    2017-07-01

    For many taxa and systems, species richness peaks at midelevations. One potential explanation for this pattern is that large-scale changes in climate and geography have, over evolutionary time, selected for traits that are favored under conditions found in contemporary midelevation regions. To test this hypothesis, we use records of historical temperature and topographic changes over the past 65 Myr to construct a general simulation model of plethodontid salamander evolution in eastern North America. We then explore possible mechanisms constraining species to midelevation bands by using the model to predict plethodontid evolutionary history and contemporary geographic distributions. Our results show that models that incorporate both temperature and topographic changes are better able to predict these patterns, suggesting that both processes may have played an important role in driving plethodontid evolution in the region. Additionally, our model (whose annotated source code is included as a supplement) represents a proof of concept to encourage future work that takes advantage of recent advances in computing power to combine models of ecology, evolution, and earth history to better explain the abundance and distribution of species over time.

  20. The effects of food level and conspecific density on biting and cannibalism in larval long-toed salamanders, Ambystoma macrodactylum.

    Science.gov (United States)

    Wildy, Erica L; Chivers, Douglas P; Kiesecker, Joseph M; Blaustein, Andrew R

    2001-07-01

    Previous studies have examined abiotic and biotic factors that facilitate agonistic behavior. For larval amphibians, food availability and conspecific density have been suggested as important factors influencing intraspecific aggression and cannibalism. In this study, we examined the separate and combined effects of food availability and density on the agonistic behavior and life history of larval long-toed salamanders, Ambystoma macrodactylum. We designed a 2×2 factorial experiment in which larvae were raised with either a high or low density of conspecifics and fed either a high or low level of food. For each treatment, we quantified the amount of group size variation, biting, and cannibalism occurring. Additionally, we examined survival to, time to and size at metamorphosis for all larvae. Results indicated that differences in both density and food level influenced all three life history traits measured. Moreover, differences in food level at which larvae were reared resulted in higher within-group size variation and heightened intraspecific biting while both density and food level contributed to increased cannibalism. We suggest that increased hunger levels and an uneven size structure promoted biting among larvae in the low food treatments. Moreover, these factors combined with a higher encounter rate with conspecifics in the high density treatments may have prompted larger individuals to seek an alternative food source in the form of smaller conspecifics.

  1. Temperature and ontogenetic effects on color change in the larval salamander species Ambystoma barbouri and Ambystoma texanum

    International Nuclear Information System (INIS)

    Garcia, T.S.; Straus, R.; Sih, A.

    2003-01-01

    Temperature has been shown to affect body color in several species of amphibians. The interaction between color and temperature may also change over larval ontogeny, perhaps because of age-related or seasonal changes in selection pressures on color. We quantified the effects of temperature on the color of the salamander sister species Ambystoma barbouri and Ambystoma texanum over larval ontogeny. We found that early-stage larvae responded to cold temperatures with a dark color relative to that of the warm temperature response. Both species then exhibited an ontogenetic shift in larval color, with larvae becoming lighter with age. Interestingly, older larvae showed decreased plasticity in color change to temperature when compared with younger stages. Older A. texanum larvae exhibited a reversal in the direction of color change, with cold temperatures inducing a lighter color relative to warm temperatures. We suggest that the overall pattern of color change (a plastic color response to temperature for young larvae, a progressive lightening of larvae over development, and an apparent loss of color plasticity to temperature over ontogeny) can be plausibly explained by seasonal changes in environmental factors (temperature, ultraviolet radiation) selecting for body color. (author)

  2. Environmental DNA method for estimating salamander distribution in headwater streams, and a comparison of water sampling methods.

    Science.gov (United States)

    Katano, Izumi; Harada, Ken; Doi, Hideyuki; Souma, Rio; Minamoto, Toshifumi

    2017-01-01

    Environmental DNA (eDNA) has recently been used for detecting the distribution of macroorganisms in various aquatic habitats. In this study, we applied an eDNA method to estimate the distribution of the Japanese clawed salamander, Onychodactylus japonicus, in headwater streams. Additionally, we compared the detection of eDNA and hand-capturing methods used for determining the distribution of O. japonicus. For eDNA detection, we designed a qPCR primer/probe set for O. japonicus using the 12S rRNA region. We detected the eDNA of O. japonicus at all sites (with the exception of one), where we also observed them by hand-capturing. Additionally, we detected eDNA at two sites where we were unable to observe individuals using the hand-capturing method. Moreover, we found that eDNA concentrations and detection rates of the two water sampling areas (stream surface and under stones) were not significantly different, although the eDNA concentration in the water under stones was more varied than that on the surface. We, therefore, conclude that eDNA methods could be used to determine the distribution of macroorganisms inhabiting headwater systems by using samples collected from the surface of the water.

  3. Identification of polymorphic inversions from genotypes

    Directory of Open Access Journals (Sweden)

    Cáceres Alejandro

    2012-02-01

    Full Text Available Abstract Background Polymorphic inversions are a source of genetic variability with a direct impact on recombination frequencies. Given the difficulty of their experimental study, computational methods have been developed to infer their existence in a large number of individuals using genome-wide data of nucleotide variation. Methods based on haplotype tagging of known inversions attempt to classify individuals as having a normal or inverted allele. Other methods that measure differences between linkage disequilibrium attempt to identify regions with inversions but unable to classify subjects accurately, an essential requirement for association studies. Results We present a novel method to both identify polymorphic inversions from genome-wide genotype data and classify individuals as containing a normal or inverted allele. Our method, a generalization of a published method for haplotype data 1, utilizes linkage between groups of SNPs to partition a set of individuals into normal and inverted subpopulations. We employ a sliding window scan to identify regions likely to have an inversion, and accumulation of evidence from neighboring SNPs is used to accurately determine the inversion status of each subject. Further, our approach detects inversions directly from genotype data, thus increasing its usability to current genome-wide association studies (GWAS. Conclusions We demonstrate the accuracy of our method to detect inversions and classify individuals on principled-simulated genotypes, produced by the evolution of an inversion event within a coalescent model 2. We applied our method to real genotype data from HapMap Phase III to characterize the inversion status of two known inversions within the regions 17q21 and 8p23 across 1184 individuals. Finally, we scan the full genomes of the European Origin (CEU and Yoruba (YRI HapMap samples. We find population-based evidence for 9 out of 15 well-established autosomic inversions, and for 52 regions

  4. HFE genotype affects exosome phenotype in cancer.

    Science.gov (United States)

    Mrowczynski, Oliver D; Madhankumar, A B; Slagle-Webb, Becky; Lee, Sang Y; Zacharia, Brad E; Connor, James R

    2017-08-01

    Neuroblastoma is the third most common childhood cancer, and timely diagnosis and sensitive therapeutic monitoring remain major challenges. Tumor progression and recurrence is common with little understanding of mechanisms. A major recent focus in cancer biology is the impact of exosomes on metastatic behavior and the tumor microenvironment. Exosomes have been demonstrated to contribute to the oncogenic effect on the surrounding tumor environment and also mediate resistance to therapy. The effect of genotype on exosomal phenotype has not yet been explored. We interrogated exosomes from human neuroblastoma cells that express wild-type or mutant forms of the HFE gene. HFE, one of the most common autosomal recessive polymorphisms in the Caucasian population, originally associated with hemochromatosis, has also been associated with increased tumor burden, therapeutic resistance boost, and negative impact on patient survival. Herein, we demonstrate that changes in genotype cause major differences in the molecular and functional properties of exosomes; specifically, HFE mutant derived exosomes have increased expression of proteins relating to invasion, angiogenesis, and cancer therapeutic resistance. HFE mutant derived exosomes were also shown to transfer this cargo to recipient cells and cause an increased oncogenic functionality in those recipient cells. Copyright © 2017. Published by Elsevier B.V.

  5. Equine cryptosporidial infection associated with Cryptosporidium hedgehog genotype in Algeria

    Czech Academy of Sciences Publication Activity Database

    Laatamna, A.E.; Wágnerová, P.; Sak, Bohumil; Květoňová, Dana; Aissi, M.; Rost, M.; Kváč, Martin

    2013-01-01

    Roč. 197, 1-2 (2013), s. 350-353 ISSN 0304-4017 Grant - others:GAJU(CZ) 022/2010/Z; GAJU(CZ) 011/2013/Z Institutional support: RVO:60077344 Keywords : horses * Cryptosporidium hedgehog genotype * PCR * SSU * GP60 Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.545, year: 2013

  6. A new moss salamander, genus Nototriton (Caudata: Plethodontidae), from the Cordillera de Talamanca, in the Costa Rica-Panama border region.

    Science.gov (United States)

    Arias, Erick; Kubicki, Brian

    2018-01-07

    A new salamander belonging to the genus Nototriton, subgenus Nototriton, is described from the Caribbean slopes of the southeastern Cordillera de Talamanca in Costa Rica, within Parque Internacional La Amistad, at an elevation ca. 1500 m a.s.l. This new taxon is distinguished from its congeners by its morphological characteristics and by its differentiation in DNA sequences of the 16S rRNA, cytochrome oxidase subunit I (COI), and cytochrome b mitochondrial genes. This new species represents the southernmost extension known for the genus Nototriton.

  7. FTO genotype and weight loss

    DEFF Research Database (Denmark)

    Livingstone, Katherine M; Celis-Morales, Carlos; Papandonatos, George D

    2016-01-01

    : Ovid Medline, Scopus, Embase, and Cochrane from inception to November 2015. ELIGIBILITY CRITERIA FOR STUDY SELECTION: Randomised controlled trials in overweight or obese adults reporting reduction in body mass index, body weight, or waist circumference by FTO genotype (rs9939609 or a proxy) after...

  8. FTO genotype and weight loss

    DEFF Research Database (Denmark)

    Livingstone, Katherine M; Celis-Morales, Carlos; Papandonatos, George D

    2016-01-01

    OBJECTIVE: To assess the effect of the FTO genotype on weight loss after dietary, physical activity, or drug based interventions in randomised controlled trials. DESIGN: Systematic review and random effects meta-analysis of individual participant data from randomised controlled trials. DATA SOURC...

  9. Molecular characterization of rotavirus genotypes in immunosuppressed and non-immunosuppressed pediatric patients

    Directory of Open Access Journals (Sweden)

    Luciane A. Pereira

    2013-05-01

    Conclusion: RVA infections can be associated with severe clinical manifestations, and the surveillance of genotypic variability of this virus is crucial to monitor the emergence of new strains and the impact of the immunization in these patients.

  10. Effects of simulated solar UVB radiation on early developmental stages of the northwestern salamander (Ambystoma gracile) from three lakes

    Science.gov (United States)

    Calfee, R.D.; Little, E.E.; Pearl, C.A.; Hoffman, R.L.

    2010-01-01

    Solar ultraviolet radiation (UV) has received much attention as a factor that could play a role in amphibian population declines. UV can be hazardous to some amphibians, but the resultant effects depend on a variety of environmental and behavioral factors. In this study, the potential effects of UV on the Northwestern Salamander, Ambystoma gracile, from three lakes were assessed in the laboratory using a solar simulator. We measured the survival of embryos and the survival and growth of larvae exposed to four UV treatments in controlled laboratory studies, the UV absorbance of egg jelly, oviposition depths in the lakes, and UV absorbance in water samples from the three lakes. Hatching success of embryos decreased in the higher UV treatments as compared to the control treatments, and growth of surviving larvae was significantly reduced in the higher UVB irradiance treatments. The egg jelly exhibited a small peak of absorbance within the UVB range (290-320 nm). The magnitude of UV absorbance differed among egg jellies from the three lakes. Oviposition depths at the three sites averaged 1.10 m below the water surface. Approximately 66 of surface UVB radiation was attenuated at 10-cm depth in all three lakes. Results of this study indicate that larvae may be sensitive to UVB exposure under laboratory conditions; however, in field conditions the depths of egg deposition in the lakes, absorbance of UV radiation by the water column, and the potential for behavioral adjustments may mitigate severe effects of UV radiation. Copyright 2010 Society for the Study of Amphibians and Reptiles.

  11. Reproduction of the salamander Siren intermedia le conte with especial reference to oviducal anatomy and mode of fertilization.

    Science.gov (United States)

    Sever, David M; Rania, Lisa C; Krenz, John D

    1996-03-01

    Reproduction was studied in a South Carolina population of the paedomorphic salamander Siren intermedia with emphasis on anatomy of the female oviduct. The oviduct forms 67-79% of the snout-vent length in this elongate species and can be divided into three portions. The atrium, 7-13% of oviducal length, is the narrow anteriormost portion, with the ostial opening immediately caudad of the transverse septum. The ampulla, 63-75% of oviducal length, is the highly convoluted, middle portion in which gelatinous coverings are added to the eggs during their passage. Hypertrophy of the oviducal glands in the ampulla causes the ampulla to increase in diameter during the ovipository season. The secretion of the eosinophilic oviducal glands is intensely positive following staining with the periodic acid-Schiff procedure and does not react with alcian blue at pH 2.5. This staining reaction, coupled with the presence of abundant rough endoplasmic reticulum and Golgi complexes, indicates that the secretion contains a glycoprotein. The ovisac, 16-25% of oviducal length, is the most posterior portion of the oviduct and holds up to 10-11 eggs prior to oviposition. Oviducal glands similar to those in the ampulla are absent in the ovisac. Oviposition in female sirens occurs during February-April in this population, and male spermiation is concurrent. Entire oviducts were sectioned from three females collected during the ovipository season and from two collected prior to the breeding season, and sperm were not found in the oviducts of these specimens. Thus no evidence was found for internal fertilization or sperm storage in the oviducts of sirens. © 1996 Wiley-Liss, Inc. Copyright © 1996 Wiley-Liss, Inc.

  12. Effects of Tail Clipping on Larval Performance and Tail Regeneration Rates in the Near Eastern Fire Salamander, Salamandra infraimmaculata.

    Directory of Open Access Journals (Sweden)

    Ori Segev

    Full Text Available Tail-tip clipping is a common technique for collecting tissue samples from amphibian larvae and adults. Surprisingly, studies of this invasive sampling procedure or of natural tail clipping--i.e., bites inflicted by predators including conspecifics--on the performance and fitness of aquatic larval stages of urodeles are scarce. We conducted two studies in which we assessed the effects of posterior tail clipping (~30 percent of tail on Near Eastern fire salamander (Salamandra infraimmaculata larvae. In a laboratory study, we checked regeneration rates of posterior tail-tip clipping at different ages. Regeneration rates were hump-shaped, peaking at the age of ~30 days and then decreasing. This variation in tail regeneration rates suggests tradeoffs in resource allocation between regeneration and somatic growth during early and advanced development. In an outdoor artificial pond experiment, under constant larval densities, we assessed how tail clipping of newborn larvae affects survival to, time to, and size at metamorphosis. Repeated measures ANOVA on mean larval survival per pond revealed no effect of tail clipping. Tail clipping had correspondingly no effect on larval growth and development expressed in size (mass and snout-vent length at, and time to, metamorphosis. We conclude that despite the given variation in tail regeneration rates throughout larval ontogeny, clipping of 30% percent of the posterior tail area seems to have no adverse effects on larval fitness and survival. We suggest that future use of this imperative tool for the study of amphibian should take into account larval developmental stage during the time of application and not just the relative size of the clipped tail sample.

  13. Multilocus Phylogeography and Species Delimitation in the Cumberland Plateau Salamander, Plethodon kentucki: Incongruence among Data Sets and Methods.

    Directory of Open Access Journals (Sweden)

    Shawn R Kuchta

    Full Text Available Species are a fundamental unit of biodiversity, yet can be challenging to delimit objectively. This is particularly true of species complexes characterized by high levels of population genetic structure, hybridization between genetic groups, isolation by distance, and limited phenotypic variation. Previous work on the Cumberland Plateau Salamander, Plethodon kentucki, suggested that it might constitute a species complex despite occupying a relatively small geographic range. To examine this hypothesis, we sampled 135 individuals from 43 populations, and used four mitochondrial loci and five nuclear loci (5693 base pairs to quantify phylogeographic structure and probe for cryptic species diversity. Rates of evolution for each locus were inferred using the multidistribute package, and time calibrated gene trees and species trees were inferred using BEAST 2 and *BEAST 2, respectively. Because the parameter space relevant for species delimitation is large and complex, and all methods make simplifying assumptions that may lead them to fail, we conducted an array of analyses. Our assumption was that strongly supported species would be congruent across methods. Putative species were first delimited using a Bayesian implementation of the GMYC model (bGMYC, Geneland, and Brownie. We then validated these species using the genealogical sorting index and BPP. We found substantial phylogeographic diversity using mtDNA, including four divergent clades and an inferred common ancestor at 14.9 myr (95% HPD: 10.8-19.7 myr. By contrast, this diversity was not corroborated by nuclear sequence data, which exhibited low levels of variation and weak phylogeographic structure. Species trees estimated a far younger root than did the mtDNA data, closer to 1.0 myr old. Mutually exclusive putative species were identified by the different approaches. Possible causes of data set discordance, and the problem of species delimitation in complexes with high levels of population

  14. Management and monitoring of the endangered Shenandoah salamander under climate change: Workshop report 10-12 April 2012

    Science.gov (United States)

    Grant, Evan H. Campbell; Wofford, John E.B.; Smith, D.R.; Dennis, J.; Hawkins-Hoffman, C.; Schaberl, J.; Foley, M.; Bogle, M.

    2014-01-01

    Here we report on a structured decision making (SDM) process to identify management strategies to ensure persistence of the federally endangered Shenandoah salamander (Plethodon shenandoah), given that it may be at increased extinction risk under projected climate change. The focus of this report is the second of two SDM workshops; in the first workshop, participants developed a prototype of the decision, including problem frame, management objectives and a suite of potential management strategies, predictive models to inform the decision and link alternatives with the objectives to identify potential solutions, and identified data needs to reduce key uncertainties in the decision. Participants in this second workshop included experts in National Park Service policy at multiple administrative levels, who refined objectives, further evaluated the initial management alternatives, and discussed policy constraints on implementing active management for the species and its high-elevation habitat. The conclusion of the second workshop was similar to that of the first: the current state of information and objectives suggest that there is some value in considering active management to reduce the long-term extinction risk for the species, though there are institutional conservative policies to implementing active management at range-wide scales. The workshop participants also emphasized a conservative NPS management philosophy, including caution in implementing management actions that may ultimately harm the system, a stated assumption that ecosystem changes were “natural” unless demonstrated otherwise (therefore not warranting active management to mitigate), and a need to demonstrate that extinction risk is tied to anthropogenic influence prior to taking active management to mitigate specific anthropogenic influences. Even within a protected area having minimal human disturbance, intertwined environmental variables and interspecific relationships that drive population

  15. Evaluation of microorganisms cultured from injured and repressed tissue regeneration sites in endangered giant aquatic Ozark Hellbender salamanders.

    Directory of Open Access Journals (Sweden)

    Cheryl A Nickerson

    cultured from a Cryptobranchid salamander. The incidence of abnormalities/injury and retarded regeneration in C. a. bishopi may have many contributing factors including disease and habitat degradation. Results from this study may provide insight into other amphibian population declines.

  16. Physiological responses of genotypes soybean to simulated drought stress

    Directory of Open Access Journals (Sweden)

    Eleonóra Krivosudská

    2016-12-01

    Full Text Available The objective of this research was to investigate possible genetic variation in the sensitivity of soybean cultivars for nitrogen fixation rates in response to soil drying. The work confirmed that the selected physiological characteristics (RWC, osmotic potential, stress index and created nodules on roots are good evaluating parameters for the determination of water stress in plant. In the floricultural year 2014 an experiment with four genetic resources of soybean was launched. Sowing of Maverick (USA, Drina (HRV, Nigra (SVK and Polanka (CZK genotypes was carried out in the containers of 15 l capacity. This stress had a negative impact on the physiological parameters. By comparing the RWC values, the decrease was more significant at the end of dehydration, which was monitored in Maverick and Drina genotypes using the Nitrazon inoculants and water stress effect. Inoculated stressed Nigra and Polanka genotypes have kept higher water content till the end of dehydration period. Also the proline accumulation was monitored during the water stress, whilst higher content of free proline reached of Maverick. More remarkable decrease of osmotic potential was again registered in a foreign Drina and Maverick genotypes in the inoculated variations. Nigra and Polanka genotypes responses not so significant in the given conditions.

  17. Hepatitis C Virus: Virology and Genotypes

    KAUST Repository

    Abdelaziz, Ahmed

    2017-01-01

    Hepatitis C virus (HCV) is a major causative agent of chronic liver disease worldwide. HCV is characterized by genetic heterogeneity, with at least six genotypes identified. The geographic distribution of genotypes has shown variations in different

  18. Response of Red-Backed Salamanders (Plethodon Cinereus to Changes in Hemlock Forest Soil Driven by Invasive Hemlock Woolly Adelgid (Adelges Tsugae

    Directory of Open Access Journals (Sweden)

    Alison Ochs

    2017-01-01

    Full Text Available Hemlock forests of the northeastern United States are declining due to the invasive hemlock woolly adelgid (HWA (Adelges tsugae. Hardwood species replace these forests, which affects soil properties that may influence other communities, such as red-backed salamanders (red-backs (Plethodon cinereus. This study examined the effects of HWA invasion on soil properties and how this affects red-backs at the Hemlock Removal Experiment at Harvard Forest, which consists of eight 0.8 ha plots treated with girdling to simulate HWA invasion, logging to simulate common management practices, or hemlock- or hardwood-dominated controls. Coverboard surveys were used to determine the relative abundance of red-backs between plots during June and July 2014 and soil cores were collected from which the bulk density, moisture, pH, temperature, leaf litter, and carbon-nitrogen ratio were measured. Ordination provided a soil quality index based on temperature, pH, and carbon-to-nitrogen ratio, which was significantly different between plot treatments (p < 0.05 and showed a significant negative correlation with the red-back relative abundance (p < 0.05. The findings support the hypothesis that red-backs are affected by soil quality, which is affected by plot treatment and thus HWA invasion. Further studies should explore how salamanders react in the long term towards changing environments and consider the use of red-backs as indicator species.

  19. Genotype x environment interaction and optimum resource ...

    African Journals Online (AJOL)

    ... x E) interaction and to determine the optimum resource allocation for cassava yield trials. The effects of environment, genotype and G x E interaction were highly significant for all yield traits. Variations due to G x E interaction were greater than those due to genotypic differences for all yield traits. Genotype x location x year ...

  20. Mineral Composition of Organically Grown Wheat Genotypes: Contribution to Daily Minerals Intake

    Science.gov (United States)

    Hussain, Abrar; Larsson, Hans; Kuktaite, Ramune; Johansson, Eva

    2010-01-01

    In this study, 321 winter and spring wheat genotypes were analysed for twelve nutritionally important minerals (B, Cu, Fe, Se, Mg, Zn, Ca, Mn, Mo, P, S and K). Some of the genotypes used were from multiple locations and years, resulting in a total number of 493 samples. Investigated genotypes were divided into six genotype groups i.e., selections, old landraces, primitive wheat, spelt, old cultivars and cultivars. For some of the investigated minerals higher concentrations were observed in selections, primitive wheat, and old cultivars as compared to more modern wheat material, e.g., cultivars and spelt wheat. Location was found to have a significant effect on mineral concentration for all genotype groups, although for primitive wheat, genotype had a higher impact than location. Spring wheat was observed to have significantly higher values for B, Cu, Fe, Zn, Ca, S and K as compared to winter wheat. Higher levels of several minerals were observed in the present study, as compared to previous studies carried out in inorganic systems, indicating that organic conditions with suitable genotypes may enhance mineral concentration in wheat grain. This study also showed that a very high mineral concentration, close to daily requirements, can be produced by growing specific primitive wheat genotypes in an organic farming system. Thus, by selecting genotypes for further breeding, nutritional value of the wheat flour for human consumption can be improved. PMID:20948934

  1. Allelopathic interference of alfalfa (Medicago sativa L.) genotypes to annual ryegrass (Lolium rigidum).

    Science.gov (United States)

    Zubair, Hasan Muhammad; Pratley, James E; Sandral, G A; Humphries, A

    2017-07-01

    Alfalfa (Medicago sativa L.) genotypes at varying densities were investigated for allelopathic impact using annual ryegrass (Lolium rigidum) as the target species in a laboratory bioassay. Three densities (15, 30, and 50 seedlings/beaker) and 40 alfalfa genotypes were evaluated by the equal compartment agar method (ECAM). Alfalfa genotypes displayed a range of allelopathic interference in ryegrass seedlings, reducing root length from 5 to 65%. The growth of ryegrass decreased in response to increasing density of alfalfa seedlings. At the lowest density, Q75 and Titan9 were the least allelopathic genotypes. An overall inhibition index was calculated to rank each alfalfa genotype. Reduction in seed germination of annual ryegrass occurred in the presence of several alfalfa genotypes including Force 10, Haymaster7 and SARDI Five. A comprehensive metabolomic analysis using Quadruple Time of Flight (Q-TOF), was conducted to compare six alfalfa genotypes. Variation in chemical compounds was found between alfalfa root extracts and exudates and also between genotypes. Further individual compound assessments and quantitative study at greater chemical concentrations are needed to clarify the allelopathic activity. Considerable genetic variation exists among alfalfa genotypes for allelopathic activity creating the opportunity for its use in weed suppression through selection.

  2. Genetic Divergence in Sugarcane Genotypes

    OpenAIRE

    Tahir, Mohammad; Rahman, Hidayatur; Gul, Rahmani; Ali, Amjad; Khalid, Muhammad

    2012-01-01

    To assess genetic divergence of sugarcane germplasm, an experiment comprising 25 sugarcane genotypes was conducted at Sugar Crops Research Institute (SCRI), Mardan, Khyber Pakhtunkhwa, Pakistan, in quadruple lattice design during 2008-09. Among the 14 parameters evaluated, majority exhibited significant differences while some showed nonsignificant mean squares. The initial correlation matrix revealed medium to high correlations. Principal Component Analysis (PCA) showed that there were two pr...

  3. Impact of "Killer Immunoglobulin-Like Receptor /Ligand" Genotypes on Outcome following Surgery among Patients with Colorectal Cancer: Activating KIRs Are Associated with Long-Term Disease Free Survival.

    Directory of Open Access Journals (Sweden)

    Kemal Beksac

    Full Text Available Approximately 30% of patients with stage II/III colorectal cancer develop recurrence following surgery. How individual regulation of host mediated anti-tumor cytotoxicity is modified by the killer-cell immunoglobulin-like receptor (KIRs genotype is essential for prediction of outcome. We analyzed the frequency of KIR and KIR ligand Human Leukocyte Antigen Class I genotypes, and their effects on recurrence and disease-free survival (DFS. Out of randomly selected 87 colorectal cancer patients who underwent R0 resection operations between 2005 and 2008, 29 patients whose cancers progressed within a median five-year follow-up period were compared with 58 patients with no recurrence within the same time period. Recurrent cases shared similar tumor stages with non-recurrent cases, but had different localizations. We used DNA isolated from pathological archival lymphoid and tumor tissues for KIR and KIR ligand (HLA-C, group C1, group C2, and HLA-A-Bw4 genotyping. Among cases with recurrence, KIR2DL1 (inhibitory KIR and A-Bw4 (ligand for inhibitory KIR3DL1 were observed more frequently (p=0.017 and p=0.024; and KIR2DS2 and KIR2DS3 (both activating KIRs were observed less frequently (p=0.005 and p=0.043. Similarly, in the non-recurrent group, inhibitory KIR-ligand combinations 2DL1-C2 and 2DL3-C1 were less frequent, while the activating combination 2DS2-C1 was more frequent. The lack of KIR2DL1, 2DL1-C2, and 2DL3-C1 improved disease-free survival (DFS (100% vs. 62.3%, p=0.05; 93.8% vs. 60.0%, p=0.035; 73.6% vs. 55.9%, p=0.07. The presence of KIR2DS2, 2DS3, and 2DS2-C1 improved DFS (77.8% vs. 48.5%, p=0.01; 79.4% vs. 58.5%, p=0.003; 76.9% vs. 51.4%, p=0.023. KIR2DS3 reduced the risk of recurrence (HR=0.263, 95% CI = 0.080-0.863, p=0.028. The number of activating KIRs are correlated strongly with DFS, none/ one/ two KIR : 54/77/98 months (p=0.004. In conclusion the inheritance of increasing numbers of activating KIRs and lack of inhibitory KIRs

  4. Hepatitis C genotype distribution in patient and blood donor samples in South Africa for the period 2008-2012.

    Science.gov (United States)

    Prabdial-Sing, N; Chirwa, T; Thaver, J; Smuts, H; Vermeulen, M; Suchard, M; Puren, A J

    2016-11-01

    There are limited molecular epidemiological studies of hepatitis C at a national level in South Africa. The introduction of newer treatment modalities for hepatitis C requires knowledge of the genotypes as these may have different prognostic and therapeutic implications. This retrospective study describes genotype distributions of patients attending specialist clinics and a blood donor group studied during the period 2008-2012 in South Africa. Residual samples from diagnostic viral load testing from specialist clinics in South Africa (n=941) and from the South African National Blood Service (n=294) were analysed quantitatively by real-time PCR and genotyped using the Versant line probe assay or sequencing. Genotype 1 was predominant in blood donors (34%), whilst genotype 5a was prevalent in patients (36%). In the blood donor group, genotype 4 was detected for the first time. Genotype 2 was rare in the patient group and not detected in blood donors. Genotype 1 was the predominant genotype in the younger age groups (less than 30 years), whereas genotype 5a was found at higher proportions in the older age groups for both the patient and blood donor groups, comprising more than 60% of genotypes in those older than 50 years. Genotypes 1 and 5 were at highest proportions across all provinces compared to other genotypes. In blood donors, genotype 1 was predominant among Caucasians (43%) and genotype 5a among Blacks (54%). Such information is required for planning the impact on the health sector with regard to newly emerging therapies for hepatitis C and burden of disease. © 2016 John Wiley & Sons Ltd.

  5. A refined ecological risk assessment for California red-legged frog, Delta smelt, and California tiger salamander exposed to malathion.

