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Sample records for greater ancestral rocky

  1. Ancestral Rocky Mountian Tectonics: A Sedimentary Record of Ancestral Front Range and Uncompahgre Exhumation

    Science.gov (United States)

    Smith, T. M.; Saylor, J. E.; Lapen, T. J.

    2015-12-01

    The Ancestral Rocky Mountains (ARM) encompass multiple crustal provinces with characteristic crystallization ages across the central and western US. Two driving mechanisms have been proposed to explain ARM deformation. (1) Ouachita-Marathon collision SE of the ARM uplifts has been linked to an E-to-W sequence of uplift and is consistent with proposed disruption of a larger Paradox-Central Colorado Trough Basin by exhumation of the Uncompahgre Uplift. Initial exhumation of the Amarillo-Wichita Uplift to the east would provide a unique ~530 Ma signal absent from source areas to the SW, and result in initial exhumation of the Ancestral Front Range. (2) Alternatively, deformation due to flat slab subduction along a hypothesized plate boundary to the SW suggests a SW-to-NE younging of exhumation. This hypothesis suggests a SW-derived Grenville signature, and would trigger uplift of the Uncompahgre first. We analyzed depositional environments, sediment dispersal patterns, and sediment and basement zircon U-Pb and (U-Th)/He ages in 3 locations in the Paradox Basin and Central Colorado Trough (CCT). The Paradox Basin exhibits an up-section transition in fluvial style that suggests a decrease in overbank stability and increased lateral migration. Similarly, the CCT records a long-term progradation of depositional environments from marginal marine to fluvial, indicating that sediment supply in both basins outpaced accommodation. Preliminary provenance results indicate little to no input from the Amarillo-Wichita uplift in either basin despite uniformly westward sediment dispersal systems in both basins. Results also show that the Uncompahgre Uplift was the source for sediment throughout Paradox Basin deposition. These observations are inconsistent with the predictions of scenario 1 above. Rather, they suggest either a synchronous response to tectonic stress across the ARM provinces or an SW-to-NE pattern of deformation.

  2. Reinterpretation of Halokinetic Features in the Ancestral Rocky Mountains Paradox Salt Basin, Utah and Colorado

    Science.gov (United States)

    Thompson, J. A.; Giles, K. A.; Rowan, M. G.; Hearon, T. E., IV

    2016-12-01

    The Paradox Basin in southeastern Utah and southwestern Colorado is a foreland basin formed in response to flexural loading by the Pennsylvanian-aged Uncompaghre uplift during the Ancestral Rocky Mountain orogen. Thick sequences of evaporites (Paradox Formation) were deposited within the foreland basin, which interfinger with clastic sediments in the foredeep and carbonates around the basin margin. Differential loading of the Pennsylvanian-Jurassic sediments onto the evaporites drove synsedimentary halokinesis, creating a series of salt walls and adjacent minibasins within the larger foreland basin. The growing salt walls within the basin influenced patterns of sediment deposition from the Pennsylvanian through the Cretaceous. By integrating previously published mapping with recent field observations, mapping, and subsurface interpretations of well logs and 2D seismic lines, we present interpretations of the timing, geometry, and nature of halokinesis within the Paradox Basin, which record the complex salt tectonic history in the basin. Furthermore, we present recent work on the relationships between the local passive salt history and the formation of syndepositional counter-regional extensional fault systems within the foreland. These results will be integrated into a new regional salt-tectonic and stratigraphic framework of the Paradox Basin, and have broader implications for interpreting sedimentary records in other basins with a mobile substrate.

  3. Derived (mutated)-types of TRPV6 channels elicit greater Ca²+ influx into the cells than ancestral-types of TRPV6: evidence from Xenopus oocytes and mammalian cell expression system.

    Science.gov (United States)

    Sudo, Yuka; Matsuo, Kiyotaka; Tetsuo, Tomoyuki; Tsutsumi, Satoshi; Ohkura, Masamichi; Nakai, Junichi; Uezono, Yasuhito

    2010-01-01

    The frequency of the allele containing three derived nonsynonymous SNPs (157C, 378M, 681M) of the gene encoding calcium permeable TRPV6 channels expressed in the intestine has been increased by positive selection in non-African populations. To understand the nature of these SNPs, we compared the properties of Ca²+ influx of ancestral (in African populations) and derived-TRPV6 (in non-African populations) channels with electrophysiological, Ca²+-imaging, and morphological methods using both the Xenopus oocyte and mammalian cell expression systems. Functional electrophysiological and Ca²+-imaging analyses indicated that the derived-TRPV6 elicited more Ca²+ influx than the ancestral one in TRPV6-expressing cells where both channels were equally expressed in the cells. Ca²+-inactivation properties in the ancestral- and derived-TRPV6 were almost the same. Furthermore, fluorescence resonance energy transfer (FRET) analysis showed that both channels have similar multimeric formation properties, suggesting that derived-TRPV6 itself could cause higher Ca²+ influx. These findings suggest that populations having derived-TRPV6 in non-African areas may absorb higher Ca²+ from the intestine than ancestral-TRPV6 in the African area.

  4. Assessing the accuracy of ancestral protein reconstruction methods.

    Directory of Open Access Journals (Sweden)

    Paul D Williams

    2006-06-01

    Full Text Available The phylogenetic inference of ancestral protein sequences is a powerful technique for the study of molecular evolution, but any conclusions drawn from such studies are only as good as the accuracy of the reconstruction method. Every inference method leads to errors in the ancestral protein sequence, resulting in potentially misleading estimates of the ancestral protein's properties. To assess the accuracy of ancestral protein reconstruction methods, we performed computational population evolution simulations featuring near-neutral evolution under purifying selection, speciation, and divergence using an off-lattice protein model where fitness depends on the ability to be stable in a specified target structure. We were thus able to compare the thermodynamic properties of the true ancestral sequences with the properties of "ancestral sequences" inferred by maximum parsimony, maximum likelihood, and Bayesian methods. Surprisingly, we found that methods such as maximum parsimony and maximum likelihood that reconstruct a "best guess" amino acid at each position overestimate thermostability, while a Bayesian method that sometimes chooses less-probable residues from the posterior probability distribution does not. Maximum likelihood and maximum parsimony apparently tend to eliminate variants at a position that are slightly detrimental to structural stability simply because such detrimental variants are less frequent. Other properties of ancestral proteins might be similarly overestimated. This suggests that ancestral reconstruction studies require greater care to come to credible conclusions regarding functional evolution. Inferred functional patterns that mimic reconstruction bias should be reevaluated.

  5. Assessing the accuracy of ancestral protein reconstruction methods.

    Science.gov (United States)

    Williams, Paul D; Pollock, David D; Blackburne, Benjamin P; Goldstein, Richard A

    2006-06-23

    The phylogenetic inference of ancestral protein sequences is a powerful technique for the study of molecular evolution, but any conclusions drawn from such studies are only as good as the accuracy of the reconstruction method. Every inference method leads to errors in the ancestral protein sequence, resulting in potentially misleading estimates of the ancestral protein's properties. To assess the accuracy of ancestral protein reconstruction methods, we performed computational population evolution simulations featuring near-neutral evolution under purifying selection, speciation, and divergence using an off-lattice protein model where fitness depends on the ability to be stable in a specified target structure. We were thus able to compare the thermodynamic properties of the true ancestral sequences with the properties of "ancestral sequences" inferred by maximum parsimony, maximum likelihood, and Bayesian methods. Surprisingly, we found that methods such as maximum parsimony and maximum likelihood that reconstruct a "best guess" amino acid at each position overestimate thermostability, while a Bayesian method that sometimes chooses less-probable residues from the posterior probability distribution does not. Maximum likelihood and maximum parsimony apparently tend to eliminate variants at a position that are slightly detrimental to structural stability simply because such detrimental variants are less frequent. Other properties of ancestral proteins might be similarly overestimated. This suggests that ancestral reconstruction studies require greater care to come to credible conclusions regarding functional evolution. Inferred functional patterns that mimic reconstruction bias should be reevaluated.

  6. Are palaeoscolecids ancestral ecdysozoans?

    Science.gov (United States)

    Harvey, Thomas H P; Dong, Xiping; Donoghue, Philip C J

    2010-01-01

    The reconstruction of ancestors is a central aim of comparative anatomy and evolutionary developmental biology, not least in attempts to understand the relationship between developmental and organismal evolution. Inferences based on living taxa can and should be tested against the fossil record, which provides an independent and direct view onto historical character combinations. Here, we consider the nature of the last common ancestor of living ecdysozoans through a detailed analysis of palaeoscolecids, an early and extinct group of introvert-bearing worms that have been proposed to be ancestral ecdysozoans. In a review of palaeoscolecid anatomy, including newly resolved details of the internal and external cuticle structure, we identify specific characters shared with various living nematoid and scalidophoran worms, but not with panarthropods. Considered within a formal cladistic context, these characters provide most overall support for a stem-priapulid affinity, meaning that palaeoscolecids are far-removed from the ecdysozoan ancestor. We conclude that previous interpretations in which palaeoscolecids occupy a deeper position in the ecdysozoan tree lack particular morphological support and rely instead on a paucity of preserved characters. This bears out a more general point that fossil taxa may appear plesiomorphic merely because they preserve only plesiomorphies, rather than the mélange of primitive and derived characters anticipated of organisms properly allocated to a position deep within animal phylogeny.

  7. Rocky Mountain Spotted Fever

    Science.gov (United States)

    ... with facebook share with twitter share with linkedin Rocky Mountain Spotted Fever Credit: CDC A male cayenne tick, Amblyomma cajennense, ... and New Mexico. Why Is the Study of Rocky Mountain Spotted Fever a Priority for NIAID? Tickborne diseases are becoming ...

  8. Rocky Mountain spotted fever

    Science.gov (United States)

    ... spotted fever on the foot Rocky Mountain spotted fever, petechial rash Antibodies Deer and dog tick References McElligott SC, Kihiczak GG, Schwartz RA. Rocky Mountain spotted fever and other rickettsial infections. In: Lebwohl MG, Heymann ...

  9. Integrating Principles Underlying Ancestral Spirits Belief in ...

    African Journals Online (AJOL)

    , associated with ancestral spirits and its use as powerful therapeutic agent for influencing behavior or lifestyle changes. Explanatory models of attachment to ancestral spirits by living descendants are first discussed, followed by a discussion ...

  10. REGEN: Ancestral Genome Reconstruction for Bacteria

    OpenAIRE

    Yang, Kuan; Heath, Lenwood S.; Setubal, João C.

    2012-01-01

    Ancestral genome reconstruction can be understood as a phylogenetic study with more details than a traditional phylogenetic tree reconstruction. We present a new computational system called REGEN for ancestral bacterial genome reconstruction at both the gene and replicon levels. REGEN reconstructs gene content, contiguous gene runs, and replicon structure for each ancestral genome. Along each branch of the phylogenetic tree, REGEN infers evolutionary events, including gene creation and deleti...

  11. Rocky Flats Compliance Program

    International Nuclear Information System (INIS)

    1994-02-01

    The Department of Energy (DOE) established the Office of Technology Development (EM-50) (OTD) as an element of Environmental Restoration and Waste Management (EM) in November 1989. The primary objective of the Office of Technology Development, Rocky Flats Compliance Program (RFCP), is to develop altemative treatment technologies for mixed low-level waste (wastes containing both hazardous and radioactive components) to use in bringing the Rocky Flats Plant (RFP) into compliance with Federal and state regulations and agreements. Approximately 48,000 cubic feet of untreated low-level mixed waste, for which treatment has not been specified, are stored at the RFP. The cleanup of the Rocky Flats site is driven by agreements between DOE, the Environmental Protection Agency (EPA), and the Colorado Department of Health (CDH). Under these agreements, a Comprehensive Treatment and Management Plan (CTMP) was drafted to outline the mechanisms by which RFP will achieve compliance with the regulations and agreements. This document describes DOE's strategy to treat low-level mixed waste to meet Land Disposal Restrictions and sets specific milestones related to the regulatory aspects of technology development. These milestones detail schedules for the development of technologies to treat all of the mixed wastes at the RFP. Under the Federal Facilities Compliance Act (FFCA), the CTMP has been incorporated into Rocky Flats Plant Conceptual Site Treatment Plan (CSTP). The CSTP will become the Rocky Flats Plant site Treatment Plan in 1995 and will supersede the CTMP

  12. Ancestral sequence reconstruction with Maximum Parsimony

    OpenAIRE

    Herbst, Lina; Fischer, Mareike

    2017-01-01

    One of the main aims in phylogenetics is the estimation of ancestral sequences based on present-day data like, for instance, DNA alignments. One way to estimate the data of the last common ancestor of a given set of species is to first reconstruct a phylogenetic tree with some tree inference method and then to use some method of ancestral state inference based on that tree. One of the best-known methods both for tree inference as well as for ancestral sequence inference is Maximum Parsimony (...

  13. Rocky Mountain Riparian Digest

    Science.gov (United States)

    Deborah M. Finch

    2008-01-01

    The Rocky Mountain Riparian Digest presents the many facets of riparian research at the station. Included are articles about protecting the riparian habitat, the social and economic values of riparian environments, watershed restoration, remote sensing tools, and getting kids interested in the science.

  14. Ancestral sequence alignment under optimal conditions

    Directory of Open Access Journals (Sweden)

    Brown Daniel G

    2005-11-01

    Full Text Available Abstract Background Multiple genome alignment is an important problem in bioinformatics. An important subproblem used by many multiple alignment approaches is that of aligning two multiple alignments. Many popular alignment algorithms for DNA use the sum-of-pairs heuristic, where the score of a multiple alignment is the sum of its induced pairwise alignment scores. However, the biological meaning of the sum-of-pairs of pairs heuristic is not obvious. Additionally, many algorithms based on the sum-of-pairs heuristic are complicated and slow, compared to pairwise alignment algorithms. An alternative approach to aligning alignments is to first infer ancestral sequences for each alignment, and then align the two ancestral sequences. In addition to being fast, this method has a clear biological basis that takes into account the evolution implied by an underlying phylogenetic tree. In this study we explore the accuracy of aligning alignments by ancestral sequence alignment. We examine the use of both maximum likelihood and parsimony to infer ancestral sequences. Additionally, we investigate the effect on accuracy of allowing ambiguity in our ancestral sequences. Results We use synthetic sequence data that we generate by simulating evolution on a phylogenetic tree. We use two different types of phylogenetic trees: trees with a period of rapid growth followed by a period of slow growth, and trees with a period of slow growth followed by a period of rapid growth. We examine the alignment accuracy of four ancestral sequence reconstruction and alignment methods: parsimony, maximum likelihood, ambiguous parsimony, and ambiguous maximum likelihood. Additionally, we compare against the alignment accuracy of two sum-of-pairs algorithms: ClustalW and the heuristic of Ma, Zhang, and Wang. Conclusion We find that allowing ambiguity in ancestral sequences does not lead to better multiple alignments. Regardless of whether we use parsimony or maximum likelihood, the

  15. REGEN: Ancestral Genome Reconstruction for Bacteria

    Directory of Open Access Journals (Sweden)

    João C. Setubal

    2012-07-01

    Full Text Available Ancestral genome reconstruction can be understood as a phylogenetic study with more details than a traditional phylogenetic tree reconstruction. We present a new computational system called REGEN for ancestral bacterial genome reconstruction at both the gene and replicon levels. REGEN reconstructs gene content, contiguous gene runs, and replicon structure for each ancestral genome. Along each branch of the phylogenetic tree, REGEN infers evolutionary events, including gene creation and deletion and replicon fission and fusion. The reconstruction can be performed by either a maximum parsimony or a maximum likelihood method. Gene content reconstruction is based on the concept of neighboring gene pairs. REGEN was designed to be used with any set of genomes that are sufficiently related, which will usually be the case for bacteria within the same taxonomic order. We evaluated REGEN using simulated genomes and genomes in the Rhizobiales order.

  16. REGEN: Ancestral Genome Reconstruction for Bacteria.

    Science.gov (United States)

    Yang, Kuan; Heath, Lenwood S; Setubal, João C

    2012-07-18

    Ancestral genome reconstruction can be understood as a phylogenetic study with more details than a traditional phylogenetic tree reconstruction. We present a new computational system called REGEN for ancestral bacterial genome reconstruction at both the gene and replicon levels. REGEN reconstructs gene content, contiguous gene runs, and replicon structure for each ancestral genome. Along each branch of the phylogenetic tree, REGEN infers evolutionary events, including gene creation and deletion and replicon fission and fusion. The reconstruction can be performed by either a maximum parsimony or a maximum likelihood method. Gene content reconstruction is based on the concept of neighboring gene pairs. REGEN was designed to be used with any set of genomes that are sufficiently related, which will usually be the case for bacteria within the same taxonomic order. We evaluated REGEN using simulated genomes and genomes in the Rhizobiales order.

  17. Resolution effects in reconstructing ancestral genomes.

    Science.gov (United States)

    Zheng, Chunfang; Jeong, Yuji; Turcotte, Madisyn Gabrielle; Sankoff, David

    2018-05-09

    The reconstruction of ancestral genomes must deal with the problem of resolution, necessarily involving a trade-off between trying to identify genomic details and being overwhelmed by noise at higher resolutions. We use the median reconstruction at the synteny block level, of the ancestral genome of the order Gentianales, based on coffee, Rhazya stricta and grape, to exemplify the effects of resolution (granularity) on comparative genomic analyses. We show how decreased resolution blurs the differences between evolving genomes, with respect to rate, mutational process and other characteristics.

  18. Kepler's first rocky planet

    DEFF Research Database (Denmark)

    Batalha, N.M.; Borucki, W.J.; Bryson, S.T.

    2011-01-01

    NASA's Kepler Mission uses transit photometry to determine the frequency of Earth-size planets in or near the habitable zone of Sun-like stars. The mission reached a milestone toward meeting that goal: the discovery of its first rocky planet, Kepler-10b. Two distinct sets of transit events were...... tests on the photometric and pixel flux time series established the viability of the planet candidates triggering ground-based follow-up observations. Forty precision Doppler measurements were used to confirm that the short-period transit event is due to a planetary companion. The parent star is bright...

  19. Ancestral Sequence Reconstruction with Maximum Parsimony.

    Science.gov (United States)

    Herbst, Lina; Fischer, Mareike

    2017-12-01

    One of the main aims in phylogenetics is the estimation of ancestral sequences based on present-day data like, for instance, DNA alignments. One way to estimate the data of the last common ancestor of a given set of species is to first reconstruct a phylogenetic tree with some tree inference method and then to use some method of ancestral state inference based on that tree. One of the best-known methods both for tree inference and for ancestral sequence inference is Maximum Parsimony (MP). In this manuscript, we focus on this method and on ancestral state inference for fully bifurcating trees. In particular, we investigate a conjecture published by Charleston and Steel in 1995 concerning the number of species which need to have a particular state, say a, at a particular site in order for MP to unambiguously return a as an estimate for the state of the last common ancestor. We prove the conjecture for all even numbers of character states, which is the most relevant case in biology. We also show that the conjecture does not hold in general for odd numbers of character states, but also present some positive results for this case.

  20. Cascading effects of fire exclusion in the Rocky Mountain ecosystems: a literature review

    Science.gov (United States)

    Robert E. Keane; Kevin C. Ryan; Tom T. Veblen; Craig D. Allen; Jessie Logan; Brad Hawkes

    2002-01-01

    The health of many Rocky Mountain ecosystems is in decline because of the policy of excluding fire in the management of these ecosystems. Fire exclusion has actually made it more difficult to fight fires, and this poses greater risks to the people who fight fires and for those who live in and around Rocky Mountain forests and rangelands. This paper discusses the extent...

  1. Assessing the Accuracy of Ancestral Protein Reconstruction Methods

    OpenAIRE

    Williams, Paul D; Pollock, David D; Blackburne, Benjamin P; Goldstein, Richard A

    2006-01-01

    The phylogenetic inference of ancestral protein sequences is a powerful technique for the study of molecular evolution, but any conclusions drawn from such studies are only as good as the accuracy of the reconstruction method. Every inference method leads to errors in the ancestral protein sequence, resulting in potentially misleading estimates of the ancestral protein's properties. To assess the accuracy of ancestral protein reconstruction methods, we performed computational population evolu...

  2. Animal regeneration: ancestral character or evolutionary novelty?

    Science.gov (United States)

    Slack, Jonathan Mw

    2017-09-01

    An old question about regeneration is whether it is an ancestral character which is a general property of living matter, or whether it represents a set of specific adaptations to the different circumstances faced by different types of animal. In this review, some recent results on regeneration are assessed to see if they can throw any new light on this question. Evidence in favour of an ancestral character comes from the role of Wnt and bone morphogenetic protein signalling in controlling the pattern of whole-body regeneration in acoels, which are a basal group of bilaterian animals. On the other hand, there is some evidence for adaptive acquisition or maintenance of the regeneration of appendages based on the occurrence of severe non-lethal predation, the existence of some novel genes in regenerating organisms, and differences at the molecular level between apparently similar forms of regeneration. It is tentatively concluded that whole-body regeneration is an ancestral character although has been lost from most animal lineages. Appendage regeneration is more likely to represent a derived character resulting from many specific adaptations. © 2017 The Author.

  3. The removal of plutonium contaminants from Rocky Flats Plant soil

    International Nuclear Information System (INIS)

    Sunderland, N.R.

    1987-01-01

    This research was undertaken to determine if the TRUclean process could effectively remove radioactive elements from soils other than derived coral. This is an interim report prior to the project report and discusses the outcome of the tests of the Rocky Flats Plant (RFP) soil. The soil tested contained plutonium particulates in the micron and submicron range. Volume reduction and activity removal were accomplished with an overall efficiency of greater than 90%. The TRUclean process is a very practical and economical solution to soil contamination problems at the Rocky Flats Plant

  4. Rocky road in the Rockies: Challenges to biodiversity

    Science.gov (United States)

    Tomback, Diana F.; Kendall, Katherine C.; Baron, Jill S.

    2002-01-01

    To people worldwide, the Rocky Mountains of the United States and Canada represent a last bastion of nature in its purest and rawest form-unspoiled forests teeming with elk and deer stalked by mountain lions and grizzly bears; bald eagles nesting near lakes and rivers; fat, feisty native trout in rushing mountain streams; and dazzling arrays of wildflowers in lush meadows. In fact, the total biodiversity of the Rocky Mountains is considerable, with relatively high diversity in birds, mammals, butterflies, reptiles, and conifers (Ricketts et al. 1999) and with geographic variation in the flora and fauna of alpine, forest, foothill, and adjacent shortgrass prairie and shrub communities over more than 20 degrees of latitude and more than 10' of longitude. Although the biodiversity of most North American regions has declined because of anthropogenic influences, the perception remains that the biodiversity of the Rocky Mountains is intact. This view exists in part because the Rocky Mountains are remote from urban centers, in part because so much of the land comprises protected areas such as national parks and wilderness areas, and in part because of wishful thinking-that nothing bad could happen to the biodiversity that is so much a part of the history, national self-image, legends, nature films, and movies of the United States and Canada. Despite modern technology and the homogenization and globalization of their cities and towns, at heart North Americans still regard their land as the New World, with pristine nature and untamed landscapes epitomized by the Rockies. The reality is that the biodiversity of the Rocky Mountains has not been free of anthropogenic influences since the West was settled in the 1800s, and in fact it was altered by Native Americans for centuries prior to settlement. A number of escalating problems and consequences of management choices are currently changing Rocky Mountain ecological communities at a dizzying pace. In Order to maintain some

  5. Approximate maximum parsimony and ancestral maximum likelihood.

    Science.gov (United States)

    Alon, Noga; Chor, Benny; Pardi, Fabio; Rapoport, Anat

    2010-01-01

    We explore the maximum parsimony (MP) and ancestral maximum likelihood (AML) criteria in phylogenetic tree reconstruction. Both problems are NP-hard, so we seek approximate solutions. We formulate the two problems as Steiner tree problems under appropriate distances. The gist of our approach is the succinct characterization of Steiner trees for a small number of leaves for the two distances. This enables the use of known Steiner tree approximation algorithms. The approach leads to a 16/9 approximation ratio for AML and asymptotically to a 1.55 approximation ratio for MP.

  6. Robustness of ancestral sequence reconstruction to phylogenetic uncertainty.

    Science.gov (United States)

    Hanson-Smith, Victor; Kolaczkowski, Bryan; Thornton, Joseph W

    2010-09-01

    Ancestral sequence reconstruction (ASR) is widely used to formulate and test hypotheses about the sequences, functions, and structures of ancient genes. Ancestral sequences are usually inferred from an alignment of extant sequences using a maximum likelihood (ML) phylogenetic algorithm, which calculates the most likely ancestral sequence assuming a probabilistic model of sequence evolution and a specific phylogeny--typically the tree with the ML. The true phylogeny is seldom known with certainty, however. ML methods ignore this uncertainty, whereas Bayesian methods incorporate it by integrating the likelihood of each ancestral state over a distribution of possible trees. It is not known whether Bayesian approaches to phylogenetic uncertainty improve the accuracy of inferred ancestral sequences. Here, we use simulation-based experiments under both simplified and empirically derived conditions to compare the accuracy of ASR carried out using ML and Bayesian approaches. We show that incorporating phylogenetic uncertainty by integrating over topologies very rarely changes the inferred ancestral state and does not improve the accuracy of the reconstructed ancestral sequence. Ancestral state reconstructions are robust to uncertainty about the underlying tree because the conditions that produce phylogenetic uncertainty also make the ancestral state identical across plausible trees; conversely, the conditions under which different phylogenies yield different inferred ancestral states produce little or no ambiguity about the true phylogeny. Our results suggest that ML can produce accurate ASRs, even in the face of phylogenetic uncertainty. Using Bayesian integration to incorporate this uncertainty is neither necessary nor beneficial.

  7. Reconstructed Ancestral Enzymes Impose a Fitness Cost upon Modern Bacteria Despite Exhibiting Favourable Biochemical Properties.

    Science.gov (United States)

    Hobbs, Joanne K; Prentice, Erica J; Groussin, Mathieu; Arcus, Vickery L

    2015-10-01

    Ancestral sequence reconstruction has been widely used to study historical enzyme evolution, both from biochemical and cellular perspectives. Two properties of reconstructed ancestral proteins/enzymes are commonly reported--high thermostability and high catalytic activity--compared with their contemporaries. Increased protein stability is associated with lower aggregation rates, higher soluble protein abundance and a greater capacity to evolve, and therefore, these proteins could be considered "superior" to their contemporary counterparts. In this study, we investigate the relationship between the favourable in vitro biochemical properties of reconstructed ancestral enzymes and the organismal fitness they confer in vivo. We have previously reconstructed several ancestors of the enzyme LeuB, which is essential for leucine biosynthesis. Our initial fitness experiments revealed that overexpression of ANC4, a reconstructed LeuB that exhibits high stability and activity, was only able to partially rescue the growth of a ΔleuB strain, and that a strain complemented with this enzyme was outcompeted by strains carrying one of its descendants. When we expanded our study to include five reconstructed LeuBs and one contemporary, we found that neither in vitro protein stability nor the catalytic rate was correlated with fitness. Instead, fitness showed a strong, negative correlation with estimated evolutionary age (based on phylogenetic relationships). Our findings suggest that, for reconstructed ancestral enzymes, superior in vitro properties do not translate into organismal fitness in vivo. The molecular basis of the relationship between fitness and the inferred age of ancestral LeuB enzymes is unknown, but may be related to the reconstruction process. We also hypothesise that the ancestral enzymes may be incompatible with the other, contemporary enzymes of the metabolic network.

  8. Ancestral Relationships Using Metafounders: Finite Ancestral Populations and Across Population Relationships.

    Science.gov (United States)

    Legarra, Andres; Christensen, Ole F; Vitezica, Zulma G; Aguilar, Ignacio; Misztal, Ignacy

    2015-06-01

    Recent use of genomic (marker-based) relationships shows that relationships exist within and across base population (breeds or lines). However, current treatment of pedigree relationships is unable to consider relationships within or across base populations, although such relationships must exist due to finite size of the ancestral population and connections between populations. This complicates the conciliation of both approaches and, in particular, combining pedigree with genomic relationships. We present a coherent theoretical framework to consider base population in pedigree relationships. We suggest a conceptual framework that considers each ancestral population as a finite-sized pool of gametes. This generates across-individual relationships and contrasts with the classical view which each population is considered as an infinite, unrelated pool. Several ancestral populations may be connected and therefore related. Each ancestral population can be represented as a "metafounder," a pseudo-individual included as founder of the pedigree and similar to an "unknown parent group." Metafounders have self- and across relationships according to a set of parameters, which measure ancestral relationships, i.e., homozygozities within populations and relationships across populations. These parameters can be estimated from existing pedigree and marker genotypes using maximum likelihood or a method based on summary statistics, for arbitrarily complex pedigrees. Equivalences of genetic variance and variance components between the classical and this new parameterization are shown. Segregation variance on crosses of populations is modeled. Efficient algorithms for computation of relationship matrices, their inverses, and inbreeding coefficients are presented. Use of metafounders leads to compatibility of genomic and pedigree relationship matrices and to simple computing algorithms. Examples and code are given. Copyright © 2015 by the Genetics Society of America.

  9. Soil decontamination at Rocky Flats

    International Nuclear Information System (INIS)

    Olsen, R.L.; Hayden, J.A.; Alford, C.E.; Kochen, R.L.; Stevens, J.R.

    1979-01-01

    A soils decontamination project was initiated, to remove actinides from soils at Rocky Flats. Wet screening, attrition scrubbing with Calgon at high pH, attrition scrubbing at low pH, and cationic flotation were investigated. Pilot plant studies were carried out. Conceptual designs have been generated for mounting the process in semi-trailers

  10. Rocky Mountain spotted fever, Panama.

    Science.gov (United States)

    Estripeaut, Dora; Aramburú, María Gabriela; Sáez-Llorens, Xavier; Thompson, Herbert A; Dasch, Gregory A; Paddock, Christopher D; Zaki, Sherif; Eremeeva, Marina E

    2007-11-01

    We describe a fatal pediatric case of Rocky Mountain spotted fever in Panama, the first, to our knowledge, since the 1950s. Diagnosis was established by immunohistochemistry, PCR, and isolation of Rickettsia rickettsii from postmortem tissues. Molecular typing demonstrated strong relatedness of the isolate to strains of R. rickettsii from Central and South America.

  11. Rocky Mountain spotted fever, Colombia.

    Science.gov (United States)

    Hidalgo, Marylin; Orejuela, Leonora; Fuya, Patricia; Carrillo, Pilar; Hernandez, Jorge; Parra, Edgar; Keng, Colette; Small, Melissa; Olano, Juan P; Bouyer, Donald; Castaneda, Elizabeth; Walker, David; Valbuena, Gustavo

    2007-07-01

    We investigated 2 fatal cases of Rocky Mountain spotted fever that occurred in 2003 and 2004 near the same locality in Colombia where the disease was first reported in the 1930s. A retrospective serosurvey of febrile patients showed that > 21% of the serum samples had antibodies aaainst spotted fever group rickettsiae.

  12. Managing Rocky Mountain spotted fever.

    Science.gov (United States)

    Minniear, Timothy D; Buckingham, Steven C

    2009-11-01

    Rocky Mountain spotted fever is caused by the tick-borne bacterium Rickettsia rickettsii. Symptoms range from moderate illness to severe illness, including cardiovascular compromise, coma and death. The disease is prevalent in most of the USA, especially during warmer months. The trademark presentation is fever and rash with a history of tick bite, although tick exposure is unappreciated in over a third of cases. Other signature symptoms include headache and abdominal pain. The antibiotic therapy of choice for R. rickettsii infection is doxycycline. Preventive measures for Rocky Mountain spotted fever and other tick-borne diseases include: wearing long-sleeved, light colored clothing; checking for tick attachment and removing attached ticks promptly; applying topical insect repellent; and treating clothing with permethrin.

  13. Residue management at Rocky Flats

    International Nuclear Information System (INIS)

    Olencz, J.

    1995-01-01

    Past plutonium production and manufacturing operations conducted at the Rocky Flats Environmental Technology Site (RFETS) produced a variety of plutonium-contaminated by-product materials. Residues are a category of these materials and were categorized as open-quotes materials in-processclose quotes to be recovered due to their inherent plutonium concentrations. In 1989 all RFETS plutonium production and manufacturing operations were curtailed. This report describes the management of plutonium bearing liquid and solid wastes

  14. Why Meillassoux’s Speculative Materialism Struggles with Ancestrality

    Directory of Open Access Journals (Sweden)

    Ciprian Jeler

    2014-12-01

    Full Text Available This paper shows that Quentin Meillassoux’s speculative materialism doesn’t offer us the means to account for the ancestral statements that the modern sciences produce, i.e. for the scientific statements about events preceding all forms of life. An analysis of the reasons why Meillassoux thinks that the problem of ancestrality problematizes the contemporary self-evidence of correlationism is first offered. The results of this analysis are then applied to speculative materialism itself and the consequences are not very promising: very much like correlationism, speculative materialism explicitly denies what I call the “generalized version of the realistic assumption of science” and, in so doing, renders scientific ancestral statements de jure unverifiable. Therefore, if correlationism is rendered suspicious by the issue of ancestrality, the same can be said of speculative materialism.

  15. WARACS: Wrappers to Automate the Reconstruction of Ancestral Character States.

    Science.gov (United States)

    Gruenstaeudl, Michael

    2016-02-01

    Reconstructions of ancestral character states are among the most widely used analyses for evaluating the morphological, cytological, or ecological evolution of an organismic lineage. The software application Mesquite remains the most popular application for such reconstructions among plant scientists, even though its support for automating complex analyses is limited. A software tool is needed that automates the reconstruction and visualization of ancestral character states with Mesquite and similar applications. A set of command line-based Python scripts was developed that (a) communicates standardized input to and output from the software applications Mesquite, BayesTraits, and TreeGraph2; (b) automates the process of ancestral character state reconstruction; and (c) facilitates the visualization of reconstruction results. WARACS provides a simple tool that streamlines the reconstruction and visualization of ancestral character states over a wide array of parameters, including tree distribution, character state, and optimality criterion.

  16. Why Meillassoux’s Speculative Materialism Struggles with Ancestrality

    OpenAIRE

    Ciprian Jeler

    2014-01-01

    This paper shows that Quentin Meillassoux’s speculative materialism doesn’t offer us the means to account for the ancestral statements that the modern sciences produce, i.e. for the scientific statements about events preceding all forms of life. An analysis of the reasons why Meillassoux thinks that the problem of ancestrality problematizes the contemporary self-evidence of correlationism is first offered. The results of this analysis are then applied to speculative materialism itself and the...

  17. Rocky Mountain Research Station: 2011 Annual Accomplishments

    Science.gov (United States)

    Rick Fletcher

    2011-01-01

    The Rocky Mountain Research Station is one of seven regional units that make up the USDA Forest Service Research and Development organization ­ the most extensive natural resources research organization in the world. We maintain 12 field laboratories throughout a 12-state territory encompassing the Great Basin, Southwest, Rocky Mountains, and parts of the Great Plains...

  18. Rocky Mountain Research Station: 2010 Research Accomplishments

    Science.gov (United States)

    Rick Fletcher

    2010-01-01

    The Rocky Mountain Research Station is one of seven regional units that make up the USDA Forest Service Research and Development organization ­ the most extensive natural resources research organization in the world. We maintain 12 field laboratories throughout a 12-state territory encompassing the Great Basin, Southwest, Rocky Mountains, and parts of the Great Plains...

  19. Rocky Mountain spotted fever in children.

    Science.gov (United States)

    Woods, Charles R

    2013-04-01

    Rocky Mountain spotted fever is typically undifferentiated from many other infections in the first few days of illness. Treatment should not be delayed pending confirmation of infection when Rocky Mountain spotted fever is suspected. Doxycycline is the drug of choice even for infants and children less than 8 years old. Copyright © 2013 Elsevier Inc. All rights reserved.

  20. Rocky Mountain Spotted Fever: Statistics and Epidemiology

    Science.gov (United States)

    ... Search Form Controls Cancel Submit Search the CDC Rocky Mountain Spotted Fever (RMSF) Note: Javascript is disabled or is not ... message, please visit this page: About CDC.gov . Rocky Mountain Spotted Fever (RMSF) Transmission Signs and Symptoms Diagnosis and Testing ...

  1. Radiation monitor training program at Rocky Flats

    International Nuclear Information System (INIS)

    Medina, L.C.; Kittinger, W.D.; Vogel, R.M.

    The Rocky Flats Radiation Monitor Training Program is tailored to train new health physics personnel in the field of radiation monitoring. The purpose of the prescribed materials and media is to be consistent in training in all areas of Rocky Flats radiation monitoring job involvement

  2. Closing Rocky Flats by 2006

    International Nuclear Information System (INIS)

    Tuor, N. R.; Schubert, A. L.

    2002-01-01

    Safely accelerating the closure of Rocky Flats to 2006 is a goal shared by many: the State of Colorado, the communities surrounding the site, the U.S. Congress, the Department of Energy, Kaiser-Hill and its team of subcontractors, the site's employees, and taxpayers across the country. On June 30, 2000, Kaiser-Hill (KH) submitted to the Department of Energy (DOE), KH's plan to achieve closure of Rocky Flats by December 15, 2006, for a remaining cost of $3.96 billion (February 1, 2000, to December 15, 2006). The Closure Project Baseline (CPB) is the detailed project plan for accomplishing this ambitious closure goal. This paper will provide a status report on the progress being made toward the closure goal. This paper will: provide a summary of the closure contract completion criteria; give the current cost and schedule variance of the project and the status of key activities; detail important accomplishments of the past year; and discuss the challenges ahead

  3. Numerical Modeling of Large-Scale Rocky Coastline Evolution

    Science.gov (United States)

    Limber, P.; Murray, A. B.; Littlewood, R.; Valvo, L.

    2008-12-01

    Seventy-five percent of the world's ocean coastline is rocky. On large scales (i.e. greater than a kilometer), many intertwined processes drive rocky coastline evolution, including coastal erosion and sediment transport, tectonics, antecedent topography, and variations in sea cliff lithology. In areas such as California, an additional aspect of rocky coastline evolution involves submarine canyons that cut across the continental shelf and extend into the nearshore zone. These types of canyons intercept alongshore sediment transport and flush sand to abyssal depths during periodic turbidity currents, thereby delineating coastal sediment transport pathways and affecting shoreline evolution over large spatial and time scales. How tectonic, sediment transport, and canyon processes interact with inherited topographic and lithologic settings to shape rocky coastlines remains an unanswered, and largely unexplored, question. We will present numerical model results of rocky coastline evolution that starts with an immature fractal coastline. The initial shape is modified by headland erosion, wave-driven alongshore sediment transport, and submarine canyon placement. Our previous model results have shown that, as expected, an initial sediment-free irregularly shaped rocky coastline with homogeneous lithology will undergo smoothing in response to wave attack; headlands erode and mobile sediment is swept into bays, forming isolated pocket beaches. As this diffusive process continues, pocket beaches coalesce, and a continuous sediment transport pathway results. However, when a randomly placed submarine canyon is introduced to the system as a sediment sink, the end results are wholly different: sediment cover is reduced, which in turn increases weathering and erosion rates and causes the entire shoreline to move landward more rapidly. The canyon's alongshore position also affects coastline morphology. When placed offshore of a headland, the submarine canyon captures local sediment

  4. Ancestrality and evolution of trait syndromes in finches (Fringillidae).

    Science.gov (United States)

    Ponge, Jean-François; Zuccon, Dario; Elias, Marianne; Pavoine, Sandrine; Henry, Pierre-Yves; Théry, Marc; Guilbert, Éric

    2017-12-01

    Species traits have been hypothesized by one of us (Ponge, 2013) to evolve in a correlated manner as species colonize stable, undisturbed habitats, shifting from "ancestral" to "derived" strategies. We predicted that generalism, r-selection, sexual monomorphism, and migration/gregariousness are the ancestral states (collectively called strategy A) and evolved correlatively toward specialism, K-selection, sexual dimorphism, and residence/territoriality as habitat stabilized (collectively called B strategy). We analyzed the correlated evolution of four syndromes, summarizing the covariation between 53 traits, respectively, involved in ecological specialization, r-K gradient, sexual selection, and dispersal/social behaviors in 81 species representative of Fringillidae, a bird family with available natural history information and that shows variability for all these traits. The ancestrality of strategy A was supported for three of the four syndromes, the ancestrality of generalism having a weaker support, except for the core group Carduelinae (69 species). It appeared that two different B-strategies evolved from the ancestral state A, both associated with highly predictable environments: one in poorly seasonal environments, called B1, with species living permanently in lowland tropics, with "slow pace of life" and weak sexual dimorphism, and one in highly seasonal environments, called B2, with species breeding out-of-the-tropics, migratory, with a "fast pace of life" and high sexual dimorphism.

  5. Reproductive function in mice exposed to ancestral and direct irradiation

    International Nuclear Information System (INIS)

    Nash, D.J.; Sprackling, L.S.

    1978-01-01

    Reproduction was studied in 13 inbred strains of mice that had been exposed continuously to 60 Co gamma radiation for varying numbers of generations. At weaning the mice were removed from the irradiation chamber and were tested for reproductive performance. Ancestral and direct levels of irradiation were determined for each animal. Each irradiated or control female was scored as fertile or sterile, and in utero litter counts were made in pregnant females that were dissected past the 10th day of pregnancy. The number of resorptions, dead embryos, and live embryos were counted, and the ratio of living embryos to the total number of embryos was determined for each litter. The overall fertility curves were sigmoid in the range of doses below those which caused complete sterility, which indicated some sort of cumulative damage. In 11 of the 13 strains studied, an increase in ancestral and/or direct irradiation led to significant decreases in fertility. The means of the number alive in the litters for the control and irradiated mice in each strain showed a definite trend toward fewer live mice in utero after irradiation. Least-squares analyses of variance were made to detect possible effects of any of six irradiation variables (ancestral linear, ancestral quadratic, ancestral cubic, direct linear, direct quadratic, or direct cubic) or of strain differences on total litter size and on ratio. Strain effects were significant in each instance. Litter size was more likely to be affected by radiation variables than ratios were

  6. Enzyme functional evolution through improved catalysis of ancestrally nonpreferred substrates

    Science.gov (United States)

    Huang, Ruiqi; Hippauf, Frank; Rohrbeck, Diana; Haustein, Maria; Wenke, Katrin; Feike, Janie; Sorrelle, Noah; Piechulla, Birgit; Barkman, Todd J.

    2012-01-01

    In this study, we investigated the role for ancestral functional variation that may be selected upon to generate protein functional shifts using ancestral protein resurrection, statistical tests for positive selection, forward and reverse evolutionary genetics, and enzyme functional assays. Data are presented for three instances of protein functional change in the salicylic acid/benzoic acid/theobromine (SABATH) lineage of plant secondary metabolite-producing enzymes. In each case, we demonstrate that ancestral nonpreferred activities were improved upon in a daughter enzyme after gene duplication, and that these functional shifts were likely coincident with positive selection. Both forward and reverse mutagenesis studies validate the impact of one or a few sites toward increasing activity with ancestrally nonpreferred substrates. In one case, we document the occurrence of an evolutionary reversal of an active site residue that reversed enzyme properties. Furthermore, these studies show that functionally important amino acid replacements result in substrate discrimination as reflected in evolutionary changes in the specificity constant (kcat/KM) for competing substrates, even though adaptive substitutions may affect KM and kcat separately. In total, these results indicate that nonpreferred, or even latent, ancestral protein activities may be coopted at later times to become the primary or preferred protein activities. PMID:22315396

  7. Mortality among plutonium and other workers at Rocky Flats

    International Nuclear Information System (INIS)

    Wilkinson, G.S.; Acquavella, J.F.; Reyes, M.; Tietjen, G.L.; Wiggs, L.d.; Voelz, G.L.

    1985-01-01

    A detailed study of mortality and radiation exposure for Rocky Flats workers was reported at the Sixteenth Mid-Year Topical Symposium of the Health Physics Society in January 1983. Significantly fewer deaths were found than were expected due to all causes, all malignant neoplasms, lung cancer, and cancer of the digestive organs. No bone cancers were observed and cancers commonly associated with radiation exposure were not more frequent than expected. Significantly more deaths than expected were observed for two causes, cancer of the prostate and benign and unspecified neoplasms. Further investigation revealed that the deaths from benign and unspecified neoplasms all involved intracranial tumors. A case control study found no association between these brain tumors and exposure to radiation, including plutonium depositions or type of occupation. The excess deaths from intracranial tumors remain unexplained but do not appear to be associated with employment at Rocky Flats. Relative risks among Rocky Flats workers with cumulative plutonium depositions of 2 nCi or more did not indicate a significantly greater risk of death among workers exposed to plutonium than among unexposed workers. Similar results were found for workers with cumulative radiation exposure of at least 1 rem. 2 references, 3 tables

  8. Long-range Rocky Flats utilization study

    International Nuclear Information System (INIS)

    1983-02-01

    The purpose of this Study was to provide information concerning the Rocky Flats Plant and its operations that will be useful to the Nation's decision-makers in determining the long-range future of the Plant. This Study was conducted under the premise that national defense policy must be supported and, accordingly, the capabilities at Rocky Flats must be maintained there or at some other location(s). The Study, therefore, makes no attempt to speculate on how possible future changes in national defense policy might affect decisions regarding the utilization of Rocky Flats. Factors pertinent to decisions regarding Rocky Flats, which are included in the Study, are: physical condition of the Plant and its vulnerabilities to natural phenomena; risks associated with plutonium to Plant workers and the public posed by postulated natural phenomena and operational accidents; identification of alternative actions regarding the future use of the Rocky Flats Plant with associated costs and time scales; local socioeconomic impacts if Rocky Flats operations were relocated; and potential for other uses if Rocky Flats facilities were vacated. The results of the tasks performed in support of this Study are summarized in the context of these five factors

  9. Rocky Flats Plant fluidized-bed incinerator

    International Nuclear Information System (INIS)

    Meile, L.J.; Meyer, F.G.; Johnson, A.J.; Ziegler, D.L.

    1982-01-01

    Laboratory and pilot-scale testing of a fluidized-bed incineration process for radioactive wastes led to the installation of an 82-kg/hr demonstration unit at Rocky Flats Plant in 1978. Design philosophy and criteria were formulated to fulfill the needs and objectives of an improved radwaste-incineration system. Unique process concepts include low-temperature (550 0 C), flameless, fluidized-bed combustion and catalytic afterburning; in-situ neutralization of acid gases; and dry off-gas cleanup. Detailed descriptions of the process and equipment are presented along with a summary of the equipment and process performance during a 2-1/2 year operational-testing period. Equipment modifications made during the test period are described. Operating personnel requirements for solid-waste burning are shown to be greater than those required for liquid-waste incineration; differences are discussed. Process-utility and raw-materials consumption rates for full-capacity operation are presented and explained. Improvements in equipment and operating procedures are recommended for any future installations. Process flow diagrams, an area floor plan, a process-control-system schematic, and equipment sketches are included

  10. Isolation of Ancestral Sylvatic Dengue Virus Type 1, Malaysia

    Science.gov (United States)

    Teoh, Boon-Teong; Sam, Sing-Sin; Abd-Jamil, Juraina

    2010-01-01

    Ancestral sylvatic dengue virus type 1, which was isolated from a monkey in 1972, was isolated from a patient with dengue fever in Malaysia. The virus is neutralized by serum of patients with endemic DENV-1 infection. Rare isolation of this virus suggests a limited spillover infection from an otherwise restricted sylvatic cycle. PMID:21029545

  11. An Epistemological Analysis of the African Ontology of `Ancestral ...

    African Journals Online (AJOL)

    The paper explores the contemporary debate surrounding the idea of ancestral reincarnation in African society and philosophy. It analyzes various problem areas having to do with the physical and spiritual status of ancestors, their relationship with their societies of orientation, the philosophical contexts of their existence, ...

  12. Musculature in sipunculan worms: ontogeny and ancestral states.

    Science.gov (United States)

    Schulze, Anja; Rice, Mary E

    2009-01-01

    Molecular phylogenetics suggests that the Sipuncula fall into the Annelida, although they are morphologically very distinct and lack segmentation. To understand the evolutionary transformations from the annelid to the sipunculan body plan, it is important to reconstruct the ancestral states within the respective clades at all life history stages. Here we reconstruct the ancestral states for the head/introvert retractor muscles and the body wall musculature in the Sipuncula using Bayesian statistics. In addition, we describe the ontogenetic transformations of the two muscle systems in four sipunculan species with different developmental modes, using F-actin staining with fluorescent-labeled phalloidin in conjunction with confocal laser scanning microscopy. All four species, which have smooth body wall musculature and less than the full set of four introvert retractor muscles as adults, go through developmental stages with four retractor muscles that are eventually reduced to a lower number in the adult. The circular and sometimes the longitudinal body wall musculature are split into bands that later transform into a smooth sheath. Our ancestral state reconstructions suggest with nearly 100% probability that the ancestral sipunculan had four introvert retractor muscles, longitudinal body wall musculature in bands and circular body wall musculature arranged as a smooth sheath. Species with crawling larvae have more strongly developed body wall musculature than those with swimming larvae. To interpret our findings in the context of annelid evolution, a more solid phylogenetic framework is needed for the entire group and more data on ontogenetic transformations of annelid musculature are desirable.

  13. A comparison of ancestral state reconstruction methods for quantitative characters.

    Science.gov (United States)

    Royer-Carenzi, Manuela; Didier, Gilles

    2016-09-07

    Choosing an ancestral state reconstruction method among the alternatives available for quantitative characters may be puzzling. We present here a comparison of seven of them, namely the maximum likelihood, restricted maximum likelihood, generalized least squares under Brownian, Brownian-with-trend and Ornstein-Uhlenbeck models, phylogenetic independent contrasts and squared parsimony methods. A review of the relations between these methods shows that the maximum likelihood, the restricted maximum likelihood and the generalized least squares under Brownian model infer the same ancestral states and can only be distinguished by the distributions accounting for the reconstruction uncertainty which they provide. The respective accuracy of the methods is assessed over character evolution simulated under a Brownian motion with (and without) directional or stabilizing selection. We give the general form of ancestral state distributions conditioned on leaf states under the simulation models. Ancestral distributions are used first, to give a theoretical lower bound of the expected reconstruction error, and second, to develop an original evaluation scheme which is more efficient than comparing the reconstructed and the simulated states. Our simulations show that: (i) the distributions of the reconstruction uncertainty provided by the methods generally make sense (some more than others); (ii) it is essential to detect the presence of an evolutionary trend and to choose a reconstruction method accordingly; (iii) all the methods show good performances on characters under stabilizing selection; (iv) without trend or stabilizing selection, the maximum likelihood method is generally the most accurate. Copyright © 2016 Elsevier Ltd. All rights reserved.

  14. Modeling X-linked ancestral origins in multiparental populations

    NARCIS (Netherlands)

    Zheng, Chaozhi

    2015-01-01

    The models for the mosaic structure of an individual's genome from multiparental populations have been developed primarily for autosomes, whereas X chromosomes receive very little attention. In this paper, we extend our previous approach to model ancestral origin processes along two X chromosomes

  15. Effects of Climate Change on Cultural Resources in the Northern Rockies Region [Chapter 12

    Science.gov (United States)

    Carl M. Davis

    2018-01-01

    People have inhabited the Northern Rocky Mountains of the United States since the close of the last Pleistocene glacial period, some 14,000 years B.P. (Fagan 1990; Meltzer 2009). Evidence of this ancient and more recent human occupation is found throughout the Forest Service, U.S. Department of Agriculture (USFS) Northern Region and the Greater Yellowstone Area,...

  16. Effects of climate change on ecosystem services in the Northern Rockies Region [Chapter 11

    Science.gov (United States)

    Travis Warziniack; Megan Lawson; S. Karen Dante-Wood

    2018-01-01

    In this chapter, we focus on the ecosystem services provided to people who visit, live adjacent to, or otherwise benefit from natural resources on public lands. Communities in the Forest Service, U.S. Department of Agriculture (USFS) Northern Region and the Greater Yellowstone Area (GYA), hereafter called the Northern Rockies region, are highly dependent on ecosystem...

  17. Historian: accurate reconstruction of ancestral sequences and evolutionary rates.

    Science.gov (United States)

    Holmes, Ian H

    2017-04-15

    Reconstruction of ancestral sequence histories, and estimation of parameters like indel rates, are improved by using explicit evolutionary models and summing over uncertain alignments. The previous best tool for this purpose (according to simulation benchmarks) was ProtPal, but this tool was too slow for practical use. Historian combines an efficient reimplementation of the ProtPal algorithm with performance-improving heuristics from other alignment tools. Simulation results on fidelity of rate estimation via ancestral reconstruction, along with evaluations on the structurally informed alignment dataset BAliBase 3.0, recommend Historian over other alignment tools for evolutionary applications. Historian is available at https://github.com/evoldoers/historian under the Creative Commons Attribution 3.0 US license. ihholmes+historian@gmail.com. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  18. Using Resurrected Ancestral Proviral Proteins to Engineer Virus Resistance

    Directory of Open Access Journals (Sweden)

    Asunción Delgado

    2017-05-01

    Full Text Available Proviral factors are host proteins hijacked by viruses for processes essential for virus propagation such as cellular entry and replication. Pathogens and their hosts co-evolve. It follows that replacing a proviral factor with a functional ancestral form of the same protein could prevent viral propagation without fatally compromising organismal fitness. Here, we provide proof of concept of this notion. Thioredoxins serve as general oxidoreductases in all known cells. We report that several laboratory resurrections of Precambrian thioredoxins display substantial levels of functionality within Escherichia coli. Unlike E. coli thioredoxin, however, these ancestral thioredoxins are not efficiently recruited by the bacteriophage T7 for its replisome and therefore prevent phage propagation in E. coli. These results suggest an approach to the engineering of virus resistance. Diseases caused by viruses may have a devastating effect in agriculture. We discuss how the suggested approach could be applied to the engineering of plant virus resistance.

  19. Perianth evolution in Ranunculaceae: are petals ancestral in the family?

    Directory of Open Access Journals (Sweden)

    Sophie Nadot

    2016-04-01

    Full Text Available Progress has been made recently towards the elucidation of phylogenetic relationships among subfamilies and tribes of the Ranunculaceae – the most recent hypothesis was published in 2016 by our team. Although relationships among the 10 tribes of the subfamily Ranunculoideae remain incompletely supported, this hypothesis provides an interesting framework to address the key issue of the ancestral vs. derived nature of a differentiated perianth within the family, and at the level of Ranunculales as a whole. Here, we present ancestral state reconstructions for several perianth characters, such as differentiation into sepals and petals, shape of petals, presence/absence of nectaries, and petaloid or sepaloid aspect of sepals. Characters were scored using the PROTEUS database and optimized on the most recent phylogeny of Ranunculaceae using parsimony and maximum likelihood methods. The results are discussed with regard to recent evo-devo studies focused on identifying genes involved in floral organs identity (the so-called ABC model in Ranunculales.

  20. The ancestral selection graph under strong directional selection.

    Science.gov (United States)

    Pokalyuk, Cornelia; Pfaffelhuber, Peter

    2013-08-01

    The ancestral selection graph (ASG) was introduced by  Neuhauser and Krone (1997) in order to study populations of constant size which evolve under selection. Coalescence events, which occur at rate 1 for every pair of lines, lead to joint ancestry. In addition, splitting events in the ASG at rate α, the scaled selection coefficient, produce possible ancestors, such that the real ancestor depends on the ancestral alleles. Here, we use the ASG in the case without mutation in order to study fixation of a beneficial mutant. Using our main tool, a reversibility property of the ASG, we provide a new proof of the fact that a beneficial allele fixes roughly in time (2logα)/α if α is large. Copyright © 2012 Elsevier Inc. All rights reserved.

  1. Prenatal effects of ancestral irradiation in inbred mice

    International Nuclear Information System (INIS)

    Sprackling, L.E.S.

    1975-01-01

    Mice from 13 inbred strains (S, Z, E, Bab, BaB, BrR, C, K, N, Q, G, CFW, CF1) received continuous cobalt 60 irradiation at low dose rates for varying numbers of consecutive generations. Some Bab and BaB mice had received continuous irradiation for from 24 to 31 generations and the other mice had up to six generations of continuous irradiation in their ancestry. At weaning, the mice were removed from the irradiation room and were mated within strains either to sibs or nonsibs. Ancestral and direct irradiation doses were calculated. The ancestral dose was the effective accumulated dose to the progeny of the mated mice. The direct dose was the amount of irradiation received by any mated female from her conception to her weaning. Each irradiated or control female was scored as fertile or sterile and in utero litter counts were made in pregnant females that were dissected past the tenth day of pregnancy; the sum of moles, dead embryos, and live embryos was the total in utero litter size. A ratio of the living embryos to the total number of embryos in utero was determined for each litter. An increase in ancestral or direct irradiation dose significantly decreased fertility in 11 of the 13 strains. The fertility curves for the pooled data were sigmoid in the area of the doses below those that caused complete sterility. Among the controls, there were significant strain differences in total litter size and in the ratio. Strain X--Y plots, with ancestral or direct doses plotted against total litter size or ratio, revealed the tendency for litter size to decrease as dose increased. The only trend shown for ratio was for the litters with ratios of 0.50 or less to appear more frequently among the irradiated mice. The few corpora lutea counts revealed nothing of significance. Generally, there was a definite trend toward fewer mice alive in utero among the irradiated mice

  2. Ancestrality and evolution of trait syndromes in finches (Fringillidae)

    OpenAIRE

    Ponge, Jean‐François; Zuccon, Dario; Elias, Marianne; Pavoine, Sandrine; Henry, Pierre‐Yves; Théry, Marc; Guilbert, Éric

    2017-01-01

    International audience; Species traits have been hypothesized by one of us (Ponge, 2013) to evolve in a correlated manner as species colonize stable, undisturbed habitats, shifting from “ancestral” to “derived” strategies. We predicted that generalism, r-selection, sexual monomorphism, and migration/gregariousness are the ancestral states (collectively called strategy A) and evolved correlatively toward specialism, K-selection, sexual dimorphism, and residence/territoriality as habitat stabil...

  3. Reconstruction of ancestral RNA sequences under multiple structural constraints

    OpenAIRE

    Tremblay-Savard, Olivier; Reinharz, Vladimir; Waldisp?hl, J?r?me

    2016-01-01

    Background Secondary structures form the scaffold of multiple sequence alignment of non-coding RNA (ncRNA) families. An accurate reconstruction of ancestral ncRNAs must use this structural signal. However, the inference of ancestors of a single ncRNA family with a single consensus structure may bias the results towards sequences with high affinity to this structure, which are far from the true ancestors. Methods In this paper, we introduce achARNement, a maximum parsimony approach that, given...

  4. Infant and juvenile growth in ancestral Pueblo Indians.

    Science.gov (United States)

    Schillaci, Michael A; Nikitovic, Dejana; Akins, Nancy J; Tripp, Lianne; Palkovich, Ann M

    2011-06-01

    The present study examines patterns of infant and juvenile growth in a diachronic sample of ancestral Pueblo Indians (AD 1300-1680) from the American Southwest. An assessment of growth patterns is accompanied by an evaluation of pathological conditions often considered to be indicators of nutritional deficiencies and/or gastrointestinal infections. Growth patterns and the distribution of pathological conditions are interpreted relative to culturally relevant age categories defined by Puebloan rites of passage described in the ethnographic literature. A visual comparison of growth distance curves revealed that relative to a modern comparative group our sample of ancestral Pueblo infant and juveniles exhibited faltering growth beginning soon after birth to about 5 years of age. A comparison of curves describing growth relative to adult femoral length, however, indicated reduced growth occurring later, by around 2 years of age. Similar to previous studies, we observed a high proportion of nonsurvivors exhibiting porotic cranial lesions during the first 2 years of life. Contrary to expectations, infants and juveniles without evidence of porotic cranial lesions exhibited a higher degree of stunting. Our study is generally consistent with previous research reporting poor health and high mortality for ancestral Pueblo Indian infants and juveniles. Through use of a culturally relevant context defining childhood, we argue that the observed poor health and high mortality in our sample occur before the important transition from young to older child and the concomitant initial incorporation into tribal ritual organization. Copyright © 2011 Wiley-Liss, Inc.

  5. Cases in which ancestral maximum likelihood will be confusingly misleading.

    Science.gov (United States)

    Handelman, Tomer; Chor, Benny

    2017-05-07

    Ancestral maximum likelihood (AML) is a phylogenetic tree reconstruction criteria that "lies between" maximum parsimony (MP) and maximum likelihood (ML). ML has long been known to be statistically consistent. On the other hand, Felsenstein (1978) showed that MP is statistically inconsistent, and even positively misleading: There are cases where the parsimony criteria, applied to data generated according to one tree topology, will be optimized on a different tree topology. The question of weather AML is statistically consistent or not has been open for a long time. Mossel et al. (2009) have shown that AML can "shrink" short tree edges, resulting in a star tree with no internal resolution, which yields a better AML score than the original (resolved) model. This result implies that AML is statistically inconsistent, but not that it is positively misleading, because the star tree is compatible with any other topology. We show that AML is confusingly misleading: For some simple, four taxa (resolved) tree, the ancestral likelihood optimization criteria is maximized on an incorrect (resolved) tree topology, as well as on a star tree (both with specific edge lengths), while the tree with the original, correct topology, has strictly lower ancestral likelihood. Interestingly, the two short edges in the incorrect, resolved tree topology are of length zero, and are not adjacent, so this resolved tree is in fact a simple path. While for MP, the underlying phenomenon can be described as long edge attraction, it turns out that here we have long edge repulsion. Copyright © 2017. Published by Elsevier Ltd.

  6. Choosing the best ancestral character state reconstruction method.

    Science.gov (United States)

    Royer-Carenzi, Manuela; Pontarotti, Pierre; Didier, Gilles

    2013-03-01

    Despite its intrinsic difficulty, ancestral character state reconstruction is an essential tool for testing evolutionary hypothesis. Two major classes of approaches to this question can be distinguished: parsimony- or likelihood-based approaches. We focus here on the second class of methods, more specifically on approaches based on continuous-time Markov modeling of character evolution. Among them, we consider the most-likely-ancestor reconstruction, the posterior-probability reconstruction, the likelihood-ratio method, and the Bayesian approach. We discuss and compare the above-mentioned methods over several phylogenetic trees, adding the maximum-parsimony method performance in the comparison. Under the assumption that the character evolves according a continuous-time Markov process, we compute and compare the expectations of success of each method for a broad range of model parameter values. Moreover, we show how the knowledge of the evolution model parameters allows to compute upper bounds of reconstruction performances, which are provided as references. The results of all these reconstruction methods are quite close one to another, and the expectations of success are not so far from their theoretical upper bounds. But the performance ranking heavily depends on the topology of the studied tree, on the ancestral node that is to be inferred and on the parameter values. Consequently, we propose a protocol providing for each parameter value the best method in terms of expectation of success, with regard to the phylogenetic tree and the ancestral node to infer. Copyright © 2012 Elsevier Inc. All rights reserved.