    Science.gov (United States)

    Clemow, Yvonne H; Manning, Gillian E; Breton, Roger L; Winchell, Michael F; Padilla, Lauren; Rodney, Sara I; Hanzas, John P; Estes, Tammara L; Budreski, Katherine; Toth, Brent N; Hill, Katie L; Priest, Colleen D; Teed, R Scott; Knopper, Loren D; Moore, Dwayne Rj; Stone, Christopher T; Whatling, Paul

    2018-03-01

    The California red-legged frog (CRLF), Delta smelt (DS), and California tiger salamander (CTS) are 3 species listed under the United States Federal Endangered Species Act (ESA), all of which inhabit aquatic ecosystems in California. The US Environmental Protection Agency (USEPA) has conducted deterministic screening-level risk assessments for these species potentially exposed to malathion, an organophosphorus insecticide and acaricide. Results from our screening-level analyses identified potential risk of direct effects to DS as well as indirect effects to all 3 species via reduction in prey. Accordingly, for those species and scenarios in which risk was identified at the screening level, we conducted a refined probabilistic risk assessment for CRLF, DS, and CTS. The refined ecological risk assessment (ERA) was conducted using best available data and approaches, as recommended by the 2013 National Research Council (NRC) report "Assessing Risks to Endangered and Threatened Species from Pesticides." Refined aquatic exposure models including the Pesticide Root Zone Model (PRZM), the Vegetative Filter Strip Modeling System (VFSMOD), the Variable Volume Water Model (VVWM), the Exposure Analysis Modeling System (EXAMS), and the Soil and Water Assessment Tool (SWAT) were used to generate estimated exposure concentrations (EECs) for malathion based on worst-case scenarios in California. Refined effects analyses involved developing concentration-response curves for fish and species sensitivity distributions (SSDs) for fish and aquatic invertebrates. Quantitative risk curves, field and mesocosm studies, surface-water monitoring data, and incident reports were considered in a weight-of-evidence approach. Currently, labeled uses of malathion are not expected to result in direct effects to CRLF, DS or CTS, or indirect effects due to effects on fish and invertebrate prey. Integr Environ Assess Manag 2018;14:224-239. © 2017 The Authors. Integrated Environmental Assessment and

  6. Variability of traits quinoa introduced genotypes (Chenopodium quinoa Willd.

    Directory of Open Access Journals (Sweden)

    Dražić Slobodan

    2013-01-01

    Full Text Available We analyzed variability and influence of investigated factors on grain yield of quinoa during three year period (2009, 2010, 2011. The experiment was conducted at two locations (Nova Pazova and Surduk, using two introduced genotypes of quinoa: KVL 37 and KVL 52. We detected that location and genotype had important impact. Grain yield varied according to years of study (1224 kg/ha to 1671 kg/ha. Results of regression and correlation analysis indicate on variation of the impact of plant height and number of plants per meter on the grain yield. Correlation coefficients were generally low and didn't show as significant. This indicates that these studies included small number of properties that can affect grain yield. In further work with this introduced species, more properties should be included.

  7. Chemical composition, nutritional value and antioxidant properties of Mediterranean okra genotypes in relation to harvest stage.

    Science.gov (United States)

    Petropoulos, Spyridon; Fernandes, Ângela; Barros, Lillian; Ferreira, Isabel C F R

    2018-03-01

    The aim of the present study was to determine the effect of fruit size on nutritional value, chemical composition and antioxidant properties of Mediterranean okra genotypes. For this purpose, pods from four okra cultivars and local landraces commonly cultivated in Greece, as well as pods from four commercial cultivars from North America were collected at two sizes (3-5 and>7cm). Significant differences were observed between the studied genotypes for both nutritional value and chemical composition parameters. Small fruit had a higher nutritional value, whereas chemical composition differed in a genotype dependent manner with most of the studied cultivars showing better results when harvested in small size. In conclusion, fruit size has a genotype dependent impact on chemical composition and nutritional value of okra pods and the common practice of harvesting okra fruit while they still have a small size helps to increase nutritional value for most of the studied genotypes. Copyright © 2017 Elsevier Ltd. All rights reserved.

  8. Applications of blood group genotyping

    Directory of Open Access Journals (Sweden)

    Mariza A. Mota

    2006-03-01

    Full Text Available Introduction: The determination of blood group polymorphism atthe genomic level facilitates the resolution of clinical problemsthat cannot be addressed by hemagglutination. They are useful to(a determine antigen types for which currently available antibodiesare weakly reactive; (b type patients who have been recentlytransfused; (c identify fetuses at risk for hemolytic disease of thenewborn; and (d to increase the reliability of repositories of antigennegative RBCs for transfusion. Objectives: This review assessedthe current applications of blood group genotyping in transfusionmedicine and hemolytic disease of the newborn. Search strategy:Blood group genotyping studies and reviews were searched ingeneral database (MEDLINE and references were reviewed.Selection criteria: All published data and reviews were eligible forinclusion provided they reported results for molecular basis ofblood group antigens, DNA analysis for blood group polymorphisms,determination of fetal group status and applications of blood groupgenotyping in blood transfusion. Data collection: All data werecollected based on studies and reviews of blood grouppolymorphisms and their clinical applications.

  9. Grain yield stability of early maize genotypes

    Directory of Open Access Journals (Sweden)

    Chitra Bahadur Kunwar

    2016-12-01

    Full Text Available The objective of this study was to estimate grain yield stability of early maize genotypes. Five early maize genotypes namely Pool-17, Arun1EV, Arun-4, Arun-2 and Farmer’s variety were evaluated using Randomized Complete Block Design along with three replications at four different locations namely Rampur, Rajahar, Pakhribas and Kabre districts of Nepal during summer seasons of three consecutive years from 2010 to 2012 under farmer’s fields. Genotype and genotype × environment (GGE biplot was used to identify superior genotype for grain yield and stability pattern. The genotypes Arun-1 EV and Arun-4 were better adapted for Kabre and Pakhribas where as pool-17 for Rajahar environments. The overall findings showed that Arun-1EV was more stable followed by Arun-2 therefore these two varieties can be recommended to farmers for cultivation in both environments.

  10. Translation of Genotype to Phenotype by a Hierarchy of Cell Subsystems.

    Science.gov (United States)

    Yu, Michael Ku; Kramer, Michael; Dutkowski, Janusz; Srivas, Rohith; Licon, Katherine; Kreisberg, Jason; Ng, Cherie T; Krogan, Nevan; Sharan, Roded; Ideker, Trey

    2016-02-24

    Accurately translating genotype to phenotype requires accounting for the functional impact of genetic variation at many biological scales. Here we present a strategy for genotype-phenotype reasoning based on existing knowledge of cellular subsystems. These subsystems and their hierarchical organization are defined by the Gene Ontology or a complementary ontology inferred directly from previously published datasets. Guided by the ontology's hierarchical structure, we organize genotype data into an "ontotype," that is, a hierarchy of perturbations representing the effects of genetic variation at multiple cellular scales. The ontotype is then interpreted using logical rules generated by machine learning to predict phenotype. This approach substantially outperforms previous, non-hierarchical methods for translating yeast genotype to cell growth phenotype, and it accurately predicts the growth outcomes of two new screens of 2,503 double gene knockouts impacting DNA repair or nuclear lumen. Ontotypes also generalize to larger knockout combinations, setting the stage for interpreting the complex genetics of disease.

  11. Heterogeneous recombination among Hepatitis B virus genotypes.

    Science.gov (United States)

    Castelhano, Nadine; Araujo, Natalia M; Arenas, Miguel

    2017-10-01

    The rapid evolution of Hepatitis B virus (HBV) through both evolutionary forces, mutation and recombination, allows this virus to generate a large variety of adapted variants at both intra and inter-host levels. It can, for instance, generate drug resistance or the diverse viral genotypes that currently exist in the HBV epidemics. Concerning the latter, it is known that recombination played a major role in the emergence and genetic diversification of novel genotypes. In this regard, the quantification of viral recombination in each genotype can provide relevant information to devise expectations about the evolutionary trends of the epidemic. Here we measured the amount of this evolutionary force by estimating global and local recombination rates in >4700 HBV complete genome sequences corresponding to nine (A to I) HBV genotypes. Counterintuitively, we found that genotype E presents extremely high levels of recombination, followed by genotypes B and C. On the other hand, genotype G presents the lowest level, where recombination is almost negligible. We discuss these findings in the light of known characteristics of these genotypes. Additionally, we present a phylogenetic network to depict the evolutionary history of the studied HBV genotypes. This network clearly classified all genotypes into specific groups and indicated that diverse pairs of genotypes are derived from a common ancestor (i.e., C-I, D-E and, F-H) although still the origin of this virus presented large uncertainty. Altogether we conclude that the amount of observed recombination is heterogeneous among HBV genotypes and that this heterogeneity can influence on the future expansion of the epidemic. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. Novel, non-invasive method for distinguishing the individuals of the fire salamander (Salamandra salamandra in capture-mark-recapture studies

    Directory of Open Access Journals (Sweden)

    Goran Šukalo

    2013-07-01

    Full Text Available Recently we started implementing a highly efficient, non-invasive method of direct individual marking (i.e., typifying in a population study of the fire salamander, Salamandra salamandra. Our technique is based on the unique alphanumeric code for every individual, generated upon the numbers of openings of repellent/toxic skin glands in the yellow areas of the selected regions of the body. This code was proved reliable in the sample of 159 individuals from two separate populations and enabled easy and quick recognition of recaptured animals. The proposed method is inexpensive, easily applicable in the field, involves minimum stress for the animals and does not affect their behaviour and the possibility of repeated captures of “marked” (i.e., coded individuals. It is particularly suitable for dense populations.

  13. A new species of dusky salamander (Amphibia: Plethodontidae: Desmognathus) from the Eastern Gulf Coastal Plain of the United States and a redescription of D. auriculatus

    Science.gov (United States)

    Means, D Bruce; Lamb, Jennifer Y; Bernardo, Joseph

    2017-05-10

    The Coastal Plain of the southeastern U. S. is one of the planet's top biodiversity hotspots and yet many taxa have not been adequately studied. The plethodontid salamander, Desmognathus auriculatus, was originally thought to occur from east Texas to Virginia, a range spanning dozens of interfluves and large river systems. Beamer and Lamb (2008) found five independent mitochondrial lineages of what has been called D. auriculatus in the Atlantic Coastal Plain, but did not examine the extensive distribution of D. auriculatus in the Gulf Coastal Plain. We present morphological and molecular genetic data distinguishing two evolutionarily independent and distantly related lineages that are currently subsumed under the taxon D. auriculatus in the eastern Gulf Coastal Plain. We describe one of these as a new species, Desmognathus valentinei sp. nov., and assign the second one to D. auriculatus which we formally redescribe.

  14. The role of HFE genotype in macrophage phenotype.

    Science.gov (United States)

    Nixon, Anne M; Neely, Elizabeth; Simpson, Ian A; Connor, James R

    2018-02-01

    Iron regulation is essential for cellular energy production. Loss of cellular iron homeostasis has critical implications for both normal function and disease progression. The H63D variant of the HFE gene is the most common gene variant in Caucasians. The resulting mutant protein alters cellular iron homeostasis and is associated with a number of neurological diseases and cancer. In the brain, microglial and infiltrating macrophages are critical to maintaining iron homeostasis and modulating inflammation associated with the pathogenic process in multiple diseases. This study addresses whether HFE genotype affects macrophage function and the implications of these findings for disease processes. Bone marrow macrophages were isolated from wildtype and H67D HFE knock-in mice. The H67D gene variant in mice is the human equivalent of the H63D variant. Upon differentiation, the macrophages were used to analyze iron regulatory proteins, cellular iron release, migration, phagocytosis, and cytokine expression. The results of this study demonstrate that the H67D HFE genotype significantly impacts a number of critical macrophage functions. Specifically, fundamental activities such as proliferation in response to iron exposure, L-ferritin expression in response to iron loading, secretion of BMP6 and cytokines, and migration and phagocytic activity were all found to be impacted by genotype. Furthermore, we demonstrated that exposure to apo-Tf (iron-poor transferrin) can increase the release of iron from macrophages. In normal conditions, 70% of circulating transferrin is unsaturated. Therefore, the ability of apo-Tf to induce iron release could be a major regulatory mechanism for iron release from macrophages. These studies demonstrate that the HFE genotype impacts fundamental components of macrophage phenotype that could alter their role in degenerative and reparative processes in neurodegenerative disorders.

  15. Hepatitis C virus genotypes in Myanmar.

    Science.gov (United States)

    Win, Nan Nwe; Kanda, Tatsuo; Nakamoto, Shingo; Yokosuka, Osamu; Shirasawa, Hiroshi

    2016-07-21

    Myanmar is adjacent to India, Bangladesh, Thailand, Laos and China. In Myanmar, the prevalence of hepatitis C virus (HCV) infection is 2%, and HCV infection accounts for 25% of hepatocellular carcinoma. In this study, we reviewed the prevalence of HCV genotypes in Myanmar. HCV genotypes 1, 3 and 6 were observed in volunteer blood donors in and around the Myanmar city of Yangon. Although there are several reports of HCV genotype 6 and its variants in Myanmar, the distribution of the HCV genotypes has not been well documented in areas other than Yangon. Previous studies showed that treatment with peginterferon and a weight-based dose of ribavirin for 24 or 48 wk could lead to an 80%-100% sustained virological response (SVR) rates in Myanmar. Current interferon-free treatments could lead to higher SVR rates (90%-95%) in patients infected with almost all HCV genotypes other than HCV genotype 3. In an era of heavy reliance on direct-acting antivirals against HCV, there is an increasing need to measure HCV genotypes, and this need will also increase specifically in Myanmar. Current available information of HCV genotypes were mostly from Yangon and other countries than Myanmar. The prevalence of HCV genotypes in Myanmar should be determined.

  16. Hepatitis C Virus: Virology and Genotypes

    KAUST Repository

    Abdelaziz, Ahmed

    2017-12-01

    Hepatitis C virus (HCV) is a major causative agent of chronic liver disease worldwide. HCV is characterized by genetic heterogeneity, with at least six genotypes identified. The geographic distribution of genotypes has shown variations in different parts of the world over the past decade because of variations in population structure, immigration, and routes of transmission. Genotype differences are of epidemiologic interest and help the study of viral transmission dynamics to trace the source of HCV infection in a given population. HCV genotypes are also of considerable clinical importance because they affect response to antiviral therapy and represent a challenging obstacle for vaccine development.

  17. Comparative limb bone loading in the humerus and femur of the tiger salamander: testing the 'mixed-chain' hypothesis for skeletal safety factors.

    Science.gov (United States)

    Kawano, Sandy M; Economy, D Ross; Kennedy, Marian S; Dean, Delphine; Blob, Richard W

    2016-02-01

    Locomotion imposes some of the highest loads upon the skeleton, and diverse bone designs have evolved to withstand these demands. Excessive loads can fatally injure organisms; however, bones have a margin of extra protection, called a 'safety factor' (SF), to accommodate loads that are higher than normal. The extent to which SFs might vary amongst an animal's limb bones is unclear. If the limbs are likened to a chain composed of bones as 'links', then similar SFs might be expected for all limb bones because failure of the system would be determined by the weakest link, and extra protection in other links could waste energetic resources. However, Alexander proposed that a 'mixed-chain' of SFs might be found amongst bones if: (1) their energetic costs differ, (2) some elements face variable demands, or (3) SFs are generally high. To test whether such conditions contribute to diversity in limb bone SFs, we compared the biomechanical properties and locomotor loading of the humerus and femur in the tiger salamander (Ambystoma tigrinum). Despite high SFs in salamanders and similar sizes of the humerus and femur that would suggest similar energetic costs, the humerus had lower bone stresses, higher mechanical hardness and larger SFs. SFs were greatest in the anatomical regions where yield stresses were highest in the humerus and lowest in the femur. Such intraspecific variation between and within bones may relate to their different biomechanical functions, providing insight into the emergence of novel locomotor capabilities during the invasion of land by tetrapods. © 2016. Published by The Company of Biologists Ltd.

  18. Structural insights into the evolution of a sexy protein: novel topology and restricted backbone flexibility in a hypervariable pheromone from the red-legged salamander, Plethodon shermani.

    Science.gov (United States)

    Wilburn, Damien B; Bowen, Kathleen E; Doty, Kari A; Arumugam, Sengodagounder; Lane, Andrew N; Feldhoff, Pamela W; Feldhoff, Richard C

    2014-01-01

    In response to pervasive sexual selection, protein sex pheromones often display rapid mutation and accelerated evolution of corresponding gene sequences. For proteins, the general dogma is that structure is maintained even as sequence or function may rapidly change. This phenomenon is well exemplified by the three-finger protein (TFP) superfamily: a diverse class of vertebrate proteins co-opted for many biological functions - such as components of snake venoms, regulators of the complement system, and coordinators of amphibian limb regeneration. All of the >200 structurally characterized TFPs adopt the namesake "three-finger" topology. In male red-legged salamanders, the TFP pheromone Plethodontid Modulating Factor (PMF) is a hypervariable protein such that, through extensive gene duplication and pervasive sexual selection, individual male salamanders express more than 30 unique isoforms. However, it remained unclear how this accelerated evolution affected the protein structure of PMF. Using LC/MS-MS and multidimensional NMR, we report the 3D structure of the most abundant PMF isoform, PMF-G. The high resolution structural ensemble revealed a highly modified TFP structure, including a unique disulfide bonding pattern and loss of secondary structure, that define a novel protein topology with greater backbone flexibility in the third peptide finger. Sequence comparison, models of molecular evolution, and homology modeling together support that this flexible third finger is the most rapidly evolving segment of PMF. Combined with PMF sequence hypervariability, this structural flexibility may enhance the plasticity of PMF as a chemical signal by permitting potentially thousands of structural conformers. We propose that the flexible third finger plays a critical role in PMF:receptor interactions. As female receptors co-evolve, this flexibility may allow PMF to still bind its receptor(s) without the immediate need for complementary mutations. Consequently, this unique

  19. Structural insights into the evolution of a sexy protein: novel topology and restricted backbone flexibility in a hypervariable pheromone from the red-legged salamander, Plethodon shermani.

    Directory of Open Access Journals (Sweden)

    Damien B Wilburn

    Full Text Available In response to pervasive sexual selection, protein sex pheromones often display rapid mutation and accelerated evolution of corresponding gene sequences. For proteins, the general dogma is that structure is maintained even as sequence or function may rapidly change. This phenomenon is well exemplified by the three-finger protein (TFP superfamily: a diverse class of vertebrate proteins co-opted for many biological functions - such as components of snake venoms, regulators of the complement system, and coordinators of amphibian limb regeneration. All of the >200 structurally characterized TFPs adopt the namesake "three-finger" topology. In male red-legged salamanders, the TFP pheromone Plethodontid Modulating Factor (PMF is a hypervariable protein such that, through extensive gene duplication and pervasive sexual selection, individual male salamanders express more than 30 unique isoforms. However, it remained unclear how this accelerated evolution affected the protein structure of PMF. Using LC/MS-MS and multidimensional NMR, we report the 3D structure of the most abundant PMF isoform, PMF-G. The high resolution structural ensemble revealed a highly modified TFP structure, including a unique disulfide bonding pattern and loss of secondary structure, that define a novel protein topology with greater backbone flexibility in the third peptide finger. Sequence comparison, models of molecular evolution, and homology modeling together support that this flexible third finger is the most rapidly evolving segment of PMF. Combined with PMF sequence hypervariability, this structural flexibility may enhance the plasticity of PMF as a chemical signal by permitting potentially thousands of structural conformers. We propose that the flexible third finger plays a critical role in PMF:receptor interactions. As female receptors co-evolve, this flexibility may allow PMF to still bind its receptor(s without the immediate need for complementary mutations. Consequently

  20. Assessment of intra and interregional genetic variation in the Eastern Red-backed Salamander, Plethodon cinereus, via analysis of novel microsatellite markers.

    Directory of Open Access Journals (Sweden)

    Alexander C Cameron

    Full Text Available The red-backed salamander (Plethodon cinereus has long-served as a model system in ecology, evolution, and behavior, and studies surveying molecular variation in this species have become increasingly common over the past decade. However, difficulties are commonly encountered when extending microsatellite markers to populations that are unstudied from a genetic perspective due to high levels of genetic differentiation across this species' range. To ameliorate this issue, we used 454 pyrosequencing to identify hundreds of microsatellite loci. We then screened 40 of our top candidate loci in populations in Virginia, Pennsylvania, and Ohio-including an isolated island population ~ 4.5 km off the shore of Lake Erie (South Bass Island. We identified 25 loci that are polymorphic in a well-studied region of Virginia and 11 of these loci were polymorphic in populations located in the genetically unstudied regions of Ohio and Pennsylvania. Use of these loci to examine patterns of variation within populations revealed that South Bass Island has low diversity in comparison to other sites. However, neither South Bass Island nor isolated populations around Cleveland are inbred. Assessment of variation between populations revealed three well defined genetic clusters corresponding to Virginia, mainland Ohio/Pennsylvania, and South Bass Island. Comparisons of our results to those of others working in various parts of the range are consistent with the idea that differentiation is lower in regions that were once glaciated. However, these comparisons also suggest that well differentiated isolated populations in the formerly glaciated portion of the range are not uncommon. This work provides novel genetic resources that will facilitate population genetic studies in a part of the red-backed salamander's range that has not previously been studied in this manner. Moreover, this work refines our understanding of how neutral variation is distributed in this ecologically

  1. Impact of edible chitosan-cassava starch coatings enriched with Lippia gracilis Schauer genotype mixtures on the shelf life of guavas (Psidium guajava L.) during storage at room temperature.

    Science.gov (United States)

    de Aquino, Alana Bezerra; Blank, Arie Fitzgerald; Santana, Luciana Cristina Lins de Aquino

    2015-03-15

    The effect of edible chitosan-cassava starch (CH-CS) coatings containing a mixture of Lippia gracilis Schauer genotypes (EOM) on the shelf life of guavas during storage at room temperature for 10 days was studied. Sixteen formulations were prepared with a range of chitosan and essential oil mixtures concentrations, and the in vitro antimicrobial activity was tested. Formulations containing 2.0% cassava starch, 2.0% chitosan and 1.0%, 2.0% or 3.0% EOM were most effective in inhibiting the growth of the majority of bacteria. The edible CH-CS coating and CH-CS with 1.0% (CH-CS-EOM1) or 3.0% EOM (CH-CS-EOM3) were added to guavas and the shelf life was evaluated. On the tenth day of storage, total aerobic mesophilic bacteria and mould and yeast counts were statistically lower (p<0.05) in the CH-CS-EOM1- or CH-CS-EOM3-coated fruits than CH-CS-coated fruits. In addition, fruits coated with CH-CS or CH-CS-EOM showed no significant changes of total soluble solids content, while CH-CS-EOM-coated fruits showed lower titratable acidity than CH-CS-coated fruits at the end of storage. CH-CS-EOM3-coated guavas showed lower a(∗) and b(∗) values and higher L(∗) and hue values than those with other coatings. Copyright © 2014 Elsevier Ltd. All rights reserved.

  2. Evaluation of the Abbott Real Time HCV genotype II assay for Hepatitis C virus genotyping.

    Science.gov (United States)

    Sariguzel, Fatma Mutlu; Berk, Elife; Gokahmetoglu, Selma; Ercal, Baris Derya; Celik, Ilhami

    2015-01-01

    The determination of HCV genotypes and subtypes is very important for the selection of antiviral therapy and epidemiological studies. The aim of this study was to evaluate the performance of Abbott Real Time HCV Genotype II assay in HCV genotyping of HCV infected patients in Kayseri, Turkey. One hundred patients with chronic hepatitis C admitted to our hospital were evaluated between June 2012 and December 2012, HCV RNA levels were determined by the COBAS® AmpliPrep/COBAS® TaqMan® 48 HCV test. HCV genotyping was investigated by the Abbott Real Time HCV Genotype II assay. With the exception of genotype 1, subtypes of HCV genotypes could not be determined by Abbott assay. Sequencing analysis was used as the reference method. Genotypes 1, 2, 3 and 4 were observed in 70, 4, 2 and 24 of the 100 patients, respectively, by two methods. The concordance between the two systems to determine HCV major genotypes was 100%. Of 70 patients with genotype 1, 66 showed infection with subtype 1b and 4 with subtype 1a by Abbott Real Time HCV Genotype II assay. Using sequence analysis, 61 showed infection with subtype 1b and 9 with subtype 1a. In determining of HCV genotype 1 subtypes, the difference between the two methods was not statistically significant (P>0.05). HCV genotype 4 and 3 samples were found to be subtype 4d and 3a, respectively, by sequence analysis. There were four patients with genotype 2. Sequence analysis revealed that two of these patients had type 2a and the other two had type 2b. The Abbott Real Time HCV Genotype II assay yielded results consistent with sequence analysis. However, further optimization of the Abbott Real Time HCV Genotype II assay for subtype identification of HCV is required.

  3. High yielding biomass genotypes of willow (Salix spp.) show differences in below ground biomass allocation

    International Nuclear Information System (INIS)

    Cunniff, Jennifer; Purdy, Sarah J.; Barraclough, Tim J.P.; Castle, March; Maddison, Anne L.; Jones, Laurence E.; Shield, Ian F.; Gregory, Andrew S.; Karp, Angela

    2015-01-01

    Willows (Salix spp.) grown as short rotation coppice (SRC) are viewed as a sustainable source of biomass with a positive greenhouse gas (GHG) balance due to their potential to fix and accumulate carbon (C) below ground. However, exploiting this potential has been limited by the paucity of data available on below ground biomass allocation and the extent to which it varies between genotypes. Furthermore, it is likely that allocation can be altered considerably by environment. To investigate the role of genotype and environment on allocation, four willow genotypes were grown at two replicated field sites in southeast England and west Wales, UK. Above and below ground biomass was intensively measured over two two-year rotations. Significant genotypic differences in biomass allocation were identified, with below ground allocation differing by up to 10% between genotypes. Importantly, the genotype with the highest below ground biomass also had the highest above ground yield. Furthermore, leaf area was found to be a good predictor of below ground biomass. Growth environment significantly impacted allocation; the willow genotypes grown in west Wales had up to 94% more biomass below ground by the end of the second rotation. A single investigation into fine roots showed the same pattern with double the volume of fine roots present. This greater below ground allocation may be attributed primarily to higher wind speeds, plus differences in humidity and soil characteristics. These results demonstrate that the capacity exists to breed plants with both high yields and high potential for C accumulation. - Highlights: • SRC willows are a source of biomass and act as carbon (C) sinks. • Biomass allocation was measured in 4 willow genotypes grown in two UK field sites. • The greatest yielding genotype had the greatest below ground biomass at both sites. • Below ground biomass allocation differed by up to 10% between genotypes and 94% between sites. • Environment e.g. wind

  4. Genotyping isolates of the entomopathogenic fungus Beauveria ...

    African Journals Online (AJOL)

    Multi-locus denaturing gradient gel electrophoresis (DGGE) analysis was developed to investigate the genotypes of Beauveria bassiana sensu lato. ... These results demonstrated that multi-locus DGGE is a potentially useful molecular marker for genotyping, identifying and tracking the fates of experimentally released ...

  5. Genetic relationship among Musa genotypes revealed by ...

    African Journals Online (AJOL)

    enoh

    2012-03-29

    Mar 29, 2012 ... A banana germplasm was established containing 44 Musa genotypes collected from various locations in Malaysia. To detect their genetic variation and to rule out duplicates among cultivar, microsatellite markers were used in their analysis. The microsatellite profiles of 44 Musa genotypes of various origins.

  6. Toward fully automated genotyping: Genotyping microsatellite markers by deconvolution

    Energy Technology Data Exchange (ETDEWEB)

    Perlin, M.W.; Lancia, G.; See-Kiong, Ng [Carnegie Mellon Univ., Pittsburgh, PA (United States)

    1995-11-01

    Dense genetic linkage maps have been constructed for the human and mouse genomes, with average densities of 2.9 cM and 0.35 cM, respectively. These genetic maps are crucial for mapping both Mendelian and complex traits and are useful in clinical genetic diagnosis. Current maps are largely comprised of abundant, easily assayed, and highly polymorphic PCR-based microsatellite markers, primarily dinucleotide (CA){sub n} repeats. One key limitation of these length polymorphisms is the PCR stutter (or slippage) artifact that introduces additional stutter bands. With two (or more) closely spaced alleles, the stutter bands overlap, and it is difficult to accurately determine the correct alleles; this stutter phenomenon has all but precluded full automation, since a human must visually inspect the allele data. We describe here novel deconvolution methods for accurate genotyping that mathematically remove PCR stutter artifact from microsatellite markers. These methods overcome the manual interpretation bottleneck and thereby enable full automation of genetic map construction and use. New functionalities, including the pooling of DNAs and the pooling of markers, are described that may greatly reduce the associated experimentation requirements. 32 refs., 5 figs., 3 tabs.

  7. Impacts

    NARCIS (Netherlands)

    Hellmuth, M.; Kabat, P.

    2003-01-01

    Even without the impacts of climate change, water managers face prodigious challenges in meeting sustainable development goals. Growing populations need affordable food, water and energy. Industrial development demands a growing share of water resources and contaminates those same resources with its

  8. Genomic evaluations with many more genotypes

    Directory of Open Access Journals (Sweden)

    Wiggans George R

    2011-03-01

    Full Text Available Abstract Background Genomic evaluations in Holstein dairy cattle have quickly become more reliable over the last two years in many countries as more animals have been genotyped for 50,000 markers. Evaluations can also include animals genotyped with more or fewer markers using new tools such as the 777,000 or 2,900 marker chips recently introduced for cattle. Gains from more markers can be predicted using simulation, whereas strategies to use fewer markers have been compared using subsets of actual genotypes. The overall cost of selection is reduced by genotyping most animals at less than the highest density and imputing their missing genotypes using haplotypes. Algorithms to combine different densities need to be efficient because numbers of genotyped animals and markers may continue to grow quickly. Methods Genotypes for 500,000 markers were simulated for the 33,414 Holsteins that had 50,000 marker genotypes in the North American database. Another 86,465 non-genotyped ancestors were included in the pedigree file, and linkage disequilibrium was generated directly in the base population. Mixed density datasets were created by keeping 50,000 (every tenth of the markers for most animals. Missing genotypes were imputed using a combination of population haplotyping and pedigree haplotyping. Reliabilities of genomic evaluations using linear and nonlinear methods were compared. Results Differing marker sets for a large population were combined with just a few hours of computation. About 95% of paternal alleles were determined correctly, and > 95% of missing genotypes were called correctly. Reliability of breeding values was already high (84.4% with 50,000 simulated markers. The gain in reliability from increasing the number of markers to 500,000 was only 1.6%, but more than half of that gain resulted from genotyping just 1,406 young bulls at higher density. Linear genomic evaluations had reliabilities 1.5% lower than the nonlinear evaluations with 50

  9. Expression of Hepatitis B virus surface antigen (HBsAg from genotypes A, D and F and influence of amino acid variations related or not to genotypes on HBsAg detection

    Directory of Open Access Journals (Sweden)

    Natalia M. Araujo

    Full Text Available The impact of hepatitis B virus (HBV genotypes on the sensitivity of surface antigen (HBsAg detection assays has been poorly investigated. Here, plasmids carrying consensus or variant coding sequences for HBV surface proteins from genotypes A, D and F, were constructed. HBsAg levels were evaluated in medium and extracts of transfected CHO cells by a commercial polyclonal-based assay. We show that HBsAg detection values of consensus forms from genotypes D and F were, respectively, 37% and 30% lower than those obtained by genotype A. However, the presence of two single variations, T143M in genotype A, and T125M in genotype D, produced a decrease of 44% and an increase of 34%, respectively, on HBsAg mean values in comparison with their consensus forms. In conclusion, HBsAg detection levels varied among HBV genotypes. However, unique amino acid substitutions not linked to genotypes, such as T125M and T143M described here, should have more implications in HBV immunological diagnostics than the set of variations characteristic of each HBV genotype.