  7. A case of Rocky Mountain spotted fever.

    Science.gov (United States)

    Rubel, Barry S

    2007-01-01

    Rocky Mountain spotted fever is a serious, generalized infection that is spread to humans through the bite of infected ticks. It can be lethal but it is curable. The disease gets its name from the Rocky Mountain region where it was first identified in 1896. The fever is caused by the bacterium Rickettsia rickettsii and is maintained in nature in a complex life cycle involving ticks and mammals. Humans are considered to be accidental hosts and are not involved in the natural transmission cycle of this pathogen. The author examined a 47-year-old woman during a periodic recall appointment. The patient had no dental problems other than the need for routine prophylaxis but mentioned a recent problem with swelling of her extremities with an accompanying rash and general malaise and soreness in her neck region. Tests were conducted and a diagnosis of Rocky Mountain spotted fever was made.

  8. Issues evaluation process at Rocky Flats Plant

    International Nuclear Information System (INIS)

    Smith, L.C.

    1992-01-01

    This report describes the issues evaluation process for Rocky Flats Plant as established in July 1990. The issues evaluation process was initiated February 27, 1990 with a Charter and Process Overview for short-term implementation. The purpose of the process was to determine the projects required for completion before the Phased Resumption of Plutonium Operations. To determine which projects were required, the issues evaluation process and emphasized risk mitigation, based on a ranking system. The purpose of this report is to document the early design of the issues evaluation process to record the methodologies used that continue as the basis for the ongoing Issues Management Program at Rocky Flats Plant

  9. Canadian Rockies Ecoregion: Chapter 4 in Status and trends of land change in the Western United States--1973 to 2000

    Science.gov (United States)

    Taylor, Janis L.

    2012-01-01

    The Canadian Rockies Ecoregion covers approximately 18,494 km2 (7,141 mi2) in northwestern Montana (Omernik, 1987; U.S. Environmental Protection Agency, 1997). The east side of the ecoregion is bordered by the Montana Valley and Foothill Prairies Ecoregion, which also forms a large part of the western border of the ecoregion. In addition, the Northern Rockies Ecoregion wraps around the ecoregion to the northwest and south (fig. 1). As the name implies, the Canadian Rocky Mountains are located mostly in Canada, straddling the border between Alberta and British Columbia. However, this ecoregion only includes the part of the northern Rocky Mountains that is in the United States. This ecoregion is characterized by steep, high-elevation mountain ranges similar to most of the rest of the Rocky Mountains. Compared to the Northern Rockies Ecoregion, however, the Canadian Rockies Ecoregion reaches higher elevations and contains a greater proportion of perennial snow and ice (Omernik, 1987) (fig. 2). Over the years, this section of the Rocky Mountains has garnered many different names, including “Crown of the Continent” by George Bird Grinnell (Waldt, 2008) and “Backbone of the World” by the Blackfeet (Pikuni) Nation. Throughout the ecoregion, montane, subalpine, and alpine ecosystems have distinct flora and fauna elevation zones. Glaciers, permanent snowfields, and seasonal snowpack are found at the highest elevations. Spring and summer runoff fills lakes and tarns that form the headwaters of numerous streams and rivers, including the Columbia and Missouri Rivers that flow west and east, respectively, from the Continental Divide.

  10. Effects of ancestral x irradiation followed by random mating on body weight of rats

    International Nuclear Information System (INIS)

    Gianola, D.; Chapman, A.B.; Rutledge, J.J.

    1977-01-01

    Effects of nine generations of 450R per generation of ancestral spermatogonial x irradiation of inbred rats on body weight were examined. After six generations of random mating (avoiding inbreeding) following the termination of irradiation, descendants of irradiated males (R) were significantly lighter than their controls (C) at 3 and 6 weeks, but not at 10 weeks of age. However, differences in growth between R and C populations were small. Among-litter and within-litter variance estimates were generally larger in the R lines than in the C lines, suggesting that selection responses would be greater in R than in C lines. In conjunction with previous evidence--obtained during the irradiation phase of the experiment--this suggested that more rapid response to selection for 6-week body weight, in particular, might accrue in the R lines

  11. Limber pine health in the Canadian Rockies

    Science.gov (United States)

    Cyndi M. Smith; David Langor; Colin Myrholm; Jim Weber; Cameron Gillies; Jon Stuart-Smith

    2011-01-01

    Limber pine (Pinus flexilis) reaches the northern limit of its range at about 52 degrees latitude in Alberta (AB) and 51 degrees latitude in British Columbia (BC). Most populations are found on the eastern slopes of the Rocky Mountains, with a few disjunct populations west of the Continental Divide in southeastern BC.

  12. Rocky Mountain spotted fever in dogs, Brazil.

    Science.gov (United States)

    Labruna, Marcelo B; Kamakura, Orson; Moraes-Filho, Jonas; Horta, Mauricio C; Pacheco, Richard C

    2009-03-01

    Clinical illness caused by Rickettsia rickettsii in dogs has been reported solely in the United States. We report 2 natural clinical cases of Rocky Mountain spotted fever in dogs in Brazil. Each case was confirmed by seroconversion and molecular analysis and resolved after doxycycline therapy.

  13. Visual system evolution and the nature of the ancestral snake.

    Science.gov (United States)

    Simões, B F; Sampaio, F L; Jared, C; Antoniazzi, M M; Loew, E R; Bowmaker, J K; Rodriguez, A; Hart, N S; Hunt, D M; Partridge, J C; Gower, D J

    2015-07-01

    The dominant hypothesis for the evolutionary origin of snakes from 'lizards' (non-snake squamates) is that stem snakes acquired many snake features while passing through a profound burrowing (fossorial) phase. To investigate this, we examined the visual pigments and their encoding opsin genes in a range of squamate reptiles, focusing on fossorial lizards and snakes. We sequenced opsin transcripts isolated from retinal cDNA and used microspectrophotometry to measure directly the spectral absorbance of the photoreceptor visual pigments in a subset of samples. In snakes, but not lizards, dedicated fossoriality (as in Scolecophidia and the alethinophidian Anilius scytale) corresponds with loss of all visual opsins other than RH1 (λmax 490-497 nm); all other snakes (including less dedicated burrowers) also have functional sws1 and lws opsin genes. In contrast, the retinas of all lizards sampled, even highly fossorial amphisbaenians with reduced eyes, express functional lws, sws1, sws2 and rh1 genes, and most also express rh2 (i.e. they express all five of the visual opsin genes present in the ancestral vertebrate). Our evidence of visual pigment complements suggests that the visual system of stem snakes was partly reduced, with two (RH2 and SWS2) of the ancestral vertebrate visual pigments being eliminated, but that this did not extend to the extreme additional loss of SWS1 and LWS that subsequently occurred (probably independently) in highly fossorial extant scolecophidians and A. scytale. We therefore consider it unlikely that the ancestral snake was as fossorial as extant scolecophidians, whether or not the latter are para- or monophyletic. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

  14. Ancestral Variations in the Shape and Size of the Zygoma.

    Science.gov (United States)

    Oettlé, Anna C; Demeter, Fabrice P; L'abbé, Ericka N

    2017-01-01

    The variable development of the zygoma, dictating its shape and size variations among ancestral groups, has important clinical implications and valuable anthropological and evolutionary inferences. The purpose of the study was to review the literature regarding the variations in the zygoma with ancestry. Ancestral variation in the zygoma reflects genetic variations because of genetic drift as well as natural selection and epigenetic changes to adapt to diet and climate variations with possible intensification by isolation. Prominence of the zygoma, zygomaxillary tuberosity, and malar tubercle have been associated with Eastern Asian populations in whom these features intensified. Prominence of the zygoma is also associated with groups from Eastern Europe and the rest of Asia. Diffusion of these traits occurred across the Behring Sea to the Arctic areas and to North and South America. The greatest zygomatic projections are exhibited in Arctic groups as an adaptation to extreme cold conditions, while Native South American groups also present with other features of facial robusticity. Groups from Australia, Malaysia, and Oceania show prominence of the zygoma to a certain extent, possibly because of archaic occupations by undifferentiated Southeast Asian populations. More recent interactions with Chinese groups might explain the prominent cheekbones noted in certain South African groups. Many deductions regarding evolutionary processes and diversifications of early groups have been made. Cognisance of these ancestral variations also have implications for forensic anthropological assessments as well as plastic and reconstructive surgery. More studies are needed to improve accuracy of forensic anthropological identification techniques. Anat Rec, 300:196-208, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  15. Effectiveness of ancestral irradiation on the direct and correlated responses to selection for body weight in rats

    International Nuclear Information System (INIS)

    Gianola, D.

    1975-01-01

    The effects of ancestral irradiation of rat spermatogonia (a cumulative total of 4050 r of x-rays) were studied in a highly inbred line of rats to explore the feasibility of using irradiation to enhance the effectiveness of selection. Six generations after irradiation was terminated, a selection experiment for body weight at six weeks of age was started in both ancestrally irradiated and non-irradiated populations. There were two non-contemporaneous replicates in each of the populations. Within each of the ancestral treatment-replicate combinations one line was selected for high, one for low body weight at six weeks of age, and a third line was maintained by random selection. In each line, avoidance of mating of animals with grandparents in common was attempted. Data on the first ten progeny generations of selection were included in this study. Five types of covariances among relatives were used to estimate causal components of variance for five different genetic models within the ''non-irradiated'' and ''irradiated'' randomly selected models. The parameters in the genetic models were estimated by generalized least-squares. This analysis suggested that a genetic model including direct genetic and maternal genetic effects was adequate to describe the body weights at 3, 6 and 10 weeks of age and the weight gains between these ages. Ancestral irradiation seemed to have enhanced the maternal genetic variance and the covariance between the direct genetic and the maternal genetic effects. On the basis of the above analysis, it was deduced that mass selection should have been more effective in the descendants of irradiated males than in those of the non-irradiated males as a consequence of greater phenotypic variability in their progeny and an enhancement in the regression of the genetic value on the selection criterion

  16. Using Resurrected Ancestral Proviral Proteins to Engineer Virus Resistance.

    Science.gov (United States)

    Delgado, Asunción; Arco, Rocio; Ibarra-Molero, Beatriz; Sanchez-Ruiz, Jose M

    2017-05-09

    Proviral factors are host proteins hijacked by viruses for processes essential for virus propagation such as cellular entry and replication. Pathogens and their hosts co-evolve. It follows that replacing a proviral factor with a functional ancestral form of the same protein could prevent viral propagation without fatally compromising organismal fitness. Here, we provide proof of concept of this notion. Thioredoxins serve as general oxidoreductases in all known cells. We report that several laboratory resurrections of Precambrian thioredoxins display substantial levels of functionality within Escherichia coli. Unlike E. coli thioredoxin, however, these ancestral thioredoxins are not efficiently recruited by the bacteriophage T7 for its replisome and therefore prevent phage propagation in E. coli. These results suggest an approach to the engineering of virus resistance. Diseases caused by viruses may have a devastating effect in agriculture. We discuss how the suggested approach could be applied to the engineering of plant virus resistance. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  17. Reconstruction of ancestral RNA sequences under multiple structural constraints

    Directory of Open Access Journals (Sweden)

    Olivier Tremblay-Savard

    2016-11-01

    Full Text Available Abstract Background Secondary structures form the scaffold of multiple sequence alignment of non-coding RNA (ncRNA families. An accurate reconstruction of ancestral ncRNAs must use this structural signal. However, the inference of ancestors of a single ncRNA family with a single consensus structure may bias the results towards sequences with high affinity to this structure, which are far from the true ancestors. Methods In this paper, we introduce achARNement, a maximum parsimony approach that, given two alignments of homologous ncRNA families with consensus secondary structures and a phylogenetic tree, simultaneously calculates ancestral RNA sequences for these two families. Results We test our methodology on simulated data sets, and show that achARNement outperforms classical maximum parsimony approaches in terms of accuracy, but also reduces by several orders of magnitude the number of candidate sequences. To conclude this study, we apply our algorithms on the Glm clan and the FinP-traJ clan from the Rfam database. Conclusions Our results show that our methods reconstruct small sets of high-quality candidate ancestors with better agreement to the two target structures than with classical approaches. Our program is freely available at: http://csb.cs.mcgill.ca/acharnement .

  18. Reconstruction of ancestral RNA sequences under multiple structural constraints.

    Science.gov (United States)

    Tremblay-Savard, Olivier; Reinharz, Vladimir; Waldispühl, Jérôme

    2016-11-11

    Secondary structures form the scaffold of multiple sequence alignment of non-coding RNA (ncRNA) families. An accurate reconstruction of ancestral ncRNAs must use this structural signal. However, the inference of ancestors of a single ncRNA family with a single consensus structure may bias the results towards sequences with high affinity to this structure, which are far from the true ancestors. In this paper, we introduce achARNement, a maximum parsimony approach that, given two alignments of homologous ncRNA families with consensus secondary structures and a phylogenetic tree, simultaneously calculates ancestral RNA sequences for these two families. We test our methodology on simulated data sets, and show that achARNement outperforms classical maximum parsimony approaches in terms of accuracy, but also reduces by several orders of magnitude the number of candidate sequences. To conclude this study, we apply our algorithms on the Glm clan and the FinP-traJ clan from the Rfam database. Our results show that our methods reconstruct small sets of high-quality candidate ancestors with better agreement to the two target structures than with classical approaches. Our program is freely available at: http://csb.cs.mcgill.ca/acharnement .

  19. Greater autonomy at work

    NARCIS (Netherlands)

    Houtman, I.L.D.

    2004-01-01

    In the past 10 years, workers in the Netherlands increasingly report more decision-making power in their work. This is important for an economy in recession and where workers face greater work demands. It makes work more interesting, creates a healthier work environment, and provides opportunities

  20. Resurrecting ancestral genes in bacteria to interpret ancient biosignatures

    Science.gov (United States)

    Kacar, Betul; Guy, Lionel; Smith, Eric; Baross, John

    2017-11-01

    Two datasets, the geologic record and the genetic content of extant organisms, provide complementary insights into the history of how key molecular components have shaped or driven global environmental and macroevolutionary trends. Changes in global physico-chemical modes over time are thought to be a consistent feature of this relationship between Earth and life, as life is thought to have been optimizing protein functions for the entirety of its approximately 3.8 billion years of history on the Earth. Organismal survival depends on how well critical genetic and metabolic components can adapt to their environments, reflecting an ability to optimize efficiently to changing conditions. The geologic record provides an array of biologically independent indicators of macroscale atmospheric and oceanic composition, but provides little in the way of the exact behaviour of the molecular components that influenced the compositions of these reservoirs. By reconstructing sequences of proteins that might have been present in ancient organisms, we can downselect to a subset of possible sequences that may have been optimized to these ancient environmental conditions. How can one use modern life to reconstruct ancestral behaviours? Configurations of ancient sequences can be inferred from the diversity of extant sequences, and then resurrected in the laboratory to ascertain their biochemical attributes. One way to augment sequence-based, single-gene methods to obtain a richer and more reliable picture of the deep past, is to resurrect inferred ancestral protein sequences in living organisms, where their phenotypes can be exposed in a complex molecular-systems context, and then to link consequences of those phenotypes to biosignatures that were preserved in the independent historical repository of the geological record. As a first step beyond single-molecule reconstruction to the study of functional molecular systems, we present here the ancestral sequence reconstruction of the

  1. Inferring genome-wide patterns of admixture in Qataris using fifty-five ancestral populations

    Directory of Open Access Journals (Sweden)

    Omberg Larsson

    2012-06-01

    Full Text Available Abstract Background Populations of the Arabian Peninsula have a complex genetic structure that reflects waves of migrations including the earliest human migrations from Africa and eastern Asia, migrations along ancient civilization trading routes and colonization history of recent centuries. Results Here, we present a study of genome-wide admixture in this region, using 156 genotyped individuals from Qatar, a country located at the crossroads of these migration patterns. Since haplotypes of these individuals could have originated from many different populations across the world, we have developed a machine learning method "SupportMix" to infer loci-specific genomic ancestry when simultaneously analyzing many possible ancestral populations. Simulations show that SupportMix is not only more accurate than other popular admixture discovery tools but is the first admixture inference method that can efficiently scale for simultaneous analysis of 50-100 putative ancestral populations while being independent of prior demographic information. Conclusions By simultaneously using the 55 world populations from the Human Genome Diversity Panel, SupportMix was able to extract the fine-scale ancestry of the Qatar population, providing many new observations concerning the ancestry of the region. For example, as well as recapitulating the three major sub-populations in Qatar, composed of mainly Arabic, Persian, and African ancestry, SupportMix additionally identifies the specific ancestry of the Persian group to populations sampled in Greater Persia rather than from China and the ancestry of the African group to sub-Saharan origin and not Southern African Bantu origin as previously thought.

  2. Release fractions for Rocky Flats specific accidents

    International Nuclear Information System (INIS)

    Weiss, R.C.

    1992-01-01

    As Rocky Flats and other DOE facilities begin the transition process towards decommissioning, the nature of the scenarios to be studied in safety analysis will change. Whereas the previous emphasis in safety accidents related to production, now the emphasis is shifting to accidents related tc decommissioning and waste management. Accident scenarios of concern at Rocky Flats now include situations of a different nature and different scale than are represented by most of the existing experimental accident data. This presentation will discuss approaches at sign to use for applying the existing body of release fraction data to this new emphasis. Mention will also be made of ongoing efforts to produce new data and improve the understanding of physical mechanisms involved

  3. History of Rocky Flats waste streams

    International Nuclear Information System (INIS)

    Luckett, L.L.; Dickman, A.A.; Wells, C.R.; Vickery, D.J.

    1982-01-01

    An analysis of the waste streams at Rocky Flats was done to provide information for the Waste Certification program. This program has involved studying the types and amounts of retrievable transuranic (TRU) waste from Rocky Flats that is stored at the Idaho National Engineering Laboratory (INEL). The information can be used to estimate the types and amounts of waste that will need to be permanently stored in the Waste Isolation Pilot Plant (WIPP). The study covered mostly the eight-year period from June 1971 to June 1979. The types, amounts, and plutonium content of TRU waste and the areas or operations responsible for generating the waste are summarized in this waste stream history report. From the period studied, a total of 24,546,153 lbs of waste containing 211,148 g of plutonium currently occupies 709,497 cu ft of storage space at INEL

  4. Rocky Flats cleanup receives new deadline

    International Nuclear Information System (INIS)

    Anon.

    1993-01-01

    The Rocky Flats nuclear weapon plant near Denver narrowly missed a court-ordered shutdown of virtually all cleanup activities when it failed to meet an Aug. 22 deadline for a state permit to store mixed radioactive and hazardous wastes on site. US District Court Judge Lewis Babcock granted a 90-day stay of contempt charges against the US Dept. of Energy, but left open the possibility of civil penalties under the Resource Conservation and Recovery Act. DOE's problems stem from a lawsuit the Sierra Club won two years ago in which Babcock gave Rocky Flats until Aug. 22 to obtain a RCRA permit or interim status from Colorado to store 600 cu yd of mixed wastes. If DOE failed to do so, the court said it could not generate further hazardous wastes at the site

  5. Rocky Mountain spotted fever: a clinician's dilemma.

    Science.gov (United States)

    Masters, Edwin J; Olson, Gary S; Weiner, Scott J; Paddock, Christopher D

    2003-04-14

    Rocky Mountain spotted fever is still the most lethal tick-vectored illness in the United States. We examine the dilemmas facing the clinician who is evaluating the patient with possible Rocky Mountain spotted fever, with particular attention to the following 8 pitfalls in diagnosis and treatment: (1) waiting for a petechial rash to develop before diagnosis; (2) misdiagnosing as gastroenteritis; (3) discounting a diagnosis when there is no history of a tick bite; (4) using an inappropriate geographic exclusion; (5) using an inappropriate seasonal exclusion; (6) failing to treat on clinical suspicion; (7) failing to elicit an appropriate history; and (8) failing to treat with doxycycline. Early diagnosis and proper treatment save lives.

  6. THERMODYNAMIC LIMITS ON MAGNETODYNAMOS IN ROCKY EXOPLANETS

    International Nuclear Information System (INIS)

    Gaidos, Eric; Conrad, Clinton P.; Manga, Michael; Hernlund, John

    2010-01-01

    To ascertain whether magnetic dynamos operate in rocky exoplanets more massive or hotter than the Earth, we developed a parametric model of a differentiated rocky planet and its thermal evolution. Our model reproduces the established properties of Earth's interior and magnetic field at the present time. When applied to Venus, assuming that planet lacks plate tectonics and has a dehydrated mantle with an elevated viscosity, the model shows that the dynamo shuts down or never operated. Our model predicts that at a fixed planet mass, dynamo history is sensitive to core size, but not to the initial inventory of long-lived, heat-producing radionuclides. It predicts that rocky planets larger than 2.5 Earth masses will not develop inner cores because the temperature-pressure slope of the iron solidus becomes flatter than that of the core adiabat. Instead, iron 'snow' will condense near or at the top of these cores, and the net transfer of latent heat upward will suppress convection and a dynamo. More massive planets can have anemic dynamos due to core cooling, but only if they have mobile lids (plate tectonics). The lifetime of these dynamos is shorter with increasing planet mass but longer with higher surface temperature. Massive Venus-like planets with stagnant lids and more viscous mantles will lack dynamos altogether. We identify two alternative sources of magnetic fields on rocky planets: eddy currents induced in the hot or molten upper layers of planets on very short-period orbits, and dynamos in the ionic conducting layers of 'ocean' planets with ∼10% mass in an upper mantle of water (ice).

  7. Basic TRUEX process for Rocky Flats Plant

    International Nuclear Information System (INIS)

    Leonard, R.A.; Chamberlain, D.B.; Dow, J.A.; Farley, S.E.; Nunez, L.; Regalbuto, M.C.; Vandegrift, G.F.

    1994-08-01

    The Generic TRUEX Model was used to develop a TRUEX process flowsheet for recovering the transuranics (Pu, Am) from a nitrate waste stream at Rocky Flats Plant. The process was designed so that it is relatively insensitive to changes in process feed concentrations and flow rates. Related issues are considered, including solvent losses, feed analysis requirements, safety, and interaction with an evaporator system for nitric acid recycle

  8. Microwave solidification development for Rocky Flats waste

    Energy Technology Data Exchange (ETDEWEB)

    Dixon, D.; Erle, R.; Eschen, V. [and others

    1994-04-01

    The Microwave Engineering Team at the Rocky Flats Plant has developed a production-scale system for the treatment of hazardous, radioactive, and mixed wastes using microwave energy. The system produces a vitreous final form which meets the acceptance criteria for shipment and disposal. The technology also has potential for application on various other waste streams from the public and private sectors. Technology transfer opportunities are being identified and pursued for commercialization of the microwave solidification technology.

  9. Microwave solidification development for Rocky Flats waste

    International Nuclear Information System (INIS)

    Dixon, D.; Erle, R.; Eschen, V.

    1994-04-01

    The Microwave Engineering Team at the Rocky Flats Plant has developed a production-scale system for the treatment of hazardous, radioactive, and mixed wastes using microwave energy. The system produces a vitreous final form which meets the acceptance criteria for shipment and disposal. The technology also has potential for application on various other waste streams from the public and private sectors. Technology transfer opportunities are being identified and pursued for commercialization of the microwave solidification technology

  10. Computational analysis and functional expression of ancestral copepod luciferase.

    Science.gov (United States)

    Takenaka, Yasuhiro; Noda-Ogura, Akiko; Imanishi, Tadashi; Yamaguchi, Atsushi; Gojobori, Takashi; Shigeri, Yasushi

    2013-10-10

    We recently reported the cDNA sequences of 11 copepod luciferases from the superfamily Augaptiloidea in the order Calanoida. They were classified into two groups, Metridinidae and Heterorhabdidae/Lucicutiidae families, by phylogenetic analyses. To elucidate the evolutionary processes, we have now further isolated 12 copepod luciferases from Augaptiloidea species (Metridia asymmetrica, Metridia curticauda, Pleuromamma scutullata, Pleuromamma xiphias, Lucicutia ovaliformis and Heterorhabdus tanneri). Codon-based synonymous/nonsynonymous tests of positive selection for 25 identified copepod luciferases suggested that positive Darwinian selection operated in the evolution of Heterorhabdidae luciferases, whereas two types of Metridinidae luciferases had diversified via neutral mechanism. By in silico analysis of the decoded amino acid sequences of 25 copepod luciferases, we inferred two protein sequences as ancestral copepod luciferases. They were expressed in HEK293 cells where they exhibited notable luciferase activity both in intracellular lysates and cultured media, indicating that the luciferase activity was established before evolutionary diversification of these copepod species. © 2013.

  11. Ancestral dichlorodiphenyltrichloroethane (DDT) exposure promotes epigenetic transgenerational inheritance of obesity

    Science.gov (United States)

    2013-01-01

    Background Ancestral environmental exposures to a variety of environmental factors and toxicants have been shown to promote the epigenetic transgenerational inheritance of adult onset disease. The present work examined the potential transgenerational actions of the insecticide dichlorodiphenyltrichloroethane (DDT) on obesity and associated disease. Methods Outbred gestating female rats were transiently exposed to a vehicle control or DDT and the F1 generation offspring bred to generate the F2 generation and F2 generation bred to generate the F3 generation. The F1 and F3 generation control and DDT lineage rats were aged and various pathologies investigated. The F3 generation male sperm were collected to investigate methylation between the control and DDT lineage male sperm. Results The F1 generation offspring (directly exposed as a fetus) derived from the F0 generation exposed gestating female rats were not found to develop obesity. The F1 generation DDT lineage animals did develop kidney disease, prostate disease, ovary disease and tumor development as adults. Interestingly, the F3 generation (great grand-offspring) had over 50% of males and females develop obesity. Several transgenerational diseases previously shown to be associated with metabolic syndrome and obesity were observed in the testis, ovary and kidney. The transgenerational transmission of disease was through both female (egg) and male (sperm) germlines. F3 generation sperm epimutations, differential DNA methylation regions (DMR), induced by DDT were identified. A number of the genes associated with the DMR have previously been shown to be associated with obesity. Conclusions Observations indicate ancestral exposure to DDT can promote obesity and associated disease transgenerationally. The etiology of disease such as obesity may be in part due to environmentally induced epigenetic transgenerational inheritance. PMID:24228800

  12. Palaeohistological Evidence for Ancestral High Metabolic Rate in Archosaurs.

    Science.gov (United States)

    Legendre, Lucas J; Guénard, Guillaume; Botha-Brink, Jennifer; Cubo, Jorge

    2016-11-01

    Metabolic heat production in archosaurs has played an important role in their evolutionary radiation during the Mesozoic, and their ancestral metabolic condition has long been a matter of debate in systematics and palaeontology. The study of fossil bone histology provides crucial information on bone growth rate, which has been used to indirectly investigate the evolution of thermometabolism in archosaurs. However, no quantitative estimation of metabolic rate has ever been performed on fossils using bone histological features. Moreover, to date, no inference model has included phylogenetic information in the form of predictive variables. Here we performed statistical predictive modeling using the new method of phylogenetic eigenvector maps on a set of bone histological features for a sample of extant and extinct vertebrates, to estimate metabolic rates of fossil archosauromorphs. This modeling procedure serves as a case study for eigenvector-based predictive modeling in a phylogenetic context, as well as an investigation of the poorly known evolutionary patterns of metabolic rate in archosaurs. Our results show that Mesozoic theropod dinosaurs exhibit metabolic rates very close to those found in modern birds, that archosaurs share a higher ancestral metabolic rate than that of extant ectotherms, and that this derived high metabolic rate was acquired at a much more inclusive level of the phylogenetic tree, among non-archosaurian archosauromorphs. These results also highlight the difficulties of assigning a given heat production strategy (i.e., endothermy, ectothermy) to an estimated metabolic rate value, and confirm findings of previous studies that the definition of the endotherm/ectotherm dichotomy may be ambiguous. © The Author(s) 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  13. Greater-confinement disposal

    International Nuclear Information System (INIS)

    Trevorrow, L.E.; Schubert, J.P.

    1989-01-01

    Greater-confinement disposal (GCD) is a general term for low-level waste (LLW) disposal technologies that employ natural and/or engineered barriers and provide a degree of confinement greater than that of shallow-land burial (SLB) but possibly less than that of a geologic repository. Thus GCD is associated with lower risk/hazard ratios than SLB. Although any number of disposal technologies might satisfy the definition of GCD, eight have been selected for consideration in this discussion. These technologies include: (1) earth-covered tumuli, (2) concrete structures, both above and below grade, (3) deep trenches, (4) augered shafts, (5) rock cavities, (6) abandoned mines, (7) high-integrity containers, and (8) hydrofracture. Each of these technologies employ several operations that are mature,however, some are at more advanced stages of development and demonstration than others. Each is defined and further described by information on design, advantages and disadvantages, special equipment requirements, and characteristic operations such as construction, waste emplacement, and closure

  14. Symposium 9: Rocky Mountain futures: preserving, utilizing, and sustaining Rocky Mountain ecosystems

    Science.gov (United States)

    Baron, Jill S.; Seastedt, Timothy; Fagre, Daniel B.; Hicke, Jeffrey A.; Tomback, Diana; Garcia, Elizabeth; Bowen, Zachary H.; Logan, Jesse A.

    2013-01-01

    In 2002 we published Rocky Mountain Futures, an Ecological Perspective (Island Press) to examine the cumulative ecological effects of human activity in the Rocky Mountains. We concluded that multiple local activities concerning land use, hydrologic manipulation, and resource extraction have altered ecosystems, although there were examples where the “tyranny of small decisions” worked in a positive way toward more sustainable coupled human/environment interactions. Superimposed on local change was climate change, atmospheric deposition of nitrogen and other pollutants, regional population growth, and some national management policies such as fire suppression.

  15. Criteria impacting shipments of Rocky Flats Plant radioactive mixed wastes

    International Nuclear Information System (INIS)

    Clawson, R.L.; Eide, J.H.

    1992-05-01

    Westinghouse Hanford Company, Transportation and Packaging Division, under contract for the Los Alamos Technology Office-Rocky Flats Plant, has developed this synopsis report to be used as a reference in the development of the Rocky Flats Plant Comprehensive Treatment and Management Plan and the Rocky Flats Plant Residue Elimination Plan. This report represents the criteria for packaging, shipping, and transporting Rocky Flats Plant radioactive mixed wastes. It is a compilation of state and federal regulations, US Department of Energy orders, and acceptance criteria specific to US Department of Energy radioactive mixed waste treatment, storage and disposal facilities

  16. More features, greater connectivity.

    Science.gov (United States)

    Hunt, Sarah

    2015-09-01

    Changes in our political infrastructure, the continuing frailties of our economy, and a stark growth in population, have greatly impacted upon the perceived stability of the NHS. Healthcare teams have had to adapt to these changes, and so too have the technologies upon which they rely to deliver first-class patient care. Here Sarah Hunt, marketing co-ordinator at Aid Call, assesses how the changing healthcare environment has affected one of its fundamental technologies - the nurse call system, argues the case for wireless such systems in terms of what the company claims is greater adaptability to changing needs, and considers the ever-wider range of features and functions available from today's nurse call equipment, particularly via connectivity with both mobile devices, and ancillaries ranging from enuresis sensors to staff attack alert 'badges'.

  17. Greater oil investment opportunities

    International Nuclear Information System (INIS)

    Arenas, Ismael Enrique

    1997-01-01

    Geologically speaking, Colombia is a very attractive country for the world oil community. According to this philosophy new and important steps are being taken to reinforce the oil sector: Expansion of the exploratory frontier by including a larger number of sedimentary areas, and the adoption of innovative contracting instruments. Colombia has to offer, Greater economic incentives for the exploration of new areas to expand the exploratory frontier, stimulation of exploration in areas with prospectivity for small fields. Companies may offer Ecopetrol a participation in production over and above royalties, without it's participating in the investments and costs of these fields, more favorable conditions for natural gas seeking projects, in comparison with those governing the terms for oil

  18. Estimation of the ancestral effective population sizes of African great apes under different selection regimes.

    Science.gov (United States)

    Schrago, Carlos G

    2014-08-01

    Reliable estimates of ancestral effective population sizes are necessary to unveil the population-level phenomena that shaped the phylogeny and molecular evolution of the African great apes. Although several methods have previously been applied to infer ancestral effective population sizes, an analysis of the influence of the selective regime on the estimates of ancestral demography has not been thoroughly conducted. In this study, three independent data sets under different selective regimes were used were composed to tackle this issue. The results showed that selection had a significant impact on the estimates of ancestral effective population sizes of the African great apes. The inference of the ancestral demography of African great apes was affected by the selection regime. The effects, however, were not homogeneous along the ancestral populations of great apes. The effective population size of the ancestor of humans and chimpanzees was more impacted by the selection regime when compared to the same parameter in the ancestor of humans, chimpanzees and gorillas. Because the selection regime influenced the estimates of ancestral effective population size, it is reasonable to assume that a portion of the discrepancy found in previous studies that inferred the ancestral effective population size may be attributable to the differential action of selection on the genes sampled.

  19. The role of macrobiota in structuring microbial communities along rocky shores

    Directory of Open Access Journals (Sweden)

    Catherine A. Pfister

    2014-10-01

    Full Text Available Rocky shore microbial diversity presents an excellent system to test for microbial habitat specificity or generality, enabling us to decipher how common macrobiota shape microbial community structure. At two coastal locations in the northeast Pacific Ocean, we show that microbial composition was significantly different between inert surfaces, the biogenic surfaces that included rocky shore animals and an alga, and the water column plankton. While all sampled entities had a core of common OTUs, rare OTUs drove differences among biotic and abiotic substrates. For the mussel Mytilus californianus, the shell surface harbored greater alpha diversity compared to internal tissues of the gill and siphon. Strikingly, a 7-year experimental removal of this mussel from tidepools did not significantly alter the microbial community structure of microbes associated with inert surfaces when compared with unmanipulated tidepools. However, bacterial taxa associated with nitrate reduction had greater relative abundance with mussels present, suggesting an impact of increased animal-derived nitrogen on a subset of microbial metabolism. Because the presence of mussels did not affect the structure and diversity of the microbial community on adjacent inert substrates, microbes in this rocky shore environment may be predominantly affected through direct physical association with macrobiota.

  20. Wind energy resource atlas. Volume 8. The southern Rocky Mountain region

    Energy Technology Data Exchange (ETDEWEB)

    Andersen, S.R.; Freeman, D.L.; Hadley, D.L.; Elliott, D.L.; Barchet, W.R.; George, R.L.

    1981-03-01

    The Southern Rocky Mountain atlas assimilates five collections of wind resource data: one for the region and one for each of the four states that compose the Southern Rocky Mountain region (Arizona, Colorado, New Mexico, and Utah). At the state level, features of the climate, topography and wind resource are discussed in greater detail than is provided in the regional discussion, and the data locations on which the assessment is based are mapped. Variations, over several time scales, in the wind resource at selected stations in each state are shown on graphs of monthly average and interannual wind speed and power, and hourly average wind speed for each season. Other graphs present speed, direction, and duration frequencies of the wind at these locations.

  1. What's new in Rocky Mountain spotted fever?

    Science.gov (United States)

    Chen, Luke F; Sexton, Daniel J

    2008-09-01

    Rocky Mountain spotted fever (RMSF) remains an important illness despite an effective therapy because it is difficult to diagnose and is capable of producing a fatal outcome. The pathogenesis of RMSF remains, in large part, an enigma. However, recent research has helped shed light on this mystery. Importantly, the diagnosis of RMSF must be considered in all febrile patients who have known or possible exposure to ticks, especially if they live in or have traveled to endemic regions during warmer months. Decisions about giving empiric therapy to such patients are difficult and require skill and careful judgement.

  2. Inference of Ancestral Recombination Graphs through Topological Data Analysis

    Science.gov (United States)

    Cámara, Pablo G.; Levine, Arnold J.; Rabadán, Raúl

    2016-01-01

    The recent explosion of genomic data has underscored the need for interpretable and comprehensive analyses that can capture complex phylogenetic relationships within and across species. Recombination, reassortment and horizontal gene transfer constitute examples of pervasive biological phenomena that cannot be captured by tree-like representations. Starting from hundreds of genomes, we are interested in the reconstruction of potential evolutionary histories leading to the observed data. Ancestral recombination graphs represent potential histories that explicitly accommodate recombination and mutation events across orthologous genomes. However, they are computationally costly to reconstruct, usually being infeasible for more than few tens of genomes. Recently, Topological Data Analysis (TDA) methods have been proposed as robust and scalable methods that can capture the genetic scale and frequency of recombination. We build upon previous TDA developments for detecting and quantifying recombination, and present a novel framework that can be applied to hundreds of genomes and can be interpreted in terms of minimal histories of mutation and recombination events, quantifying the scales and identifying the genomic locations of recombinations. We implement this framework in a software package, called TARGet, and apply it to several examples, including small migration between different populations, human recombination, and horizontal evolution in finches inhabiting the Galápagos Islands. PMID:27532298

  3. Mitochondrial introgression suggests extensive ancestral hybridization events among Saccharomyces species.

    Science.gov (United States)

    Peris, David; Arias, Armando; Orlić, Sandi; Belloch, Carmela; Pérez-Través, Laura; Querol, Amparo; Barrio, Eladio

    2017-03-01

    Horizontal gene transfer (HGT) in eukaryotic plastids and mitochondrial genomes is common, and plays an important role in organism evolution. In yeasts, recent mitochondrial HGT has been suggested between S. cerevisiae and S. paradoxus. However, few strains have been explored given the lack of accurate mitochondrial genome annotations. Mitochondrial genome sequences are important to understand how frequent these introgressions occur, and their role in cytonuclear incompatibilities and fitness. Indeed, most of the Bateson-Dobzhansky-Muller genetic incompatibilities described in yeasts are driven by cytonuclear incompatibilities. We herein explored the mitochondrial inheritance of several worldwide distributed wild Saccharomyces species and their hybrids isolated from different sources and geographic origins. We demonstrated the existence of several recombination points in mitochondrial region COX2-ORF1, likely mediated by either the activity of the protein encoded by the ORF1 (F-SceIII) gene, a free-standing homing endonuclease, or mostly facilitated by A+T tandem repeats and regions of integration of GC clusters. These introgressions were shown to occur among strains of the same species and among strains of different species, which suggests a complex model of Saccharomyces evolution that involves several ancestral hybridization events in wild environments. Copyright © 2017 Elsevier Inc. All rights reserved.

  4. Time-Dependent-Asymmetric-Linear-Parsimonious Ancestral State Reconstruction.

    Science.gov (United States)

    Didier, Gilles

    2017-10-01

    The time-dependent-asymmetric-linear parsimony is an ancestral state reconstruction method which extends the standard linear parsimony (a.k.a. Wagner parsimony) approach by taking into account both branch lengths and asymmetric evolutionary costs for reconstructing quantitative characters (asymmetric costs amount to assuming an evolutionary trend toward the direction with the lowest cost). A formal study of the influence of the asymmetry parameter shows that the time-dependent-asymmetric-linear parsimony infers states which are all taken among the known states, except for some degenerate cases corresponding to special values of the asymmetry parameter. This remarkable property holds in particular for the Wagner parsimony. This study leads to a polynomial algorithm which determines, and provides a compact representation of, the parametric reconstruction of a phylogenetic tree, that is for all the unknown nodes, the set of all the possible reconstructed states associated with the asymmetry parameters leading to them. The time-dependent-asymmetric-linear parsimony is finally illustrated with the parametric reconstruction of the body size of cetaceans.

  5. Rocky Mountain Research Station: 2012-2013 Annual Report

    Science.gov (United States)

    Cass Cairns

    2013-01-01

    The Rocky Mountain Research Station is one of seven regional units that make up the USDA Forest Service Research and Development organization - the most extensive natural resources research organization in the world. We maintain 12 field laboratories throughout a 12-state territory encompassing the Great Basin, Southwest, Rocky Mountains, and parts of the...

  6. Ancestral gene reconstruction and synthesis of ancient rhodopsins in the laboratory.

    Science.gov (United States)

    Chang, Belinda S W

    2003-08-01

    Laboratory synthesis of ancestral proteins offers an intriguing opportunity to study the past directly. The development of Bayesian methods to infer ancestral sequences, combined with advances in models of molecular evolution, and synthetic gene technology make this an increasingly promising approach in evolutionary studies of molecular function. Visual pigments form the first step in the biochemical cascade of events in the retina in all animals known to possess visual capabilities. In vertebrates, the necessity of spanning a dynamic range of light intensities of many orders of magnitude has given rise to two different types of photoreceptors, rods specialized for dim-light conditions, and cones for daylight and color vision. These photoreceptors contain different types of visual pigment genes. Reviewed here are methods of inferring ancestral sequences, chemical synthesis of artificial ancestral genes in the laboratory, and applications to the evolution of vertebrate visual systems and the experimental recreation of an archosaur rod visual pigment. The ancestral archosaurs gave rise to several notable lineages of diapsid reptiles, including the birds and the dinosaurs, and would have existed over 200 MYA. What little is known of their physiology comes from fossil remains, and inference based on the biology of their living descendants. Despite its age, an ancestral archosaur pigment was successfully recreated in the lab, and showed interesting properties of its wavelength sensitivity that may have implications for the visual capabilities of the ancestral archosaurs in dim light.

  7. Characterization of Reconstructed Ancestral Proteins Suggests a Change in Temperature of the Ancient Biosphere.

    Science.gov (United States)

    Akanuma, Satoshi

    2017-08-06

    Understanding the evolution of ancestral life, and especially the ability of some organisms to flourish in the variable environments experienced in Earth's early biosphere, requires knowledge of the characteristics and the environment of these ancestral organisms. Information about early life and environmental conditions has been obtained from fossil records and geological surveys. Recent advances in phylogenetic analysis, and an increasing number of protein sequences available in public databases, have made it possible to infer ancestral protein sequences possessed by ancient organisms. However, the in silico studies that assess the ancestral base content of ribosomal RNAs, the frequency of each amino acid in ancestral proteins, and estimate the environmental temperatures of ancient organisms, show conflicting results. The characterization of ancestral proteins reconstructed in vitro suggests that ancient organisms had very thermally stable proteins, and therefore were thermophilic or hyperthermophilic. Experimental data supports the idea that only thermophilic ancestors survived the catastrophic increase in temperature of the biosphere that was likely associated with meteorite impacts during the early history of Earth. In addition, by expanding the timescale and including more ancestral proteins for reconstruction, it appears as though the Earth's surface temperature gradually decreased over time, from Archean to present.

  8. Disposal of Rocky Flats residues as waste

    International Nuclear Information System (INIS)

    Dustin, D.F.; Sendelweck, V.S.

    1993-01-01

    Work is underway at the Rocky Flats Plant to evaluate alternatives for the removal of a large inventory of plutonium-contaminated residues from the plant. One alternative under consideration is to package the residues as transuranic wastes for ultimate shipment to the Waste Isolation Pilot Plant. Current waste acceptance criteria and transportation regulations require that approximately 1000 cubic yards of residues be repackaged to produce over 20,000 cubic yards of WIPP certified waste. The major regulatory drivers leading to this increase in waste volume are the fissile gram equivalent, surface radiation dose rate, and thermal power limits. In the interest of waste minimization, analyses have been conducted to determine, for each residue type, the controlling criterion leading to the volume increase, the impact of relaxing that criterion on subsequent waste volume, and the means by which rules changes may be implemented. The results of this study have identified the most appropriate changes to be proposed in regulatory requirements in order to minimize the costs of disposing of Rocky Flats residues as transuranic wastes

  9. Risk, media, and stigma at Rocky Flats

    International Nuclear Information System (INIS)

    Flynn, J.; Peters, E.; Mertz, C.K.; Slovic, P.

    1998-01-01

    Public responses to nuclear technologies are often strongly negative. Events, such as accidents or evidence of unsafe conditions at nuclear facilities, receive extensive and dramatic coverage by the news media. These news stories affect public perceptions of nuclear risks and the geographic areas near nuclear facilities. One result of these perceptions, avoidance behavior, is a form of technological stigma that leads to losses in property values near nuclear facilities. The social amplification of risk is a conceptual framework that attempts to explain how stigma is created through media transmission of information about hazardous places and public perceptions and decisions. This paper examines stigma associated with the US Department of energy's Rocky Flats facility, a major production plant in the nation's nuclear weapons complex, located near Denver, Colorado. This study, based upon newspaper analyses and a survey of Denver area residents, finds that the social amplification theory provides a reasonable framework for understanding the events and public responses that took place in regard to Rocky Flats during a 6-year period, beginning with an FBI raid of the facility in 1989

  10. Numerical Modeling of Rocky Mountain Paleoglaciers - Insights into the Climate of the Last Glacial Maximum and the Subsequent Deglaciation

    Science.gov (United States)

    Leonard, E. M.; Laabs, B. J. C.; Plummer, M. A.

    2014-12-01

    Numerical modeling of paleoglaciers can yield information on the climatic conditions necessary to sustain those glaciers. In this study we apply a coupled 2-d mass/energy balance and flow model (Plummer and Phillips, 2003) to reconstruct local last glacial maximum (LLGM) glaciers and paleoclimate in ten study areas along the crest of the U.S. Rocky Mountains between 33°N and 49°N. In some of the areas, where timing of post-LLGM ice recession is constrained by surface exposure ages on either polished bedrock upvalley from the LLGM moraines or post-LLGM recessional moraines, we use the model to assess magnitudes and rates of climate change during deglaciation. The modeling reveals a complex pattern of LLGM climate. The magnitude of LLGM-to-modern climate change (temperature and/or precipitation change) was greater in both the northern (Montana) Rocky Mountains and southern (New Mexico) Rocky Mountains than in the middle (Wyoming and Colorado) Rocky Mountains. We use temperature depression estimates from global and regional climate models to infer LLGM precipitation from our glacier model results. Our results suggest a reduction of precipitation coupled with strongly depressed temperatures in the north, contrasted with strongly enhanced precipitation and much more modest temperature depression in the south. The middle Rocky Mountains of Colorado and Wyoming appear to have experienced a reduction in precipitation at the LLGM without the strong temperature depression of the northern Rocky Mountains. Preliminary work on modeling of deglaciation in the Sangre de Cristo Range in southern Colorado suggests that approximately half of the LLGM-to-modern climate change took place during the initial ~2400 years of deglaciation. If increasing temperature and changing solar insolation were the sole drivers of this initial deglaciation, then temperature would need to have risen by slightly more than 1°C/ky through this interval to account for the observed rate of ice recession.

  11. The Microcephalin Ancestral Allele in a Neanderthal Individual

    Science.gov (United States)

    Lari, Martina; Rizzi, Ermanno; Milani, Lucio; Corti, Giorgio; Balsamo, Carlotta; Vai, Stefania; Catalano, Giulio; Pilli, Elena; Longo, Laura; Condemi, Silvana; Giunti, Paolo; Hänni, Catherine; De Bellis, Gianluca; Orlando, Ludovic; Barbujani, Guido; Caramelli, David

    2010-01-01

    Background The high frequency (around 0.70 worlwide) and the relatively young age (between 14,000 and 62,000 years) of a derived group of haplotypes, haplogroup D, at the microcephalin (MCPH1) locus led to the proposal that haplogroup D originated in a human lineage that separated from modern humans >1 million years ago, evolved under strong positive selection, and passed into the human gene pool by an episode of admixture circa 37,000 years ago. The geographic distribution of haplogroup D, with marked differences between Africa and Eurasia, suggested that the archaic human form admixing with anatomically modern humans might have been Neanderthal. Methodology/Principal Findings Here we report the first PCR amplification and high- throughput sequencing of nuclear DNA at the microcephalin (MCPH1) locus from Neanderthal individual from Mezzena Rockshelter (Monti Lessini, Italy). We show that a well-preserved Neanderthal fossil dated at approximately 50,000 years B.P., was homozygous for the ancestral, non-D, allele. The high yield of Neanderthal mtDNA sequences of the studied specimen, the pattern of nucleotide misincorporation among sequences consistent with post-mortem DNA damage and an accurate control of the MCPH1 alleles in all personnel that manipulated the sample, make it extremely unlikely that this result might reflect modern DNA contamination. Conclusions/Significance The MCPH1 genotype of the Monti Lessini (MLS) Neanderthal does not prove that there was no interbreeding between anatomically archaic and modern humans in Europe, but certainly shows that speculations on a possible Neanderthal origin of what is now the most common MCPH1 haplogroup are not supported by empirical evidence from ancient DNA. PMID:20498832

  12. Genetic Diversity, Population Structure and Ancestral Origin of Australian Wheat

    Directory of Open Access Journals (Sweden)

    Reem Joukhadar

    2017-12-01

    Full Text Available Since the introduction of wheat into Australia by the First Fleet settlers, germplasm from different geographical origins has been used to adapt wheat to the Australian climate through selection and breeding. In this paper, we used 482 cultivars, representing the breeding history of bread wheat in Australia since 1840, to characterize their diversity and population structure and to define the geographical ancestral background of Australian wheat germplasm. This was achieved by comparing them to a global wheat collection using in-silico chromosome painting based on SNP genotyping. The global collection involved 2,335 wheat accessions which was divided into 23 different geographical subpopulations. However, the whole set was reduced to 1,544 accessions to increase the differentiation and decrease the admixture among different global subpopulations to increase the power of the painting analysis. Our analysis revealed that the structure of Australian wheat germplasm and its geographic ancestors have changed significantly through time, especially after the Green Revolution. Before 1920, breeders used cultivars from around the world, but mainly Europe and Africa, to select potential cultivars that could tolerate Australian growing conditions. Between 1921 and 1970, a dependence on African wheat germplasm became more prevalent. Since 1970, a heavy reliance on International Maize and Wheat Improvement Center (CIMMYT germplasm has persisted. Combining the results from linkage disequilibrium, population structure and in-silico painting revealed that the dependence on CIMMYT materials has varied among different Australian States, has shrunken the germplasm effective population size and produced larger linkage disequilibrium blocks. This study documents the evolutionary history of wheat breeding in Australia and provides an understanding for how the wheat genome has been adapted to local growing conditions. This information provides a guide for industry to

  13. Genetic Diversity, Population Structure and Ancestral Origin of Australian Wheat.

    Science.gov (United States)

    Joukhadar, Reem; Daetwyler, Hans D; Bansal, Urmil K; Gendall, Anthony R; Hayden, Matthew J

    2017-01-01

    Since the introduction of wheat into Australia by the First Fleet settlers, germplasm from different geographical origins has been used to adapt wheat to the Australian climate through selection and breeding. In this paper, we used 482 cultivars, representing the breeding history of bread wheat in Australia since 1840, to characterize their diversity and population structure and to define the geographical ancestral background of Australian wheat germplasm. This was achieved by comparing them to a global wheat collection using in-silico chromosome painting based on SNP genotyping. The global collection involved 2,335 wheat accessions which was divided into 23 different geographical subpopulations. However, the whole set was reduced to 1,544 accessions to increase the differentiation and decrease the admixture among different global subpopulations to increase the power of the painting analysis. Our analysis revealed that the structure of Australian wheat germplasm and its geographic ancestors have changed significantly through time, especially after the Green Revolution. Before 1920, breeders used cultivars from around the world, but mainly Europe and Africa, to select potential cultivars that could tolerate Australian growing conditions. Between 1921 and 1970, a dependence on African wheat germplasm became more prevalent. Since 1970, a heavy reliance on International Maize and Wheat Improvement Center (CIMMYT) germplasm has persisted. Combining the results from linkage disequilibrium, population structure and in-silico painting revealed that the dependence on CIMMYT materials has varied among different Australian States, has shrunken the germplasm effective population size and produced larger linkage disequilibrium blocks. This study documents the evolutionary history of wheat breeding in Australia and provides an understanding for how the wheat genome has been adapted to local growing conditions. This information provides a guide for industry to assist with

  14. The Korarchaeota: Archaeal orphans representing an ancestral lineage of life

    Energy Technology Data Exchange (ETDEWEB)

    Elkins, James G.; Kunin, Victor; Anderson, Iain; Barry, Kerrie; Goltsman, Eugene; Lapidus, Alla; Hedlund, Brian; Hugenholtz, Phil; Kyrpides, Nikos; Graham, David; Keller, Martin; Wanner, Gerhard; Richardson, Paul; Stetter, Karl O.

    2007-05-01

    Based on conserved cellular properties, all life on Earth can be grouped into different phyla which belong to the primary domains Bacteria, Archaea, and Eukarya. However, tracing back their evolutionary relationships has been impeded by horizontal gene transfer and gene loss. Within the Archaea, the kingdoms Crenarchaeota and Euryarchaeota exhibit a profound divergence. In order to elucidate the evolution of these two major kingdoms, representatives of more deeply diverged lineages would be required. Based on their environmental small subunit ribosomal (ss RNA) sequences, the Korarchaeota had been originally suggested to have an ancestral relationship to all known Archaea although this assessment has been refuted. Here we describe the cultivation and initial characterization of the first member of the Korarchaeota, highly unusual, ultrathin filamentous cells about 0.16 {micro}m in diameter. A complete genome sequence obtained from enrichment cultures revealed an unprecedented combination of signature genes which were thought to be characteristic of either the Crenarchaeota, Euryarchaeota, or Eukarya. Cell division appears to be mediated through a FtsZ-dependent mechanism which is highly conserved throughout the Bacteria and Euryarchaeota. An rpb8 subunit of the DNA-dependent RNA polymerase was identified which is absent from other Archaea and has been described as a eukaryotic signature gene. In addition, the representative organism possesses a ribosome structure typical for members of the Crenarchaeota. Based on its gene complement, this lineage likely diverged near the separation of the two major kingdoms of Archaea. Further investigations of these unique organisms may shed additional light onto the evolution of extant life.

  15. The microcephalin ancestral allele in a Neanderthal individual.

    Directory of Open Access Journals (Sweden)

    Martina Lari

    Full Text Available BACKGROUND: The high frequency (around 0.70 worldwide and the relatively young age (between 14,000 and 62,000 years of a derived group of haplotypes, haplogroup D, at the microcephalin (MCPH1 locus led to the proposal that haplogroup D originated in a human lineage that separated from modern humans >1 million years ago, evolved under strong positive selection, and passed into the human gene pool by an episode of admixture circa 37,000 years ago. The geographic distribution of haplogroup D, with marked differences between Africa and Eurasia, suggested that the archaic human form admixing with anatomically modern humans might have been Neanderthal. METHODOLOGY/PRINCIPAL FINDINGS: Here we report the first PCR amplification and high-throughput sequencing of nuclear DNA at the microcephalin (MCPH1 locus from Neanderthal individual from Mezzena Rockshelter (Monti Lessini, Italy. We show that a well-preserved Neanderthal fossil dated at approximately 50,000 years B.P., was homozygous for the ancestral, non-D, allele. The high yield of Neanderthal mtDNA sequences of the studied specimen, the pattern of nucleotide misincorporation among sequences consistent with post-mortem DNA damage and an accurate control of the MCPH1 alleles in all personnel that manipulated the sample, make it extremely unlikely that this result might reflect modern DNA contamination. CONCLUSIONS/SIGNIFICANCE: The MCPH1 genotype of the Monti Lessini (MLS Neanderthal does not prove that there was no interbreeding between anatomically archaic and modern humans in Europe, but certainly shows that speculations on a possible Neanderthal origin of what is now the most common MCPH1 haplogroup are not supported by empirical evidence from ancient DNA.

  16. Analysis on the reconstruction accuracy of the Fitch method for inferring ancestral states

    Directory of Open Access Journals (Sweden)

    Grünewald Stefan

    2011-01-01

    Full Text Available Abstract Background As one of the most widely used parsimony methods for ancestral reconstruction, the Fitch method minimizes the total number of hypothetical substitutions along all branches of a tree to explain the evolution of a character. Due to the extensive usage of this method, it has become a scientific endeavor in recent years to study the reconstruction accuracies of the Fitch method. However, most studies are restricted to 2-state evolutionary models and a study for higher-state models is needed since DNA sequences take the format of 4-state series and protein sequences even have 20 states. Results In this paper, the ambiguous and unambiguous reconstruction accuracy of the Fitch method are studied for N-state evolutionary models. Given an arbitrary phylogenetic tree, a recurrence system is first presented to calculate iteratively the two accuracies. As complete binary tree and comb-shaped tree are the two extremal evolutionary tree topologies according to balance, we focus on the reconstruction accuracies on these two topologies and analyze their asymptotic properties. Then, 1000 Yule trees with 1024 leaves are generated and analyzed to simulate real evolutionary scenarios. It is known that more taxa not necessarily increase the reconstruction accuracies under 2-state models. The result under N-state models is also tested. Conclusions In a large tree with many leaves, the reconstruction accuracies of using all taxa are sometimes less than those of using a leaf subset under N-state models. For complete binary trees, there always exists an equilibrium interval [a, b] of conservation probability, in which the limiting ambiguous reconstruction accuracy equals to the probability of randomly picking a state. The value b decreases with the increase of the number of states, and it seems to converge. When the conservation probability is greater than b, the reconstruction accuracies of the Fitch method increase rapidly. The reconstruction

  17. Assessment of lake sensitivity to acidic deposition in national parks of the Rocky Mountains

    Science.gov (United States)

    Nanus, L.; Williams, M.W.; Campbell, D.H.; Tonnessen, K.A.; Blett, T.; Clow, D.W.

    2009-01-01

    The sensitivity of high-elevation lakes to acidic deposition was evaluated in five national parks of the Rocky Mountains based on statistical relations between lake acid-neutralizing capacity concentrations and basin characteristics. Acid-neutralizing capacity (ANC) of 151 lakes sampled during synoptic surveys and basin-characteristic information derived from geographic information system (GIS) data sets were used to calibrate the statistical models. The explanatory basin variables that were considered included topographic parameters, bedrock type, and vegetation type. A logistic regression model was developed, and modeling results were cross-validated through lake sampling during fall 2004 at 58 lakes. The model was applied to lake basins greater than 1 ha in area in Glacier National Park (n = 244 lakes), Grand Teton National Park (n = 106 lakes), Great Sand Dunes National Park and Preserve (n = 11 lakes), Rocky Mountain National Park (n = 114 lakes), and Yellowstone National Park (n = 294 lakes). Lakes that had a high probability of having an ANC concentration 3000 m, with 80% of the catchment bedrock having low buffering capacity. The modeling results indicate that the most sensitive lakes are located in Rocky Mountain National Park and Grand Teton National Park. This technique for evaluating the lake sensitivity to acidic deposition is useful for designing long-term monitoring plans and is potentially transferable to other remote mountain areas of the United States and the world.

  18. Historical Exposures to Chemicals at the Rocky Flats Nuclear Weapons Plant: A Pilot Retrospective Exposure Assessment

    Energy Technology Data Exchange (ETDEWEB)

    Robertson, Janeen Denise [Univ. of New Mexico, Albuquerque, NM (United States)

    1999-02-01

    In a mortality study of white males who had worked at the Rocky Flats Nuclear Weapons Plant between 1952 and 1979, an increased number of deaths from benign and unspecified intracranial neoplasms was found. A case-control study nested within this cohort investigated the hypothesis that an association existed between brain tumor death and exposure to either internally deposited plutonium or external ionizing radiation. There was no statistically significant association found between estimated radiation exposure from internally deposited plutonium and the development of brain tumors. Exposure by job or work area showed no significant difference between the cohort and the control groups. An update of the study found elevated risk estimates for (1) all lymphopoietic neoplasms, and (2) all causes of death in employees with body burdens greater than or equal to two nanocuries of plutonium. There was an excess of brain tumors for the entire cohort. Similar cohort studies conducted on worker populations from other plutonium handling facilities have not yet shown any elevated risks for brain tumors. Historically, the Rocky Flats Nuclear Weapons Plant used large quantities of chemicals in their production operations. The use of solvents, particularly carbon tetrachloride, was unique to Rocky Flats. No investigation of the possible confounding effects of chemical exposures was done in the initial studies. The objectives of the present study are to (1) investigate the history of chemical use at the Rocky Flats facility; (2) locate and analyze chemical monitoring information in order to assess employee exposure to the chemicals that were used in the highest volume; and (3) determine the feasibility of establishing a chemical exposure assessment model that could be used in future epidemiology studies.

  19. WARACS: Wrappers to Automate the Reconstruction of Ancestral Character States1

    Science.gov (United States)

    Gruenstaeudl, Michael

    2016-01-01

    Premise of the study: Reconstructions of ancestral character states are among the most widely used analyses for evaluating the morphological, cytological, or ecological evolution of an organismic lineage. The software application Mesquite remains the most popular application for such reconstructions among plant scientists, even though its support for automating complex analyses is limited. A software tool is needed that automates the reconstruction and visualization of ancestral character states with Mesquite and similar applications. Methods and Results: A set of command line–based Python scripts was developed that (a) communicates standardized input to and output from the software applications Mesquite, BayesTraits, and TreeGraph2; (b) automates the process of ancestral character state reconstruction; and (c) facilitates the visualization of reconstruction results. Conclusions: WARACS provides a simple tool that streamlines the reconstruction and visualization of ancestral character states over a wide array of parameters, including tree distribution, character state, and optimality criterion. PMID:26949580

  20. NEPA/CERCLA integration at Rocky Flats

    International Nuclear Information System (INIS)

    Schassburger, R.J.

    1991-01-01

    Integration of two laws, the Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) and the National Environmental Policy Act (NEPA) was mandated by the US Department of Energy (DOE) with issuance of DOE Order 5400.4 in October 6, 1989. NEPA documentation is required for all federal actions to thereby consider the impacts of such actions prior to the action taking place. On the other hand, CERCLA actions taken by the US Environmental Protection Agency (EPA) at non-federal and federal sites do not normally take NEPA into consideration, although it is not exempted at federal sites. EPA claims that CERCLA is functionally equivalent to N-EPA and therefore NEPA is not required. Although EPA maintains the functional equivalency of the two laws and formerly resisted to recognize NEPA even in Inter-Agency Agreements (IAGs), Rocky Flats has been integrating the two laws within documents to avoid duplication of information and effort

  1. Rocky Mountain spotted fever in Argentina.

    Science.gov (United States)

    Paddock, Christopher D; Fernandez, Susana; Echenique, Gustavo A; Sumner, John W; Reeves, Will K; Zaki, Sherif R; Remondegui, Carlos E

    2008-04-01

    We describe the first molecular confirmation of Rickettsia rickettsii, the cause of Rocky Mountain spotted fever (RMSF), from a tick vector, Amblyomma cajennense, and from a cluster of fatal spotted fever cases in Argentina. Questing A. cajennense ticks were collected at or near sites of presumed or confirmed cases of spotted fever rickettsiosis in Jujuy Province and evaluated by polymerase chain reaction assays for spotted fever group rickettsiae. DNA of R. rickettsii was amplified from a pool of A. cajennense ticks and from tissues of one of four patients who died during 2003-2004 after illnesses characterized by high fever, severe headache, myalgias, and petechial rash. The diagnosis of spotted fever rickettsiosis was confirmed in the other patients by indirect immunofluorescence antibody and immunohistochemical staining techniques. These findings show the existence of RMSF in Argentina and emphasize the need for clinicians throughout the Americas to consider RMSF in patients with febrile rash illnesses.

  2. Rapid maximum likelihood ancestral state reconstruction of continuous characters: A rerooting-free algorithm.

    Science.gov (United States)

    Goolsby, Eric W

    2017-04-01

    Ancestral state reconstruction is a method used to study the evolutionary trajectories of quantitative characters on phylogenies. Although efficient methods for univariate ancestral state reconstruction under a Brownian motion model have been described for at least 25 years, to date no generalization has been described to allow more complex evolutionary models, such as multivariate trait evolution, non-Brownian models, missing data, and within-species variation. Furthermore, even for simple univariate Brownian motion models, most phylogenetic comparative R packages compute ancestral states via inefficient tree rerooting and full tree traversals at each tree node, making ancestral state reconstruction extremely time-consuming for large phylogenies. Here, a computationally efficient method for fast maximum likelihood ancestral state reconstruction of continuous characters is described. The algorithm has linear complexity relative to the number of species and outperforms the fastest existing R implementations by several orders of magnitude. The described algorithm is capable of performing ancestral state reconstruction on a 1,000,000-species phylogeny in fewer than 2 s using a standard laptop, whereas the next fastest R implementation would take several days to complete. The method is generalizable to more complex evolutionary models, such as phylogenetic regression, within-species variation, non-Brownian evolutionary models, and multivariate trait evolution. Because this method enables fast repeated computations on phylogenies of virtually any size, implementation of the described algorithm can drastically alleviate the computational burden of many otherwise prohibitively time-consuming tasks requiring reconstruction of ancestral states, such as phylogenetic imputation of missing data, bootstrapping procedures, Expectation-Maximization algorithms, and Bayesian estimation. The described ancestral state reconstruction algorithm is implemented in the Rphylopars

  3. Plutonium in a grassland ecosystem. [Rocky Flats Plant

    Energy Technology Data Exchange (ETDEWEB)

    Little, C.A.

    1976-08-01

    A study was made of plutonium contamination of grassland at the Rocky Flats plant northwest of Denver, Colorado. Of interest were: the definition of major plutonium-containing ecosystem compartments; the relative amounts in those compartments; how those values related to studies done in other geographical areas; whether or not the predominant isotopes, /sup 238/Pu and /sup 239/Pu, behaved differently; and what mechanisms might have allowed for the observed patterns of contamination. Samples of soil, litter, vegetation, arthropods, and small mammals were collected for Pu analysis and mass determination from each of two macroplots. Small aliquots (5 g or less) were analyzed by a rapid liquid scintillation technique and by alpha spectrometry. Of the compartments sampled, greater than 99 percent of the total plutonium was contained in the soil and the concentrations were significantly inversely correlated with distance from the contamination source, depth of the sample, and particle size of the sieved soil samples. The soil data suggested that the distribution of contamination largely resulted from physical transport processes.

  4. The rocky flats controversy on radionuclide soil action levels

    International Nuclear Information System (INIS)

    Earle, T.C.

    2004-01-01

    This report describes how stakeholder involvement processes led to the successful resolution of a dispute over radionuclide soil action levels at the Rocky Flats Site near Denver, Colorado. During the Cold War Era, Rocky Flats, a plutonium fabrication plant, was part of the American government's multi-site nuclear weapons production facilities. Although the Rocky Flats plant had significant positive effects on the local economy, it became a target of public protest due to concerns over both public safety in the area surrounding the site and global nuclear proliferation. In the late 1980's, local safety concerns led to investigations by state and federal agencies. In 1992, with the Cold War ended, the Department of Energy decided to decommission the Rocky Flats site and to begin the long process of decontamination. (author)

  5. Why sulfonamides are contraindicated in Rocky Mountain spotted fever

    OpenAIRE

    Ren, Vicky; Hsu, Sylvia

    2014-01-01

    Sulfonamide antibiotics are not effective for the treatment of Rocky Mountain spotted fever (RMSF). Patients suspected of having RMSF based on history and physical exam should be treated with doxycycline and not a sulfonamide to avoid increased morbidity and mortality.

  6. Why sulfonamides are contraindicated in Rocky Mountain spotted fever.

    Science.gov (United States)

    Ren, Vicky; Hsu, Sylvia

    2014-02-18

    Sulfonamide antibiotics are not effective for the treatment of Rocky Mountain spotted fever (RMSF). Patients suspected of having RMSF based on history and physical exam should be treated with doxycycline and not a sulfonamide to avoid increased morbidity and mortality.

  7. Ongoing Cerebral Vasculitis During Treatment of Rocky Mountain Spotted Fever.

    Science.gov (United States)

    Sun, Lisa R; Huisman, Thierry A G M; Yeshokumar, Anusha K; Johnston, Michael V

    2015-11-01

    Rocky Mountain spotted fever is a tickborne infection that produces a systemic small-vessel vasculitis; its prognosis is excellent if appropriate treatment is initiated early. Because the advent of effective antirickettsial therapies predates the widespread use of brain magnetic resonance imaging, there are limited data on the effect of untreated Rocky Mountain spotted fever infection on neuroimaging studies. We describe a 7-year-old girl with delayed treatment of Rocky Mountain spotted fever who suffered severe neurological impairment. Serial brain magnetic resonance images revealed a progressive "starry sky appearance," which is proposed to result from the same small vessel vasculitis that causes the characteristic skin rash of this infection. Neurological injury can continue to occur despite specific antirickettsial therapy in Rocky Mountain spotted fever. This child's clinical features raise questions about the optimal management of this infection, particularly the utility of immune modulating therapies in cases of delayed treatment and neurological involvement. Copyright © 2015 Elsevier Inc. All rights reserved.

  8. Benchmarking and performance improvement at Rocky Flats Technology Site

    International Nuclear Information System (INIS)

    Elliott, C.; Doyle, G.; Featherman, W.L.

    1997-03-01

    The Rocky Flats Environmental Technology Site has initiated a major work process improvement campaign using the tools of formalized benchmarking and streamlining. This paper provides insights into some of the process improvement activities performed at Rocky Flats from November 1995 through December 1996. It reviews the background, motivation, methodology, results, and lessons learned from this ongoing effort. The paper also presents important gains realized through process analysis and improvement including significant cost savings, productivity improvements, and an enhanced understanding of site work processes

  9. KEPLER'S FIRST ROCKY PLANET: KEPLER-10b

    International Nuclear Information System (INIS)

    Batalha, Natalie M.; Borucki, William J.; Bryson, Stephen T.; Haas, Michael R.; Koch, David G.; Lissauer, Jack J.; Rowe, Jason F.; Buchhave, Lars A.; Fressin, Francois; Latham, David W.; Caldwell, Douglas A.; Jenkins, Jon M.; Christensen-Dalsgaard, Joergen; Kjeldsen, Hans; Ciardi, David; Dunham, Edward W.; Gautier, Thomas N. III; Gilliland, Ronald L.; Howell, Steve B.; Marcy, Geoffrey W.

    2011-01-01

    NASA's Kepler Mission uses transit photometry to determine the frequency of Earth-size planets in or near the habitable zone of Sun-like stars. The mission reached a milestone toward meeting that goal: the discovery of its first rocky planet, Kepler-10b. Two distinct sets of transit events were detected: (1) a 152 ± 4 ppm dimming lasting 1.811 ± 0.024 hr with ephemeris T [BJD] =2454964.57375 +0.00060 -0.00082 + N*0.837495 +0.000004 -0.000005 days and (2) a 376 ± 9 ppm dimming lasting 6.86 ± 0.07 hr with ephemeris T [BJD] =2454971.6761 +0.0020 -0.0023 + N*45.29485 +0.00065 -0.00076 days. Statistical tests on the photometric and pixel flux time series established the viability of the planet candidates triggering ground-based follow-up observations. Forty precision Doppler measurements were used to confirm that the short-period transit event is due to a planetary companion. The parent star is bright enough for asteroseismic analysis. Photometry was collected at 1 minute cadence for >4 months from which we detected 19 distinct pulsation frequencies. Modeling the frequencies resulted in precise knowledge of the fundamental stellar properties. Kepler-10 is a relatively old (11.9 ± 4.5 Gyr) but otherwise Sun-like main-sequence star with T eff = 5627 ± 44 K, M * = 0.895 ± 0.060 M sun , and R * = 1.056 ± 0.021 R sun . Physical models simultaneously fit to the transit light curves and the precision Doppler measurements yielded tight constraints on the properties of Kepler-10b that speak to its rocky composition: M P = 4.56 +1.17 -1.29 M + , R P = 1.416 +0.033 -0.036 R + , and ρ P = 8.8 +2.1 -2.9 g cm -3 . Kepler-10b is the smallest transiting exoplanet discovered to date.

  10. Ancestral sequence reconstruction in primate mitochondrial DNA: compositional bias and effect on functional inference.

    Science.gov (United States)

    Krishnan, Neeraja M; Seligmann, Hervé; Stewart, Caro-Beth; De Koning, A P Jason; Pollock, David D

    2004-10-01

    Reconstruction of ancestral DNA and amino acid sequences is an important means of inferring information about past evolutionary events. Such reconstructions suggest changes in molecular function and evolutionary processes over the course of evolution and are used to infer adaptation and convergence. Maximum likelihood (ML) is generally thought to provide relatively accurate reconstructed sequences compared to parsimony, but both methods lead to the inference of multiple directional changes in nucleotide frequencies in primate mitochondrial DNA (mtDNA). To better understand this surprising result, as well as to better understand how parsimony and ML differ, we constructed a series of computationally simple "conditional pathway" methods that differed in the number of substitutions allowed per site along each branch, and we also evaluated the entire Bayesian posterior frequency distribution of reconstructed ancestral states. We analyzed primate mitochondrial cytochrome b (Cyt-b) and cytochrome oxidase subunit I (COI) genes and found that ML reconstructs ancestral frequencies that are often more different from tip sequences than are parsimony reconstructions. In contrast, frequency reconstructions based on the posterior ensemble more closely resemble extant nucleotide frequencies. Simulations indicate that these differences in ancestral sequence inference are probably due to deterministic bias caused by high uncertainty in the optimization-based ancestral reconstruction methods (parsimony, ML, Bayesian maximum a posteriori). In contrast, ancestral nucleotide frequencies based on an average of the Bayesian set of credible ancestral sequences are much less biased. The methods involving simpler conditional pathway calculations have slightly reduced likelihood values compared to full likelihood calculations, but they can provide fairly unbiased nucleotide reconstructions and may be useful in more complex phylogenetic analyses than considered here due to their speed and

  11. LHC Report: Rocky re-start

    CERN Multimedia

    Barbara Holzer for the LHC Team

    2012-01-01

    A rocky re-start with beam followed a successful machine development period and the first technical stop of 2012. Today, Friday 11 May, the machine began running again with 1380 bunches.   A short, two-day machine development period was successfully completed on 21-22 April. It focused on topics relevant for the 2012 physics beam operation. This was then followed by a five-day technical stop, the first of the year. The technical stop finished on time on Friday 26 April. The re-start with beam was somewhat tortuous and hampered by an unlucky succession of technical faults leading to extended periods of downtime. The planned intensity increase was put on hold for three days with the machine operating with 1092 bunches and a moderate bunch intensity of 1.3x1011 protons. This delivered a reasonable peak luminosity of 3.6x1033 cm-2s-1 to ATLAS and CMS. Higher than usual beam losses were observed in the ramp and squeeze, and time was required to investigate the causes and to implement mitigati...

  12. Elemental compositions of two extrasolar rocky planetesimals

    Energy Technology Data Exchange (ETDEWEB)

    Xu, S.; Jura, M.; Klein, B.; Zuckerman, B. [Department of Physics and Astronomy, University of California, Los Angeles, CA 90095-1562 (United States); Koester, D., E-mail: sxu@astro.ucla.edu, E-mail: jura@astro.ucla.edu, E-mail: kleinb@astro.ucla.edu, E-mail: ben@astro.ucla.edu, E-mail: koester@astrophysik.uni-kiel.de [Institut fur Theoretische Physik und Astrophysik, University of Kiel, D-24098 Kiel (Germany)

    2014-03-10

    We report Keck/HIRES and Hubble Space Telescope/COS spectroscopic studies of extrasolar rocky planetesimals accreted onto two hydrogen atmosphere white dwarfs, G29-38 and GD 133. In G29-38, eight elements are detected, including C, O, Mg, Si, Ca, Ti, Cr, and Fe while in GD 133, O, Si, Ca, and marginally Mg are seen. These two extrasolar planetesimals show a pattern of refractory enhancement and volatile depletion. For G29-38, the observed composition can be best interpreted as a blend of a chondritic object with some refractory-rich material, a result from post-nebular processing. Water is very depleted in the parent body accreted onto G29-38, based on the derived oxygen abundance. The inferred total mass accretion rate in GD 133 is the lowest of all known dusty white dwarfs, possibly due to non-steady state accretion. We continue to find that a variety of extrasolar planetesimals all resemble to zeroth order the elemental composition of bulk Earth.

  13. The HARPS-N Rocky Planet Search

    DEFF Research Database (Denmark)

    Motalebi, F.; Udry, S.; Gillon, M.

    2015-01-01

    We know now from radial velocity surveys and transit space missions that planets only a few times more massive than our Earth are frequent around solar-type stars. Fundamental questions about their formation history, physical properties, internal structure, and atmosphere composition are, however......, still to be solved. We present here the detection of a system of four low-mass planets around the bright (V = 5.5) and close-by (6.5 pc) star HD 219134. This is the first result of the Rocky Planet Search programme with HARPS-N on the Telescopio Nazionale Galileo in La Palma. The inner planet orbits...... on a close-in, quasi-circular orbit with a period of 6.767 ± 0.004 days. The third planet in the system has a period of 46.66 ± 0.08 days and a minimum-mass of 8.94 ± 1.13 M⊕, at 0.233 ± 0.002 AU from the star. Its eccentricity is 0.46 ± 0.11. The period of this planet is close to the rotational period...

  14. Rocky Planet Formation: Quick and Neat

    Science.gov (United States)

    Kenyon, Scott J.; Najita, Joan R.; Bromley, Benjamin C.

    2016-11-01

    We reconsider the commonly held assumption that warm debris disks are tracers of terrestrial planet formation. The high occurrence rate inferred for Earth-mass planets around mature solar-type stars based on exoplanet surveys (˜20%) stands in stark contrast to the low incidence rate (≤2%-3%) of warm dusty debris around solar-type stars during the expected epoch of terrestrial planet assembly (˜10 Myr). If Earth-mass planets at au distances are a common outcome of the planet formation process, this discrepancy suggests that rocky planet formation occurs more quickly and/or is much neater than traditionally believed, leaving behind little in the way of a dust signature. Alternatively, the incidence rate of terrestrial planets has been overestimated, or some previously unrecognized physical mechanism removes warm dust efficiently from the terrestrial planet region. A promising removal mechanism is gas drag in a residual gaseous disk with a surface density ≳10-5 of the minimum-mass solar nebula.

  15. Commercial Decommissioning at DOE's Rocky Flats

    International Nuclear Information System (INIS)

    Freiboth, C.; Sandlin, N.; Schubert, A.; Hansen, S.

    2002-01-01

    Due in large part to the number of nuclear facilities that make up the DOE complex, DOE-EM work has historically been paperwork intensive and driven by extensive regulations. Requirements for non-nuclear facilities are often grouped with those of nuclear facilities, driving up costs. Kaiser-Hill was interested in applying a commercial model to demolition of these facilities and wanted to apply necessary and sufficient standards to the work activities, but avoid applying unnecessary requirements. Faced with demolishing hundreds of uncontaminated or non-radiologically contaminated facilities, Kaiser-Hill has developed a subcontracting strategy to drastically reduce the cost of demolishing these facilities at Rocky Flats. Aiming to tailor the demolition approach of such facilities to more closely follow commercial practices, Kaiser-Hill recently released a Request for Proposals (RFP) for the demolition of the site's former central administration facility. The RFP significantly reduced requirements for compliance with specific DOE directives. Instead, the RFP required subcontractors to comply with health and safety requirements commonly found in the demolition of similar facilities in a commercial setting. This resulted in a number of bids from companies who have normally not bid on DOE work previously and at a reduced cost over previous approaches. This paper will discuss the details of this subcontracting strategy

  16. Ancestral effect on HOMA-IR levels quantitated in an American population of Mexican origin.

    Science.gov (United States)

    Qu, Hui-Qi; Li, Quan; Lu, Yang; Hanis, Craig L; Fisher-Hoch, Susan P; McCormick, Joseph B

    2012-12-01

    An elevated insulin resistance index (homeostasis model assessment of insulin resistance [HOMA-IR]) is more commonly seen in the Mexican American population than in European populations. We report quantitative ancestral effects within a Mexican American population, and we correlate ancestral components with HOMA-IR. We performed ancestral analysis in 1,551 participants of the Cameron County Hispanic Cohort by genotyping 103 ancestry-informative markers (AIMs). These AIMs allow determination of the percentage (0-100%) ancestry from three major continental populations, i.e., European, African, and Amerindian. We observed that predominantly Amerindian ancestral components were associated with increased HOMA-IR (β = 0.124, P = 1.64 × 10(-7)). The correlation was more significant in males (Amerindian β = 0.165, P = 5.08 × 10(-7)) than in females (Amerindian β = 0.079, P = 0.019). This unique study design demonstrates how genomic markers for quantitative ancestral information can be used in admixed populations to predict phenotypic traits such as insulin resistance.

  17. Rocky desertification in Southwest China: Impacts, causes, and restoration

    Science.gov (United States)

    Jiang, Zhongcheng; Lian, Yanqing; Qin, Xiaoqun

    2014-05-01

    Rocky desertification, which is relatively less well known than desertification, refers to the processes and human activities that transform a karst area covered by vegetation and soil into a rocky landscape. It has occurred in various countries and regions, including the European Mediterranean and Dinaric Karst regions of the Balkan Peninsula, Southwest China on a large scale, and alarmingly, even in tropical rainforests such as Haiti and Barbados, and has had tremendous negative impacts to the environment and social and economic conditions at local and regional scales. The goal of this paper is to provide a thorough review of the impacts, causes, and restoration measures of rocky desertification based on decades of studies in the southwest karst area of China and reviews of studies in Europe and other parts of the world. The low soil formation rate and high permeability of carbonate rocks create a fragile and vulnerable environment that is susceptible to deforestation and soil erosion. Other natural processes related to hydrology and ecology could exacerbate rocky desertification. However, disturbances from a wide variety of human activities are ultimately responsible for rocky desertification wherever it has occurred. This review shows that reforestation can be successful in Southwest China and even in the Dinaric Karst region when the land, people, water, and other resources are managed cohesively. However, new challenges may arise as more frequent droughts and extreme floods induced by global climate change and variability may slow the recovery process or even expand rocky desertification. This review is intended to bring attention to this challenging issue and provide information needed to advance research and engineering practices to combat rocky desertification and to aid in sustainable development.

  18. New summer areas and mixing of two greater sandhill crane populations in the Intermountain West

    Science.gov (United States)

    Collins, Daniel P.; Grisham, Blake A.; Conring, Courtenay M.; Knetter, Jeffrey M.; Conway, Warren C.; Carleton, Scott A.; Boggie, Matthew A.

    2016-01-01

    Population delineation throughout the annual life cycle for migratory birds is needed to formulate regional and national management and conservation strategies. Despite being well studied continentally, connectivity of sandhill crane Grus canadensis populations throughout the western portion of their North American range remains poorly described. Our objectives were to 1) use global positioning system satellite transmitter terminals to identify summer distributions for the Lower Colorado River Valley Population of greater sandhill cranes Grus canadensis tabida and 2) determine whether intermingling occurs among any of the western greater sandhill crane populations: Rocky Mountain Population, Lower Colorado River Valley Population, and Central Valley Population. Capture and marking occurred during winter and summer on private lands in California and Idaho as well as on two National Wildlife Refuges: Cibola and Sonny Bono Salton Sea National Wildlife Refuges. A majority of marked greater sandhill cranes summered in what is established Lower Colorado River Valley Population breeding areas in northeastern Nevada and southwestern Idaho. A handful of greater sandhill cranes summered outside of traditional breeding areas in west-central Idaho around Cascade Reservoir near Donnelly and Cascade, Idaho. For example, a greater sandhill crane colt captured near Donnelly in July 2014 survived to winter migration and moved south to areas associated with the Rocky Mountain Population. The integration of the greater sandhill crane colt captured near Donnelly provides the first evidence of potential intermingling between the Lower Colorado River Population and Rocky Mountain Population. We suggest continued marking and banding efforts of all three western populations of greater sandhill cranes will accurately delineate population boundaries and connectivity and inform management decisions for the three populations.

  19. Social capital and health: evidence that ancestral trust promotes health among children of immigrants.

    Science.gov (United States)

    Ljunge, Martin

    2014-12-01

    This paper presents evidence that generalized trust promotes health. Children of immigrants in a broad set of European countries with ancestry from across the world are studied. Individuals are examined within country of residence using variation in trust across countries of ancestry. The approach addresses reverse causality and concerns that the trust measure picks up institutional factors in the individual's contextual setting. There is a significant positive estimate of ancestral trust in explaining self-assessed health. The finding is robust to accounting for individual, parental, and extensive ancestral country characteristics. Individuals with higher ancestral trust are also less likely to be hampered by health problems in their daily life, providing evidence of trust influencing real life outcomes. Individuals with high trust feel and act healthier, enabling a more productive life.

  20. On the Accuracy of Ancestral Sequence Reconstruction for Ultrametric Trees with Parsimony.

    Science.gov (United States)

    Herbst, Lina; Fischer, Mareike

    2018-04-01

    We examine a mathematical question concerning the reconstruction accuracy of the Fitch algorithm for reconstructing the ancestral sequence of the most recent common ancestor given a phylogenetic tree and sequence data for all taxa under consideration. In particular, for the symmetric four-state substitution model which is also known as Jukes-Cantor model, we answer affirmatively a conjecture of Li, Steel and Zhang which states that for any ultrametric phylogenetic tree and a symmetric model, the Fitch parsimony method using all terminal taxa is more accurate, or at least as accurate, for ancestral state reconstruction than using any particular terminal taxon or any particular pair of taxa. This conjecture had so far only been answered for two-state data by Fischer and Thatte. Here, we focus on answering the biologically more relevant case with four states, which corresponds to ancestral sequence reconstruction from DNA or RNA data.

  1. Ancestral TCDD exposure promotes epigenetic transgenerational inheritance of imprinted gene Igf2: Methylation status and DNMTs

    International Nuclear Information System (INIS)

    Ma, Jing; Chen, Xi; Liu, Yanan; Xie, Qunhui; Sun, Yawen; Chen, Jingshan; Leng, Ling; Yan, Huan; Zhao, Bin; Tang, Naijun

    2015-01-01

    Ancestral TCDD exposure could induce epigenetic transgenerational phenotypes, which may be mediated in part by imprinted gene inheritance. The aim of our study was to evaluate the transgenerational effects of ancestral TCDD exposure on the imprinted gene insulin-like growth factor-2 (Igf2) in rat somatic tissue. TCDD was administered daily by oral gavage to groups of F0 pregnant SD rats at dose levels of 0 (control), 200 or 800 ng/kg bw during gestation day 8–14. Animal transgenerational model of ancestral exposure to TCDD was carefully built, avoiding sibling inbreeding. Hepatic Igf2 expression of the TCDD male progeny was decreased concomitantly with hepatic damage and increased activities of serum hepatic enzymes both in the F1 and F3 generation. Imprinted Control Region (ICR) of Igf2 manifested a hypermethylated pattern, whereas methylation status in the Differentially Methylated Region 2 (DMR2) showed a hypomethylated manner in the F1 generation. These epigenetic alterations in these two regions maintained similar trends in the F3 generation. Meanwhile, the expressions of DNA methyltransferases (DNMT1, DNMT3A and DNMT3B) changed in a non-monotonic manner both in the F1 and F3 generation. This study provides evidence that ancestral TCDD exposure may promote epigenetic transgenerational alterations of imprinted gene Igf2 in adult somatic tissue. - Highlights: • Ancestral TCDD exposure induces epigenetic transgenerational inheritance. • Ancestral TCDD exposure affects methylation status in ICR and DMR2 region of Igf2. • DNMTs play a role in TCDD induced epigenetic transgenerational changes of Igf2.

  2. Asymptotic distributions of coalescence times and ancestral lineage numbers for populations with temporally varying size.

    Science.gov (United States)

    Chen, Hua; Chen, Kun

    2013-07-01

    The distributions of coalescence times and ancestral lineage numbers play an essential role in coalescent modeling and ancestral inference. Both exact distributions of coalescence times and ancestral lineage numbers are expressed as the sum of alternating series, and the terms in the series become numerically intractable for large samples. More computationally attractive are their asymptotic distributions, which were derived in Griffiths (1984) for populations with constant size. In this article, we derive the asymptotic distributions of coalescence times and ancestral lineage numbers for populations with temporally varying size. For a sample of size n, denote by Tm the mth coalescent time, when m + 1 lineages coalesce into m lineages, and An(t) the number of ancestral lineages at time t back from the current generation. Similar to the results in Griffiths (1984), the number of ancestral lineages, An(t), and the coalescence times, Tm, are asymptotically normal, with the mean and variance of these distributions depending on the population size function, N(t). At the very early stage of the coalescent, when t → 0, the number of coalesced lineages n - An(t) follows a Poisson distribution, and as m → n, $$n\\left(n-1\\right){T}_{m}/2N\\left(0\\right)$$ follows a gamma distribution. We demonstrate the accuracy of the asymptotic approximations by comparing to both exact distributions and coalescent simulations. Several applications of the theoretical results are also shown: deriving statistics related to the properties of gene genealogies, such as the time to the most recent common ancestor (TMRCA) and the total branch length (TBL) of the genealogy, and deriving the allele frequency spectrum for large genealogies. With the advent of genomic-level sequencing data for large samples, the asymptotic distributions are expected to have wide applications in theoretical and methodological development for population genetic inference.

  3. Environmental enrichment mitigates the impact of ancestral stress on motor skill and corticospinal tract plasticity.

    Science.gov (United States)

    McCreary, J Keiko; Erickson, Zachary T; Metz, Gerlinde A S

    2016-10-06

    An adverse fetal environment in utero has been associated with long-term alterations in brain structure and function, and a higher risk of neurological disorders in later life. A common consequence of early adverse experience is impaired motor system function. A causal relationship for stress-associated impairments and a suitable therapy, however, have not been determined yet. To investigate the impact of ancestral stress on corticospinal tract (CST) morphology and fine motor performance in rats, and to determine if adverse programming by ancestral stress can be mitigated by environmental enrichment therapy in rats. The study examined F3 offspring generated by three lineages; one with prenatal stress only in the F1 generation, one with compounding effects of multigenerational prenatal stress, and a non-stress control lineage. F3 offspring from each lineage were injected with biotinylated dextran amine (BDA) into the motor cortex for anterograde tracing of the CST. Examination of the CST revealed reduced axonal density in the ancestrally stressed lineages. These anatomical changes were associated with significant impairments in skilled walking, as indicated by reduced foot placement accuracy and disturbed inter-limb coordination. Therapeutic intervention by environmental enrichment reduced the neuromorphological consequences of ancestral stress and restored skilled walking ability. The data suggest a causal relationship between stress-induced abnormal CST function and loss of fine motor performance. Thus, ancestral stress may be a determinant of motor system development and motor skill. Environmental enrichment may represent an effective intervention for the adverse programming by ancestral stress and trauma. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  4. Ancestral TCDD exposure promotes epigenetic transgenerational inheritance of imprinted gene Igf2: Methylation status and DNMTs

    Energy Technology Data Exchange (ETDEWEB)

    Ma, Jing; Chen, Xi; Liu, Yanan [Department of Occupational and Environmental Health, School of Public Health, Tianjin Medical University, Tianjin 300070 (China); Xie, Qunhui [State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085 (China); Sun, Yawen; Chen, Jingshan; Leng, Ling; Yan, Huan [Department of Occupational and Environmental Health, School of Public Health, Tianjin Medical University, Tianjin 300070 (China); Zhao, Bin, E-mail: binzhao@rcees.ac.cn [State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085 (China); Tang, Naijun, E-mail: tangnaijun@tijmu.edu.cn [Department of Occupational and Environmental Health, School of Public Health, Tianjin Medical University, Tianjin 300070 (China)

    2015-12-01

    Ancestral TCDD exposure could induce epigenetic transgenerational phenotypes, which may be mediated in part by imprinted gene inheritance. The aim of our study was to evaluate the transgenerational effects of ancestral TCDD exposure on the imprinted gene insulin-like growth factor-2 (Igf2) in rat somatic tissue. TCDD was administered daily by oral gavage to groups of F0 pregnant SD rats at dose levels of 0 (control), 200 or 800 ng/kg bw during gestation day 8–14. Animal transgenerational model of ancestral exposure to TCDD was carefully built, avoiding sibling inbreeding. Hepatic Igf2 expression of the TCDD male progeny was decreased concomitantly with hepatic damage and increased activities of serum hepatic enzymes both in the F1 and F3 generation. Imprinted Control Region (ICR) of Igf2 manifested a hypermethylated pattern, whereas methylation status in the Differentially Methylated Region 2 (DMR2) showed a hypomethylated manner in the F1 generation. These epigenetic alterations in these two regions maintained similar trends in the F3 generation. Meanwhile, the expressions of DNA methyltransferases (DNMT1, DNMT3A and DNMT3B) changed in a non-monotonic manner both in the F1 and F3 generation. This study provides evidence that ancestral TCDD exposure may promote epigenetic transgenerational alterations of imprinted gene Igf2 in adult somatic tissue. - Highlights: • Ancestral TCDD exposure induces epigenetic transgenerational inheritance. • Ancestral TCDD exposure affects methylation status in ICR and DMR2 region of Igf2. • DNMTs play a role in TCDD induced epigenetic transgenerational changes of Igf2.

  5. Which came first: The lizard or the egg? Robustness in phylogenetic reconstruction of ancestral states.

    Science.gov (United States)

    Wright, April M; Lyons, Kathleen M; Brandley, Matthew C; Hillis, David M

    2015-09-01

    Changes in parity mode between egg-laying (oviparity) and live-bearing (viviparity) have occurred repeatedly throughout vertebrate evolution. Oviparity is the ancestral amniote state, and viviparity has evolved many times independently within amniotes (especially in lizards and snakes), with possibly a few reversions to oviparity. In amniotes, the shelled egg is considered a complex structure that is unlikely to re-evolve if lost (i.e., it is an example of Dollo's Principle). However, a recent ancestral state reconstruction analysis concluded that viviparity was the ancestral state of squamate reptiles (lizards and snakes), and that oviparity re-evolved from viviparity many times throughout the evolutionary history of squamates. Here, we re-evaluate support for this provocative conclusion by testing the sensitivity of the analysis to model assumptions and estimates of squamate phylogeny. We found that the models and methods used for parity mode reconstruction are highly sensitive to the specific estimate of phylogeny used, and that the point estimate of phylogeny used to suggest that viviparity is the root state of the squamate tree is far from an optimal phylogenetic solution. The ancestral state reconstructions are also highly sensitive to model choice and specific values of model parameters. A method that is designed to account for biases in taxon sampling actually accentuates, rather than lessens, those biases with respect to ancestral state reconstructions. In contrast to recent conclusions from the same data set, we find that ancestral state reconstruction analyses provide highly equivocal support for the number and direction of transitions between oviparity and viviparity in squamates. Moreover, the reconstructions of ancestral parity state are highly dependent on the assumptions of each model. We conclude that the common ancestor of squamates was oviparous, and subsequent evolutionary transitions to viviparity were common, but reversals to oviparity were

  6. ROCKY PLANETESIMAL FORMATION VIA FLUFFY AGGREGATES OF NANOGRAINS

    Energy Technology Data Exchange (ETDEWEB)

    Arakawa, Sota; Nakamoto, Taishi, E-mail: arakawa.s.ac@m.titech.ac.jp [Department of Earth and Planetary Sciences, Tokyo Institute of Technology, Meguro, Tokyo 152-8551 (Japan)

    2016-12-01

    Several pieces of evidence suggest that silicate grains in primitive meteorites are not interstellar grains but condensates formed in the early solar system. Moreover, the size distribution of matrix grains in chondrites implies that these condensates might be formed as nanometer-sized grains. Therefore, we propose a novel scenario for rocky planetesimal formation in which nanometer-sized silicate grains are produced by evaporation and recondensation events in early solar nebula, and rocky planetesimals are formed via aggregation of these nanograins. We reveal that silicate nanograins can grow into rocky planetesimals via direct aggregation without catastrophic fragmentation and serious radial drift, and our results provide a suitable condition for protoplanet formation in our solar system.

  7. The rocky flats controversy on radionuclide soil action levels

    International Nuclear Information System (INIS)

    Earle, T.C.

    2004-01-01

    This report describes the Rocky Flats radionuclide soil action level controversy as a case study for the purpose of understanding the nature and value of stakeholder involvement in the management of radiological hazards. The report consists of three main sections. The first section outlines the Rocky Flats story, including the Cold War era, the post-Cold War era, and the transition between the two. This provides the context necessary to understand the radionuclide soil action level controversy, the main events of which are described in the second section. In the final section, the Rocky Flats case is briefly discussed within the framework of a general model of stakeholder involvement and the lessons learned from the case are identified. (author)

  8. Kawasaki disease following Rocky Mountain spotted fever: a case report

    Directory of Open Access Journals (Sweden)

    Bal Aswine K

    2009-07-01

    Full Text Available Abstract Introduction Kawasaki disease is an idiopathic acute systemic vasculitis of childhood. Although it simulates the clinical features of many infectious diseases, an infectious etiology has not been established. This is the first reported case of Kawasaki disease following Rocky Mountain spotted fever. Case presentation We report the case of a 4-year-old girl who presented with fever and petechial rash. Serology confirmed Rocky Mountain spotted fever. While being treated with intravenous doxycycline, she developed swelling of her hands and feet. She had the clinical features of Kawasaki disease which resolved after therapy with intravenous immune globulin (IVIG and aspirin. Conclusion This case report suggests that Kawasaki disease can occur concurrently or immediately after a rickettsial illness such as Rocky Mountain spotted fever, hypothesizing an antigen-driven immune response to a rickettsial antigen.

  9. Kawasaki disease following Rocky Mountain spotted fever: a case report.

    Science.gov (United States)

    Bal, Aswine K; Kairys, Steven W

    2009-07-06

    Kawasaki disease is an idiopathic acute systemic vasculitis of childhood. Although it simulates the clinical features of many infectious diseases, an infectious etiology has not been established. This is the first reported case of Kawasaki disease following Rocky Mountain spotted fever. We report the case of a 4-year-old girl who presented with fever and petechial rash. Serology confirmed Rocky Mountain spotted fever. While being treated with intravenous doxycycline, she developed swelling of her hands and feet. She had the clinical features of Kawasaki disease which resolved after therapy with intravenous immune globulin (IVIG) and aspirin. This case report suggests that Kawasaki disease can occur concurrently or immediately after a rickettsial illness such as Rocky Mountain spotted fever, hypothesizing an antigen-driven immune response to a rickettsial antigen.

  10. Evolutionary relationships in the sand-dwelling cichlid lineage of lake tanganyika suggest multiple colonization of rocky habitats and convergent origin of biparental mouthbrooding.

    Science.gov (United States)

    Koblmüller, Stephan; Salzburger, Walter; Sturmbauer, Christian

    2004-01-01

    The cichlid species flock of Lake Tanganyika is comprised of seven seeding lineages that evolved in step with changes of the lake environment. One seeding lineage diversified into at least six lineages within a short period of time. Our study focuses on the diversification of one of these lineages, the Ectodini, comprising highly specialized, sand- and rock-dwelling species. They display two distinct breeding styles: maternal and biparental mouthbrooding. By analyzing three mtDNA gene segments in 30 species representing all 13 described genera, we show that the Ectodini rapidly diversified into four clades at the onset of their radiation. The monotypic genus Grammatotria is likely to represent the most ancestral split, followed by the almost contemporary origin of three additional clades, the first comprising the benthic genus Callochromis, the second comprising the benthic genera Asprotilapia, Xenotilapia, Enantiopus, and Microdontochromis, and the third comprising the semi-pelagic genera Ophthalmotilapia, Cardiopharynx, Cyathopharynx, Ectodus, Aulonocranus, Lestradea, and Cunningtonia. Our study confirms the benthic and sand-dwelling life-style as ancestral. Rocky habitats were colonized independently in the Xenotilapia- and Ophthalmotilapia-clade. The Xenotilapia-clade comprises both maternal and biparental mouthbrooders. Their mode of breeding appears to be highly plastic: biparental mouthbrooding either evolved once in the common ancestor of the clade, to be reverted at least three times, or evolved at least five times independently from a maternally mouthbrooding ancestor. Furthermore, the genera Xenotilapia, Microdontochromis, Lestradea, and Ophthalmotilapia appeared paraphyletic in our analyses, suggesting the need of taxonomic revision.

  11. Developmental geology of coalbed methane from shallow to deep in Rocky Mountain basins and in Cook Inlet-Matanuska Basin, Alaska, USA and Canada

    Science.gov (United States)

    Johnson, R.C.; Flores, R.M.

    1998-01-01

    The Rocky Mountain basins of western North America contain vast deposits of coal of Cretaceous through early Tertiary age. Coalbed methane is produced in Rocky Mountain basins at depths ranging from 45 m (150 ft) to 1981 m (6500 ft) from coal of lignite to low-volatile bituminous rank. Although some production has been established in almost all Rocky Mountain basins, commercial production occurs in only a few. despite more than two decades of exploration for coalbed methane in the Rocky Mountain region, it is still difficult to predict production characteristics of coalbed methane wells prior to drilling. Commonly cited problems include low permeabilities, high water production, and coals that are significantly undersaturated with respect to methane. Sources of coalbed gases can be early biogenic, formed during the early stages of coalification, thermogenic, formed during the main stages of coalification, or late stage biogenic, formed as a result of the reintroduction of methane-gnerating bacteria by groundwater after uplift and erosion. Examples of all three types of coalbed gases, and combinations of more than one type, can be found in the Rocky Mountain region. Coals in the Rocky Mountain region achieved their present ranks largely as a result of burial beneath sediments that accumulated during the Laramide orogeny (Late Cretaceous through the end of the eocene) or shortly after. Thermal events since the end of the orogeny have also locally elevated coal ranks. Coal beds in the upper part of high-volatile A bituminous rank or greater commonly occur within much more extensive basin-centered gas deposits which cover large areas of the deeper parts of most Rocky Mountain basins. Within these basin-centered deposits all lithologies, including coals, sandstones, and shales, are gas saturated, and very little water is produced. The interbedded coals and carbonaceous shales are probably the source of much of this gas. Basin-centered gas deposits become overpressured

  12. A skull might lie: modelling ancestral ranges and diet from genes and shape of tree squirrels

    Czech Academy of Sciences Publication Activity Database

    Pečnerová, Patrícia; Moravec, Jiří C.; Martínková, Natália

    2015-01-01

    Roč. 64, č. 6 (2015), s. 1074-1088 ISSN 1063-5157 EU Projects: European Commission(XE) CZ.1.07/2.4.00/17.0138 Institutional support: RVO:68081766 Keywords : Sciurini * multilocus phylogeny * geometric morphometry * speciation * ancestral range reconstruction * diet modelling Subject RIV: EG - Zoology Impact factor: 8.225, year: 2015

  13. Language Shift and Maintenance in Multilingual Mauritius: The Case of Indian Ancestral Languages

    Science.gov (United States)

    Bissoonauth, Anu

    2011-01-01

    This paper reports on a research study conducted in Mauritius between June and July 2009. The aim of this research was to investigate the use of Indian ancestral languages in the domestic domain by the younger generations. The data were collected in the field by means of a questionnaire and interviews from a quota sample of secondary school…

  14. Inferring ancestral distribution area and survival vegetation of Caragana (Fabaceae) in Tertiary

    Science.gov (United States)

    Mingli Zhang; Juanjuan Xue; Qiang Zhang; Stewart C. Sanderson

    2015-01-01

    Caragana, a leguminous genus mainly restricted to temperate Central and East Asia, occurs in arid, semiarid, and humid belts, and has forest, grassland, and desert ecotypes. Based on the previous molecular phylogenetic tree and dating, biogeographical analyses of extant species area and ecotype were conducted by means of four ancestral optimization approaches: S-DIVA,...

  15. The structured ancestral selection graph and the many-demes limit.

    Science.gov (United States)

    Slade, Paul F; Wakeley, John

    2005-02-01

    We show that the unstructured ancestral selection graph applies to part of the history of a sample from a population structured by restricted migration among subpopulations, or demes. The result holds in the limit as the number of demes tends to infinity with proportionately weak selection, and we have also made the assumptions of island-type migration and that demes are equivalent in size. After an instantaneous sample-size adjustment, this structured ancestral selection graph converges to an unstructured ancestral selection graph with a mutation parameter that depends inversely on the migration rate. In contrast, the selection parameter for the population is independent of the migration rate and is identical to the selection parameter in an unstructured population. We show analytically that estimators of the migration rate, based on pairwise sequence differences, derived under the assumption of neutrality should perform equally well in the presence of weak selection. We also modify an algorithm for simulating genealogies conditional on the frequencies of two selected alleles in a sample. This permits efficient simulation of stronger selection than was previously possible. Using this new algorithm, we simulate gene genealogies under the many-demes ancestral selection graph and identify some situations in which migration has a strong effect on the time to the most recent common ancestor of the sample. We find that a similar effect also increases the sensitivity of the genealogy to selection.

  16. Indigenous ancestral sayings contribute to modern conservation partnerships: examples using Phormium tenax.

    Science.gov (United States)

    Wehi, Priscilla M

    2009-01-01

    Traditional ecological knowledge (TEK) is central to indigenous worldviews and practices and is one of the most important contributions that indigenous people can bring to conservation management partnerships. However, researchers and managers may have difficulty accessing such knowledge, particularly where knowledge transmission has been damaged. A new methodological approach analyzes ancestral sayings from Maori oral traditions for ecological information about Phormium tenax, a plant with high cultural value that is a dominant component in many threatened wetland systems, and frequently used in restoration plantings in New Zealand. Maori ancestral sayings record an association with nectar-feeding native parrots that has only rarely been reported, as well as indications of important environmental parameters (rainfall and drought) for this species. These sayings provide evidence of indigenous management that has not been reported from interviews with elders, including evidence of fire use to create Phormium cultivations. TEK in Maori ancestral sayings imply landscape-scale processes in comparison to intensive, small-scale management methods often reported in interviews. TEK in ancestral sayings can be used to generate new scientific hypotheses, negotiate collaborative pathways, and identify ecological management strategies that support biodiversity retention. TEK can inform restoration ecology, historical ecology, and conservation management of species and ecosystems, especially where data from pollen records and archaeological artifacts are incomplete.

  17. Benchmarking and Performance Improvement at Rocky Flats Environmental Technology Site

    Energy Technology Data Exchange (ETDEWEB)

    Elliott, C. [Kaiser-Hill Co., LLC, Golden, CO (United States)], Doyle, D. [USDOE Rocky Flats Office, Golden, CO (United States)], Featherman, W.D. [Project Performance Corp., Sterline, VA (United States)

    1997-12-31

    The Rocky Flats Environmental Technology Site (RFETS) has initiated a major work process improvement campaign using the tools of formalized benchmarking and streamlining. This paper provides insights into some of the process improvement activities performed at Rocky Flats from November 1995 through December 1996. It reviews the background, motivation, methodology, results, and lessons learned from this ongoing effort. The paper also presents important gains realized through process analysis and improvement including significant cost savings, productivity improvements, and an enhanced understanding of site work processes.

  18. Invasion of Ancestral Mammals into Dim-light Environments Inferred from Adaptive Evolution of the Phototransduction Genes.

    Science.gov (United States)

    Wu, Yonghua; Wang, Haifeng; Hadly, Elizabeth A

    2017-04-20

    Nocturnality is a key evolutionary innovation of mammals that enables mammals to occupy relatively empty nocturnal niches. Invasion of ancestral mammals into nocturnality has long been inferred from the phylogenetic relationships of crown Mammalia, which is primarily nocturnal, and crown Reptilia, which is primarily diurnal, although molecular evidence for this is lacking. Here we used phylogenetic analyses of the vision genes involved in the phototransduction pathway to predict the diel activity patterns of ancestral mammals and reptiles. Our results demonstrated that the common ancestor of the extant Mammalia was dominated by positive selection for dim-light vision, supporting the predominate nocturnality of the ancestral mammals. Further analyses showed that the nocturnality of the ancestral mammals was probably derived from the predominate diurnality of the ancestral amniotes, which featured strong positive selection for bright-light vision. Like the ancestral amniotes, the common ancestor of the extant reptiles and various taxa in Squamata, one of the main competitors of the temporal niches of the ancestral mammals, were found to be predominate diurnality as well. Despite this relatively apparent temporal niche partitioning between ancestral mammals and the relevant reptiles, our results suggested partial overlap of their temporal niches during crepuscular periods.

  19. Reconstruction of Ancestral Genomes in Presence of Gene Gain and Loss.

    Science.gov (United States)

    Avdeyev, Pavel; Jiang, Shuai; Aganezov, Sergey; Hu, Fei; Alekseyev, Max A

    2016-03-01

    Since most dramatic genomic changes are caused by genome rearrangements as well as gene duplications and gain/loss events, it becomes crucial to understand their mechanisms and reconstruct ancestral genomes of the given genomes. This problem was shown to be NP-complete even in the "simplest" case of three genomes, thus calling for heuristic rather than exact algorithmic solutions. At the same time, a larger number of input genomes may actually simplify the problem in practice as it was earlier illustrated with MGRA, a state-of-the-art software tool for reconstruction of ancestral genomes of multiple genomes. One of the key obstacles for MGRA and other similar tools is presence of breakpoint reuses when the same breakpoint region is broken by several different genome rearrangements in the course of evolution. Furthermore, such tools are often limited to genomes composed of the same genes with each gene present in a single copy in every genome. This limitation makes these tools inapplicable for many biological datasets and degrades the resolution of ancestral reconstructions in diverse datasets. We address these deficiencies by extending the MGRA algorithm to genomes with unequal gene contents. The developed next-generation tool MGRA2 can handle gene gain/loss events and shares the ability of MGRA to reconstruct ancestral genomes uniquely in the case of limited breakpoint reuse. Furthermore, MGRA2 employs a number of novel heuristics to cope with higher breakpoint reuse and process datasets inaccessible for MGRA. In practical experiments, MGRA2 shows superior performance for simulated and real genomes as compared to other ancestral genome reconstruction tools.

  20. Analyzing Whitebark Pine Distribution in the Northern Rocky Mountains in Support of Grizzly Bear Recovery

    Science.gov (United States)

    Lawrence, R.; Landenburger, L.; Jewett, J.

    2007-12-01

    Whitebark pine seeds have long been identified as the most significant vegetative food source for grizzly bears in the Greater Yellowstone Ecosystem (GYE) and, hence, a crucial element of suitable grizzly bear habitat. The overall health and status of whitebark pine in the GYE is currently threatened by mountain pine beetle infestations and the spread of whitepine blister rust. Whitebark pine distribution (presence/absence) was mapped for the GYE using Landsat 7 Enhanced Thematic Mapper (ETM+) imagery and topographic data as part of a long-term inter-agency monitoring program. Logistic regression was compared with classification tree analysis (CTA) with and without boosting. Overall comparative classification accuracies for the central portion of the GYE covering three ETM+ images along a single path ranged from 91.6% using logistic regression to 95.8% with See5's CTA algorithm with the maximum 99 boosts. The analysis is being extended to the entire northern Rocky Mountain Ecosystem and extended over decadal time scales. The analysis is being extended to the entire northern Rocky Mountain Ecosystem and extended over decadal time scales.

  1. Rocky Flats Cleanup Agreement implementation successes and challenges

    International Nuclear Information System (INIS)

    Shelton, D.C.

    1997-01-01

    On July 19, 1996 the US Department of Energy (DOE), State of Colorado (CDPHE), and US Environmental Protection Agency (EPA) entered into an agreement called the Rocky Flats Cleanup Agreement (RFCA) for the cleanup and closure of the Rocky Flats Environmental Technology Site (RFETS or Rocky Flats). Major elements of the agreement include: an Integrated Site-Wide Baseline; up to twelve significant enforceable milestones per year; agreed upon soil and water action levels and standards for cleanup; open space as the likely foreseeable land use; the plutonium and TRU waste removed by 2015; streamlined regulatory process; agreement with the Defense Nuclear Facilities Safety Board (DNFSB) to coordinate activities; and a risk reduction focus. Successful implementation of RFCA requires a substantial effort by the parties to change their way of thinking about RFETS and meet the deliverables and commitments. Substantial progress toward Site closure through the implementation of RFCA has been accomplished in the short time since the signing, yet much remains to be done. Much can be learned from the Rocky Flats experience by other facilities in similar situations

  2. Rocky Flats Plant Site Environmental Report for 1992

    International Nuclear Information System (INIS)

    Cirrincione, D.A.; Erdmann, N.L.

    1992-01-01

    The Rocky Rats Plant Site Environmental Report provides summary information on the plant's environmental monitoring programs and the results recorded during 1992. The report contains a compliance summary, results of environmental monitoring and other related programs, a review of environmental remediation activities, information on external gamma radiation dose monitoring, and radiation dose estimates for the surrounding population

  3. Public involvement in cleanup - the Rocky Flats experience

    International Nuclear Information System (INIS)

    Paukert, J.; Pennock, S.; Schassburger, R.

    1992-01-01

    The U.S. Department of Energy's Rocky Flats Plant recently completed and implemented the Rocky Flats Plant Community Relations Plan for public involvement in environmental restoration of the site. The plan was developed in cooperation with the plant's regulators, the U.S. Environmental Protection Agency and the Colorado Department of Health. In addition, citizens near the plant played a significant role in shaping the document through extensive community interviews and public comment. The result of these cooperative efforts is a plan that meets and exceeds the applicable federal and state community relations requirements for a cleanup program. In fact, the U.S. Environmental Protection Agency has used the Rocky Flats Plant Community Relations Plants a model for similar plans at other federal facilities. Plan development, however, is only the starting point for an effective community relations effort. The Rocky Flats Plant and the public will face many challenges together as we implement the plan and build a partnership for addressing environmental cleanup issues. (author)

  4. Progress towards a lightning ignition model for the Northern Rockies

    Science.gov (United States)

    Paul Sopko; Don Latham

    2010-01-01

    We are in the process of constructing a lightning ignition model specific to the Northern Rockies using fire occurrence, lightning strike, ecoregion, and historical weather, NFDRS (National Fire Danger Rating System), lightning efficiency and lightning "possibility" data. Daily grids for each of these categories were reconstructed for the 2003 fire season (...

  5. Biological impacts of oil pollution: rocky shores. V. 7

    International Nuclear Information System (INIS)

    1997-01-01

    Most people with access to the sea have at one time enjoyed looking into rockpools and searching for crabs under boulders. Rocky shores have a great deal of fascination for people and they are the closest that many of them will get to the mysteries below the low tide mark. They are found, in some form, on most of the world's coasts and their ecology has been the subject of many books, reports and scientific papers. Rocky shores encompass a variety of intertidal habitats and have a range of vulnerabilities to oil. While some areas are quickly and easily cleaned by natural forces others can trap oil in sensitive sub-habitats which may then be damaged and take many years to recover. Furthermore, rocky shores have an importance in the wider context of marine ecosystems and some provide important local fisheries resources, tourism and amenities. This report describes the factors that make some rocky shores more sensitive to oil spills than others and considers the most appropriate methods of clean-up. Case histories are used to illustrate the effects of spills and spill clean-up, as well as typical recovery rates. (UK)

  6. Rocky Mountain Research Station invasive species visionary white paper

    Science.gov (United States)

    D. E. Pearson; M. Kim; J. Butler

    2011-01-01

    Invasive species represent one of the single greatest threats to natural ecosystems and the services they provide. Effectively addressing the invasive species problem requires management that is based on sound research. We provide an overview of recent and ongoing invasive species research conducted by Rocky Mountain Research Station scientists in the Intermountain...

  7. Adsorption study for uranium in Rocky Flats groundwater

    International Nuclear Information System (INIS)

    Laul, J.C.; Rupert, M.C.; Harris, M.J.; Duran, A.

    1995-01-01

    Six adsorbents were studied to determine their effectiveness in removing uranium in Rocky Flats groundwater. The bench column and batch (Kd) tests showed that uranium can be removed (>99.9%) by four adsorbents. Bone Charcoal (R1O22); F-1 Alumina (granular activated alumina); BIOFIX (immobilized biological agent); SOPBPLUS (mixed metal oxide); Filtrasorb 300 (granular activated carbon); and Zeolite (clinoptilolite)

  8. Field guide to diseases & insects of the Rocky Mountain Region

    Science.gov (United States)

    Forest Health Protection. Rocky Mountain Region

    2010-01-01

    This field guide is a forest management tool for field identification of biotic and abiotic agents that damage native trees in Colorado, Kansas, Nebraska, South Dakota, and Wyoming, which constitute the USDA Forest Service's Rocky Mountain Region. The guide focuses only on tree diseases and forest insects that have significant economic, ecological, and/ or...

  9. Rocky Flats Plant Site Environmental Report for 1992

    Energy Technology Data Exchange (ETDEWEB)

    Cirrincione, D.A.; Erdmann, N.L. [eds.

    1992-12-31

    The Rocky Rats Plant Site Environmental Report provides summary information on the plant`s environmental monitoring programs and the results recorded during 1992. The report contains a compliance summary, results of environmental monitoring and other related programs, a review of environmental remediation activities, information on external gamma radiation dose monitoring, and radiation dose estimates for the surrounding population.

  10. Immune Thrombocytopenia as a Consequence of Rocky Mountain Spotted Fever.

    Science.gov (United States)

    Baldeo, Cherisse; Seegobin, Karan; Zuberi, Lara

    2017-01-01

    Primary immune thrombocytopenia (ITP) - also called idiopathic thrombocytopenic purpura or immune thrombocytopenic purpura - is an acquired thrombocytopenia caused by autoantibodies against platelet antigens. It is one of the more common causes of thrombocytopenia in otherwise asymptomatic adults. Rocky Mountain spotted fever (RMSF) is a potentially lethal, but curable, tick-borne disease. We present a case of ITP that was triggered by RMSF.

  11. Natural phenomena risk assessment at Rocky Flats Plant

    International Nuclear Information System (INIS)

    Foppe, T.L.

    1985-01-01

    A realistic approach is currently being used at the Rocky Flats Plant to assess the risks of natural phenomena events. The methodology addresses frequency of occurrence estimates, damage stress on the facility and vital equipment, material-at-risk, release fractions and source terms, leakpath, dispersion and dosimetric models, risk curves, and an uncertainty analysis. 28 references, 1 figure

  12. Aquatic Resources of Rocky Mountain Arsenal Adams County, Colorado

    Science.gov (United States)

    1989-09-01

    Consequently, temperatures rise and oxygen levels fall. Primary producers in these stretches shift from periphyton to phytoplankton (suspended algae ...trees and have rocky substrates. Primary production in these cold- water and coolwater reaches is generally limited to periphyton (attached algae ...Adams County. Biotic components investigated included phytoplankton , zooplankton, aquatic macrophytes, benthic macroinvertebrates, fish eggs and

  13. Erratum: Vascular epiphyte vegetation in rocky savannas of southeastern Brazil

    Czech Academy of Sciences Publication Activity Database

    Alves, R. J. V.; Kolbek, Jiří; Becker, J.

    2009-01-01

    Roč. 27, č. 4 (2009), s. 351-352 ISSN 0107-055X Institutional research plan: CEZ:AV0Z60050516 Keywords : epiphytes * Brazil * rocky savannas Subject RIV: EF - Botanics Impact factor: 0.868, year: 2009

  14. Rocky Planetary Debris Around Young WDs

    Science.gov (United States)

    Gaensicke, B.

    2014-04-01

    , the low C/Si ratio demonstrates that the planetary material is of rocky nature. * None of the 9 systems where we measure the C/O ratio shows evidence for carbon-dominated chemistry, implying that "carbon planets" are not common. * In the most polluted white dwarfs, we measure the debris abundances of up to 11 elements, enabling a detailed comparison between the chemistry of exo-planetary material with that of solar system meteorites. We find that the exo-planetary debris shares many characteristics of solar-system material, i.e. a wide spread in the relative abundances of Mg, Fe, Si, and O, a constant Al/Ca ratio, and evidence for differentiation in the form of Fe over-abundances All of the above is suggestive that thermal and collisional processing of planetary material in those systems might have been similar to that in the solar system.

  15. Study on comprehensive planning of rocky desertification in karst area of Chongqing

    Science.gov (United States)

    Zang, Yajun

    2017-11-01

    Chongqing is a key area for comprehensive treatment of rocky desertification in karst areas of china. Strengthening the comprehensive management of karst rocky desertification area, for the maintenance of ecological safety of Three Gorges Reservoir area, expanding the karst rocky desertification area people survival and development space, and improving the regional ecological conditions, have important practical significance to the construction of ecological civilization and building a harmonious society. Based on the investigation, analysis and arrangement of the data in the rocky desertification area, the paper puts forward the corresponding measures and phased targets for the treatment of the Rocky Desertification in the karst areas of Chongqing.

  16. The challenge and future of rocky desertification control in karst areas in southwest China

    Science.gov (United States)

    Zhang, J. Y.; Dai, M. H.; Wang, L. C.; Zeng, C. F.; Su, W. C.

    2016-01-01

    Karst rocky desertification occurs after vegetation deteriorates as a result of intensive land use, which leads to severe water loss and soil erosion and exposes basement rocks, creating a rocky landscape. Karst rocky desertification is found in humid areas in southwest China, the region most seriously affected by rocky desertification in the world. In order to promote ecological restoration and help peasants out of poverty, the Chinese government carried out the first phase of a rocky desertification control project from 2006 to 2015, which initially contained the expansion of rocky desertification. Currently, the Chinese government is prepared to implement the second phase of the rocky desertification control project, and therefore it is essential to summarise the lessons learned over the last 10 years of the first phase. In this paper, we analyse the driving social and economic factors behind rocky desertification, summarise the scientific research on rocky desertification in the region, and finally identify the main problems facing rocky desertification control. In addition, we put forward several policy suggestions that take into account the perspective of local peasants, scientific research, and China's economic development and urbanisation process. These suggestions include promoting the non-agriculturalization of household livelihoods, improving ecological compensation, strengthening the evaluation of rocky desertification control and dynamic monitoring, and strengthening research on key ecological function recovery technologies and supporting technologies.

  17. Flavor in the context of ancestral human diets

    Directory of Open Access Journals (Sweden)

    Richard Wrangham

    2014-07-01

    . Evidence that honey has been a major part of the diet for thousands of generations comes from a co-evolved symbiosis between humans and an African bird, the greater honeyguide Indicator indicator. The relationship depends on honeyguides being born with a tendency to guide humans to honey, and on humans extracting honey from the hives to which the honeyguide leads them. Large intakes of fructose and glucose by humans are thus an ancient phenomenon, suggesting that humans have had the opportunity to at least partially adapt to this aspect of a diabetogenic diet [2]. The second dimension of difference between humans and other primates is food processing. Humans are the only species that processes their food with heat, i.e. by cooking. Cooked meat or tubers provide more energy than the same items eaten raw [3]. Studies of human raw-foodists (individuals who choose to eat their diets raw indicate that most adherents suffer chronic energy shortage and in the case of women, amenorrea [4]. Yet raw-foodist diets are high-quality compared to what a hunter-gatherer could eat raw. Raw-foodist eat agriculturally derived foods, so plant items are low in fiber and rich in sugar compared to wild foods, and meats (since not all raw-foodists are vegan are fat-rich. Raw-foodists live in industrial societies with access to global markets and no serious seasonal shortages of food. They often process their food non-thermally and tend to take less exercise than hunter-gatherers. The fact that despite all these advantages, raw-foodists experience severe energy shortages and impaired reproduction indicates that hunter-gatherers would not be able to survive on raw diets. Humans have a different kind of digestion from other animals: we are not biologically adapted to eating our food raw. Little is still known about how the human digestive system is functionally constrained to including a substantial component of cooked food in the diet but compared to all other primates humans have smallest relative

  18. Expression, purification and crystallization of the ancestral androgen receptor-DHT complex.

    Science.gov (United States)

    Colucci, Jennifer K; Ortlund, Eric A

    2013-09-01

    Steroid receptors (SRs) are a closely related family of ligand-dependent nuclear receptors that mediate the transcription of genes critical for development, reproduction and immunity. SR dysregulation has been implicated in cancer, inflammatory diseases and metabolic disorders. SRs bind their cognate hormone ligand with exquisite specificity, offering a unique system to study the evolution of molecular recognition. The SR family evolved from an estrogen-sensitive ancestor and diverged to become sensitive to progestagens, corticoids and, most recently, androgens. To understand the structural mechanisms driving the evolution of androgen responsiveness, the ancestral androgen receptor (ancAR1) was crystallized in complex with 5α-dihydrotestosterone (DHT) and a fragment of the transcriptional mediator/intermediary factor 2 (Tif2). Crystals diffracted to 2.1 Å resolution and the resulting structure will permit a direct comparison with its progestagen-sensitive ancestor, ancestral steroid receptor 2 (AncSR2).

  19. Inference of the ancestral vertebrate phenotype through vestiges of the whole-genome duplications.

    Science.gov (United States)

    Onimaru, Koh; Kuraku, Shigehiro

    2018-03-16

    Inferring the phenotype of the last common ancestor of living vertebrates is a challenging problem because of several unresolvable factors. They include the lack of reliable out-groups of living vertebrates, poor information about less fossilizable organs and specialized traits of phylogenetically important species, such as lampreys and hagfishes (e.g. secondary loss of vertebrae in adult hagfishes). These factors undermine the reliability of ancestral reconstruction by traditional character mapping approaches based on maximum parsimony. In this article, we formulate an approach to hypothesizing ancestral vertebrate phenotypes using information from the phylogenetic and functional properties of genes duplicated by genome expansions in early vertebrate evolution. We named the conjecture as 'chronological reconstruction of ohnolog functions (CHROF)'. This CHROF conjecture raises the possibility that the last common ancestor of living vertebrates may have had more complex traits than currently thought.

  20. Ancestral genes can control the ability of horizontally acquired loci to confer new traits.

    Directory of Open Access Journals (Sweden)

    H Deborah Chen

    2011-07-01

    Full Text Available Horizontally acquired genes typically function as autonomous units conferring new abilities when introduced into different species. However, we reasoned that proteins preexisting in an organism might constrain the functionality of a horizontally acquired gene product if it operates on an ancestral pathway. Here, we determine how the horizontally acquired pmrD gene product activates the ancestral PmrA/PmrB two-component system in Salmonella enterica but not in the closely related bacterium Escherichia coli. The Salmonella PmrD protein binds to the phosphorylated PmrA protein (PmrA-P, protecting it from dephosphorylation by the PmrB protein. This results in transcription of PmrA-dependent genes, including those conferring polymyxin B resistance. We now report that the E. coli PmrD protein can activate the PmrA/PmrB system in Salmonella even though it cannot do it in E. coli, suggesting that these two species differ in an additional component controlling PmrA-P levels. We establish that the E. coli PmrB displays higher phosphatase activity towards PmrA-P than the Salmonella PmrB, and we identified a PmrB subdomain responsible for this property. Replacement of the E. coli pmrB gene with the Salmonella homolog was sufficient to render E. coli resistant to polymyxin B under PmrD-inducing conditions. Our findings provide a singular example whereby quantitative differences in the biochemical activities of orthologous ancestral proteins dictate the ability of a horizontally acquired gene product to confer species-specific traits. And they suggest that horizontally acquired genes can potentiate selection at ancestral loci.