  10. IMPACTS !

    CERN Multimedia

    2008-01-01

    (Photo courtesy of Don Davis / NASA)The University of Geneva (UNIGE) and the Ecole Polytechnique Fédérale of Lausanne (EPFL) are organising the 4th series of public lectures on astronomy, on the theme of "Impacts". The schedule is as follows: Il y a 100 ans : une explosion dans la Tunguska – Dr. Frédéric COURBIN, EPFL Les impacts sur Terre – Prof. Didier Queloz, UNIGE La fin des dinosaures – Dr. Stéphane Paltani, UNIGE Wednesday 7 May 2008, from 7.00 p.m. to 9.00 p.m. Auditoire CO1, EPFL, Ecublens Thursday 08 May 2008, from 7.00 p.m. to 9.00 p.m. Auditoire Rouiller, Uni-Dufour, Genève All 3 lectures will be givent each evening! Admission free Information: 022 379 22 00

  11. Simultaneous circulation of genotypes I and III of dengue virus 3 in Colombia

    Directory of Open Access Journals (Sweden)

    Domingo Cristina

    2008-09-01

    Full Text Available Abstract Background Dengue is a major health problem in tropical and subtropical regions. In Colombia, dengue viruses (DENV cause about 50,000 cases annually, 10% of which involve Dengue Haemorrhagic Fever/Dengue Shock Syndrome. The picture is similar in other surrounding countries in the Americas, with recent outbreaks of severe disease, mostly associated with DENV serotype 3, strains of the Indian genotype, introduced into the Americas in 1994. Results The analysis of the 3'end (224 bp of the envelope gene from 32 DENV-3 strains recently recovered in Colombia confirms the circulation of the Indian genotype, and surprisingly the co-circulation of an Asian-Pacific genotype only recently described in the Americas. Conclusion These results have important implications for epidemiology and surveillance of DENV infection in Central and South America. Molecular surveillance of the DENV genotypes infecting humans could be a very valuable tool for controlling/mitigating the impact of the DENV infection.

  12. Developmental plasticity: re-conceiving the genotype.

    Science.gov (United States)

    Sultan, Sonia E

    2017-10-06

    In recent decades, the phenotype of an organism (i.e. its traits and behaviour) has been studied as the outcome of a developmental 'programme' coded in its genotype. This deterministic view is implicit in the Modern Synthesis approach to adaptive evolution as a sorting process among genetic variants. Studies of developmental pathways have revealed that genotypes are in fact differently expressed depending on environmental conditions. Accordingly, the genotype can be understood as a repertoire of potential developmental outcomes or norm of reaction. Reconceiving the genotype as an environmental response repertoire rather than a fixed developmental programme leads to three critical evolutionary insights. First, plastic responses to specific conditions often comprise functionally appropriate trait adjustments, resulting in an individual-level, developmental mode of adaptive variation. Second, because genotypes are differently expressed depending on the environment, the genetic diversity available to natural selection is itself environmentally contingent. Finally, environmental influences on development can extend across multiple generations via cytoplasmic and epigenetic factors transmitted to progeny individuals, altering their responses to their own, immediate environmental conditions and, in some cases, leading to inherited but non-genetic adaptations. Together, these insights suggest a more nuanced understanding of the genotype and its evolutionary role, as well as a shift in research focus to investigating the complex developmental interactions among genotypes, environments and previous environments.

  13. Genotype X/C recombinant (putative genotype I) of hepatitis B virus is rare in Hanoi, Vietnam--genotypes B4 and C1 predominate.

    Science.gov (United States)

    Phung, Thi Bich Thuy; Alestig, Erik; Nguyen, Thanh Liem; Hannoun, Charles; Lindh, Magnus

    2010-08-01

    There are eight known genotypes of hepatitis B virus, A-H, and several subgenotypes, with rather well-defined geographic distributions. HBV genotypes were evaluated in 153 serum samples from Hanoi, Vietnam. Of the 87 samples that could be genotyped, genotype B was found in 67 (77%) and genotype C in 19 (22%). All genotype C strains were of subgenotype C1, and the majority of genotype B strains were B4, while a few were B2. The genotype X/C recombinant strain, identified previously in Swedish patients of indigenous Vietnamese origin, was found in one sample. This variant, proposed to be classified as genotype I, has been found recently also by others in Vietnam and Laos. The current study indicates that the genotype X/C recombinant may represent approximately 1% of the HBV strains circulating in Vietnam. (c) 2010 Wiley-Liss, Inc.

  14. Effects of drought stress on morphological traits in chickpea (Cicer arientinum L. genotypes in greenhouse

    Directory of Open Access Journals (Sweden)

    ali masoomi

    2009-06-01

    Full Text Available This research was conducted in a research greenhouse at the College of Agriculture in Ferdowsi University of Mashhad to investigate the impact of five drought levels (-0.3, -3, -6, -9 and -12 bar on physiological and morphological characteristics of nine chickpea genotypes including MCC101, MCC174, MCC276, MCC477, MCC327, MCC476, JAM, Karaj12-60-31and ILC482. The experiment used 5×9 factorial laid out in randomized complete design with 4 replications. The genotypes were exposed to drought stress 10 days after emergence. Some traits were measured during growth season (including plant height, leaf number, flower and pod number, length and number of lateral branch that all of them shown significant differences in the first stage of stress between genotypes and then the effects of drought were appeared. In majority of genotypes reduction in the flowering and podding time were observed. Flower number is a favor parameter in the assessment of drought tolerance genotypes. Most measured traits imposed significant differences in all levels of drought stress, genotypes and interaction of them at the end of growth season. The highest amount of all measured parameters were observed in the field capacity (-0.3 bar. Among the levels of water potential tested -3 and -6 bar were the best treatment for evaluating drought stress of chickpea genotypes. Pod and seed weight did not form in heavy drought stress. Among genotypes tested ILC482, MCC276 and MCC 477 were the best genotypes in terms of responsing to drought stress.

  15. NS5A Sequence Heterogeneity and Mechanisms of Daclatasvir Resistance in Hepatitis C Virus Genotype 4 Infection.

    Science.gov (United States)

    Zhou, Nannan; Hernandez, Dennis; Ueland, Joseph; Yang, Xiaoyan; Yu, Fei; Sims, Karen; Yin, Philip D; McPhee, Fiona

    2016-01-15

    Daclatasvir is an NS5A inhibitor approved for treatment of infection due to hepatitis C virus (HCV) genotypes (GTs) 1-4. To support daclatasvir use in HCV genotype 4 infection, we examined a diverse genotype 4-infected population for HCV genotype 4 subtype prevalence, NS5A polymorphisms at residues associated with daclatasvir resistance (positions 28, 30, 31, or 93), and their effects on daclatasvir activity in vitro and clinically. We performed phylogenetic analysis of genotype 4 NS5A sequences from 186 clinical trial patients and 43 sequences from the European HCV database, and susceptibility analyses of NS5A polymorphisms and patient-derived NS5A sequences by using genotype 4 NS5A hybrid genotype 2a replicons. The clinical trial patients represented 14 genotype 4 subtypes; most prevalent were genotype 4a (55%) and genotype 4d (27%). Daclatasvir 50% effective concentrations for 10 patient-derived NS5A sequences representing diverse phylogenetic clusters were ≤0.080 nM. Most baseline sequences had ≥1 NS5A polymorphism at residues associated with daclatasvir resistance; however, only 3 patients (1.6%) had polymorphisms conferring ≥1000-fold daclatasvir resistance in vitro. Among 46 patients enrolled in daclatasvir trials, all 20 with baseline resistance polymorphisms achieved a sustained virologic response. Circulating genotype 4 subtypes are genetically diverse. Polymorphisms conferring high-level daclatasvir resistance in vitro are uncommon before therapy, and clinical data suggest that genotype 4 subtype and baseline polymorphisms have minimal impact on responses to daclatasvir-containing regimens. © The Author 2015. Published by Oxford University Press for the Infectious Diseases Society of America.

  16. Geographical Distribution of Trypanosoma cruzi Genotypes in Venezuela

    Science.gov (United States)

    Carrasco, Hernán J.; Segovia, Maikell; Llewellyn, Martin S.; Morocoima, Antonio; Urdaneta-Morales, Servio; Martínez, Cinda; Martínez, Clara E.; Garcia, Carlos; Rodríguez, Marlenes; Espinosa, Raul; de Noya, Belkisyolé A.; Díaz-Bello, Zoraida; Herrera, Leidi; Fitzpatrick, Sinead; Yeo, Matthew; Miles, Michael A.; Feliciangeli, M. Dora

    2012-01-01

    Chagas disease is an endemic zoonosis native to the Americas and is caused by the kinetoplastid protozoan parasite Trypanosoma cruzi. The parasite is also highly genetically diverse, with six discrete typing units (DTUs) reported TcI – TcVI. These DTUs broadly correlate with several epidemiogical, ecological and pathological features of Chagas disease. In this manuscript we report the most comprehensive evaluation to date of the genetic diversity of T. cruzi in Venezuela. The dataset includes 778 samples collected and genotyped over the last twelve years from multiple hosts and vectors, including nine wild and domestic mammalian host species, and seven species of triatomine bug, as well as from human sources. Most isolates (732) can be assigned to the TcI clade (94.1%); 24 to the TcIV group (3.1%) and 22 to TcIII (2.8%). Importantly, among the 95 isolates genotyped from human disease cases, 79% belonged to TcI - a DTU common in the Americas, however, 21% belonged to TcIV- a little known genotype previously thought to be rare in humans. Furthermore, were able to assign multiple oral Chagas diseases cases to TcI in the area around the capital, Caracas. We discuss our findings in the context of T. cruzi DTU distributions elsewhere in the Americas, and evaluate the impact they have on the future of Chagas disease control in Venezuela. PMID:22745843

  17. DRD4 genotype predicts longevity in mouse and human.

    Science.gov (United States)

    Grady, Deborah L; Thanos, Panayotis K; Corrada, Maria M; Barnett, Jeffrey C; Ciobanu, Valentina; Shustarovich, Diana; Napoli, Anthony; Moyzis, Alexandra G; Grandy, David; Rubinstein, Marcelo; Wang, Gene-Jack; Kawas, Claudia H; Chen, Chuansheng; Dong, Qi; Wang, Eric; Volkow, Nora D; Moyzis, Robert K

    2013-01-02

    Longevity is influenced by genetic and environmental factors. The brain's dopamine system may be particularly relevant, since it modulates traits (e.g., sensitivity to reward, incentive motivation, sustained effort) that impact behavioral responses to the environment. In particular, the dopamine D4 receptor (DRD4) has been shown to moderate the impact of environments on behavior and health. We tested the hypothesis that the DRD4 gene influences longevity and that its impact is mediated through environmental effects. Surviving participants of a 30-year-old population-based health survey (N = 310; age range, 90-109 years; the 90+ Study) were genotyped/resequenced at the DRD4 gene and compared with a European ancestry-matched younger population (N = 2902; age range, 7-45 years). We found that the oldest-old population had a 66% increase in individuals carrying the DRD4 7R allele relative to the younger sample (p = 3.5 × 10(-9)), and that this genotype was strongly correlated with increased levels of physical activity. Consistent with these results, DRD4 knock-out mice, when compared with wild-type and heterozygous mice, displayed a 7-9.7% decrease in lifespan, reduced spontaneous locomotor activity, and no lifespan increase when reared in an enriched environment. These results support the hypothesis that DRD4 gene variants contribute to longevity in humans and in mice, and suggest that this effect is mediated by shaping behavioral responses to the environment.

  18. Forensic SNP genotyping with SNaPshot

    DEFF Research Database (Denmark)

    Fondevila, M; Børsting, C; Phillips, C

    2017-01-01

    to routine STR profiling, use of SNaPshot is an important part of the development of SNP sets for a wide range of forensic applications with these markers, from genotyping highly degraded DNA with very short amplicons to the introduction of SNPs to ascertain the ancestry and physical characteristics......This review explores the key factors that influence the optimization, routine use, and profile interpretation of the SNaPshot single-base extension (SBE) system applied to forensic single-nucleotide polymorphism (SNP) genotyping. Despite being a mainly complimentary DNA genotyping technique...... of an unidentified contact trace donor. However, this technology, as resourceful as it is, displays several features that depart from the usual STR genotyping far enough to demand a certain degree of expertise from the forensic analyst before tackling the complex casework on which SNaPshot application provides...

  19. HMSRP Hawaiian Monk Seal Microsatellite Genotypes

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Currently ~2,400 Hawaiian monk seal specimens have been analyzed genetically, providing genotypes at 18 microsatellite loci. These data are organized by individual,...

  20. Global distribution of novel rhinovirus genotype

    DEFF Research Database (Denmark)

    Briese, Thomas; Renwick, Neil; Venter, Marietjie

    2008-01-01

    Global surveillance for a novel rhinovirus genotype indicated its association with community outbreaks and pediatric respiratory disease in Africa, Asia, Australia, Europe, and North America. Molecular dating indicates that these viruses have been circulating for at least 250 years Udgivelsesdato...

  1. Assessment of antibiotic susceptibilities, genotypic characteristics ...

    African Journals Online (AJOL)

    Jane

    2011-09-28

    Sep 28, 2011 ... Staphylococcus aureus and Salmonella Typhimurium ... This study was designed to evaluate the antibiotic susceptibilities, genotypic characteristics and ..... Distribution of reference and virulence genes among antibiotic-sensitive S. aureus (SAS), .... environmental factors such as temperature, water activity,.

  2. Hepatitis C Virus: Viral Quasispecies and Genotypes

    Directory of Open Access Journals (Sweden)

    Kyoko Tsukiyama-Kohara

    2017-12-01

    Full Text Available Hepatitis C virus (HCV mainly replicates in the cytoplasm, where it easily establishes persistent infection, resulting in chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma. Due to its high rate of mutation, HCV forms viral quasispecies, categorized based on the highly variable regions in the envelope protein and nonstructural 5A protein. HCV possesses seven major genotypes, among which genotype 1 is the most prevalent globally. The distribution of HCV genotypes varies based on geography, and each genotype has a different sensitivity to interferon treatment. Recently-developed direct-acting antivirals (DAAs, which target viral proteases or polymerases, mediate drastically better antiviral effects than previous therapeutics. Although treatment with DAAs has led to the development of drug-resistant HCV mutants, the most recently approved DAAs show improved pan-genomic activity, with a higher barrier to viral resistance.

  3. Hepatitis C Virus: Viral Quasispecies and Genotypes.

    Science.gov (United States)

    Tsukiyama-Kohara, Kyoko; Kohara, Michinori

    2017-12-22

    Hepatitis C virus (HCV) mainly replicates in the cytoplasm, where it easily establishes persistent infection, resulting in chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma. Due to its high rate of mutation, HCV forms viral quasispecies, categorized based on the highly variable regions in the envelope protein and nonstructural 5A protein. HCV possesses seven major genotypes, among which genotype 1 is the most prevalent globally. The distribution of HCV genotypes varies based on geography, and each genotype has a different sensitivity to interferon treatment. Recently-developed direct-acting antivirals (DAAs), which target viral proteases or polymerases, mediate drastically better antiviral effects than previous therapeutics. Although treatment with DAAs has led to the development of drug-resistant HCV mutants, the most recently approved DAAs show improved pan-genomic activity, with a higher barrier to viral resistance.

  4. Early seedling development of Medicago truncatula genotypes ...

    African Journals Online (AJOL)

    adel

    2014-01-08

    Jan 8, 2014 ... heat shock proteins; ABA, abscisic acid. Page 2. Amar et al. 323. Figure 1. Seed vigor of M. truncatula genotypes under different salt stress conditions. Results are means ..... (HSPs) that accumulate during seed late maturation.

  5. Hearing impairment in genotyped Wolfram syndrome patients.

    NARCIS (Netherlands)

    Plantinga, R.F.; Pennings, R.J.E.; Huygen, P.L.M.; Bruno, R.; Eller, P.; Barrett, T.G.; Vialettes, B.; Paquis-Fluklinger, V.; Lombardo, F.; Cremers, C.W.R.J.

    2008-01-01

    OBJECTIVES: Wolfram syndrome is a progressive neurodegenerative syndrome characterized by the features "DIDMOAD" (diabetes insipidus, diabetes mellitus, optic atrophy, and deafness). We sought to study the audiometric data of genotyped Wolfram syndrome patients with sensorineural hearing impairment.

  6. Existence of various human parvovirus B19 genotypes in Chinese plasma pools: genotype 1, genotype 3, putative intergenotypic recombinant variants and new genotypes.

    Science.gov (United States)

    Jia, Junting; Ma, Yuyuan; Zhao, Xiong; Huangfu, Chaoji; Zhong, Yadi; Fang, Chi; Fan, Rui; Lv, Maomin; Zhang, Jingang

    2016-09-17

    Human parvovirus B19 (B19V) is a frequent contaminant of blood and plasma-derived medicinal products. Three distinct genotypes of B19V have been identified. The distribution of the three B19V genotypes has been investigated in various regions or countries. However, in China, data on the existence of different B19V genotypes are limited. One hundred and eighteen B19V-DNA positive source plasma pool samples collected from three Chinese blood products manufacturers were analyzed. The subgenomic NS1/VP1u region junction of B19V was amplified by nested PCR. These amplified products were then cloned and subsequently sequenced. For genotyping, their phylogenetic inferences were constructed based on the NS1/VP1-unique region. Then putative recombination events were analyzed and identified. Phylogenetic analysis of 118 B19V sequences attributed 61.86 % to genotype 1a, 10.17 % to genotype 1b, and 17.80 % to genotype 3b. All the genotype 3b sequences obtained in this study grouped as a specific, closely related cluster with B19V strain D91.1. Four 1a/3b recombinants and 5 new atypical B19V variants with no recombination events were identified. There were at least 3 subtypes (1a, 1b and 3b) of B19V circulating in China. Furthermore, putative B19V 1a/3b recombinants and unclassified strains were identified as well. Such recombinant and unclassified strains may contribute to the genetic diversity of B19V and consequently complicate the B19V infection diagnosis and NAT screening. Further studies will be required to elucidate the biological significance of the recombinant and unclassified strains.

  7. Analysis of genotype diversity and evolution of Dengue virus serotype 2 using complete genomes

    Directory of Open Access Journals (Sweden)

    Vaishali P. Waman

    2016-08-01

    Full Text Available Background Dengue is one of the most common arboviral diseases prevalent worldwide and is caused by Dengue viruses (genus Flavivirus, family Flaviviridae. There are four serotypes of Dengue Virus (DENV-1 to DENV-4, each of which is further subdivided into distinct genotypes. DENV-2 is frequently associated with severe dengue infections and epidemics. DENV-2 consists of six genotypes such as Asian/American, Asian I, Asian II, Cosmopolitan, American and sylvatic. Comparative genomic study was carried out to infer population structure of DENV-2 and to analyze the role of evolutionary and spatiotemporal factors in emergence of diversifying lineages. Methods Complete genome sequences of 990 strains of DENV-2 were analyzed using Bayesian-based population genetics and phylogenetic approaches to infer genetically distinct lineages. The role of spatiotemporal factors, genetic recombination and selection pressure in the evolution of DENV-2 is examined using the sequence-based bioinformatics approaches. Results DENV-2 genetic structure is complex and consists of fifteen subpopulations/lineages. The Asian/American genotype is observed to be diversified into seven lineages. The Asian I, Cosmopolitan and sylvatic genotypes were found to be subdivided into two lineages, each. The populations of American and Asian II genotypes were observed to be homogeneous. Significant evidence of episodic positive selection was observed in all the genes, except NS4A. Positive selection operational on a few codons in envelope gene confers antigenic and lineage diversity in the American strains of Asian/American genotype. Selection on codons of non-structural genes was observed to impact diversification of lineages in Asian I, cosmopolitan and sylvatic genotypes. Evidence of intra/inter-genotype recombination was obtained and the uncertainty in classification of recombinant strains was resolved using the population genetics approach. Discussion Complete genome-based analysis

  8. Popcorn genotypes resistance to fall armyworm

    Directory of Open Access Journals (Sweden)

    Nádia Cristina de Oliveira

    2018-02-01

    Full Text Available ABSTRACT: The aim of this study was to evaluate popcorn genotypes for resistance to the fall armyworm, Spodoptera frugiperda. The experiment used a completely randomized design with 30 replicates. The popcorn genotypes Aelton, Arzm 05 083, Beija-Flor, Colombiana, Composto Chico, Composto Gaúcha, Márcia, Mateus, Ufvm Barão Viçosa, Vanin, and Viviane were evaluated,along with the common maize variety Zapalote Chico. Newly hatched fall armyworm larvae were individually assessed with regard to biological development and consumption of food. The data were subjected to multivariate analyses of variance and genetic divergence among genotypes was evaluated through the clustering methods of Tocher based on generalized Mahalanobis distances and canonical variable analyses. Seven popcorn genotypes, namely, Aelton, Arzm 05 083, Composto Chico, Composto Gaúcha, Márcia, Mateus, and Viviane,were shown to form a cluster (cluster I that had antibiosis as the mechanism of resistance to the pest. Cluster I genotypes and the Zapalote Chico genotype could be used for stacking genes for antibiosis and non-preference resistance.

  9. Differences in viral load among human respiratory syncytial virus genotypes in hospitalized children with severe acute respiratory infections in the Philippines.

    Science.gov (United States)

    Kadji, Francois Marie Ngako; Okamoto, Michiko; Furuse, Yuki; Tamaki, Raita; Suzuki, Akira; Lirio, Irene; Dapat, Clyde; Malasao, Rungnapa; Saito, Mariko; Pedrera-Rico, Gay Anne Granada; Tallo, Veronica; Lupisan, Socorro; Saito, Mayuko; Oshitani, Hitoshi

    2016-06-27

    Human respiratory syncytial virus (HRSV) is a leading viral etiologic agent of pediatric lower respiratory infections, including bronchiolitis and pneumonia. Two antigenic subgroups, HRSV-A and B, each contain several genotypes. While viral load may vary among HRSV genotypes and affect the clinical course of disease, data are scarce regarding the actual differences among genotypes. Therefore, this study estimated and compared viral load among NA1 and ON1 genotypes of HRSV-A and BA9 of HRSV-B. ON1 is a newly emerged genotype with a 72-nucleotide duplication in the G gene as observed previously with BA genotypes in HRSV-B. Children <5 years of age with an initial diagnosis of severe or very severe pneumonia at a hospital in the Philippines from September 2012 to December 2013 were enrolled. HRSV genotypes were determined and the viral load measured from nasopharyngeal swabs (NPS). The viral load of HRSV genotype NA1 were significantly higher than those of ON1 and BA9. Regression analysis showed that both genotype NA1 and younger age were significantly associated with high HRSV viral load. The viral load of NA1 was higher than that of ON1 and BA9 in NPS samples. HRSV genotypes may be associated with HRSV viral load. The reasons and clinical impacts of these differences in viral load among HRSV genotypes require further evaluation.

  10. Association of the TYMS 3G/3G genotype with poor response and GGH 354GG genotype with the bone marrow toxicity of the methotrexate in RA patients.

    Science.gov (United States)

    Jekic, Biljana; Lukovic, Ljiljana; Bunjevacki, Vera; Milic, Vera; Novakovic, Ivana; Damnjanovic, Tatjana; Milasin, Jelena; Popovic, Branka; Maksimovic, Nela; Damjanov, Nemanja; Radunovic, Goran; Kovacevic, Ljiljana; Krajinovic, Maja

    2013-03-01

    Gamma-glutamyl hydrolase (GGH), cyclin D1 (CCND1) and thymidylate synthase (TS) genes encode enzymes that are involved in methotrexate (MTX) action. In a group of 184 RA patients treated with MTX, we have investigated whether selected polymorphisms in these genes modulate MTX efficacy and/or have impact on adverse drug effects (ADEs). The efficacy of the MTX therapy has been estimated using the disease activity score in 28 joints (DAS28-ESR) based on EULAR criteria and relative DAS28 values (rDAS28). All adverse drug events were recorded. Patients were genotyped for selected polymorphisms of the GGH (-354 G > T and 452 C > T), CCND1 (870 A > G) and TYMS (variable number of tandem repeats, VNTR, and G to C substitution of triple repeat, 3R allele) gene. Association studies have been performed between obtained genotypes and the efficacy and toxicity of MTX. According to the EULAR response criteria, 146 RA patients (79.3 %) were classified as responders (good/moderate response) and 38 (20.7 %) as non-responders (poor response). Higher frequency of the TYMS 3 G/3 G genotype has been found among non-responders as compared to individuals with remaining genotypes (p = 0.02). ADEs were recorded in 53 patients. Among those patients eight experienced bone marrow toxicity, all of them carried GGH -354GG genotype (p = 0.003). No other significant association were observed. The 3 G/3 G genotype of the TYMS gene may indicate predisposition of poor response to MTX and GG genotype of GGH -354 T > G polymorphism may have high predictive value for myelosuppression in RA patients.

  11. Morphology and evolutionary implications of the annual cycle of secretion and sperm storage in spermathecae of the salamander Ambystoma opacum (Amphibia: Ambystomatidae).

    Science.gov (United States)

    Sever, David M; Krenz, John D; Johnson, Kristin M; Rania, Lisa C

    1995-01-01

    Females of the marbled salamander, Ambystoma opacum, store sperm in exocrine glands called spermathecae in the roof of the cloaca. Eggs are fertilized by sperm released from the spermathecae during oviposition. Some sperm remain in the spermathecae following oviposition, but these sperm degenerate within a month and none persists more than 6 mo after oviposition. Thus, sperm storage between successive breeding seasons does not occur. Apical secretory vaculoes are abundant during the fall mating season and contain a substance that is alcian blue+ at pH 2.5. Production of secretory vacuoles decreases markedly after oviposition, and the glands are inactive by the summer months. Ambystoma opacum is a terrestrial breeder, and some mating occurs prior to arrival at pond basins where oviposition occurs. Mating prior to arrival at the ovipository site may prolong the breeding season, leading to fitness implications for both males and females. Females have opportunities for more matings, and the possibilities for sperm competition in the spermathecae are enhanced. © 1995 Wiley-Liss, Inc. Copyright © 1995 Wiley-Liss, Inc.

  12. Effects of metamorphosis and captivity on the in vitro sensitivity of thyroid glands from the tiger salamander, Ambystoma tigrinum, to bovine thyrotropin

    International Nuclear Information System (INIS)

    Norman, M.F.; Norris, D.O.

    1987-01-01

    The sensitivity of thyroid glands from the tiger salamander, Ambystoma tigrinum, to bovine thyrotropin (bTSH) was tested in vitro. Thyroids were taken from subjects representing metamorphic stages I (premetamorphic larvae), II (onset of climax), and VII (completion of gill resorption), as well as from captivity control larvae. Exogenous TSH reduced the cumulative uptake of 125 I in vitro by thyroids from stage I larvae after 24 and 48 hr. The capacity of thyroids to release thyroxine (T4) in vitro was used subsequently as a measure of their responsiveness to TSH. Baseline levels of T4 release in vitro were variable but did not differ significantly among developmental stages. A low dose of bTSH (5 X 10(-6) IU/ml) did not increase in vitro T4 release compared with that of controls. A larger dose (5 X 10(-4) IU/ml) caused greater increases in T4 release from thyroids of stage II and VII subjects than from those of controls. This dose produced only a small response by thyroids from captivity-control subjects. The results suggest that the thyroids of Ambystoma increase in their capacity to respond to TSH during the process of metamorphosis

  13. CYP2D6 genotype dependent oxycodone metabolism in postoperative patients.

    Science.gov (United States)

    Stamer, Ulrike M; Zhang, Lan; Book, Malte; Lehmann, Lutz E; Stuber, Frank; Musshoff, Frank

    2013-01-01

    The impact of polymorphic cytochrome P450 CYP2D6 enzyme on oxycodone's metabolism and clinical efficacy is currently being discussed. However, there are only spare data from postoperative settings. The hypothesis of this study is that genotype dependent CYP2D6 activity influences plasma concentrations of oxycodone and its metabolites and impacts analgesic consumption. Patients received oxycodone 0.05 mg/kg before emerging from anesthesia and patient-controlled analgesia (PCA) for the subsequent 48 postoperative hours. Blood samples were drawn at 30, 90 and 180 minutes after the initial oxycodone dose. Plasma concentrations of oxycodone and its metabolites oxymorphone, noroxycodone and noroxymorphone were analyzed by liquid chromatography-mass spectrometry with electrospray ionization. CYP2D6 genotyping was performed and 121 patients were allocated to the following genotype groups: PM (poor metabolizer: no functionally active CYP2D6 allele), HZ/IM (heterozygous subjects, intermediate metabolizers with decreased CYP2D6 activity), EM (extensive metabolizers, normal CYP2D6 activity) and UM (ultrarapid metabolizers, increased CYP2D6 activity). Primary endpoint was the genotype dependent metabolite ratio of plasma concentrations oxymorphone/oxycodone. Secondary endpoint was the genotype dependent analgesic consumption with calculation of equianalgesic doses compared to the standard non-CYP dependent opioid piritramide. Metabolism differed between CYP2D6 genotypes. Mean (95%-CI) oxymophone/oxycodone ratios were 0.10 (0.02/0.19), 0.13 (0.11/0.16), 0.18 (0.16/0.20) and 0.28 (0.07/0.49) in PM, HZ/IM, EM and UM, respectively (p = 0.005). Oxycodone consumption up to the 12(th) hour was highest in PM (p = 0.005), resulting in lowest equianalgesic doses of piritramide versus oxycodone for PM (1.6 (1.4/1.8); EM and UM 2.2 (2.1/2.3); p<0.001). Pain scores did not differ between genotypes. In this postoperative setting, the number of functionally active CYP2D6 alleles had an impact

  14. CYP2D6 genotype dependent oxycodone metabolism in postoperative patients.

    Directory of Open Access Journals (Sweden)

    Ulrike M Stamer

    Full Text Available BACKGROUND: The impact of polymorphic cytochrome P450 CYP2D6 enzyme on oxycodone's metabolism and clinical efficacy is currently being discussed. However, there are only spare data from postoperative settings. The hypothesis of this study is that genotype dependent CYP2D6 activity influences plasma concentrations of oxycodone and its metabolites and impacts analgesic consumption. METHODS: Patients received oxycodone 0.05 mg/kg before emerging from anesthesia and patient-controlled analgesia (PCA for the subsequent 48 postoperative hours. Blood samples were drawn at 30, 90 and 180 minutes after the initial oxycodone dose. Plasma concentrations of oxycodone and its metabolites oxymorphone, noroxycodone and noroxymorphone were analyzed by liquid chromatography-mass spectrometry with electrospray ionization. CYP2D6 genotyping was performed and 121 patients were allocated to the following genotype groups: PM (poor metabolizer: no functionally active CYP2D6 allele, HZ/IM (heterozygous subjects, intermediate metabolizers with decreased CYP2D6 activity, EM (extensive metabolizers, normal CYP2D6 activity and UM (ultrarapid metabolizers, increased CYP2D6 activity. Primary endpoint was the genotype dependent metabolite ratio of plasma concentrations oxymorphone/oxycodone. Secondary endpoint was the genotype dependent analgesic consumption with calculation of equianalgesic doses compared to the standard non-CYP dependent opioid piritramide. RESULTS: Metabolism differed between CYP2D6 genotypes. Mean (95%-CI oxymophone/oxycodone ratios were 0.10 (0.02/0.19, 0.13 (0.11/0.16, 0.18 (0.16/0.20 and 0.28 (0.07/0.49 in PM, HZ/IM, EM and UM, respectively (p = 0.005. Oxycodone consumption up to the 12(th hour was highest in PM (p = 0.005, resulting in lowest equianalgesic doses of piritramide versus oxycodone for PM (1.6 (1.4/1.8; EM and UM 2.2 (2.1/2.3; p<0.001. Pain scores did not differ between genotypes. CONCLUSIONS: In this postoperative setting, the number of

  15. Cotton genotypes selection through artificial neural networks.

    Science.gov (United States)

    Júnior, E G Silva; Cardoso, D B O; Reis, M C; Nascimento, A F O; Bortolin, D I; Martins, M R; Sousa, L B

    2017-09-27

    Breeding programs currently use statistical analysis to assist in the identification of superior genotypes at various stages of a cultivar's development. Differently from these analyses, the computational intelligence approach has been little explored in genetic improvement of cotton. Thus, this study was carried out with the objective of presenting the use of artificial neural networks as auxiliary tools in the improvement of the cotton to improve fiber quality. To demonstrate the applicability of this approach, this research was carried out using the evaluation data of 40 genotypes. In order to classify the genotypes for fiber quality, the artificial neural networks were trained with replicate data of 20 genotypes of cotton evaluated in the harvests of 2013/14 and 2014/15, regarding fiber length, uniformity of length, fiber strength, micronaire index, elongation, short fiber index, maturity index, reflectance degree, and fiber quality index. This quality index was estimated by means of a weighted average on the determined score (1 to 5) of each characteristic of the HVI evaluated, according to its industry standards. The artificial neural networks presented a high capacity of correct classification of the 20 selected genotypes based on the fiber quality index, so that when using fiber length associated with the short fiber index, fiber maturation, and micronaire index, the artificial neural networks presented better results than using only fiber length and previous associations. It was also observed that to submit data of means of new genotypes to the neural networks trained with data of repetition, provides better results of classification of the genotypes. When observing the results obtained in the present study, it was verified that the artificial neural networks present great potential to be used in the different stages of a genetic improvement program of the cotton, aiming at the improvement of the fiber quality of the future cultivars.