  1. Temperature-dependent respiration-growth relations in ancestral maize cultivars

    Science.gov (United States)

    Bruce N. Smith; Jillian L. Walker; Rebekka L. Stone; Angela R. Jones; Lee D. Hansen

    2001-01-01

    Shoots from 4- to 6-day old seedlings of seven ancestral or old cultivars of Zea mays L. were placed in a calorimeter. Dark metabolic heat rate (q) and CO2 production rate (RCO2) were measured at nine temperatures (5, 10, 15, 20, 25, 30, 35, 40, and 45 °C). Temperature dependencies of q and RCO2 were used to model response of both growth and substrate carbon conversion...

  2. Ancestral diet leads to dynamic transgenerational plasticity for five generations in Drosophila melanogaster

    OpenAIRE

    Mikheyev, Alexander; Emborski, Carmen

    2018-01-01

    Ancestral exposures can influence phenotypic expression in subsequent generations, which influence diverse biological processes ranging from phenotypic plasticity to obesity. Currently, most transgenerational studies work under the assumption of transgenerational response stability and reproducibility through time and across exposure differences, relying on short-term (i.e. 2-3 generations) single-exposure experiments. Yet, little evidence exists in the literature to validate this assumption,...

  3. Perianth evolution in Ranunculaceae: are petals ancestral in the family?

    OpenAIRE

    Nadot S.; Sauquet H.; Damerval C.; Jabbour F.; Domenech B.

    2016-01-01

    Progress has been made recently towards the elucidation of phylogenetic relationships among subfamilies and tribes of the Ranunculaceae – the most recent hypothesis was published in 2016 by our team. Although relationships among the 10 tribes of the subfamily Ranunculoideae remain incompletely supported, this hypothesis provides an interesting framework to address the key issue of the ancestral vs. derived nature of a differentiated perianth within the family, and at the level of Ranunculales...

  4. Sampling design for long-term regional trends in marine rocky intertidal communities

    Science.gov (United States)

    Irvine, Gail V.; Shelley, Alice

    2013-01-01

    Probability-based designs reduce bias and allow inference of results to the pool of sites from which they were chosen. We developed and tested probability-based designs for monitoring marine rocky intertidal assemblages at Glacier Bay National Park and Preserve (GLBA), Alaska. A multilevel design was used that varied in scale and inference. The levels included aerial surveys, extensive sampling of 25 sites, and more intensive sampling of 6 sites. Aerial surveys of a subset of intertidal habitat indicated that the original target habitat of bedrock-dominated sites with slope ≤30° was rare. This unexpected finding illustrated one value of probability-based surveys and led to a shift in the target habitat type to include steeper, more mixed rocky habitat. Subsequently, we evaluated the statistical power of different sampling methods and sampling strategies to detect changes in the abundances of the predominant sessile intertidal taxa: barnacles Balanomorpha, the mussel Mytilus trossulus, and the rockweed Fucus distichus subsp. evanescens. There was greatest power to detect trends in Mytilus and lesser power for barnacles and Fucus. Because of its greater power, the extensive, coarse-grained sampling scheme was adopted in subsequent years over the intensive, fine-grained scheme. The sampling attributes that had the largest effects on power included sampling of “vertical” line transects (vs. horizontal line transects or quadrats) and increasing the number of sites. We also evaluated the power of several management-set parameters. Given equal sampling effort, sampling more sites fewer times had greater power. The information gained through intertidal monitoring is likely to be useful in assessing changes due to climate, including ocean acidification; invasive species; trampling effects; and oil spills.

  5. Lack of Social Support Raises Stress Vulnerability in Rats with a History of Ancestral Stress.

    Science.gov (United States)

    Faraji, Jamshid; Soltanpour, Nabiollah; Lotfi, Hamid; Moeeini, Reza; Moharreri, Ali-Reza; Roudaki, Shabnam; Hosseini, S Abedin; Olson, David M; Abdollahi, Ali-Akbar; Soltanpour, Nasrin; Mohajerani, Majid H; Metz, Gerlinde A S

    2017-07-13

    Stress is a primary risk factor for psychiatric disorders. However, it is not fully understood why some stressed individuals are more vulnerable to psychiatric disorders than others. Here, we investigated whether multigenerational ancestral stress produces phenotypes that are sensitive to depression-like symptoms in rats. We also examined whether social isolation reveals potentially latent sensitivity to depression-like behaviours. F4 female rats born to a lineage of stressed mothers (F0-F3) received stress in adulthood while housed in pairs or alone. Social isolation during stress induced cognitive and psychomotor retardation only in rats exposed to ancestral stress. Social isolation also hampered the resilience of the hypothalamic-pituitary-adrenal axis to chronic stress and reduced hippocampal volume and brain-derived neurotrophic factor (BDNF) expression. Thus, synergy between social isolation and stress may unmask a latent history of ancestral stress, and raises vulnerability to mental health conditions. The findings support the notion that social support critically promotes stress coping and resilience.

  6. Ancestral state reconstruction, rate heterogeneity, and the evolution of reptile viviparity.

    Science.gov (United States)

    King, Benedict; Lee, Michael S Y

    2015-05-01

    Virtually all models for reconstructing ancestral states for discrete characters make the crucial assumption that the trait of interest evolves at a uniform rate across the entire tree. However, this assumption is unlikely to hold in many situations, particularly as ancestral state reconstructions are being performed on increasingly large phylogenies. Here, we show how failure to account for such variable evolutionary rates can cause highly anomalous (and likely incorrect) results, while three methods that accommodate rate variability yield the opposite, more plausible, and more robust reconstructions. The random local clock method, implemented in BEAST, estimates the position and magnitude of rate changes on the tree; split BiSSE estimates separate rate parameters for pre-specified clades; and the hidden rates model partitions each character state into a number of rate categories. Simulations show the inadequacy of traditional models when characters evolve with both asymmetry (different rates of change between states within a character) and heterotachy (different rates of character evolution across different clades). The importance of accounting for rate heterogeneity in ancestral state reconstruction is highlighted empirically with a new analysis of the evolution of viviparity in squamate reptiles, which reveal a predominance of forward (oviparous-viviparous) transitions and very few reversals. © The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  7. Preliminary appraisal of ground water in and near the ancestral Missouri River Valley, northeastern Montana

    Science.gov (United States)

    Levings, G.W.

    1986-01-01

    A preliminary appraisal was conducted in and near the ancestral Missouri River valley in northeastern Montana to describe the groundwater resources and to establish a data base for the area. The data base then could be used for future evaluation of possible changes in water levels or water quality. In this area, consolidated aquifers are the Upper Cretaceous Fox Hills-lower Hell Creek aquifer and the overlying Paleocene Fort Union Formation. Unconsolidated aquifers are Pleistocene terrace gravel and glacial deposits and Holocene alluvial deposits. Aquifers are recharged by precipitation, infiltration of streamflow, and possibly leakage from lakes and potholes. Groundwater moves from topographically higher areas to the ancestral valley, then along the ancestral valley to the southwest. Water is discharged from aquifers by evapotranspiration, springs and seeps, movement directly into streams and lakes, and from pumping wells. Average well yields are greatest for irrigation wells completed in outwash gravel (886 gallons/min). Eighteen wells were completed in various aquifers to monitor potential long-term changes in water levels and water quality. Measured water levels declined about 2 ft. or less during the study (1982-85). Chemical analysis of groundwater samples indicated that concentrations of some dissolved constituents exceeded U.S. Environmental Protection Agency standards for drinking water. (USGS)

  8. An allele of an ancestral transcription factor dependent on a horizontally acquired gene product.

    Science.gov (United States)

    Chen, H Deborah; Jewett, Mollie W; Groisman, Eduardo A

    2012-01-01

    Changes in gene regulatory circuits often give rise to phenotypic differences among closely related organisms. In bacteria, these changes can result from alterations in the ancestral genome and/or be brought about by genes acquired by horizontal transfer. Here, we identify an allele of the ancestral transcription factor PmrA that requires the horizontally acquired pmrD gene product to promote gene expression. We determined that a single amino acid difference between the PmrA proteins from the human adapted Salmonella enterica serovar Paratyphi B and the broad host range S. enterica serovar Typhimurium rendered transcription of PmrA-activated genes dependent on the PmrD protein in the former but not the latter serovar. Bacteria harboring the serovar Typhimurium allele exhibited polymyxin B resistance under PmrA- or under PmrA- and PmrD-inducing conditions. By contrast, isogenic strains with the serovar Paratyphi B allele displayed PmrA-regulated polymyxin B resistance only when experiencing activating conditions for both PmrA and PmrD. We establish that the two PmrA orthologs display quantitative differences in several biochemical properties. Strains harboring the serovar Paratyphi B allele showed enhanced biofilm formation, a property that might promote serovar Paratyphi B's chronic infection of the gallbladder. Our findings illustrate how subtle differences in ancestral genes can impact the ability of horizontally acquired genes to confer new properties.

  9. Distinct actions of ancestral vinclozolin and juvenile stress on neural gene expression in the male rat

    Directory of Open Access Journals (Sweden)

    Ross eGillette

    2015-03-01

    Full Text Available Exposure to the endocrine disrupting chemical vinclozolin during gestation of an F0 generation and/or chronic restraint stress during adolescence of the F3 descendants affects behavior, physiology, and gene expression in the brain. Genes related to the networks of growth factors, signaling peptides and receptors, steroid hormone receptors and enzymes, and epigenetic related factors were measured using quantitative polymerase chain reaction via Taqman low density arrays targeting 48 genes in the central amygdaloid nucleus, medial amygdaloid nucleus, medial preoptic area, lateral hypothalamus, and the ventromedial nucleus of the hypothalamus. We found that growth factors are particularly vulnerable to ancestral exposure in the central and medial amygdala; restraint stress during adolescence affected neural growth factors in the medial amygdala. Signaling peptides were affected by both ancestral exposure and stress during adolescence primarily in hypothalamic nuclei. Steroid hormone receptors and enzymes were strongly affected by restraint stress in the medial preoptic area. Epigenetic related genes were affected by stress in the ventromedial hypothalamus and by both ancestral exposure and stress during adolescence independently in the central amygdala. It is noteworthy that the lateral hypothalamus showed no effects of either manipulation. Gene expression is discussed in the context of behavioral and physiological measures previously published.

  10. Distinct actions of ancestral vinclozolin and juvenile stress on neural gene expression in the male rat.

    Science.gov (United States)

    Gillette, Ross; Miller-Crews, Isaac; Skinner, Michael K; Crews, David

    2015-01-01

    Exposure to the endocrine disrupting chemical vinclozolin during gestation of an F0 generation and/or chronic restraint stress during adolescence of the F3 descendants affects behavior, physiology, and gene expression in the brain. Genes related to the networks of growth factors, signaling peptides, and receptors, steroid hormone receptors and enzymes, and epigenetic related factors were measured using quantitative polymerase chain reaction via Taqman low density arrays targeting 48 genes in the central amygdaloid nucleus, medial amygdaloid nucleus, medial preoptic area (mPOA), lateral hypothalamus (LH), and the ventromedial nucleus of the hypothalamus. We found that growth factors are particularly vulnerable to ancestral exposure in the central and medial amygdala; restraint stress during adolescence affected neural growth factors in the medial amygdala. Signaling peptides were affected by both ancestral exposure and stress during adolescence primarily in hypothalamic nuclei. Steroid hormone receptors and enzymes were strongly affected by restraint stress in the mPOA. Epigenetic related genes were affected by stress in the ventromedial nucleus and by both ancestral exposure and stress during adolescence independently in the central amygdala. It is noteworthy that the LH showed no effects of either manipulation. Gene expression is discussed in the context of behavioral and physiological measures previously published.

  11. Ancestral informative marker selection and population structure visualization using sparse Laplacian eigenfunctions.

    Directory of Open Access Journals (Sweden)

    Jun Zhang

    Full Text Available Identification of a small panel of population structure informative markers can reduce genotyping cost and is useful in various applications, such as ancestry inference in association mapping, forensics and evolutionary theory in population genetics. Traditional methods to ascertain ancestral informative markers usually require the prior knowledge of individual ancestry and have difficulty for admixed populations. Recently Principal Components Analysis (PCA has been employed with success to select SNPs which are highly correlated with top significant principal components (PCs without use of individual ancestral information. The approach is also applicable to admixed populations. Here we propose a novel approach based on our recent result on summarizing population structure by graph laplacian eigenfunctions, which differs from PCA in that it is geometric and robust to outliers. Our approach also takes advantage of the priori sparseness of informative markers in the genome. Through simulation of a ring population and the real global population sample HGDP of 650K SNPs genotyped in 940 unrelated individuals, we validate the proposed algorithm at selecting most informative markers, a small fraction of which can recover the similar underlying population structure efficiently. Employing a standard Support Vector Machine (SVM to predict individuals' continental memberships on HGDP dataset of seven continents, we demonstrate that the selected SNPs by our method are more informative but less redundant than those selected by PCA. Our algorithm is a promising tool in genome-wide association studies and population genetics, facilitating the selection of structure informative markers, efficient detection of population substructure and ancestral inference.

  12. Pollination and reproduction of an invasive plant inside and outside its ancestral range

    Science.gov (United States)

    Petanidou, Theodora; Price, Mary V.; Bronstein, Judith L.; Kantsa, Aphrodite; Tscheulin, Thomas; Kariyat, Rupesh; Krigas, Nikos; Mescher, Mark C.; De Moraes, Consuelo M.; Waser, Nickolas M.

    2018-05-01

    Comparing traits of invasive species within and beyond their ancestral range may improve our understanding of processes that promote aggressive spread. Solanum elaeagnifolium (silverleaf nightshade) is a noxious weed in its ancestral range in North America and is invasive on other continents. We compared investment in flowers and ovules, pollination success, and fruit and seed set in populations from Arizona, USA ("AZ") and Greece ("GR"). In both countries, the populations we sampled varied in size and types of present-day disturbance. Stature of plants increased with population size in AZ samples whereas GR plants were uniformly tall. Taller plants produced more flowers, and GR plants produced more flowers for a given stature and allocated more ovules per flower. Similar functional groups of native bees pollinated in AZ and GR populations, but visits to flowers decreased with population size and we observed no visits in the largest GR populations. As a result, plants in large GR populations were pollen-limited, and estimates of fecundity were lower on average in GR populations despite the larger allocation to flowers and ovules. These differences between plants in our AZ and GR populations suggest promising directions for further study. It would be useful to sample S. elaeagnifolium in Mediterranean climates within the ancestral range (e.g., in California, USA), to study asexual spread via rhizomes, and to use common gardens and genetic studies to explore the basis of variation in allocation patterns and of relationships between visitation and fruit set.

  13. [Autoerotic fatalities in Greater Dusseldorf].

    Science.gov (United States)

    Hartung, Benno; Hellen, Florence; Borchard, Nora; Huckenbeck, Wolfgang

    2011-01-01

    Autoerotic fatalities in the Greater Dusseldorf area correspond to the relevant medicolegal literature. Our results included exclusively young to middle-aged, usually single men who were found dead in their city apartments. Clothing and devices used showed a great variety. Women's or fetish clothing and complex shackling or hanging devices were disproportionately frequent. In most cases, death occurred due to hanging or ligature strangulation. There was no increased incidence of underlying psychiatric disorders. In most of the deceased no or at least no remarkable alcohol intoxication was found. Occasionally, it may be difficult to reliably differentiate autoerotic accidents, accidents occurring in connection with practices of bondage & discipline, dominance & submission (BDSM) from natural death, suicide or homicide.

  14. Planning for greater confinement disposal

    International Nuclear Information System (INIS)

    Gilbert, T.L.; Luner, C.; Meshkov, N.K.; Trevorrow, L.E.; Yu, C.

    1985-01-01

    A report that provides guidance for planning for greater-confinement disposal (GCD) of low-level radioactive waste is being prepared. The report addresses procedures for selecting a GCD technology and provides information for implementing these procedures. The focus is on GCD; planning aspects common to GCD and shallow-land burial are covered by reference. Planning procedure topics covered include regulatory requirements, waste characterization, benefit-cost-risk assessment and pathway analysis methodologies, determination of need, waste-acceptance criteria, performance objectives, and comparative assessment of attributes that support these objectives. The major technologies covered include augered shafts, deep trenches, engineered structures, hydrofracture, improved waste forms, and high-integrity containers. Descriptive information is provided, and attributes that are relevant for risk assessment and operational requirements are given. 10 refs., 3 figs., 2 tabs

  15. Polymer solidification of mixed wastes at the Rocky Flats Plant

    International Nuclear Information System (INIS)

    Faucette, A.M.; Logsdon, B.W.; Lucerna, J.J.; Yudnich, R.J.

    1994-01-01

    The Rocky Flats Plant is pursuing polymer solidification as a viable treatment option for several mixed waste streams that are subject to land disposal restrictions within the Resource Conservation and Recovery Act provisions. Tests completed to date using both surrogate and actual wastes indicate that polyethylene microencapsulation is a viable treatment option for several mixed wastes at the Rocky Flats Plant, including nitrate salts, sludges, and secondary wastes such as ash. Treatability studies conducted on actual salt waste demonstrated that the process is capable of producing waste forms that comply with all applicable regulatory criteria, including the Toxicity Characteristic Leaching Procedure. Tests have also been conducted to evaluate the feasibility of macroencapsulating certain debris wastes in polymers. Several methods and plastics have been tested for macroencapsulation, including post-consumer recycle and regrind polyethylene

  16. Implementing DOE guidance for hazards assessments at Rocky Flats Plant

    International Nuclear Information System (INIS)

    Zimmerman, G.A.

    1993-01-01

    Hazards Assessments are performed for a variety of activities and facilities at Rocky Flats Plant. Prior to 1991, there was no guidance for performing Hazards Assessments. Each organization that performed Hazards Assessments used its own methodology with no attempt at standardization. In 1991, DOE published guidelines for the performance of Hazards Assessments for Emergency Planning (DOE-EPG-5500.1, ''Guidance for a Hazards Assessment Methodology''). Subsequently, in 1992, DOE published a standard for the performance of Hazards Assessments (DOE-STD-1027-92, ''Hazard Categorization and Accident Analysis, Techniques for Compliance with DOE Order 5480.23, Nuclear Safety Analysis Reports''). Although these documents are a step in the direction of standardization, there remains a great deal of interpretation and subjective implementation in the performance of Hazards Assessments. Rocky Flats Plant has initiated efforts to develop a uniform and standard process to be used for Hazards Assessments

  17. Actinide solution processing at the Rocky Flats Environmental Technology Site

    International Nuclear Information System (INIS)

    1995-04-01

    The Department of Energy (DOE) has prepared an Environmental Assessment (EA), DOE/EA-1039, for radioactive solution removal and processing at Rocky Flats Environmental Technology Site, Golden, Colorado. The proposal for solution removal and processing is in response to independent safety assessments and an agreement with the State of Colorado to remove mixed residues at Rocky Flats and reduce the risk of future accidents. Monthly public meetings were held during the scoping and preparation of the EA. The scope of the EA included evaluations of alternative methods and locations of solution processing. A comment period from February 20, 1995 through March 21, 1995 was provided to the public and the State of Colorado to offer written comment on the EA. Comments were received from the State of Colorado and the U.S. Environmental Protection Agency. A response to the agency comments is included in the Final EA

  18. Facility overview for commercial application of selected Rocky Flats facilities

    International Nuclear Information System (INIS)

    1996-11-01

    The purpose of this Facility Overview is to support the Rocky Flats Local Impacts Initiative's Request for Interest, to solicit interest from commercial corporations for utilizing buildings 865 and 883, and the equipment contained within each building, for a commercial venture. In the following sections, this document describes the Rocky Flats Site, the buildings available for lease, the equipment within these buildings, the site services available to a tenant, the human resources available to support operations in buildings 865 and 883, and the environmental condition of the buildings and property. In addition, a brief description is provided of the work performed to date to explore the potential products that might be manufactured in Buildings 865 and 883, and the markets for these products

  19. Taino and African maternal heritage in the Greater Antilles.

    Science.gov (United States)

    Bukhari, Areej; Luis, Javier Rodriguez; Alfonso-Sanchez, Miguel A; Garcia-Bertrand, Ralph; Herrera, Rene J

    2017-12-30

    Notwithstanding the general interest and the geopolitical importance of the island countries in the Greater Antilles, little is known about the specific ancestral Native American and African populations that settled them. In an effort to alleviate this lacuna of information on the genetic constituents of the Greater Antilles, we comprehensively compared the mtDNA compositions of Cuba, Dominican Republic, Haiti, Jamaica and Puerto Rico. To accomplish this, the mtDNA HVRI and HVRII regions, as well as coding diagnostic sites, were assessed in the Haitian general population and compared to data from reference populations. The Taino maternal DNA is prominent in the ex-Spanish colonies (61.3%-22.0%) while it is basically non-existent in the ex-French and ex-English colonies of Haiti (0.0%) and Jamaica (0.5%), respectively. The most abundant Native American mtDNA haplogroups in the Greater Antilles are A2, B2 and C1. The African mtDNA component is almost fixed in Haiti (98.2%) and Jamaica (98.5%), and the frequencies of specific African haplogroups vary considerably among the five island nations. The strong persistence of Taino mtDNA in the ex-Spanish colonies (and especially in Puerto Rico), and its absence in the French and English excolonies is likely the result of different social norms regarding mixed marriages with Taino women during the early years after the first contact with Europeans. In addition, this article reports on the results of an integrative approach based on mtDNA analysis and demographic data that tests the hypothesis of a southward shift in raiding zones along the African west coast during the period encompassing the Transatlantic Slave Trade. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. Quantitative respirator man-testing at Rocky Flats

    International Nuclear Information System (INIS)

    Leigh, J.D.

    The dioctyl phthalate quantitative respirator man-testing method used at Rocky Flats is outlined. Using this method, 93 persons trained to use self contained breathing equipment were tested with eight respiratory protective devices. Test results obtained with the seven devices using high efficiency particulate filters are compared to the results obtained with the self contained breathing equipment. Also comparison is made for these results to test results for 1667 other employees

  1. Restoration of genetic connectivity among Northern Rockies wolf populations.

    Science.gov (United States)

    Hebblewhite, Mark; Musiani, Marco; Mills, L Scott

    2010-10-01

    Probably no conservation genetics issue is currently more controversial than the question of whether grey wolves (Canis lupus) in the Northern Rockies have recovered to genetically effective levels. Following the dispersal-based recolonization of Northwestern Montana from Canada, and reintroductions to Yellowstone and Central Idaho, wolves have vastly exceeded population recovery goals of 300 wolves distributed in at least 10 breeding pairs in each of Wyoming, Idaho and Montana. With >1700 wolves currently, efforts to delist wolves from endangered status have become mired in legal battles over the distinct population segment (DPS) clause of the Endangered Species Act (ESA), and whether subpopulations within the DPS were genetically isolated. An earlier study by vonHoldt et al. (2008) suggested Yellowstone National Park wolves were indeed isolated and was used against delisting in 2008. Since then, wolves were temporarily delisted, and a first controversial hunting season occurred in fall of 2009. Yet, concerns over the genetic recovery of wolves in the Northern Rockies remain, and upcoming District court rulings in the summer of 2010 will probably include consideration of gene flow between subpopulations. In this issue of Molecular Ecology, vonHoldt et al. (2010) conduct the largest analysis of gene flow and population structure of the Northern Rockies wolves to date. Using an impressive sampling design and novel analytic methods, vonHoldt et al. (2010) show substantial levels of gene flow between three identified subpopulations of wolves within the Northern Rockies, clarifying previous analyses and convincingly showing genetic recovery. © 2010 Blackwell Publishing Ltd.

  2. Rocky Flats Plant Site Environmental Report: 1993 Highlights

    Energy Technology Data Exchange (ETDEWEB)

    1993-12-31

    The Rocky Flats Plant Site Environmental Report provides summary information on the plant`s environmental monitoring programs and the results recorded during 1993. The report contains a compliance summary, results of environmental monitoring and other related programs, a review of environmental remediation activities, information on external gamma radiation dose monitoring, and radiation dose estimates for the surrounding population. This section provides an overview of these topics and summarizes more comprehensive discussions found in the main text of this annual report.

  3. Properties of vitrified rocky flats TRUW with different waste loadings

    International Nuclear Information System (INIS)

    Eddy, T.L.; Sears, J.W.; Grandy, J.D.; Miley, D.V.; Erickson, A.W.; Farnsworth, R.N.; Larsen, E.D.

    1994-01-01

    Leach rates, phase structures, and mechanical properties of simulated Rocky Flats Plant 1st and 2nd slate sludge vitrified in an arc melter are described as a function of waste to soil fraction and method of devitrification to produce the glass-ceramic waste form. Volatile, hazardous, and transuranic (TRU) surrogate metals were added to assess dissolution effects. Zirconia and titania were also added to confirm their ability as transuranic-surrogate getters

  4. Impacts and effects of ocean warming on intertidal rocky habitats

    OpenAIRE

    Hawkins, Stephen J.; Evans, A J; Firth, L B; Genner, Martin J; Herbert, R J H; Adams, L C; Moore, P J; Mieszkowska, N; Thompson, R.C.; Burrows, M.T.; Fenberg, P.B.

    2016-01-01

    • Intertidal rocky habitats comprise over 50% of the shorelines of the world, supporting a diversity of marine life and providing extensive ecosystem services worth in the region of US$ 5-10 trillion per year. • They are valuable indicators of the impacts of climate change on the wider marine environment and ecosystems. • Changes in species distributions, abundance and phenology have already been observed around the world in response to recent rapid climate change. • Species-level responses w...

  5. Reseeding of mussels on denuded rocky shores: preliminary studies ...

    African Journals Online (AJOL)

    A method is developed to establish clumps of mussels Perna perna in denuded areas on high-energy rocky shores on the south-east coast of South Africa. A total of 20 small (20–30 mm total length) mussels is placed under a 30 cm half-section of perforated PVC drainage pipe bolted to the rock surface. The pipe is left in ...

  6. Quantitative respirator man-testing at Rocky Flats

    Energy Technology Data Exchange (ETDEWEB)

    Leigh, J. D.

    1978-01-01

    The dioctyl phthalate quantitative respirator man-testing method used at Rocky Flats is outlined. Using this method, 93 persons trained to use self contained breathing equipment were tested with eight respiratory protective devices. Test results obtained with the seven devices using high efficiency particulate filters are compared to the results obtained with the self contained breathing equipment. Also comparison is made for these results to test results for 1667 other employees.

  7. Rocky Flats Plant Site Environmental Report: 1993 Highlights

    International Nuclear Information System (INIS)

    1993-01-01

    The Rocky Flats Plant Site Environmental Report provides summary information on the plant's environmental monitoring programs and the results recorded during 1993. The report contains a compliance summary, results of environmental monitoring and other related programs, a review of environmental remediation activities, information on external gamma radiation dose monitoring, and radiation dose estimates for the surrounding population. This section provides an overview of these topics and summarizes more comprehensive discussions found in the main text of this annual report

  8. Immune Thrombocytopenia as a Consequence of Rocky Mountain Spotted Fever

    OpenAIRE

    Baldeo, Cherisse; Seegobin, Karan; Zuberi, Lara

    2017-01-01

    Primary immune thrombocytopenia (ITP) – also called idiopathic thrombocytopenic purpura or immune thrombocytopenic purpura – is an acquired thrombocytopenia caused by autoantibodies against platelet antigens. It is one of the more common causes of thrombocytopenia in otherwise asymptomatic adults. Rocky Mountain spotted fever (RMSF) is a potentially lethal, but curable, tick-borne disease. We present a case of ITP that was triggered by RMSF.

  9. Immune Thrombocytopenia as a Consequence of Rocky Mountain Spotted Fever

    Directory of Open Access Journals (Sweden)

    Cherisse Baldeo

    2017-10-01

    Full Text Available Primary immune thrombocytopenia (ITP – also called idiopathic thrombocytopenic purpura or immune thrombocytopenic purpura – is an acquired thrombocytopenia caused by autoantibodies against platelet antigens. It is one of the more common causes of thrombocytopenia in otherwise asymptomatic adults. Rocky Mountain spotted fever (RMSF is a potentially lethal, but curable, tick-borne disease. We present a case of ITP that was triggered by RMSF.

  10. Rocky Mountain spotted fever acquired in Florida, 1973-83.

    Science.gov (United States)

    Sacks, J J; Janowski, H T

    1985-01-01

    From 1973 to 1983, 49 Florida residents were reported with confirmed Rocky Mountain spotted fever (RMSF), 25 of whom were considered to have had Florida-acquired disease. Although there was no history of tick exposure for six of these 25 persons, all had contact with dogs or outdoor activities during the incubation period. The tick vectors of RMSF are widely distributed throughout Florida. We conclude that RMSF, although rare in Florida, can be acquired in the state. PMID:4061716

  11. DOE awards first economic conversion project at Rocky Flats

    International Nuclear Information System (INIS)

    Lobsenz, G.

    1993-01-01

    In the first economic conversion project at an Energy Department weapons facility, a Colorado company this week was given permission to refurbish four buildings at DOE's Rocky Flats plant to recycle slightly radioactive scrap metal. DOE, acting in conjunction with the Environmental Protection Agency and Colorado authorities, announced Tuesday it had given the go-ahead to Manufacturing Sciences Corp. of Golden, Colorado, to proceed with planning for the project

  12. Treatment of pond sludge at the Rocky Flats Plant

    International Nuclear Information System (INIS)

    Wienand, J.; Tyler, R.; Baldwin, C.

    1992-01-01

    The treatment of low-level radioactive/hazardous materials sludges from five inactive solar evaporation settling ponds at the Rocky Flats Plant is discussed. The paper presents information on the following topics: history of the ponds; previous pond cleanout activities; current approach to the problem with respect to water management, sludge management, regulatory actions, and disposal; and future processing technology needs in the areas of polymer solidification, microwave solidification, joule-heated glass melters, and advanced technology incineration

  13. Litigation Technical Support and Services, Rocky Mountain Arsenal

    Science.gov (United States)

    1989-05-01

    34 d V) W C > - d) 4- -~ 0 - - .4 ..- di L *..L 3~1 3-~ v mi a- a t - --- w- Vdi 4 - ý 0 -4 0 m~ -j m0 m’ .- us 0 Ill i to -v .4 I 4 1 t A ~ 3Ul t -4...2060. Marlow, D. J. 1979g, November 8. Pest control report, October 1979. Rocky Mountain Arsenal. Microfilm RMA182, Franes 2048 -2053 Marlow, D. J

  14. The ancestral chromosomes of Dromiciops gliroides (Microbiotheridae), and its bearings on the karyotypic evolution of American marsupials

    OpenAIRE

    Su?rez-Villota, Elkin Y.; Haro, Ronie E.; Vargas, Rodrigo A.; Gallardo, Milton H.

    2016-01-01

    Background The low-numbered 14-chromosome karyotype of marsupials has falsified the fusion hypothesis claiming ancestrality from a 22-chromosome karyotype. Since the 14-chromosome condition of the relict Dromiciops gliroides is reminecent of ancestrality, its interstitial traces of past putative fusions and heterochromatin banding patterns were studied and added to available marsupials? cytogenetic data. Fluorescent in situ hybridization (FISH) and self-genomic in situ hybridization (self-GIS...

  15. Evidence that the ancestral haplotype in Australian hemochromatosis patients may be associated with a common mutation in the gene.

    OpenAIRE

    Crawford, D H; Powell, L W; Leggett, B A; Francis, J S; Fletcher, L M; Webb, S I; Halliday, J W; Jazwinska, E C

    1995-01-01

    Hemochromatosis (HC) is a common inherited disorder of iron metabolism for which neither the gene nor biochemical defect have yet been identified. The aim of this study was to look for clinical evidence that the predominant ancestral haplotype in Australian patients is associated with a common mutation in the gene. We compared indices of iron metabolism and storage in three groups of HC patients categorized according to the presence of the ancestral haplotype (i.e., patients with two copies, ...

  16. The rocky flats controversy on radionuclide soil action levels

    International Nuclear Information System (INIS)

    Earle, T.C.

    2004-01-01

    An account of the Rocky Flats radionuclide soil action level controversy is presented as: a case study for the purpose of understanding the nature and value of stakeholder involvement in the management of radiological hazards. The report consists of three main sections. The first section outlines the Rocky Flats story, including the Cold War era, which was characterised by secrecy and distrust, the post-Cold War era, in which trust and co-operation between risk managers and the public began to develop. This contrast between these two historical periods provides the context necessary to understand the radionuclide soil action level controversy, the main events of which are described in the second section. In the final section, the Rocky Flats case is briefly discussed within the framework of a general model of stakeholder involvement and the lessons learned from the case are identified: (1) without a basis in shared values, collaborative public involvement in the management of radiological hazards is not possible; (2) given a basis in shared values, collaborative public involvement can lead to improved solutions to the management of radiological hazards; and (3) risk managers should therefore seek to understand the values of public stakeholders and to identify ways, through stakeholder involvement, that those values can be incorporated in management practice. (author)

  17. Rocky flats closure project - lessons learned in worker stakeholder engagement

    Energy Technology Data Exchange (ETDEWEB)

    Sweeney, Laura [Des Moines Area Community College, Ankeny, Iowa (United States); Mazur, Robert E. [Iowa State University, Ames, Iowa (United States); Edelson, Martin [Ames Laboratory-USDOE (Retired), Ames, Iowa (United States)

    2013-07-01

    The Rocky Flats Environmental Technology Site (EPA Superfund site near Denver, Colorado) produced plutonium components for nuclear weapons for the U.S. defense program. The facility shut down in 1989 and clean up began in 1992. To ensure safe remediation of inactive nuclear sites, site owners have begun to consult stakeholders more widely in recent years. The closure of Rocky Flats aimed to set the standard for stakeholder involvement in doing the work safely, complying with regulations/standards, in a cost-effective manner. We have studied, using ethnographic methods, the extent to which workers at Rocky Flats were involved in communication and decision making strategies. Our results point out that workers can have perceptions of the site remediation process that differ from management and even other workers and that a significant number of workers questioned the commitment by management to engage the worker as stakeholder. The most effective remediation efforts should involve careful consideration of the insights and observations of all workers, particularly those who face immediate and high-level health and safety risks. (authors)

  18. [Rocky Mountain spotted fever in an American tourist].

    Science.gov (United States)

    de Pender, A M G; Bauer, A G C; van Genderen, P J J

    2005-04-02

    In a 28-year-old male American tourist who presented in the hospital with fever, cold shivers, headache, nausea, myalgia and arthralgia, Rocky Mountain spotted fever was suspected, partly because he came from an endemic region (the state of Georgia). The patient was treated with doxycycline, 100 mg b.i.d.; 9 days after the first appearance of the symptoms, the diagnosis was confirmed by the report of a positive antibody titre against Rickettsia rickettsii. The patient did not have exanthema. He was discharged in good general condition after two weeks of treatment. Rocky Mountain spotted fever, caused by the Gram-negative bacterium R. rickettsii, is a serious rickettsiosis. The disease is seen only sporadically in the Netherlands because the ticks in the Netherlands do not carry the bacterium. The travel history is still not a standard component of the anamnesis and is therefore often forgotten. This can lead to under-diagnosis and delayed treatment of diseases that were formerly limited to the continent. The early recognition and treatment of Rocky Mountain spotted fever is important since delayed treatment is associated with a clear increase in both morbidity and mortality.

  19. Rocky Mountain spotted fever in Mexico: past, present, and future.

    Science.gov (United States)

    Álvarez-Hernández, Gerardo; Roldán, Jesús Felipe González; Milan, Néstor Saúl Hernández; Lash, R Ryan; Behravesh, Casey Barton; Paddock, Christopher D

    2017-06-01

    Rocky Mountain spotted fever, a tick-borne zoonosis caused by Rickettsia rickettsii, is among the most lethal of all infectious diseases in the Americas. In Mexico, the disease was first described during the early 1940s by scientists who carefully documented specific environmental determinants responsible for devastating outbreaks in several communities in the states of Sinaloa, Sonora, Durango, and Coahuila. These investigators also described the pivotal roles of domesticated dogs and Rhipicephalus sanguineus sensu lato (brown dog ticks) as drivers of epidemic levels of Rocky Mountain spotted fever. After several decades of quiescence, the disease re-emerged in Sonora and Baja California during the early 21st century, driven by the same environmental circumstances that perpetuated outbreaks in Mexico during the 1940s. This Review explores the history of Rocky Mountain spotted fever in Mexico, current epidemiology, and the multiple clinical, economic, and social challenges that must be considered in the control and prevention of this life-threatening illness. Copyright © 2017 Elsevier Ltd. All rights reserved.

  20. Rocky flats closure project - lessons learned in worker stakeholder engagement

    International Nuclear Information System (INIS)

    Sweeney, Laura; Mazur, Robert E.; Edelson, Martin

    2013-01-01

    The Rocky Flats Environmental Technology Site (EPA Superfund site near Denver, Colorado) produced plutonium components for nuclear weapons for the U.S. defense program. The facility shut down in 1989 and clean up began in 1992. To ensure safe remediation of inactive nuclear sites, site owners have begun to consult stakeholders more widely in recent years. The closure of Rocky Flats aimed to set the standard for stakeholder involvement in doing the work safely, complying with regulations/standards, in a cost-effective manner. We have studied, using ethnographic methods, the extent to which workers at Rocky Flats were involved in communication and decision making strategies. Our results point out that workers can have perceptions of the site remediation process that differ from management and even other workers and that a significant number of workers questioned the commitment by management to engage the worker as stakeholder. The most effective remediation efforts should involve careful consideration of the insights and observations of all workers, particularly those who face immediate and high-level health and safety risks. (authors)

  1. Map of mixed prairie grassland vegetation, Rocky Flats, Colorado

    Energy Technology Data Exchange (ETDEWEB)

    Clark, S J.V.; Webber, P J; Komarkova, V; Weber, W A

    1980-01-01

    A color vegetation map at the scale of 1:12,000 of the area surrounding the Rocky Flats, Rockwell International Plant near Boulder, Colorado, provides a permanent record of baseline data which can be used to monitor changes in both vegetation and environment and thus to contribute to future land management and land-use policies. Sixteen mapping units based on species composition were identified, and characterized by two 10-m/sup 2/ vegetation stands each. These were grouped into prairie, pasture, and valley side on the basis of their species composition. Both the mapping units and these major groups were later confirmed by agglomerative clustering analysis of the 32 vegetation stands on the basis of species composition. A modified Bray and Curtis ordination was used to determine the environmental factor complexes controlling the distribution of vegetation at Rocky flats. Recommendations are made for future policies of environmental management and predictions of the response to environmental change of the present vegetation at the Rocky Flats site.

  2. Evidence that the ancestral haplotype in Australian hemochromatosis patients may be associated with a common mutation in the gene

    Energy Technology Data Exchange (ETDEWEB)

    Crawford, D.H.G.; Powell, L.W.; Leggett, B.A. [Univ. of Queensland (Australia)] [and others

    1995-08-01

    Hemochromatosis (HC) is a common inherited disorder of iron metabolism for which neither the gene nor biochemical defect have yet been identified. The aim of this study was to look for clinical evidence that the predominant ancestral haplotype in Australian patients is associated with a common mutation in the gene. We compared indices of iron metabolism and storage in three groups of HC patients categorized according to the presence of the ancestral haplotype (i.e., patients with two copies, one copy, and no copies of the ancestral haplotype). We also examined iron indices in two groups of HC heterozygotes (those with the ancestral haplotype and those without) and in age-matched controls. These analyses indicate that (i) HC patients with two copies of the ancestral haplotype show significantly more severe expression of the disorder than those with one copy or those without, (ii) HC heterozygotes have partial clinical expression, which may be influenced by the presence of the ancestral haplotype in females but not in males, and (iii) the high population frequency of the HC gene may be the result of the selective advantage conferred by protecting heterozygotes against iron deficiency. 18 refs., 3 tabs.

  3. Waste management in Greater Vancouver

    Energy Technology Data Exchange (ETDEWEB)

    Carrusca, K. [Greater Vancouver Regional District, Burnaby, BC (Canada); Richter, R. [Montenay Inc., Vancouver, BC (Canada)]|[Veolia Environmental Services, Vancouver, BC (Canada)

    2006-07-01

    An outline of the Greater Vancouver Regional District (GVRD) waste-to-energy program was presented. The GVRD has an annual budget for solid waste management of $90 million. Energy recovery revenues from solid waste currently exceed $10 million. Over 1,660,00 tonnes of GVRD waste is recycled, and another 280,000 tonnes is converted from waste to energy. The GVRD waste-to-energy facility combines state-of-the-art combustion and air pollution control, and has processed over 5 million tonnes of municipal solid waste since it opened in 1988. Its central location minimizes haul distance, and it was originally sited to utilize steam through sales to a recycle paper mill. The facility has won several awards, including the Solid Waste Association of North America award for best facility in 1990. The facility focuses on continual improvement, and has installed a carbon injection system; an ammonia injection system; a flyash stabilization system; and heat capacity upgrades in addition to conducting continuous waste composition studies. Continuous air emissions monitoring is also conducted at the plant, which produces a very small percentage of the total air emissions in metropolitan Vancouver. The GVRD is now seeking options for the management of a further 500,000 tonnes per year of solid waste, and has received 23 submissions from a range of waste energy technologies which are now being evaluated. It was concluded that waste-to-energy plants can be located in densely populated metropolitan areas and provide a local disposal solution as well as a source of renewable energy. Other GVRD waste reduction policies were also reviewed. refs., tabs., figs.

  4. The effect of a small creek valley on drainage flows in the Rocky Flats region

    International Nuclear Information System (INIS)

    Porch, W.

    1996-01-01

    Regional scale circulation and mountain-plain interactions and effects on boundary layer development are important for understanding the fate of an atmospheric release from Rocky Flats, Colorado. Numerical modeling of Front Range topographic effects near Rocky Flats have shown that though the Front Range dominates large scale flow features, small-scale terrain features near Rocky Flats are important to local transport during nighttime drainage flow conditions. Rocky Flats has been the focus of interest for the Department of Energy's Atmospheric Studies in Complex Terrain (ASCOT) program

  5. Evolution of sexes from an ancestral mating-type specification pathway.

    Directory of Open Access Journals (Sweden)

    Sa Geng

    2014-07-01

    Full Text Available Male and female sexes have evolved repeatedly in eukaryotes but the origins of dimorphic sexes and their relationship to mating types in unicellular species are not understood. Volvocine algae include isogamous species such as Chlamydomonas reinhardtii, with two equal-sized mating types, and oogamous multicellular species such as Volvox carteri with sperm-producing males and egg-producing females. Theoretical work predicts genetic linkage of a gamete cell-size regulatory gene(s to an ancestral mating-type locus as a possible step in the evolution of dimorphic gametes, but this idea has not been tested. Here we show that, contrary to predictions, a single conserved mating locus (MT gene in volvocine algae-MID, which encodes a RWP-RK domain transcription factor-evolved from its ancestral role in C. reinhardtii as a mating-type specifier, to become a determinant of sperm and egg development in V. carteri. Transgenic female V. carteri expressing male MID produced functional sperm packets during sexual development. Transgenic male V. carteri with RNA interference (RNAi-mediated knockdowns of VcMID produced functional eggs, or self-fertile hermaphrodites. Post-transcriptional controls were found to regulate cell-type-limited expression and nuclear localization of VcMid protein that restricted its activity to nuclei of developing male germ cells and sperm. Crosses with sex-reversed strains uncoupled sex determination from sex chromosome identity and revealed gender-specific roles for male and female mating locus genes in sexual development, gamete fitness and reproductive success. Our data show genetic continuity between the mating-type specification and sex determination pathways of volvocine algae, and reveal evidence for gender-specific adaptations in the male and female mating locus haplotypes of Volvox. These findings will enable a deeper understanding of how a master regulator of mating-type determination in an ancestral unicellular species was

  6. What was the ancestral sex-determining mechanism in amniote vertebrates?

    Science.gov (United States)

    Johnson Pokorná, Martina; Kratochvíl, Lukáš

    2016-02-01

    Amniote vertebrates, the group consisting of mammals and reptiles including birds, possess various mechanisms of sex determination. Under environmental sex determination (ESD), the sex of individuals depends on the environmental conditions occurring during their development and therefore there are no sexual differences present in their genotypes. Alternatively, through the mode of genotypic sex determination (GSD), sex is determined by a sex-specific genotype, i.e. by the combination of sex chromosomes at various stages of differentiation at conception. As well as influencing sex determination, sex-specific parts of genomes may, and often do, develop specific reproductive or ecological roles in their bearers. Accordingly, an individual with a mismatch between phenotypic (gonadal) and genotypic sex, for example an individual sex-reversed by environmental effects, should have a lower fitness due to the lack of specialized, sex-specific parts of their genome. In this case, evolutionary transitions from GSD to ESD should be less likely than transitions in the opposite direction. This prediction contrasts with the view that GSD was the ancestral sex-determining mechanism for amniote vertebrates. Ancestral GSD would require several transitions from GSD to ESD associated with an independent dedifferentiation of sex chromosomes, at least in the ancestors of crocodiles, turtles, and lepidosaurs (tuataras and squamate reptiles). In this review, we argue that the alternative theory postulating ESD as ancestral in amniotes is more parsimonious and is largely concordant with the theoretical expectations and current knowledge of the phylogenetic distribution and homology of sex-determining mechanisms. © 2014 Cambridge Philosophical Society.

  7. Analysis of ancestral and functionally relevant CD5 variants in systemic lupus erythematosus patients.

    Directory of Open Access Journals (Sweden)

    Maria Carmen Cenit

    Full Text Available CD5 plays a crucial role in autoimmunity and is a well-established genetic risk factor of developing RA. Recently, evidence of positive selection has been provided for the CD5 Pro224-Val471 haplotype in East Asian populations. The aim of the present work was to further analyze the functional relevance of non-synonymous CD5 polymorphisms conforming the ancestral and the newly derived haplotypes (Pro224-Ala471 and Pro224-Val471, respectively as well as to investigate the potential role of CD5 on the development of SLE and/or SLE nephritis.The CD5 SNPs rs2241002 (C/T; Pro224Leu and rs2229177 (C/T; Ala471Val were genotyped using TaqMan allelic discrimination assays in a total of 1,324 controls and 681 SLE patients of Spanish origin. In vitro analysis of CD3-mediated T cell proliferative and cytokine response profiles of healthy volunteers homozygous for the above mentioned CD5 haplotypes were also analyzed.T-cell proliferation and cytokine release were significantly increased showing a bias towards to a Th2 profile after CD3 cross-linking of peripheral mononuclear cells from healthy individuals homozygous for the ancestral Pro224-Ala471 (CC haplotype, compared to the more recently derived Pro224-Val471 (CT. The same allelic combination was statistically associated with Lupus nephritis.The ancestral Ala471 CD5 allele confers lymphocyte hyper-responsiveness to TCR/CD3 cross-linking and is associated with nephritis in SLE patients.

  8. Do Père David's deer lose memories of their ancestral predators?

    Directory of Open Access Journals (Sweden)

    Chunwang Li

    Full Text Available Whether prey retains antipredator behavior after a long period of predator relaxation is an important question in predator-prey evolution. Père David's deer have been raised in enclosures for more than 1200 years and this isolation provides an opportunity to study whether Père David's deer still respond to the cues of their ancestral predators or to novel predators. We played back the sounds of crows (familiar sound and domestic dogs (familiar non-predators, of tigers and wolves (ancestral predators, and of lions (potential naïve predator to Père David's deer in paddocks, and blank sounds to the control group, and videoed the behavior of the deer during the experiment. We also showed life-size photo models of dog, leopard, bear, tiger, wolf, and lion to the deer and video taped their responses after seeing these models. Père David's deer stared at and approached the hidden loudspeaker when they heard the roars of tiger or lion. The deer listened to tiger roars longer, approached to tiger roars more and spent more time staring at the tiger model. The stags were also found to forage less in the trials of tiger roars than that of other sound playbacks. Additionally, it took longer for the deer to restore their normal behavior after they heard tiger roars, which was longer than that after the trial of other sound playbacks. Moreover, the deer were only found to walk away after hearing the sounds of tiger and wolf. Therefore, the tiger was probably the main predator for Père David's deer in ancient time. Our study implies that Père David's deer still retain the memories of the acoustic and visual cues of their ancestral predators in spite of the long term isolation from natural habitat.

  9. The mammary gland-specific marsupial ELP and eutherian CTI share a common ancestral gene.

    Science.gov (United States)

    Pharo, Elizabeth A; De Leo, Alison A; Renfree, Marilyn B; Thomson, Peter C; Lefèvre, Christophe M; Nicholas, Kevin R

    2012-06-08

    The marsupial early lactation protein (ELP) gene is expressed in the mammary gland and the protein is secreted into milk during early lactation (Phase 2A). Mature ELP shares approximately 55.4% similarity with the colostrum-specific bovine colostrum trypsin inhibitor (CTI) protein. Although ELP and CTI both have a single bovine pancreatic trypsin inhibitor (BPTI)-Kunitz domain and are secreted only during the early lactation phases, their evolutionary history is yet to be investigated. Tammar ELP was isolated from a genomic library and the fat-tailed dunnart and Southern koala ELP genes cloned from genomic DNA. The tammar ELP gene was expressed only in the mammary gland during late pregnancy (Phase 1) and early lactation (Phase 2A). The opossum and fat-tailed dunnart ELP and cow CTI transcripts were cloned from RNA isolated from the mammary gland and dog CTI from cells in colostrum. The putative mature ELP and CTI peptides shared 44.6%-62.2% similarity. In silico analyses identified the ELP and CTI genes in the other species examined and provided compelling evidence that they evolved from a common ancestral gene. In addition, whilst the eutherian CTI gene was conserved in the Laurasiatherian orders Carnivora and Cetartiodactyla, it had become a pseudogene in others. These data suggest that bovine CTI may be the ancestral gene of the Artiodactyla-specific, rapidly evolving chromosome 13 pancreatic trypsin inhibitor (PTI), spleen trypsin inhibitor (STI) and the five placenta-specific trophoblast Kunitz domain protein (TKDP1-5) genes. Marsupial ELP and eutherian CTI evolved from an ancestral therian mammal gene before the divergence of marsupials and eutherians between 130 and 160 million years ago. The retention of the ELP gene in marsupials suggests that this early lactation-specific milk protein may have an important role in the immunologically naïve young of these species.

  10. The mammary gland-specific marsupial ELP and eutherian CTI share a common ancestral gene

    Directory of Open Access Journals (Sweden)

    Pharo Elizabeth A

    2012-06-01

    Full Text Available Abstract Background The marsupial early lactation protein (ELP gene is expressed in the mammary gland and the protein is secreted into milk during early lactation (Phase 2A. Mature ELP shares approximately 55.4% similarity with the colostrum-specific bovine colostrum trypsin inhibitor (CTI protein. Although ELP and CTI both have a single bovine pancreatic trypsin inhibitor (BPTI-Kunitz domain and are secreted only during the early lactation phases, their evolutionary history is yet to be investigated. Results Tammar ELP was isolated from a genomic library and the fat-tailed dunnart and Southern koala ELP genes cloned from genomic DNA. The tammar ELP gene was expressed only in the mammary gland during late pregnancy (Phase 1 and early lactation (Phase 2A. The opossum and fat-tailed dunnart ELP and cow CTI transcripts were cloned from RNA isolated from the mammary gland and dog CTI from cells in colostrum. The putative mature ELP and CTI peptides shared 44.6%-62.2% similarity. In silico analyses identified the ELP and CTI genes in the other species examined and provided compelling evidence that they evolved from a common ancestral gene. In addition, whilst the eutherian CTI gene was conserved in the Laurasiatherian orders Carnivora and Cetartiodactyla, it had become a pseudogene in others. These data suggest that bovine CTI may be the ancestral gene of the Artiodactyla-specific, rapidly evolving chromosome 13 pancreatic trypsin inhibitor (PTI, spleen trypsin inhibitor (STI and the five placenta-specific trophoblast Kunitz domain protein (TKDP1-5 genes. Conclusions Marsupial ELP and eutherian CTI evolved from an ancestral therian mammal gene before the divergence of marsupials and eutherians between 130 and 160 million years ago. The retention of the ELP gene in marsupials suggests that this early lactation-specific milk protein may have an important role in the immunologically naïve young of these species.

  11. Bayesian phylogeography of influenza A/H3N2 for the 2014-15 season in the United States using three frameworks of ancestral state reconstruction.

    Directory of Open Access Journals (Sweden)

    Daniel Magee

    2017-02-01

    Full Text Available Ancestral state reconstructions in Bayesian phylogeography of virus pandemics have been improved by utilizing a Bayesian stochastic search variable selection (BSSVS framework. Recently, this framework has been extended to model the transition rate matrix between discrete states as a generalized linear model (GLM of genetic, geographic, demographic, and environmental predictors of interest to the virus and incorporating BSSVS to estimate the posterior inclusion probabilities of each predictor. Although the latter appears to enhance the biological validity of ancestral state reconstruction, there has yet to be a comparison of phylogenies created by the two methods. In this paper, we compare these two methods, while also using a primitive method without BSSVS, and highlight the differences in phylogenies created by each. We test six coalescent priors and six random sequence samples of H3N2 influenza during the 2014-15 flu season in the U.S. We show that the GLMs yield significantly greater root state posterior probabilities than the two alternative methods under five of the six priors, and significantly greater Kullback-Leibler divergence values than the two alternative methods under all priors. Furthermore, the GLMs strongly implicate temperature and precipitation as driving forces of this flu season and nearly unanimously identified a single root state, which exhibits the most tropical climate during a typical flu season in the U.S. The GLM, however, appears to be highly susceptible to sampling bias compared with the other methods, which casts doubt on whether its reconstructions should be favored over those created by alternate methods. We report that a BSSVS approach with a Poisson prior demonstrates less bias toward sample size under certain conditions than the GLMs or primitive models, and believe that the connection between reconstruction method and sampling bias warrants further investigation.

  12. Sustainability of ancestral methods of agricultural production in Perú: ¿keep or replace?

    Directory of Open Access Journals (Sweden)

    Dani Eduardo Vargas Huanca

    2016-09-01

    Full Text Available Based on the success of some Andean products such as quinoa, potatoes or maca in international food trade and the growing environmental degradation facing developing countries, resulting from intensive exploitation activities; Our research seeks to show the trend that is assumed from the academic / scientific community and public officials in the food sector in Peru, against the need to maintain sustainable various ancestral modes of agricultural production (case quinoa, for it analyze quantitative and qualitative obtained from public institutions and Peruvian universities.

  13. Comparative analysis of rosaceous genomes and the reconstruction of a putative ancestral genome for the family.

    Science.gov (United States)

    Illa, Eudald; Sargent, Daniel J; Lopez Girona, Elena; Bushakra, Jill; Cestaro, Alessandro; Crowhurst, Ross; Pindo, Massimo; Cabrera, Antonio; van der Knaap, Esther; Iezzoni, Amy; Gardiner, Susan; Velasco, Riccardo; Arús, Pere; Chagné, David; Troggio, Michela

    2011-01-12

    Comparative genome mapping studies in Rosaceae have been conducted until now by aligning genetic maps within the same genus, or closely related genera and using a limited number of common markers. The growing body of genomics resources and sequence data for both Prunus and Fragaria permits detailed comparisons between these genera and the recently released Malus × domestica genome sequence. We generated a comparative analysis using 806 molecular markers that are anchored genetically to the Prunus and/or Fragaria reference maps, and physically to the Malus genome sequence. Markers in common for Malus and Prunus, and Malus and Fragaria, respectively were 784 and 148. The correspondence between marker positions was high and conserved syntenic blocks were identified among the three genera in the Rosaceae. We reconstructed a proposed ancestral genome for the Rosaceae. A genome containing nine chromosomes is the most likely candidate for the ancestral Rosaceae progenitor. The number of chromosomal translocations observed between the three genera investigated was low. However, the number of inversions identified among Malus and Prunus was much higher than any reported genome comparisons in plants, suggesting that small inversions have played an important role in the evolution of these two genera or of the Rosaceae.

  14. Comparative analysis of rosaceous genomes and the reconstruction of a putative ancestral genome for the family

    Directory of Open Access Journals (Sweden)

    Velasco Riccardo

    2011-01-01

    Full Text Available Abstract Background Comparative genome mapping studies in Rosaceae have been conducted until now by aligning genetic maps within the same genus, or closely related genera and using a limited number of common markers. The growing body of genomics resources and sequence data for both Prunus and Fragaria permits detailed comparisons between these genera and the recently released Malus × domestica genome sequence. Results We generated a comparative analysis using 806 molecular markers that are anchored genetically to the Prunus and/or Fragaria reference maps, and physically to the Malus genome sequence. Markers in common for Malus and Prunus, and Malus and Fragaria, respectively were 784 and 148. The correspondence between marker positions was high and conserved syntenic blocks were identified among the three genera in the Rosaceae. We reconstructed a proposed ancestral genome for the Rosaceae. Conclusions A genome containing nine chromosomes is the most likely candidate for the ancestral Rosaceae progenitor. The number of chromosomal translocations observed between the three genera investigated was low. However, the number of inversions identified among Malus and Prunus was much higher than any reported genome comparisons in plants, suggesting that small inversions have played an important role in the evolution of these two genera or of the Rosaceae.

  15. Ancestral state reconstruction infers phytopathogenic origins of sooty blotch and flyspeck fungi on apple.

    Science.gov (United States)

    Ismail, Siti Izera; Batzer, Jean Carlson; Harrington, Thomas C; Crous, Pedro W; Lavrov, Dennis V; Li, Huanyu; Gleason, Mark L

    2016-01-01

    Members of the sooty blotch and flyspeck (SBFS) complex are epiphytic fungi in the Ascomycota that cause economically damaging blemishes of apples worldwide. SBFS fungi are polyphyletic, but approx. 96% of SBFS species are in the Capnodiales. Evolutionary origins of SBFS fungi remain unclear, so we attempted to infer their origins by means of ancestral state reconstruction on a phylogenetic tree built utilizing genes for the nuc 28S rDNA (approx. 830 bp from near the 59 end) and the second largest subunit of RNA polymerase II (RPB2). The analyzed taxa included the well-known genera of SBFS as well as non-SBFS fungi from seven families within the Capnodiales. The non-SBFS taxa were selected based on their distinct ecological niches, including plant-parasitic and saprophytic species. The phylogenetic analyses revealed that most SBFS species in the Capnodiales are closely related to plant-parasitic fungi. Ancestral state reconstruction provided strong evidence that plant-parasitic fungi were the ancestors of the major SBFS lineages. Knowledge gained from this study may help to better understand the ecology and evolution of epiphytic fungi. © 2016 by The Mycological Society of America.

  16. Reconstructing an ancestral mammalian immune supercomplex from a marsupial major histocompatibility complex.

    Directory of Open Access Journals (Sweden)

    Katherine Belov

    2006-03-01

    Full Text Available The first sequenced marsupial genome promises to reveal unparalleled insights into mammalian evolution. We have used the Monodelphis domestica (gray short-tailed opossum sequence to construct the first map of a marsupial major histocompatibility complex (MHC. The MHC is the most gene-dense region of the mammalian genome and is critical to immunity and reproductive success. The marsupial MHC bridges the phylogenetic gap between the complex MHC of eutherian mammals and the minimal essential MHC of birds. Here we show that the opossum MHC is gene dense and complex, as in humans, but shares more organizational features with non-mammals. The Class I genes have amplified within the Class II region, resulting in a unique Class I/II region. We present a model of the organization of the MHC in ancestral mammals and its elaboration during mammalian evolution. The opossum genome, together with other extant genomes, reveals the existence of an ancestral "immune supercomplex" that contained genes of both types of natural killer receptors together with antigen processing genes and MHC genes.

  17. Evidence for Ancestral Programming of Resilience in a Two-Hit Stress Model

    Directory of Open Access Journals (Sweden)

    Jamshid Faraji

    2017-05-01

    Full Text Available In a continuously stressful environment, the effects of recurrent prenatal stress (PS may accumulate across generations and alter stress vulnerability and resilience. Here, we report in female rats that a family history of recurrent ancestral PS facilitates certain aspects of movement performance, and that these benefits are abolished by the experience of a second hit, induced by a silent ischemia during adulthood. Female F4-generation rats with and without a family history of cumulative multigenerational PS (MPS were tested for skilled motor function before and after the induction of a minor ischemic insult by endothelin-1 infusion into the primary motor cortex. MPS resulted in improved skilled motor abilities and blunted hypothalamic-pituitary-adrenal (HPA axis function compared to non-stressed rats. Deep sequencing revealed downregulation of miR-708 in MPS rats along with upregulation of its predicted target genes Mapk10 and Rasd2. Through miR-708 stress may regulate mitogen-activated protein kinase (MAPK pathway activity. Hair trace elemental analysis revealed an increased Na/K ratio, which suggests a chronic shift in adrenal gland function. The ischemic lesion activated the HPA axis in MPS rats only; the lesion, however, abolished the advantage of MPS in skilled reaching. The findings indicate that MPS generates adaptive flexibility in movement, which is challenged by a second stressor, such as a neuropathological condition. Thus, a second “hit” by a stressor may limit behavioral flexibility and neural plasticity associated with ancestral stress.

  18. Bearing the unbearable: ancestral transmission through dreams and moving metaphors in the analtyic field.

    Science.gov (United States)

    Pickering, Judith

    2012-11-01

    This paper explores how untold and unresolved intergenerational trauma may be transmitted through unconscious channels of communication, manifesting in the dreams of descendants. Unwitting carriers for that which was too horrific for their ancestors to bear, descendants may enter analysis through an unconscious need to uncover past secrets, piece together ancestral histories before the keys to comprehending their terrible inheritance die with their forebears. They seek the relational containment of the analytic relationship to provide psychological conditions to bear the unbearable, know the unknowable, speak the unspeakable and redeem the unredeemable. In the case of 'Rachael', initial dreams gave rise to what Hobson (1984) called 'moving metaphors of self' in the analytic field. Dream imagery, projective and introjective processes in the transference-countertransference dynamics gradually revealed an unknown ancestral history. I clarify the back and forth process from dream to waking dream thoughts to moving metaphors and differentiate the moving metaphor from a living symbol. I argue that the containment of the analytic relationship nested within the security of the analytic space is a necessary precondition for such healing processes to occur. © 2012, The Society of Analytical Psychology.

  19. Sexually dimorphic effects of ancestral exposure to vinclozolin on stress reactivity in rats.

    Science.gov (United States)

    Gillette, Ross; Miller-Crews, Isaac; Nilsson, Eric E; Skinner, Michael K; Gore, Andrea C; Crews, David

    2014-10-01

    How an individual responds to the environment depends upon both personal life history as well as inherited genetic and epigenetic factors from ancestors. Using a 2-hit, 3 generations apart model, we tested how F3 descendants of rats given in utero exposure to the environmental endocrine-disrupting chemical (EDC) vinclozolin reacted to stress during adolescence in their own lives, focusing on sexually dimorphic phenotypic outcomes. In adulthood, male and female F3 vinclozolin- or vehicle-lineage rats, stressed or nonstressed, were behaviorally characterized on a battery of tests and then euthanized. Serum was used for hormone assays, and brains were used for quantitative PCR and transcriptome analyses. Results showed that the effects of ancestral exposure to vinclozolin converged with stress experienced during adolescence in a sexually dimorphic manner. Debilitating effects were seen at all levels of the phenotype, including physiology, behavior, brain metabolism, gene expression, and genome-wide transcriptome modifications in specific brain nuclei. Additionally, females were significantly more vulnerable than males to transgenerational effects of vinclozolin on anxiety but not sociality tests. This fundamental transformation occurs in a manner not predicted by the ancestral exposure or the proximate effects of stress during adolescence, an interaction we refer to as synchronicity.

  20. Phylogenetic signal from rearrangements in 18 Anopheles species by joint scaffolding extant and ancestral genomes.

    Science.gov (United States)

    Anselmetti, Yoann; Duchemin, Wandrille; Tannier, Eric; Chauve, Cedric; Bérard, Sèverine

    2018-05-09

    Genomes rearrangements carry valuable information for phylogenetic inference or the elucidation of molecular mechanisms of adaptation. However, the detection of genome rearrangements is often hampered by current deficiencies in data and methods: Genomes obtained from short sequence reads have generally very fragmented assemblies, and comparing multiple gene orders generally leads to computationally intractable algorithmic questions. We present a computational method, ADSEQ, which, by combining ancestral gene order reconstruction, comparative scaffolding and de novo scaffolding methods, overcomes these two caveats. ADSEQ provides simultaneously improved assemblies and ancestral genomes, with statistical supports on all local features. Compared to previous comparative methods, it runs in polynomial time, it samples solutions in a probabilistic space, and it can handle a significantly larger gene complement from the considered extant genomes, with complex histories including gene duplications and losses. We use ADSEQ to provide improved assemblies and a genome history made of duplications, losses, gene translocations, rearrangements, of 18 complete Anopheles genomes, including several important malaria vectors. We also provide additional support for a differentiated mode of evolution of the sex chromosome and of the autosomes in these mosquito genomes. We demonstrate the method's ability to improve extant assemblies accurately through a procedure simulating realistic assembly fragmentation. We study a debated issue regarding the phylogeny of the Gambiae complex group of Anopheles genomes in the light of the evolution of chromosomal rearrangements, suggesting that the phylogenetic signal they carry can differ from the phylogenetic signal carried by gene sequences, more prone to introgression.

  1. A branch-heterogeneous model of protein evolution for efficient inference of ancestral sequences.

    Science.gov (United States)

    Groussin, M; Boussau, B; Gouy, M

    2013-07-01

    Most models of nucleotide or amino acid substitution used in phylogenetic studies assume that the evolutionary process has been homogeneous across lineages and that composition of nucleotides or amino acids has remained the same throughout the tree. These oversimplified assumptions are refuted by the observation that compositional variability characterizes extant biological sequences. Branch-heterogeneous models of protein evolution that account for compositional variability have been developed, but are not yet in common use because of the large number of parameters required, leading to high computational costs and potential overparameterization. Here, we present a new branch-nonhomogeneous and nonstationary model of protein evolution that captures more accurately the high complexity of sequence evolution. This model, henceforth called Correspondence and likelihood analysis (COaLA), makes use of a correspondence analysis to reduce the number of parameters to be optimized through maximum likelihood, focusing on most of the compositional variation observed in the data. The model was thoroughly tested on both simulated and biological data sets to show its high performance in terms of data fitting and CPU time. COaLA efficiently estimates ancestral amino acid frequencies and sequences, making it relevant for studies aiming at reconstructing and resurrecting ancestral amino acid sequences. Finally, we applied COaLA on a concatenate of universal amino acid sequences to confirm previous results obtained with a nonhomogeneous Bayesian model regarding the early pattern of adaptation to optimal growth temperature, supporting the mesophilic nature of the Last Universal Common Ancestor.

  2. A phylogenetic Kalman filter for ancestral trait reconstruction using molecular data.

    Science.gov (United States)

    Lartillot, Nicolas

    2014-02-15

    Correlation between life history or ecological traits and genomic features such as nucleotide or amino acid composition can be used for reconstructing the evolutionary history of the traits of interest along phylogenies. Thus far, however, such ancestral reconstructions have been done using simple linear regression approaches that do not account for phylogenetic inertia. These reconstructions could instead be seen as a genuine comparative regression problem, such as formalized by classical generalized least-square comparative methods, in which the trait of interest and the molecular predictor are represented as correlated Brownian characters coevolving along the phylogeny. Here, a Bayesian sampler is introduced, representing an alternative and more efficient algorithmic solution to this comparative regression problem, compared with currently existing generalized least-square approaches. Technically, ancestral trait reconstruction based on a molecular predictor is shown to be formally equivalent to a phylogenetic Kalman filter problem, for which backward and forward recursions are developed and implemented in the context of a Markov chain Monte Carlo sampler. The comparative regression method results in more accurate reconstructions and a more faithful representation of uncertainty, compared with simple linear regression. Application to the reconstruction of the evolution of optimal growth temperature in Archaea, using GC composition in ribosomal RNA stems and amino acid composition of a sample of protein-coding genes, confirms previous findings, in particular, pointing to a hyperthermophilic ancestor for the kingdom. The program is freely available at www.phylobayes.org.

  3. Cascading effects of ocean acidification in a rocky subtidal community.

    Directory of Open Access Journals (Sweden)

    Valentina Asnaghi

    Full Text Available Temperate marine rocky habitats may be alternatively characterized by well vegetated macroalgal assemblages or barren grounds, as a consequence of direct and indirect human impacts (e.g. overfishing and grazing pressure by herbivorous organisms. In future scenarios of ocean acidification, calcifying organisms are expected to be less competitive: among these two key elements of the rocky subtidal food web, coralline algae and sea urchins. In order to highlight how the effects of increased pCO2 on individual calcifying species will be exacerbated by interactions with other trophic levels, we performed an experiment simultaneously testing ocean acidification effects on primary producers (calcifying and non-calcifying algae and their grazers (sea urchins. Artificial communities, composed by juveniles of the sea urchin Paracentrotus lividus and calcifying (Corallina elongata and non-calcifying (Cystoseira amentacea var stricta, Dictyota dichotoma macroalgae, were subjected to pCO2 levels of 390, 550, 750 and 1000 µatm in the laboratory. Our study highlighted a direct pCO2 effect on coralline algae and on sea urchin defense from predation (test robustness. There was no direct effect on the non-calcifying macroalgae. More interestingly, we highlighted diet-mediated effects on test robustness and on the Aristotle's lantern size. In a future scenario of ocean acidification a decrease of sea urchins' density is expected, due to lower defense from predation, as a direct consequence of pH decrease, and to a reduced availability of calcifying macroalgae, important component of urchins' diet. The effects of ocean acidification may therefore be contrasting on well vegetated macroalgal assemblages and barren grounds: in the absence of other human impacts, a decrease of biodiversity can be predicted in vegetated macroalgal assemblages, whereas a lower density of sea urchin could help the recovery of shallow subtidal rocky areas affected by overfishing from

  4. Cascading effects of ocean acidification in a rocky subtidal community.

    Science.gov (United States)

    Asnaghi, Valentina; Chiantore, Mariachiara; Mangialajo, Luisa; Gazeau, Frédéric; Francour, Patrice; Alliouane, Samir; Gattuso, Jean-Pierre

    2013-01-01

    Temperate marine rocky habitats may be alternatively characterized by well vegetated macroalgal assemblages or barren grounds, as a consequence of direct and indirect human impacts (e.g. overfishing) and grazing pressure by herbivorous organisms. In future scenarios of ocean acidification, calcifying organisms are expected to be less competitive: among these two key elements of the rocky subtidal food web, coralline algae and sea urchins. In order to highlight how the effects of increased pCO2 on individual calcifying species will be exacerbated by interactions with other trophic levels, we performed an experiment simultaneously testing ocean acidification effects on primary producers (calcifying and non-calcifying algae) and their grazers (sea urchins). Artificial communities, composed by juveniles of the sea urchin Paracentrotus lividus and calcifying (Corallina elongata) and non-calcifying (Cystoseira amentacea var stricta, Dictyota dichotoma) macroalgae, were subjected to pCO2 levels of 390, 550, 750 and 1000 µatm in the laboratory. Our study highlighted a direct pCO2 effect on coralline algae and on sea urchin defense from predation (test robustness). There was no direct effect on the non-calcifying macroalgae. More interestingly, we highlighted diet-mediated effects on test robustness and on the Aristotle's lantern size. In a future scenario of ocean acidification a decrease of sea urchins' density is expected, due to lower defense from predation, as a direct consequence of pH decrease, and to a reduced availability of calcifying macroalgae, important component of urchins' diet. The effects of ocean acidification may therefore be contrasting on well vegetated macroalgal assemblages and barren grounds: in the absence of other human impacts, a decrease of biodiversity can be predicted in vegetated macroalgal assemblages, whereas a lower density of sea urchin could help the recovery of shallow subtidal rocky areas affected by overfishing from barren grounds to

  5. Rocky Flats Neutron Detector Testing at Valduc, France

    International Nuclear Information System (INIS)

    Kim, S.S.; Dulik, G.M.

    2011-01-01

    Recent program requirements of the US Department of Energy/NNSA have led to a need for a criticality accident alarm system to be installed at a newly activated facility. The Criticality Safety Group of the Lawrence Livermore National Laboratory (LLNL) was able to recover and store for possible future use approximately 200 neutron criticality detectors and 20 master alarm panels from the former Rocky Flats Plant in Golden, Colorado when the plant was closed. The Criticality Safety Group participated in a facility analysis and evaluation, the engineering design and review process, as well as the refurbishment, testing, and recalibration of the Rocky Flats criticality alarm system equipment to be used in the new facility. In order to demonstrate the functionality and survivability of the neutron detectors to the effects of an actual criticality accident, neutron detector testing was performed at the French CEA Valduc SILENE reactor from October 7 to October 19, 2010. The neutron detectors were exposed to three criticality events or pulses generated by the SILENE reactor. The first excursion was performed with a bare or unshielded reactor, and the second excursion was made with a lead shielded/reflected reactor, and the third excursion with a polyethylene reflected core. These tests of the Rocky Flats neutron detectors were performed as a part of the 2010 Criticality Accident Alarm System Benchmark Measurements at the SILENE Reactor. The principal investigators for this series of experiments were Thomas M. Miller and John C. Wagner of the Oak Ridge National Laboratory, with Nicolas Authier and Nathalie Baclet of CEA Valduc. Several other organizations were also represented, including the Y-12 National Security Complex, Lawrence Livermore National Laboratory, Los Alamos National Laboratory, CEA Saclay, and Babcock International Group.

  6. Plutonium dissolution from Rocky Flats Plant incinerator ash

    International Nuclear Information System (INIS)

    Delegard, C.H.

    1985-06-01

    Rockwell Hanford Operations (Rockwell) soon will commence recovery of plutonium from Rocky Flats Plant incinerator ash. In preparation for this processing, Rockwell undertook literature and laboratory studies to identify, select and optimize plutonium dissolution methods for treating the ash. Ash reburning, followed by dissolution in nitric acid containing calcium fluoride, was selected as the processing method for the ash. Recommended values of process parameters were identified. Using the selected process, 99.5% plutonium recovery was achieved, leaving about 12.7 wt % heel residue for an equal weight composite of the three ashes tested. 15 refs., 26 figs

  7. Thermal Structure and Mantle Dynamics of Rocky Exoplanets

    Science.gov (United States)

    Wagner, F. W.; Tosi, N.; Hussmann, H.; Sohl, F.

    2011-12-01

    The confirmed detections of CoRoT-7b and Kepler-10b reveal that rocky exoplanets exist. Moreover, recent theoretical studies suggest that small planets beyond the Solar System are indeed common and many of them will be discovered by increasingly precise observational surveys in the years ahead. The knowledge about the interior structure and thermal state of exoplanet interiors provides crucial theoretical input not only for classification and characterization of individual planetary bodies, but also to better understand the origin and evolution of the Solar System and the Earth in general. These developments and considerations have motivated us to address several questions concerning thermal structure and interior dynamics of terrestrial exoplanets. In the present study, depth-dependent structural models of solid exoplanet interiors have been constructed in conjunction with a mixing length approach to calculate self-consistently the radial distribution of temperature and heat flux. Furthermore, 2-D convection simulations using the compressible anelastic approximation have been carried through to examine the effect of thermodynamic quantities (e.g., thermal expansivity) on mantle convection pattern within rocky planets more massive than the Earth. In comparison to parameterized convection models, our calculated results predict generally hotter planetary interiors, which are mainly attributed to a viscosity-regulating feedback mechanism involving temperature and pressure. We find that density and thermal conductivity increase with depth by a factor of two to three, however, thermal expansivity decreases by more than an order of magnitude across the mantle for planets as massive as CoRoT-7b or Kepler-10b. The specific heat capacity is observed to stay almost constant over an extended region of the lower mantle. The planform of mantle convection is strongly modified in the presence of depth-dependent thermodynamic quantities with hot upwellings (plumes) rising across

  8. The Rocky Flats Environmental Technology Site beryllium characterization project

    International Nuclear Information System (INIS)

    Morrell, D.M.; Miller, J.R.; Allen, D.F.

    1999-01-01

    A site beryllium characterization project was completed at the Rocky Flats Environmental Technology Site (RFETS) in 1997. Information from historical reviews, previous sampling surveys, and a new sampling survey were used to establish a more comprehensive understanding of the locations and levels of beryllium contamination in 35 buildings. A feature of the sampling strategy was to test if process knowledge was a good predictor of where beryllium contamination could be found. Results revealed that this technique was effective at identifying where surface contamination levels might exceed the RFETS smear control level but that it was not effective in identifying where low concentrations of beryllium might be found

  9. Recovery of plutonium from incinerator ash at Rocky Flats

    International Nuclear Information System (INIS)

    Johnson, T.C.

    1976-01-01

    Incineration of combustible materials highly contaminated with plutonium produces a residue of incinerator ash. Recovery of plutonium from incinerator ash residues at Rocky Flats is accomplished by a continuous leaching operation with nitric acid containing fluoride ion. Special equipment used in the leaching operation consists of a screw feeder, air-lift dissolvers, filters, solids dryer, and vapor collection system. Each equipment item is described in detail. The average dissolution efficiency of plutonium experienced with the process was 68% on the first pass, 74% on the second pass, and 64% on each subsequent pass. Total-solids dissolution efficiencies averaged 47% on the first pass and about 25% on each subsequent pass

  10. [Rocky mountain spotted fever: report of two cases].

    Science.gov (United States)

    Martínez-Medina, Miguel Angel; Padilla-Zamudio, Guillermo; Solís-Gallardo, Lilia Patricia; Guevara-Tovar, Marcela

    2005-01-01

    Rocky Mountain spotted fever (RMSF) is an acute febrile illness caused by infection with Ricketsia Rickettsii, characterized by the presence of petechial rash. Even though the etiology, clinical characteristics and availability of effective antibiotics are known, RMSF related deaths have a prevalence of 4%. In its early stages RMFS can resemble many others infectious conditions and the diagnosis can be difficult. The present paper reports two patients with RMSF; these cases underscore the importance of prompt diagnosis and appropriate antimicrobial therapy, and consider RMSF as a differential diagnosis in any patient who develops fever and rash in an endemic area.

  11. Distinct crustal isostasy trends east and west of the Rocky Mountain Front

    KAUST Repository

    Schmandt, Brandon

    2015-12-14

    © 2015. American Geophysical Union. All Rights Reserved. Seismic structure beneath the contiguous U.S. was imaged with multimode receiver function stacking and inversion of Rayleigh wave dispersion and ellipticity measurements. Crust thickness and elevation are weakly correlated across the contiguous U.S., but the correlation is ∼3-4 times greater for separate areas east and west of the Rocky Mountain Front (RMF). Greater lower crustal shear velocities east of the RMF, particularly in low-elevation areas with thick crust, are consistent with deep crustal density as the primary cause of the contrasting crust thickness versus elevation trends. Separate eastern and western trends are best fit by Airy isostasy models that assume lower crust to uppermost mantle density increases of 0.18 g/cm3 and 0.40 g/cm3, respectively. The former value is near the minimum that is plausible for felsic lower crust. Location of the transition at the RMF suggests that Laramide to post-Laramide processes reduced western U.S. lower crustal density.

  12. A history of forest entomology in the Intermountain and Rocky Mountain areas, 1901 to 1982

    Science.gov (United States)

    Malcolm M. Furniss

    2007-01-01

    This account spans the time from A.D. Hopkins' trip to the Black Hills, SD, in 1901 to my retirement in 1982. The focus is on personnel and the work of the Division of Forest Insect Investigations, USDA, and the Forest Service experiment stations in the Rocky Mountain and Intermountain areas. Information for the Intermountain and Northern Rocky Mountain station...

  13. 76 FR 9350 - Patient Safety Organizations: Voluntary Delisting From Rocky Mountain Patient Safety Organization

    Science.gov (United States)

    2011-02-17

    ... Organizations: Voluntary Delisting From Rocky Mountain Patient Safety Organization AGENCY: Agency for Healthcare... Organization: AHRQ has accepted a notification of voluntary relinquishment from Rocky Mountain Patient Safety Organization, a component entity of Colorado Hospital Association, of its status as a Patient Safety...

  14. 78 FR 70033 - Encana Marketing (USA) Inc. v. Rockies Express Pipeline LLC; Notice of Complaint

    Science.gov (United States)

    2013-11-22

    ... Marketing (USA) Inc. v. Rockies Express Pipeline LLC; Notice of Complaint Take notice that on November 15... Commission (Commission), 18 CFR 385.206, Encana Marketing (USA) Inc. (Encana Marketing or Complainant), filed... Rockies Express has unlawfully denied Encana Marketing's request to make changes to the primary delivery...

  15. Vascular plant flora of the alpine zone in the southern Rocky Mountains, U.S.A

    Science.gov (United States)

    James F. Fowler; B. E. Nelson; Ronald L. Hartman

    2014-01-01

    Field detection of changes in occurrence, distribution, or abundance of alpine plant species is predicated on knowledge of which species are in specific locations. The alpine zone of the Southern Rocky Mountain Region has been systematically inventoried by the staff and floristics graduate students from the Rocky Mountain Herbarium over the last 27 years. It is...

  16. Co-Infection of Rickettsia rickettsii and Streptococcus pyogenes: Is Fatal Rocky Mountain Spotted Fever Underdiagnosed?

    Science.gov (United States)

    Raczniak, Gregory A.; Kato, Cecilia; Chung, Ida H.; Austin, Amy; McQuiston, Jennifer H.; Weis, Erica; Levy, Craig; Carvalho, Maria da Gloria S.; Mitchell, Audrey; Bjork, Adam; Regan, Joanna J.

    2014-01-01

    Rocky Mountain spotted fever, a tick-borne disease caused by Rickettsia rickettsii, is challenging to diagnose and rapidly fatal if not treated. We describe a decedent who was co-infected with group A β-hemolytic streptococcus and R. rickettsii. Fatal cases of Rocky Mountain spotted fever may be underreported because they present as difficult to diagnose co-infections. PMID:25331804

  17. Thermotolerant Yeast Strains Adapted by Laboratory Evolution Show Trade-Off at Ancestral Temperatures and Preadaptation to Other Stresses

    DEFF Research Database (Denmark)

    Caspeta, Luis; Nielsen, Jens

    2015-01-01

    adaptive laboratory evolution, we previously isolated seven Saccharomyces cerevisiae strains with improved growth at 40°C. Here, we show that genetic adaptations to high temperature caused a growth trade-off at ancestral temperatures, reduced cellular functions, and improved tolerance of other stresses...... in the ancestral strain. The latter is an advantageous attribute for acquiring thermotolerance and correlates with the reduction of yeast functions associated with loss of respiration capacity. This trait caused glycerol overproduction that was associated with the growth trade-off at ancestral temperatures....... In combination with altered sterol composition of cellular membranes, glycerol overproduction was also associated with yeast osmotolerance and improved tolerance of high concentrations of glucose and ethanol. Our study shows that thermal adaptation of yeast is suitable for improving yeast resistance...

  18. Estimating Divergence Time and Ancestral Effective Population Size of Bornean and Sumatran Orangutan Subspecies Using a Coalescent Hidden Markov Model

    DEFF Research Database (Denmark)

    Mailund, Thomas; Dutheil, Julien; Hobolth, Asger

    2011-01-01

    event has occurred to split them apart. The size of these segments of constant divergence depends on the recombination rate, but also on the speciation time, the effective population size of the ancestral population, as well as demographic effects and selection. Thus, inference of these parameters may......, and the ancestral effective population size. The model is efficient enough to allow inference on whole-genome data sets. We first investigate the power and consistency of the model with coalescent simulations and then apply it to the whole-genome sequences of the two orangutan sub-species, Bornean (P. p. pygmaeus......) and Sumatran (P. p. abelii) orangutans from the Orangutan Genome Project. We estimate the speciation time between the two sub-species to be thousand years ago and the effective population size of the ancestral orangutan species to be , consistent with recent results based on smaller data sets. We also report...

  19. Extraction of Rocky Desertification from Disp Imagery: a Case Study of Liupanshui, Guizhou, China

    Science.gov (United States)

    Zhou, G.; Wu, Z.; Wang, W.; Shi, Y.; Mao, G.; Huang, Y.; Jia, B.; Gao, G.; Chen, P.

    2017-09-01

    Karst rocky desertification is a typical type of land degradation in Guizhou Province, China. It causes great ecological and economical implications to the local people. This paper utilized the declassified intelligence satellite photography (DISP) of 1960s to extract the karst rocky desertification area to analyze the early situation of karst rocky desertification in Liupanshui, Guizhou, China. Due to the lack of ground control points and parameters of the satellite, a polynomial orthographic correction model with considering altitude difference correction is proposed for orthorectification of DISP imagery. With the proposed model, the 96 DISP images from four missions are orthorectified. The images are assembled into a seamless image map of the karst area of Guizhou, China. The assembled image map is produced to thematic map of karst rocky desertification by visual interpretation in Liupanshui city. With the assembled image map, extraction of rocky desertification is conducted.

  20. EXTRACTION OF ROCKY DESERTIFICATION FROM DISP IMAGERY: A CASE STUDY OF LIUPANSHUI, GUIZHOU, CHINA

    Directory of Open Access Journals (Sweden)

    G. Zhou

    2017-09-01

    Full Text Available Karst rocky desertification is a typical type of land degradation in Guizhou Province, China. It causes great ecological and economical implications to the local people. This paper utilized the declassified intelligence satellite photography (DISP of 1960s to extract the karst rocky desertification area to analyze the early situation of karst rocky desertification in Liupanshui, Guizhou, China. Due to the lack of ground control points and parameters of the satellite, a polynomial orthographic correction model with considering altitude difference correction is proposed for orthorectification of DISP imagery. With the proposed model, the 96 DISP images from four missions are orthorectified. The images are assembled into a seamless image map of the karst area of Guizhou, China. The assembled image map is produced to thematic map of karst rocky desertification by visual interpretation in Liupanshui city. With the assembled image map, extraction of rocky desertification is conducted.

  1. Dust Allergens within Rural Northern Rocky Mountain Residences.

    Science.gov (United States)

    Weiler, Emily; Semmens, Erin; Noonan, Curtis; Cady, Carol; Ward, Tony

    2015-01-23

    To date, few studies have characterized allergens within residences located in rural areas of the northern Rocky Mountain region. In this study, we collected dust samples from 57 homes located throughout western Montana and northern Idaho. Dust samples were collected and later analyzed for dust mite allergens Der f 1 and Der p 1 , Group 2 mite allergens ( Der p 2 and Der f 2 ), domestic feline ( Fel d 1 ), and canine ( Can f 1 ). Indoor temperature and humidity levels were also measured during the sampling program, as were basic characteristics of each home. Dog (96%) and cat (82%) allergens were the most prevalent allergens found in these homes (even when a feline or canine did not reside in the home). Results also revealed the presence of dust mites. Seven percent (7%) of homes tested positive for Der p 1 , 19% of homes were positive for Der f 1 , and 5% of homes were positive for the Group 2 mite allergens. Indoor relative humidity averaged 27.0 ± 7.6% within the homes. Overall, humidity was not significantly associated with dust mite presence, nor was any of the other measured home characteristics. This study provides a descriptive assessment of indoor allergen presence (including dust mites) in rural areas of the northern Rocky Mountains, and provides new information to assist regional patients with reducing allergen exposure using in-home intervention strategies.

  2. ROCKY EXTRASOLAR PLANETARY COMPOSITIONS DERIVED FROM EXTERNALLY POLLUTED WHITE DWARFS

    International Nuclear Information System (INIS)

    Klein, B.; Jura, M.; Zuckerman, B.; Koester, D.

    2011-01-01

    We report Keck High Resolution Echelle Spectrometer data and model atmosphere analysis of two helium-dominated white dwarfs, PG1225–079 and HS2253+8023, whose heavy pollutions most likely derive from the accretion of terrestrial-type planet(esimal)s. For each system, the minimum accreted mass is ∼10 22 g, that of a large asteroid. In PG1225–079, Mg, Cr, Mn, Fe, and Ni have abundance ratios similar to bulk Earth values, while we measure four refractory elements, Ca, Sc, Ti, and V, all at a factor of ∼2-3 higher abundance than in the bulk Earth. For HS2253+8023 the swallowed material was compositionally similar to bulk Earth in being more than 85% by mass in the major element species, O, Mg, Si, and Fe, and with abundances in the distinctive proportions of mineral oxides—compelling evidence for an origin in a rocky parent body. Including previous studies we now know of four heavily polluted white dwarfs where the measured oxygen and hydrogen are consistent with the view that the parents' bodies formed with little ice, interior to any snow line in their nebular environments. The growing handful of polluted white dwarf systems with comprehensive abundance measurements form a baseline for characterizing rocky exoplanet compositions that can be compared with bulk Earth.

  3. Whole-community facilitation regulates biodiversity on Patagonian rocky shores.

    Directory of Open Access Journals (Sweden)

    Brian R Silliman

    Full Text Available Understanding the factors that generate and maintain biodiversity is a central goal in ecology. While positive species interactions (i.e., facilitation have historically been underemphasized in ecological research, they are increasingly recognized as playing important roles in the evolution and maintenance of biodiversity. Dominant habitat-forming species (foundation species buffer environmental conditions and can therefore facilitate myriad associated species. Theory predicts that facilitation will be the dominant community-structuring force under harsh environmental conditions, where organisms depend on shelter for survival and predation is diminished. Wind-swept, arid Patagonian rocky shores are one of the most desiccating intertidal rocky shores ever studied, providing an opportunity to test this theory and elucidate the context-dependency of facilitation.Surveys across 2100 km of southern Argentinean coastline and experimental manipulations both supported theoretical predictions, with 43 out of 46 species in the animal assemblage obligated to living within the matrices of mussels for protection from potentially lethal desiccation stress and predators having no detectable impact on diversity.These results provide the first experimental support of long-standing theoretical predictions and reveal that in extreme climates, maintenance of whole-community diversity can be maintained by positive interactions that ameliorate physical stress. These findings have important conservation implications and emphasize that preserving foundation species should be a priority in remediating the biodiversity consequences of global climate change.

  4. Stabilization of mixed waste - Rocky Flats solar ponds

    International Nuclear Information System (INIS)

    Bittner, T.A.; Mathew, S.A.; Henderson, W.C.

    1993-01-01

    Among the wastes that require disposal as part of the Department of Energy's (DOE's) Environmental Restoration Program are large amounts of contaminated sludge and inorganic wastes. Halliburton NUS Corporation was awarded a contract by EG ampersand G Rocky Flats in March 1991 to stabilize mixed waste sludge contained in five solar evaporator ponds and to reprocess billets of solidified waste called Pondcrete and Saltcrete at DOE's Rocky Flats Plant. The scope of the project consists of waste characterization and treatability studies for process development, followed by design, construction and operation of various process trains to remediate different waste forms ranging from solid Pondcrete/Saltcrete blocks to aqueous brine solutions. One of the significant advances made was the development of a durable and certifiable stabilization formulation capable of treating concentrated nitrate solution wastes. The project uses high-volume grout mixing and pumping technologies with process control techniques that accommodate the heterogeneity of the wastes. To comply with all relevant environmental regulations and to provide a safe working atmosphere for plant personnel, Halliburton NUS designed process trains such that all emissions were eliminated during the remediation process. Personnel protection equipment requirements have been downgraded due to safeguards incorporated in the design. The technical and regulatory issues that were encountered would be typical of stabilization efforts underway at other DOE sites. Thus the lessons learned and concepts developed can be expected to have widespread application

  5. Land disposal restriction (LDR) waste management strategy at Rocky Flats

    International Nuclear Information System (INIS)

    Tyler, R.W.; Anderson, S.A.; Rising, T.L.

    1993-01-01

    The Rocky Flats Plant (RFP) is a government-owned, contractor-operated facility which is a part of the nationwide DOE nuclear weapons production complex. Rocky Flats has accumulated (and will continue to generate) a substantial quantity of mixed waste subject to regulation under the land disposal restrictions (LDR) of the Resource Conservation and Recovery Act (RCRA). These waste streams include low level mixed waste and transuranic mixed waste which are LDR primarily due to solvent and heavy metal contamination. DOE and EPA have entered into a Federal Facility Compliance Agreement (FFCA) which requires actions to be taken to ensure the accurate identification, safe storage and minimization of LDR mixed wastes prior to their ultimate treatment and/or disposal. As required by the FFCA, DOE has prepared a Comprehensive Treatment and Management Plant (CTMP) which describes the strategy and commitments for bringing LDR wastes at RFP into compliance with applicable regulations. This strategy includes waste characterization and reclassification, utilization of existing commercial and DOE treatment capacity, as well as, the development and implementation of treatment systems (and other management systems) for the purpose of achieving LDR regulatory compliance and ultimate waste disposal. This paper will give an overview of this strategy including a description of the major waste streams being addressed, the regulatory drivers, and plans and status of ongoing treatment systems technology development and implementation efforts

  6. Adult Onset Still's Disease and Rocky Mountain Spotted Fever

    Directory of Open Access Journals (Sweden)

    Paul Persad

    2010-01-01

    Full Text Available Adult Still's Disease was first described in 1971 by Bywaters in fourteen adult female patients who presented with symptoms indistinguishable from that of classic childhood Still's Disease (Bywaters, 1971. George Still in 1896 first recognized this triad of quotidian (daily fevers, evanescent rash, and arthritis in children with what later became known as juvenile inflammatory arthritis (Still, 1990. Adult Onset Still's Disease (AOSD is an inflammatory condition of unknown etiology characterized by an evanescent rash, quotidian fevers, and arthralgias. Numerous infectious agents have been associated with its presentation. This case is to our knowledge the first presentation of AOSD in the setting of Rocky Mountain Spotted Fever. Although numerous infectious agents have been suggested, the etiology of this disorder remains elusive. Nevertheless, infection may in fact play a role in triggering the onset of symptoms in those with this disorder. Our case presentation is, to our knowledge, the first case of Adult Onset Still's Disease associated with Rocky Mountain spotted fever (RMSF.

  7. Validation of KENO-based criticality calculations at Rocky Flats

    International Nuclear Information System (INIS)

    Felsher, P.D.; McKamy, J.N.; Monahan, S.P.

    1992-01-01

    In the absence of experimental data, it is necessary to rely on computer-based computational methods in evaluating the criticality condition of a nuclear system. The validity of the computer codes is established in a two-part procedure as outlined in ANSI/ANS 8.1. The first step, usually the responsibility of the code developer, involves verification that the algorithmic structure of the code is performing the intended mathematical operations correctly. The second step involves an assessment of the code's ability to realistically portray the governing physical processes in question. This is accomplished by determining the code's bias, or systematic error, through a comparison of computational results to accepted values obtained experimentally. In this paper, the authors discuss the validation process for KENO and the Hansen-Roach cross sections in use at EG and G Rocky Flats. The validation process at Rocky Flats consists of both global and local techniques. The global validation resulted in a maximum k eff limit of 0.95 for the limiting-accident scanarios of a criticality evaluation

  8. Circumscribing campo rupestre – megadiverse Brazilian rocky montane savanas

    Directory of Open Access Journals (Sweden)

    RJV. Alves

    Full Text Available Currently campo rupestre (CR is a name accepted and used internationally by botanists, zoologists, and other naturalists, usually applied to a very specific ecosystem, despite the lack of a consensual published circumscription. We present a tentative geographic circumscription of the term, combining data on climate, geology, geomorphology, soil, flora, fauna and vegetation. The circumscription of campo rupestre proposed herein is based on the following premises: (1 the classification of vegetation is not an exact science, and it is difficult to attain a high degree of consensus to the circumscription of vegetation names; (2 despite this, vegetation classification is useful for conservation and management. It is thus desirable to circumscribe vegetation types with the greatest attainable precision; (3 there is a need to preserve all montane and rocky vegetation types, regardless of classification, biome, etc; (4 the CRs are formed by a complex mosaic of vegetation types including rock-dwelling, psammophilous, aquatic, epiphytic, and penumbral plant communities. Campos rupestres stricto sensu are a Neotropical, azonal vegetation complex endemic to Brazil, forming a mosaic of rocky mountaintop “archipelagos” inserted within a matrix of zonal vegetation, mainly in the Cerrado and Caatinga provinces of the Brazilian Shield (southeastern, northeastern and central-western regions, occurring mainly above 900 m asl. up to altitudes exceeding 2000 m, having measured annual precipitation between 800 and 1500 mm, and an arid season of two to five months.

  9. Circumscribing campo rupestre - megadiverse Brazilian rocky montane savanas.

    Science.gov (United States)

    Alves, R J V; Silva, N G; Oliveira, J A; Medeiros, D

    2014-05-01

    Currently campo rupestre (CR) is a name accepted and used internationally by botanists, zoologists, and other naturalists, usually applied to a very specific ecosystem, despite the lack of a consensual published circumscription. We present a tentative geographic circumscription of the term, combining data on climate, geology, geomorphology, soil, flora, fauna and vegetation. The circumscription of campo rupestre proposed herein is based on the following premises: (1) the classification of vegetation is not an exact science, and it is difficult to attain a high degree of consensus to the circumscription of vegetation names; (2) despite this, vegetation classification is useful for conservation and management. It is thus desirable to circumscribe vegetation types with the greatest attainable precision; (3) there is a need to preserve all montane and rocky vegetation types, regardless of classification, biome, etc; (4) the CRs are formed by a complex mosaic of vegetation types including rock-dwelling, psammophilous, aquatic, epiphytic, and penumbral plant communities. Campos rupestres stricto sensu are a Neotropical, azonal vegetation complex endemic to Brazil, forming a mosaic of rocky mountaintop "archipelagos" inserted within a matrix of zonal vegetation, mainly in the Cerrado and Caatinga provinces of the Brazilian Shield (southeastern, northeastern and central-western regions), occurring mainly above 900 m asl. up to altitudes exceeding 2000 m, having measured annual precipitation between 800 and 1500 mm, and an arid season of two to five months.

  10. Interplay between field observations and numerical modeling to understand temporal pulsing of tree root throw processes, Canadian Rockies, Canada

    Science.gov (United States)

    Martin, Y. E.; Johnson, E. A.; Chaikina, O.

    2013-10-01

    During the cycle of forest disturbance, regeneration, and maturity, tree mortality leading to topple is a regular occurrence. When tree topple occurs relatively soon after mortality and if the tree has attained some threshold diameter at breast height (dbh) at the time of death, then notable amounts of soil may be upheaved along with the root wad. This upheaval may result in sediment transfers and soil production. A combination of field evidence and numerical modeling is used herein to gain insights regarding the temporal dynamics of tree topple, associated root throw processes, and pit-mound microtopography. Results from our model of tree population dynamics demonstrate temporal patterns in root throw processes in subalpine forests of the Canadian Rockies, a region in which forests are affected largely by wildfire disturbance. As the forest regenerates after disturbance, the new cohort of trees has to reach a critical dbh before significant root plate upheaval can occur; in the subalpine forests of the Canadian Rockies, this may take up to ~ 102 years. Once trees begin to reach this critical dbh for root plate upheaval, a period of sporadic root throw arises that is caused by mortality of trees during competition. In due course, another wildfire will occur on the landscape and a period of much increased root throw activity then takes place for the next several decades; tree sizes and, therefore, the amount of sediment disturbance will be greater the longer the time period since the previous fire. Results of previous root throw studies covering a number of regional settings are used to guide an exercise in diffusion modeling with the aim of defining a range of reasonable diffusion coefficients for pit-mound degradation; the most appropriate values to fit the field data ranged from 0.01 m2 y- 1 to 0.1 m2 y- 1. A similar exercise is then undertaken that is guided by our field observations in subalpine forests of the Canadian Rockies. For these forests, the most

  11. Main factors determining bioerosion patterns on rocky cliffs in a drowned valley estuary in the Colombian Pacific (Eastern Tropical Pacific)

    Science.gov (United States)

    Cobo-Viveros, Alba Marina; Cantera-Kintz, Jaime Ricardo

    2015-10-01

    Bioerosion is an important process that destroys coastal rocks in the tropics. However, the rates at which this process occurs, the organisms involved, and the dynamics of rocky cliffs in tropical latitudes have been less studied than in temperate and subtropical latitudes. To contribute to the knowledge of the bioerosion process in rocky cliffs on the Pacific coast of Colombia (Eastern Tropical Pacific) we compared: 1) boring volume, 2) grain size distribution of the rocks, and 3) rock porosity, across three tidal zones of two cliffs with different wave exposure; these factors were related to the bioeroding community found. We observed that cliffs that were not exposed to wave action (IC, internal cliffs) exhibited high percentages of clays in their grain size composition, and a greater porosity (47.62%) and perforation (15.86%) than exposed cliffs (EC, external cliffs). However, IC also exhibited less diversity and abundance of bioeroding species (22 species and 314 individuals, respectively) compared to the values found in EC (41.11%, 14.34%, 32 and 491, respectively). The most abundant bioeroders were Petrolisthes zacae in IC and Pachygrapsus transversus in EC. Our findings show that the tidal zone is the common factor controlling bioerosion on both cliffs; in addition to the abundance of bioeroders on IC and the number of bioeroding species on EC. The integration of geology, sedimentology, and biology allows us to obtain a more comprehensive view of the patterns and trends in the process of bioerosion.

  12. Where did the chili get its spice? Biogeography of capsaicinoid production in ancestral wild chili species.

    Science.gov (United States)

    Tewksbury, Joshua J; Manchego, Carlos; Haak, David C; Levey, Douglas J

    2006-03-01

    The biogeography of pungency in three species of wild chili in the chaco and surrounding highland habitats of southeastern Bolivia is described. We report that Capsicum chacoense, C. baccatum, and C. eximium are polymorphic for production of capsaicin and its analogs, such that completely pungent and completely nonpungent individuals co-occur in some populations. In C. chacoense, the density of plants and the proportion of pungent plants increased with elevation. Above 900 m, all individuals in all populations except two were pungent; nonpungent individuals in at least one of the two polymorphic populations were likely a result of spreading by humans. The occurrence of pungent and nonpungent individuals in three species of ancestral Capsicum and the geographic variation of pungency within species suggest that production of capsaicin and its analogs entails both costs and benefits, which shift from one locality to another. Determining the selection pressures behind such shifts is necessary to understand the evolution of pungency in chilies.

  13. Novel ancestral Dysferlin splicing mutation which migrated from the Iberian peninsula to South America.

    Science.gov (United States)

    Vernengo, Luis; Oliveira, Jorge; Krahn, Martin; Vieira, Emilia; Santos, Rosário; Carrasco, Luisa; Negrão, Luís; Panuncio, Ana; Leturcq, France; Labelle, Veronique; Bronze-da-Rocha, Elsa; Mesa, Rosario; Pizzarossa, Carlos; Lévy, Nicolas; Rodriguez, Maria-Mirta

    2011-05-01

    Primary dysferlinopathies are a group of recessive heterogeneous muscular dystrophies. The most common clinical presentations are Miyoshi myopathy and LGMD2B. Additional presentations range from isolated hyperCKemia to severe functional disability. Symptomatology begins in the posterior muscle compartment of the calf and its clinical course progresses slowly in Miyoshi myopathy whereas LGMD2B involves predominantly the proximal muscles of the lower limbs. The age of onset ranges from 13 to 60years in Caucasians. We present five patients that carry a novel mutation in the exon12/intron12 boundary: c.1180_1180+7delAGTGCGTG (r.1054_1284del). We provide evidence of a founder effect due to a common ancestral origin of this mutation, detected in heterozygosity in four patients and in homozygosity in one patient. Copyright © 2011 Elsevier B.V. All rights reserved.

  14. Loop Replacement Enhances the Ancestral Antibacterial Function of a Bifunctional Scorpion Toxin

    Directory of Open Access Journals (Sweden)

    Shangfei Zhang

    2018-06-01

    Full Text Available On the basis of the evolutionary relationship between scorpion toxins targeting K+ channels (KTxs and antibacterial defensins (Zhu S., Peigneur S., Gao B., Umetsu Y., Ohki S., Tytgat J. Experimental conversion of a defensin into a neurotoxin: Implications for origin of toxic function. Mol. Biol. Evol. 2014, 31, 546–559, we performed protein engineering experiments to modify a bifunctional KTx (i.e., weak inhibitory activities on both K+ channels and bacteria via substituting its carboxyl loop with the structurally equivalent loop of contemporary defensins. As expected, the engineered peptide (named MeuTXKα3-KFGGI remarkably improved the antibacterial activity, particularly on some Gram-positive bacteria, including several antibiotic-resistant opportunistic pathogens. Compared with the unmodified toxin, its antibacterial spectrum also enlarged. Our work provides a new method to enhance the antibacterial activity of bifunctional scorpion venom peptides, which might be useful in engineering other proteins with an ancestral activity.

  15. Did warfare among ancestral hunter-gatherers affect the evolution of human social behaviors?

    Science.gov (United States)

    Bowles, Samuel

    2009-06-05

    Since Darwin, intergroup hostilities have figured prominently in explanations of the evolution of human social behavior. Yet whether ancestral humans were largely "peaceful" or "warlike" remains controversial. I ask a more precise question: If more cooperative groups were more likely to prevail in conflicts with other groups, was the level of intergroup violence sufficient to influence the evolution of human social behavior? Using a model of the evolutionary impact of between-group competition and a new data set that combines archaeological evidence on causes of death during the Late Pleistocene and early Holocene with ethnographic and historical reports on hunter-gatherer populations, I find that the estimated level of mortality in intergroup conflicts would have had substantial effects, allowing the proliferation of group-beneficial behaviors that were quite costly to the individual altruist.

  16. Evolution of sweet taste perception in hummingbirds by transformation of the ancestral umami receptor

    Science.gov (United States)

    Baldwin, Maude W.; Toda, Yasuka; Nakagita, Tomoya; O'Connell, Mary J.; Klasing, Kirk C.; Misaka, Takumi; Edwards, Scott V.; Liberles, Stephen D.

    2015-01-01

    Sensory systems define an animal's capacity for perception and can evolve to promote survival in new environmental niches. We have uncovered a noncanonical mechanism for sweet taste perception that evolved in hummingbirds since their divergence from insectivorous swifts, their closest relatives. We observed the widespread absence in birds of an essential subunit (T1R2) of the only known vertebrate sweet receptor, raising questions about how specialized nectar feeders such as hummingbirds sense sugars. Receptor expression studies revealed that the ancestral umami receptor (the T1R1-T1R3 heterodimer) was repurposed in hummingbirds to function as a carbohydrate receptor. Furthermore, the molecular recognition properties of T1R1-T1R3 guided taste behavior in captive and wild hummingbirds. We propose that changing taste receptor function enabled hummingbirds to perceive and use nectar, facilitating the massive radiation of hummingbird species. PMID:25146290

  17. Sensory biology. Evolution of sweet taste perception in hummingbirds by transformation of the ancestral umami receptor.

    Science.gov (United States)

    Baldwin, Maude W; Toda, Yasuka; Nakagita, Tomoya; O'Connell, Mary J; Klasing, Kirk C; Misaka, Takumi; Edwards, Scott V; Liberles, Stephen D

    2014-08-22

    Sensory systems define an animal's capacity for perception and can evolve to promote survival in new environmental niches. We have uncovered a noncanonical mechanism for sweet taste perception that evolved in hummingbirds since their divergence from insectivorous swifts, their closest relatives. We observed the widespread absence in birds of an essential subunit (T1R2) of the only known vertebrate sweet receptor, raising questions about how specialized nectar feeders such as hummingbirds sense sugars. Receptor expression studies revealed that the ancestral umami receptor (the T1R1-T1R3 heterodimer) was repurposed in hummingbirds to function as a carbohydrate receptor. Furthermore, the molecular recognition properties of T1R1-T1R3 guided taste behavior in captive and wild hummingbirds. We propose that changing taste receptor function enabled hummingbirds to perceive and use nectar, facilitating the massive radiation of hummingbird species. Copyright © 2014, American Association for the Advancement of Science.

  18. Wiring a periscope--ocelli, retinula axons, visual neuropils and the ancestrality of sea spiders.

    Science.gov (United States)

    Lehmann, Tobias; Hess, Martin; Melzer, Roland R

    2012-01-01

    The Pycnogonida or sea spiders are cryptic, eight-legged arthropods with four median ocelli in a 'periscope' or eye tubercle. In older attempts at reconstructing phylogeny they were Arthropoda incertae sedis, but recent molecular trees placed them as the sister group either to all other euchelicerates or even to all euarthropods. Thus, pycnogonids are among the oldest extant arthropods and hold a key position for the understanding of arthropod evolution. This has stimulated studies of new sets of characters conductive to cladistic analyses, e.g. of the chelifores and of the hox gene expression pattern. In contrast knowledge of the architecture of the visual system is cursory. A few studies have analysed the ocelli and the uncommon "pseudoinverted" retinula cells. Moreover, analyses of visual neuropils are still at the stage of Hanström's early comprehensive works. We have therefore used various techniques to analyse the visual fibre pathways and the structure of their interrelated neuropils in several species. We found that pycnogonid ocelli are innervated to first and second visual neuropils in close vicinity to an unpaired midline neuropil, i.e. possibly the arcuate body, in a way very similar to ancestral euarthropods like Euperipatoides rowelli (Onychophora) and Limulus polyphemus (Xiphosura). This supports the ancestrality of pycnogonids and sheds light on what eyes in the pycnogonid ground plan might have 'looked' like. Recently it was suggested that arthropod eyes originated from simple ocelli similar to larval eyes. Hence, pycnogonid eyes would be one of the early offshoots among the wealth of more sophisticated arthropod eyes.

  19. Wiring a periscope--ocelli, retinula axons, visual neuropils and the ancestrality of sea spiders.

    Directory of Open Access Journals (Sweden)

    Tobias Lehmann

    Full Text Available The Pycnogonida or sea spiders are cryptic, eight-legged arthropods with four median ocelli in a 'periscope' or eye tubercle. In older attempts at reconstructing phylogeny they were Arthropoda incertae sedis, but recent molecular trees placed them as the sister group either to all other euchelicerates or even to all euarthropods. Thus, pycnogonids are among the oldest extant arthropods and hold a key position for the understanding of arthropod evolution. This has stimulated studies of new sets of characters conductive to cladistic analyses, e.g. of the chelifores and of the hox gene expression pattern. In contrast knowledge of the architecture of the visual system is cursory. A few studies have analysed the ocelli and the uncommon "pseudoinverted" retinula cells. Moreover, analyses of visual neuropils are still at the stage of Hanström's early comprehensive works. We have therefore used various techniques to analyse the visual fibre pathways and the structure of their interrelated neuropils in several species. We found that pycnogonid ocelli are innervated to first and second visual neuropils in close vicinity to an unpaired midline neuropil, i.e. possibly the arcuate body, in a way very similar to ancestral euarthropods like Euperipatoides rowelli (Onychophora and Limulus polyphemus (Xiphosura. This supports the ancestrality of pycnogonids and sheds light on what eyes in the pycnogonid ground plan might have 'looked' like. Recently it was suggested that arthropod eyes originated from simple ocelli similar to larval eyes. Hence, pycnogonid eyes would be one of the early offshoots among the wealth of more sophisticated arthropod eyes.

  20. Wiring a Periscope – Ocelli, Retinula Axons, Visual Neuropils and the Ancestrality of Sea Spiders

    Science.gov (United States)

    Lehmann, Tobias; Heß, Martin; Melzer, Roland R.

    2012-01-01

    The Pycnogonida or sea spiders are cryptic, eight-legged arthropods with four median ocelli in a ‘periscope’ or eye tubercle. In older attempts at reconstructing phylogeny they were Arthropoda incertae sedis, but recent molecular trees placed them as the sister group either to all other euchelicerates or even to all euarthropods. Thus, pycnogonids are among the oldest extant arthropods and hold a key position for the understanding of arthropod evolution. This has stimulated studies of new sets of characters conductive to cladistic analyses, e.g. of the chelifores and of the hox gene expression pattern. In contrast knowledge of the architecture of the visual system is cursory. A few studies have analysed the ocelli and the uncommon “pseudoinverted” retinula cells. Moreover, analyses of visual neuropils are still at the stage of Hanström's early comprehensive works. We have therefore used various techniques to analyse the visual fibre pathways and the structure of their interrelated neuropils in several species. We found that pycnogonid ocelli are innervated to first and second visual neuropils in close vicinity to an unpaired midline neuropil, i.e. possibly the arcuate body, in a way very similar to ancestral euarthropods like Euperipatoides rowelli (Onychophora) and Limulus polyphemus (Xiphosura). This supports the ancestrality of pycnogonids and sheds light on what eyes in the pycnogonid ground plan might have ‘looked’ like. Recently it was suggested that arthropod eyes originated from simple ocelli similar to larval eyes. Hence, pycnogonid eyes would be one of the early offshoots among the wealth of more sophisticated arthropod eyes. PMID:22279594

  1. Genes Suggest Ancestral Colour Polymorphisms Are Shared across Morphologically Cryptic Species in Arctic Bumblebees.

    Directory of Open Access Journals (Sweden)

    Paul H Williams

    Full Text Available Our grasp of biodiversity is fine-tuned through the process of revisionary taxonomy. If species do exist in nature and can be discovered with available techniques, then we expect these revisions to converge on broadly shared interpretations of species. But for the primarily arctic bumblebees of the subgenus Alpinobombus of the genus Bombus, revisions by some of the most experienced specialists are unusual for bumblebees in that they have all reached different conclusions on the number of species present. Recent revisions based on skeletal morphology have concluded that there are from four to six species, while variation in colour pattern of the hair raised questions as to whether at least seven species might be present. Even more species are supported if we accept the recent move away from viewing species as morphotypes to viewing them instead as evolutionarily independent lineages (EILs using data from genes. EILs are recognised here in practice from the gene coalescents that provide direct evidence for their evolutionary independence. We show from fitting both general mixed Yule/coalescent (GMYC models and Poisson-tree-process (PTP models to data for the mitochondrial COI gene that there is support for nine species in the subgenus Alpinobombus. Examination of the more slowly evolving nuclear PEPCK gene shows further support for a previously unrecognised taxon as a new species in northwestern North America. The three pairs of the most morphologically similar sister species are separated allopatrically and prevented from interbreeding by oceans. We also find that most of the species show multiple shared colour patterns, giving the appearance of mimicry among parts of the different species. However, reconstructing ancestral colour-pattern states shows that speciation is likely to have cut across widespread ancestral polymorphisms, without or largely without convergence. In the particular case of Alpinobombus, morphological, colour-pattern, and

  2. Characterisation of monotreme caseins reveals lineage-specific expansion of an ancestral casein locus in mammals.

    Science.gov (United States)

    Lefèvre, Christophe M; Sharp, Julie A; Nicholas, Kevin R

    2009-01-01

    Using a milk-cell cDNA sequencing approach we characterised milk-protein sequences from two monotreme species, platypus (Ornithorhynchus anatinus) and echidna (Tachyglossus aculeatus) and found a full set of caseins and casein variants. The genomic organisation of the platypus casein locus is compared with other mammalian genomes, including the marsupial opossum and several eutherians. Physical linkage of casein genes has been seen in the casein loci of all mammalian genomes examined and we confirm that this is also observed in platypus. However, we show that a recent duplication of beta-casein occurred in the monotreme lineage, as opposed to more ancient duplications of alpha-casein in the eutherian lineage, while marsupials possess only single copies of alpha- and beta-caseins. Despite this variability, the close proximity of the main alpha- and beta-casein genes in an inverted tail-tail orientation and the relative orientation of the more distant kappa-casein genes are similar in all mammalian genome sequences so far available. Overall, the conservation of the genomic organisation of the caseins indicates the early, pre-monotreme development of the fundamental role of caseins during lactation. In contrast, the lineage-specific gene duplications that have occurred within the casein locus of monotremes and eutherians but not marsupials, which may have lost part of the ancestral casein locus, emphasises the independent selection on milk provision strategies to the young, most likely linked to different developmental strategies. The monotremes therefore provide insight into the ancestral drivers for lactation and how these have adapted in different lineages.

  3. Origin of amphibian and avian chromosomes by fission, fusion, and retention of ancestral chromosomes

    Science.gov (United States)

    Voss, Stephen R.; Kump, D. Kevin; Putta, Srikrishna; Pauly, Nathan; Reynolds, Anna; Henry, Rema J.; Basa, Saritha; Walker, John A.; Smith, Jeramiah J.

    2011-01-01

    Amphibian genomes differ greatly in DNA content and chromosome size, morphology, and number. Investigations of this diversity are needed to identify mechanisms that have shaped the evolution of vertebrate genomes. We used comparative mapping to investigate the organization of genes in the Mexican axolotl (Ambystoma mexicanum), a species that presents relatively few chromosomes (n = 14) and a gigantic genome (>20 pg/N). We show extensive conservation of synteny between Ambystoma, chicken, and human, and a positive correlation between the length of conserved segments and genome size. Ambystoma segments are estimated to be four to 51 times longer than homologous human and chicken segments. Strikingly, genes demarking the structures of 28 chicken chromosomes are ordered among linkage groups defining the Ambystoma genome, and we show that these same chromosomal segments are also conserved in a distantly related anuran amphibian (Xenopus tropicalis). Using linkage relationships from the amphibian maps, we predict that three chicken chromosomes originated by fusion, nine to 14 originated by fission, and 12–17 evolved directly from ancestral tetrapod chromosomes. We further show that some ancestral segments were fused prior to the divergence of salamanders and anurans, while others fused independently and randomly as chromosome numbers were reduced in lineages leading to Ambystoma and Xenopus. The maintenance of gene order relationships between chromosomal segments that have greatly expanded and contracted in salamander and chicken genomes, respectively, suggests selection to maintain synteny relationships and/or extremely low rates of chromosomal rearrangement. Overall, the results demonstrate the value of data from diverse, amphibian genomes in studies of vertebrate genome evolution. PMID:21482624

  4. Ancestral Variations of the PCDHG Gene Cluster Predispose to Dyslexia in a Multiplex Family

    Directory of Open Access Journals (Sweden)

    Teesta Naskar

    2018-02-01

    Full Text Available Dyslexia is a heritable neurodevelopmental disorder characterized by difficulties in reading and writing. In this study, we describe the identification of a set of 17 polymorphisms located across 1.9 Mb region on chromosome 5q31.3, encompassing genes of the PCDHG cluster, TAF7, PCDH1 and ARHGAP26, dominantly inherited with dyslexia in a multi-incident family. Strikingly, the non-risk form of seven variations of the PCDHG cluster, are preponderant in the human lineage, while risk alleles are ancestral and conserved across Neanderthals to non-human primates. Four of these seven ancestral variations (c.460A > C [p.Ile154Leu], c.541G > A [p.Ala181Thr], c.2036G > C [p.Arg679Pro] and c.2059A > G [p.Lys687Glu] result in amino acid alterations. p.Ile154Leu and p.Ala181Thr are present at EC2: EC3 interacting interface of γA3-PCDH and γA4-PCDH respectively might affect trans-homophilic interaction and hence neuronal connectivity. p.Arg679Pro and p.Lys687Glu are present within the linker region connecting trans-membrane to extracellular domain. Sequence analysis indicated the importance of p.Ile154, p.Arg679 and p.Lys687 in maintaining class specificity. Thus the observed association of PCDHG genes encoding neural adhesion proteins reinforces the hypothesis of aberrant neuronal connectivity in the pathophysiology of dyslexia. Additionally, the striking conservation of the identified variants indicates a role of PCDHG in the evolution of highly specialized cognitive skills critical to reading.

  5. Metamorphosis Is Ancestral for Crown Euarthropods, and Evolved in the Cambrian or Earlier.

    Science.gov (United States)

    Wolfe, Joanna M

    2017-09-01

    Macroevolutionary developmental biology employs fossilized ontogenetic data and phylogenetic comparative methods to probe the evolution of development at ancient nodes. Despite the prevalence of ecologically differentiated larval forms in marine invertebrates, it has been frequently presumed that the ancestors of arthropods were direct developers, and that metamorphosis may not have evolved until the Ordovician or later. Using fossils and new dated phylogenies, I infer that metamorphosis was likely ancestral for crown arthropods, contradicting this assumption. Based on a published morphological dataset encompassing 217 exceptionally preserved fossil and 96 extant taxa, fossils were directly incorporated into both the topology and age estimates, as in "tip dating" analyses. Using data from post-embryonic fossils representing 25 species throughout stem and crown arthropod lineages (as well as most of the 96 extant taxa), characters for metamorphosis were assigned based on inferred ecological changes in development (e.g., changes in habitat and adaptive landscape). Under all phylogenetic hypotheses, metamorphosis was supported as most likely ancestral to both ecdysozoans and euarthropods. Care must be taken to account for potential drastic post-embryonic morphological changes in evolutionary analyses. Many stem group euarthrpods may have had ecologically differentiated larval stages that did not preserve in the fossil record. Moreover, a complex life cycle and planktonic ecology may have evolved in the Ediacaran or earlier, and may have typified the pre-Cambrian explosion "wormworld" prior to the origin of crown group euarthropods. © The Author 2017. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

  6. Magmatism and Epithermal Gold-Silver Deposits of the Southern Ancestral Cascade Arc, Western Nevada and Eastern California

    Science.gov (United States)

    John, David A.; du Bray, Edward A.; Henry, Christopher D.; Vikre, Peter

    2015-01-01

    Many epithermal gold-silver deposits are temporally and spatially associated with late Oligocene to Pliocene magmatism of the southern ancestral Cascade arc in western Nevada and eastern California. These deposits, which include both quartz-adularia (low- and intermediate-sulfidation; Comstock Lode, Tonopah, Bodie) and quartz-alunite (high-sulfidation; Goldfield, Paradise Peak) types, were major producers of gold and silver. Ancestral Cascade arc magmatism preceded that of the modern High Cascades arc and reflects subduction of the Farallon plate beneath North America. Ancestral arc magmatism began about 45 Ma, continued until about 3 Ma, and extended from near the Canada-United States border in Washington southward to about 250 km southeast of Reno, Nevada. The ancestral arc was split into northern and southern segments across an inferred tear in the subducting slab between Mount Shasta and Lassen Peak in northern California. The southern segment extends between 42°N in northern California and 37°N in western Nevada and was active from about 30 to 3 Ma. It is bounded on the east by the northeast edge of the Walker Lane. Ancestral arc volcanism represents an abrupt change in composition and style of magmatism relative to that in central Nevada. Large volume, caldera-forming, silicic ignimbrites associated with the 37 to 19 Ma ignimbrite flareup are dominant in central Nevada, whereas volcanic centers of the ancestral arc in western Nevada consist of andesitic stratovolcanoes and dacitic to rhyolitic lava domes that mostly formed between 25 and 4 Ma. Both ancestral arc and ignimbrite flareup magmatism resulted from rollback of the shallowly dipping slab that began about 45 Ma in northeast Nevada and migrated south-southwest with time. Most southern segment ancestral arc rocks have oxidized, high potassium, calc-alkaline compositions with silica contents ranging continuously from about 55 to 77 wt%. Most lavas are porphyritic and contain coarse plagioclase

  7. The mechanistic basis of hemoglobin adaptation in the high-flying barheaded goose: insights from ancestral protein resurrection

    DEFF Research Database (Denmark)

    Natarajan, Chandrasekhar; Kumar, Amit; Moriyama, Hideaki

    2016-01-01

    the functional effects of causative mutations on the genetic background in which they actually occurred during evolution (i.e., in the BHG ancestor). An alternative ‘vertical’ approach is to reconstruct and resurrect ancestral proteins to test the effects of historical mutations on the genetic background...

  8. ReAS: Recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun

    DEFF Research Database (Denmark)

    Li, Ruiqiang; Ye, Jia; Li, Songgang

    2005-01-01

    in comparison to their ancestral sequences. Tested on the japonica rice genome, ReAS was able to reconstruct all of the high copy sequences in the Repbase repository of known TEs, and increase the effectiveness of RepeatMasker in identifying TEs from genome sequences. Udgivelsesdato: 2005-Sep...

  9. Cementation and solidification of Rocky Flats Plant incinerator ash

    International Nuclear Information System (INIS)

    Phillips, J.A.; Semones, G.B.

    1994-01-01

    Cementation studies on various aqueous waste streams at Rocky Flats have shown this technology to be effective for immobilizing the RCRA constituents in the waste. Cementation is also being evaluated for encapsulation of incinerator ash. Experiments will initially evaluate a surrogate ash waste using a Taguchi experimental design to optimize the cement formulation and waste loading levels for this application. Variables of waste loading, fly ash additions, water/cement ratio, and cement type will be tested at three levels each during the course of this work. Tests will finally be conducted on actual waste using the optimized cement formulation developed from this testing. This progression of tests will evaluate the effectiveness of cement encapsulation for this waste stream without generating any additional wastes

  10. Epidemiologic surveillance. Annual report for EG&G Rocky Flats

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1994-12-31

    Epidemiologic surveillance at U.S. Department of Energy (DOE) facilities consists of regular and systematic collection, analysis, and interpretation of data on absences resulting from illness and injury in the work force. Its purpose is to provide an early warning system for health problems occurring among employees at participating sites. Data are collected by coordinators at each site and submitted to the Epidemiologic Surveillance Data Center, located at the Oak Ridge Institute for Science and Education, where quality control procedures and analyses are carried out. Rates of absences and rates of diagnoses associated with absences are analyzed by occupation and other relevant variables. They may be compared with the disease experience of different groups within the DOE work force and with populations that do not work for DOE to identify disease patterns or clusters that may be associated with work activities. This report presents the 1994 morbidity data for the Rocky Flats plant.