  16. A two-step real-time PCR assay for quantitation and genotyping of human parvovirus 4.

    Science.gov (United States)

    Väisänen, E; Lahtinen, A; Eis-Hübinger, A M; Lappalainen, M; Hedman, K; Söderlund-Venermo, M

    2014-01-01

    Human parvovirus 4 (PARV4) of the family Parvoviridae was discovered in a plasma sample of a patient with an undiagnosed acute infection in 2005. Currently, three PARV4 genotypes have been identified, however, with an unknown clinical significance. Interestingly, these genotypes seem to differ in epidemiology. In Northern Europe, USA and Asia, genotypes 1 and 2 have been found to occur mainly in persons with a history of injecting drug use or other parenteral exposure. In contrast, genotype 3 appears to be endemic in sub-Saharan Africa, where it infects children and adults without such risk behaviour. In this study, a novel straightforward and cost-efficient molecular assay for both quantitation and genotyping of PARV4 DNA was developed. The two-step method first applies a single-probe pan-PARV4 qPCR for screening and quantitation of this relatively rare virus, and subsequently, only the positive samples undergo a real-time PCR-based multi-probe genotyping. The new qPCR-GT method is highly sensitive and specific regardless of the genotype, and thus being suitable for studying the clinical impact and occurrence of the different PARV4 genotypes. Copyright © 2013 Elsevier B.V. All rights reserved.

  17. Discordant genotyping results using DNA isolated from anti-doping control urine samples.

    Science.gov (United States)

    Choong, Eva; Schulze, Jenny J; Ericsson, Magnus; Rane, Anders; Ekström, Lena

    2017-07-01

    The UGT2B17 gene deletion polymorphism is known to correlate to urinary concentration of testosterone-glucuronide and hence this genotype exerts a large impact on the testosterone/epitestosterone (T/E) ratio, a biomarker for testosterone doping. The objective of this study was to assess if DNA isolated from athletes' urine samples (n = 713) obtained in routine doping controls could be targeted for genotyping analysis for future integration in the athlete's passport. A control population (n = 21) including both urine and blood DNA was used for genotyping concordance test. Another aim was to study a large group (n = 596) of authentic elite athletes in respect of urinary steroid profile in relation to genetic variation. First we found that the genotype results when using urine-derived DNA did not correlate sufficiently with the genotype obtained from whole blood DNA. Secondly we found males with one or two UGT2B17 alleles had higher T/E (mean 1.63 ± 0.93) than females (mean 1.28 ± 1.08), p˂0.001. Unexpectedly, we found that several male del/del athletes in power sports had a T/E ˃1. If men in power sport exert a different urinary steroid profile needs to be further investigated. The other polymorphisms investigated in the CYP17A1, UGT2B7 and UGT2B15 genes did not show any associations with testosterone and epitestosterone concentrations. Our results show that genotyping using urine samples according to our method is not useful in an anti-doping setting. Instead, it is of importance for the anti-doping test programs to include baseline values in the ABP to minimize any putative impact of genotype. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  18. Hepatitis C virus genotypes in Bahawalpur

    International Nuclear Information System (INIS)

    Qazi, M.A.; Fayyaz, M.; Chaudhry, G.M.D.; Jamil, A.

    2006-01-01

    This study was conducted at Medical Unit-II Bahawal Victoria Hospital / Quaid-e-Azam Medical College Bahawalpur from May 1st , 2005 to December 31st 2005. The objective of this study was to determine hepatitis C virus (HCV) genotypes in Bahawalpur, Pakistan. In consecutive 105 anti-HCV (ELISA-3) positive patients, complete history and physical examination was performed. Liver function tests, complete blood counts and platelet count, blood sugar fasting and 2 hours after breakfast, prothrombin time, serum albumin, serum globulin and abdominal ultrasound were carried out in all the patients. Tru cut biopsy was performed on 17 patients. We studied HCV RNA in all these patients by Nested PCR method. HCV RNA was detected in 98 patients and geno typing assay was done by genotype specific PCR. Among total of 105 anti-HCV positive patients, HCV-RNA was detected in 98 patients. Out of these 98 patients there were 57 (58.2%) males and 41 (42.8%) females. Their age range was 18-75 years. The age 18-29 years 26 (26.5%), 30-39 years 35 (35.7%) and 40-75 37 (37.8%), while 10 (10.2%) patients were diabetics and 34 (34.7%) patients were obese. Liver cirrhosis was present in 10 (10.2%) patients. Forty two (43.9%) patients were symptomatic while 56 (57.1%) were asymptomatic. Out of 98 patients 11 (11.2%) were un type-able and 87 (88.8%) were type able. 70/98 (71.4%) were genotype 3; 10/98 (10.2%) were genotype 1; 03/98 (3.1%) were genotype 2; 03/98 (3.1%) were mixed genotype 2 and 3; 01/98 (1%) were mixed genotype 3a and 3b. Genotype 3 is the most common HCV virus in our area which shows that both virological and biochemical response will be better. Because HCV genotype 3 is more frequent among the drug users which points towards unsafe injection practices in our area. (author)

  19. The influence of al-madinah al-munawwara treated and untreated domestic wastewater on growth and physiology of three tomato (lycopersicon esculentum mill.) genotypes

    International Nuclear Information System (INIS)

    Akhkha, A.; Boutraa, T.; Shoaibi, A.K.

    2017-01-01

    The impact of irrigation with Al-Madinah Al-Munawwara domestic wastewater on three tomato genotypes (AL, P and VF) was investigated. Five treatments including Tap water, untreated (TN), primary (T1), secondary (T2) and tertiary (T3) treated wastewaters were used for irrigation. The physico-chemical characteristics of wastewater were determined. Leaves were analysed for N, P, K and heavy metals (Copper, Cadmium, Lead and Nickel). The growth parameters assessed were % germination, plant height, shoot and root dry weights, and total leaf dry weight. Some physiological parameters such as photosynthetic light response curve, maximum gross photosynthesis (Amax), dark respiration (DR), chlorophyll fluorescence parameters (Fo, Fm and Fv / Fm), chlorophyll content index and stomatal conductance were detected. % germination was decreased in both A1 and P genotype, with no effect on VF genotype. Most growth parameters were increased in genotype A1, followed by VF then P genotype which had a sensitive leaf dry weight to T2 and T3. Photosynthesis was mainly increased in A1 genotype with a decrease in VF genotype. DR was negatively affected in VF genotype with no response of A1 genotype. Chlorophyll fluorescence showed an increase in Fo in VF genotype but a decrease in Fv / Fm in both A1 and VF genotypes. Chlorophyll content index was decreased but only in A1 and VF genotypes under TN. Treatment with TN and / or T1 decreased stomatal conductance in all genotypes. The levels of heavy metals in wastewaters used were lower than the standard limits; however, plant chemical analysis showed that the leaves of the three tomato genotypes accumulated heavy metals but differently with higher levels at TN and lower levels at T3. (author)

  20. Phenotypic and genotypic variation in Iranian Pistachios

    Directory of Open Access Journals (Sweden)

    Somayeh Tayefeh Aliakbarkhani

    2015-12-01

    Full Text Available As Iran is one of the richest pistachio germplasms a few studies have been conducted on different sexes of pistachio trees, in areas where this crop emerged. To this end, 40 male and female Iranian pistachio genotypes from Feizabad region, Khorasan, Iran; were evaluated using morphological characters and randomly amplified polymorphic DNA (RAPD markers. For morphological assessments, 54 variables were considered to investigate similarities between and among the studied genotypes. Morphological data indicated relative superiority in some female genotypes (such as Sefid 1, Sefid Sabuni 2, Garmesiah, and Ghermezdorosht Z regarding characters such as halfcrackedness, the percentages of protein and fat content. 115 polymorphic bands were recorded with 92.83% average polymorphism among all primers. The total resolving power (Rp of the primers was 74.54. The range of genetic similarity varied from about 0.31 to about 0.70. Genotypes were segregated into eight groups at the similarity limit of 0.41. Results of present investigation could be helpful for strategic decisions for maintaining Iranian pistachio genotypes.

  1. Precise genotyping and recombination detection of Enterovirus

    Science.gov (United States)

    2015-01-01

    Enteroviruses (EV) with different genotypes cause diverse infectious diseases in humans and mammals. A correct EV typing result is crucial for effective medical treatment and disease control; however, the emergence of novel viral strains has impaired the performance of available diagnostic tools. Here, we present a web-based tool, named EVIDENCE (EnteroVirus In DEep conception, http://symbiont.iis.sinica.edu.tw/evidence), for EV genotyping and recombination detection. We introduce the idea of using mixed-ranking scores to evaluate the fitness of prototypes based on relatedness and on the genome regions of interest. Using phylogenetic methods, the most possible genotype is determined based on the closest neighbor among the selected references. To detect possible recombination events, EVIDENCE calculates the sequence distance and phylogenetic relationship among sequences of all sliding windows scanning over the whole genome. Detected recombination events are plotted in an interactive figure for viewing of fine details. In addition, all EV sequences available in GenBank were collected and revised using the latest classification and nomenclature of EV in EVIDENCE. These sequences are built into the database and are retrieved in an indexed catalog, or can be searched for by keywords or by sequence similarity. EVIDENCE is the first web-based tool containing pipelines for genotyping and recombination detection, with updated, built-in, and complete reference sequences to improve sensitivity and specificity. The use of EVIDENCE can accelerate genotype identification, aiding clinical diagnosis and enhancing our understanding of EV evolution. PMID:26678286

  2. Differential effects of the ApoE4 genotype on brain structure and function

    NARCIS (Netherlands)

    Matura, S.; Prvulovic, D.; Jurcoane, A.; Hartmann, D.; Miller, J.; Scheibe, M.; O'Dwyer, L.G.; Oertel-Knochel, V.; Knochel, C.; Reinke, B.; Karakaya, T.; Fusser, F.; Pantel, J.

    2014-01-01

    The apolipoprotein E epsilon4 allele is a well established genetic risk factor for sporadic Alzheimer's disease. It is associated with structural and functional brain changes in healthy young, middle-aged and elderly subjects. In the current study, we assessed the impact of the ApoE genotype on

  3. Maternal and pup genotype contribution to growth in wild-type and tau mutant Syrian hamsters

    NARCIS (Netherlands)

    Oklejewicz, Malgorzata; Pen, Ido; Durieux, Geesje C.R.; Daan, Serge

    The single gene mutation tau in the Syrian hamster-apart from its effect on the circadian organization of locomotor activity-has a pronounced influence on body weight. In this study we investigate the impact of maternal and pup genotypes at the tau-locus on the growth rate of pups. Homozygous tau

  4. Lethal Encephalitozoon cuniculi genotype III infection in Steppe lemmings (Lagurus lagurus)

    Czech Academy of Sciences Publication Activity Database

    Hofmannová, L.; Sak, Bohumil; Jekl, V.; Mináriková, A.; Škorič, M.; Kváč, Martin

    2014-01-01

    Roč. 205, 1-2 (2014), s. 357-360 ISSN 0304-4017 R&D Projects: GA ČR(CZ) GAP505/11/1163 Institutional support: RVO:60077344 Keywords : Encephalitozoon cuniculi genotype III * Steppe lemmings * Lethal infection * PCR * Histology Subject RIV: EG - Zoology Impact factor: 2.460, year: 2014

  5. Photosynthetic performance of two maize genotypes as affected by chilling stress

    Czech Academy of Sciences Publication Activity Database

    Kosová, K.; Haisel, Daniel; Tichá, I.

    2005-01-01

    Roč. 51, č. 5 (2005), s. 206-212 ISSN 1214-1178 R&D Projects: GA ČR GA522/01/0846 Institutional research plan: CEZ:AV0Z50380511; MSM 113100004 Keywords : maize ( Zea mays L.) * genotype * light dependence of photosynthetic characteristics Subject RIV: EF - Botanics Impact factor: 0.170, year: 2004

  6. Saponin profile of green asparagus genotypes.

    Science.gov (United States)

    Vázquez-Castilla, Sara; Jaramillo-Carmona, Sara; Fuentes-Alventosa, Jose María; Jiménez-Araujo, Ana; Rodríguez-Arcos, Rocío; Cermeño-Sacristán, Pedro; Espejo-Calvo, Juan Antonio; Guillén-Bejarano, Rafael

    2013-11-20

    The main goal of this study was to determine the saponin profiles of different "triguero" asparagus genotypes and to compare them to green asparagus commercial hybrids. The samples consisted of 31 commercial hybrids and 58 genotypes from the Huétor-Tájar (HT) population variety ("triguero"). The saponin analysis by high-performance liquid chromatography-mass spectrometry allowed for the determination of 12 saponins derived from a furostan-type steroidal genin, 4 of which had never been described in the edible part of asparagus. The saponin profile of "triguero" asparagus was a combination of these new saponins and protodioscin. Although protodioscin was the major saponin found in commercial hybrids, some of these 12 saponins were detected as major components in some of the commercial hybrids. The total contents of saponins described in some of these HT genotypes reach values as high as 10-100 times higher than those found in commercial hybrids.

  7. Carcass traits of four rabbit genotypes

    Directory of Open Access Journals (Sweden)

    Ajda Kermauner

    2010-01-01

    Full Text Available Seventy-three rabbits of four genotypes (A - SIKA maternal line; C - SIKA sire line; AxC - hybrids between line A and C; AxCal - crossbreds between line A and the Californian breed were used to evaluate the effect of genotype on carcass traits. Rabbits were weaned at 35 days and slaughtered at 93 days of age. Rabbits were fed standard feed mixture ad libitum. The highest live weight at slaughter and dressing percentage was achieved by line C, and the lowest in line A. Hybrids between line A and C exhibited slightly worse carcass traits than rabbits in line C, but the differences were not statistically significant. The Californian breed gave worse results than crossbreeding with line C, though in most cases the differences between AxC and AxCal were not significant. The differences between genotypes in hind leg tissue composition, pH and meat colour were not statistically significant.

  8. Precise control of miR-125b levels is required to create a regeneration-permissive environment after spinal cord injury: a cross-species comparison between salamander and rat

    Directory of Open Access Journals (Sweden)

    Juan Felipe Diaz Quiroz

    2014-06-01

    Full Text Available Most spinal cord injuries lead to permanent paralysis in mammals. By contrast, the remarkable regenerative abilities of salamanders enable full functional recovery even from complete spinal cord transections. The molecular differences underlying this evolutionary divergence between mammals and amphibians are poorly understood. We focused on upstream regulators of gene expression as primary entry points into this question. We identified a group of microRNAs (miRNAs that are conserved between the Mexican axolotl salamander (Ambystoma mexicanum and mammals but show marked cross-species differences in regulation patterns following spinal cord injury. We found that precise post-injury levels of one of these miRNAs (miR-125b is essential for functional recovery, and guides correct regeneration of axons through the lesion site in a process involving the direct downstream target Sema4D in axolotls. Translating these results to a mammalian model, we increased miR-125b levels in the rat through mimic treatments following spinal cord transection. These treatments downregulated Sema4D and other glial-scar-related genes, and enhanced the animal’s functional recovery. Our study identifies a key regulatory molecule conserved between salamander and mammal, and shows that the expression of miR-125b and Sema4D must be carefully controlled in the right cells at the correct level to promote regeneration. We also show that these molecular components of the salamander’s regeneration-permissive environment can be experimentally harnessed to improve treatment outcomes for mammalian spinal cord injuries.

  9. Genotype x environment interaction for grain yield of wheat genotypes tested under water stress conditions

    International Nuclear Information System (INIS)

    Sail, M.A.; Dahot, M.U.; Mangrio, S.M.; Memon, S.

    2007-01-01

    Effect of water stress on grain yield in different wheat genotypes was studied under field conditions at various locations. Grain yield is a complex polygenic trait influenced by genotype, environment and genotype x environment (GxE) interaction. To understand the stability among genotypes for grain yield, twenty-one wheat genotypes developed Through hybridization and radiation-induced mutations at Nuclear Institute of Agriculture (NIA) TandoJam were evaluated with four local check varieties (Sarsabz, Thori, Margalla-99 and Chakwal-86) in multi-environmental trails (MET/sub s/). The experiments were conducted over 5 different water stress environments in Sindh. Data on grain yield were recorded from each site and statistically analyzed. Combined analysis of variance for all the environments indicated that the genotype, environment and genotype x environment (GxE) interaction were highly significant (P greater then 0.01) for grain yield. Genotypes differed in their response to various locations. The overall highest site mean yield (4031 kg/ha) recorded at Moro and the lowest (2326 kg/ha) at Thatta. Six genotypes produced significantly (P=0.01) the highest grain yield overall the environments. Stability analysis was applied to estimate stability parameters viz., regression coefficient (b), standard error of regression coefficient and variance due to deviation from regression (S/sub 2/d) genotypes 10/8, BWS-78 produced the highest mean yield over all the environments with low regression coefficient (b=0.68, 0.67 and 0.63 respectively and higher S/sup 2/ d value, showing specific adaptation to poor (un favorable) environments. Genotype 8/7 produced overall higher grain yield (3647 kg/ha) and ranked as third high yielding genotype had regression value close to unity (b=0.9) and low S/sup d/ value, indicating more stability and wide adaptation over the all environments. The knowledge of the presence and magnitude of genotype x environment (GE) interaction is important to

  10. Oilseed rape genotypes response to boron toxicity

    Directory of Open Access Journals (Sweden)

    Savić Jasna

    2013-01-01

    Full Text Available Response of 16 oilseed rape genotypes to B (boron toxicity was analyzed by comparing the results of two experiments conducted in a glasshouse. In Experiment 1 plants were grown in standard nutrient solutions with 10 µMB (control and 1000 µM B. Relative root and shoot growth varied from 20-120% and 31-117%, respectively. Variation in B concentration in shoots was also wide (206.5-441.7 µg B g-1 DW as well as total B uptake by plant (62.3-281.2 µg B g1. Four selected genotypes were grown in Experiment 2 in pots filled with high B soil (8 kg ha-1 B; B8. Shoot growth was not affected by B8 treatment, while root and shoot B concentration was significantly increased compared to control. Genotypes Panther and Pronto which performed low relative root and shoot growth and high B accumulation in plants in Experiment 1, had good growth in B8 treatment. In Experiment 2 genotype NS-L-7 had significantly lower B concentration in shots under treatment B8, but also very high B accumulation in Experiment 1. In addition, cluster analyses classified genotypes in three groups according to traits contrasting in their significance for analyzing response to B toxicity. The first group included four varieties based on their shared characteristics that have small value for the relative growth of roots and shoots and large values of B concentration in shoot. In the second largest group were connected ten genotypes that are heterogeneous in traits and do not stand out on any characteristic. Genotypes NS-L-7 and Navajo were separated in the third group because they had big relative growth of root and shoot, but also a high concentration of B in the shoot, and high total B uptake. Results showed that none of tested genotypes could not be recommended for breeding process to tolerance for B toxicity. [Projekat Ministarstva nauke Republike Srbije, br. OI 173028

  11. American foulbrood of the honey bee: occurrence and distribution of different genotypes of Paenibacillus larvae in the administrative district of Arnsberg (North Rhine-Westphalia).

    Science.gov (United States)

    Peters, M; Kilwinski, J; Beringhoff, A; Reckling, D; Genersch, E

    2006-03-01

    Between March 2003 and October 2004, Paenibacillus larvae, the aetiological agent of American foulbrood disease of the honey bee, was isolated from broodcombs and honey samples of 54 apiaries in the administrative district of Arnsberg (North Rhine-Westphalia, Germany). Genotyping of 176 P. larvae isolates with repetitive element polymerase chain reaction fingerprinting (rep-PCR) using BOX A1R and MBO REP1 primers revealed five different genotypes (AB, Ab, ab, ass, Acapital BE, Cyrillic). In samples of three apiaries, more than one genotype was detected. A combination of two genotypes was isolated from honey samples of the same hive two times (ab/ass and Ab/ab). The five genotypes were not randomly distributed in the district, but revealed a certain geographical clustering. Possible factors with impact on the genotype diversity and the distribution pattern are discussed.

  12. Specificity of the Linear Array HPV Genotyping Test for detecting human papillomavirus genotype 52 (HPV-52)

    OpenAIRE

    Kocjan, Boštjan; Poljak, Mario; Oštrbenk, Anja

    2015-01-01

    Introduction: HPV-52 is one of the most frequent human papillomavirus (HPV) genotypes causing significant cervical pathology. The most widely used HPV genotyping assay, the Roche Linear Array HPV Genotyping Test (Linear Array), is unable to identify HPV- 52 status in samples containing HPV-33, HPV-35, and/or HPV-58. Methods: Linear Array HPV-52 analytical specificity was established by testing 100 specimens reactive with the Linear Array HPV- 33/35/52/58 cross-reactive probe, but not with the...

  13. An integrative approach to phylogeography: investigating the effects of ancient seaways, climate, and historical geology on multi-locus phylogeographic boundaries of the Arboreal Salamander (Aneides lugubris).

    Science.gov (United States)

    Reilly, Sean B; Corl, Ammon; Wake, David B

    2015-11-04

    Phylogeography is an important tool that can be used to reveal cryptic biodiversity and to better understand the processes that promote lineage diversification. We studied the phylogeographic history of the Arboreal Salamander (Aneides lugubris), a wide-ranging species endemic to the California floristic province. We used multi-locus data to reconstruct the evolutionary history of A. lugubris and to discover the geographic location of major genetic breaks within the species. We also used species distribution modeling and comparative phylogeography to better understand the environmental factors that have shaped the genetic history of A. lugubris. We found six major mitochondrial clades in A. lugubris. Nuclear loci supported the existence of at least three genetically distinct groups, corresponding to populations north of the San Francisco Bay and in the Sierra Nevada, in the Santa Cruz Mountains, and in the central coast and southern California. All of the genetic breaks in mitochondrial and nuclear loci corresponded to regions where historical barriers to dispersal have been observed in other species. Geologic or water barriers likely were the most important factors restricting gene flow among clades. Climatic unsuitability during glacial maximum may have contributed to the isolation of the mitochondrial clades in the central coast and southern California. A projection of our species distribution model to a future scenario with a moderate amount of climate change suggests that most of the range of A. lugubris will remain climatically suitable, but climatic conditions in the Sierra Nevada and low elevation areas in Southern California are likely to deteriorate. Aneides lugubris contains substantial cryptic genetic diversity as a result of historical isolation of populations. At least two (and perhaps three) evolutionarily significant units in A. lugubris merit protection; all six mitochondrial clades should be considered as management units within the species.

  14. Concurrent speciation in the eastern woodland salamanders (Genus Plethodon):DNA sequences of the complete albumin nuclear and partialmitochondrial 12s genes

    Science.gov (United States)

    Highton, Richard; Hastings, Amy Picard; Palmer, Catherine; Watts, Richard; Hass, Carla A.; Culver, Melanie; Arnold, Stevan

    2012-01-01

    Salamanders of the North American plethodontid genus Plethodon are important model organisms in a variety of studies that depend on a phylogenetic framework (e.g., chemical communication, ecological competition, life histories, hybridization, and speciation), and consequently their systematics has been intensively investigated over several decades. Nevertheless, we lack a synthesis of relationships among the species. In the analyses reported here we use new DNA sequence data from the complete nuclear albumin gene (1818 bp) and the 12s mitochondrial gene (355 bp), as well as published data for four other genes (Wiens et al., 2006), up to a total of 6989 bp, to infer relationships. We relate these results to past systematic work based on morphology, allozymes, and DNA sequences. Although basal relationships show a strong consensus across studies, many terminal relationships remain in flux despite substantial sequencing and other molecular and morphological studies. This systematic instability appears to be a consequence of contemporaneous bursts of speciation in the late Miocene and Pliocene, yielding many closely related extant species in each of the four eastern species groups. Therefore we conclude that many relationships are likely to remain poorly resolved in the face of additional sequencing efforts. On the other hand, the current classification of the 45 eastern species into four species groups is supported. The Plethodon cinereus group (10 species) is the sister group to the clade comprising the other three groups, but these latter groups (Plethodon glutinosus [28 species], Plethodon welleri [5 species], and Plethodon wehrlei [2 species]) probably diverged from each other at approximately the same time.

  15. An Affymetrix Microarray Design for Microbial Genotyping

    Science.gov (United States)

    2009-10-01

    les échantillons qui ne se prêtent pas aux méthodes culturales de la microbiologie classique. La puce à ADN est une technologie qui permet la... area of microbial genotyping there are multiple platforms that can identify one or a few microbial targets in a single assay iteration. For most

  16. Human papillomavirus genotyping by multiplex pyrosequencing in ...

    Indian Academy of Sciences (India)

    PRAKASH KUMAR G

    malignant cervical samples ... low- and high-risk HPV genotypes without identifying ... Since these samples were not from “healthy .... major capsid protein, any variation in its coding sequence is .... worldwide: a meta-analysis; Br. J. Cancer 88 63–73.

  17. Physicochemical and sensorial quality of banana genotypes

    Directory of Open Access Journals (Sweden)

    Ronielli Cardoso Reis

    2016-03-01

    Full Text Available Despite the diversity of banana varieties in Brazil, only a few cultivars have the proper agronomic traits and fruit quality for commercial exploitation. This study aimed at evaluating the physicochemical traits and sensorial acceptance of banana genotypes, in order to identify those with potential for commercial growing. Six improved banana genotypes were assessed (BRS Maravilha, PC 0101, FHIA 18, TM 2803, YB 4203 and BRS Caipira, as well as three commercial cultivars (Grand Naine, Pacovan and Prata Anã. Analyses of peel and pulp color, peel thickness, pulp yield, moisture, pH, soluble solids, titratable acidity, total carotenoids and sensorial acceptance were performed. The BRS Maravilha, FHIA 18, YB 4203 and BRS Caipira genotypes presented physicochemical traits similar to the Grand Naine, Pacovan and Prata Anã commercial cultivars. The BRS Maravilha and TM 2803 genotypes had sensorial acceptance similar to the Prata Anã and Grand Naine cultivars, and are therefore promising for commercial growing, with the advantage of being resistant to the black Sigatoka and Panama disease.

  18. Genotyping of human pappilomavirus in cervical precancerous ...

    African Journals Online (AJOL)

    Background: Cervical cancer caused by human papilloma virus (HPV), is the second most common cancer for women. This cancer is distributed worldwide, with ~80% of cases are found in the developing countries. In Indonesia, data of HPV genotypes are still limited and do not represent all regions of the country. Thus ...

  19. Morphometric characteristics of Lotus corniculatus L. genotypes ...

    African Journals Online (AJOL)

    The aim of this study was to examine the degree of variability in morphological and agronomic characteristics of 20 Lotus corniculatus L. local genotypes, and also to set aside germplasm that will be used as a source of genetic basis for improvement of the studied properties. In poor quality soils, L. corniculatus L. plays an ...

  20. Genotype X Fertility Interactions in Seedling Sweetgum

    Science.gov (United States)

    Scott X. Chang; Daniel J. Robison

    2002-01-01

    Genotype x fertility interactions may affect the suitability of sweetgum (Liquidambar styraciflua L.) for specific sites or the efficiency of nutrient use. To gain a better understanding of these interactions, 2-year-old sweetgum seedlings from two half-sib families were tested for growth response to N (0 and 100 kg/ha equivalent) and P (0 and 50 kg...

  1. (AMMI) and genotype by environment interaction

    African Journals Online (AJOL)

    SARAH

    2014-04-30

    Apr 30, 2014 ... Background and justification: Lack of stable high yielding cultivars is one ... of advanced finger millet genotypes evaluated in multiple environments, and (ii) identify stable high yielding .... for interaction principal component axis (IPCA) n, γgn ..... Table 2: Analysis of variance for grain yield using AMMI model.

  2. Effect of knowledge of APOE genotype on subjective and objective memory performance in healthy older adults.

    Science.gov (United States)

    Lineweaver, Tara T; Bondi, Mark W; Galasko, Douglas; Salmon, David P

    2014-02-01

    The knowledge that one carries the apolipoprotein E (APOE) ε4 allele risk factor for Alzheimer's disease was recently found to have little short-term psychological risk. The authors investigated the impact of knowledge of carrying the risk allele on subjective ratings of memory and objective memory test performance of older adults. Using a nested case-control design, the authors administered objective verbal and visual memory tests and self-rating scales of memory function to 144 cognitively normal older adults (ages 52-89) with known APOE genotype who knew (ε4+, N=25; ε4-, N=49) or did not know (ε4+, N=25; ε4-, N=45) their genotype and genetic risk for Alzheimer's disease prior to neuropsychological evaluation. Significant genotype-by-disclosure interaction effects were observed on several memory rating scales and tests of immediate and delayed verbal recall. Older adults who knew their ε4+ genotype judged their memory more harshly and performed worse on an objective verbal memory test than did ε4+ adults who did not know. In contrast, older adults who knew their ε4- genotype judged their memory more positively than did ε4- adults who did not know, but these groups did not differ in objective memory test performance. Informing older adults that they have an APOE genotype associated with an increased risk of Alzheimer's disease can have adverse consequences on their perception of their memory abilities and their performance on objective memory tests. The patient's knowledge of his or her genotype and risk of Alzheimer's disease should be considered when evaluating cognition in the elderly.