  11. Status of Americium-241 recovery at Rocky Flats Plant

    International Nuclear Information System (INIS)

    Knighton, J.B.; Hagan, P.G.; Navratil, J.D.; Thompson, G.H.

    1981-01-01

    This paper is presented in two parts: Part I, Molten Salt Extraction of Americium from Molten Plutonium Metal, and Part II, Aqueous Recovery of Americium from Extraction Salts. The Rocky Flats recovery process used for waste salts includes (1) dilute hydrochloric acid dissolution of residues; (2) cation exchange to convert from the chloride to the nitrate system and to remove gross amounts of monovalent impurities; (3) anion exchange separation of plutonium; (4) oxalate precipitation of americium; and (5) calcination of the oxalate at 600 0 C to yield americium oxide. The aqueous process portion describes attempts to improve the recovery of americium. The first part deals with modifications to the cation exchange step; the second describes development of a solvent extractions process that will recovery americium from residues containing aluminium as well as other common impurities. Results of laboratory work are described. 3 figures, 6 tables. (DP)

  12. Rocky Flats Plant Live-Fire Range Risk Analysis Report

    Energy Technology Data Exchange (ETDEWEB)

    Nicolosi, S.L.; Rodriguez, M.A.

    1994-04-01

    The objective of the Live-Fire Range Risk Analysis Report (RAR) is to provide an authorization basis for operation as required by DOE 5480.16. The existing Live-Fire Range does not have a safety analysis-related authorization basis. EG&G Rocky Flats, Inc. has worked with DOE and its representatives to develop a format and content description for development of an RAR for the Live-Fire Range. Development of the RAR is closely aligned with development of the design for a baffle system to control risks from errant projectiles. DOE 5480.16 requires either an RAR or a safety analysis report (SAR) for live-fire ranges. An RAR rather than a SAR was selected in order to gain flexibility to more closely address the safety analysis and conduct of operation needs for a live-fire range in a cost-effective manner.

  13. Rockwell International - Rocky Flats Plant: Occupational Health Information System

    International Nuclear Information System (INIS)

    Bistine, R.W.; Petrocchi, A.; Wright, W.L.; Yoder, R.E.; Fischer, C.M.

    1984-01-01

    The Rockwell International-Rocky Flats Occupational Health Information System uses the FLOW GEMINI software on a VAX computer system. The system is extremely user friendly, flexible, comprehensive, and easily customized by the user. The system contains the editioned files (i.e., time organized historical data) of the Medical, Industrial Hygiene, Health Physics, and Safety Departments. It maintains, analyzes and reports on data from employee medical and work histories, medical exams, workplace monitoring, and health effects related to specific hazards or locations in the workplace. It identifies and reports potential individual and group problems through regular reports and responses to on-line queries. In addition, it schedules examination, sampling, produces standard user-defined reports, and provides statistical analysis capabilities. The system presently contains a file of more than 20,000 Material Data Safety Sheets. A user group provides a mechanism for sharing ideas and continual software enhancement. 11 figures

  14. Rocky Mountain spotted fever in Panama: a cluster description.

    Science.gov (United States)

    Tribaldos, Maribel; Zaldivar, Yamitzel; Bermudez, Sergio; Samudio, Franklyn; Mendoza, Yaxelis; Martinez, Alexander A; Villalobos, Rodrigo; Eremeeva, Marina E; Paddock, Christopher D; Page, Kathleen; Smith, Rebecca E; Pascale, Juan Miguel

    2011-10-13

    Rocky Mountain spotted fever (RMSF) is a tick-borne infection caused by Rickettsia rickettsii. We report a cluster of fatal cases of RMSF in 2007 in Panama, involving a pregnant woman and two children from the same family.  The woman presented with a fever followed by respiratory distress, maculopapular rash, and an eschar at the site from which a tick had been removed.  She died four days after disease onset.  This is the second published report of an eschar in a patient confirmed by PCR to be infected with R. rickettsii.  One month later, the children presented within days of one another with fever and rash and died three and four days after disease onset. The diagnosis was confirmed by immunohistochemistry, PCR and sequencing of the genes of R. rickettsii in tissues obtained at autopsy. 

  15. Association between sepsis and Rocky Mountain spotted fever.

    Science.gov (United States)

    Bacci, Marcelo Rodrigues; Namura, José Jorge

    2012-12-06

    Rocky Mountain spotted fever (RMSF) is a disease caused by the Gram-negative coccobacillus Rickettsia ricketsii which has been on the rise since the last decade in the USA. The symptoms are common to the many viral diseases, and the classic triad of fever, rash and headache is not always present when RMSF is diagnosed. It may progress to severe cases such as renal failure, disseminated intravascular coagulation and septicaemia. This report aims to present a fulminant case of RMSF associated with sepsis. It describes a female patient's case that quickly progressed to sepsis and death. The patient showed non-specific symptoms for 5 days before being admitted to a hospital. The fact that she lived in an area highly infested with Amblyomma aureolatum ticks was unknown to the medical staff until the moment she died.

  16. Characterization and storage of the Rocky Flats plutonium oxide legacy

    International Nuclear Information System (INIS)

    Stakebake, J.L.

    1997-01-01

    Prior to 1989, plutonium oxide storage at the U.S. Department of Energy (DOE) Rocky Flats Environmental Technology Site (RFETS) could generally be considered as short term. Packaging configurations for short-term storage consisted of slip-lid cans and sealed produce cans. Prior to packaging, most of the oxide had been stabilized by heating to ∼500 degrees C. When storage times were relatively short, few problems were attributed to either packaging or storage. However, with projected storage times extended up to 50 yr, most of the old packaging of RFETS plutonium oxide will be in two welded steel containers in compliance with the DOE Standard 3013-96, which defines processing and packaging criteria for safe, long-term storage of plutonium oxide

  17. [Rocky Mountain spotted fever in children: clinical and epidemiological features].

    Science.gov (United States)

    Martínez-Medina, Miguel Angel; Alvarez-Hernández, Gerardo; Padilla-Zamudioa, José Guillermo; Rojas-Guerra, Maria Guadalupe

    2007-01-01

    To report the clinical features of the Rocky Mountain spotted fever (RMSF) in children of southern Sonora, Mexico. Nine cases were studied at the Sonora State Children's Hospital. One case was defined by clinical features and positive serological tests (indirect immunofluorescence assay or reaction to Proteus OX 19). Demographic and clinical characteristics of the patients were registered. The study subjects were children from two to twelve years ofage. All patients have had contact with tick-infested dogs and had fever, as well as petechial rash. Laboratory findings included high levels of hepatic aminotransferase, hyponatremia and thrombocytopenia. Therapy with chloramphenicol and doxyciclyne was administered after the first seven days of the onset of illness. The mortality rate was 22%. This study supports the presence of RMSF in the state of Sonora, Mexico, which should be considered as a public health hazard, requiring immediate actions for prevention and control.

  18. Sitewide risk perspectives for the Rocky Flats Environmental Technology Site

    International Nuclear Information System (INIS)

    Olinger, S.J.

    1998-05-01

    The US Department of Energy (DOE) has recently finalized a closure plan (originally called the Ten Year Plan) for closure and environmental cleanup of previous nuclear weapons facilities. The DOE Rocky Flats Field Office has established priorities for risk reduction work to Support closure activities, as well as addressing those hazards associated with storage and management of radioactive materials and hazardous chemicals. To provide information for future National Environmental Policy Act (NEPA) or other regulatory assessments of specific risk reduction projects identified in the Closure Plan, a risk assessment of normal operations and potential accidents was recently prepared to provide an updated baseline of the cumulative impacts to the worker, public and environment due to the Site's operations, activities, and environmental conditions in light of the Site's change in mission, and of future closure projects. This paper summarizes the risk assessment approach, results, and conclusions

  19. Atmospheric Circulations of Rocky Planets as Heat Engines

    Science.gov (United States)

    Koll, D. D. B.

    2017-12-01

    Rocky planets are extremely common in the galaxy and include Earth, Mars, Venus, and hundreds of exoplanets. To understand and compare the climates of these planets, we need theories that are general enough to accommodate drastically different atmospheric and planetary properties. Unfortunately, few such theories currently exist.For Earth, there is a well-known principle that its atmosphere resembles a heat engine - the atmosphere absorbs heat near the surface, at a hot temperature, and emits heat to space in the upper troposphere, at a cold temperature, which allows it to perform work and balance dissipative processes such as friction. However, previous studies also showed that Earth's hydrological cycle uses up a large fraction of the heat engine's work output, which makes it difficult to view other atmospheres as heat engines.In this work I extend the heat engine principle from Earth towards other rocky planets. I explore both dry and moist atmospheres in an idealized general circulation model (GCM), and quantify their work output using entropy budgets. First, I show that convection and turbulent heat diffusion are important entropy sources in dry atmospheres. I develop a scaling that accounts for its effects, which allows me to predict the strength of frictional dissipation in dry atmospheres. There are strong parallels between my scaling and so-called potential intensity theory, which is a seminal theory for understanding tropical cyclones on Earth. Second, I address how moisture affects atmospheric heat engines. Moisture modifies both the thermodynamic properties of air and releases latent heat when water vapor condenses. I explore the impact of both effects, and use numerical simulations to explore the difference between dry and moist atmospheric circulations across a wide range of climates.

  20. Sampling for Soil Carbon Stock Assessment in Rocky Agricultural Soils

    Science.gov (United States)

    Beem-Miller, Jeffrey P.; Kong, Angela Y. Y.; Ogle, Stephen; Wolfe, David

    2016-01-01

    Coring methods commonly employed in soil organic C (SOC) stock assessment may not accurately capture soil rock fragment (RF) content or soil bulk density (rho (sub b)) in rocky agricultural soils, potentially biasing SOC stock estimates. Quantitative pits are considered less biased than coring methods but are invasive and often cost-prohibitive. We compared fixed-depth and mass-based estimates of SOC stocks (0.3-meters depth) for hammer, hydraulic push, and rotary coring methods relative to quantitative pits at four agricultural sites ranging in RF content from less than 0.01 to 0.24 cubic meters per cubic meter. Sampling costs were also compared. Coring methods significantly underestimated RF content at all rocky sites, but significant differences (p is less than 0.05) in SOC stocks between pits and corers were only found with the hammer method using the fixed-depth approach at the less than 0.01 cubic meters per cubic meter RF site (pit, 5.80 kilograms C per square meter; hammer, 4.74 kilograms C per square meter) and at the 0.14 cubic meters per cubic meter RF site (pit, 8.81 kilograms C per square meter; hammer, 6.71 kilograms C per square meter). The hammer corer also underestimated rho (sub b) at all sites as did the hydraulic push corer at the 0.21 cubic meters per cubic meter RF site. No significant differences in mass-based SOC stock estimates were observed between pits and corers. Our results indicate that (i) calculating SOC stocks on a mass basis can overcome biases in RF and rho (sub b) estimates introduced by sampling equipment and (ii) a quantitative pit is the optimal sampling method for establishing reference soil masses, followed by rotary and then hydraulic push corers.

  1. Cost-benefit of three different methods for studying Mediterranean rocky benthic assemblages

    Directory of Open Access Journals (Sweden)

    Natàlia Sant

    2017-03-01

    Full Text Available Here we compare the applicability, the information provided and the cost-benefit of three sampling methods usually used in the study of rocky benthic assemblages. For comparative purposes, sampling was performed seasonally and along a depth gradient (0-50 m in the Cabrera Archipelago (western Mediterranean. The destructive scraping (collection method was the least cost-effective but provided the best qualitative and quantitative information. The in situ visual method was the most time-effective but provided low levels of taxonomic resolution and its accuracy decreased with depth due to the increasing difficulty of recognizing species in situ due to nitrogen narcosis, reduced light and cold. The photoquadrat method showed intermediate values of cost-effectiveness and information but was not suitable for multilayered assemblages, as it only accounted for the overstory. A canonical correspondence analysis showed that depth was highlighted as the main environmental gradient (16.0% of variance by the three methods. However, differences due to the sampling method (7.9% of variance were greater than differences due to temporal variability (5.8% of variance, suggesting that the three methods are valid but their selection has to be carefully assessed in relation to the targeted assemblages and the specific goals of each study.

  2. Effects of climate change on ecological disturbance in the Northern Rockies Region [Chapter 8

    Science.gov (United States)

    Loehman, Rachel A.; Bentz, Barbara J.; DeNitto, Gregg A.; Keane, Robert E.; Manning, Mary E.; Duncan, Jacob P.; Egan, Joel M.; Jackson, Marcus B.; Kegley, Sandra; Lockman, I. Blakey; Pearson, Dean E.; Powell, James A.; Shelly, Steve; Steed, Brytten E.; Zambino, Paul J.

    2018-01-01

    This chapter describes the ecology of important disturbance regimes in the Forest Service, U.S. Department of Agriculture (USFS) Northern Region and the Greater Yellowstone Area, hereafter called the Northern Rockies region, and potential shifts in these regimes as a consequence of observed and projected climate change. The term disturbance regime describes the general temporal and spatial characteristics of a disturbance agent - insect, disease, fire, weather, even human activity - and the effects of that agent on the landscape (table 8.1). More specifically, a disturbance regime is the cumulative effect of multiple disturbance events over space and time (Keane 2013). Disturbances disrupt an ecosystem, community, or population structure and change elements of the biological environment, physical environment, or both (White and Pickett 1985). The resulting shifting mosaic of diverse ecological patterns and structures in turn affects future patterns of disturbance, in a reciprocal, linked relationship that shapes the fundamental character of landscapes and ecosystems. Disturbance creates and maintains biological diversity in the form of shifting, heterogeneous mosaics of diverse communities and habitats across a landscape (McKinney and Drake 1998), and biodiversity is generally highest when disturbance is neither too rare nor too frequent on the landscape (Grime 1973).

  3. Foods and nutritional components of diets of black bear in Rocky Mountain National Park, Colorado

    Science.gov (United States)

    Baldwin, R.A.; Bender, L.C.

    2009-01-01

    We used scat analysis to determine diets and relative nutritional values of diets for black bears (Ursus americanus Pallas, 1780) in Rocky Mountain National Park, Colorado, from 2003 to 2006, and compared foods consumed and nutritional components to identify important sources of fecal gross energy (GE), crude fat (CF), and fecal nitrogen (FN) in annual and seasonal diets. Patterns of use of food classes followed typical seasonal patterns for bears, although use of animal matter was among the highest reported (>49% annually). Use of animal matter increased after spring, although crude protein levels in bear diets were always >25%. GE was typically lowest for grasses and other herbaceous plants and highest for ants and ungulates; FN was strongly positively related to most animal sources, but negatively correlated with vegetative matter; and CF showed the strongest positive relationship with ungulates and berries, with the latter likely influenced by the presence of seeds. Compared with historic data (1984-1991), contemporary diets included substantially greater prevalence of anthropogenic foods, which likely contributed to increases in size, condition, and productivity of the contemporary bear population. Management strategies are needed to increase quantity and quality of natural foods while minimizing dependence on anthropogenic sources.

  4. Trends in clinical diagnoses of Rocky Mountain spotted fever among American Indians, 2001-2008.

    Science.gov (United States)

    Folkema, Arianne M; Holman, Robert C; McQuiston, Jennifer H; Cheek, James E

    2012-01-01

    American Indians are at greater risk for Rocky Mountain spotted fever (RMSF) than the general U.S. population. The epidemiology of RMSF among American Indians was examined by using Indian Health Service inpatient and outpatient records with an RMSF International Classification of Diseases, Ninth Revision, Clinical Modification diagnosis. For 2001-2008, 958 American Indian patients with clinical diagnoses of RMSF were reported. The average annual RMSF incidence was 94.6 per 1,000,000 persons, with a significant increasing incidence trend from 24.2 in 2001 to 139.4 in 2008 (P = 0.006). Most (89%) RMSF hospital visits occurred in the Southern Plains and Southwest regions, where the average annual incidence rates were 277.2 and 49.4, respectively. Only the Southwest region had a significant increasing incidence trend (P = 0.005), likely linked to the emergence of brown dog ticks as an RMSF vector in eastern Arizona. It is important to continue monitoring RMSF infection to inform public health interventions that target RMSF reduction in high-risk populations.

  5. Rocky Mountain spotted fever in the United States, 1997-2002.

    Science.gov (United States)

    Chapman, Alice S; Murphy, Staci M; Demma, Linda J; Holman, Robert C; Curns, Aaron T; McQuiston, Jennifer H; Krebs, John W; Swerdlow, David L

    2006-01-01

    Rocky Mountain spotted fever (RMSF) is the most commonly reported fatal tick-borne disease in the United States. During 1997-2002, 3,649 cases of RMSF were reported to the Centers for Disease Control and Prevention via the National Electronic Telecommunications System for Surveillance; 2,589 case report forms, providing supplemental information, were also submitted. The average annual RMSF incidence during 1997-2002 was 2.2 cases/million persons. The annual incidence increased during 1997-2002 to a rate of 3.8 cases/million persons in 2002. The incidence was lowest among persons aged<5 and 10-29 years, and highest among adults aged 60-69 years. The overall case-fatality rate was 1.4%; the rate peaked in 1998 at 2.9% and declined to 0.7% in 2001 and 2002. Children<5 years of age had a case-fatality rate (5%) that was significantly greater than the rates for age groups<60 years of age, except for that for 40-49 years of age. Continued national surveillance is needed to assess the effectiveness of prevention efforts and early treatment in decreasing severe morbidity and mortality associated with RMSF.

  6. Trends in Clinical Diagnoses of Rocky Mountain Spotted Fever among American Indians, 2001–2008

    Science.gov (United States)

    Folkema, Arianne M.; Holman, Robert C.; McQuiston, Jennifer H.; Cheek, James E.

    2012-01-01

    American Indians are at greater risk for Rocky Mountain spotted fever (RMSF) than the general U.S. population. The epidemiology of RMSF among American Indians was examined by using Indian Health Service inpatient and outpatient records with an RMSF International Classification of Diseases, Ninth Revision, Clinical Modification diagnosis. For 2001–2008, 958 American Indian patients with clinical diagnoses of RMSF were reported. The average annual RMSF incidence was 94.6 per 1,000,000 persons, with a significant increasing incidence trend from 24.2 in 2001 to 139.4 in 2008 (P = 0.006). Most (89%) RMSF hospital visits occurred in the Southern Plains and Southwest regions, where the average annual incidence rates were 277.2 and 49.4, respectively. Only the Southwest region had a significant increasing incidence trend (P = 0.005), likely linked to the emergence of brown dog ticks as an RMSF vector in eastern Arizona. It is important to continue monitoring RMSF infection to inform public health interventions that target RMSF reduction in high-risk populations. PMID:22232466

  7. Public distrust and hazard management success at the Rocky Flats nuclear weapons plant

    International Nuclear Information System (INIS)

    Hohenemser, C.

    1987-01-01

    Based on experience gained while serving a public oversight commission appointed by the governor of Colorado, hazard management at the Department of Energy's Rocky Flats nuclear weapons plant is reviewed. Specific reference is made to the plant's history of controversy, its defense-in-depth strategy of hazard control, occupational health issues, public exposure to plutonium, and the assessment of low-probability, high-consequence risks. This leads to the conclusion that Rocky flats is, by any objective standard, a hazard management success. It follows that public distrust of Rocky Flats arises as much from fear and loathing of nuclear weapons themselves as from the manufacturing process by which they are made

  8. Structure Changes of Macrobenthic Community on Rocky Shores After the Hebei Spirit Oil Spill

    OpenAIRE

    Yun-Hwan Jung; Heung-Sik Park; Kon-Tak Yoon; Hyung-Gon Lee; Chae-Woo Ma

    2013-01-01

    In Korea, more than 300 oil spill accidents occur every year. Despite the frequency, only a small pool of data is available on the initial effect of oil spill on macrobenthic fauna inhabiting rocky shores. The aim of this study was to analyze the variation of macrobenthic fauna composition and community structure on rocky shores, and understand the impact of oil on rocky shore organisms after the Hebei Spirit oil spill. Field surveys were carried out in five regions dose to the wreck site in ...

  9. Chromosome evolution in kangaroos (Marsupialia: Macropodidae): cross species chromosome painting between the tammar wallaby and rock wallaby spp. with the 2n = 22 ancestral macropodid karyotype.

    Science.gov (United States)

    O'Neill, R J; Eldridge, M D; Toder, R; Ferguson-Smith, M A; O'Brien, P C; Graves, J A

    1999-06-01

    Marsupial mammals show extraordinary karyotype stability, with 2n = 14 considered ancestral. However, macropodid marsupials (kangaroos and wallabies) exhibit a considerable variety of karyotypes, with a hypothesised ancestral karyotype of 2n = 22. Speciation and karyotypic diversity in rock wallabies (Petrogale) is exceptional. We used cross species chromosome painting to examine the chromosome evolution between the tammar wallaby (2n = 16) and three 2n = 22 rock wallaby species groups with the putative ancestral karyotype. Hybridization of chromosome paints prepared from flow sorted chromosomes of the tammar wallaby to Petrogale spp., showed that this ancestral karyotype is largely conserved among 2n = 22 rock wallaby species, and confirmed the identity of ancestral chromosomes which fused to produce the bi-armed chromosomes of the 2n = 16 tammar wallaby. These results illustrate the fission-fusion process of karyotype evolution characteristic of the kangaroo group.

  10. Creation of Functional Viruses from Non-Functional cDNA Clones Obtained from an RNA Virus Population by the Use of Ancestral Reconstruction

    DEFF Research Database (Denmark)

    Fahnøe, Ulrik; Pedersen, Anders Gorm; Dräger, Carolin

    2015-01-01

    necessarily be the descendant of a functional ancestor, we hypothesized that it should be possible to produce functional clones by reconstructing ancestral sequences. To test this we used phylogenetic methods to infer two ancestral sequences, which were then reconstructed as cDNA clones. Viruses rescued from...... the reconstructed cDNAs were tested in cell culture and pigs. Both reconstructed ancestral genomes proved functional, and displayed distinct phenotypes in vitro and in vivo. We suggest that reconstruction of ancestral viruses is a useful tool for experimental and computational investigations of virulence and viral...... evolution. Importantly, ancestral reconstruction can be done even on the basis of a set of sequences that all correspond to non-functional variants....

  11. Fire Regime and Ecosystem Effects of Climate-driven Changes in Rocky Mountains Hydrology

    Science.gov (United States)

    Westerling, A. L.; Das, T.; Lubetkin, K.; Romme, W.; Ryan, M. G.; Smithwick, E. A.; Turner, M.

    2009-12-01

    Western US Forest managers face more wildfires than ever before, and it is increasingly imperative to anticipate the consequences of this trend. Large fires in the northern Rocky Mountains have increased in association with warmer temperatures, earlier snowmelt, and longer fire seasons (1), and this trend is likely to continue with global warming (2). Increased wildfire occurrence is already a concern shared by managers from many federal land-management agencies (3). However, new analyses for the western US suggest that future climate could diverge even more rapidly from past climate than previously suggested. Current model projections suggest end-of-century hydroclimatic conditions like those of 1988 (the year of the well-known Yellowstone Fires) may represent close to the average year rather than an extreme year. The consequences of a shift of this magnitude for the fire regime, post-fire succession and carbon (C) balance of western forest ecosystems are well beyond what scientists have explored to date, and may fundamentally change the potential of western forests to sequester atmospheric C. We link hydroclimatic extremes (spring and summer temperature and cumulative water-year moisture deficit) to extreme fire years in northern Rockies forests, using large forest fire histories and 1/8-degree gridded historical hydrologic simulations (1950 - 2005) (4) forced with historical gridded temperature and precipitation (5). The frequency of extremes in hydroclimate associated with historic severe fire years in the northern Rocky Mountains is compared to those projected under a range of climate change projections, using global climate model runs for the A2 and B1 emissions pathways for three global climate models (NCAR PCM1, GFDL CM2.1, CNRM CM3). Coarse-scale climatic variables are downscaled to a 1/8 degree grid and used to force hydrologic simulations (6, 7). We will present preliminary results using these hydrologic simulations to model spatially explicit annual

  12. Department of Energy treatment capabilities for greater-than-Class C low-level radioactive waste

    International Nuclear Information System (INIS)

    Morrell, D.K.; Fischer, D.K.

    1995-01-01

    This report provides brief profiles for 26 low-level and high-level waste treatment capabilities available at the Idaho National Engineering Laboratory (INEL), Lawrence Livermore National Laboratory (LLNL), Los Alamos National Laboratory (LANL), Oak Ridge National Laboratory (ORNL), Pacific Northwest Laboratory (PNL), Rocky Flats Plant (RFP), Savannah River Site (SRS), and West Valley Demonstration Plant (WVDP). Six of the treatments have potential use for greater-than-Class C low-level waste (GTCC LLW). They include: (a) the glass ceramic process and (b) the Waste Experimental Reduction Facility incinerator at INEL; (c) the Super Compaction and Repackaging Facility and (d) microwave melting solidification at RFP; (e) the vitrification plant at SRS; and (f) the vitrification plant at WVDP. No individual treatment has the capability to treat all GTCC LLW streams. It is recommended that complete physical and chemical characterizations be performed for each GTCC waste stream, to permit using multiple treatments for GTCC LLW

  13. Esthetic evaluation of timber harvesting in the Northern Rockies - a progressive report

    Science.gov (United States)

    Dennis L. Schweitzer; James R. Ullrich; Robert E. Benson

    1976-01-01

    Panels of judges have been evaluating the esthetic dimension of harvested areas in the Northern Rockies. Studies conducted in Wyoming and Montana agree with intuition in that forest scenes are generally liked less as the evidence of man's activities increases.

  14. Synthetic Minor NSR Permit: Tesoro Logistics-Rockies - Ponderosa Compressor Station

    Science.gov (United States)

    This page contains documents related to the synthetic minor NSR permit for the Tesoro Logistics-Rockies Ponderosa Compressor Station, located on the Uintah and Ouray Indian Reservation in Uintah County, UT.

  15. Good Days on the Trail, 1938-1942: Film Footage of the Rocky Mountains, Colorado

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This film documents student hiking trips conducted by the University of Colorado at Boulder in the Rocky Mountains, Colorado, USA during the summers of 1938-1942....

  16. Compaction-Driven Evolution of Pluto's Rocky Core: Implications for Water-Rock Interactions

    Science.gov (United States)

    Gabasova, L. R.; Tobie, G.; Choblet, G.

    2018-05-01

    We model the compaction of Pluto's rocky core after accretion and explore the potential for hydrothermal circulation within the porous layer, as well as examine its effect on core cooling and the persistence of a liquid internal ocean.

  17. Numerical simulation of atmospheric dispersion in the vicinity of the Rocky Flats plant

    International Nuclear Information System (INIS)

    Bossert, J.E.; Poulos, G.S.

    1993-01-01

    The Atmospheric Studies in Complex Terrain (ASCOT) program sponsored a field experiment in the winter of 1991 near Rocky Flats, Colorado. Both meteorological and tracer dispersion measurements were taken. These two data sets provided an opportunity to investigate the influence of terrain-generated, radiatively-driven flows on the dispersion of the tracer. In this study, we use the Regional Atmospheric Modeling System (RAMS) to simulate meteorological conditions and tracer dispersion on the case night of 4--5 February 1991. The simulations were developed to examine the influence of nocturnal drainage flow from various topography regimes on the dispersion of tracer from the Rocky Flats plant. The simulation described herein demonstrates the extent to which Rocky Mountain drainage winds influence the flow at the mountain/plain interface for a particular case night, and shows the potential importance of canyon drainage on dispersion from the Rocky Flats area

  18. Discrepancies in Weil-Felix and microimmunofluorescence test results for Rocky Mountain spotted fever.

    Science.gov (United States)

    Hechemy, K E; Stevens, R W; Sasowski, S; Michaelson, E E; Casper, E A; Philip, R N

    1979-01-01

    Only 4.2% of 284 single specimens and 17.6% of 51 pairs of sera reactive in Weil-Felix agglutination tests for Rocky Mountain spotted fever were confirmed by a specific Rickettsia rickettsii microimmunofluorescence test. PMID:107194

  19. Proceedings of the second symposium on the geology of Rocky Mountain coal, 1977

    Energy Technology Data Exchange (ETDEWEB)

    Hodgson, H. E. [ed.

    1978-01-01

    The 1977 Symposium on the Geology of Rocky Mountain Coal was held May 9 and 10 on the campus of the Colorado School of Mines in Golden, Colorado. The 1977 Symposium was sponsored by the Colorado Geological Survey and the US Geological Survey. The 1977 Symposium consisted of four technical sessions: Depositional Models for Coal Exploration in the Rocky Mountain Cretaceous; Stratigraphy and Depositional Environments of Rocky Mountain Tertiary Coal Deposits; Depositional Models for Coal Exploration in non-Rocky Mountain Regions; and Application of Geology to Coal Mining and Coal Mine Planning. Several papers discuss geophysical survey and well logging techniques applied to the exploration of coal deposits and for mine planning. Fouteen papers have been entered individually into EDB and ERA. (LTN)

  20. Comparative wood anatomy of some shrubs native to the Northern Rocky Mountains

    Science.gov (United States)

    Arlene Dale

    1968-01-01

    This paper describes some xylem characteristics of the more important shrub species of the Northern Rockies and presents a key for identifying shrub-wood specimens by microscopic characters. The paper contains photomicrographs of 55 shrub woods.

  1. SITE Technology Capsule. Demonstration of Rocky Mountain Remediation Services Soil Amendment

    Science.gov (United States)

    This report briefly summarizes the Rocky Mountain Remediation Services treatment technology demonstration of a soil amendment process for lead contaminated soil at Roseville, OH. The evaluation included leaching, bioavailability, geotechnical, and geochemical methods.

  2. NPDES Permit for Rocky Mountain Arsenal Recycled Water Pipeline in Colorado

    Science.gov (United States)

    Under NPDES permit CO-0035009, the U.S. Department of Interior's Fish and Wildlife Service is authorized to discharge from the Rocky Mountain Arsenal recycled water pipeline to Lower Derby Lake in Adams County, Colo.

  3. Bat population monitoring and conservation at the Rocky Mountain Arsenal NWR

    Data.gov (United States)

    Department of the Interior — A study of the bat populations at Rocky Mountain Arsenal National Wildlife Refuge (RMA) was conducted from 1997–1998, which provided basic population and contaminant...

  4. Fire, fuels, and restoration of ponderosa pine-Douglas-fir forests in the Rocky Mountains, USA

    OpenAIRE

    Baker, W. L.; Veblen, T. T.; Sherriff, R. L.

    2007-01-01

    Forest restoration in ponderosa pine and mixed ponderosa pine–Douglas fir forests in the US Rocky Mountains has been highly influenced by a historical model of frequent, low-severity surface fires developed for the ponderosa pine forests of the Southwestern USA. A restoration model, based on this low-severity fire model, focuses on thinning and prescribed burning to restore historical forest structure. However, in the US Rocky Mountains, research on fire history and forest structure, and earl...

  5. Sintopy of two Tropidurus lizard species (Squamata: Tropiduridae) in a rocky Cerrado habitat in Central Brazil

    OpenAIRE

    Faria,R. G.; Araujo,A. F. B.

    2004-01-01

    We studied the ecology of Tropidurus itambere and T. oreadicus that occur syntopically in rocky habitats of Cerrado vegetation in central Brazil during the dry season (April to September 2000). The two species are ecologically similar, but somewhat differentiated in vertical microhabitat use. The two species preferred rocky surface microhabitat. Both species demonstrated a unimodal activity pattern, with a peak between 10 and 15 h. Their diets were similar in composition and prey size. The mo...

  6. The evolution of brachiation in ateline primates, ancestral character states and history.

    Science.gov (United States)

    Jones, Andrea L

    2008-10-01

    This study examines how brachiation locomotion evolved in ateline primates using recently-developed molecular phylogenies and character reconstruction algorithms, and a newly-collected dataset including the fossils Protopithecus, Caipora, and Cebupithecia. Fossils are added to two platyrrhine molecular phylogenies to create several phylogenetic scenarios. A generalized least squares algorithm reconstructs ateline and atelin ancestral character states for 17 characters that differentiate between ateline brachiators and nonbrachiators. Histories of these characters are mapped out on these phylogenies, producing two scenarios of ateline brachiation evolution that have four commonalities: First, many characters change towards the Ateles condition on the ateline stem lineage before Alouatta splits off from the atelins, suggesting that an ateline energy-maximizing strategy began before the atelines diversified. Second, the ateline last common ancestor is always reconstructed as an agile quadruped, usually with suspensory abilities. It is never exactly like Alouatta and many characters reverse and change towards the Alouatta condition after Alouatta separates from the atelins. Third, most characters undergo homoplastic change in all ateline lineages, especially on the Ateles and Brachyteles terminal branches. Fourth, ateline character evolution probably went through a hindlimb suspension with tail-bracing phase. The atelines most likely diversified via a quick adaptive radiation, with bursts of punctuated change occurring in their postcranial skeletons, due to changing climatic conditions, which may have caused competition among the atelines and between atelines and pitheciines.

  7. An ancestral role for the mitochondrial pyruvate carrier in glucose-stimulated insulin secretion

    Directory of Open Access Journals (Sweden)

    Kyle S. McCommis

    2016-08-01

    Full Text Available Objective: Transport of pyruvate into the mitochondrial matrix by the Mitochondrial Pyruvate Carrier (MPC is an important and rate-limiting step in its metabolism. In pancreatic β-cells, mitochondrial pyruvate metabolism is thought to be important for glucose sensing and glucose-stimulated insulin secretion. Methods: To evaluate the role that the MPC plays in maintaining systemic glucose homeostasis, we used genetically-engineered Drosophila and mice with loss of MPC activity in insulin-producing cells. Results: In both species, MPC deficiency results in elevated blood sugar concentrations and glucose intolerance accompanied by impaired glucose-stimulated insulin secretion. In mouse islets, β-cell MPC-deficiency resulted in decreased respiration with glucose, ATP-sensitive potassium (KATP channel hyperactivity, and impaired insulin release. Moreover, treatment of pancreas-specific MPC knockout mice with glibenclamide, a sulfonylurea KATP channel inhibitor, improved defects in islet insulin secretion and abnormalities in glucose homeostasis in vivo. Finally, using a recently-developed biosensor for MPC activity, we show that the MPC is rapidly stimulated by glucose treatment in INS-1 insulinoma cells suggesting that glucose sensing is coupled to mitochondrial pyruvate carrier activity. Conclusions: Altogether, these studies suggest that the MPC plays an important and ancestral role in insulin-secreting cells in mediating glucose sensing, regulating insulin secretion, and controlling systemic glycemia. Keywords: Stimulus-coupled secretion, Insulin, β-Cell, Diabetes, Pyruvate, Mitochondria, Drosophila

  8. Mitogenomics and phylogenomics reveal priapulid worms as extant models of the ancestral Ecdysozoan.

    Science.gov (United States)

    Webster, Bonnie L; Copley, Richard R; Jenner, Ronald A; Mackenzie-Dodds, Jacqueline A; Bourlat, Sarah J; Rota-Stabelli, Omar; Littlewood, D T J; Telford, Maximilian J

    2006-01-01

    Research into arthropod evolution is hampered by the derived nature and rapid evolution of the best-studied out-group: the nematodes. We consider priapulids as an alternative out-group. Priapulids are a small phylum of bottom-dwelling marine worms; their tubular body with spiny proboscis or introvert has changed little over 520 million years and recognizable priapulids are common among exceptionally preserved Cambrian fossils. Using the complete mitochondrial genome and 42 nuclear genes from Priapulus caudatus, we show that priapulids are slowly evolving ecdysozoans; almost all these priapulid genes have evolved more slowly than nematode orthologs and the priapulid mitochondrial gene order may be unchanged since the Cambrian. Considering their primitive bodyplan and embryology and the great conservation of both nuclear and mitochondrial genomes, priapulids may deserve the popular epithet of "living fossil." Their study is likely to yield significant new insights into the early evolution of the Ecdysozoa and the origins of the arthropods and their kin as well as aiding inference of the morphology of ancestral Ecdysozoa and Bilateria and their genomes.

  9. Multiple chromosomal rearrangements structured the ancestral vertebrate Hox-bearing protochromosomes.

    Directory of Open Access Journals (Sweden)

    Vincent J Lynch

    2009-01-01

    Full Text Available While the proposal that large-scale genome expansions occurred early in vertebrate evolution is widely accepted, the exact mechanisms of the expansion--such as a single or multiple rounds of whole genome duplication, bloc chromosome duplications, large-scale individual gene duplications, or some combination of these--is unclear. Gene families with a single invertebrate member but four vertebrate members, such as the Hox clusters, provided early support for Ohno's hypothesis that two rounds of genome duplication (the 2R-model occurred in the stem lineage of extant vertebrates. However, despite extensive study, the duplication history of the Hox clusters has remained unclear, calling into question its usefulness in resolving the role of large-scale gene or genome duplications in early vertebrates. Here, we present a phylogenetic analysis of the vertebrate Hox clusters and several linked genes (the Hox "paralogon" and show that different phylogenies are obtained for Dlx and Col genes than for Hox and ErbB genes. We show that these results are robust to errors in phylogenetic inference and suggest that these competing phylogenies can be resolved if two chromosomal crossover events occurred in the ancestral vertebrate. These results resolve conflicting data on the order of Hox gene duplications and the role of genome duplication in vertebrate evolution and suggest that a period of genome reorganization occurred after genome duplications in early vertebrates.

  10. Detection of Weakly Conserved Ancestral Mammalian RegulatorySequences by Primate Comparisons

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Qian-fei; Prabhakar, Shyam; Chanan, Sumita; Cheng,Jan-Fang; Rubin, Edward M.; Boffelli, Dario

    2006-06-01

    Genomic comparisons between human and distant, non-primatemammals are commonly used to identify cis-regulatory elements based onconstrained sequence evolution. However, these methods fail to detectcryptic functional elements, which are too weakly conserved among mammalsto distinguish from nonfunctional DNA. To address this problem, weexplored the potential of deep intra-primate sequence comparisons. Wesequenced the orthologs of 558 kb of human genomic sequence, coveringmultiple loci involved in cholesterol homeostasis, in 6 nonhumanprimates. Our analysis identified 6 noncoding DNA elements displayingsignificant conservation among primates, but undetectable in more distantcomparisons. In vitro and in vivo tests revealed that at least three ofthese 6 elements have regulatory function. Notably, the mouse orthologsof these three functional human sequences had regulatory activity despitetheir lack of significant sequence conservation, indicating that they arecryptic ancestral cis-regulatory elements. These regulatory elementscould still be detected in a smaller set of three primate speciesincluding human, rhesus and marmoset. Since the human and rhesus genomesequences are already available, and the marmoset genome is activelybeing sequenced, the primate-specific conservation analysis describedhere can be applied in the near future on a whole-genome scale, tocomplement the annotation provided by more distant speciescomparisons.

  11. Anomalously high variation in postnatal development is ancestral for dinosaurs but lost in birds

    Science.gov (United States)

    Griffin, Christopher T.; Nesbitt, Sterling J.

    2016-12-01

    Compared with all other living reptiles, birds grow extremely fast and possess unusually low levels of intraspecific variation during postnatal development. It is now clear that birds inherited their high rates of growth from their dinosaurian ancestors, but the origin of the avian condition of low variation during development is poorly constrained. The most well-understood growth trajectories of later Mesozoic theropods (e.g., Tyrannosaurus, Allosaurus) show similarly low variation to birds, contrasting with higher variation in extant crocodylians. Here, we show that deep within Dinosauria, among the earliest-diverging dinosaurs, anomalously high intraspecific variation is widespread but then is lost in more derived theropods. This style of development is ancestral for dinosaurs and their closest relatives, and, surprisingly, this level of variation is far higher than in living crocodylians. Among early dinosaurs, this variation is widespread across Pangaea in the Triassic and Early Jurassic, and among early-diverging theropods (ceratosaurs), this variation is maintained for 165 million years to the end of the Cretaceous. Because the Late Triassic environment across Pangaea was volatile and heterogeneous, this variation may have contributed to the rise of dinosaurian dominance through the end of the Triassic Period.

  12. Fixation Probability in a Two-Locus Model by the Ancestral Recombination–Selection Graph

    Science.gov (United States)

    Lessard, Sabin; Kermany, Amir R.

    2012-01-01

    We use the ancestral influence graph (AIG) for a two-locus, two-allele selection model in the limit of a large population size to obtain an analytic approximation for the probability of ultimate fixation of a single mutant allele A. We assume that this new mutant is introduced at a given locus into a finite population in which a previous mutant allele B is already segregating with a wild type at another linked locus. We deduce that the fixation probability increases as the recombination rate increases if allele A is either in positive epistatic interaction with B and allele B is beneficial or in no epistatic interaction with B and then allele A itself is beneficial. This holds at least as long as the recombination fraction and the selection intensity are small enough and the population size is large enough. In particular this confirms the Hill–Robertson effect, which predicts that recombination renders more likely the ultimate fixation of beneficial mutants at different loci in a population in the presence of random genetic drift even in the absence of epistasis. More importantly, we show that this is true from weak negative epistasis to positive epistasis, at least under weak selection. In the case of deleterious mutants, the fixation probability decreases as the recombination rate increases. This supports Muller’s ratchet mechanism to explain the accumulation of deleterious mutants in a population lacking recombination. PMID:22095080

  13. Comparative Genomics of Facultative Bacterial Symbionts Isolated from European Orius Species Reveals an Ancestral Symbiotic Association

    Directory of Open Access Journals (Sweden)

    Xiaorui Chen

    2017-10-01

    Full Text Available Pest control in agriculture employs diverse strategies, among which the use of predatory insects has steadily increased. The use of several species within the genus Orius in pest control is widely spread, particularly in Mediterranean Europe. Commercial mass rearing of predatory insects is costly, and research efforts have concentrated on diet manipulation and selective breeding to reduce costs and improve efficacy. The characterisation and contribution of microbial symbionts to Orius sp. fitness, behaviour, and potential impact on human health has been neglected. This paper provides the first genome sequence level description of the predominant culturable facultative bacterial symbionts associated with five Orius species (O. laevigatus, O. niger, O. pallidicornis, O. majusculus, and O. albidipennis from several geographical locations. Two types of symbionts were broadly classified as members of the genera Serratia and Leucobacter, while a third constitutes a new genus within the Erwiniaceae. These symbionts were found to colonise all the insect specimens tested, which evidenced an ancestral symbiotic association between these bacteria and the genus Orius. Pangenome analyses of the Serratia sp. isolates offered clues linking Type VI secretion system effector–immunity proteins from the Tai4 sub-family to the symbiotic lifestyle.

  14. Comparative Genomics of Facultative Bacterial Symbionts Isolated from European Orius Species Reveals an Ancestral Symbiotic Association

    Science.gov (United States)

    Chen, Xiaorui; Hitchings, Matthew D.; Mendoza, José E.; Balanza, Virginia; Facey, Paul D.; Dyson, Paul J.; Bielza, Pablo; Del Sol, Ricardo

    2017-01-01

    Pest control in agriculture employs diverse strategies, among which the use of predatory insects has steadily increased. The use of several species within the genus Orius in pest control is widely spread, particularly in Mediterranean Europe. Commercial mass rearing of predatory insects is costly, and research efforts have concentrated on diet manipulation and selective breeding to reduce costs and improve efficacy. The characterisation and contribution of microbial symbionts to Orius sp. fitness, behaviour, and potential impact on human health has been neglected. This paper provides the first genome sequence level description of the predominant culturable facultative bacterial symbionts associated with five Orius species (O. laevigatus, O. niger, O. pallidicornis, O. majusculus, and O. albidipennis) from several geographical locations. Two types of symbionts were broadly classified as members of the genera Serratia and Leucobacter, while a third constitutes a new genus within the Erwiniaceae. These symbionts were found to colonise all the insect specimens tested, which evidenced an ancestral symbiotic association between these bacteria and the genus Orius. Pangenome analyses of the Serratia sp. isolates offered clues linking Type VI secretion system effector–immunity proteins from the Tai4 sub-family to the symbiotic lifestyle. PMID:29067021

  15. Phylogenetic uncertainty can bias the number of evolutionary transitions estimated from ancestral state reconstruction methods.

    Science.gov (United States)

    Duchêne, Sebastian; Lanfear, Robert

    2015-09-01

    Ancestral state reconstruction (ASR) is a popular method for exploring the evolutionary history of traits that leave little or no trace in the fossil record. For example, it has been used to test hypotheses about the number of evolutionary origins of key life-history traits such as oviparity, or key morphological structures such as wings. Many studies that use ASR have suggested that the number of evolutionary origins of such traits is higher than was previously thought. The scope of such inferences is increasing rapidly, facilitated by the construction of very large phylogenies and life-history databases. In this paper, we use simulations to show that the number of evolutionary origins of a trait tends to be overestimated when the phylogeny is not perfect. In some cases, the estimated number of transitions can be several fold higher than the true value. Furthermore, we show that the bias is not always corrected by standard approaches to account for phylogenetic uncertainty, such as repeating the analysis on a large collection of possible trees. These findings have important implications for studies that seek to estimate the number of origins of a trait, particularly those that use large phylogenies that are associated with considerable uncertainty. We discuss the implications of this bias, and methods to ameliorate it. © 2015 Wiley Periodicals, Inc.

  16. Reconstruction of chromosome rearrangements between the two most ancestral duckweed species Spirodela polyrhiza and S. intermedia.

    Science.gov (United States)

    Hoang, Phuong T N; Schubert, Ingo

    2017-12-01

    The monophyletic duckweeds comprising five genera within the monocot order Alismatales are neotenic, free-floating, aquatic organisms with fast vegetative propagation. Some species are considered for efficient biomass production, for life stock feeding, and for (simultaneous) wastewater phytoremediation. The ancestral genus Spirodela consists of only two species, Spirodela polyrhiza and Spirodela intermedia, both with a similar small genome (~160 Mbp/1C). Reference genome drafts and a physical map of 96 BACs on the 20 chromosome pairs of S. polyrhiza strain 7498 are available and provide useful tools for further evolutionary studies within and between duckweed genera. Here we applied sequential comparative multicolor fluorescence in situ hybridization (mcFISH) to address homeologous chromosomes in S. intermedia (2n = 36), to detect chromosome rearrangements between both species and to elucidate the mechanisms which may have led to the chromosome number alteration after their evolutionary separation. Ten chromosome pairs proved to be conserved between S. polyrhiza and S. intermedia, the remaining ones experienced, depending on the assumed direction of evolution, translocations, inversion, and fissions, respectively. These results represent a first step to unravel karyotype evolution among duckweeds and are anchor points for future genome assembly of S. intermedia.

  17. Convergent evolution of caffeine in plants by co-option of exapted ancestral enzymes.

    Science.gov (United States)

    Huang, Ruiqi; O'Donnell, Andrew J; Barboline, Jessica J; Barkman, Todd J

    2016-09-20

    Convergent evolution is a process that has occurred throughout the tree of life, but the historical genetic and biochemical context promoting the repeated independent origins of a trait is rarely understood. The well-known stimulant caffeine, and its xanthine alkaloid precursors, has evolved multiple times in flowering plant history for various roles in plant defense and pollination. We have shown that convergent caffeine production, surprisingly, has evolved by two previously unknown biochemical pathways in chocolate, citrus, and guaraná plants using either caffeine synthase- or xanthine methyltransferase-like enzymes. However, the pathway and enzyme lineage used by any given plant species is not predictable from phylogenetic relatedness alone. Ancestral sequence resurrection reveals that this convergence was facilitated by co-option of genes maintained over 100 million y for alternative biochemical roles. The ancient enzymes of the Citrus lineage were exapted for reactions currently used for various steps of caffeine biosynthesis and required very few mutations to acquire modern-day enzymatic characteristics, allowing for the evolution of a complete pathway. Future studies aimed at manipulating caffeine content of plants will require the use of different approaches given the metabolic and genetic diversity revealed by this study.

  18. Greater trochanteric pain syndrome diagnosis and treatment.

    Science.gov (United States)

    Mallow, Michael; Nazarian, Levon N

    2014-05-01

    Lateral hip pain, or greater trochanteric pain syndrome, is a commonly seen condition; in this article, the relevant anatomy, epidemiology, and evaluation strategies of greater trochanteric pain syndrome are reviewed. Specific attention is focused on imaging of this syndrome and treatment techniques, including ultrasound-guided interventions. Copyright © 2014 Elsevier Inc. All rights reserved.

  19. Accuracy of Genomic Prediction in Synthetic Populations Depending on the Number of Parents, Relatedness, and Ancestral Linkage Disequilibrium.

    Science.gov (United States)

    Schopp, Pascal; Müller, Dominik; Technow, Frank; Melchinger, Albrecht E

    2017-01-01

    Synthetics play an important role in quantitative genetic research and plant breeding, but few studies have investigated the application of genomic prediction (GP) to these populations. Synthetics are generated by intermating a small number of parents ([Formula: see text] and thereby possess unique genetic properties, which make them especially suited for systematic investigations of factors contributing to the accuracy of GP. We generated synthetics in silico from [Formula: see text]2 to 32 maize (Zea mays L.) lines taken from an ancestral population with either short- or long-range linkage disequilibrium (LD). In eight scenarios differing in relatedness of the training and prediction sets and in the types of data used to calculate the relationship matrix (QTL, SNPs, tag markers, and pedigree), we investigated the prediction accuracy (PA) of Genomic best linear unbiased prediction (GBLUP) and analyzed contributions from pedigree relationships captured by SNP markers, as well as from cosegregation and ancestral LD between QTL and SNPs. The effects of training set size [Formula: see text] and marker density were also studied. Sampling few parents ([Formula: see text]) generates substantial sample LD that carries over into synthetics through cosegregation of alleles at linked loci. For fixed [Formula: see text], [Formula: see text] influences PA most strongly. If the training and prediction set are related, using [Formula: see text] parents yields high PA regardless of ancestral LD because SNPs capture pedigree relationships and Mendelian sampling through cosegregation. As [Formula: see text] increases, ancestral LD contributes more information, while other factors contribute less due to lower frequencies of closely related individuals. For unrelated prediction sets, only ancestral LD contributes information and accuracies were poor and highly variable for [Formula: see text] due to large sample LD. For large [Formula: see text], achieving moderate accuracy requires

  20. [Relationships between landscape structure and rocky desertification in karst region of northwestern Guangxi].

    Science.gov (United States)

    Zhang, Xiao-nan; Wang, Ke-lin; Chen, Hong-song; Zhang, Wei

    2008-11-01

    By using canonical correspondence analysis (CCA), sixteen landscape indices were adopted to quantitatively analyze the relationships between the landscape structure and rocky desertification in karst region of Huanjiang County, Guangxi Province. The results showed that the first and the second ordination axis of CCA were strongly correlated to the factors of average patch area, average dry land patch area, landscape shape index, and landscape aggregation index. The potential rocky desertification in the region was highly positively correlated with the average dry land patch area and the average fractal dimensions of dry land and shrub land, but negatively correlated with the patch numbers of dry land. Light rocky desertification had obvious positive correlations with the fractal dimension index, average fractal dimension of unused land, and patch numbers of shrub land; while moderate and strong rocky desertification had high positive correlations with the average unused land patch area but negative correlation with the average fractal dimension of shrub land. To some extent, rocky desertification degree might be represented by the values of landscape indices. The gradient variation in karst rocky desertification along landscape structure was clearly presented by the results of CCA.

  1. Idaho National Engineering Laboratory code assessment of the Rocky Flats transuranic waste

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-07-01

    This report is an assessment of the content codes associated with transuranic waste shipped from the Rocky Flats Plant in Golden, Colorado, to INEL. The primary objective of this document is to characterize and describe the transuranic wastes shipped to INEL from Rocky Flats by item description code (IDC). This information will aid INEL in determining if the waste meets the waste acceptance criteria (WAC) of the Waste Isolation Pilot Plant (WIPP). The waste covered by this content code assessment was shipped from Rocky Flats between 1985 and 1989. These years coincide with the dates for information available in the Rocky Flats Solid Waste Information Management System (SWIMS). The majority of waste shipped during this time was certified to the existing WIPP WAC. This waste is referred to as precertified waste. Reassessment of these precertified waste containers is necessary because of changes in the WIPP WAC. To accomplish this assessment, the analytical and process knowledge available on the various IDCs used at Rocky Flats were evaluated. Rocky Flats sources for this information include employee interviews, SWIMS, Transuranic Waste Certification Program, Transuranic Waste Inspection Procedure, Backlog Waste Baseline Books, WIPP Experimental Waste Characterization Program (headspace analysis), and other related documents, procedures, and programs. Summaries are provided of: (a) certification information, (b) waste description, (c) generation source, (d) recovery method, (e) waste packaging and handling information, (f) container preparation information, (g) assay information, (h) inspection information, (i) analytical data, and (j) RCRA characterization.

  2. Identification of the ancestral haplotype for apolipoprotein B suggests an African origin of Homo sapiens sapiens and traces their subsequent migration to Europe and the Pacific

    Energy Technology Data Exchange (ETDEWEB)

    Rapacz, J.; Hasler-Rapacz, J.O. (Univ. of Wisconsin, Madison (United States)); Chen, L.; Wu, Mingjiuan; Schumaker, V.N. (Univ. of California, Los Angeles (United States)); Butler-Brunner, E.; Butler, R. (Swiss Red Cross Blood Transfusion Service, Bern (Switzerland))

    1991-02-15

    The probable ancestral haplotype for human apolipoprotein B (apoB) has been identified through immunological analysis of chimpanzee and gorilla serum and sequence analysis of their DNA. Moreover, the frequency of this ancestral apoB haplotype among different human populations provides strong support for the African origin of Homo sapiens sapiens and their subsequent migration from Africa to Europe and to the Pacific. The approach used here for the identification of the ancestral human apoB haplotype is likely to be applicable to many other genes.

  3. Identification of the ancestral haplotype for apolipoprotein B suggests an African origin of Homo sapiens sapiens and traces their subsequent migration to Europe and the Pacific

    International Nuclear Information System (INIS)

    Rapacz, J.; Hasler-Rapacz, J.O.; Chen, L.; Wu, Mingjiuan; Schumaker, V.N.; Butler-Brunner, E.; Butler, R.

    1991-01-01

    The probable ancestral haplotype for human apolipoprotein B (apoB) has been identified through immunological analysis of chimpanzee and gorilla serum and sequence analysis of their DNA. Moreover, the frequency of this ancestral apoB haplotype among different human populations provides strong support for the African origin of Homo sapiens sapiens and their subsequent migration from Africa to Europe and to the Pacific. The approach used here for the identification of the ancestral human apoB haplotype is likely to be applicable to many other genes

  4. Effect of the assignment of ancestral CpG state on the estimation of nucleotide substitution rates in mammals

    Directory of Open Access Journals (Sweden)

    Keightley Peter D

    2008-09-01

    Full Text Available Abstract Background Molecular evolutionary studies in mammals often estimate nucleotide substitution rates within and outside CpG dinucleotides separately. Frequently, in alignments of two sequences, the division of sites into CpG and non-CpG classes is based simply on the presence or absence of a CpG dinucleotide in either sequence, a procedure that we refer to as CpG/non-CpG assignment. Although it likely that this procedure is biased, it is generally assumed that the bias is negligible if species are very closely related. Results Using simulations of DNA sequence evolution we show that assignment of the ancestral CpG state based on the simple presence/absence of the CpG dinucleotide can seriously bias estimates of the substitution rate, because many true non-CpG changes are misassigned as CpG. Paradoxically, this bias is most severe between closely related species, because a minimum of two substitutions are required to misassign a true ancestral CpG site as non-CpG whereas only a single substitution is required to misassign a true ancestral non-CpG site as CpG in a two branch tree. We also show that CpG misassignment bias differentially affects fourfold degenerate and noncoding sites due to differences in base composition such that fourfold degenerate sites can appear to be evolving more slowly than noncoding sites. We demonstrate that the effects predicted by our simulations occur in a real evolutionary setting by comparing substitution rates estimated from human-chimp coding and intronic sequence using CpG/non-CpG assignment with estimates derived from a method that is largely free from bias. Conclusion Our study demonstrates that a common method of assigning sites into CpG and non CpG classes in pairwise alignments is seriously biased and recommends against the adoption of ad hoc methods of ancestral state assignment.

  5. Genotype-based ancestral background consistently predicts efficacy and side effects across treatments in CATIE and STAR*D.

    Directory of Open Access Journals (Sweden)

    Daniel E Adkins

    Full Text Available Only a subset of patients will typically respond to any given prescribed drug. The time it takes clinicians to declare a treatment ineffective leaves the patient in an impaired state and at unnecessary risk for adverse drug effects. Thus, diagnostic tests robustly predicting the most effective and safe medication for each patient prior to starting pharmacotherapy would have tremendous clinical value. In this article, we evaluated the use of genetic markers to estimate ancestry as a predictive component of such diagnostic tests. We first estimated each patient's unique mosaic of ancestral backgrounds using genome-wide SNP data collected in the Clinical Antipsychotic Trials of Intervention Effectiveness (CATIE (n = 765 and the Sequenced Treatment Alternatives to Relieve Depression (STAR*D (n = 1892. Next, we performed multiple regression analyses to estimate the predictive power of these ancestral dimensions. For 136/89 treatment-outcome combinations tested in CATIE/STAR*D, results indicated 1.67/1.84 times higher median test statistics than expected under the null hypothesis assuming no predictive power (p<0.01, both samples. Thus, ancestry showed robust and pervasive correlations with drug efficacy and side effects in both CATIE and STAR*D. Comparison of the marginal predictive power of MDS ancestral dimensions and self-reported race indicated significant improvements to model fit with the inclusion of MDS dimensions, but mixed evidence for self-reported race. Knowledge of each patient's unique mosaic of ancestral backgrounds provides a potent immediate starting point for developing algorithms identifying the most effective and safe medication for a wide variety of drug-treatment response combinations. As relatively few new psychiatric drugs are currently under development, such personalized medicine offers a promising approach toward optimizing pharmacotherapy for psychiatric conditions.

  6. Effects of ancestral populations on entrepreneurial founding and failure: private liquor stores in Alberta, 1994--2003

    OpenAIRE

    Glen Dowell; Robert J. David

    2011-01-01

    Until 1993, all liquor stores in the Canadian province of Alberta were government owned and run. In the fall of 1993, the provincial government exited liquor retailing, all government stores were shut down, and entrepreneurs were allowed to open private liquor stores. In this article, we take advantage of this abrupt regulatory change in the Alberta liquor-retailing industry to address two related issues that have received little empirical attention. First, we investigate how an ancestral pop...

  7. Accretion of Planetesimals and the Formation of Rocky Planets

    Science.gov (United States)

    Chambers, John E.; O'Brien, David P.; Davis, Andrew M.

    2010-02-01

    Here we describe the formation of rocky planets and asteroids in the context of the planetesimal hypothesis. Small dust grains in protoplanetary disks readily stick together forming mm-to-cm-sized aggregates, many of which experience brief heating episodes causing melting. Growth to km-sized planetesimals might proceed via continued pairwise sticking, turbulent concentration, or gravitational instability of a thin particle layer. Gravitational interactions between planetesimals lead to rapid runaway and oligarchic growth forming lunar-to-Mars-sized protoplanets in 10^5 to 10^6 years. Giant impacts between protoplanets form Earth-mass planets in 10^7 to 10^8 years, and occasionally lead to the formation of large satellites. Protoplanets may migrate far from their formation locations due to tidal interactions with the surrounding disk. Radioactive decay and impact heating cause melting and differentiation of planetesimals and protoplanets, forming iron-rich cores and silicate mantles, and leading to some loss of volatiles. Dynamical perturbations from giant planets eject most planetesimals and protoplanets from regions near orbital resonances, leading to asteroid-belt formation. Some of this scattered material will collide with growing terrestrial planets, altering their composition as a result. Numerical simulations and radioisotope dating indicate that the terrestrial planets of the Solar System were essentially fully formed in 100-200 million years.

  8. DISPOSITION PATHS FOR ROCKY FLATS GLOVEBOXES: EVALUATING OPTIONS

    International Nuclear Information System (INIS)

    Lobdell, D.; Geimer, R.; Larsen, P.; Loveland, K.

    2003-01-01

    The Kaiser-Hill Company, LLC has the responsibility for closure activities at the Rocky Flats Environmental Technology Site (RFETS). One of the challenges faced for closure is the disposition of radiologically contaminated gloveboxes. Evaluation of the disposition options for gloveboxes included a detailed analysis of available treatment capabilities, disposal facilities, and lifecycle costs. The Kaiser-Hill Company, LLC followed several processes in determining how the gloveboxes would be managed for disposition. Currently, multiple disposition paths have been chosen to accommodate the needs of the varying styles and conditions of the gloveboxes, meet the needs of the decommissioning team, and to best manage lifecycle costs. Several challenges associated with developing a disposition path that addresses both the radiological and RCRA concerns as well as offering the most cost-effective solution were encountered. These challenges included meeting the radiological waste acceptance criteria of available disposal facilities, making a RCRA determination, evaluating treatment options and costs, addressing void requirements associated with disposal, and identifying packaging and transportation options. The varying disposal facility requirements affected disposition choices. Facility conditions that impacted decisions included radiological and chemical waste acceptance criteria, physical requirements, and measurement for payment options. The facility requirements also impacted onsite activities including management strategies, decontamination activities, and life-cycle cost

  9. Differential concentration of plutonium isotopes in Rocky Flats Biota

    International Nuclear Information System (INIS)

    Little, Craig A.

    1978-01-01

    Data for 238 Pu and 239 Pu concentrations in samples from grassland biota and soil at Rocky Flats, Colorado, were studied to compare environmental behavior of these isotopes. Mean isotope ratios ( 239,240 Pu pCi/g / 238 Pu pCi/g) were lower for the small mammals and arthropods than for the soil, litter, and standing vegetation. The isotopic ratio was also found to be inversely related to soil sample depth. These results suggested that, relative to 239 Pu, 238 Pu was concentrating in small mammals and arthropods and moving downward into the soil at a faster rate. Further investigations, however, indicated that isotopic ratios were likely biased towards lower values of the ratio as the total plutonium concentration in a sample decreased. This bias can be understood as a leftward shift of the value of the most probable and mean ratio. This shift occurs when the frequency distribution of the numerator ( 239 Pu) and denominator ( 238 Pu) of the ratio are truncated (have their lower tail removed) by eliminating values below some detection limit. If, as in this example, the distribution of the denominator variable is of lower magnitude than the numerator and, therefore, nearer the detection limit and truncated to a larger degree, the resulting ratio frequency distribution is shifted to lower values compared to the ratio of two untruncated variables. (author)

  10. Environmental Survey preliminary report, Rocky Flats Plant, Golden, Colorado

    Energy Technology Data Exchange (ETDEWEB)

    1987-06-01

    This report presents the preliminary findings of the Environmental Survey of the United States Department of Energy (DOE), Rocky Flats Plant (RFP), conducted August 11 through 22, 1986. The Survey is being conducted by an multidisciplinary team of environmental specialists, led and managed by the Office of Environment, Safety and Health's Office of Environmental Audit. Individual team members are outside experts supplied by a private contractor. The objective of the Survey is to identify environmental problems and areas of environmental risk associated with the RFP. The Survey covers all environmental media and all areas of environmental regulations. It is being performed in accordance with the DOE Environmental Survey Manual. The on-site phase of the Survey involves the review of existing site environmental data observations of the operations carried on at RFP, and interviews with site personnel. The Survey team developed a Sampling and Analysis Plan to assist in further assessing certain environmental problems identified during its on-site activates. The Sampling and Analysis Plan is being executed by DOE's Oak Ridge National Laboratory. When completed, the results will be incorporated into the RFP Environmental Survey Interim Report. The Interim Report will reflect the final determinations of the RFP Survey. 75 refs., 24 figs., 33 tabs.

  11. Cure electrocoagulation demonstration at Rocky Flats Environmental Technology Site

    International Nuclear Information System (INIS)

    Bridges, J.L.; Jones, J.; Ball, T.

    1996-01-01

    A demonstration of an innovative technology for remediating radionuclide contamination in water took place at the Rocky Flats Environmental Technology Site (RFETS) in Golden, Colorado, during the summer of 1995. The demonstration was part of the U.S. Environmental Protection Agency (EPA) Superfund Innovative Technology Evaluation (SITE) program and was conducted by EPA, the U.S. Department of Energy (DOE), and General Environmental Corporation (GEC). The SITE program encourages the development and demonstration of innovative treatment and monitoring technologies. The purpose of the demonstration was to evaluate the ability of GEC's innovative CURE technology to remove uranium, plutonium, and americium from water taken from the A and B solar evaporation ponds at RFETS. The CURE electrocoagulation process uses an anode and cathode in a patented geometry to remove contaminants, including radionuclides, from wastewater in a continuous flow process. Electrocoagulation has been recognized as a method of removing a variety of contaminants from wastewaters. With the CURE process, GEC has refined the technology and adapted it to hazardous waste cleanup. Bench scale treatability testing conducted in April 1995 indicated 99 percent removal efficiencies were possible for uranium, plutonium-239/240, and americium-241. During the field scale demonstration in August and September 1995, samples were collected from four demonstration runs at RFETS. A removal efficiency of approximately 50 percent was achieved for uranium and nearly 99 percent for plutonium and americium

  12. Technical Safety Appraisal of the Rocky Flats Plant

    Energy Technology Data Exchange (ETDEWEB)

    Brown, Blake P.

    1989-01-01

    This report provides the results of a Technical Safety Appraisal (TSA) of the Rocky Flats Plant (RFP) conducted November 14 to 18 and November 28 to December 9, 1988. This appraisal covered the effectiveness and improvements in the RFP safety program across the site, evaluating progress to date against standards of accepted practice. The appraisal included coverage of the timeliness and effectiveness of actions taken in response to the recommendations/concerns in three previous Technical Safety Appraisals (TSAs) of RFP Bldg. 707 conducted in July 1986, Bldgs. 771/774 conducted in October/November 1986, and Bldgs. 776/777 conducted in January/February 1988. Results of this appraisal are given in Section IV for each of 14 technical safety areas at RFP. These results include a discussion, conclusions and any new safety concerns for each technical safety area. Appendix A contains a description of the system for categorizing concerns, and the concerns are tabulated in Appendix B. Appendix C reports on the evaluation of the contractor's actions and the current status of each of the 230 recommendations and concerns contained in the three previous TSA reports.

  13. Environmental Survey preliminary report, Rocky Flats Plant, Golden, Colorado

    International Nuclear Information System (INIS)

    1987-06-01

    This report presents the preliminary findings of the Environmental Survey of the United States Department of Energy (DOE), Rocky Flats Plant (RFP), conducted August 11 through 22, 1986. The Survey is being conducted by an multidisciplinary team of environmental specialists, led and managed by the Office of Environment, Safety and Health's Office of Environmental Audit. Individual team members are outside experts supplied by a private contractor. The objective of the Survey is to identify environmental problems and areas of environmental risk associated with the RFP. The Survey covers all environmental media and all areas of environmental regulations. It is being performed in accordance with the DOE Environmental Survey Manual. The on-site phase of the Survey involves the review of existing site environmental data observations of the operations carried on at RFP, and interviews with site personnel. The Survey team developed a Sampling and Analysis Plan to assist in further assessing certain environmental problems identified during its on-site activates. The Sampling and Analysis Plan is being executed by DOE's Oak Ridge National Laboratory. When completed, the results will be incorporated into the RFP Environmental Survey Interim Report. The Interim Report will reflect the final determinations of the RFP Survey. 75 refs., 24 figs., 33 tabs

  14. Cure electrocoagulation demonstration at Rocky Flats Environmental Technology Site

    Energy Technology Data Exchange (ETDEWEB)

    Bridges, J.L.; Jones, J.; Ball, T. [PRC Environmental Management, Inc., Denver, CO (United States)] [and others

    1996-12-31

    A demonstration of an innovative technology for remediating radionuclide contamination in water took place at the Rocky Flats Environmental Technology Site (RFETS) in Golden, Colorado, during the summer of 1995. The demonstration was part of the U.S. Environmental Protection Agency (EPA) Superfund Innovative Technology Evaluation (SITE) program and was conducted by EPA, the U.S. Department of Energy (DOE), and General Environmental Corporation (GEC). The SITE program encourages the development and demonstration of innovative treatment and monitoring technologies. The purpose of the demonstration was to evaluate the ability of GEC`s innovative CURE technology to remove uranium, plutonium, and americium from water taken from the A and B solar evaporation ponds at RFETS. The CURE electrocoagulation process uses an anode and cathode in a patented geometry to remove contaminants, including radionuclides, from wastewater in a continuous flow process. Electrocoagulation has been recognized as a method of removing a variety of contaminants from wastewaters. With the CURE process, GEC has refined the technology and adapted it to hazardous waste cleanup. Bench scale treatability testing conducted in April 1995 indicated 99 percent removal efficiencies were possible for uranium, plutonium-239/240, and americium-241. During the field scale demonstration in August and September 1995, samples were collected from four demonstration runs at RFETS. A removal efficiency of approximately 50 percent was achieved for uranium and nearly 99 percent for plutonium and americium.

  15. Efficient cooling of rocky planets by intrusive magmatism

    Science.gov (United States)

    Lourenço, Diogo L.; Rozel, Antoine B.; Gerya, Taras; Tackley, Paul J.

    2018-05-01

    The Earth is in a plate tectonics regime with high surface heat flow concentrated at constructive plate boundaries. Other terrestrial bodies that lack plate tectonics are thought to lose their internal heat by conduction through their lids and volcanism: hotter planets (Io and Venus) show widespread volcanism whereas colder ones (modern Mars and Mercury) are less volcanically active. However, studies of terrestrial magmatic processes show that less than 20% of melt volcanically erupts, with most melt intruding into the crust. Signatures of large magmatic intrusions are also found on other planets. Yet, the influence of intrusive magmatism on planetary cooling remains unclear. Here we use numerical magmatic-thermo-mechanical models to simulate global mantle convection in a planetary interior. In our simulations, warm intrusive magmatism acts to thin the lithosphere, leading to sustained recycling of overlying crustal material and cooling of the mantle. In contrast, volcanic eruptions lead to a thick lithosphere that insulates the upper mantle and prevents efficient cooling. We find that heat loss due to intrusive magmatism can be particularly efficient compared to volcanic eruptions if the partitioning of heat-producing radioactive elements into the melt phase is weak. We conclude that the mode of magmatism experienced by rocky bodies determines the thermal and compositional evolution of their interior.

  16. Retrospective Study of Rocky Mountain Spotted Fever in Children.

    Science.gov (United States)

    Tull, Rechelle; Ahn, Christine; Daniel, Alyssa; Yosipovitch, Gil; Strowd, Lindsay C

    2017-03-01

    Rocky Mountain spotted fever (RMSF), a lethal tick-borne illness, is prevalent in the south central United States. Children younger than 10 years old have the greatest risk of fatal outcome from RMSF. The objective of the current study was to review pediatric cases of RMSF seen in the dermatology consult service and to evaluate dermatology's role in the diagnosis and management of this disease. A retrospective review was performed of inpatient dermatology consultations at a tertiary care center in North Carolina from 2001 to 2011. Data collected included patient demographic characteristics, symptoms, pre- and postconsultation diagnoses, diagnostic procedures, length of hospital stay, and outcome. A total of 3,912 consultations were conducted in the dermatology service over 10 years. Six patients with RMSF, ranging in age from 22 months to 10 years (mean 5.1 years), were evaluated during April, May, and June. All preconsultation diagnoses included RMSF in the differential diagnosis. All patients underwent skin biopsies, and a culture was obtained in one case. Fifty percent of patients died within 4 days of hospitalization. Variables associated with mortality from RMSF are delayed diagnosis and initiation of antirickettsial therapy. Physicians should consider RMSF in children presenting with fever and rash during the summer months. Dermatology consultation is useful in evaluating patients with suspicious clinical features of RMSF with skin findings. © 2016 Wiley Periodicals, Inc.

  17. Atypical Rocky Mountain spotted fever with polyarticular arthritis.

    Science.gov (United States)

    Chaudhry, Muhammad A; Scofield, Robert Hal

    2013-11-01

    Rocky Mountain spotted fever (RMSF) is an acute, serious tick borne illness caused by Rickettsia rickettsi. Frequently, RMSF is manifested by headache, a typical rash and fever but atypical disease is common, making diagnosis difficult. Inflammatory arthritis as a manifestation is rare. The purpose of this study is to describe a patient with serologically proven RMSF who presented in an atypical manner with inflammatory arthritis of the small joints of the hands and to review the previously reported patients with rickettsial infection and inflammatory arthritis. An 18-year-old woman presented with a rash that began on the distal extremities and spread centrally, along with hand pain and swelling. She had tenderness and swelling of the metacarpophlangeal joints on examination in addition to an erythematosus macular rash and occasional fever. Acute and convalescent serology demonstrated R rickettsi infection. She was successfully treated with doxycycline. Inflammatory arthritis is a rare manifestation of RMSF or other rickettsial infection with 8 previously reported patients, only 1 of whom had RMSF. Physician must have a high index of suspicion for RMSF because of atypical presentations.

  18. Rocky mountain spotted fever hospitalizations among American Indians.

    Science.gov (United States)

    Demma, Linda J; Holman, Robert C; Mikosz, Christina A; Curns, Aaron T; Swerdlow, David L; Paisano, Edna L; Cheek, James E

    2006-09-01

    To describe the epidemiology of Rocky Mountain spotted fever (RMSF) among American Indians/Alaska Natives (AI/ANs), we conducted a retrospective analysis of hospitalization records with an RMSF diagnosis using Indian Health Service (IHS) hospital discharge data for calendar years 1980-2003. A total of 261 RMSF hospitalizations were reported among AIs, for an average annual hospitalization rate of 1.21 per 100,000 persons; two deaths were reported (0.8%). Most hospitalizations (88.5%) occurred in the Southern Plains region, where the rate was 4.23 per 100,000 persons. Children 1-4 years of age had the highest age-specific hospitalization rate of 2.50 per 100,000 persons. The overall annual RMSF hospitalization rate declined during the study period. Understanding the epidemiology of RMSF among AI/ANs and educating IHS/tribal physicians on the diagnosis of tick-borne diseases remain important for the prompt treatment of RMSF and the reduction of the disease occurrence among AI/ANs, particularly in high-risk areas.

  19. Regional-scale analysis of subtidal rocky shore community

    Science.gov (United States)

    Derrien-Courtel, Sandrine; Le Gal, Aodren; Grall, Jacques

    2013-12-01

    The French monitoring network, REseau BENThique (REBENT), was launched by the Ministry of the Environment in 2003 following the 1999 Erika oil spill. REBENT aimed to acquire baseline knowledge of coastal benthic habitat distributions with a special focus on biological diversity. This study analyzed data from 38 subtidal rocky reef sites collected by a single diving team of marine biologists along the coast of Brittany from 2004 to 2010. At each site, the depth limits of the algal belts were determined between 0 and -40 m Chart Datum (CD); the flora and fauna compositions and abundances were sampled at -3 and -8 m CD. A total of 364 taxa (156 flora and 208 fauna), belonging to 12 phyla, were identified. The results showed that the depth limit and density of kelp beds increased as water turbidity decreased; moreover, several changes in community structure could be related to water turbidity and temperature. Thus, northern and southern Brittany showed strong differences in diversity and structure of the dominant kelp species ( Laminaria hyperborea and Saccorhiza polyschides). The results from this kelp habitat composition survey (dominant kelp species and indicator species) provided important information for local pressure assessments, like increases in turbidity. The data also provided a reference that could be useful for detecting changes in coastal water temperatures due to global warming.

  20. Ancestral origins and invasion pathways in a globally invasive bird correlate with climate and influences from bird trade.

    Science.gov (United States)

    Jackson, Hazel; Strubbe, Diederik; Tollington, Simon; Prys-Jones, Robert; Matthysen, Erik; Groombridge, Jim J

    2015-08-01

    Invasive species present a major threat to global biodiversity. Understanding genetic patterns and evolutionary processes that reinforce successful establishment is paramount for elucidating mechanisms underlying biological invasions. Among birds, the ring-necked parakeet (Psittacula krameri) is one of the most successful invasive species, established in over 35 countries. However, little is known about the evolutionary genetic origins of this species and what population genetic signatures tell us about patterns of invasion. We reveal the ancestral origins of populations across the invasive range and explore the potential influence of climate and propagule pressure from the pet trade on observed genetic patterns. Ring-necked parakeet samples representing the ancestral native range (n = 96) were collected from museum specimens, and modern samples from the invasive range (n = 855) were gathered from across Europe, Mauritius and Seychelles, and sequenced for two mitochondrial DNA markers comprising 868 bp of cytochrome b and control region, and genotyped at 10 microsatellite loci. Invasive populations comprise birds that originate predominantly from Pakistan and northern areas of India. Haplotypes associated with more northerly distribution limits in the ancestral native range were more prevalent in invasive populations in Europe, and the predominance of Asian haplotypes in Europe is consistent with the higher number of Asian birds transported by the pet trade outside the native range. Successful establishment of invasive species is likely to be underpinned by a combination of environmental and anthropogenic influences. © 2015 John Wiley & Sons Ltd.

  1. The ancestral chromosomes of Dromiciops gliroides (Microbiotheridae), and its bearings on the karyotypic evolution of American marsupials.

    Science.gov (United States)

    Suárez-Villota, Elkin Y; Haro, Ronie E; Vargas, Rodrigo A; Gallardo, Milton H

    2016-01-01

    The low-numbered 14-chromosome karyotype of marsupials has falsified the fusion hypothesis claiming ancestrality from a 22-chromosome karyotype. Since the 14-chromosome condition of the relict Dromiciops gliroides is reminecent of ancestrality, its interstitial traces of past putative fusions and heterochromatin banding patterns were studied and added to available marsupials' cytogenetic data. Fluorescent in situ hybridization (FISH) and self-genomic in situ hybridization (self-GISH) were used to detect telomeric and repetitive sequences, respectively. These were complemented with C-, fluorescent banding, and centromere immunodetection over mitotic spreads. The presence of interstitial telomeric sequences (ITS) and diploid numbers were reconstructed and mapped onto the marsupial phylogenetic tree. No interstitial, fluorescent signals, but clearly stained telomeric regions were detected by FISH and self-GISH. Heterochromatin distribution was sparse in the telomeric/subtelomeric regions of large submetacentric chromosomes. Large AT-rich blocks were detected in the long arm of four submetacentrics and CG-rich block in the telomeric regions of all chromosomes. The ancestral reconstructions both ITS presence and diploid numbers suggested that ITS are unrelated to fusion events. Although the lack of interstitial signals in D. gliroides' karyotype does not prove absence of past fusions, our data suggests its non-rearranged plesiomorphic condition.

  2. Emergence, Retention and Selection: A Trilogy of Origination for Functional De Novo Proteins from Ancestral LncRNAs in Primates.

    Directory of Open Access Journals (Sweden)

    Jia-Yu Chen

    2015-07-01

    Full Text Available While some human-specific protein-coding genes have been proposed to originate from ancestral lncRNAs, the transition process remains poorly understood. Here we identified 64 hominoid-specific de novo genes and report a mechanism for the origination of functional de novo proteins from ancestral lncRNAs with precise splicing structures and specific tissue expression profiles. Whole-genome sequencing of dozens of rhesus macaque animals revealed that these lncRNAs are generally not more selectively constrained than other lncRNA loci. The existence of these newly-originated de novo proteins is also not beyond anticipation under neutral expectation, as they generally have longer theoretical lifespan than their current age, due to their GC-rich sequence property enabling stable ORFs with lower chance of non-sense mutations. Interestingly, although the emergence and retention of these de novo genes are likely driven by neutral forces, population genetics study in 67 human individuals and 82 macaque animals revealed signatures of purifying selection on these genes specifically in human population, indicating a proportion of these newly-originated proteins are already functional in human. We thus propose a mechanism for creation of functional de novo proteins from ancestral lncRNAs during the primate evolution, which may contribute to human-specific genetic novelties by taking advantage of existed genomic contexts.

  3. When ancestral heritage is a source of discomfort: culture, pre-object relatedness, and self-alienation.

    Science.gov (United States)

    Kradin, Richard L

    2012-04-01

    The ancestral claims on an individual can evoke mental conflict when they involve separating from an ethnic group whose beliefs and customs are devalued by the dominant culture. However, these claims are engraved on the psyche early in development by caretakers to the level of pre-object relatedness, where contents and affect tones are implicit and may be unavailable for later psychoanalytical interventions. In addition, as the anthropologist Clifford Geertz notes, one's culture of origin precedes the development of psyche and creates its own set of claims that must be renegotiated when one encounters a different domain of cultural symbols, a confrontation that can produce psychological dissonance and self-alienation. In this paper, three cases are examined in which mental conflicts were evoked by attempts at divesting ancestral claims in response to conscious efforts to assimilate into the dominant culture. These patients suffered from separation guilt and unstable self-esteem and reported dream imagery suggesting psychological imbalance. The requirement to carefully delineate the ancestral claims on psyche as well as those contents and affects that may not be accessible to therapeutic intervention is emphasized, and the importance of compromise and acceptance with respect to the psychological demands of the unconscious are considered. 2012, The Society of Analytical Psychology.

  4. Are Hox genes ancestrally involved in axial patterning? Evidence from the hydrozoan Clytia hemisphaerica (Cnidaria.

    Directory of Open Access Journals (Sweden)

    Roxane Chiori

    Full Text Available BACKGROUND: The early evolution and diversification of Hox-related genes in eumetazoans has been the subject of conflicting hypotheses concerning the evolutionary conservation of their role in axial patterning and the pre-bilaterian origin of the Hox and ParaHox clusters. The diversification of Hox/ParaHox genes clearly predates the origin of bilaterians. However, the existence of a "Hox code" predating the cnidarian-bilaterian ancestor and supporting the deep homology of axes is more controversial. This assumption was mainly based on the interpretation of Hox expression data from the sea anemone, but growing evidence from other cnidarian taxa puts into question this hypothesis. METHODOLOGY/PRINCIPAL FINDINGS: Hox, ParaHox and Hox-related genes have been investigated here by phylogenetic analysis and in situ hybridisation in Clytia hemisphaerica, an hydrozoan species with medusa and polyp stages alternating in the life cycle. Our phylogenetic analyses do not support an origin of ParaHox and Hox genes by duplication of an ancestral ProtoHox cluster, and reveal a diversification of the cnidarian HOX9-14 genes into three groups called A, B, C. Among the 7 examined genes, only those belonging to the HOX9-14 and the CDX groups exhibit a restricted expression along the oral-aboral axis during development and in the planula larva, while the others are expressed in very specialised areas at the medusa stage. CONCLUSIONS/SIGNIFICANCE: Cross species comparison reveals a strong variability of gene expression along the oral-aboral axis and during the life cycle among cnidarian lineages. The most parsimonious interpretation is that the Hox code, collinearity and conservative role along the antero-posterior axis are bilaterian innovations.

  5. Toxic and nontoxic components of botulinum neurotoxin complex are evolved from a common ancestral zinc protein

    International Nuclear Information System (INIS)

    Inui, Ken; Sagane, Yoshimasa; Miyata, Keita; Miyashita, Shin-Ichiro; Suzuki, Tomonori; Shikamori, Yasuyuki; Ohyama, Tohru; Niwa, Koichi; Watanabe, Toshihiro

    2012-01-01

    Highlights: ► BoNT and NTNHA proteins share a similar protein architecture. ► NTNHA and BoNT were both identified as zinc-binding proteins. ► NTNHA does not have a classical HEXXH zinc-coordinating motif similar to that found in all serotypes of BoNT. ► Homology modeling implied probable key residues involved in zinc coordination. -- Abstract: Zinc atoms play an essential role in a number of enzymes. Botulinum neurotoxin (BoNT), the most potent toxin known in nature, is a zinc-dependent endopeptidase. Here we identify the nontoxic nonhemagglutinin (NTNHA), one of the BoNT-complex constituents, as a zinc-binding protein, along with BoNT. A protein structure classification database search indicated that BoNT and NTNHA share a similar domain architecture, comprising a zinc-dependent metalloproteinase-like, BoNT coiled-coil motif and concanavalin A-like domains. Inductively coupled plasma-mass spectrometry analysis demonstrated that every single NTNHA molecule contains a single zinc atom. This is the first demonstration of a zinc atom in this protein, as far as we know. However, the NTNHA molecule does not possess any known zinc-coordinating motif, whereas all BoNT serotypes possess the classical HEXXH motif. Homology modeling of the NTNHA structure implied that a consensus K-C-L-I-K-X 35 -D sequence common among all NTNHA serotype molecules appears to coordinate a single zinc atom. These findings lead us to propose that NTNHA and BoNT may have evolved distinct functional specializations following their branching out from a common ancestral zinc protein.

  6. Allelic lineages of the ficolin genes (FCNs are passed from ancestral to descendant primates.

    Directory of Open Access Journals (Sweden)

    Tina Hummelshøj

    Full Text Available The ficolins recognize carbohydrates and acetylated compounds on microorganisms and dying host cells and are able to activate the lectin pathway of the complement system. In humans, three ficolin genes have been identified: FCN1, FCN2 and FCN3, which encode ficolin-1, ficolin-2 and ficolin-3, respectively. Rodents have only two ficolins designated ficolin-A and ficolin-B that are closely related to human ficolin-1, while the rodent FCN3 orthologue is a pseudogene. Ficolin-2 and ficolin-3 have so far only been observed in humans. Thus, we performed a systematic investigation of the FCN genes in non-human primates. The exons and intron-exon boundaries of the FCN1-3 genes were sequenced in the following primate species: chimpanzee, gorilla, orangutan, rhesus macaque, cynomolgus macaque, baboon and common marmoset. We found that the exon organisation of the FCN genes was very similar between all the non-human primates and the human FCN genes. Several variations in the FCN genes were found in more than one primate specie suggesting that they were carried from one species to another including humans. The amino acid diversity of the ficolins among human and non-human primate species was estimated by calculating the Shannon entropy revealing that all three proteins are generally highly conserved. Ficolin-1 and ficolin-2 showed the highest diversity, whereas ficolin-3 was more conserved. Ficolin-2 and ficolin-3 were present in non-human primate sera with the same characteristic oligomeric structures as seen in human serum. Taken together all the FCN genes show the same characteristics in lower and higher primates. The existence of trans-species polymorphisms suggests that different FCN allelic lineages may be passed from ancestral to descendant species.

  7. COMPONENTES NUTRICIONALES Y ANTIOXIDANTES DE DOS ESPECIES DE GUAJE (Leucaena spp.: UN RECURSO ANCESTRAL SUBUTILIZADO

    Directory of Open Access Journals (Sweden)

    Nallely Román-Cortés

    2014-01-01

    Full Text Available El guaje ( Leucaena spp. es una planta de vaina y semillas comestibles, un recurso ancestral subutilizado por los pueblos mesoamericanos. El valor nutricional y nutracéutico del guaje se desconoce pese a su consumo vigente en las poblaciones rurales. El objetivo de este trabajo fue evaluar el contenido de minerales, compo - nentes nutricionales y antioxidantes para contribuir a la revalorización alimentaria del guaje rojo ( L. esculenta Benth. y verde ( L. leucocephala Lam.. Los contenidos de antocianinas, flavonoides, fenoles totales, taninos y actividad antioxidante se cuantificaron, así como la composición proximal y mineral. Las semillas de guaje rojo superaron a las de guaje verde en los contenidos de N, Mg, Mn, P y Zn; en contraste, las semillas de guaje verde presentaron niveles mayores de Na y de Fe. El contenido de fibra cruda fue 10.55 y 10.07 % en guaje rojo y verde, respectivamente, mientras que el de proteína fue 33.12 % en guaje rojo y 31.7 % en el verde. El alto contenido de compuestos fenólicos fue mayor en las semillas frescas de guaje rojo (1,088.70 mg equivalentes de ácido gálico [EAG]·100 g -1 p. f. que en las verdes (969.09 mg EAG·100 g -1 p. f., pero las últimas presen - taron mayor cantidad de taninos. La elevada actividad secuestradora de radicales libres (97.22 a 98.11 % obtenida por el método ABTS ( á cido 2,2’-azino-bis(3-etilben-zotiazolin-6-sulfónico, puede estar asociada al contenido de compuestos fenólicos. En conclusión, las semillas de guaje podrían considerarse un alimento funcional, principalmente las de guaje rojo debido a su calidad nutricional y mayor actividad antioxidante.

  8. Evolutionary history of Lissotriton helveticus: multilocus assessment of ancestral vs. recent colonization of the Iberian Peninsula.

    Science.gov (United States)

    Recuero, Ernesto; García-París, Mario

    2011-07-01

    The Pleistocene was characterized by climatic changes that greatly altered the distribution of organisms. Population extinctions, bottlenecks, isolation, range expansions and contractions were often associated with glaciations, leaving signatures in the spatial patterns of genetic diversity across species. Lissotriton helveticus belongs to a Pan-European lineage of newts that were strongly affected by glaciations and represent an excellent model to analyse the effect of generalized climatic changes in phylogeographic patterns. We studied the genetic diversity of the species using data from two mitochondrial and three nuclear genes analyzed in a Bayesian phylogenetic framework to investigate the historical processes shaping spatial patterns of genetic diversity. Mitochondrial haplotypes cluster in four different groups present in the Iberian Peninsula and of Pleistocene origin, probably by allopatric fragmentation. Nuclear genes present no obvious geographic structure patterns, suggesting gene flow and generalized incomplete lineage sorting. Populations north of the Pyrenees are closely related to those from northeastern Iberia, suggesting recent range expansion from this region. Historical demographic analyses indicate a demographic expansion starting about 100,000years ago and more recent population declines. Compared to other Lissotriton species, L. helveticus includes only relatively young genetic lineages, suggesting a Central European pre-Pleistocene distribution followed by complete extirpation of the species during glaciations in that area. Historical demographic trends in the Iberian Peninsula are reversed with respect to the more Mediterranean species Lissotriton boscai, indicating different responses of both species to climate changes. Diversity patterns among Lissotriton species seem to be defined by four main factors: ancestral distributions, colonization capabilities, interactions with other species and effective population sizes. Differences in these

  9. Evolution of neural crest and placodes: amphioxus as a model for the ancestral vertebrate?

    Science.gov (United States)

    Holland, L. Z.; Holland, N. D.

    2001-01-01

    Recent studies of protochordates (ascidian tunicates and amphioxus) have given insights into possible ancestors of 2 of the characteristic features of the vertebrate head: neural crest and placodes. The neural crest probably evolved from cells on either side of the neural plate-epidermis boundary in a protochordate ancestral to the vertebrates. In amphioxus, homologues of several vertebrate neural crest marker genes (BMP2/4, Pax3/7, Msx, Dll and Snail) are expressed at the edges of the neural plate and/or adjacent nonneural ectoderm. Some of these markers are also similarly expressed in tunicates. In protochordates, however, these cells, unlike vertebrate neural crest, neither migrate as individuals through embryonic tissues nor differentiate into a wide spectrum of cell types. Therefore, while the protochordate ancestor of the vertebrates probably had the beginnings of a genetic programme for neural crest formation, this programme was augmented in the earliest vertebrates to attain definitive neural crest. Clear homologues of vertebrate placodes are lacking in protochordates. However, both amphioxus and tunicates have ectodermal sensory cells. In tunicates these are all primary neurons, sending axons to the central nervous system, while in amphioxus, the ectodermal sensory cells include both primary neurons and secondary neurons lacking axons. Comparisons of developmental gene expression suggest that the anterior ectoderm in amphioxus may be homologous to the vertebrate olfactory placode, the only vertebrate placode with primary, not secondary, neurons. Similarly, biochemical, morphological and gene expression data suggest that amphioxus and tunicates also have homologues of the adenohypophysis, one of the few vertebrate structures derived from nonneurogenic placodes. In contrast, the origin of the other vertebrate placodes is very uncertain.

  10. Functions of two distinct prolactin-releasing peptides evolved from a common ancestral gene

    Directory of Open Access Journals (Sweden)

    Tetsuya eTachibana

    2014-11-01

    Full Text Available Prolactin-releasing peptide (PrRP is one of the RF-amide peptides and was originally identified in the bovine hypothalamus as a stimulator of prolactin (PRL release. Independently, another RF-amide peptide was found in Japanese crucian carp and named Carassius RFa (C-RFa, which shows high homology to PrRP and stimulates PRL secretion in teleost fish. Therefore, C-RFa has been recognized as fish PrRP. However, recent work has revealed that PrRP and C-RFa in non-mammalian vertebrates are encoded by separate genes originated through duplication of an ancestral gene. Indeed, both PrRP and C-RFa are suggested to exist in teleost, amphibian, reptile, and avian species. Therefore, we propose that non-mammalian PrRP (C-RFa be renamed PrRP2. Despite a common evolutionary origin, PrRP2 appears to be a physiological regulator of PRL, whereas this is not a consistent role for PrRP itself. Further work revealed that the biological functions of PrRP and PrRP2 are not limited solely to PRL release, because they are also neuromodulators of several hypothalamus-pituitary axes and are involved in some brain circuits related to the regulation of food intake, stress, and cardiovascular functions. However, these actions appear to be different among vertebrates. For example, central injection of PrRP inhibits feeding behavior in rodents and teleosts while it stimulates it in chicks. Therefore, both PrRP and PrRP2 have acquired diverse actions through evolution. In this review, we integrate the burgeoning information of structures, expression profiles, and multiple biological actions of PrRP in higher vertebrates, as well as those of PrRP2 in non-mammals.

  11. CHAAJ (JUEGO DE PELOTA MESOAMERICANO: UN jUEGO ANCESTRAL ENTRE EMERGENCIAS CULTURALES

    Directory of Open Access Journals (Sweden)

    Jairzinho Francisco Panqueba Cifuentes

    2012-06-01

    Full Text Available Los juegos de pelota mesoamericanos son manifestaciones corporales que han sido exploradasprincipalmente desde perspectivas arqueológicas e históricas, pero también han sido retomadosdesde distintas iniciativas para ponerlos en práctica. Desde la frontera entre Estados Unidos conMéxico, pasando por distintos Estados del país “azteca”, son practicadas diferentes modalidades deeste juego. Sin embargo, decir que el chaaj en Mesoamérica es hoy en día una alternativa recreativay deportiva, es quedarse corto respecto a su ya demostrado potencial. La sacralidad manifestada através de los movimientos corporales está ofreciendo opciones de innovación en varios espacios de lassociedades actuales. En su dimensión ceremonial, revela una comunicación ancestral muy actual. Allíse ponen en juego los códices, las interpretaciones arqueológicas y los conocimientos territoriales depersonas sabedoras de las comunidades. En su dimensión lúdica, el juego reúne elementos culturales,deportivos y pedagógicos. Ha sido una práctica corporal, técnica y motora ejecutada constantementeen algunas regiones mexicanas y guatemaltecas. No obstante su antigüedad, en los últimos años seviene registrando una promoción inusitada, en medio de los actuales tiempos de cambio que fueronanunciados desde tiempos inmemoriales por los sabedores y las sabedoras mayas.

  12. Toxic and nontoxic components of botulinum neurotoxin complex are evolved from a common ancestral zinc protein

    Energy Technology Data Exchange (ETDEWEB)

    Inui, Ken [Department of Food and Cosmetic Science, Faculty of Bioindustry, Tokyo University of Agriculture, 196 Yasaka, Abashiri 099-2493 (Japan); Japan Society for the Promotion of Science, 1-8 Chiyoda-ku, Tokyo 102-8472 (Japan); Sagane, Yoshimasa [Department of Food and Cosmetic Science, Faculty of Bioindustry, Tokyo University of Agriculture, 196 Yasaka, Abashiri 099-2493 (Japan); Miyata, Keita [Department of Food and Cosmetic Science, Faculty of Bioindustry, Tokyo University of Agriculture, 196 Yasaka, Abashiri 099-2493 (Japan); Japan Society for the Promotion of Science, 1-8 Chiyoda-ku, Tokyo 102-8472 (Japan); Miyashita, Shin-Ichiro [Department of Food and Cosmetic Science, Faculty of Bioindustry, Tokyo University of Agriculture, 196 Yasaka, Abashiri 099-2493 (Japan); Suzuki, Tomonori [Department of Bacteriology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558 (Japan); Shikamori, Yasuyuki [Agilent Technologies International Japan, Ltd. Takaura-cho 9-1, Hachioji-shi, Tokyo 192-0033 (Japan); Ohyama, Tohru; Niwa, Koichi [Department of Food and Cosmetic Science, Faculty of Bioindustry, Tokyo University of Agriculture, 196 Yasaka, Abashiri 099-2493 (Japan); Watanabe, Toshihiro, E-mail: t-watana@bioindustry.nodai.ac.jp [Department of Food and Cosmetic Science, Faculty of Bioindustry, Tokyo University of Agriculture, 196 Yasaka, Abashiri 099-2493 (Japan)

    2012-03-16

    Highlights: Black-Right-Pointing-Pointer BoNT and NTNHA proteins share a similar protein architecture. Black-Right-Pointing-Pointer NTNHA and BoNT were both identified as zinc-binding proteins. Black-Right-Pointing-Pointer NTNHA does not have a classical HEXXH zinc-coordinating motif similar to that found in all serotypes of BoNT. Black-Right-Pointing-Pointer Homology modeling implied probable key residues involved in zinc coordination. -- Abstract: Zinc atoms play an essential role in a number of enzymes. Botulinum neurotoxin (BoNT), the most potent toxin known in nature, is a zinc-dependent endopeptidase. Here we identify the nontoxic nonhemagglutinin (NTNHA), one of the BoNT-complex constituents, as a zinc-binding protein, along with BoNT. A protein structure classification database search indicated that BoNT and NTNHA share a similar domain architecture, comprising a zinc-dependent metalloproteinase-like, BoNT coiled-coil motif and concanavalin A-like domains. Inductively coupled plasma-mass spectrometry analysis demonstrated that every single NTNHA molecule contains a single zinc atom. This is the first demonstration of a zinc atom in this protein, as far as we know. However, the NTNHA molecule does not possess any known zinc-coordinating motif, whereas all BoNT serotypes possess the classical HEXXH motif. Homology modeling of the NTNHA structure implied that a consensus K-C-L-I-K-X{sub 35}-D sequence common among all NTNHA serotype molecules appears to coordinate a single zinc atom. These findings lead us to propose that NTNHA and BoNT may have evolved distinct functional specializations following their branching out from a common ancestral zinc protein.

  13. The vomeronasal complex of nocturnal strepsirhines and implications for the ancestral condition in primates.

    Science.gov (United States)

    Garrett, Eva C; Dennis, John C; Bhatnagar, Kunwar P; Durham, Emily L; Burrows, Anne M; Bonar, Christopher J; Steckler, Natalie K; Morrison, Edward E; Smith, Timothy D

    2013-12-01

    This study investigates the vomeronasal organ in extant nocturnal strepsirhines as a model for ancestral primates. Cadaveric samples from 10 strepsirhine species, ranging from fetal to adult ages, were studied histologically. Dimensions of structures in the vomeronasal complex, such as the vomeronasal neuroepithelium (VNNE) and vomeronasal cartilage (VNC) were measured in serial sections and selected specimens were studied immunohistochemically to determine physiological aspects of the vomeronasal sensory neurons (VSNs). Osteological features corresponding to vomeronasal structures were studied histologically and related to 3-D CT reconstructions. The VNC consistently rests in a depression on the palatal portion of the maxilla, which we refer to as the vomeronasal groove (VNG). Most age comparisons indicate that in adults VNNE is about twice the length compared with perinatal animals. In VNNE volume, adults are 2- to 3-fold larger compared with perinatal specimens. Across ages, a strong linear relationship exists between VNNE dimensions and body length, mass, and midfacial length. Results indicate that the VNNE of nocturnal strepsirhines is neurogenic postnatally based on GAP43 expression. In addition, based on Olfactory Marker Protein expression, terminally differentiated VSNs are present in the VNNE. Therefore, nocturnal strepsirhines have basic similarities to rodents in growth and maturational characteristics of VSNs. These results indicate that a functional vomeronasal system is likely present in all nocturnal strepsirhines. Finally, given that osteological features such as the VNG are visible on midfacial bones, primate fossils can be assessed to determine whether primate ancestors possessed a vomeronasal complex morphologically similar to that of modern nocturnal strepsirhines. Copyright © 2013 Wiley Periodicals, Inc.

  14. Middle Rockies Ecoregion: Chapter 5 in Status and trends of land change in the Western United States--1973 to 2000

    Science.gov (United States)

    Taylor, Janis L.

    2012-01-01

    The Middle Rockies Ecoregion—characterized by steep, high-elevation mountain ranges and intermountain valleys—is a disjunct ecoregion composed of three distinct geographic areas: the Greater Yellowstone area in northwest Wyoming, southwest Montana, and eastern Idaho; the Bighorn Mountains in north-central Wyoming and south-central Montana; and the Black Hills in western South Dakota and eastern Wyoming (Omernik, 1987; U.S. Environmental Protection Agency, 1997). The ecoregion covers approximately 90,160 km2 (34,881 mi2), and its three distinct geographic sections are bordered by several other ecoregions (fig. 1). The Yellowstone section abuts the Montana Valley and Foothill Prairies and the Northern Rockies Ecoregions to the north, the Snake River Basin and the Central Basin and Range Ecoregions to the west, and the Wyoming Basin Ecoregion to the south and east. The Bighorn Mountains section lies between the Wyoming Basin Ecoregion to the west and the Northwestern Great Plains Ecoregion to the east, and it abuts the Montana Valleys and Foothill Prairies Ecoregion to the north. The Black Hills section is entirely surrounded by the Northwestern Great Plains Ecoregion. The Continental Divide crosses the ecoregion from the southeast along the Wind River Range, through Yellowstone National Park, and west along the Montana-Idaho border. On both sides of the divide, topographic relief causes local climate variability, particularly the effects of aspect, exposure to prevailing wind, thermal inversions, and rain-shadow effects, that are reflected in the wide variety of flora and fauna within the ecoregion (Ricketts and others, 1999).

  15. Decapod crustaceans from rocky shore at Farol Island, Matinhos, Paraná, Brazil. I: temporal distribution of population densities

    OpenAIRE

    Masunari, Setuko; Oliveira, Edinalva; Kowalczuk, Vânia Graciele Lezan

    1998-01-01

    A study of the temporal distribution of the decapod populations from a rocky shore at Farol Isle, Matinhos, State of Paraná, Brazil (25o51'S e48o32'W) was carried out. The rocky shore is 13m wide when the tidal level is zero meter and about 8o inclination. In the supralittoral, the rocky basins is mostly covered by a layer of litter coming from the terrestrial environment. In the midlittoral and upper infralittoral, the rocky slope is overlayed by boulders and pebbles and they constitute a hi...

  16. Rocky Mountain spotted fever from an unexpected tick vector in Arizona.

    Science.gov (United States)

    Demma, Linda J; Traeger, Marc S; Nicholson, William L; Paddock, Christopher D; Blau, Dianna M; Eremeeva, Marina E; Dasch, Gregory A; Levin, Michael L; Singleton, Joseph; Zaki, Sherif R; Cheek, James E; Swerdlow, David L; McQuiston, Jennifer H

    2005-08-11

    Rocky Mountain spotted fever is a life-threatening, tick-borne disease caused by Rickettsia rickettsii. This disease is rarely reported in Arizona, and the principal vectors, Dermacentor species ticks, are uncommon in the state. From 2002 through 2004, a focus of Rocky Mountain spotted fever was investigated in rural eastern Arizona. We obtained blood and tissue specimens from patients with suspected Rocky Mountain spotted fever and ticks from patients' homesites. Serologic, molecular, immunohistochemical, and culture assays were performed to identify the causative agent. On the basis of specific laboratory criteria, patients were classified as having confirmed or probable Rocky Mountain spotted fever infection. A total of 16 patients with Rocky Mountain spotted fever infection (11 with confirmed and 5 with probable infection) were identified. Of these patients, 13 (81 percent) were children 12 years of age or younger, 15 (94 percent) were hospitalized, and 2 (12 percent) died. Dense populations of Rhipicephalus sanguineus ticks were found on dogs and in the yards of patients' homesites. All patients with confirmed Rocky Mountain spotted fever had contact with tick-infested dogs, and four had a reported history of tick bite preceding the illness. R. rickettsii DNA was detected in nonengorged R. sanguineus ticks collected at one home, and R. rickettsii isolates were cultured from these ticks. This investigation documents the presence of Rocky Mountain spotted fever in eastern Arizona, with common brown dog ticks (R. sanguineus) implicated as a vector of R. rickettsii. The broad distribution of this common tick raises concern about its potential to transmit R. rickettsii in other settings. Copyright 2005 Massachusetts Medical Society.

  17. Simultaneous bilateral isolated greater trochanter fracture

    Directory of Open Access Journals (Sweden)

    Maruti Kambali

    2013-01-01

    Full Text Available A 48-year-old woman sustained simultaneous isolated bilateral greater trochanteric fracture, following a road traffic accident. The patient presented to us 1 month after the injury. She presented with complaints of pain in the left hip and inability to walk. Roentgenograms revealed displaced comminuted bilateral greater trochanter fractures. The fracture of the left greater trochanter was reduced and fixed internally using the tension band wiring technique. The greater trochanter fracture on the right side was asymptomatic and was managed conservatively. The patient regained full range of motion and use of her hips after a postoperative follow-up of 6 months. Isolated fractures of the greater trochanter are unusual injuries. Because of their relative rarity and the unsettled controversy regarding their etiology and pathogenesis, several methods of treatment have been advocated. Furthermore, the reports of this particular type of injury are not plentiful and the average textbook coverage afforded to this entity is limited. In our study we discuss the mechanism of injury and the various treatment options available.

  18. Excess unsupported sup(210)Pb in lake sediment from Rocky Mountain lakes

    International Nuclear Information System (INIS)

    Norton, S.A.; Hess, C.T.; Blake, G.M.; Morrison, M.L.; Baron, J.

    1985-01-01

    Sediment cores from four high-altitude (approximately 3200 m) lakes in Rocky Mountain National Park, Colorado, were dated by sup(210)Pb chronology. Background (supported) sup(210)Pb activities for the four cores range from 0.26 to 0.93 Beq/g dry weight, high for typical oligotrophic lakes. Integrated unsupported sup(210)Pb ranges from 0.81 (a typical value for most lakes) to 11.0 Beq/cmsup(2). The sup(210)Pb activity in the surface sediments ranges from 1.48 to 22.2 Beq/g dry weight. Sedimentation from Lake Louise, the most unusual of the four, has 22.2 Beq/g dry weight at the sediment surface, an integrated unsupported sup(210)Pb=11.0 Beq/cmsup(2), and supported sup(210)Pb=0.74 Beq/g dry weight. sup(226)Ra content of the sediment is insufficient to explain either the high unsupported sup(210)Pb or the sup(222)Rn content of the water column of Lake Louise, which averaged 96.2 Beq/L. We concluded that sup(222)Rn-rich groundwater entering the lake is the source of the high sup(222)Rn in the water column. This, in turn, is capable of supporting the unusually high sup(210)Pb flux to the sediment surface. Groundwater with high sup(222)Rn may control the sup(210)Pb budget of lakes where sediment cores have integrated unsupported sup(210)Pb greater than 2 Beq/cmsup(2)

  19. Complete tribal sampling reveals basal split in Muscidae (Diptera), confirms saprophagy as ancestral feeding mode, and reveals an evolutionary correlation between instar numbers and carnivory

    DEFF Research Database (Denmark)

    Kutty, Sujatha Narayanan; Pont, Adrian C.; Meier, Rudolf

    2014-01-01

    split within this family. The ancestral larval feeding habit is reconstructed to be saprophagy with more specialised coprophagous saprophagy, phytophagy, and carnivory evolving multiple times from saprophagous ancestors. The origins of carnivory in larvae are significantly correlated with a reduction...

  20. Patterns of LGM precipitation in the U.S. Rocky Mountains: results from regional application of a glacier mass/energy balance and flow model

    Science.gov (United States)

    Leonard, E. M.; Laabs, B. J.; Refsnider, K. A.; Plummer, M. A.; Jacobsen, R. E.; Wollenberg, J. A.

    2010-12-01

    Global climate model (GCM) simulations of the last glacial maximum (LGM) in the western United States predict changes in atmospheric circulation and storm tracks that would have resulted in significantly less-than-modern precipitation in the Northwest and northern Rockies, and significantly more-than-modern precipitation in the Southwest and southern Rockies. Model simulations also suggest that late Pleistocene pluvial lakes in the intermontane West may have modified local moisture regimes in areas immediately downwind. In this study, we present results of the application of a coupled energy/mass balance and glacier-flow model (Plummer and Phillips, 2003) to reconstructed paleoglaciers in Rocky Mountains of Utah, New Mexico, Colorado, and Wyoming to assess the changes from modern climate that would have been necessary to sustain each glacier in mass-balance equilibrium at its LGM extent. Results demonstrate that strong west-to-east and north-to-south gradients in LGM precipitation, relative to present, would be required if a uniform LGM temperature depression with respect to modern is assumed across the region. At an assumed 7oC temperature depression, approximately modern precipitation would have been necessary to support LGM glaciation in the Colorado Front Range, significantly less than modern precipitation to support glaciation in the Teton Range, and almost twice modern precipitation to sustain glaciers in the Wasatch and Uinta ranges of Utah and the New Mexico Sangre de Cristo Range. The observed west-to-east (Utah-to-Colorado) LGM moisture gradient is consistent with precipitation enhancement from pluvial Lake Bonneville, decreasing with distance downwind from the lake. The north-to-south (Wyoming-to-New Mexico) LGM moisture gradient is consistent with a southward LGM displacement of the mean winter storm track associated with the winter position of the Pacific Jet Stream across the western U.S. Our analysis of paleoglacier extents in the Rocky Mountain

  1. A Detailed Study of Rocky Planetary Material in the Hyades

    Science.gov (United States)

    Farihi, Jay

    2017-08-01

    The Hyades is the nearest open cluster, relatively young, and containing numerous A-type stars. Its youth, distance, and metallicity make it an ideal site to study planet formation around 2-3 Msun stars, and in a dynamically challenging environment.During our HST COS Snapshot, we discovered the ongoing accretion of Si-rich and C-deficient material in two white dwarf Hyads. The lower limit Si/C ratios determined from these 400s exposures indicate the material is more C-depleted than in chondritic meteorites, the most primitive rocks in the Solar System. Our 2013 Keck discovery of metal pollution in a third Hyades white dwarf indicates that planet formation is common in the cluster. Together, these three stars indicate that substantial minor bodies persist at several AU or more, and provide an unprecedented opportunity for a detailed study of rocky exoplanet precursors in a cluster environment.We propose to obtain detailed abundances of the planetary debris at these three polluted Hyads, which requires a modest investment of observatory time. The mass ratios between C, O, Mg, and Si are accurate indicators of the temperature and orbital regions where the parent bodies formed, their water and volatile contents. We will also detect Al and Fe, which are key indicators of differentiation and giant impacts among planetary embryos.Our proposed observations will provide legacy value for planet formation models, and especially those in cluster enviroments. These observations cannot be done from the ground or at optical or longer wavelengths, and must be carried out by HST in the ultraviolet.

  2. Technical safety appraisal: Buildings 776/777 Rocky Flats Plant

    Energy Technology Data Exchange (ETDEWEB)

    Field, H C

    1988-03-01

    Buildings 776/777 at the Rocky Flats Plant are major components of the production complex at the plant site. They have been in operation since 1957. The operations taking place in the buildings are nuclear weapons production support, processing of weapons assemblies returned from Pantex, waste processing, research and development in support of production, special projects, and those generated by support groups, such as maintenance. The appraisal team identified nine deficiencies that it believed required prompt attention. DOE management for EH, the program office (Defense Programs), and the field office analyzed the information provided by the appraisal team and instituted compensatory measures for closer monitoring of contractor activities by knowledgeable DOE staff and staff from other sites. Concurrently, the contractor was requested to address both short-term and long-term remedial measures to correct the identified issues as well as the underlying problems. The contractor has provided his action plan, which is included. This plan was under evaluation by EH and the DOE program office at the time this report was prepared. In addressing the major areas of concern identified above, a well as the specific deficiencies identified by the appraisal team, the contractor and the field office are cautioned to search for the root causes for the problems and to direct corrective actions to those root causes rather than solely to the symptoms to assure the sustainability of the improvements being made. The results of prior TSAs led DOE to conclude that previous corrective actions were not sufficient in that a large number of the individual findings are recurrent. Pending completion of remedial actions over the next few months, enhanced DOE oversight of the contractor is warranted.

  3. Distal Ejecta from Lunar Impacts: Extensive Regions of Rocky Deposits

    Science.gov (United States)

    Bandfield, Joshua L.; Cahill, Joshua T. S.; Carter, Lynn M.; Neish, Catherine D.; Patterson, G. Wesley; Williams, Jean-Pierre; Paige, David A.

    2016-01-01

    Lunar Reconnaissance Orbiter (LRO) Diviner Radiometer, Mini-RF, and LRO Camera data were used to identify and characterize rocky lunar deposits that appear well separated from any potential source crater. Two regions are described: 1) A approximate 18,000 sq km area with elevated rock abundance and extensive melt ponds and veneers near the antipode of Tycho crater (167.5 deg E, 42.5 deg N). This region has been identified previously, using radar and aging data. 2) A much larger and more diffuse region, covering approximately 730,000 sq km, centered near 310 deg E, 35 deg S, containing elevated rock abundance and numerous granular flow deposits on crater walls. The rock distributions in both regions favor certain slope azimuths over others, indicating a directional component to the formation of these deposits. The spatial distribution of rocks is consistent with the arrival of ejecta from the west and northwest at low angles (approximately 10-30 deg) above the horizon in both regions. The derived age and slope orientations of the deposits indicate that the deposits likely originated as ejecta from the Tycho impact event. Despite their similar origin, the deposits in the two regions show significant differences in the datasets. The Tycho crater antipode deposit covers a smaller area, but the deposits are pervasive and appear to be dominated by impact melts. By contrast, the nearside deposits cover a much larger area and numerous granular flows were triggered. However, the features in this region are less prominent with no evidence for the presence of impact melts. The two regions appear to be surface expressions of a distant impact event that can modify surfaces across wide regions, resulting in a variety of surface morphologies. The Tycho impact event may only be the most recent manifestation of these processes, which likely have played a role in the development of the regolith throughout lunar history

  4. Transportation of pyrochemical salts from Rocky Flats to Los Alamos

    International Nuclear Information System (INIS)

    Schreiber, S.B.

    1997-01-01

    Radioactive legacy wastes or residues are currently being stored on numerous Sites around the former Department of Energy's (DOE) Nuclear Weapons Complex. Since most of the operating facilities were shut down and have not operated since before the declared end to the Cold War in 1993, the historical method for treating these residues no longer exists. The risk associated with continued storage of these residues will dramatically increase with time. Thus, the DOE was directed by the Defense Nuclear Facility Safety Board in its Recommendation 94-1 to address and stabilize these residues and established an eight year time frame for doing so. There are only two options available to respond to this requirement: (1) restart existing facilities to treat and package the residues for disposal or (2) transport the residues to another operating facility within the Complex where they can be treated and packaged for disposal. This paper focuses on one such residue type, pyrochemical salts, produced at one Complex site, the Rocky Flats Plant located northwest of Denver, Colorado. One option for treating the salts is their shipment to Los Alamos, New Mexico, for handling at the Plutonium Facility. The safe transportation of these salts can be accomplished at present with several shipping containers including a DOT 6M, a DOE 9968, Type A or Type B quantity 55-gallon drum overpacks, or even the TRUPACT II. The tradeoffs between each container is examined with the conclusion that none of the available shipping containers is fully satisfactory. Thus, the advantageous aspects of each container must be utilized in an integrated and efficient way to effectively manage the risk involved. 1 fig

  5. Plutonium in the aquatic environment around the Rocky Flats facility

    International Nuclear Information System (INIS)

    Thompson, M.A.

    1975-01-01

    The Rocky Flats Plant of the United States Energy Research and Development Administration has been fabricating and chemically recovering plutonium for over 20 years. During that time, small amounts of plutonium have been released with liquid process and sanitary waste discharges. The liquid waste flows through a series of holding ponds from which it is discharged into a creek that is part of a municipal drinking water supply. The water flows for about 1.5 km between the last holding pond and the municipal drinking water reservoir. In addition, liquid wastes containing high levels of chemical contaminants and plutonium concentrations less than allowable drinking water standards have been discharged to large evaporation ponds. The fate of the plutonium in both the surface and subsurface aquatic environment has been extensively monitored and studied. It has been found that plutonium does not move very far or very rapidly through subsurface water. The majority of the plutonium released through surface water has been contained in the sediments of the plant holding ponds. Small amounts of plutonium have also been found in the sediments of the draining creek and in the sediments of the receiving reservoir. Higher than normal amounts of plutonium were released from the waste treatment plants during times when suspended solids were high. Various biological species have been examined and plutonium concentration factors determined. Considerably less than 1% of the 210 mCi of plutonium released has been detected in biological systems including man. After more than 20 years of large scale operations, no health or environmental hazard has been identified due to the release of small amounts of plutonium. (author)

  6. Isotopes in North American Rocky Mountain snowpack 1993–2014

    Science.gov (United States)

    Anderson, Lesleigh; Max Berkelhammer,; Mast, M. Alisa

    2015-01-01

    We present ∼1300 new isotopic measurements (δ18O and δ2H) from a network of snowpack sites in the Rocky Mountains that have been sampled since 1993. The network includes 177 locations where depth-integrated snow samples are collected each spring near peak accumulation. At 57 of these locations snowpack samples were obtained for 10–21 years and their isotopic measurements provide unprecedented spatial and temporal documentation of snowpack isotope values at mid-latitudes. For environments where snowfall accounts for the majority of annual precipitation, snowmelt is likely to have the strongest influence on isotope values retained in proxy archives. In this first presentation of the dataset we (1) describe the basic features of the isotope values in relation to the Global Meteoric Water Line (GMWL), (2) evaluate space for time substitutions traditionally used to establish δ18O-temperature relations, (3) evaluate site-to-site similarities across the network and identify those that are the most regionally representative, (4) examine atmospheric circulation patterns for several years with spatially coherent isotope patterns, and (5) provide examples of the implications this new dataset has for interpreting paleoclimate records (Bison Lake, Colorado and Minnetonka Cave, Idaho). Results indicate that snowpack δ18O is rarely a simple proxy of temperature. Instead, it exhibits a high degree of spatial heterogeneity and temporal variance that reflect additional processes such as vapor transport and post-depositional modification. Despite these complexities we identify consistent climate-isotope patterns and regionally representative locations that serve to better define Holocene hydroclimate estimates and their uncertainty. Climate change has and will affect western U.S. snowpack and we suggest these changes can be better understood and anticipated by oxygen and hydrogen isotope-based reconstructions of Holocene hydroclimate using a process-based understanding of the

  7. Technical safety appraisal: Buildings 776/777 Rocky Flats Plant

    International Nuclear Information System (INIS)

    Field, H.C.

    1988-03-01

    Buildings 776/777 at the Rocky Flats Plant are major components of the production complex at the plant site. They have been in operation since 1957. The operations taking place in the buildings are nuclear weapons production support, processing of weapons assemblies returned from Pantex, waste processing, research and development in support of production, special projects, and those generated by support groups, such as maintenance. The appraisal team identified nine deficiencies that it believed required prompt attention. DOE management for EH, the program office (Defense Programs), and the field office analyzed the information provided by the appraisal team and instituted compensatory measures for closer monitoring of contractor activities by knowledgeable DOE staff and staff from other sites. Concurrently, the contractor was requested to address both short-term and long-term remedial measures to correct the identified issues as well as the underlying problems. The contractor has provided his action plan, which is included. This plan was under evaluation by EH and the DOE program office at the time this report was prepared. In addressing the major areas of concern identified above, a well as the specific deficiencies identified by the appraisal team, the contractor and the field office are cautioned to search for the root causes for the problems and to direct corrective actions to those root causes rather than solely to the symptoms to assure the sustainability of the improvements being made. The results of prior TSAs led DOE to conclude that previous corrective actions were not sufficient in that a large number of the individual findings are recurrent. Pending completion of remedial actions over the next few months, enhanced DOE oversight of the contractor is warranted

  8. The Rocky Flats Decontamination and Decommissioning (D and D) Challenge

    International Nuclear Information System (INIS)

    Parker, A.M.; Mathis, B.W.; Stevens, J.L.

    1999-01-01

    At the Rocky Flats Environmental Technology Site (RFETS), the D and D task is enormous. Tons of plutonium has been processed over the years in approximately 1,000 gloveboxes, This represents nearly half of the gloveboxes in the DOE complex. In addition, more than a thousand tanks of various designs, with miles of associated piping, supported the processes. A wide variety of operations were performed at RFETS, including aqueous processing, pyrophoric processing, hydriding and dehydriding, metal casting, and machining of plutonium. Various materials have been handled at the facility, including plutonium, uranium, americium, tantalum, beryllium, chloride salts, and various acids and solvents. Significant amounts of plutonium residues remain in inaccessible equipment in the facilities, which create criticality safety issues. Some of the plutonium has been at RFETS for many years, and there is significant in-growth of americium, a decay product that emits gamma radiation, which potentially increases exposure to the workers. The size reduction portion of the D and D will be difficult and costly. The gloveboxes and tanks are constructed of stainless steel, frequently with lead shielding or double walls that hold water for neutron shielding. Window mountings, glove port rings, site gages, bolted flanges, and various penetrations reinforce the walls. Tanks may be filled with berated glass rings for criticality control, or double walled to hold the process fluid in the space between walls. The gloveboxes and tanks are generally tall enough to require workers to stand on scaffolding or platforms to perform D and D. Gloveboxes and tanks were individually constructed over a span of many years with evolving design specifications; therefore, most gloveboxes are unique and few tank designs are duplicated in more than pairs. This paper describes the cultural transition and technical approaches taken for D and D at RFETS to achieve 2006 closure. Specific emphasis is placed on

  9. Strategy and plan for siting and licensing a Rocky Mountain low-level radioactive waste facility

    International Nuclear Information System (INIS)

    Whitman, M.

    1983-09-01

    In 1979, the States of Nevada and Washington temporarily closed their commercial low-level radioactive waste (LLW) disposal facilities and South Carolina, the only other state hosting such a facility, restricted the amount of waste it would accept. All three states then announced that they did not intend to continue the status quo of accepting all of the country's commercial low-level radioactive waste. Faced with this situation, other states began considering alternative LLW management and disposal options. In the Rocky Mountain region, this evolved into discussions for the development of an interstate compact to manage low-level waste. Inherent in this management plan was a strategy to site and license a new LLW disposal facility for the Rocky Mountain region. The Rocky Mountain Low-Level Radioactive Waste Compact was negotiated over the course of a year, with final agreement on the language of the compact agreed to in early 1982. States eligible to join the compact are Arizona, Colorado, Nevada, New Mexico, Utah, and Wyoming. Colorado adopted the compact into law in 1982, and Nevada, New Mexico and Wyoming adopted it in 1983. Utah has joined the Northwest Compact, although it may decide to join the Rocky Mountain Compact after a new disposal facility is developed for the region. Arizona has taken no action on the Rocky Mountain Compact

  10. Establishing bounding internal dose estimates for thorium activities at Rocky Flats.

    Science.gov (United States)

    Ulsh, Brant A; Rich, Bryce L; Chew, Melton H; Morris, Robert L; Sharfi, Mutty; Rolfes, Mark R

    2008-07-01

    As part of an evaluation of a Special Exposure Cohort petition filed on behalf of workers at the Rocky Flats Plant, the National Institute for Occupational Safety and Health (NIOSH) was required to demonstrate that bounding values could be established for radiation doses due to the potential intake of all radionuclides present at the facility. The main radioactive elements of interest at Rocky Flats were plutonium and uranium, but much smaller quantities of several other elements, including thorium, were occasionally handled at the site. Bounding potential doses from thorium has proven challenging at other sites due to the early historical difficulty in detecting this element through urinalysis methods and the relatively high internal dose delivered per unit intake. This paper reports the results of NIOSH's investigation of the uses of thorium at Rocky Flats and provides bounding dose reconstructions for these operations. During this investigation, NIOSH reviewed unclassified reports, unclassified extracts of classified materials, material balance and inventory ledgers, monthly progress reports from various groups, and health physics field logbooks, and conducted interviews with former Rocky Flats workers. Thorium operations included: (1) an experimental metal forming project with 240 kg of thorium in 1960; (2) the use of pre-formed parts in weapons mockups; (3) the removal of Th from U; (4) numerous analytical procedures involving trace quantities of thorium; and (5) the possible experimental use of thorium as a mold coating compound. The thorium handling operations at Rocky Flats were limited in scope, well-monitored and documented, and potential doses can be bounded.

  11. Hanford/Rocky Flats collaboration on development of supercritical carbon dioxide extraction to treat mixed waste

    International Nuclear Information System (INIS)

    Hendrickson, D.W.; Biyani, R.K.; Brown, C.M.; Teter, W.L.

    1995-11-01

    Proposals for demonstration work under the Department of Energy's Mixed Waste Focus Area, during the 1996 through 1997 fiscal years included two applications of supercritical carbon dioxide to mixed waste pretreatment. These proposals included task RF15MW58 of Rocky Flats and task RL46MW59 of Hanford. Analysis of compatibilities in wastes and work scopes yielded an expectation of substantial collaboration between sites whereby Hanford waste streams may undergo demonstration testing at Rocky Flats, thereby eliminating the need for test facilities at Hanford. This form of collaboration is premised the continued deployment at Rocky Flats and the capability for Hanford samples to be treated at Rocky Flats. The recent creation of a thermal treatment contract for a facility near Hanford may alleviate the need to conduct organic extraction upon Rocky Flats wastes by providing a cost effective thermal treatment alternative, however, some waste streams at Hanford will continue to require organic extraction. Final site waste stream treatment locations are not within the scope of this document

  12. Are seagrass beds indicators of anthropogenic nutrient stress in the rocky intertidal?

    International Nuclear Information System (INIS)

    Honig, Susanna E.; Mahoney, Brenna; Glanz, Jess S.; Hughes, Brent B.