  3. Validation of the DNATyper™15 PCR Genotyping System for Forensic Application

    Directory of Open Access Journals (Sweden)

    Jian Ye

    2015-01-01

    Full Text Available We describe the optimization and validation of the DNATyper™15 multiplex polymerase chain reaction (PCR genotyping system for autosomal short tandem repeat (STR amplification at 14 autosomal loci (D6S1043, D21S11, D7S820, CSF1PO, D2S1338, D3S1358, D13S317, D8S1179, D16S539, Penta E, D5S818, vWA, D18S51, and FGA and  amelogenin, a sex-determining locus. Several DNATyper™15 assay variables were optimized, including hot start Taq polymerase concentration, Taq polymerase activation time, magnesium concentration, primer concentration, annealing temperature, reaction volume, and cycle number. The performance of the assay was validated with respect to species specificity, sensitivity to template concentration, stability, accuracy, influence of the DNA extraction methods, and the ability to genotype the mixture samples. The performance of the DNATyper™15 system on casework samples was compared with that of two widely used STR amplification kits, Identifiler™ (Applied Biosystems, Carlsbad, CA, USA and PowerPlex 16 ® (Promega, Madison, WI, USA. The conditions for PCR-based DNATyper™15 genotyping were optimized. Contamination from forensically relevant nonhuman DNA was not found to impact genotyping results, and full profiles were generated for all the reactions containing ≥ 0.125 ng of DNA template. No significant difference in performance was observed even after the DNATyper™15 assay components were subjected to 20 freeze-thaw cycles. The performances of DNATyper™15, Identifiler™, and PowerPlex 16 ® were comparable in terms of sensitivity and the ability to genotype the mixed samples and case-type samples, with the assays giving the same genotyping results for all the shared loci. The DNA extraction methods did not affect the performance of any of the systems. Our results demonstrate that the DNATyper™15 system is suitable for genotyping in both forensic DNA database work and case-type samples.

  4. Molecular epidemiology and genotyping of hepatitis B virus of HBsAg-positive patients in Oman.

    Science.gov (United States)

    Al Baqlani, Said Ali; Sy, Bui Tien; Ratsch, Boris A; Al Naamani, Khalid; Al Awaidy, Salah; Busaidy, Suleiman Al; Pauli, Georg; Bock, C-Thomas

    2014-01-01

    Hepatitis B virus (HBV) infection is a major global health burden with distinct geographic public health significance. Oman is a country with intermediate HBV carrier prevalence; however, little is known about the incidence of HBV variants in circulation. We investigated the HBV genotype distribution, the occurrence of antiviral resistance, and HBV surface antigen (HBsAg) escape mutations in HBsAg-positive patients in Oman. Serum samples were collected from 179 chronically HBV-infected patients enrolled in various gastroenterology clinics in Oman. HBV genotypes were determined by sequencing and phylogenetic analysis. Mutations in the HBV polymerase and the HBsAg gene were characterized by mutational analysis. HBV genotypes D (130/170; 76.47%) and A (32/170; 18.28%) are predominant in Oman. The HBV genotypes C and E were less frequent (each 1.18%), while the HBV genotypes B, G, F, and H were not detected. Four patients revealed HBV genotype mixtures (HBV-A/D and D/C). The analyses of vaccine escape mutations yield that 148/170 (87.06%) HBV sequences were wild type. 22/170 (12.94%) HBV sequences showed mutations in the "a" determinant of the HBsAg domain. Two patients showed the described HBV vaccine escape mutation sP120T. 8/146 (5.48%) HBV isolates harbored mutations in the HBV polymerase known to confer resistance against antiviral therapy. Especially the lamivudine resistance mutations rtL180M/rtM204V and rtM204I were detected. This study shows the distribution of HBV genotypes, therapy resistance, and vaccine escape mutations in HBV-infected patients in Oman. Our findings will have a major impact on therapy management and diagnostics of chronic HBV infections in Oman to control HBV infection in this intermediate HBV-endemic country.

  5. Field study of dried blood spot specimens for HIV-1 drug resistance genotyping.

    Science.gov (United States)

    Parry, C M; Parkin, N; Diallo, K; Mwebaza, S; Batamwita, R; DeVos, J; Bbosa, N; Lyagoba, F; Magambo, B; Jordan, M R; Downing, R; Zhang, G; Kaleebu, P; Yang, C; Bertagnolio, S

    2014-08-01

    Dried blood spots (DBS) are an alternative specimen type for HIV drug resistance genotyping in resource-limited settings. Data relating to the impact of DBS storage and shipment conditions on genotyping efficiency under field conditions are limited. We compared the genotyping efficiencies and resistance profiles of DBS stored and shipped at different temperatures to those of plasma specimens collected in parallel from patients receiving antiretroviral therapy in Uganda. Plasma and four DBS cards from anti-coagulated venous blood and a fifth card from finger-prick blood were prepared from 103 HIV patients with a median viral load (VL) of 57,062 copies/ml (range, 1,081 to 2,964,191). DBS were stored at ambient temperature for 2 or 4 weeks or frozen at -80 °C and shipped from Uganda to the United States at ambient temperature or frozen on dry ice for genotyping using a broadly sensitive in-house method. Plasma (97.1%) and DBS (98.1%) stored and shipped frozen had similar genotyping efficiencies. DBS stored frozen (97.1%) or at ambient temperature for 2 weeks (93.2%) and shipped at ambient temperature also had similar genotyping efficiencies. Genotyping efficiency was reduced for DBS stored at ambient temperature for 4 weeks (89.3%, P = 0.03) or prepared from finger-prick blood and stored at ambient temperature for 2 weeks (77.7%, P blood and handled similarly. Resistance profiles were similar between plasma and DBS specimens. This report delineates the optimal DBS collection, storage, and shipping conditions and opens a new avenue for cost-saving ambient-temperature DBS specimen shipments for HIV drug resistance (HIVDR) surveillances in resource-limited settings. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  6. A review of best management practices and the mitigation of stream-breeding salamanders in the eastern deciduous forest

    Science.gov (United States)

    Thomas A. Maigret; John J. Cox

    2014-01-01

    Timber harvest has been implicated as a causative factor in the decline of amphibian populations and diversity in many areas of the world. The adoption of best management practices (BMPs) is intended to minimize the impacts of timber harvest on the biotic community, including amphibians and their habitat requirements. Herein, we synthesize the current scientific...

  7. In Vitro Conservation of Sweet Potato Genotypes

    Directory of Open Access Journals (Sweden)

    Maria de Fátima Arrigoni-Blank

    2014-01-01

    Full Text Available The aim of this study was to develop a protocol for the in vitro conservation of sweet potato genotypes using the slow growth technique. The first experiment was conducted in a 4×5×2 factorial scheme, testing four genotypes (IPB-007, IPB-052, IPB-072, and IPB-137, five concentrations of abscisic acid (ABA (0.0, 1.0, 2.0, 4.0, and 8.0 mg·L−1, and two temperatures (18 and 25°C. The second experiment was conducted in a 4×3×3 factorial scheme at 18°C, testing four genotypes (IPB-007, IPB-052, IPB-072, and IPB-137, three variations of MS salts (50, 75, and 100%, and three concentrations of sucrose (10, 20, and 30 g·L−1. Every three months, we evaluated the survival (%, shoot height, and shoot viability. In vitro conservation of the sweet potato genotypes IPB-052 and IPB-007 was obtained over three and six months, respectively, using MS medium plus 2.0 mg·L−1 of ABA at either 18 or 25°C. Genotypes IPB-072 and IPB-137 can be kept for three and six months, respectively, in MS medium without ABA at 18°C. It is possible to store IPB-052 and IPB-072 for six months and IPB-007 and IPB-137 for nine months using 30 g·L−1 of sucrose and 50% MS salts.

  8. Genotypic variability enhances the reproducibility of an ecological study.

    Science.gov (United States)

    Milcu, Alexandru; Puga-Freitas, Ruben; Ellison, Aaron M; Blouin, Manuel; Scheu, Stefan; Freschet, Grégoire T; Rose, Laura; Barot, Sebastien; Cesarz, Simone; Eisenhauer, Nico; Girin, Thomas; Assandri, Davide; Bonkowski, Michael; Buchmann, Nina; Butenschoen, Olaf; Devidal, Sebastien; Gleixner, Gerd; Gessler, Arthur; Gigon, Agnès; Greiner, Anna; Grignani, Carlo; Hansart, Amandine; Kayler, Zachary; Lange, Markus; Lata, Jean-Christophe; Le Galliard, Jean-François; Lukac, Martin; Mannerheim, Neringa; Müller, Marina E H; Pando, Anne; Rotter, Paula; Scherer-Lorenzen, Michael; Seyhun, Rahme; Urban-Mead, Katherine; Weigelt, Alexandra; Zavattaro, Laura; Roy, Jacques

    2018-02-01

    Many scientific disciplines are currently experiencing a 'reproducibility crisis' because numerous scientific findings cannot be repeated consistently. A novel but controversial hypothesis postulates that stringent levels of environmental and biotic standardization in experimental studies reduce reproducibility by amplifying the impacts of laboratory-specific environmental factors not accounted for in study designs. A corollary to this hypothesis is that a deliberate introduction of controlled systematic variability (CSV) in experimental designs may lead to increased reproducibility. To test this hypothesis, we had 14 European laboratories run a simple microcosm experiment using grass (Brachypodium distachyon L.) monocultures and grass and legume (Medicago truncatula Gaertn.) mixtures. Each laboratory introduced environmental and genotypic CSV within and among replicated microcosms established in either growth chambers (with stringent control of environmental conditions) or glasshouses (with more variable environmental conditions). The introduction of genotypic CSV led to 18% lower among-laboratory variability in growth chambers, indicating increased reproducibility, but had no significant effect in glasshouses where reproducibility was generally lower. Environmental CSV had little effect on reproducibility. Although there are multiple causes for the 'reproducibility crisis', deliberately including genetic variability may be a simple solution for increasing the reproducibility of ecological studies performed under stringently controlled environmental conditions.

  9. Selection of ectomycorrhizal willow genotype in phytoextraction of heavy metals.

    Science.gov (United States)

    Hrynkiewicz, Katarzyna; Baum, Christel

    2013-01-01

    Willow clones are used for the phytoextraction of heavy metals from contaminated soils and are usually mycorrhizal. The receptiveness of willow clones for mycorrhizal inoculum varies specific to genotype; however, it is unknown if this might have a significant impact on their efficiency in phytoextraction of heavy metals. Therefore, a model system with mycorrhizal and non-mycorrhizal willows of two different genotypes--one with usually stronger natural mycorrhizal colonization (Salix dasyclados), and one with lower natural mycorrhizal colonization (S. viminalis)--was investigated for its efficiency of phytoextraction of heavy metals (Cd, Pb, Cu, Zn) from contaminated soil. Inoculation with the ectomycorrhizal fungus Amanita muscaria significantly decreased the biomass of leaves of both inoculated willow clones, and increased or had no effect on the biomass of trunks and roots of S. dasyclados and S. viminalis, respectively. The concentrations of heavy metals in the biomass of S. dasyclados were in general higher than in S. viminalis irrespective of inoculation with the ectomycorrhizal fungus. Inoculation with A. muscaria significantly decreased the concentration of Cu in the trunks of both Salix taxa, but did not affected the concentrations of other heavy metals in the biomass. In conclusion, stronger receptiveness of willow clones for mycorrhizal inoculum was correlated with an increased total extraction of heavy metals from contaminated soils. Therefore, this seems to be a suitable criterion for effective willow clone selection for phytoremediation. Increased biomass production with relatively constant metal concentrations seems to be a major advantage of mycorrhizal formation of willows in phytoremediation of contaminated soils.

  10. The potential of plant viruses to promote genotypic diversity via genotype x environment interactions

    DEFF Research Database (Denmark)

    van Mölken, Tamara; Stuefer, Josef F.

    2011-01-01

    † Background and Aims Genotype by environment (G × E) interactions are important for the long-term persistence of plant species in heterogeneous environments. It has often been suggested that disease is a key factor for the maintenance of genotypic diversity in plant populations. However, empirical...... and the G × E interactions were examined with respect to genotypespecific plant responses to WClMV infection. Thus, the environment is defined as the presence or absence of the virus. † Key Results WClMV had a negative effect on plant performance as shown by a decrease in biomass and number of ramets...... evidence for this contention is scarce. Here virus infection is proposed as a possible candidate for maintaining genotypic diversity in their host plants. † Methods The effects of White clover mosaic virus (WClMV) on the performance and development of different Trifolium repens genotypes were analysed...

  11. Genotypic Variation of Early Maturing Soybean Genotypes for Phosphorus Utilization Efficiency under Field Grown Conditions

    Energy Technology Data Exchange (ETDEWEB)

    Abaidoo, R. C. [Kwame Nkrumah University of Technology, Kumasi (Ghana); International Institute of Tropical Agriculture, Ibadan (Nigeria); Opoku, A.; Boahen, S. [Kwame Nkrumah University of Technology, Kumasi (Ghana); Dare, M. O. [Federal University of Agriculture, Abeokuta (Nigeria)

    2013-11-15

    Variability in the utilization of phosphorus (P) by 64 early-maturing soybean (Glycine max L. Merr.) genotypes under low-P soil conditions were evaluated in 2009 and 2010 at Shika, Nigeria. Fifteen phenotypic variables; number of nodules, nodule dry weight, grain yield, plant biomass, total biomass, biomass N and P content, Phosphorus Utilization Index (PUI), shoot P Utilization efficiency (PUIS), grain P Utilization efficiency (PUIG), Harvest Index (HI), Biological N fixed (BNF), total N fixed and N and P uptake were measured. The four clusters revealed by cluster analysis were basically divided along (1) plant biomass and uptake, (2) nutrient acquisition and utilization and (3) nodulation components. Three early maturing genotypes, TGx1842-14E, TGx1912-11F and TGx1913-5F, were identified as having high P utilization index and low P uptake. These genotypes could be a potential source for breeding for P use efficiency in early maturing soybean genotypes. (author)

  12. In situ assessment of morpho-physiological response of wheat (triticum aestivum L.) genotypes to drought

    International Nuclear Information System (INIS)

    Raziuddin; Faratullah; Ullah, N.; Hassan, G.; Swati, Z.A.; Bakht, J.; Shafi, M.; Akmal, M.

    2010-01-01

    In situ studies were conducted to assess the morpho-physiological responses of wheat genotypes to PEG-induced water stress. Wheat genotypes were raised in hydroponic cultures where plants were nourished with half strength Hoagland solution. Plants were exposed to 00, 10, 20, 30 and 40% PEG-6000 at 4-leaf stage. PEG was applied in split doses at the rate of 10% with an interval of 15 days. Significant differences (p=0.05) were recorded for all the parameters studied due to genotypes and PEG concentrations. Wheat genotypes showed negative but variable response to PEG concentrations for shoot length, root length, root/ shoot ratio and root mass whereas PEG imposed stress had positive impact on proline content and abscisic acid (ABA). Genotype Khattakwal attained maximum shoot length in PEG induced stress. Maximum root/shoot ratio and root mass was recorded in Ghaznavi-98 while Tatara and Khattakwal attained maximum relative water content. Endogenous proline and ABA content increased up to 10 fold in response to 40% PEG. Maximum proline was accumulated by Khattakwal whereas maximum ABA by ICP-3. (author)

  13. Nutritional value of dual-purpose wheat genotypes pastures under grazing by dairy cows

    Directory of Open Access Journals (Sweden)

    Mauricio Pase Quatrin

    2017-07-01

    Full Text Available In the south of Brazil, one of the major limitations to milk production is the low forage availability during autumn and early winter. The use of dual-purpose wheat genotypes is one alternative to minimize the impact of low forage availability in addition to produce grains. Therefore, this study aimed to evaluate the nutritional value of two dual-purpose wheat genotypes (BRS Tarumã and BRS Umbu. Structural composition and forage nitrogen uptake were evaluated. The nutritional value of the forage was analyzed for mineral matter (MM, organic matter (OM, neutral detergent fiber (NDF, crude protein (CP, total digestible nutrients (TDN, in situ organic matter digestibility (ISOMD and in situ dry matter digestibility (ISDMD. Differences in NDF (49.03 vs. 46.44%, CP (24.4 vs. 27.4%, ISOMD (83.53 vs. 85.45%, ISDMD (83.59 vs. 86.65% and TDN (75.37 vs. 78.39 for BRS Umbu and BRS Tarumã genotypes were detected, respectively. The BRS Umbu genotype had a lower leaf blade proportion and forage nitrogen uptake. The dual-purpose wheat genotype BRS Tarumã was superior in nutritive value.

  14. Phenotype, Genotype, and Drug Resistance in Subtype C HIV-1 Infection.

    Science.gov (United States)

    Derache, Anne; Wallis, Carole L; Vardhanabhuti, Saran; Bartlett, John; Kumarasamy, Nagalingeswaran; Katzenstein, David

    2016-01-15

    Virologic failure in subtype C is characterized by high resistance to first-line antiretroviral (ARV) drugs, including efavirenz, nevirapine, and lamivudine, with nucleoside resistance including type 2 thymidine analog mutations, K65R, a T69del, and M184V. However, genotypic algorithms predicting resistance are mainly based on subtype B viruses and may under- or overestimate drug resistance in non-B subtypes. To explore potential treatment strategies after first-line failure, we compared genotypic and phenotypic susceptibility of subtype C human immunodeficiency virus 1 (HIV-1) following first-line ARV failure. AIDS Clinical Trials Group 5230 evaluated patients failing an initial nonnucleoside reverse-transcriptase inhibitor (NNRTI) regimen in Africa and Asia, comparing the genotypic drug resistance and phenotypic profile from the PhenoSense (Monogram). Site-directed mutagenesis studies of K65R and T69del assessed the phenotypic impact of these mutations. Genotypic algorithms overestimated resistance to etravirine and rilpivirine, misclassifying 28% and 32%, respectively. Despite K65R with the T69del in 9 samples, tenofovir retained activity in >60%. Reversion of the K65R increased susceptibility to tenofovir and other nucleosides, while reversion of the T69del showed increased resistance to zidovudine, with little impact on other NRTI. Although genotype and phenotype were largely concordant for first-line drugs, estimates of genotypic resistance to etravirine and rilpivirine may misclassify subtype C isolates compared to phenotype. © The Author 2015. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail journals.permissions@oup.com.

  15. Different natural courses of chronic hepatitis B with genotypes B and C after the fourth decade of life

    Institute of Scientific and Technical Information of China (English)

    Tatsuji Maeshiro; Tomofumi Nakayoshi; Tomokuni Nakayoshi; Masashi Mizokami; Jiro Fujita; Hiroshi Sakugawa; Shingo Arakaki; Takako Watanabe; Hajime Aoyama; Joji Shiroma; Tsuyoshi Yamashiro; Tetsuo Hirata; Akira Hokama; Fukunori Kinjo

    2007-01-01

    AIM: To investigate the different impact of genotypes B and C on the development of liver cirrhosis (LC) among different age groups of patients with chronic hepatitis B (CH-B).METHODS: We examined the outcome of 121 patients with CH-B, divided by age and genotype. Univariate analyses were used to compare different groups. The Cox proportional hazard model was employed to evaluate factors affecting the development of LC.RESULTS: In patients < 30 years old, there were no significant predictors for development of LC. However,in patients ≥ 30 years old, genotype C was the only significant predictor. In the genotype C group, 8 of 12patients who progressed to LC were 30-49 years old at initial diagnosis of chronic hepatitis (7 patients were positive for HBeAg). In the genotype B group, 4 of 8patients who developed LC were ≥ 50 years old at initial diagnosis and were HBeAg-negative.CONCLUSION: The rate of development of LC was comparable in patients infected with genotypes B and C when CH-B occurred at < 30 years old. However,CH-B patients infected with genotype C showed poor prognosis if they were 30-49 years old and were positive for HBeAg. Age-specific natural course of CH-B should be considered when patients with CH-B are treated with antiviral drugs.

  16. Distribution of genotype network sizes in sequence-to-structure genotype-phenotype maps.

    Science.gov (United States)

    Manrubia, Susanna; Cuesta, José A

    2017-04-01

    An essential quantity to ensure evolvability of populations is the navigability of the genotype space. Navigability, understood as the ease with which alternative phenotypes are reached, relies on the existence of sufficiently large and mutually attainable genotype networks. The size of genotype networks (e.g. the number of RNA sequences folding into a particular secondary structure or the number of DNA sequences coding for the same protein structure) is astronomically large in all functional molecules investigated: an exhaustive experimental or computational study of all RNA folds or all protein structures becomes impossible even for moderately long sequences. Here, we analytically derive the distribution of genotype network sizes for a hierarchy of models which successively incorporate features of increasingly realistic sequence-to-structure genotype-phenotype maps. The main feature of these models relies on the characterization of each phenotype through a prototypical sequence whose sites admit a variable fraction of letters of the alphabet. Our models interpolate between two limit distributions: a power-law distribution, when the ordering of sites in the prototypical sequence is strongly constrained, and a lognormal distribution, as suggested for RNA, when different orderings of the same set of sites yield different phenotypes. Our main result is the qualitative and quantitative identification of those features of sequence-to-structure maps that lead to different distributions of genotype network sizes. © 2017 The Author(s).

  17. Pollen diversity, viability and floral structure of some Musa genotypes

    African Journals Online (AJOL)

    Pollen diversity, viability and floral structure of some Musa genotypes. ... This experiment was designed to study the floral structure, pollen morphology and the potential pollen viability of five Musa genotypes obtained ... HOW TO USE AJOL.

  18. Behavior of durum wheat genotypes under normal irrigation and ...

    African Journals Online (AJOL)

    Behavior of durum wheat genotypes under normal irrigation and drought stress conditions in the greenhouse. ... African Journal of Biotechnology ... Genotypes were grouped in cluster analysis (using Ward's method) based on Yp, Ys and ...

  19. Genetic variability in cowpea (Vigna unguiculata (L.) Walp.) genotypes

    African Journals Online (AJOL)

    sive protein in human diets with grains containing about. 23–25% protein ... Keywords: heritability, phenotype, principal component analysis, variance. Introduction .... be due to genotype, environment, and the interaction of genotype and ...

  20. magnitude of genotype x environment interaction for bacterial leaf

    African Journals Online (AJOL)

    ACSS

    African Crop Science Journal, Vol. ... effects of treatments into genotype, environment, and genotype x environment (G x E) interactions. Results .... method is economically effective (Niño-Liu et al., ..... This phenomenon indicated differences in.

  1. Genotype 3 is the predominant hepatitis C genotype in a multi-ethnic Asian population in Malaysia.

    Science.gov (United States)

    Ho, Shiaw-Hooi; Ng, Kee-Peng; Kaur, Harvinder; Goh, Khean-Lee

    2015-06-01

    Genotypes of hepatitis C virus (HCV) are distributed differently across the world. There is a paucity of such data in a multi-ethnic Asian population like Malaysia. The objectives of this study were to determine the distribution of HCV genotypes between major ethnic groups and to ascertain their association with basic demographic variables like age and gender. This was a cross-sectional prospective study conducted from September 2007 to September 2013. Consecutive patients who were detected to have anti-HCV antibodies in the University of Malaya Medical Centre were included and tested for the presence of HCV RNA using Roche Cobas Amplicor Analyzer and HCV genotype using Roche single Linear Array HCV Genotyping strip. Five hundred and ninety-six subjects were found to have positive anti-HCV antibodies during this period of time. However, only 396 (66.4%) were HCV RNA positive and included in the final analysis. Our results showed that HCV genotype 3 was the predominant genotype with overall frequency of 61.9% followed by genotypes 1 (35.9%), 2 (1.8%) and 6 (0.5%). There was a slightly higher prevalence of HCV genotype 3 among the Malays when compared to the Chinese (P=0.043). No other statistical significant differences were observed in the distribution of HCV genotypes among the major ethnic groups. There was also no association between the predominant genotypes and basic demographic variables. In a multi-ethnic Asian society in Malaysia, genotype 3 is the predominant genotype among all the major ethnic groups with genotype 1 as the second commonest genotype. Both genotypes 2 and 6 are uncommon. Neither genotype 4 nor 5 was detected. There is no identification of HCV genotype according to ethnic origin, age and gender.

  2. HPV genotypes in invasive cervical cancer in Danish women

    DEFF Research Database (Denmark)

    Kirschner, Benny; Junge, Jette; Holl, Katsiaryna

    2013-01-01

    Human papillomavirus (HPV) genotype distribution in invasive cervical cancers may differ by geographic region. The primary objective of this study was to estimate HPV-genotype distribution in Danish women with a diagnosis of invasive cervical cancer.......Human papillomavirus (HPV) genotype distribution in invasive cervical cancers may differ by geographic region. The primary objective of this study was to estimate HPV-genotype distribution in Danish women with a diagnosis of invasive cervical cancer....

  3. Evaluation of promising sweetpotato genotypes for high altitude ...

    African Journals Online (AJOL)

    The trials were set up to identify sweetpotato genotypes with adaptation to highland agroecologies with special reference to resistance to Ahemaria blight ... growth and at harvest, four genotypes and the local check, Magabari, bad high levels of resistance toA/Jemaria blight. Eight genotypes had total storage root yield ...

  4. Hepatitis B virus Genotypes in West Azarbayjan Province, Northwest Iran

    Directory of Open Access Journals (Sweden)

    Mohammad Hasan Khadem Ansari

    2017-12-01

    CONCLUSIONS: The results reveal that D genotype is the main genotype of HBV in West Azarbayjan province. Presence of this genotype conformed with the low rate of acute liver diseases caused by hepatitis B chronic infection, cirrhosis of the liver and hepatocellular carcinoma.

  5. Genotype-based personalised nutrition for obesity prevention and ...

    African Journals Online (AJOL)

    Typically, genotype-based personalised nutrition involves genotyping for a number of susceptibility SNPs associated with the prevention, or management, of a particular disease. Dietary advice is then personalised to the individual's genotype to ensure optimal prevention or treatment outcomes. To ensure evidence-based ...

  6. Introduction to a special issue on genotype by environment interaction

    Science.gov (United States)

    Expression of a phenotype is a function of the genotype, the environment, and the differential sensitivity of certain genotypes to different environments, also known as genotype by environment (G × E) interaction. This special issue of Crop Science includes a collection of manuscripts that reviews t...

  7. Core Gene Expression and Association of Genotypes with Viral ...

    African Journals Online (AJOL)

    Purpose: To determine genotypic distribution, ribonucleic acid (RNA) RNA viral load and express core gene from Hepatitis C Virus (HCV) infected patients in Punjab, Pakistan. Methods: A total of 1690 HCV RNA positive patients were included in the study. HCV genotyping was tested by type-specific genotyping assay, viral ...

  8. Effect of Genotype and Age on Some Morphometric, Body Linear ...

    African Journals Online (AJOL)

    A population of 231 roosters of the Nigerian indigenous chickens of normal feathered frizzle feathered and naked neck genotypes was evaluated for the effect of genotype and age on some morphometric body linear measurements and semen characteristics of three Nigerian chicken genotypes. 20 roosters from each ...

  9. 21 CFR 862.3360 - Drug metabolizing enzyme genotyping system.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Drug metabolizing enzyme genotyping system. 862... Test Systems § 862.3360 Drug metabolizing enzyme genotyping system. (a) Identification. A drug metabolizing enzyme genotyping system is a device intended for use in testing deoxyribonucleic acid (DNA...

  10. Relationship of status of polymorphic rapd bands with genotypic ...

    African Journals Online (AJOL)

    Relationship of status of polymorphic rapd bands with genotypic adaptation in early finger millet genotypes. S Das, RC Misra, GR Rout, MC Pattanaik, S Aparajita. Abstract. Molecular characterisation of the 15 early duration finger millet (Eleusine coracana G) genotypes was done through RAPD markers. Twenty-five ...

  11. Genotype x Environment Interaction for Tuber Yield, Dry Matter ...

    African Journals Online (AJOL)

    A study was conducted to determine stability of tuber yield, dry matter content and specific gravity, and the nature and magnitude of genotype x environment (G x E) interaction in elite tetraploid potato genotypes. Eleven potato genotypes including two standard checks were evaluated in the eastern part of Ethiopia at ...

  12. [Evaluation of hepatitis B virus genotyping EIA kit].

    Science.gov (United States)

    Tanaka, Yasuhito; Sugauchi, Fuminaka; Matsuuraa, Kentaro; Naganuma, Hatsue; Tatematsu, Kanako; Takagi, Kazumi; Hiramatsu, Kumiko; Kani, Satomi; Gotoh, Takaaki; Wakimoto, Yukio; Mizokami, Masashi

    2009-01-01

    Clinical significance of Hepatitis B virus(HBV) genotyping is increasingly recognized. The aim of this study was to evaluate reproducibility, accuracy, and sensitivity of an enzyme immunoassay (EIA) based HBV genotyping kit, which designed to discriminate between genotypes to A, B, C, or D by detecting genotype-specific epitopes in PreS2 region. Using the four genotypes panels, the EIA demonstrated complete inter and intra-assay genotyping reproducibility. Serum specimens had stable results after 8 days at 4 degrees C, or 10 cycles of freezing-thawing. In 91 samples that have been genotyped by DNA sequencing, 87(95.6%) were in complete accordance with EIA genotyping. Of examined 344 HBsAg-positive serum specimens, genotypes A, B, C and D were determined in 26 (7.6%), 62 (18.0%), 228 (66.3%), and 9 (2.6%) cases, respectively. Of 19 (5.5%) specimens unclassified by the EIA, 13 were found to have low titer of HBsAg concentration (< 3 IU/ml), and the other 5 had amino acid mutations or deletions within targeted PreS2 epitopes. The EIA allowed genotyping even in HBV DNA negative samples (96.2%). In conclusion, HBV genotype EIA is reliable, sensitive and easy assay for HBV genotyping. The assay would be useful for clinical use.

  13. Genotype by environment interactions and yield stability of stem ...

    African Journals Online (AJOL)

    In a maize breeding program, potential genotypes are usually evaluated in different environments before desirable ones are selected. Genotype x environment (G x E) interaction is associated with the differential performance of genotypes tested at different locations and in different years, and influences selection and ...

  14. Genotype x environment interaction and stability analysis for yield ...

    African Journals Online (AJOL)

    Chickpea is the major pulse crop cultivated in Ethiopia. However, its production is constrained due to genotype instability and environmental variability. This research was carried out to examine the magnitude of environmental effect on yield of chickpea genotypes and to investigate the stability and adaptability of genotypes ...

  15. Reactions of some potato genotypes to late blight in Cameroon ...

    African Journals Online (AJOL)

    Reactions of some potato genotypes to late blight in Cameroon. D. K. Njualem, P. Demo, H. A. Mendoza, J. T. Koi, S. F. Nana. Abstract. Field experiments were conducted in Cameroon in 1995 and 1996 to evaluate reactions of different potato genotypes to late blight. There were significant differences among genotypes for ...

  16. Discovery of novel variants in genotyping arrays improves genotype retention and reduces ascertainment bias

    Directory of Open Access Journals (Sweden)

    Didion John P

    2012-01-01

    Full Text Available Abstract Background High-density genotyping arrays that measure hybridization of genomic DNA fragments to allele-specific oligonucleotide probes are widely used to genotype single nucleotide polymorphisms (SNPs in genetic studies, including human genome-wide association studies. Hybridization intensities are converted to genotype calls by clustering algorithms that assign each sample to a genotype class at each SNP. Data for SNP probes that do not conform to the expected pattern of clustering are often discarded, contributing to ascertainment bias and resulting in lost information - as much as 50% in a recent genome-wide association study in dogs. Results We identified atypical patterns of hybridization intensities that were highly reproducible and demonstrated that these patterns represent genetic variants that were not accounted for in the design of the array platform. We characterized variable intensity oligonucleotide (VINO probes that display such patterns and are found in all hybridization-based genotyping platforms, including those developed for human, dog, cattle, and mouse. When recognized and properly interpreted, VINOs recovered a substantial fraction of discarded probes and counteracted SNP ascertainment bias. We developed software (MouseDivGeno that identifies VINOs and improves the accuracy of genotype calling. MouseDivGeno produced highly concordant genotype calls when compared with other methods but it uniquely identified more than 786000 VINOs in 351 mouse samples. We used whole-genome sequence from 14 mouse strains to confirm the presence of novel variants explaining 28000 VINOs in those strains. We also identified VINOs in human HapMap 3 samples, many of which were specific to an African population. Incorporating VINOs in phylogenetic analyses substantially improved the accuracy of a Mus species tree and local haplotype assignment in laboratory mouse strains. Conclusion The problems of ascertainment bias and missing

  17. COMT genotype, gambling activity, and cognition

    DEFF Research Database (Denmark)

    Grant, Jon E; Leppink, Eric W; Redden, Sarah A

    2015-01-01

    adjustment and delay aversion) and the Spatial Working Memory task (total errors). This study adds to the growing literature on the role of COMT in impulsive behaviors by showing that the Val/Val genotype was associated with specific clinical and cognitive elements among young adults who gamble......Neuropsychological studies of adults with problem gambling indicate impairments across multiple cognitive domains. Catechol-O-methyltransferase (COMT) plays a unique role in the regulation of dopamine in the prefrontal cortex, and has been implicated in the cognitive dysfunction evident in problem...... gambling. This study examined adults with varying levels of gambling behavior to determine whether COMT genotype was associated with differences in gambling symptoms and cognitive functioning. 260 non-treatment-seeking adults aged 18-29 years with varying degrees of gambling behavior provided saliva...

  18. FRUIT QUALITY CHARACTERISTICS OF SOME BLUEBERRY GENOTYPES

    Directory of Open Access Journals (Sweden)

    Irina Ancu

    2013-12-01

    Full Text Available In Romania the blueberry breeding program started in 1982 and till now was conducted by dr. Paulina Mladin. For inducing the variability, different genetic resources of American blueberry cultivars (V. corymbosum, V. angustifolium were involved in a high number of crosses. For identify the genotype with the best fruit quality, some biometric quality indicators (average fruit weight, size index and basically chemical compounds of fruits including ascorbic acid, dry matter, ash, soluble solids, total sugar, titratable acidity, tanoid substances, pectic substances, protein crude, phosphorus and potassium were determined. Of the eleven chemical studied properties who reflected the fruits quality, for five of them were found no statistically significant differences. The purpose of this paper work was to evaluate fruit quality and to identify the valuable genotypes resulted from Romanian blueberry breeding program.

  19. BCL2 genotypes and prostate cancer survival

    Energy Technology Data Exchange (ETDEWEB)

    Renner, Wilfried [Medical University of Graz, Clinical Institute of Medical and Chemical Laboratory Diagnostics, Graz (Austria); Langsenlehner, Uwe [GKK Outpatient Department, Division of Internal Medicine, Graz (Austria); Krenn-Pilko, Sabine; Langsenlehner, Tanja [Medical University of Graz, Department of Therapeutic Radiology and Oncology, Graz (Austria); Eder, Petra [University Hospital Wuerzburg, Department of Internal Medicine I, Wuerzburg (Germany)

    2017-06-15

    The antiapoptotic B-cell lymphoma 2 (BCL2) gene is a key player in cancer development and progression. A functional single-nucleotide polymorphism (c.-938C>A, rs2279115) in the inhibitory P2 BCL2 gene promoter has been associated with clinical outcomes in various types of cancer. Aim of the present study was to analyze the role of BCL2-938C>A genotypes in prostate cancer mortality. The association between BCL2-938C>A (rs2279115) genotypes and prostate cancer outcome was studied within the prospective PROCAGENE study comprising 702 prostate cancer patients. During a median follow-up time of 92 months, 120 (17.1%) patients died. A univariate Cox regression model showed a significant association of the CC genotype with reduced cancer-specific survival (CSS; hazard ratio, HR, 2.13, 95% confidence interval, CI, 1.10-4.12; p = 0.024) and overall survival (OS; HR 2.34, 95% CI 1.58-3.47; p < 0.001). In a multivariate Cox regression model including age at diagnosis, risk group, and androgen deprivation therapy, the CC genotype remained a significant predictor of poor CSS (HR 2.05, 95% CI 1.05-3.99; p = 0.034) and OS (HR 2.25, 95% CI 1.51-3.36; p < 0.001). This study provides evidence that the homozygous BCL2-938 CC genotype is associated with OS and C in prostate cancer patients. (orig.) [German] Das antiapoptotische Gen B cell lymphoma 2 (BCL2) spielt eine Schluesselrolle in der Entstehung und Progression von Krebserkrankungen. Ein funktioneller Einzelnukleotid-Polymorphismus (c.-938C>A, rs2279115) im inhibitorischen P2-BCL2-Promotor wurde mit dem klinischen Outcome verschiedener Krebserkrankungen verknuepft. Ziel der vorliegenden Studie war die Untersuchung der Rolle von BCL2-938C>A-Genotypen fuer die Mortalitaet bei Patienten mit Prostatakarzinom. Der Zusammenhang zwischen BCL2-938C>A-Genotypen (rs2279115) und dem Outcome bei Prostatakrebs wurde in der prospektiven PROCAGENE-Studie, die 702 Patienten mit Prostatakarzinom umfasste, untersucht. Waehrend der medianen

  20. Multi-generational imputation of single nucleotide polymorphism marker genotypes and accuracy of genomic selection.

    Science.gov (United States)

    Toghiani, S; Aggrey, S E; Rekaya, R

    2016-07-01

    Availability of high-density single nucleotide polymorphism (SNP) genotyping platforms provided unprecedented opportunities to enhance breeding programmes in livestock, poultry and plant species, and to better understand the genetic basis of complex traits. Using this genomic information, genomic breeding values (GEBVs), which are more accurate than conventional breeding values. The superiority of genomic selection is possible only when high-density SNP panels are used to track genes and QTLs affecting the trait. Unfortunately, even with the continuous decrease in genotyping costs, only a small fraction of the population has been genotyped with these high-density panels. It is often the case that a larger portion of the population is genotyped with low-density and low-cost SNP panels and then imputed to a higher density. Accuracy of SNP genotype imputation tends to be high when minimum requirements are met. Nevertheless, a certain rate of genotype imputation errors is unavoidable. Thus, it is reasonable to assume that the accuracy of GEBVs will be affected by imputation errors; especially, their cumulative effects over time. To evaluate the impact of multi-generational selection on the accuracy of SNP genotypes imputation and the reliability of resulting GEBVs, a simulation was carried out under varying updating of the reference population, distance between the reference and testing sets, and the approach used for the estimation of GEBVs. Using fixed reference populations, imputation accuracy decayed by about 0.5% per generation. In fact, after 25 generations, the accuracy was only 7% lower than the first generation. When the reference population was updated by either 1% or 5% of the top animals in the previous generations, decay of imputation accuracy was substantially reduced. These results indicate that low-density panels are useful, especially when the generational interval between reference and testing population is small. As the generational interval

  1. Novel approach for CES1 genotyping

    DEFF Research Database (Denmark)

    Bjerre, Ditte; Berg Rasmussen, Henrik

    2018-01-01

    AIM: Development of a specific procedure for genotyping of CES1A1 (CES1) and CES1A2, a hybrid of CES1A1 and the pseudogene CES1P1. MATERIALS & METHODS: The number of CES1A1 and CES1A2 copies and that of CES1P1 were determined using real-time PCR. Long range PCRs followed by secondary PCRs allowed...

  2. Screening cotton genotypes for seedling drought tolerance

    Directory of Open Access Journals (Sweden)

    Penna Julio C. Viglioni

    1998-01-01

    Full Text Available The objectives of this study were to adapt a screening method previously used to assess seedling drought tolerance in cereals for use in cotton (Gossypium hirsutum L. and to identify tolerant accessions among a wide range of genotypes. Ninety genotypes were screened in seven growth chamber experiments. Fifteen-day-old seedlings were subjected to four 4-day drought cycles, and plant survival was evaluated after each cycle. Three cycles are probably the minimum required in cotton work. Significant differences (at the 0.05 level or lower among entries were obtained in four of the seven experiments. A "confirmation test" with entries previously evaluated as "tolerant" (high survival and "susceptible" (low survival was run. A number of entries duplicated their earlier performance, but others did not, which indicates the need to reevaluate selections. Germplasms considered tolerant included: `IAC-13-1', `IAC-RM4-SM5', `Minas Sertaneja', `Acala 1517E-1' and `4521'. In general, the technique is simple, though time-consuming, with practical value for screening a large number of genotypes. Results from the screening tests generally agreed with field information. The screening procedure is suitable to select tolerant accessions from among a large number of entries in germplasm collections as a preliminary step in breeding for drought tolerance. This research also demonstrated the need to characterize the internal lack of uniformity in growth chambers to allow for adequate designs of experiments.

  3. Identification of zoonotic genotypes of Giardia duodenalis.

    Directory of Open Access Journals (Sweden)

    Hein Sprong

    Full Text Available Giardia duodenalis, originally regarded as a commensal organism, is the etiologic agent of giardiasis, a gastrointestinal disease of humans and animals. Giardiasis causes major public and veterinary health concerns worldwide. Transmission is either direct, through the faecal-oral route, or indirect, through ingestion of contaminated water or food. Genetic characterization of G. duodenalis isolates has revealed the existence of seven groups (assemblages A to G which differ in their host distribution. Assemblages A and B are found in humans and in many other mammals, but the role of animals in the epidemiology of human infection is still unclear, despite the fact that the zoonotic potential of Giardia was recognised by the WHO some 30 years ago. Here, we performed an extensive genetic characterization of 978 human and 1440 animal isolates, which together comprise 3886 sequences from 4 genetic loci. The data were assembled into a molecular epidemiological database developed by a European network of public and veterinary health Institutions. Genotyping was performed at different levels of resolution (single and multiple loci on the same dataset. The zoonotic potential of both assemblages A and B is evident when studied at the level of assemblages, sub-assemblages, and even at each single locus. However, when genotypes are defined using a multi-locus sequence typing scheme, only 2 multi-locus genotypes (MLG of assemblage A and none of assemblage B appear to have a zoonotic potential. Surprisingly, mixtures of genotypes in individual isolates were repeatedly observed. Possible explanations are the uptake of genetically different Giardia cysts by a host, or subsequent infection of an already infected host, likely without overt symptoms, with a different Giardia species, which may cause disease. Other explanations for mixed genotypes, particularly for assemblage B, are substantial allelic sequence heterogeneity and/or genetic recombination. Although the

  4. Genotypic diversity of root and shoot characteristics of

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    ali ganjali

    2009-06-01

    Full Text Available Root and shoot characteristics of chickpea (Cicer arietinum L. genotypes are believed to be important in drought tolerance. There is a little information about the response of genotypes root growth in hydroponics and greenhouse culture, also the relationships between root size and drought tolerance. This study was conducted to observe whether genotypes differ in root size, and to see that root size is associated with drought tolerance during early vegetative growth. We found significant differences (p0.01 in root dry weight, total root length, tap root length, root area, leaf dry weight, leaf area and shoot biomass per plant among 30 genotypes of chickpea grown in hydroponics culture for three weeks. Each of these parameters correlated with all others, positively. Among 30 genotypes, 10 genotypes with different root sizes were selected and were grown in a greenhouse in sand culture experiment under drought stress (FC %30 for three weeks. There were not linear or non-linear significant correlations between root characters in hydroponics and greenhouse environments. It seems that environmental factors are dominant on genetic factors in seedling stage and so, the expression of genotypics potential for root growth characteristics of genotypes are different in hydroponic and greenhouse conditions. In this study, the selection of genotypes with vigorous roots system in hydroponic condition did not lead to genotypes with the same root characters in greenhouse environment. The genotype×drought interactions for root characters of chickpea seedlings in 30 days were not significant (p

  5. Performance of chickpea genotypes under Swat valley conditions

    International Nuclear Information System (INIS)

    Khan, A.; Rahim, M.; Ahmad, F.; Ali, A.

    2004-01-01

    Twenty-two genetically diverse chickpeas genotypes were studied for their physiological efficiency to select the most desirable genotype/genotypes for breeding program on chickpea. Genotype 'CM7-1' was found physiologically efficient stain with maximum harvest index (37.33%) followed by genotype 'CM1571-1-A' with harvest index of 35.73%. Genotype '90206' produced maximum biological yield (7463 kg ha/sup -1/) followed by genotypes 'CM31-1' and 'E-2034' with biological yield of 7352 and 7167 kg ha/sup -1/, respectively. Harvest index and economic yield showed significant positive correlation value of (r=+0.595), while negative correlation value of (r = -0.435) was observed between harvest index and biological yield. (author)

  6. Effect of Mahanarva fimbriolata (Hemiptera: Cercopidae) Attack on Photosynthetic Parameters of Sugarcane Genotypes of Contrasting Susceptibility.

    Science.gov (United States)

    Soares, Bruno Oliveira; Chaves, Vinicius de Vicente; Tomaz, Adriano Cirino; Kuki, Kacilda Naomi; Peternelli, Luiz Alexandre; Barbosa, Márcio Henrique Pereira

    2017-12-05

    The aim of this study was to compare the effect of spittlebug Mahanarva fimbriolata Stål (Hemiptera: Cercopidae) on photosynthetic parameters of both a susceptible (SP81-3250) and a resistant (H.Kawandang) sugarcane genotype. In the first assay, the susceptibility level of genotypes to spittlebug was confirmed by comparing damage score and chlorophyll content of the plants. In the second assay, the effect of spittlebug nymphs on photosynthetic characteristics was assessed using the following parameters: Net photosynthetic rate (A), carboxylation efficiency (A/Ci), stomata conductance (gS), transpiration (E), electron transport rate (ETR), maximum quantum yield of Photosystem 2 (PSII) (FV/FM), effective quantum yield (Y(II)), photochemical quenching (Y(NPQ)), and nonphotochemical quenching (Y(NO)). Spittlebug nymphs affected the photosynthetic process of the susceptible genotype SP81-3250 by decreasing the Chl content, ETR, FV/FM, and Y(II). However, this genotype was able to maintain A probably due to its ability to maintain stomata aperture, increase the carboxylation efficiency of Rubisco, and dissipate excess energy through the xanthophyll cycle, as Y(NPQ) increased under the spittlebug attack. On the other hand, the spittlebug did not affect Chl content and FV/FM of the H.Kawandang genotype. Furthermore, H.Kawandang increased A to compensate for the sink demand by the spittlebug by increasing stomatal aperture and carboxylation efficiency and increasing efficiency of the photochemical apparatus in converting light energy into chemical products. We can conclude that the feeding habits of spittlebug nymphs have different impacts on photosynthesis of susceptible and resistant sugarcane genotypes. © The Author(s) 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  7. Physiological, Biochemical, Epigenetic and Molecular Analyses of Wheat (Triticum aestivum Genotypes with Contrasting Salt Tolerance

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    Suresh Kumar

    2017-06-01

    Full Text Available Abiotic stress exerts significant impact on plant’s growth, development, and productivity. Productivity of crop plants under salt stress is lagging behind because of our limited knowledge about physiological, biochemical, epigenetic, and molecular mechanisms of salt tolerance in plants. This study aimed to investigate physio-biochemical, molecular indices and defense responses of selected wheat cultivars to identify the most contrasting salt-responsive genotypes and the mechanisms associated with their differential responses. Physio-biochemical traits specifically membrane stability index, antioxidant potential, osmoprotectants and chlorophyll contents, measured at vegetative stage, were used for multivariate analysis to identify the most contrasting genotypes. Genetic and epigenetic analyses indicated the possible mechanisms associated with differential response of the wheat genotypes under salt stress. Better antioxidant potential, membrane stability, increased accumulation of osmolytes/phytophenolics, and higher K+/Na+ ratio under 200 mM NaCl stress identified Kharchia-65 to be the most salt-tolerant cultivar. By contrast, increased MDA level, reduced soluble sugar, proline, total chlorophyll, total phenolics contents, and lower antioxidant potential in HD-2329 marked it to be sensitive to the stress. Genetic and bioinformatics analyses of HKT1;4 of contrasting genotypes (Kharchia-65 and HD-2329 revealed deletions, transitions, and transversions resulting into altered structure, loss of conserved motifs (Ser-Gly-Gly-Gly and Gly-Arg and function in salt-sensitive (HD-2329 genotype. Expression analysis of HKTs rationalized the observed responses. Epigenetic variations in cytosine methylation explained tissue- and genotype-specific differential expression of HKT2;1 and HKT2;3.

  8. Widespread recombination, reassortment, and transmission of unbalanced compound viral genotypes in natural arenavirus infections.

    Directory of Open Access Journals (Sweden)

    Mark D Stenglein

    2015-05-01

    Full Text Available Arenaviruses are one of the largest families of human hemorrhagic fever viruses and are known to infect both mammals and snakes. Arenaviruses package a large (L and small (S genome segment in their virions. For segmented RNA viruses like these, novel genotypes can be generated through mutation, recombination, and reassortment. Although it is believed that an ancient recombination event led to the emergence of a new lineage of mammalian arenaviruses, neither recombination nor reassortment has been definitively documented in natural arenavirus infections. Here, we used metagenomic sequencing to survey the viral diversity present in captive arenavirus-infected snakes. From 48 infected animals, we determined the complete or near complete sequence of 210 genome segments that grouped into 23 L and 11 S genotypes. The majority of snakes were multiply infected, with up to 4 distinct S and 11 distinct L segment genotypes in individual animals. This S/L imbalance was typical: in all cases intrahost L segment genotypes outnumbered S genotypes, and a particular S segment genotype dominated in individual animals and at a population level. We corroborated sequencing results by qRT-PCR and virus isolation, and isolates replicated as ensembles in culture. Numerous instances of recombination and reassortment were detected, including recombinant segments with unusual organizations featuring 2 intergenic regions and superfluous content, which were capable of stable replication and transmission despite their atypical structures. Overall, this represents intrahost diversity of an extent and form that goes well beyond what has been observed for arenaviruses or for viruses in general. This diversity can be plausibly attributed to the captive intermingling of sub-clinically infected wild-caught snakes. Thus, beyond providing a unique opportunity to study arenavirus evolution and adaptation, these findings allow the investigation of unintended anthropogenic impacts on

  9. Genotypic variation in transpiration efficiency due to differences in photosynthetic capacity among sugarcane-related clones.

    Science.gov (United States)

    Li, Chunjia; Jackson, Phillip; Lu, Xin; Xu, Chaohua; Cai, Qing; Basnayake, Jayapathi; Lakshmanan, Prakash; Ghannoum, Oula; Fan, Yuanhong

    2017-04-01

    Sugarcane, derived from the hybridization of Saccharum officinarum×Saccharum spontaneum, is a vegetative crop in which the final yield is highly driven by culm biomass production. Cane yield under irrigated or rain-fed conditions could be improved by developing genotypes with leaves that have high intrinsic transpiration efficiency, TEi (CO2 assimilation/stomatal conductance), provided this is not offset by negative impacts from reduced conductance and growth rates. This study was conducted to partition genotypic variation in TEi among a sample of diverse clones from the Chinese collection of sugarcane-related germplasm into that due to variation in stomatal conductance versus that due to variation in photosynthetic capacity. A secondary goal was to define protocols for optimized larger-scale screening of germplasm collections. Genotypic variation in TEi was attributed to significant variation in both stomatal and photosynthetic components. A number of genotypes were found to possess high TEi as a result of high photosynthetic capacity. This trait combination is expected to be of significant breeding value. It was determined that a small number of observations (16) is sufficient for efficiently screening TEi in larger populations of sugarcane genotypes The research methodology and results reported are encouraging in supporting a larger-scale screening and introgression of high transpiration efficiency in sugarcane breeding. However, further research is required to quantify narrow sense heritability as well as the leaf-to-field translational potential of genotypic variation in transpiration efficiency-related traits observed in this study. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology.

  10. Laboratory Information Management Software for genotyping workflows: applications in high throughput crop genotyping

    Directory of Open Access Journals (Sweden)

    Prasanth VP

    2006-08-01

    Full Text Available Abstract Background With the advances in DNA sequencer-based technologies, it has become possible to automate several steps of the genotyping process leading to increased throughput. To efficiently handle the large amounts of genotypic data generated and help with quality control, there is a strong need for a software system that can help with the tracking of samples and capture and management of data at different steps of the process. Such systems, while serving to manage the workflow precisely, also encourage good laboratory practice by standardizing protocols, recording and annotating data from every step of the workflow. Results A laboratory information management system (LIMS has been designed and implemented at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT that meets the requirements of a moderately high throughput molecular genotyping facility. The application is designed as modules and is simple to learn and use. The application leads the user through each step of the process from starting an experiment to the storing of output data from the genotype detection step with auto-binning of alleles; thus ensuring that every DNA sample is handled in an identical manner and all the necessary data are captured. The application keeps track of DNA samples and generated data. Data entry into the system is through the use of forms for file uploads. The LIMS provides functions to trace back to the electrophoresis gel files or sample source for any genotypic data and for repeating experiments. The LIMS is being presently used for the capture of high throughput SSR (simple-sequence repeat genotyping data from the legume (chickpea, groundnut and pigeonpea and cereal (sorghum and millets crops of importance in the semi-arid tropics. Conclusion A laboratory information management system is available that has been found useful in the management of microsatellite genotype data in a moderately high throughput genotyping

  11. Giardia assemblage A: human genotype in muskoxen in the Canadian Arctic

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    Nagy John

    2008-09-01

    Full Text Available Abstract As part of an ongoing program assessing the biodiversity and impacts of parasites in Arctic ungulates we examined 72 fecal samples from muskoxen on Banks Island, Northwest Territories, Canada for Giardia and Cryptosporidium. Cryptosporidium spp. were not detected, but 21% of the samples were positive for Giardia. Sequencing of four isolates of Giardia demonstrated G. duodenalis, Assemblage A, a zoonotic genotype.

  12. The course of infection caused by Encephalitozoon cuniculi genotype III in immunocompetent and immunodeficient mice

    Czech Academy of Sciences Publication Activity Database

    Kotková, Michaela; Sak, Bohumil; Hlásková, Lenka; Kváč, Martin

    2017-01-01

    Roč. 182, November (2017), s. 16-21 ISSN 0014-4894 R&D Projects: GA ČR GA17-12871S; GA ČR GA14-20684S Institutional support: RVO:60077344 Keywords : albendazole * BALB/C * Encephalitozoon cuniculi genotypes II and III * microsporidiosis * SCID Subject RIV: FN - Epidemiology, Contagious Diseases ; Clinical Immunology OBOR OECD: Infectious Diseases Impact factor: 1.724, year: 2016

  13. Genotyping of Coxiella burnetii from domestic ruminants in northern Spain

    Directory of Open Access Journals (Sweden)

    Astobiza Ianire

    2012-12-01

    Full Text Available Abstract Background Information on the genotypic diversity of Coxiella burnetii isolates from infected domestic ruminants in Spain is limited. The aim of this study was to identify the C. burnetii genotypes infecting livestock in Northern Spain and compare them to other European genotypes. A commercial real-time PCR targeting the IS1111a insertion element was used to detect the presence of C. burnetii DNA in domestic ruminants from Spain. Genotypes were determined by a 6-loci Multiple Locus Variable number tandem repeat analysis (MLVA panel and Multispacer Sequence Typing (MST. Results A total of 45 samples from 4 goat herds (placentas, N = 4, 12 dairy cattle herds (vaginal mucus, individual milk, bulk tank milk, aerosols, N = 20 and 5 sheep flocks (placenta, vaginal swabs, faeces, air samples, dust, N = 21 were included in the study. Samples from goats and sheep were obtained from herds which had suffered abortions suspected to be caused by C. burnetii, whereas cattle samples were obtained from animals with reproductive problems compatible with C. burnetii infection, or consisted of bulk tank milk (BTM samples from a Q fever surveillance programme. C. burnetii genotypes identified in ruminants from Spain were compared to those detected in other countries. Three MLVA genotypes were found in 4 goat farms, 7 MLVA genotypes were identified in 12 cattle herds and 4 MLVA genotypes were identified in 5 sheep flocks. Clustering of the MLVA genotypes using the minimum spanning tree method showed a high degree of genetic similarity between most MLVA genotypes. Overall 11 different MLVA genotypes were obtained corresponding to 4 different MST genotypes: MST genotype 13, identified in goat, sheep and cattle from Spain; MST genotype 18, only identified in goats; and, MST genotypes 8 and 20, identified in small ruminants and cattle, respectively. All these genotypes had been previously identified in animal and human clinical samples from several

  14. Audioprofiles and antioxidant enzyme genotypes in presbycusis.

    Science.gov (United States)

    Angeli, Simon I; Bared, Anthony; Ouyang, Xiaomei; Du, Li Lin; Yan, Denise; Zhong Liu, Xue

    2012-11-01

    Audiometric patterns have been shown to indirectly provide information regarding the pathophysiology of presbycusis and be useful in the phenotyping of hereditary deafness. Hospital-based cohort study of adults with presbycusis, comparing the association of audiometric patterns and polymorphisms of antioxidant enzymes that have been linked to presbycusis: GSTT1, GSTM1 and NAT2. All subjects underwent a clinical evaluation and completed questionnaires regarding ototoxicity and noise exposure. Pure-tone threshold audiometry was obtained and subjects' audiograms were classified into specific patterns. DNA was extracted from blood and the polymorphisms of GSTT1, GSTM1, and the NAT2 variants (NAT2* 5A; NAT2* 6A,B) were analyzed by PCR. The audiometric patterns that were more prevalent in our cohort were "High-Frequency Steeply Sloping" or HFSS (33%), "High-Frequency Gently Sloping" or HFGS (31%), and "Flat" (27%), with other patterns being rare. We did not find a statistical significant effect of gender, age, hearing level, and ear side on the audiometric pattern. Subjects with mutant alleles for GSTT1 were more likely to have a HFSS audiogram than subjects with the wild type genotype. In this cohort, there was a similar prevalence for the three audiometric configurations HFSS, HFGS, and Flat, with other configurations being rare. Subjects with mutant alleles for GSTT1 were more likely to have a HFSS audiogram than subjects with the wild type genotype, suggesting that the basal turn of the cochlea is susceptible to GSTT1 regulated oxidative stress. However, further studies of audioprofiles with larger sample sizes may be needed to establish phenotype-genotype correlations in presbycusis. Copyright © 2012 The American Laryngological, Rhinological, and Otological Society, Inc.

  15. Plant genotypic diversity reduces the rate of consumer resource utilization.

    Science.gov (United States)

    McArt, Scott H; Thaler, Jennifer S

    2013-07-07

    While plant species diversity can reduce herbivore densities and herbivory, little is known regarding how plant genotypic diversity alters resource utilization by herbivores. Here, we show that an invasive folivore--the Japanese beetle (Popillia japonica)--increases 28 per cent in abundance, but consumes 24 per cent less foliage in genotypic polycultures compared with monocultures of the common evening primrose (Oenothera biennis). We found strong complementarity for reduced herbivore damage among plant genotypes growing in polycultures and a weak dominance effect of particularly resistant genotypes. Sequential feeding by P. japonica on different genotypes from polycultures resulted in reduced consumption compared with feeding on different plants of the same genotype from monocultures. Thus, diet mixing among plant genotypes reduced herbivore consumption efficiency. Despite positive complementarity driving an increase in fruit production in polycultures, we observed a trade-off between complementarity for increased plant productivity and resistance to herbivory, suggesting costs in the complementary use of resources by plant genotypes may manifest across trophic levels. These results elucidate mechanisms for how plant genotypic diversity simultaneously alters resource utilization by both producers and consumers, and show that population genotypic diversity can increase the resistance of a native plant to an invasive herbivore.

  16. Relationship of some upland rice genotype after gamma irradiation

    Science.gov (United States)

    Suliartini, N. W. S.; Wijayanto, T.; Madiki, A.; Boer, D.; Muhidin; Juniawan

    2018-02-01

    The objective of the research was to group local upland rice genotypes after being treated with gamma irradiation. The research materials were upland rice genotypes resulted from mutation of the second generation and two parents: Pae Loilo (K3D0) and Pae Pongasi (K2D0) Cultivars. The research was conducted at the Indonesian Sweetener and Fiber Crops Research Institute, Malang Regency, and used the augmented design method. Research data were analyzed with R Program. Eight hundred and seventy one genotypes were selected with the selection criteria were based on yields on the average parents added 1.5 standard deviation. Based on the selection, eighty genotypes were analyzed with cluster analyses. Nine observation variables were used to develop cluster dendrogram using average linked method. Genetic distance was measured by euclidean distance. The results of cluster dendrogram showed that tested genotypes were divided into eight groups. Group 1, 2, 7, and 8 each had one genotype, group 3 and 6 each had two genotypes, group 4 had 25 genotypes, and group 5 had 51 genotypes. Check genotypes formed a separate group. Group 6 had the highest yield per plant of 126.11 gram, followed by groups 5 and 4 of 97.63 and 94.08 gram, respectively.

  17. Warfarin dose and INR related to genotypes of CYP2C9 and VKORC1 in patients with myocardial infarction

    Directory of Open Access Journals (Sweden)

    Seljeflot Ingebjørg

    2008-06-01

    Full Text Available Abstract Background Warfarin treatment has a narrow therapeutic range, requiring meticulous monitoring and dosage titration. Individual dosage requirement has recently partly been explained by genetic variation of the warfarin metabolizing enzyme CYP2C9 and the Vitamin K-activating enzyme VKORC1. In the WARIS-II study, comparing three different antithrombotic regimens after myocardial infarction, warfarin treatment reduced thrombotic events, but was associated with more frequent bleeding than use of acetylsalisylic acid (ASA alone. Aims The primary aim of the present study was to investigate the relation between genotypes of CYP2C9 and VKORC1 and warfarin maintenance dose in myocardial infarction. The secondary aim was to relate the genotypes to international normalized ratio (INR. Methods Genotyping was performed in 212 myocardial infarction patients from the WARIS-II study by robotic isolation of DNA from EDTA whole blood (MagNa Pure LC before PCR amplification (LightCycler and melting point analysis. Results The 420 C>T substitution of CYP2C9*2, the 1075 A>C substitution of CYP2C9*3 and the 1173 C>T substitution of VKORC1 had minor allele frequencies of, 11.3%, 5.7% and 36.6% respectively. Warfarin weekly dose varied between 17 mg and 74 mg among the patients. INR did not vary between genotypes. Warfarin dosage requirement was significantly associated with CYP2C9 and VKORC1 genotypes, treatment group and age. The VKORC1 genotype contributed 24.5% to the interindividual variation in warfarin dosage, whereas the combined CYP2C9 genotypes were only responsible for 7.2% of the dose variation. Conclusion CYP2C9 and VKORC1 genotype frequencies in myocardial infarction patients appear similar to other patient groups and have similar impact on warfarin maintenance dose.

  18. Emergence of new genotype and diversity of Theileria orientalis parasites from bovines in India.

    Science.gov (United States)

    George, Neena; Bhandari, Vasundhra; Reddy, D Peddi; Sharma, Paresh

    2015-12-01

    Bovine theileriosis is a serious threat to livestock worldwide. Uncertainty around species prevalence, antigenic diversity and genotypes of strains make it difficult to assess the impact of this parasite and to provide necessary treatment. We aimed to characterize genotypic diversity, phylogeny and prevalence of Theileria orientalis parasites from the states of Telangana and Andhra Pradesh, India by collecting bovine blood samples from the major districts of the two states. Bioinformatic analysis identified antigenic diversity among the prevalent parasite strains using major piroplasm surface protein (MPSP) gene. Our study revealed a prevalence rate of 4.8% (n=41/862) of T. orientalis parasites in bovine animals and a new genotype of T. orientalis parasite which was not previously reported in India. The emergence of these new genotypes could be an explanation for the frequent outbreaks of bovine theileriosis. Further, whole genome sequencing of T. orientalis strains will help to elucidate the genetic factors relevant for transmissibility and virulence as well as vaccine and new drug development. Copyright © 2015 Elsevier B.V. All rights reserved.

  19. Enzymatic Saccharification of Shrub Willow Genotypes with Differing Biomass Composition for Biofuel Production

    Directory of Open Access Journals (Sweden)

    Michelle J. Serapiglia

    2013-03-01

    Full Text Available In the conversion of woody biomass feedstocks into liquid fuel ethanol, the pretreatment process is the most critical and costly step. Variations in biomass composition based on genetic differences or environmental effects have a significant impact on the degree of accessibility accomplished by pretreatment and subsequent sugar release by enzymatic hydrolysis. To evaluate this, biomass from 10 genetically diverse, genotypes of shrub willow (Salix spp. was pretreated with a hot-water process at two levels of severity, hydrolyzed using a combination of two commercial enzyme cocktails, and the release of hexose and pentose monomers was quantified by HPLC. Among the genotypes selected for analysis, cellulose content ranged from 39 to 45% (w/w and lignin content ranged from 20 to 23% (w/w at harvest. Differences in the effectiveness of the pretreatment process were observed among the various willow genotypes. Correlations were identified between total sugar release and % cellulose and % lignin content. There was a significant effect of pretreatment severity on polysaccharide accessibility, but the response to pretreatments was different among the genotypes. At the high severity pretreatment ‘SV1’ was the least recalcitrant with sugar release representing as much as 60% of total biomass. These results suggest that structural, as well as chemical characteristics of the biomass may influence pretreatment and hydrolytic efficiency.

  20. Dopamine and cognitive control: sex-by-genotype interactions influence the capacity to switch attention.

    Science.gov (United States)

    Gurvich, C; Rossell, S L

    2015-03-15

    Cognitive performance in healthy persons varies widely between individuals. Sex differences in cognition are well reported, and there is an emerging body of evidence suggesting that the relationship between dopaminergic neurotransmission, implicated in many cognitive functions, is modulated by sex. Here, we examine the influence of sex and genetic variations along the dopaminergic pathway on aspects of cognitive control. A total of 415 healthy individuals, selected from an international consortium linked to Brain Research and Integrative Neuroscience Network (BRAINnet), were genotyped for two common and functional genetic variations of dopamine regulating genes: the catechol-O-methyltransferase [COMT] gene (rs4680) and the dopamine receptor D2 [DRD2] gene (rs6277). Cognitive measures were selected to explore sustained attention (using a continuous performance task), switching of attention (using a Trails B adaptation) and working memory (a visual computerised adaptation of digit span). While there were no main effects for genotype across any tasks, analyses revealed significant sex by genotype interactions for the capacity to switch attention. In relation to COMT, superior performance was noted in females with the Val/Val genotype and for DRD2, superior performance was seen for TT females and CC males. These findings highlight the importance of considering genetic variation in baseline dopamine levels in addition to sex, when considering the impact of dopamine on cognition in healthy populations. These findings also have important implications for the many neuropsychiatric disorders that implicate dopamine, cognitive changes and sex differences. Copyright © 2014 Elsevier B.V. All rights reserved.

  1. Phenotypic diversity of basic characteristics of genotypes from the Serbia onion collection

    Directory of Open Access Journals (Sweden)

    Gvozdanović-Varga Jelica

    2013-01-01

    Full Text Available The onion is a widely distributed vegetable crop, which takes an important place in the vegetable production in Serbia. The traditional planting method is the one from sets. Old cultivars and populations and, in recent years, foreign cultivars are grown. The large variety of genotypes, including both domestic populations and cultivars, comprises the significant gene pool of this region. The onion collection of the Institute of Field and Vegetable Crops in Novi Sad is based on the populations and cultivars from the territory of the former Yugoslavia. This paper reviews 30 onion genotypes on the basic IPGRI descriptors (ANNEX I. Variability of the reviewed characteristics was determined by PC analysis. High variability values have been established for bulb skin color, bulb flesh color, bulb hearting and bulb skin thickness. The genotypes varied in bulb skin color as well as in bulb flesh color from white to dark violet. These two characteristics had the largest impact on clustering, with a single genotype being heterogeneous exactly for these two characteristics. [Projekat Ministarstva nauke Republike Srbije, br. TR 31030

  2. Linking genotypes database with locus-specific database and genotype-phenotype correlation in phenylketonuria.

    Science.gov (United States)

    Wettstein, Sarah; Underhaug, Jarl; Perez, Belen; Marsden, Brian D; Yue, Wyatt W; Martinez, Aurora; Blau, Nenad

    2015-03-01

    The wide range of metabolic phenotypes in phenylketonuria is due to a large number of variants causing variable impairment in phenylalanine hydroxylase function. A total of 834 phenylalanine hydroxylase gene variants from the locus-specific database PAHvdb and genotypes of 4181 phenylketonuria patients from the BIOPKU database were characterized using FoldX, SIFT Blink, Polyphen-2 and SNPs3D algorithms. Obtained data was correlated with residual enzyme activity, patients' phenotype and tetrahydrobiopterin responsiveness. A descriptive analysis of both databases was compiled and an interactive viewer in PAHvdb database was implemented for structure visualization of missense variants. We found a quantitative relationship between phenylalanine hydroxylase protein stability and enzyme activity (r(s) = 0.479), between protein stability and allelic phenotype (r(s) = -0.458), as well as between enzyme activity and allelic phenotype (r(s) = 0.799). Enzyme stability algorithms (FoldX and SNPs3D), allelic phenotype and enzyme activity were most powerful to predict patients' phenotype and tetrahydrobiopterin response. Phenotype prediction was most accurate in deleterious genotypes (≈ 100%), followed by homozygous (92.9%), hemizygous (94.8%), and compound heterozygous genotypes (77.9%), while tetrahydrobiopterin response was correctly predicted in 71.0% of all cases. To our knowledge this is the largest study using algorithms for the prediction of patients' phenotype and tetrahydrobiopterin responsiveness in phenylketonuria patients, using data from the locus-specific and genotypes database.

  3. Influence of silicon treatment on antimony uptake and translocation in rice genotypes with different radial oxygen loss.

    Science.gov (United States)

    Zhang, Liping; Yang, Qianqian; Wang, Shiliang; Li, Wanting; Jiang, Shaoqing; Liu, Yan

    2017-10-01

    Antimony (Sb) pollution in soil may have a negative impact on the health of people consuming rice. This study investigated the effect of silicon (Si) application on rice biomass, iron plaque formation, and Sb uptake and speciation in rice plants with different radial oxygen loss (ROL) using pot experiments. The results demonstrated that Si addition increased the biomass of straw and grain, but had no obvious impact on the root biomass. Indica genotypes with higher ROL underwent greater iron plaque formation and exhibited more Sb sequestration in iron plaque. Silicon treatments increased iron levels in iron plaque from the different genotypes but decreased the total Sb concentration in root, straw, husk, and grain. In addition, Si treatment reduced the inorganic Sb concentrations but slightly increased the trimethylantimony (TMSb) concentrations in rice straw. Moreover, rice straw from hybrid genotypes accumulated higher concentrations of TMSb and inorganic Sb than that from indica genotypes. The conclusions from this study indicate that Sb contamination in rice can be efficiently reduced by applying Si treatment and selecting genotypes with high ROL. Copyright © 2017 Elsevier Inc. All rights reserved.

  4. Antioxidant capacity of anthocyanins from acerola genotypes

    Directory of Open Access Journals (Sweden)

    Vera Lúcia Arroxelas Galvão De Lima

    2011-03-01

    Full Text Available Anthocyanins from 12 acerola genotypes cultivated at the Active Germplasm Bank at Federal Rural University of Pernambuco were isolated for antioxidant potential evaluation. The antioxidant activity and radical scavenging capacity of the anthocyanin isolates were measured according to the β-carotene bleaching method and 1,1-diphenyl-2-picrylhydrazyl (DPPH free radical scavenging assay, respectively. The antioxidant activity varied from 25.58 to 47.04% at 0.2 mg.mL-1, and it was measured using the β-carotene bleaching method. The free radical scavenging capacity increased according to the increase in concentration and reaction time by the DPPH assay. At 16.7 μg.mL-1 concentration and after 5 minutes and 2 hours reaction time, the percentage of scavenged radicals varied from 36.97 to 63.92% and 73.27 to 94.54%, respectively. Therefore, the antioxidant capacity of acerola anthocyanins varied amongst acerola genotypes and methods used. The anthocyanins present in this fruit may supply substantial dietary source of antioxidant which may promote health and produce disease prevention effects.

  5. [Mexican phenotype and genotype Vibrio cholerae 01].

    Science.gov (United States)

    Giono, S; Gutiérrez Cogno, L; Rodríguez Angeles, G; del Rio Zolezzi, A; Valdespino González, J L; Sepúlveda Amor, J

    1995-01-01

    This paper presents the phenotypical and genotypical characterization of 26922 Vibrio cholerae 01 strains isolated in Mexico from 1991 to 1993. All strains isolated were El Tor biovar. Strains were sensitive to antibiotics excluding furazolidone, streptomycin and sulfisoxasole to which we found resistance in 97% and we are using this characteristic as epidemiological markers. We detected a marked change in frequency of Inaba serotype from 1991, when it was dominant, with 99.5%, until 1992 when Ogawa serotype turned to be dominant with 95% of isolates. All Vibrio cholerae 01 strains, except one Ogawa strain, were to igenic, and V. choleraeno 01 were not toxigenic by ELISA, PCR and cell culture tests. Dominant ribotype was 5, but we found some strains with 6a pattern and two with ribotype 12. We are searching for ribotype 2 among hemolytic strains in order to learn if there is any relation to Gulf Coast strains prevalent in the USA, but until now we have not found any V. cholerae ribotype 2 in our isolates. Even if rapid tests are recommended for immediate diagnosis of cholera, it is necessary to continue bacterial isolation in order to have strains for phenotyping and genotyping studies that may support epidemiological analysis.

  6. Haplotype-Based Genotyping in Polyploids

    Directory of Open Access Journals (Sweden)

    Josh P. Clevenger

    2018-04-01

    Full Text Available Accurate identification of polymorphisms from sequence data is crucial to unlocking the potential of high throughput sequencing for genomics. Single nucleotide polymorphisms (SNPs are difficult to accurately identify in polyploid crops due to the duplicative nature of polyploid genomes leading to low confidence in the true alignment of short reads. Implementing a haplotype-based method in contrasting subgenome-specific sequences leads to higher accuracy of SNP identification in polyploids. To test this method, a large-scale 48K SNP array (Axiom Arachis2 was developed for Arachis hypogaea (peanut, an allotetraploid, in which 1,674 haplotype-based SNPs were included. Results of the array show that 74% of the haplotype-based SNP markers could be validated, which is considerably higher than previous methods used for peanut. The haplotype method has been implemented in a standalone program, HAPLOSWEEP, which takes as input bam files and a vcf file and identifies haplotype-based markers. Haplotype discovery can be made within single reads or span paired reads, and can leverage long read technology by targeting any length of haplotype. Haplotype-based genotyping is applicable in all allopolyploid genomes and provides confidence in marker identification and in silico-based genotyping for polyploid genomics.

  7. Hearing impairment in genotyped Wolfram syndrome patients.

    Science.gov (United States)

    Plantinga, Rutger F; Pennings, Ronald J E; Huygen, Patrick L M; Bruno, Rocco; Eller, Philipp; Barrett, Timothy G; Vialettes, Bernard; Paquis-Fluklinger, Veronique; Lombardo, Fortunato; Cremers, Cor W R J

    2008-07-01

    Wolfram syndrome is a progressive neurodegenerative syndrome characterized by the features "DIDMOAD" (diabetes insipidus, diabetes mellitus, optic atrophy, and deafness). We sought to study the audiometric data of genotyped Wolfram syndrome patients with sensorineural hearing impairment. Pure tone threshold data of 23 Wolfram syndrome patients were used for cross-sectional analysis in subgroups (age less than 16 years or between 19 and 25 years, gender, and origin). All subgroups, with 1 exception, showed a fairly similar type of hearing impairment with, on average, thresholds of about 25 dB (range, 0 to 65 dB) at 0.25 to 1 kHz, gently sloping downward to about 60 dB (range, 25 to 95 dB) at 8 kHz. The subgroup of Dutch women, which was excluded from the calculations of the average hearing thresholds, showed a higher degree of hearing impairment. Only the latter subgroup showed progression; however, contrary to the previous longitudinal analysis, progression was not significant in the present cross-sectional analysis, presumably because of the high degree of cross-subject variability. This unique collection of audiometric data from genotyped Wolfram syndrome patients shows no substantial progression in sensorineural hearing impairment with advancing age, no relation to the types of WFS1 mutations identified, and, with exclusion of the subgroup of Dutch female patients, no significant sex-related differences.

  8. The first report on Cryptosporidium suis and Cryptosporidium pig genotype II in Eurasian wild boars (Sus scrofa) (Czech Republic)

    Czech Academy of Sciences Publication Activity Database

    Němejc, K.; Sak, Bohumil; Květoňová, Dana; Hanzal, V.; Jeníková, Martina; Kváč, Martin

    2012-01-01

    Roč. 184, 2/4 (2012), 122-125 ISSN 0304-4017 Grant - others:Mšk(CZ) 6007665806 Institutional research plan: CEZ:AV0Z60220518; CEZ:AV0Z50450515 Keywords : Cryptosporidium suis * Cryptosporidium pig genotype II * Eurasian wild boar * SSU * PCR Subject RIV: GJ - Animal Vermins ; Diseases, Veterinary Medicine Impact factor: 2.381, year: 2012

  9. Cryptosporidium galli and novel Cryptosporidium avian genotype VI in North American red-winged blackbirds (Agelaius phoeniceus)

    Czech Academy of Sciences Publication Activity Database

    Chelladurai, J.J.; Clark, M.E.; Kváč, Martin; Holubová, Nikola; Khan, E.; Stenger, B.L.S.; Giddings, C.W.; McEvoy, J.

    2016-01-01

    Roč. 115, č. 5 (2016), s. 1901-1906 ISSN 0932-0113 Institutional support: RVO:60077344 Keywords : Cryptosporidium * Red-winged blackbird * Passerines * Cryptosporidium galli * Avian genotypeVI * Proventriculus * Intestine Subject RIV: GJ - Animal Vermins ; Diseases, Veterinary Medicine Impact factor: 2.329, year: 2016

  10. Deep sequencing analysis of HBV genotype shift and correlation with antiviral efficiency during adefovir dipivoxil therapy.

    Directory of Open Access Journals (Sweden)

    Yuwei Wang

    Full Text Available Viral genotype shift in chronic hepatitis B (CHB patients during antiviral therapy has been reported, but the underlying mechanism remains elusive.38 CHB patients treated with ADV for one year were selected for studying genotype shift by both deep sequencing and Sanger sequencing method.Sanger sequencing method found that 7.9% patients showed mixed genotype before ADV therapy. In contrast, all 38 patients showed mixed genotype before ADV treatment by deep sequencing. 95.5% mixed genotype rate was also obtained from additional 200 treatment-naïve CHB patients. Of the 13 patients with genotype shift, the fraction of the minor genotype in 5 patients (38% increased gradually during the course of ADV treatment. Furthermore, responses to ADV and HBeAg seroconversion were associated with the high rate of genotype shift, suggesting drug and immune pressure may be key factors to induce genotype shift. Interestingly, patients with genotype C had a significantly higher rate of genotype shift than genotype B. In genotype shift group, ADV treatment induced a marked enhancement of genotype B ratio accompanied by a reduction of genotype C ratio, suggesting genotype C may be more sensitive to ADV than genotype B. Moreover, patients with dominant genotype C may have a better therapeutic effect. Finally, genotype shifts was correlated with clinical improvement in terms of ALT.Our findings provided a rational explanation for genotype shift among ADV-treated CHB patients. The genotype and genotype shift might be associated with antiviral efficiency.

  11. The genotype-phenotype map of an evolving digital organism

    OpenAIRE

    Fortuna, Miguel A.; Zaman, Luis; Ofria, Charles; Wagner, Andreas

    2017-01-01

    To understand how evolving systems bring forth novel and useful phenotypes, it is essential to understand the relationship between genotypic and phenotypic change. Artificial evolving systems can help us understand whether the genotype-phenotype maps of natural evolving systems are highly unusual, and it may help create evolvable artificial systems. Here we characterize the genotype-phenotype map of digital organisms in Avida, a platform for digital evolution. We consider digital organisms fr...

  12. Molecular genotyping of HCV infection in seropositive blood donor

    Science.gov (United States)

    Zarin, Siti Noraziah Abu; Ibrahim, Nazlina

    2013-11-01

    This study is to investigate the prevalence of hepatitis C virus infection in seropositive blood donor. RNA was extracted from 32 positive samples in National Blood Centre and Melaka Hospital. The core and NS5B sequences were obtained from 23 samples. Genotype 3a is most prevalent in this study followed by genotype 1a. Evidence of mixed-genotypes (3a and 1b) infections was found in 5 subjects.

  13. Genomic Variants Revealed by Invariably Missing Genotypes in Nelore Cattle.

    Directory of Open Access Journals (Sweden)

    Joaquim Manoel da Silva

    Full Text Available High density genotyping panels have been used in a wide range of applications. From population genetics to genome-wide association studies, this technology still offers the lowest cost and the most consistent solution for generating SNP data. However, in spite of the application, part of the generated data is always discarded from final datasets based on quality control criteria used to remove unreliable markers. Some discarded data consists of markers that failed to generate genotypes, labeled as missing genotypes. A subset of missing genotypes that occur in the whole population under study may be caused by technical issues but can also be explained by the presence of genomic variations that are in the vicinity of the assayed SNP and that prevent genotyping probes from annealing. The latter case may contain relevant information because these missing genotypes might be used to identify population-specific genomic variants. In order to assess which case is more prevalent, we used Illumina HD Bovine chip genotypes from 1,709 Nelore (Bos indicus samples. We found 3,200 missing genotypes among the whole population. NGS re-sequencing data from 8 sires were used to verify the presence of genomic variations within their flanking regions in 81.56% of these missing genotypes. Furthermore, we discovered 3,300 novel SNPs/Indels, 31% of which are located in genes that may affect traits of importance for the genetic improvement of cattle production.

  14. Phosphorus use efficiency in pima cotton (Gossypium barbadense L. genotypes

    Directory of Open Access Journals (Sweden)

    Elcio Santos

    2015-06-01

    Full Text Available In the Brazilian Cerrado, P deficiency restricts cotton production, which requires large amounts of phosphate fertilizer. To improve the yield of cotton crops, genotypes with high P use efficiency must be identified and used. The present study evaluated P uptake and use efficiency of different Gossypium barbadense L. genotypes grown in the Cerrado. The experiment was carried out in a greenhouse with a completely randomized design, 15 x 2 factorial treatment structure (15 genotypes x 2 P levels, and four replicates. The genotypes were MT 69, MT 70, MT 87, MT 91, MT 92, MT 94, MT 101, MT 102, MT 103, MT 105, MT 106, MT 110, MT 112, MT 124, and MT 125; P levels were sufficient (1000 mg pot-1, PS treatment or deficient (PD treatment. Dry matter (DM and P levels were determined in cotton plant parts and used to calculate plant P content and use efficiency. In general, DM and P content were higher in the PS than in the PD treatment, with the exception of root DM and total DM in some genotypes. Genotypes also differed in terms of P uptake and use capacity. In the PS treatment, genotypes MT 92 and MT 102 had the highest response to phosphate fertilization. Genotype MT 69 exhibited the most efficient P uptake in the PD treatment. Genotype MT 124 showed the best shoot physiological efficiency, apparent recovery efficiency, and utilization efficiency, whereas MT 110 exhibited the highest root physiological efficiency.

  15. Drastic Population Size Change in Two Populations of the Golden-Striped Salamander over a Forty-Year Period—Are Eucalypt Plantations to Blame?

    Directory of Open Access Journals (Sweden)

    Jan W. Arntzen

    2015-07-01

    Full Text Available Over the last half century the Iberian peninsula has seen the large scale planting of exotic gum trees (Eucalyptus sp. therewith reducing space for native wildlife. An additional effect of the gum tree plantations may be the lowering of the water table in adjacent streams, to which amphibian species with a larval niche in the running sections of small streams would be especially susceptible. In northwestern Iberia that niche is occupied by the Golden-striped salamander, Chioglossa lusitanica. I here report on the demographic trends of two C. lusitanica populations over a forty-year period, in two areas of one mountain range near Porto in northwestern Portugal. In both areas advantage was taken of the migration pattern of C. lusitanica to sites for aestivation and breeding in summer and fall. The area of the Silveirinhos brook was transformed in a plantation of gum trees shortly after the research started, while the area of Poço do Inferno remained virtually unaffected. At Silveirinhos the adult C. lusitanica population declined by one or two orders of magnitude, from ca. 1500 individuals to less than 50 at present. Demographic models that operate under a uniform larval mortality yielded population sizes that are compatible with field observations, including the late onset of the decline at 14 or more years after the planting of the gum trees and the near-extinction at year 32. An alternative reason for the relatively recent population collapse of C. lusitanica may have been disease, but no sick individuals or corpses have become available for clinical investigation. Conversely, the control population at Poço do Inferno increased in size by a factor of five or more. These data support the hypothesis that gum tree plantations have a strong negative effect on C. lusitanica. The population size increase at Poço do Inferno is probably attributable to the installation of wastewater treatment in the adjacent town of Valongo, with a discharge in the

  16. Influence of Genotype on Warfarin Maintenance Dose Predictions Produced Using a Bayesian Dose Individualization Tool.

    Science.gov (United States)

    Saffian, Shamin M; Duffull, Stephen B; Roberts, Rebecca L; Tait, Robert C; Black, Leanne; Lund, Kirstin A; Thomson, Alison H; Wright, Daniel F B

    2016-12-01

    A previously established Bayesian dosing tool for warfarin was found to produce biased maintenance dose predictions. In this study, we aimed (1) to determine whether the biased warfarin dose predictions previously observed could be replicated in a new cohort of patients from 2 different clinical settings, (2) to explore the influence of CYP2C9 and VKORC1 genotype on predictive performance of the Bayesian dosing tool, and (3) to determine whether the previous population used to develop the kinetic-pharmacodynamic model underpinning the Bayesian dosing tool was sufficiently different from the test (posterior) population to account for the biased dose predictions. The warfarin maintenance doses for 140 patients were predicted using the dosing tool and compared with the observed maintenance dose. The impact of genotype was assessed by predicting maintenance doses with prior parameter values known to be altered by genetic variability (eg, EC50 for VKORC1 genotype). The prior population was evaluated by fitting the published kinetic-pharmacodynamic model, which underpins the Bayesian tool, to the observed data using NONMEM and comparing the model parameter estimates with published values. The Bayesian tool produced positively biased dose predictions in the new cohort of patients (mean prediction error [95% confidence interval]; 0.32 mg/d [0.14-0.5]). The bias was only observed in patients requiring ≥7 mg/d. The direction and magnitude of the observed bias was not influenced by genotype. The prior model provided a good fit to our data, which suggests that the bias was not caused by different prior and posterior populations. Maintenance doses for patients requiring ≥7 mg/d were overpredicted. The bias was not due to the influence of genotype nor was it related to differences between the prior and posterior populations. There is a need for a more mechanistic model that captures warfarin dose-response relationship at higher warfarin doses.

  17. Plant genotype, microbial recruitment and nutritional security.

    Science.gov (United States)

    Patel, Jai S; Singh, Akanksha; Singh, Harikesh B; Sarma, Birinchi K

    2015-01-01

    Agricultural food products with high nutritional value should always be preferred over food products with low nutritional value. Efforts are being made to increase nutritional value of food by incorporating dietary supplements to the food products. The same is more desirous if the nutritional value of food is increased under natural environmental conditions especially in agricultural farms. Fragmented researches have demonstrated possibilities in achieving the same. The rhizosphere is vital in this regard for not only health and nutritional status of plants but also for the microorganisms colonizing the rhizosphere. Remarkably robust composition of plant microbiome with respect to other soil environments clearly suggests the role of a plant host in discriminating its colonizers (Zancarini et al., 2012). A large number of biotic and abiotic factors are believed to manipulate the microbial communities in the rhizosphere. However, plant genotype has proven to be the key in giving the final shape of the rhizosphere microbiome (Berendsen et al., 2012; Marques et al., 2014).

  18. Sources of Wilhelm Johannsen's genotype theory.

    Science.gov (United States)

    Roll-Hansen, Nils

    2009-01-01

    This paper describes the historical background and early formation of Wilhelm Johannsen's distinction between genotype and phenotype. It is argued that contrary to a widely accepted interpretation (For instance, W. Provine, 1971. The Origins of Theoretical Population Genetics. Chicago: The University of Chicago Press; Mayr, 1973; F. B. Churchill, 1974. Journal of the History of Biology 7: 5-30; E. Mayr, 1982. The Growth of Biological Thought, Cambridge: Harvard University Press; J. Sapp, 2003. Genesis. The Evolution of Biology. New York: Oxford University Press) his concepts referred primarily to properties of individual organisms and not to statistical averages. Johannsen's concept of genotype was derived from the idea of species in the tradition of biological systematics from Linnaeus to de Vries: An individual belonged to a group - species, subspecies, elementary species - by representing a certain underlying type (S. Müller-Wille and V. Orel, 2007. Annals of Science 64: 171-215). Johannsen sharpened this idea theoretically in the light of recent biological discoveries, not least those of cytology. He tested and confirmed it experimentally combining the methods of biometry, as developed by Francis Galton, with the individual selection method and pedigree analysis, as developed for instance by Louis Vilmorin. The term "genotype" was introduced in W. Johannsen's 1909 (Elemente der Exakten Erblichkeitslehre. Jena: Gustav Fischer) treatise, but the idea of a stable underlying biological "type" distinct from observable properties was the core idea of his classical bean selection experiment published 6 years earlier (W. Johannsen, 1903. Ueber Erblichkeit in Populationen und reinen Linien. Eine Beitrag zur Beleuchtung schwebender Selektionsfragen, Jena: Gustav Fischer, pp. 58-59). The individual ontological foundation of population analysis was a self-evident presupposition in Johannsen's studies of heredity in populations from their start in the early 1890s till his

  19. Identification of Zoonotic Genotypes of Giardia duodenalis

    DEFF Research Database (Denmark)

    Sprong, H.; Cacciò, S.M.; van der Giessen, J.W.B

    2009-01-01

    Giardia duodenalis, originally regarded as a commensal organism, is the etiologic agent of giardiasis, a gastrointestinal disease of humans and animals. Giardiasis causes major public and veterinary health concerns worldwide. Transmission is either direct, through the faecal-oral route, or indirect......, through ingestion of contaminated water or food. Genetic characterization of G. duodenalis isolates has revealed the existence of seven groups (assemblages A to G) which differ in their host distribution. Assemblages A and B are found in humans and in many other mammals, but the role of animals......, mixtures of genotypes in individual isolates were repeatedly observed. Possible explanations are the uptake of genetically different Giardia cysts by a host, or subsequent infection of an already infected host, likely without overt symptoms, with a different Giardia species, which may cause disease. Other...

  20. PNPLA 3 I148M genetic variant associates with insulin resistance and baseline viral load in HCV genotype 2 but not in genotype 3 infection

    DEFF Research Database (Denmark)

    Rembeck, Karolina; Maglio, Cristina; Lagging, Martin

    2012-01-01

    ABSTRACT: BACKGROUND: Hepatic steatosis in HCV patients has been postulated as a risk factor associated with a higher frequency of fibrosis and cirrhosis. A single genetic variant, PNPLA3 I148M, has been widely associated with increased hepatic steatosis. Previous studies of the PNPLA3 I148M...... sequence variant in HCV infected individuals have reported an association between this variant and prevalence of steatosis, fibrosis, and cirrhosis. To evaluate the impact of PNPLA3 I148M variant on metabolic traits and treatment response in HCV genotype 2 and 3 infected patients. METHODS: Three hundred...

  1. Automated genotyping of dinucleotide repeat markers

    Energy Technology Data Exchange (ETDEWEB)

    Perlin, M.W.; Hoffman, E.P. [Carnegie Mellon Univ., Pittsburgh, PA (United States)]|[Univ. of Pittsburgh, PA (United States)

    1994-09-01

    The dinucleotide repeats (i.e., microsatellites) such as CA-repeats are a highly polymorphic, highly abundant class of PCR-amplifiable markers that have greatly streamlined genetic mapping experimentation. It is expected that over 30,000 such markers (including tri- and tetranucleotide repeats) will be characterized for routine use in the next few years. Since only size determination, and not sequencing, is required to determine alleles, in principle, dinucleotide repeat genotyping is easily performed on electrophoretic gels, and can be automated using DNA sequencers. Unfortunately, PCR stuttering with these markers generates not one band for each allele, but a pattern of bands. Since closely spaced alleles must be disambiguated by human scoring, this poses a key obstacle to full automation. We have developed methods that overcome this obstacle. Our model is that the observed data is generated by arithmetic superposition (i.e., convolution) of multiple allele patterns. By quantitatively measuring the size of each component band, and exploiting the unique stutter pattern associated with each marker, closely spaced alleles can be deconvolved; this unambiguously reconstructs the {open_quotes}true{close_quotes} allele bands, with stutter artifact removed. We used this approach in a system for automated diagnosis of (X-linked) Duchenne muscular dystrophy; four multiplexed CA-repeats within the dystrophin gene were assayed on a DNA sequencer. Our method accurately detected small variations in gel migration that shifted the allele size estimate. In 167 nonmutated alleles, 89% (149/167) showed no size variation, 9% (15/167) showed 1 bp variation, and 2% (3/167) showed 2 bp variation. We are currently developing a library of dinucleotide repeat patterns; together with our deconvolution methods, this library will enable fully automated genotyping of dinucleotide repeats from sizing data.

  2. Anatomical and micromorphological characteristics of the seed coat of field pea (Pisum sativum L. genotypes in relation to cracks and damage of seeds

    Directory of Open Access Journals (Sweden)

    Lazarević Jelena

    2017-01-01

    Full Text Available In this paper, we present the morphological characteristics of the seed and micromorphological, anatomical and chemical characteristics of the seed coat of pea (Pisum sativum L. genotypes, Jezero, Javor and NS Junior. Our aim was to investigate whether these genotypes can be differentiated based on seed coat morphoanatomical characteristics, depending on the harvest treatment. The observations and measurements of seed coat cross-sections were performed using light microscopy. The seed coat surface was observed using SEM. A tuberculate seed coat surface characterized all examined pea genotypes, and the average diameter of the tubercle was about 12 μm. Statistical and laboratory analyses revealed that major damage was the most frequent defect type as the result of mechanized harvest in all the examined genotypes. Genotype NS Junior had the shortest seed length (6.1 mm. Micromorphological analysis revealed that the seed surface was tuberculate in all genotypes. The genotype Jezero had the highest number of tubercle ribs (11.0 and a significantly higher proportion of parenchyma tissue (50.6%, while NS Junior was characterized by the greatest share of macrosclereids (49.8%. The highest number of osteosclereids (832/mm2 was counted in genotype Javor. In addition, genotype NS Junior stands out due to the highest percentage of crude fiber (62.75 g/100g in the seed coat. There was a marked difference among the studied genotypes with regard to the seed coat morphoanatomical characteristics, which is confirmed by the results of multivariate discriminant analysis (MDA. These results suggested that the morphological, micromorphological and anatomical characteristics of the seed might have an impact on the seed coat damage level at harvest. [Project of the Serbian Ministry of Education, Science and Technological Development, Grant no. 31024 and Grant no. 173002

  3. The Development of Quality Control Genotyping Approaches: A Case Study Using Elite Maize Lines.

    Directory of Open Access Journals (Sweden)

    Jiafa Chen

    Full Text Available Quality control (QC of germplasm identity and purity is a critical component of breeding and conservation activities. SNP genotyping technologies and increased availability of markers provide the opportunity to employ genotyping as a low-cost and robust component of this QC. In the public sector available low-cost SNP QC genotyping methods have been developed from a very limited panel of markers of 1,000 to 1,500 markers without broad selection of the most informative SNPs. Selection of optimal SNPs and definition of appropriate germplasm sampling in addition to platform section impact on logistical and resource-use considerations for breeding and conservation applications when mainstreaming QC. In order to address these issues, we evaluated the selection and use of SNPs for QC applications from large DArTSeq data sets generated from CIMMYT maize inbred lines (CMLs. Two QC genotyping strategies were developed, the first is a "rapid QC", employing a small number of SNPs to identify potential mislabeling of seed packages or plots, the second is a "broad QC", employing a larger number of SNP, used to identify each germplasm entry and to measure heterogeneity. The optimal marker selection strategies combined the selection of markers with high minor allele frequency, sampling of clustered SNP in proportion to marker cluster distance and selecting markers that maintain a uniform genomic distribution. The rapid and broad QC SNP panels selected using this approach were further validated using blind test assessments of related re-generation samples. The influence of sampling within each line was evaluated. Sampling 192 individuals would result in close to 100% possibility of detecting a 5% contamination in the entry, and approximately a 98% probability to detect a 2% contamination of the line. These results provide a framework for the establishment of QC genotyping. A comparison of financial and time costs for use of these approaches across different

  4. Amygdala response to anticipation of dyspnea is modulated by 5-HTTLPR genotype.

    Science.gov (United States)

    Stoeckel, M Cornelia; Esser, Roland W; Gamer, Matthias; Kalisch, Raffael; Büchel, Christian; von Leupoldt, Andreas

    2015-07-01

    Dyspnea anticipation and perception varies largely between individuals. To investigate whether genetic factors related to negative affect such as the 5-HTTLPR polymorphism impact this variability, we investigated healthy, 5-HTTLPR stratified volunteers using resistive load induced dyspnea together with fMRI. Alternating blocks of severe and mild dyspnea ("perception") were differentially cued ("anticipation") and followed by intensity and unpleasantness ratings. In addition, volunteers indicated their anticipatory fear during the anticipation periods. There were no genotype-based group differences concerning dyspnea intensity and unpleasantness or brain activation during perception of severe vs. mild dyspnea. However, in risk allele carriers, higher anticipatory fear was paralleled by stronger amygdala activation during anticipation of severe vs. mild dyspnea. These results suggest a role of the 5-HTTLPR genotype in fearful dyspnea anticipation. © 2015 Society for Psychophysiological Research.

  5. Improved Ancestry Estimation for both Genotyping and Sequencing Data using Projection Procrustes Analysis and Genotype Imputation

    Science.gov (United States)

    Wang, Chaolong; Zhan, Xiaowei; Liang, Liming; Abecasis, Gonçalo R.; Lin, Xihong

    2015-01-01

    Accurate estimation of individual ancestry is important in genetic association studies, especially when a large number of samples are collected from multiple sources. However, existing approaches developed for genome-wide SNP data do not work well with modest amounts of genetic data, such as in targeted sequencing or exome chip genotyping experiments. We propose a statistical framework to estimate individual ancestry in a principal component ancestry map generated by a reference set of individuals. This framework extends and improves upon our previous method for estimating ancestry using low-coverage sequence reads (LASER 1.0) to analyze either genotyping or sequencing data. In particular, we introduce a projection Procrustes analysis approach that uses high-dimensional principal components to estimate ancestry in a low-dimensional reference space. Using extensive simulations and empirical data examples, we show that our new method (LASER 2.0), combined with genotype imputation on the reference individuals, can substantially outperform LASER 1.0 in estimating fine-scale genetic ancestry. Specifically, LASER 2.0 can accurately estimate fine-scale ancestry within Europe using either exome chip genotypes or targeted sequencing data with off-target coverage as low as 0.05×. Under the framework of LASER 2.0, we can estimate individual ancestry in a shared reference space for samples assayed at different loci or by different techniques. Therefore, our ancestry estimation method will accelerate discovery in disease association studies not only by helping model ancestry within individual studies but also by facilitating combined analysis of genetic data from multiple sources. PMID:26027497

  6. Genotypic and phenotypic characterization of Chikungunya virus of different genotypes from Malaysia.

    Directory of Open Access Journals (Sweden)

    I-Ching Sam

    Full Text Available BACKGROUND: Mosquito-borne Chikungunya virus (CHIKV has recently re-emerged globally. The epidemic East/Central/South African (ECSA strains have spread for the first time to Asia, which previously only had endemic Asian strains. In Malaysia, the ECSA strain caused an extensive nationwide outbreak in 2008, while the Asian strains only caused limited outbreaks prior to this. To gain insight into these observed epidemiological differences, we compared genotypic and phenotypic characteristics of CHIKV of Asian and ECSA genotypes isolated in Malaysia. METHODS AND FINDINGS: CHIKV of Asian and ECSA genotypes were isolated from patients during outbreaks in Bagan Panchor in 2006, and Johor in 2008. Sequencing of the CHIKV strains revealed 96.8% amino acid similarity, including an unusual 7 residue deletion in the nsP3 protein of the Asian strain. CHIKV replication in cells and Aedes mosquitoes was measured by virus titration. There were no differences in mammalian cell lines. The ECSA strain reached significantly higher titres in Ae. albopictus cells (C6/36. Both CHIKV strains infected Ae. albopictus mosquitoes at a higher rate than Ae. aegypti, but when compared to each other, the ECSA strain had much higher midgut infection and replication, and salivary gland dissemination, while the Asian strain infected Ae. aegypti at higher rates. CONCLUSIONS: The greater ability of the ECSA strain to replicate in Ae. albopictus may explain why it spread far more quickly and extensively in humans in Malaysia than the Asian strain ever did, particularly in rural areas where Ae. albopictus predominates. Intergenotypic genetic differences were found at E1, E2, and nsP3 sites previously reported to be determinants of host adaptability in alphaviruses. Transmission of CHIKV in humans is influenced by virus strain and vector species, which has implications for regions with more than one circulating CHIKV genotype and Aedes species.

  7. Epidemiology of HPV Genotypes among HIV Positive Women in Kenya: A Systematic Review and Meta-Analysis

    Science.gov (United States)

    Menon, Sonia; Wusiman, Aibibula; Boily, Marie Claude; Kariisa, Mbabazi; Mabeya, Hillary; Luchters, Stanley; Forland, Frode; Rossi, Rodolfo; Callens, Steven; vanden Broeck, Davy

    2016-01-01

    Background There is a scarcity of data on the distribution of human papillomavirus (HPV) genotypes in the HIV positive population and in invasive cervical cancer (ICC) in Kenya. This may be different from genotypes found in abnormal cytology. Yet, with the advent of preventive HPV vaccines that target HPV 16 and 18, and the nonavalent vaccine targeting 90% of all ICC cases, such HPV genotype distribution data are indispensable for predicting the impact of vaccination and HPV screening on prevention. Even with a successful vaccination program, vaccinated women will still require screening to detect those who will develop ICC from other High risk (HR) HPV genotypes not prevented by current vaccines. The aim of this review is to report on the prevalence of pHR/HR HPV types and multiple pHR/HR HPV genotypes in Kenya among HIV positive women with normal, abnormal cytology and ICC. Methods PUBMED, EMBASE, SCOPUS, and PROQUEST were searched for articles on HPV infection up to August 2nd 2016. Search terms were HIV, HPV, Cervical Cancer, Incidence or Prevalence, and Kenya. Results The 13 studies included yielded a total of 2116 HIV-infected women, of which 89 had ICC. The overall prevalence of pHR/HR HPV genotypes among HIV-infected women was 64% (95%CI: 50%-77%). There was a borderline significant difference in the prevalence of pHR/HR HPV genotypes between Female Sex workers (FSW) compared to non-FSW in women with both normal and abnormal cytology. Multiple pHR/HR HPV genotypes were highly prominent in both normal cytology/HSIL and ICC. The most prevalent HR HPV genotypes in women with abnormal cytology were HPV 16 with 26%, (95%CI: 23.0%-30.0%) followed by HPV 35 and 52, with 21% (95%CI: 18%-25%) and 18% (95%CI: 15%-21%), respectively. In women with ICC, the most prevalent HPV genotypes were HPV 16 (37%; 95%CI: 28%-47%) and HPV 18 (24%; 95%CI: 16%-33%). Conclusion HPV 16/18 gains prominence as the severity of cervical disease increases, with HPV 16/18 accounting for 61

  8. Epidemiology of HPV Genotypes among HIV Positive Women in Kenya: A Systematic Review and Meta-Analysis.

    Directory of Open Access Journals (Sweden)

    Sonia Menon

    Full Text Available There is a scarcity of data on the distribution of human papillomavirus (HPV genotypes in the HIV positive population and in invasive cervical cancer (ICC in Kenya. This may be different from genotypes found in abnormal cytology. Yet, with the advent of preventive HPV vaccines that target HPV 16 and 18, and the nonavalent vaccine targeting 90% of all ICC cases, such HPV genotype distribution data are indispensable for predicting the impact of vaccination and HPV screening on prevention. Even with a successful vaccination program, vaccinated women will still require screening to detect those who will develop ICC from other High risk (HR HPV genotypes not prevented by current vaccines. The aim of this review is to report on the prevalence of pHR/HR HPV types and multiple pHR/HR HPV genotypes in Kenya among HIV positive women with normal, abnormal cytology and ICC.PUBMED, EMBASE, SCOPUS, and PROQUEST were searched for articles on HPV infection up to August 2nd 2016. Search terms were HIV, HPV, Cervical Cancer, Incidence or Prevalence, and Kenya.The 13 studies included yielded a total of 2116 HIV-infected women, of which 89 had ICC. The overall prevalence of pHR/HR HPV genotypes among HIV-infected women was 64% (95%CI: 50%-77%. There was a borderline significant difference in the prevalence of pHR/HR HPV genotypes between Female Sex workers (FSW compared to non-FSW in women with both normal and abnormal cytology. Multiple pHR/HR HPV genotypes were highly prominent in both normal cytology/HSIL and ICC. The most prevalent HR HPV genotypes in women with abnormal cytology were HPV 16 with 26%, (95%CI: 23.0%-30.0% followed by HPV 35 and 52, with 21% (95%CI: 18%-25% and 18% (95%CI: 15%-21%, respectively. In women with ICC, the most prevalent HPV genotypes were HPV 16 (37%; 95%CI: 28%-47% and HPV 18 (24%; 95%CI: 16%-33%.HPV 16/18 gains prominence as the severity of cervical disease increases, with HPV 16/18 accounting for 61% (95%CI: 50.0%-70.0% of all ICC

  9. Methods for discovering and validating relationships among genotyped animals

    Science.gov (United States)

    Genomic selection based on single-nucleotide polymorphisms (SNPs) has led to the collection of genotypes for over 2.2 million animals by the Council on Dairy Cattle Breeding in the United States. To assure that a genotype is assigned to the correct animal and that the animal’s pedigree is correct, t...

  10. Variation of meat quality traits among five genotypes of chicken.

    Science.gov (United States)

    Tang, H; Gong, Y Z; Wu, C X; Jiang, J; Wang, Y; Li, K

    2009-10-01

    The main objective of this study was to examine the diversity of meat quality traits among 5 chicken genotypes. The genotypes included 2 Chinese native breeds (Wenchang,WCH, and Xianju), 1 commercial broiler line (Avian, AV), 1 commercial layer line (Hy-Line Brown, HLB), and 1 Chinese commercial broiler line (Lingnanhuang, LNH) synthesized by exotic and native breeds, which were slaughtered at their market ages: 16, 7, 16, and 8 wk, respectively. The effects of genotype, muscle type, and sex on meat quality traits were examined. Birds from slow-growing genotypes (WCH, Xianju, and HLB) exhibited higher shear value, inosine-5'-monophosphate concentration, lower cook loss, and more fat than those from fast-growing genotypes (AV and LNH). Chickens from WCH possessed the lowest expressible moisture, cook loss, and the highest lipid (%) among the 3 slow-growing genotypes. The HLB birds were intermediate in expressible moisture and cook loss and lowest in lipid among all genotypes. The LNH cross birds were similar to AV broilers in most meat quality parameters, although they had a lower shear force value and higher fat content than AV broilers. Breast muscle had higher expressible moisture, shear force, protein (%), inosine-5'-monophosphate content, lower cook loss, and lipid (%) than leg muscle. Muscles from male chickens had higher expressible moisture than those from the females. Variability of meat quality characteristics is mainly related to genotype and muscle type differences.

  11. Screening of Wheat Genotypes for Boron Efficiency in Bangladesh

    Science.gov (United States)

    A number of Bangladeshi wheat genotypes (varieties and advanced lines) have been tested for boron efficiency through sand culture experiments over two years (2007-08 & 2008-09) against two Thai check varieties ‘Fang 60’ (boron efficient) and ‘SW41’ (boron inefficient). Performances of the genotypes ...

  12. Crossbreeding of large white and Nsukka local pigs: Genotype and ...

    African Journals Online (AJOL)

    5-Blood samples from 80 pigs of 4 genotypes - the Nsukka local (Lo), the exotic Large White (LW), the one-way F1 (LW x Lo) and the F2 crosses belonging to 5 age groups, were analyzed, to determine the mean values of the haematological parameters in the genotypes and different age groups and to check if and how the ...

  13. Enhanced fodder yield of maize genotypes under saline irrigation is ...

    African Journals Online (AJOL)

    Poor quality irrigation water adversely affects the growth and yield of crops. This study was designed to evaluate the growth, fodder yield and ionic concentration of three promising maize (Zea mays L.) genotypes under the influence of varying quality irrigation water, with different salinity levels. The genotypes, such as ...

  14. Breeding of a Tomato Genotype Readily Accessible to Genetic Manipulation

    NARCIS (Netherlands)

    Koornneef, Maarten; Hanhart, Corrie; Jongsma, Maarten; Toma, Ingrid; Weide, Rob; Zabel, Pim; Hille, Jacques

    1986-01-01

    A tomato genotype, superior in regenerating plants from cell cultures, was obtained by transferring regeneration capacity from Lycopersicon peruvianum into L. esculentum by classical breeding. This genotype, MsK93, greatly facilitates genetic manipulation of tomato, as was demonstrated by successful

  15. Application of mixed models for the assessment genotype and ...

    African Journals Online (AJOL)

    Application of mixed models for the assessment genotype and environment interactions in cotton ( Gossypium hirsutum ) cultivars in Mozambique. ... The cultivars ISA 205, STAM 42 and REMU 40 showed superior productivity when they were selected by the Harmonic Mean of Genotypic Values (HMGV) criterion in relation ...

  16. The influence of host genotype X environment Interactions on the ...

    African Journals Online (AJOL)

    Mean squares for environments, genotypes and G x E interactions were highly significant (P<0.0001) for anthracnose infection. Significant G x E interactions, accounting for 19% of the treatment sums of squares, indicated that genotypes responded differentially to anthracnose infection across environments. The additive ...

  17. The genotype-phenotype map of an evolving digital organism.

    Directory of Open Access Journals (Sweden)

    Miguel A Fortuna

    2017-02-01

    Full Text Available To understand how evolving systems bring forth novel and useful phenotypes, it is essential to understand the relationship between genotypic and phenotypic change. Artificial evolving systems can help us understand whether the genotype-phenotype maps of natural evolving systems are highly unusual, and it may help create evolvable artificial systems. Here we characterize the genotype-phenotype map of digital organisms in Avida, a platform for digital evolution. We consider digital organisms from a vast space of 10141 genotypes (instruction sequences, which can form 512 different phenotypes. These phenotypes are distinguished by different Boolean logic functions they can compute, as well as by the complexity of these functions. We observe several properties with parallels in natural systems, such as connected genotype networks and asymmetric phenotypic transitions. The likely common cause is robustness to genotypic change. We describe an intriguing tension between phenotypic complexity and evolvability that may have implications for biological evolution. On the one hand, genotypic change is more likely to yield novel phenotypes in more complex organisms. On the other hand, the total number of novel phenotypes reachable through genotypic change is highest for organisms with simple phenotypes. Artificial evolving systems can help us study aspects of biological evolvability that are not accessible in vastly more complex natural systems. They can also help identify properties, such as robustness, that are required for both human-designed artificial systems and synthetic biological systems to be evolvable.

  18. The genotype-phenotype map of an evolving digital organism.

    Science.gov (United States)

    Fortuna, Miguel A; Zaman, Luis; Ofria, Charles; Wagner, Andreas

    2017-02-01

    To understand how evolving systems bring forth novel and useful phenotypes, it is essential to understand the relationship between genotypic and phenotypic change. Artificial evolving systems can help us understand whether the genotype-phenotype maps of natural evolving systems are highly unusual, and it may help create evolvable artificial systems. Here we characterize the genotype-phenotype map of digital organisms in Avida, a platform for digital evolution. We consider digital organisms from a vast space of 10141 genotypes (instruction sequences), which can form 512 different phenotypes. These phenotypes are distinguished by different Boolean logic functions they can compute, as well as by the complexity of these functions. We observe several properties with parallels in natural systems, such as connected genotype networks and asymmetric phenotypic transitions. The likely common cause is robustness to genotypic change. We describe an intriguing tension between phenotypic complexity and evolvability that may have implications for biological evolution. On the one hand, genotypic change is more likely to yield novel phenotypes in more complex organisms. On the other hand, the total number of novel phenotypes reachable through genotypic change is highest for organisms with simple phenotypes. Artificial evolving systems can help us study aspects of biological evolvability that are not accessible in vastly more complex natural systems. They can also help identify properties, such as robustness, that are required for both human-designed artificial systems and synthetic biological systems to be evolvable.

  19. The influence of temperature on photosynthesis of different tomato genotypes

    NARCIS (Netherlands)

    Gosiewski, W.; Nilwik, H.J.M.; Bierhuizen, J.F.

    1982-01-01

    Net photosynthesis and dark respiration from whole plants of various tomato genotypes were measured in a closed system. At low irradiance (27 W m−2) and low external CO2 concentration (550 mg m−3), net photosynthesis of 10 genotypes was found to vary between 0.122 and 0.209 mg CO2 m−2 s−1.

  20. characterisation of common bean genotypes based on storage

    African Journals Online (AJOL)

    ACSS

    of pliers and then ground to fine powder with a ... segregation of genotypes were Rm 23.75, 32.50,. 33.75, 22.50 ... Figure 1. Positions of Phaseolus vulgarisL. genotypes on the first and second correspondence scores based on storage protein.

  1. Integrated analysis for genotypic adaptation in rice | Das | African ...

    African Journals Online (AJOL)

    Integrated analysis for genotypic adaptation in rice. S Das, RC Misra, MC Pattnaik, SK Sinha. Abstract. Development of varieties with high yield potential coupled with wide adaptability is an important plant breeding objective. The presence of genotype by environment (GxE) interaction plays a crucial role in determining the ...

  2. Characteristics of Streptococcus mutans genotypes and dental caries in children

    Science.gov (United States)

    Cheon, Kyounga; Moser, Stephen A.; Wiener, Howard W.; Whiddon, Jennifer; Momeni, Stephanie S.; Ruby, John D.; Cutter, Gary R.; Childers, Noel K.

    2013-01-01

    This longitudinal cohort study evaluated the diversity, commonality, and stability of Streptococcus mutans genotypes associated with dental caries history. Sixty-seven 5 and 6 yr-old children, considered being at high caries risk, had plaque collected from baseline through 36 months for S. mutans isolation and genotyping with repetitive extragenic palindromic-PCR (4,392 total isolates). Decayed, missing, filled surfaces (dmfs/DMFS) for each child were recorded at baseline. At baseline, 18 distinct genotypes were found among 911 S. mutans isolates from 67 children (diversity) and 13 genotypes were shared by at least 2 children (commonality). The number of genotypes per individual was positively associated with the proportion of decayed surfaces (p-ds) at baseline. Twenty-four of the 39 children who were available at follow-up visits maintained a predominant genotype for the follow-up periods (stability) and was negatively associated with p-ds. The observed diversity, commonality, and stability of S. mutans genotypes represent a pattern of dental caries epidemiology in this high caries risk community, which suggest fewer decayed surfaces are significantly associated with lower diversity and stability of S. mutans genotypes. PMID:23659236

  3. Beijing/W genotype Mycobacterium tuberculosis and drug resistance.

    NARCIS (Netherlands)

    Glynn, Judith R; Kremer, Kristin; Borgdorff, Martien W; Rodriguez, Mar Pujades; Soolingen, Dick van

    2006-01-01

    Beijing/W genotype Mycobacterium tuberculosis is widespread, may be increasing, and may have a predilection for drug resistance. Individual-level data on >29,000 patients from 49 studies in 35 countries were combined to assess the Beijing genotype's prevalence worldwide, trends over time and with

  4. Apolipoprotein E genotype, cardiovascular biomarkers and risk of stroke

    DEFF Research Database (Denmark)

    Khan, Tauseef A; Shah, Tina; Prieto, David

    2013-01-01

    At the APOE gene, encoding apolipoprotein E, genotypes of the ε2/ε3/ε4 alleles associated with higher LDL-cholesterol (LDL-C) levels are also associated with higher coronary risk. However, the association of APOE genotype with other cardiovascular biomarkers and risk of ischaemic stroke is less c...

  5. Genotype dependent callus induction and shoot regeneration in ...

    African Journals Online (AJOL)

    This study aims to observe the effect of genotype, hormone and culture conditions on sunflower (Helianthus annuus L.) callus induction and indirect plant regeneration. Calli were obtained from hypocotyl and cotyledon explants of five different sunflower genotypes; Trakya 80, Trakya 129, Trakya 259, Trakya 2098 and ...

  6. Haemoglobin genotype of children with severe malaria seen at the ...

    African Journals Online (AJOL)

    Abstract: Introduction: Types of haemoglobin (Hb) genotype have been found to be crucial to the rate of red blood cell parasite invasion, multiplication, and destruction as well as outcome of malaria disease. In a bid to provide more information on the relationship between Hb genotype and level of protection conferred by ...

  7. participatory selection of mungbean genotypes in uganda abstract

    African Journals Online (AJOL)

    ACSS

    2017-05-29

    May 29, 2017 ... that there were no significant differences in genotype choices based on gender ... However, there were significant genotype preference differences between eastern and northern regions (χ2 = ..... for southern Ethiopia. ... of improved cowpea cultivars in the Guinea and Sudan savanna zones of north east.

  8. Genetic variation of response to water deficit in parental genotypes ...

    African Journals Online (AJOL)

    dgomi

    In this study, we investigated morphological and photosynthetic responses to water deficit in parental genotypes of M. ... for adaptation to water deficit in legumes is a prerequisite for any research aiming to improve legume yields. ...... tolerant genotypes in rainfed lowland rice. Field Crop. Res. 99:48-58. Rouached A, Slama I, ...

  9. Clusters of incompatible genotypes evolve with limited dispersal

    Science.gov (United States)

    Erin L. Landguth; Norman A. Johnson; Samuel A. Cushman

    2015-01-01

    Theoretical and empirical studies have shown heterogeneous selection to be the primary driver for the evolution of reproductively isolated genotypes in the absence of geographic barriers. Here, we ask whether limited dispersal alone can lead to the evolution of reproductively isolated genotypes despite the absence of any geographic barriers or heterogeneous...

  10. Evaluation of sorghum genotypes under drought stress conditions ...

    African Journals Online (AJOL)

    Seven genotypes of sorghum (Sorghum bicolour (L.) Moench) were studied in both drought and normal conditions. In each condition, the genotypes were evaluated using a split plot based randomized complete block design with three replications. Drought tolerance indices including stability tolerance index (STI), mean ...

  11. Genotyping-By-Sequencing for Plant Genetic Diversity Analysis: A Lab Guide for SNP Genotyping

    Directory of Open Access Journals (Sweden)

    Gregory W. Peterson

    2014-10-01

    Full Text Available Genotyping-by-sequencing (GBS has recently emerged as a promising genomic approach for exploring plant genetic diversity on a genome-wide scale. However, many uncertainties and challenges remain in the application of GBS, particularly in non-model species. Here, we present a GBS protocol we developed and use for plant genetic diversity analysis. It uses two restriction enzymes to reduce genome complexity, applies Illumina multiplexing indexes for barcoding and has a custom bioinformatics pipeline for genotyping. This genetic diversity-focused GBS (gd-GBS protocol can serve as an easy-to-follow lab guide to assist a researcher through every step of a GBS application with five main components: sample preparation, library assembly, sequencing, SNP calling and diversity analysis. Specifically, in this presentation, we provide a brief overview of the GBS approach, describe the gd-GBS procedures, illustrate it with an application to analyze genetic diversity in 20 flax (Linum usitatissimum L. accessions and discuss related issues in GBS application. Following these lab bench procedures and using the custom bioinformatics pipeline, one could generate genome-wide SNP genotype data for a conventional genetic diversity analysis of a non-model plant species.

  12. Genotypic character relationship and phenotypic path coefficient analysis in chili pepper genotypes grown under tropical condition.

    Science.gov (United States)

    Usman, Magaji G; Rafii, Mohd Y; Martini, Mohammad Y; Oladosu, Yusuff; Kashiani, Pedram

    2017-03-01

    Studies on genotypic and phenotypic correlations among characters of crop plants are useful in planning, evaluating and setting selection criteria for the desired characters in a breeding program. The present study aimed to estimate the phenotypic correlation coefficients among yield and yield attributed characters and to work out the direct and indirect effects of yield-related characters on yield per plant using path coefficient analysis. Twenty-six genotypes of chili pepper were laid out in a randomized complete block design with three replications. Yield per plant showed positive and highly significant (P ≤ 0.01) correlations with most of the characters studied at both the phenotypic and genotypic levels. By contrast, disease incidence and days to flowering showed a significant negative association with yield. Fruit weight and number of fruits exerted positive direct effect on yield and also had a positive and significant (P ≤ 0.01) correlation with yield per plant. However, fruit length showed a low negative direct effect with a strong and positive indirect effect through fruit weight on yield and had a positive and significant association with yield. Longer fruits, heavy fruits and a high number of fruits are variables that are related to higher yields of chili pepper under tropical conditions and hence could be used as a reliable indicator in indirect selection for yield. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

  13. Saccharification Performances of Miscanthus at the Pilot and Miniaturized Assay Scales: Genotype and Year Variabilities According to the Biomass Composition

    Directory of Open Access Journals (Sweden)

    Nassim Belmokhtar

    2017-05-01

    Full Text Available HIGHLIGHTSBiomass production and cell wall composition are differentially impacted by harvesting year and genotypes, influencing then cellulose conversion in miniaturized assay.Using a high-throughput miniaturized and semi-automated method for performing the pretreatment and saccharification steps at laboratory scale allows for the assessment of these factors on the biomass potential for producing bioethanol before moving to the industrial scale.The large genetic diversity of the perennial grass miscanthus makes it suitable for producing cellulosic ethanol in biorefineries. The saccharification potential and year variability of five genotypes belonging to Miscanthus × giganteus and Miscanthus sinensis were explored using a miniaturized and semi-automated method, allowing the application of a hot water treatment followed by an enzymatic hydrolysis. The studied genotypes highlighted distinct cellulose conversion yields due to their distinct cell wall compositions. An inter-year comparison revealed significant variations in the biomass productivity and cell wall compositions. Compared to the recalcitrant genotypes, more digestible genotypes contained higher amounts of hemicellulosic carbohydrates and lower amounts of cellulose and lignin. In contrast to hemicellulosic carbohydrates, the relationships analysis between the biomass traits and cellulose conversion clearly showed the same negative effect of cellulose and lignin on cellulose digestion. The miniaturized and semi-automated method we developed was usable at the laboratory scale and was reliable for mimicking the saccharification at the pilot scale using a steam explosion pretreatment and enzymatic hydrolysis. Therefore, this miniaturized method will allow the reliable screening of many genotypes for saccharification potential. These findings provide valuable information and tools for breeders to create genotypes combining high yield, suitable biomass composition, and high saccharification

  14. Genotypic diversity of european Phytophthora ramorum isolates based on SSR analysis

    Science.gov (United States)

    Kris Van Poucke; Annelies Vercauteren; Martine Maes; Sabine Werres; Kurt Heungens

    2013-01-01

    in Scotland were genotyped using seven microsatellite markers as described by Vercauteren et al. (2010). Thirty multilocus genotypes were identified within the Scottish population, with 51 percent of the isolates belonging to the main European genotype EU1MG1 and 13 unique detected genotypes. Ten of those genotypes were site specific, often represented by...

  15. Performance and precision of double digestion RAD (ddRAD) genotyping in large multiplexed datasets of marine fish species

    DEFF Research Database (Denmark)

    Maroso, F.; Hillen, J E J; Pardo, B. G.

    2018-01-01

    ; (ii) the discrepancy between expected and observed tag length and coverage; (iii) the performances of reference based vs. de novo approaches; (iv) the sources of potential genotyping errors of the library preparation/bioinformatics protocol, by comparing technical replicates. Our results showed use...... a standardized protocol. A common bioinformatics pipeline based on STACKS was established, with and without the use of a reference genome. We performed analyses throughout the production and analysis of ddRAD data in order to explore (i) the loss of information due to heterogeneous raw read number across samples...... of downstream analysis carried out with ddRAD vs single SNP allele specific assay genotypes provided information about the levels of genotyping imprecision that can have a significant impact on allele frequency estimations and population assignment. The results and insights presented here will help to select...

  16. Understanding the Effects of Genotype, Growing Year, and Breeding on Tunisian Durum Wheat Allergenicity. 1. The Baker's Asthma Case.

    Science.gov (United States)

    Boukid, Fatma; Prandi, Barbara; Sforza, Stefano; Sayar, Rhouma; Seo, Yong Weon; Mejri, Mondher; Yacoubi, Ines

    2017-07-19

    Baker's asthma is a serious airway disease triggered by wheat protein CM3 α-amylase/trypsin inhibitor. The purpose of the present study was to investigate the impact of genotype and crop year on allergen CM3 α-amylase/trypsin inhibitor associated with baker's asthma. A historical series of Tunisian durum wheat (100 accessions), derived from three crop years, was used to compare the amount of CM3 from landraces to advanced cultivars. CM3 protein quantification was assessed after an enzymatic cleavage of the soluble protein extracts on a UPLC/ESI-MS system, using a marker peptide for its quantification. Combined data analysis of variance revealed an important effect of genotype, crop year, and their interaction. The CM3 allergenic proteins were found to significantly vary among studied genotypes, as confirmed by genetic variability, coefficient of variance, heritability, and genetic advance.