    2017-01-01

    It is well established that anthropogenic nutrient inputs harm estuarine seagrasses, but the influence of nutrients in rocky intertidal ecosystems is less clear. In this study, we investigated the effect of anthropogenic nutrient loading on Phyllospadix spp., a rocky intertidal seagrass, at local and regional scales. At sites along California, Washington, and Oregon, we demonstrated a significant, negative correlation of urban development and Phyllospadix bed thickness. These results were echoed locally along an urban gradient on the central California coast, where Phyllospadix shoot δ 15 N was negatively associated with Phyllospadix bed thickness, and experimentally, where nutrient additions in mesocosms reduced Phyllospadix shoot formation and increased epiphytic cover on Phyllospadix shoots. These findings provide evidence that coastal development can threaten rocky intertidal seagrasses through increased epiphytism. Considering that seagrasses provide vital ecosystem services, mitigating eutrophication and other factors associated with development in the rocky intertidal coastal zone should be a management priority. - Highlights: • The effect of nutrient loading on rocky intertidal seagrasses is not well studied. • Regionally, development was negatively associated with Phyllospadix bed thickness. • Locally, shoot δ 15 N was negatively associated with Phyllospadix bed thickness. • Mesocosms with added nutrients had a net loss in shoots and increased epiphytes. • Nutrient loading may have a negative effect on intertidal seagrass bed health.

  13. Hanford/Rocky Flats collaboration on development of supercritical carbon dioxide extraction to treat mixed waste

    Energy Technology Data Exchange (ETDEWEB)

    Hendrickson, D.W.; Biyani, R.K. [Westinghouse Hanford Co., Richland, WA (United States); Brown, C.M.; Teter, W.L. [Kaiser-Hill Co., Golden, CO (United States)

    1995-11-01

    Proposals for demonstration work under the Department of Energy`s Mixed Waste Focus Area, during the 1996 through 1997 fiscal years included two applications of supercritical carbon dioxide to mixed waste pretreatment. These proposals included task RF15MW58 of Rocky Flats and task RL46MW59 of Hanford. Analysis of compatibilities in wastes and work scopes yielded an expectation of substantial collaboration between sites whereby Hanford waste streams may undergo demonstration testing at Rocky Flats, thereby eliminating the need for test facilities at Hanford. This form of collaboration is premised the continued deployment at Rocky Flats and the capability for Hanford samples to be treated at Rocky Flats. The recent creation of a thermal treatment contract for a facility near Hanford may alleviate the need to conduct organic extraction upon Rocky Flats wastes by providing a cost effective thermal treatment alternative, however, some waste streams at Hanford will continue to require organic extraction. Final site waste stream treatment locations are not within the scope of this document.

  14. FINAL REPORT FORMER RADIATION WORKER MEDICAL SURVEILLANCE PROGRAM AT ROCKY FLATS For Department of Energy Programs

    Energy Technology Data Exchange (ETDEWEB)

    Joe M. Aldrich

    2004-11-01

    The Former Radiation Worker Medical Surveillance Program at Rocky Flats was conducted in Arvada, CO, by Oak Ridge Associated Universities through the Oak Ridge Institute for Science and Education under DOE Contract DE-AC05-00OR22750. Objectives of the program were to obtain information on the value of medical surveillance among at-risk former radiation workers and to provide long-term internal radiation dosimetry information to the scientific community. This program provided the former radiation workers of the Rocky Flats Environmental Technology Site (formerly Rocky Flats Plant) an opportunity to receive follow-up medical monitoring and a re-evaluation of their internal radiation dose. The former Rocky Flats radiation worker population is distinctive because it was a reasonably stable work force that received occupational exposures, at times substantial, over several decades. This report reflects the summation of health outcomes, statistical analyses, and dose assessment information on former Rocky Flats radiation workers to the date of study termination as of March 2004.

  15. FINAL REPORT. FORMER RADIATION WORKER MEDICAL SURVEILLANCE PROGRAM AT ROCKY FLATS For Department of Energy Programs

    International Nuclear Information System (INIS)

    Aldrich, Joe M.

    2004-01-01

    The Former Radiation Worker Medical Surveillance Program at Rocky Flats was conducted in Arvada, CO, by Oak Ridge Associated Universities through the Oak Ridge Institute for Science and Education under DOE Contract DE-AC--05-00OR22750. Objectives of the program were to obtain information on the value of medical surveillance among at-risk former radiation workers and to provide long-term internal radiation dosimetry information to the scientific community. This program provided the former radiation workers of the Rocky Flats Environmental Technology Site (formerly Rocky Flats Plant) an opportunity to receive follow-up medical monitoring and a re-evaluation of their internal radiation dose. The former Rocky Flats radiation worker population is distinctive because it was a reasonably stable work force that received occupational exposures, at times substantial, over several decades. This report reflects the summation of health outcomes, statistical analyses, and dose assessment information on former Rocky Flats radiation workers to the date of study termination as of March 2004

  16. Reconstructed ancestral Myo-inositol-3-phosphate synthases indicate that ancestors of the Thermococcales and Thermotoga species were more thermophilic than their descendants.

    Science.gov (United States)

    Butzin, Nicholas C; Lapierre, Pascal; Green, Anna G; Swithers, Kristen S; Gogarten, J Peter; Noll, Kenneth M

    2013-01-01

    The bacterial genomes of Thermotoga species show evidence of significant interdomain horizontal gene transfer from the Archaea. Members of this genus acquired many genes from the Thermococcales, which grow at higher temperatures than Thermotoga species. In order to study the functional history of an interdomain horizontally acquired gene we used ancestral sequence reconstruction to examine the thermal characteristics of reconstructed ancestral proteins of the Thermotoga lineage and its archaeal donors. Several ancestral sequence reconstruction methods were used to determine the possible sequences of the ancestral Thermotoga and Archaea myo-inositol-3-phosphate synthase (MIPS). These sequences were predicted to be more thermostable than the extant proteins using an established sequence composition method. We verified these computational predictions by measuring the activities and thermostabilities of purified proteins from the Thermotoga and the Thermococcales species, and eight ancestral reconstructed proteins. We found that the ancestral proteins from both the archaeal donor and the Thermotoga most recent common ancestor recipient were more thermostable than their descendants. We show that there is a correlation between the thermostability of MIPS protein and the optimal growth temperature (OGT) of its host, which suggests that the OGT of the ancestors of these species of Archaea and the Thermotoga grew at higher OGTs than their descendants.

  17. Reconstructed ancestral Myo-inositol-3-phosphate synthases indicate that ancestors of the Thermococcales and Thermotoga species were more thermophilic than their descendants.

    Directory of Open Access Journals (Sweden)

    Nicholas C Butzin

    Full Text Available The bacterial genomes of Thermotoga species show evidence of significant interdomain horizontal gene transfer from the Archaea. Members of this genus acquired many genes from the Thermococcales, which grow at higher temperatures than Thermotoga species. In order to study the functional history of an interdomain horizontally acquired gene we used ancestral sequence reconstruction to examine the thermal characteristics of reconstructed ancestral proteins of the Thermotoga lineage and its archaeal donors. Several ancestral sequence reconstruction methods were used to determine the possible sequences of the ancestral Thermotoga and Archaea myo-inositol-3-phosphate synthase (MIPS. These sequences were predicted to be more thermostable than the extant proteins using an established sequence composition method. We verified these computational predictions by measuring the activities and thermostabilities of purified proteins from the Thermotoga and the Thermococcales species, and eight ancestral reconstructed proteins. We found that the ancestral proteins from both the archaeal donor and the Thermotoga most recent common ancestor recipient were more thermostable than their descendants. We show that there is a correlation between the thermostability of MIPS protein and the optimal growth temperature (OGT of its host, which suggests that the OGT of the ancestors of these species of Archaea and the Thermotoga grew at higher OGTs than their descendants.

  18. A Common Ancestral Mutation in CRYBB3 Identified in Multiple Consanguineous Families with Congenital Cataracts.

    Directory of Open Access Journals (Sweden)

    Xiaodong Jiao

    report a common ancestral mutation in CRYBB3 associated with autosomal recessive congenital cataracts identified in four familial cases of Pakistani origin.

  19. Greater trochanteric fracture with occult intertrochanteric extension.

    Science.gov (United States)

    Reiter, Michael; O'Brien, Seth D; Bui-Mansfield, Liem T; Alderete, Joseph

    2013-10-01

    Proximal femoral fractures are frequently encountered in the emergency department (ED). Prompt diagnosis is paramount as delay will exacerbate the already poor outcomes associated with these injuries. In cases where radiography is negative but clinical suspicion remains high, magnetic resonance imaging (MRI) is the study of choice as it has the capability to depict fractures which are occult on other imaging modalities. Awareness of a particular subset of proximal femoral fractures, namely greater trochanteric fractures, is vital for both radiologists and clinicians since it has been well documented that they invariably have an intertrochanteric component which may require surgical management. The detection of intertrochanteric or cervical extension of greater trochanteric fractures has been described utilizing MRI but is underestimated with both computed tomography (CT) and bone scan. Therefore, if MRI is unavailable or contraindicated, the diagnosis of an isolated greater trochanteric fracture should be met with caution. The importance of avoiding this potential pitfall is demonstrated in the following case of an elderly woman with hip pain and CT demonstrating an isolated greater trochanteric fracture who subsequently returned to the ED with a displaced intertrochanteric fracture.

  20. Butterfly valves: greater use in power plants

    International Nuclear Information System (INIS)

    McCoy, M.

    1975-01-01

    Improvements in butterfly valves, particularly in the areas of automatic control and leak tightness are described. The use of butterfly valves in nuclear power plants is discussed. These uses include service in component cooling, containment cooling, and containment isolation. The outlook for further improvements and greater uses is examined. (U.S.)

  1. Greater Somalia, the never-ending dream?

    DEFF Research Database (Denmark)

    Zoppi, Marco

    2015-01-01

    This paper provides an historical analysis of the concept of Greater Somalia, the nationalist project that advocates the political union of all Somali-speaking people, including those inhabiting areas in current Djibouti, Ethiopia and Kenya. The Somali territorial unification project of “lost...

  2. Comparative risk analysis for the Rocky Flats Plant integrated project planning

    International Nuclear Information System (INIS)

    Jones, M.E.; Shain, D.I.

    1994-01-01

    The Rocky Flats Plant is developing, with active stakeholder a comprehensive planning strategy that will support transition of the Rocky Flats Plant from a nuclear weapons production facility to site cleanup and final disposition. Final disposition of the Rocky Flats Plant materials and contaminants requires consideration of the interrelated nature of sitewide problems, such as material movement and disposition, facility and land use endstates, costs relative risks to workers and the public, and waste disposition. Comparative Risk Analysis employs both incremental risk and cumulative risk evaluations to compare risks from postulated options or endstates. These postulated options or endstates can be various remedial alternatives, or future endstate uses of federal agency land. Currently, there does not exist any approved methodology that aggregates various incremental risk estimates. Comparative Risk Analysis has been developed to aggregate various incremental risk estimates to develop a site cumulative risk estimate. This paper discusses development of the Comparative Risk Analysis methodology, stakeholder participation and lessons learned from these challenges

  3. [Relationships between soil and rocky desertification in typical karst mountain area based on redundancy analysis].

    Science.gov (United States)

    Long, Jian; Liao, Hong-Kai; Li, Juan; Chen, Cai-Yun

    2012-06-01

    Redundancy analysis (RDA) was employed to reveal the relationships between soil and rocky desertification through vegetation investigation and analysis of soil samples collected in typical karst mountain area of southwest Guizhou Province. The results showed that except TP, TK and ACa, all other variables including SOC, TN, MBC, ROC, DOC, available nutrients and basal respiration showed significant downward trends during the rocky desertification process. RDA results showed significant correlations between different types of desertification and soil variables, described as non-degraded > potential desertification > light desertification > moderate desertification > severe desertification. Moreover, RDA showed that using SOC, TN, AN, and BD as soil indicators, 74.4% of the variance information on soil and rocky desertification could be explained. Furthermore, the results of correlation analysis showed that soil variables were significantly affected by surface vegetation. Considering the ecological function of the aboveground vegetation and the soil quality, Zanthoxylum would be a good choice for restoration of local vegetation in karst mountain area.

  4. Structure of macroalgal communities on tropical rocky shores inside and outside a marine protected area.

    Science.gov (United States)

    Portugal, Adriana Brizon; Carvalho, Fabrício Lopes; Soares, Marcelo de Oliveira; Horta, Paulo Antunes; de Castro Nunes, José Marcos

    2017-09-01

    The structure of marine macroalgal communities and morpho-functional groups were investigated in a poorly characterized region on the Tropical Southwestern Atlantic coast, Brazil. The survey was conducted at six rocky shores located on the mainland and on coastal islands distributed inside a marine protected area (MPA) and outside the MPA (near a densely populated area). We hypothesized that tropical rocky shores inside the MPA and islands have higher species richness, diversity, and evenness of marine macroalgae. Results confirmed that species richness, diversity and evenness were significantly higher inside the MPA than in rocky shores outside the MPA. Only species richness was higher on islands than on the mainland. The results suggest that human impacts could lead to a competitive advantage and dominance in the articulated calcareous morphotype, resulting in community differences and lower benthic biodiversity in tropical ecosystems near urbanized sites. Copyright © 2017 Elsevier Ltd. All rights reserved.

  5. Reestablishment of the Ancestral Cascades Arc in Western Nevada and Eastern California by Rollback of the Shallow Farallon Slab

    Science.gov (United States)

    Henry, C. D.; Cousens, B.; John, D. A.; Colgan, J. P.

    2009-12-01

    The character and even existence of an ancestral Tertiary Cascades arc in western Nevada and eastern California south of the modern arc are controversial. Based on extensive published and new data on the regional distribution, timing, style, and composition of magmatism, we conclude that an ancestral arc was established by WSW migration of magmatism into western NV and the northeastern Sierra Nevada in the Oligocene and Miocene as a result of progressive rollback of the shallow subducted slab. Magma migration started with the well-known southward sweep through NE NV and NW UT between ~46 and 36 Ma. By ~30 Ma, migration of the leading edge and central belt of activity was much more WSW, especially after removing younger ~E-W extension. Locally sourced, initially dispersed and small volume, intermediate to mafic lavas erupted in western NV and northeastern CA by ~30 Ma and the eastern Sierra Nevada by ~28 Ma, contemporaneous with the much more voluminous ignimbrite flare-up in central NV. As migration continued, the ignimbrite flare-up tapered off. A voluminous, NNW-trending, dominantly effusive volcanic belt developed by ~22-18 Ma in western NV and was continuous from the Bodie Hills (CA/NV) to the Warner Range (northeast CA) by ~16-15 Ma. The volcanic belt was dominated by intermediate to mafic magmas compositionally similar to those of the modern south Cascades arc but reflecting melting of an old, subduction-modified lithosphere (Cousens et al. 2008; Geosphere). Extensive middle Miocene bimodal rocks related to the Yellowstone hotspot cover these rocks in NW NV, NE CA, and SE OR, but 30-23 Ma, intermediate to mafic and lesser silicic rocks are voluminous wherever older rocks are exposed below the middle Miocene rocks. Between ~25 Ma and the present, magmatism migrated WSW at an average rate of ~8 km/Ma but was at least partly stepwise, as exemplified by an ~50 km westward step at 2 Ma in the Lassen area (Guffanti et al. 1990, JGR). The magmatic belt was as much

  6. Regeneration of Rocky Mountain bristlecone pine (Pinus aristata) and limber pine (Pinus flexilis) three decades after stand-replacing fires

    Science.gov (United States)

    Jonathan D. Coop; Anna W. Schoettle

    2009-01-01

    Rocky Mountain bristlecone pine (Pinus aristata) and limber pine (Pinus flexilis) are important highelevation pines of the southern Rockies that are forecast to decline due to the recent spread of white pine blister rust (Cronartium ribicola) into this region. Proactive management strategies to promote the evolution of rust resistance and maintain ecosystem function...

  7. Self-reported treatment practices by healthcare providers could lead to death from Rocky Mountain spotted fever.

    Science.gov (United States)

    Zientek, Jillian; Dahlgren, F Scott; McQuiston, Jennifer H; Regan, Joanna

    2014-02-01

    Among 2012 Docstyle survey respondents, 80% identified doxycycline as the appropriate treatment for Rocky Mountain spotted fever in patients ≥ 8 years old, but only 35% correctly chose doxycycline in patients Rocky Mountain spotted fever observed nationally. Targeted education efforts are needed. Crown Copyright © 2014. Published by Mosby, Inc. All rights reserved.

  8. Plutonium contamination in soils in open space and residential areas near Rocky Flats, Colorado

    International Nuclear Information System (INIS)

    Litaor, M.I.

    1999-01-01

    Spatial analysis of the 240 Pu: 239 Pu isotopic ratio of 42 soil samples collected around Rocky Flats Plant near Golden, Colorado, was conducted to assess the effect of Rocky Flats Plant activity on the soil environment. Two probability maps that quantified the uncertainty of the spatial distribution of plutonium isotopic ratios were constructed using the sequential Gaussian simulation technique (sGs). Assuming a plutonium isotopic ratio range of 0.152 ± 0.003 to 0.169 ± 0.009 is characteristic to global fallout in Colorado, and a mean value of 0.155 is representative for the Rocky Flats Plant area, the main findings of the current work were (1) the areas northwest and southwest of Rocky Flats Plant exhibited a plutonium ratio ≥0.155, this were minimally impacted by the plant activity; (2) he study area east of Rocky Flats Plant exhibited a plutonium isotopic ratio ≤0.155, which is a definitive indicator of Rocky Flats Plant-derived plutonium; and (3) inventory calculations across the study area exhibited large standard error of estimates. These errors were originated from the high variability in plutonium activity over a small sampling scale and the uncertainty in the global fallout isotopic ratio. Using the mean simulated estimates of plutonium isotopic ratio, coupled with plutonium activity measured at 11 soil pits and additional plutonium information published elsewhere, the plutonium loading on the open space and residential areas amounted to 111.2 GBq, with a standard error of estimate of 50.8 GBq

  9. Utilization of wind energy in greater Hanover

    International Nuclear Information System (INIS)

    Sahling, U.

    1993-01-01

    Since the beginning of the Eighties, the association of communities of Greater Hanover has dealt intensively with energy and ecopolitical questions in the scope of regional planning. Renewable energy sources play a dominant role in this context. This brochure is the third contribution to the subject ''Energy policy and environmental protection''. Experts as well as possibly interested parties are addressed especially. For all 8 contributions contained, separate entries have been recorded in this database. (BWI) [de

  10. Small cities face greater impact from automation

    OpenAIRE

    Frank, Morgan R.; Sun, Lijun; Cebrian, Manuel; Youn, Hyejin; Rahwan, Iyad

    2017-01-01

    The city has proven to be the most successful form of human agglomeration and provides wide employment opportunities for its dwellers. As advances in robotics and artificial intelligence revive concerns about the impact of automation on jobs, a question looms: How will automation affect employment in cities? Here, we provide a comparative picture of the impact of automation across U.S. urban areas. Small cities will undertake greater adjustments, such as worker displacement and job content su...

  11. Founder haplotype analysis of Fanconi anemia in the Korean population finds common ancestral haplotypes for a FANCG variant.

    Science.gov (United States)

    Park, Joonhong; Kim, Myungshin; Jang, Woori; Chae, Hyojin; Kim, Yonggoo; Chung, Nack-Gyun; Lee, Jae-Wook; Cho, Bin; Jeong, Dae-Chul; Park, In Yang; Park, Mi Sun

    2015-05-01

    A common ancestral haplotype is strongly suggested in the Korean and Japanese patients with Fanconi anemia (FA), because common mutations have been frequently found: c.2546delC and c.3720_3724delAAACA of FANCA; c.307+1G>C, c.1066C>T, and c.1589_1591delATA of FANCG. Our aim in this study was to investigate the origin of these common mutations of FANCA and FANCG. We genotyped 13 FA patients consisting of five FA-A patients and eight FA-G patients from the Korean FA population. Microsatellite markers used for haplotype analysis included four CA repeat markers which are closely linked with FANCA and eight CA repeat markers which are contiguous with FANCG. As a result, Korean FA-A patients carrying c.2546delC or c.3720_3724delAAACA did not share the same haplotypes. However, three unique haplotypes carrying c.307+1G>C, c.1066C > T, or c.1589_1591delATA, that consisted of eight polymorphic loci covering a flanking region were strongly associated with Korean FA-G, consistent with founder haplotypes reported previously in the Japanese FA-G population. Our finding confirmed the common ancestral haplotypes on the origins of the East Asian FA-G patients, which will improve our understanding of the molecular population genetics of FA-G. To the best of our knowledge, this is the first report on the association between disease-linked mutations and common ancestral haplotypes in the Korean FA population. © 2015 John Wiley & Sons Ltd/University College London.

  12. Human Genetic Ancestral Composition Correlates with the Origin of Mycobacterium leprae Strains in a Leprosy Endemic Population.

    Directory of Open Access Journals (Sweden)

    Nora Cardona-Castro

    Full Text Available Recent reports have suggested that leprosy originated in Africa, extended to Asia and Europe, and arrived in the Americas during European colonization and the African slave trade. Due to colonization, the contemporary Colombian population is an admixture of Native-American, European and African ancestries. Because microorganisms are known to accompany humans during migrations, patterns of human migration can be traced by examining genomic changes in associated microbes. The current study analyzed 118 leprosy cases and 116 unrelated controls from two Colombian regions endemic for leprosy (Atlantic and Andean in order to determine possible associations of leprosy with patient ancestral background (determined using 36 ancestry informative markers, Mycobacterium leprae genotype and/or patient geographical origin. We found significant differences between ancestral genetic composition. European components were predominant in Andean populations. In contrast, African components were higher in the Atlantic region. M. leprae genotypes were then analyzed for cluster associations and compared with the ancestral composition of leprosy patients. Two M. leprae principal clusters were found: haplotypes C54 and T45. Haplotype C54 associated with African origin and was more frequent in patients from the Atlantic region with a high African component. In contrast, haplotype T45 associated with European origin and was more frequent in Andean patients with a higher European component. These results suggest that the human and M. leprae genomes have co-existed since the African and European origins of the disease, with leprosy ultimately arriving in Colombia during colonization. Distinct M. leprae strains followed European and African settlement in the country and can be detected in contemporary Colombian populations.

  13. Allo-allo-triploid Sphagnum × falcatulum: single individuals contain most of the Holantarctic diversity for ancestrally indicative markers.

    Science.gov (United States)

    Karlin, Eric F; Smouse, Peter E

    2017-08-01

    Allopolyploids exhibit both different levels and different patterns of genetic variation than are typical of diploids. However, scant attention has been given to the partitioning of allelic information and diversity in allopolyploids, particularly that among homeologous monoploid components of the hologenome. Sphagnum × falcatulum is a double allopolyploid peat moss that spans a considerable portion of the Holantarctic. With monoploid genomes from three ancestral species, this organism exhibits a complex evolutionary history involving serial inter-subgeneric allopolyploidizations. Studying populations from three disjunct regions [South Island (New Zealand); Tierra de Fuego archipelago (Chile, Argentina); Tasmania (Australia)], allelic information for five highly stable microsatellite markers that differed among the three (ancestral) monoploid genomes was examined. Using Shannon information and diversity measures, the holoploid information, as well as the information within and among the three component monoploid genomes, was partitioned into separate components for individuals within and among populations and regions, and those information components were then converted into corresponding diversity measures. The majority (76 %) of alleles detected across these five markers are most likely to have been captured by hybridization, but the information within each of the three monoploid genomes varied, suggesting a history of recurrent allopolyploidization between ancestral species containing different levels of genetic diversity. Information within individuals, equivalent to the information among monoploid genomes (for this dataset), was relatively stable, and represented 83 % of the grand total information across the Holantarctic, with both inter-regional and inter-population diversification each accounting for about 5 % of the total information. Sphagnum × falcatulum probably inherited the great majority of its genetic diversity at these markers by reticulation

  14. Saccharomyces cerevisiae Bat1 and Bat2 aminotransferases have functionally diverged from the ancestral-like Kluyveromyces lactis orthologous enzyme.

    Directory of Open Access Journals (Sweden)

    Maritrini Colón

    Full Text Available BACKGROUND: Gene duplication is a key evolutionary mechanism providing material for the generation of genes with new or modified functions. The fate of duplicated gene copies has been amply discussed and several models have been put forward to account for duplicate conservation. The specialization model considers that duplication of a bifunctional ancestral gene could result in the preservation of both copies through subfunctionalization, resulting in the distribution of the two ancestral functions between the gene duplicates. Here we investigate whether the presumed bifunctional character displayed by the single branched chain amino acid aminotransferase present in K. lactis has been distributed in the two paralogous genes present in S. cerevisiae, and whether this conservation has impacted S. cerevisiae metabolism. PRINCIPAL FINDINGS: Our results show that the KlBat1 orthologous BCAT is a bifunctional enzyme, which participates in the biosynthesis and catabolism of branched chain aminoacids (BCAAs. This dual role has been distributed in S. cerevisiae Bat1 and Bat2 paralogous proteins, supporting the specialization model posed to explain the evolution of gene duplications. BAT1 is highly expressed under biosynthetic conditions, while BAT2 expression is highest under catabolic conditions. Bat1 and Bat2 differential relocalization has favored their physiological function, since biosynthetic precursors are generated in the mitochondria (Bat1, while catabolic substrates are accumulated in the cytosol (Bat2. Under respiratory conditions, in the presence of ammonium and BCAAs the bat1Δ bat2Δ double mutant shows impaired growth, indicating that Bat1 and Bat2 could play redundant roles. In K. lactis wild type growth is independent of BCAA degradation, since a Klbat1Δ mutant grows under this condition. CONCLUSIONS: Our study shows that BAT1 and BAT2 differential expression and subcellular relocalization has resulted in the distribution of the

  15. Human Genetic Ancestral Composition Correlates with the Origin of Mycobacterium leprae Strains in a Leprosy Endemic Population.

    Science.gov (United States)

    Cardona-Castro, Nora; Cortés, Edwin; Beltrán, Camilo; Romero, Marcela; Badel-Mogollón, Jaime E; Bedoya, Gabriel

    2015-01-01

    Recent reports have suggested that leprosy originated in Africa, extended to Asia and Europe, and arrived in the Americas during European colonization and the African slave trade. Due to colonization, the contemporary Colombian population is an admixture of Native-American, European and African ancestries. Because microorganisms are known to accompany humans during migrations, patterns of human migration can be traced by examining genomic changes in associated microbes. The current study analyzed 118 leprosy cases and 116 unrelated controls from two Colombian regions endemic for leprosy (Atlantic and Andean) in order to determine possible associations of leprosy with patient ancestral background (determined using 36 ancestry informative markers), Mycobacterium leprae genotype and/or patient geographical origin. We found significant differences between ancestral genetic composition. European components were predominant in Andean populations. In contrast, African components were higher in the Atlantic region. M. leprae genotypes were then analyzed for cluster associations and compared with the ancestral composition of leprosy patients. Two M. leprae principal clusters were found: haplotypes C54 and T45. Haplotype C54 associated with African origin and was more frequent in patients from the Atlantic region with a high African component. In contrast, haplotype T45 associated with European origin and was more frequent in Andean patients with a higher European component. These results suggest that the human and M. leprae genomes have co-existed since the African and European origins of the disease, with leprosy ultimately arriving in Colombia during colonization. Distinct M. leprae strains followed European and African settlement in the country and can be detected in contemporary Colombian populations.

  16. Reconstructed ancestral enzymes reveal that negative selection drove the evolution of substrate specificity in ADP-dependent kinases.

    Science.gov (United States)

    Castro-Fernandez, Víctor; Herrera-Morande, Alejandra; Zamora, Ricardo; Merino, Felipe; Gonzalez-Ordenes, Felipe; Padilla-Salinas, Felipe; Pereira, Humberto M; Brandão-Neto, Jose; Garratt, Richard C; Guixe, Victoria

    2017-09-22

    One central goal in molecular evolution is to pinpoint the mechanisms and evolutionary forces that cause an enzyme to change its substrate specificity; however, these processes remain largely unexplored. Using the glycolytic ADP-dependent kinases of archaea, including the orders Thermococcales , Methanosarcinales , and Methanococcales , as a model and employing an approach involving paleoenzymology, evolutionary statistics, and protein structural analysis, we could track changes in substrate specificity during ADP-dependent kinase evolution along with the structural determinants of these changes. To do so, we studied five key resurrected ancestral enzymes as well as their extant counterparts. We found that a major shift in function from a bifunctional ancestor that could phosphorylate either glucose or fructose 6-phosphate (fructose-6-P) as a substrate to a fructose 6-P-specific enzyme was started by a single amino acid substitution resulting in negative selection with a ground-state mode against glucose and a subsequent 1,600-fold change in specificity of the ancestral protein. This change rendered the residual phosphorylation of glucose a promiscuous and physiologically irrelevant activity, highlighting how promiscuity may be an evolutionary vestige of ancestral enzyme activities, which have been eliminated over time. We also could reconstruct the evolutionary history of substrate utilization by using an evolutionary model of discrete binary characters, indicating that substrate uses can be discretely lost or acquired during enzyme evolution. These findings exemplify how negative selection and subtle enzyme changes can lead to major evolutionary shifts in function, which can subsequently generate important adaptive advantages, for example, in improving glycolytic efficiency in Thermococcales . © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  17. Estimation of the net acid load of the diet of ancestral preagricultural Homo sapiens and their hominid ancestors.

    Science.gov (United States)

    Sebastian, Anthony; Frassetto, Lynda A; Sellmeyer, Deborah E; Merriam, Renée L; Morris, R Curtis

    2002-12-01

    Natural selection has had diet resulting from the inventions of agriculture and animal husbandry. The objective was to estimate the net systemic load of acid (net endogenous acid production; NEAP) from retrojected ancestral preagricultural diets and to compare it with that of contemporary diets, which are characterized by an imbalance of nutrient precursors of hydrogen and bicarbonate ions that induces a lifelong, low-grade, pathogenically significant systemic metabolic acidosis. Using established computational methods, we computed NEAP for a large number of retrojected ancestral preagricultural diets and compared them with computed and measured values for typical American diets. The mean (+/- SD) NEAP for 159 retrojected preagricultural diets was -88 +/- 82 mEq/d; 87% were net base-producing. The computational model predicted NEAP for the average American diet (as recorded in the third National Health and Nutrition Examination Survey) as 48 mEq/d, within a few percentage points of published measured values for free-living Americans; the model, therefore, was not biased toward generating negative NEAP values. The historical shift from negative to positive NEAP was accounted for by the displacement of high-bicarbonate-yielding plant foods in the ancestral diet by cereal grains and energy-dense, nutrient-poor foods in the contemporary diet-neither of which are net base-producing. The findings suggest that diet-induced metabolic acidosis and its sequelae in humans eating contemporary diets reflect a mismatch between the nutrient composition of the diet and genetically determined nutritional requirements for optimal systemic acid-base status.

  18. The Greater Sekhukhune-CAPABILITY outreach project.

    Science.gov (United States)

    Gregersen, Nerine; Lampret, Julie; Lane, Tony; Christianson, Arnold

    2013-07-01

    The Greater Sekhukhune-CAPABILITY Outreach Project was undertaken in a rural district in Limpopo, South Africa, as part of the European Union-funded CAPABILITY programme to investigate approaches for capacity building for the translation of genetic knowledge into care and prevention of congenital disorders. Based on previous experience of a clinical genetic outreach programme in Limpopo, it aimed to initiate a district clinical genetic service in Greater Sekhukhune to gain knowledge and experience to assist in the implementation and development of medical genetic services in South Africa. Implementing the service in Greater Sekhukhune was impeded by a developing staff shortage in the province and pressure on the health service from the existing HIV/AIDS and TB epidemics. This situation underscores the need for health needs assessment for developing services for the care and prevention of congenital disorders in middle- and low-income countries. However, these impediments stimulated the pioneering of innovate ways to offer medical genetic services in these circumstances, including tele-teaching of nurses and doctors, using cellular phones to enhance clinical care and adapting and assessing the clinical utility of a laboratory test, QF-PCR, for use in the local circumstances.

  19. Operational technology for greater confinement disposal

    International Nuclear Information System (INIS)

    Dickman, P.T.; Vollmer, A.T.; Hunter, P.H.

    1984-12-01

    Procedures and methods for the design and operation of a greater confinement disposal facility using large-diameter boreholes are discussed. It is assumed that the facility would be located at an operating low-level waste disposal site and that only a small portion of the wastes received at the site would require greater confinement disposal. The document is organized into sections addressing: facility planning process; facility construction; waste loading and handling; radiological safety planning; operations procedures; and engineering cost studies. While primarily written for low-level waste management site operators and managers, a detailed economic assessment section is included that should assist planners in performing cost analyses. Economic assessments for both commercial and US government greater confinement disposal facilities are included. The estimated disposal costs range from $27 to $104 per cubic foot for a commercial facility and from $17 to $60 per cubic foot for a government facility. These costs are based on average site preparation, construction, and waste loading costs for both contact- and remote-handled wastes. 14 figures, 22 tables

  20. Characterization of Most Promising Sequestration Formations in the Rocky Mountain Region (RMCCS)

    Energy Technology Data Exchange (ETDEWEB)

    McPherson, Brian; Matthews, Vince

    2013-09-30

    The primary objective of the “Characterization of Most Promising Carbon Capture and Sequestration Formations in the Central Rocky Mountain Region” project, or RMCCS project, is to characterize the storage potential of the most promising geologic sequestration formations within the southwestern U.S. and the Central Rocky Mountain region in particular. The approach included an analysis of geologic sequestration formations under the Craig Power Station in northwestern Colorado, and application or extrapolation of those local-scale results to the broader region. A ten-step protocol for geologic carbon storage site characterization was a primary outcome of this project.

  1. The analysis of morphometric data on rocky mountain wolves and artic wolves using statistical method

    Science.gov (United States)

    Ammar Shafi, Muhammad; Saifullah Rusiman, Mohd; Hamzah, Nor Shamsidah Amir; Nor, Maria Elena; Ahmad, Noor’ani; Azia Hazida Mohamad Azmi, Nur; Latip, Muhammad Faez Ab; Hilmi Azman, Ahmad

    2018-04-01

    Morphometrics is a quantitative analysis depending on the shape and size of several specimens. Morphometric quantitative analyses are commonly used to analyse fossil record, shape and size of specimens and others. The aim of the study is to find the differences between rocky mountain wolves and arctic wolves based on gender. The sample utilised secondary data which included seven variables as independent variables and two dependent variables. Statistical modelling was used in the analysis such was the analysis of variance (ANOVA) and multivariate analysis of variance (MANOVA). The results showed there exist differentiating results between arctic wolves and rocky mountain wolves based on independent factors and gender.

  2. Stable Hydrogen-rich Atmospheres of Young Rocky Planets

    Science.gov (United States)

    Zahnle, K. J.; Catling, D. C.; Gacesa, M.

    2016-12-01

    SourceURL:file://localhost/Volumes/Lexar/Zahnle_AGU_2016.docx Understanding hydrogen escape is essential to understanding the limits to habitability, both for liquid water where the Sun is bright, but also to assess the true potential of H2 as a greenhouse gas where the Sun is faint. Hydrogen-rich primary atmospheres of Earth-like planets can result either from gravitational capture of solar nebular gases (with helium), or from impact shock processing of a wide variety of volatile-rich planetesimals (typically accompanied by H2O, CO2, and under the right circumstances, CH4). Most studies of hydrogen escape from planets focus on determining how fast the hydrogen escapes. In general this requires solving hydrodynamic equations that take into account the acceleration of hydrogen through a critical transonic point and an energy budget that should include radiative heating and cooling, thermal conduction, the work done in lifting the hydrogen against gravity, and the residual heat carried by the hydrogen as it leaves. But for planets from which hydrogen escape is modest or insignificant, the atmosphere can be approximated as hydrostatic, which is much simpler, and for which a relatively full-featured treatment of radiative cooling by embedded molecules, atoms, and ions such as CO2 and H3+ is straightforward. Previous work has overlooked the fact that the H2 molecule is extremely efficient at exciting non-LTE CO2 15 micron emission, and thus that radiative cooling can be markedly more efficient when H2 is abundant. We map out the region of phase space in which terrestrial planets keep hydrogen-rich atmospheres, which is what we actually want to know for habitability. We will use this framework to reassess Tian et al's (Science 308, pp. 1014-1017, 2005) hypothesis that H2-rich atmospheres may have been rather long-lived on Earth itself. Finally, we will address the empirical observation that rocky planets with thin or negligible atmospheres are rarely or never bigger than

  3. A seasonal nitrogen deposition budget for Rocky Mountain National Park.

    Science.gov (United States)

    Benedict, K B; Carrico, C M; Kreidenweis, S M; Schichtel, B; Malm, W C; Collett, J L

    2013-07-01

    Nitrogen deposition is a concern in many protected ecosystems around the world, yet few studies have quantified a complete reactive nitrogen deposition budget including all dry and wet, inorganic and organic compounds. Critical loads that identify the level at which nitrogen deposition negatively affects an ecosystem are often defined using incomplete reactive nitrogen budgets. Frequently only wet deposition of ammonium and nitrate are considered, despite the importance of other nitrogen deposition pathways. Recently, dry deposition pathways including particulate ammonium and nitrate and gas phase nitric acid have been added to nitrogen deposition budgets. However, other nitrogen deposition pathways, including dry deposition of ammonia and wet deposition of organic nitrogen, still are rarely included. In this study, a more complete seasonal nitrogen deposition budget was constructed based on observations during a year-long study period from November 2008 to November 2009 at a location on the east side of Rocky Mountain National Park (RMNP), Colorado, USA. Measurements included wet deposition of ammonium, nitrate, and organic nitrogen, PM2.5 (particulate matter with an aerodynamic diameter less than 2.5 microm, nitrate, and ammonium) concentrations of ammonium, nitrate, and organic nitrogen, and atmospheric gas phase concentrations of ammonia, nitric acid, and NO2. Dry deposition fluxes were determined from measured ambient concentrations and modeled deposition velocities. Total reactive nitrogen deposition by all included pathways was found to be 3.65 kg N x ha(-1) yr(-1). Monthly deposition fluxes ranged from 0.06 to 0.54 kg N x ha(-1)yr(-1), with peak deposition in the month of July and the least deposition in December. Wet deposition of ammonium and nitrate were the two largest deposition pathways, together contributing 1.97 kg N x ha(-1)yr(-1) or 54% of the total nitrogen deposition budget for this region. The next two largest deposition pathways were wet

  4. Coastal rocky reef fishes of Santa Catarina's northern islands, Brazil

    Directory of Open Access Journals (Sweden)

    Johnatas Adelir Alves

    2015-11-01

    Full Text Available The coast of the state of Santa Catarina only has non-biogenic reefs, i.e. rocky and artificial reefs, and is considered the geographic south limit for many reef fish species. At present the diversity of organisms associated with reef environments is threatened. This study aimed to record the number of families and species of reef fish fauna of the north coast of the state of Santa Catarina. The data were collected through underwater visual census performed on Graças archipelago (26°12'S /48º29'W, Tamboretes archipelago (26°22'S/48°31'W and Barra do Sul islands (26°27'S/48º35'W. A total of 166 species was observed (6 elasmobranchii and 160 actinopterygii belonging to 66 families. The families with more species richness were Carangidae (16, Epinephelidae (9, Blenidae (8, Serranidae (7, Haemulidae (6, Sparidae (6 Tetraodontidae (6, Labridae-Scarini (5, Labrisomidae (5 Pomacentridae (5, Lutjanidae (5 and Muraenidae (5. This study add to the current published list, new 115 species, including new occurrences (e.g. Chromis limbata, and some endemic (e.g. Sparisoma amplum, exotic (e.g. Omobranchus punctatus, endangered (e.g. Hippocampus erectus and overexploited (e.g. Lutjanus analis species. Twenty one species are present in the IUCN’s list, twelve in the IBAMA’s list and four in the local list. All elasmobranchii recorded here are considered threatened species, like the brazilian guitarfish (Rhinobatos horkelii, which appears in three red lists, and it is considered critically endangered. All species of Epinephelidae are mentioned in the list of risk categories of the IUCN and five are cited as overexploited or threatened with overexploitation by IBAMA. Among Epinephelidae, the goliath grouper (Epinephelus itajara, is present in all red lists and has specific protection rules in Brazil. The gathered information will allow to take appropriate conservation measures, such as the establishment of marine protected areas, monitoring of fishing

  5. Identifying organic nitrogen compounds in Rocky Mountain National Park aerosols

    Science.gov (United States)

    Beem, K. B.; Desyaterik, Y.; Ozel, M. Z.; Hamilton, J. F.; Collett, J. L.

    2010-12-01

    Nitrogen deposition is an important issue in Rocky Mountain National Park (RMNP). While inorganic nitrogen contributions to the ecosystems in this area have been studied, the sources of organic nitrogen are still largely unknown. To better understand the potential sources of organic nitrogen, filter samples were collected and analyzed for organic nitrogen species. Samples were collected in RMNP using a Thermo Fisher Scientific TSP (total suspended particulate) high-volume sampler with a PM2.5 impactor plate from April - November of 2008. The samples presented the opportunity to compare two different methods for identification of individual organic nitrogen species. The first type of analysis was performed with a comprehensive two dimensional gas chromatography (GCxGC) system using a nitrogen chemiluminescence detector (NCD). The filter samples were spiked with propanil in dichloromethane to use as an internal standard and were then extracted in water followed by solid phase extraction. The GCxGC system was comprised of a volatility based separation (DB5 column) followed by a polarity based separation (RXI-17 column). A NCD was used to specifically detect nitrogen compounds and remove the complex background matrix. Individual standards were used to identify peaks by comparing retention times. This method has the added benefit of an equimolar response for nitrogen so only a single calibration is needed for all species. In the second analysis, a portion of the same filter samples were extracted in DI water and analyzed with liquid chromatography coupled with mass spectroscopy (LC/MS). The separation was performed using a C18 column and a water-methanol gradient elution. Electrospray ionization into a time of flight mass spectrometer was used for detection. High accuracy mass measurement allowed unambiguous assignments of elemental composition of resulting ions. Positive and negative polarities were used since amines tend to show up in positive mode and nitrates in

  6. Thermotolerant Yeast Strains Adapted by Laboratory Evolution Show Trade-Off at Ancestral Temperatures and Preadaptation to Other Stresses.

    Science.gov (United States)

    Caspeta, Luis; Nielsen, Jens

    2015-07-21

    A major challenge for the production of ethanol from biomass-derived feedstocks is to develop yeasts that can sustain growth under the variety of inhibitory conditions present in the production process, e.g., high osmolality, high ethanol titers, and/or elevated temperatures (≥ 40 °C). Using adaptive laboratory evolution, we previously isolated seven Saccharomyces cerevisiae strains with improved growth at 40 °C. Here, we show that genetic adaptations to high temperature caused a growth trade-off at ancestral temperatures, reduced cellular functions, and improved tolerance of other stresses. Thermotolerant yeast strains showed horizontal displacement of their thermal reaction norms to higher temperatures. Hence, their optimal and maximum growth temperatures increased by about 3 °C, whereas they showed a growth trade-off at temperatures below 34 °C. Computational analysis of the physical properties of proteins showed that the lethal temperature for yeast is around 49 °C, as a large fraction of the yeast proteins denature above this temperature. Our analysis also indicated that the number of functions involved in controlling the growth rate decreased in the thermotolerant strains compared with the number in the ancestral strain. The latter is an advantageous attribute for acquiring thermotolerance and correlates with the reduction of yeast functions associated with loss of respiration capacity. This trait caused glycerol overproduction that was associated with the growth trade-off at ancestral temperatures. In combination with altered sterol composition of cellular membranes, glycerol overproduction was also associated with yeast osmotolerance and improved tolerance of high concentrations of glucose and ethanol. Our study shows that thermal adaptation of yeast is suitable for improving yeast resistance to inhibitory conditions found in industrial ethanol production processes. Yeast thermotolerance can significantly reduce the production costs of biomass

  7. Breadth of T cell responses after immunization with adenovirus vectors encoding ancestral antigens or polyvalent papillomavirus antigens

    DEFF Research Database (Denmark)

    Ragonnaud, Emeline; Pedersen, Anders Gorm; Holst, Peter Johannes

    2017-01-01

    to the other PV proteins. The PV sequences were fused to a T cell adjuvant, the murine invariant chain and encoded in a recombinant adenoviral vector which was administered to naïve outbred mice. By measuring T cell responses induced by these different vaccines and towards peptide pools representing 3...... circulating strains and a putative ancestor of oncogenic HPVs, we showed that the ancestral vaccine antigen has to be approximately 90% identical to the circulating PVs before a marked drop of ~90% mean CD8+ T cell responses ensues. Interestingly, the combination of two or three type-specific PV vaccines did...

  8. The Odyssey of the Ancestral Escherich Strain through Culture Collections: an Example of Allopatric Diversification.

    Science.gov (United States)

    Desroches, M; Royer, G; Roche, D; Mercier-Darty, M; Vallenet, D; Médigue, C; Bastard, K; Rodriguez, C; Clermont, O; Denamur, E; Decousser, J-W

    2018-01-01

    More than a century ago, Theodor Escherich isolated the bacterium that was to become Escherichia coli , one of the most studied organisms. Not long after, the strain began an odyssey and landed in many laboratories across the world. As laboratory culture conditions could be responsible for major changes in bacterial strains, we conducted a genome analysis of isolates of this emblematic strain from different culture collections (England, France, the United States, Germany). Strikingly, many discrepancies between the isolates were observed, as revealed by multilocus sequence typing (MLST), the presence of virulence-associated genes, core genome MLST, and single nucleotide polymorphism/indel analyses. These differences are correlated with the phylogeographic history of the strain and were due to an unprecedented number of mutations in coding DNA repair functions such as mismatch repair (MutL) and oxidized guanine nucleotide pool cleaning (MutT), conferring a specific mutational spectrum and leading to a mutator phenotype. The mutator phenotype was probably acquired during subculturing and corresponded to second-order selection. Furthermore, all of the isolates exhibited hypersusceptibility to antibiotics due to mutations in efflux pump- and porin-encoding genes, as well as a specific mutation in the sigma factor-encoding gene rpoS . These defects reflect a self-preservation and nutritional competence tradeoff allowing survival under the starvation conditions imposed by storage. From a clinical point of view, dealing with such mutator strains can lead microbiologists to draw false conclusions about isolate relatedness and may impact therapeutic effectiveness. IMPORTANCE Mutator phenotypes have been described in laboratory-evolved bacteria, as well as in natural isolates. Several genes can be impacted, each of them being associated with a typical mutational spectrum. By studying one of the oldest strains available, the ancestral Escherich strain, we were able to

  9. Evidence for an Ancestral Association of Human Coronavirus 229E with Bats.

    Science.gov (United States)

    Corman, Victor Max; Baldwin, Heather J; Tateno, Adriana Fumie; Zerbinati, Rodrigo Melim; Annan, Augustina; Owusu, Michael; Nkrumah, Evans Ewald; Maganga, Gael Darren; Oppong, Samuel; Adu-Sarkodie, Yaw; Vallo, Peter; da Silva Filho, Luiz Vicente Ribeiro Ferreira; Leroy, Eric M; Thiel, Volker; van der Hoek, Lia; Poon, Leo L M; Tschapka, Marco; Drosten, Christian; Drexler, Jan Felix

    2015-12-01

    We previously showed that close relatives of human coronavirus 229E (HCoV-229E) exist in African bats. The small sample and limited genomic characterizations have prevented further analyses so far. Here, we tested 2,087 fecal specimens from 11 bat species sampled in Ghana for HCoV-229E-related viruses by reverse transcription-PCR (RT-PCR). Only hipposiderid bats tested positive. To compare the genetic diversity of bat viruses and HCoV-229E, we tested historical isolates and diagnostic specimens sampled globally over 10 years. Bat viruses were 5- and 6-fold more diversified than HCoV-229E in the RNA-dependent RNA polymerase (RdRp) and spike genes. In phylogenetic analyses, HCoV-229E strains were monophyletic and not intermixed with animal viruses. Bat viruses formed three large clades in close and more distant sister relationships. A recently described 229E-related alpaca virus occupied an intermediate phylogenetic position between bat and human viruses. According to taxonomic criteria, human, alpaca, and bat viruses form a single CoV species showing evidence for multiple recombination events. HCoV-229E and the alpaca virus showed a major deletion in the spike S1 region compared to all bat viruses. Analyses of four full genomes from 229E-related bat CoVs revealed an eighth open reading frame (ORF8) located at the genomic 3' end. ORF8 also existed in the 229E-related alpaca virus. Reanalysis of HCoV-229E sequences showed a conserved transcription regulatory sequence preceding remnants of this ORF, suggesting its loss after acquisition of a 229E-related CoV by humans. These data suggested an evolutionary origin of 229E-related CoVs in hipposiderid bats, hypothetically with camelids as intermediate hosts preceding the establishment of HCoV-229E. The ancestral origins of major human coronaviruses (HCoVs) likely involve bat hosts. Here, we provide conclusive genetic evidence for an evolutionary origin of the common cold virus HCoV-229E in hipposiderid bats by analyzing a

  10. Development of monitoring protocols to detect change in rocky intertidal communities of Glacier Bay National Park and Preserve

    Science.gov (United States)

    Irvine, Gail V.

    2010-01-01

    Glacier Bay National Park and Preserve in southeastern Alaska includes extensive coastlines representing a major proportion of all coastlines held by the National Park Service. The marine plants and invertebrates that occupy intertidal shores form highly productive communities that are ecologically important to a number of vertebrate and invertebrate consumers and that are vulnerable to human disturbances. To better understand these communities and their sensitivity, it is important to obtain information on species abundances over space and time. During field studies from 1997 to 2001, I investigated probability-based rocky intertidal monitoring designs that allow inference of results to similar habitat within the bay and that reduce bias. Aerial surveys of a subset of intertidal habitat indicated that the original target habitat of bedrock-dominated sites with slope less than or equal to 30 degrees was rare. This finding illustrated the value of probability-based surveys and led to a shift in the target habitat type to more mixed rocky habitat with steeper slopes. Subsequently, I investigated different sampling methods and strategies for their relative power to detect changes in the abundances of the predominant sessile intertidal taxa: barnacles -Balanomorpha, the mussel Mytilus trossulus and the rockweed Fucus distichus subsp. evanescens. I found that lower-intensity sampling of 25 randomly selected sites (= coarse-grained sampling) provided a greater ability to detect changes in the abundances of these taxa than did more intensive sampling of 6 sites (= fine-grained sampling). Because of its greater power, the coarse-grained sampling scheme was adopted in subsequent years. This report provides detailed analyses of the 4 years of data and evaluates the relative effect of different sampling attributes and management-set parameters on the ability of the sampling to detect changes in the abundances of these taxa. The intent was to provide managers with information

  11. Greater happiness for a greater number: Is that possible in Austria?

    NARCIS (Netherlands)

    R. Veenhoven (Ruut)

    2011-01-01

    textabstractWhat is the final goal of public policy? Jeremy Bentham (1789) would say: greater happiness for a greater number. He thought of happiness as subjective enjoyment of life; in his words as “the sum of pleasures and pains”. In his time the happiness of the great number could not be measured

  12. Greater happiness for a greater number: Is that possible? If so how? (Arabic)

    NARCIS (Netherlands)

    R. Veenhoven (Ruut); E. Samuel (Emad)

    2012-01-01

    textabstractWhat is the final goal of public policy? Jeremy Bentham (1789) would say: greater happiness for a greater number. He thought of happiness as subjective enjoyment of life; in his words as “the sum of pleasures and pains”. In his time, the happiness of the great number could not be

  13. Greater happiness for a greater number: Is that possible in Germany?

    NARCIS (Netherlands)

    R. Veenhoven (Ruut)

    2009-01-01

    textabstractWhat is the final goal of public policy? Jeremy Bentham (1789) would say: greater happiness for a greater number. He thought of happiness as subjective enjoyment of life; in his words as “the sum of pleasures and pains”. In his time the Happiness of the great number could not be measured

  14. Search for greater stability in nuclear regulation

    International Nuclear Information System (INIS)

    Asselstine, J.K.

    1985-01-01

    The need for greater stability in nuclear regulation is discussed. Two possible approaches for dealing with the problems of new and rapidly changing regulatory requirements are discussed. The first approach relies on the more traditional licensing reform initiatives that have been considered off and on for the past decade. The second approach considers a new regulator philosophy aimed at the root causes of the proliferation of new safety requirements that have been imposed in recent years. For the past few years, the concepts of deregulation and regulatory reform have been in fashion in Washington, and the commercial nuclear power program has not remained unaffected. Many look to these concepts to provide greater stability in the regulatory program. The NRC, the nuclear industry and the administration have all been avidly pursuing regulatory reform initiatives, which take the form of both legislative and administrative proposals. Many of these proposals look to the future, and, if adopted, would have little impact on currently operating nuclear power plants or plants now under construction

  15. Greater Sudbury fuel efficient driving handbook

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2009-12-15

    Reducing the amount of fuel that people use for personal driving saves money, improves local air quality, and reduces personal contributions to climate change. This handbook was developed to be used as a tool for a fuel efficient driving pilot program in Greater Sudbury in 2009-2010. Specifically, the purpose of the handbook was to provide greater Sudbury drivers with information on how to drive and maintain their personal vehicles in order to maximize fuel efficiency. The handbook also provides tips for purchasing fuel efficient vehicles. It outlines the benefits of fuel maximization, with particular reference to reducing contributions to climate change; reducing emissions of air pollutants; safe driving; and money savings. Some tips for efficient driving are to avoid aggressive driving; use cruise control; plan trips; and remove excess weight. Tips for efficient winter driving are to avoid idling to warm up the engine; use a block heater; remove snow and ice; use snow tires; and check tire pressure. The importance of car maintenance and tire pressure was emphasized. The handbook also explains how fuel consumption ratings are developed by vehicle manufacturers. refs., figs.

  16. Women at greater risk of HIV infection.

    Science.gov (United States)

    Mahathir, M

    1997-04-01

    Although many people believe that mainly men get infected with HIV/AIDS, women are actually getting infected at a faster rate than men, especially in developing countries, and suffer more from the adverse impact of AIDS. As of mid-1996, the Joint UN Program on AIDS estimated that more than 10 million of the 25 million adults infected with HIV since the beginning of the epidemic are women. The proportion of HIV-positive women is growing, with almost half of the 7500 new infections daily occurring among women. 90% of HIV-positive women live in a developing country. In Asia-Pacific, 1.4 million women have been infected with HIV out of an estimated total 3.08 million adults from the late 1970s until late 1994. Biologically, women are more vulnerable than men to infection because of the greater mucus area exposed to HIV during penile penetration. Women under age 17 years are at even greater risk because they have an underdeveloped cervix and low vaginal mucus production. Concurrent sexually transmitted diseases increase the risk of HIV transmission. Women's risk is also related to their exposure to gender inequalities in society. The social and economic pressures of poverty exacerbate women's risk. Prevention programs are discussed.

  17. Survival relative to new and ancestral host plants, phytoplasma infection, and genetic constitution in host races of a polyphagous insect disease vector

    Science.gov (United States)

    Maixner, Michael; Albert, Andreas; Johannesen, Jes

    2014-01-01

    Dissemination of vectorborne diseases depends strongly on the vector's host range and the pathogen's reservoir range. Because vectors interact with pathogens, the direction and strength of a vector's host shift is vital for understanding epidemiology and is embedded in the framework of ecological specialization. This study investigates survival in host-race evolution of a polyphagous insect disease vector, Hyalesthes obsoletus, whether survival is related to the direction of the host shift (from field bindweed to stinging nettle), the interaction with plant-specific strains of obligate vectored pathogens/symbionts (stolbur phytoplasma), and whether survival is related to genetic differentiation between the host races. We used a twice repeated, identical nested experimental design to study survival of the vector on alternative hosts and relative to infection status. Survival was tested with Kaplan–Meier analyses, while genetic differentiation between vector populations was quantified with microsatellite allele frequencies. We found significant direct effects of host plant (reduced survival on wrong hosts) and sex (males survive longer than females) in both host races and relative effects of host (nettle animals more affected than bindweed animals) and sex (males more affected than females). Survival of bindweed animals was significantly higher on symptomatic than nonsymptomatic field bindweed, but in the second experiment only. Infection potentially had a positive effect on survival in nettle animals but due to low infection rates the results remain suggestive. Genetic differentiation was not related to survival. Greater negative plant-transfer effect but no negative effect of stolbur in the derived host race suggests preadaptation to the new pathogen/symbiont strain before strong diversifying selection during the specialization process. Physiological maladaptation or failure to accept the ancestral plant will have similar consequences, namely positive assortative

  18. Amplification of an ancestral mammalian L1 family of long interspersed repeated DNA occurred just before the murine radiation

    International Nuclear Information System (INIS)

    Pascale, E.; Valle, E.; Furano, A.V.

    1990-01-01

    Each mammalian genus examined so far contains 50,000-100,000 members of an L1 (LINE 1) family of long interspersed repeated DNA elements. Current knowledge on the evolution of L1 families presents a paradox because, although L1 families have been in mammalian genomes since before the mammalian radiation ∼80 million years ago, most members of the L1 families are only a few million years old. Accordingly it has been suggested either that the extensive amplification that characterizes present-day L1 families did not occur in the past or that old members were removed as new one were generated. However, the authors show here that an ancestral rodent L1 family was extensively amplified ∼10 million years ago and that the relics of this amplification have persisted in modern murine genomes. This amplification occurred just before the divergence of modern murine genera from their common ancestor and identifies the murine node in the lineage of modern muroid rodents The results suggest that repeated amplification of L1 elements is a feature of the evaluation of mammalian genomes and that ancestral amplification events could provide a useful tool for determining mammalian lineages

  19. The ghost of Afrikaner identity in Ancestral voices, Leap year and The long silence of Mario Salviati (Etienne van Heerden

    Directory of Open Access Journals (Sweden)

    Mariëtte van Graan

    2017-04-01

    Full Text Available Ghost characters are a characteristic of the novels of Etienne van Heerden, but little research has been done concerning the nature and function of these ghost characters. In this article I discuss Van Heerden’s use of ghost characters diachronically with reference to the novels Ancestral voices (1986, Leap year (1993 and The long silence of Mario Salviati (2000. In order to clarify the nature of these ghosts, I use the so-called science of the paranormal as a framework. The ghosts in the three novels will be classified accordingly, and then discussed within the context of the novels in which they appear. In this way, I shall show how the ghost characters in these novels can be read as a constantly changing embodiment of Afrikaner identity (a central theme in Van Heerden’s oeuvre. Van Heerden’s Afrikaner changes with the times: in Ancestral voices the ghost characters form a collective that represents a fragmented image of the stereotypical, archaic male Afrikaner identity; in Leap year a liminal character is written in a liminal time to embody a liminal Afrikaner identity; and in The long silence of Mario Salviati Van Heerden moves away from the exclusive Afrikaner identity to a broader South African identity by using ghost characters from very different backgrounds and origins. In conclusion I shall compare these identities and the historical contexts of these novels in order to show the function of Van Heerden’s ghost characters as constant rewritings of South African identities.

  20. Geographic patterns of genetic variation and population structure in Pinus aristata, Rocky Mountain bristlecone pine

    Science.gov (United States)

    Anna W. Schoettle; Betsy A. Goodrich; Valerie Hipkins; Christopher Richards; Julie Kray

    2012-01-01

    Pinus aristata Engelm., Rocky Mountain bristlecone pine, has a narrow core geographic and elevational distribution, occurs in disjunct populations, and is threatened by rapid climate change, white pine blister rust, and bark beetles. Knowledge of genetic diversity and population structure will help guide gene conservation strategies for this species. Sixteen sites...

  1. 76 FR 17439 - Nonessential Experimental Populations of Gray Wolves in the Northern Rocky Mountains; Lethal Take...

    Science.gov (United States)

    2011-03-29

    ... nonessential experimental population areas for the gray wolf under section 10(j) of the ESA: the Yellowstone...-0000-C3] Nonessential Experimental Populations of Gray Wolves in the Northern Rocky Mountains; Lethal Take of Wolves in the West Fork Elk Management Unit of Montana; Draft Environmental Assessment AGENCY...

  2. 76 FR 7875 - Nonessential Experimental Populations of Gray Wolves in the Northern Rocky Mountains; Lethal Take...

    Science.gov (United States)

    2011-02-11

    ... the central Idaho and Yellowstone area nonessential experimental populations of gray wolves in the...-0000-C3] Nonessential Experimental Populations of Gray Wolves in the Northern Rocky Mountains; Lethal Take of Wolves in the Lolo Elk Management Zone of Idaho; Draft Environmental Assessment AGENCY: Fish...

  3. Deposition of reactive nitrogen during the Rocky Mountain Airborne Nitrogen and Sulfur (RoMANS) study

    International Nuclear Information System (INIS)

    Beem, Katherine B.; Raja, Suresh; Schwandner, Florian M.; Taylor, Courtney; Lee, Taehyoung; Sullivan, Amy P.; Carrico, Christian M.; McMeeking, Gavin R.; Day, Derek; Levin, Ezra; Hand, Jenny; Kreidenweis, Sonia M.; Schichtel, Bret; Malm, William C.; Collett, Jeffrey L.

    2010-01-01

    Increases in reactive nitrogen deposition are a growing concern in the U.S. Rocky Mountain west. The Rocky Mountain Airborne Nitrogen and Sulfur (RoMANS) study was designed to improve understanding of the species and pathways that contribute to nitrogen deposition in Rocky Mountain National Park (RMNP). During two 5-week field campaigns in spring and summer of 2006, the largest contributor to reactive nitrogen deposition in RMNP was found to be wet deposition of ammonium (34% spring and summer), followed by wet deposition of nitrate (24% spring, 28% summer). The third and fourth most important reactive nitrogen deposition pathways were found to be wet deposition of organic nitrogen (17%, 12%) and dry deposition of ammonia (14%, 16%), neither of which is routinely measured by air quality/deposition networks operating in the region. Total reactive nitrogen deposition during the spring campaign was determined to be 0.45 kg ha -1 and more than doubled to 0.95 kg ha -1 during the summer campaign. - The reactive nitrogen deposition budget for Rocky Mountain National Park.

  4. Evaluating the sufficiency of protected lands for maintaining wildlife population connectivity in the northern Rocky Mountains

    Science.gov (United States)

    Samuel A. Cushman; Erin L. Landguth; Curtis H. Flather

    2012-01-01

    Aim: The goal of this study was to evaluate the sufficiency of the network of protected lands in the U.S. northern Rocky Mountains in providing protection for habitat connectivity for 105 hypothetical organisms. A large proportion of the landscape...

  5. Grizzly bears as a filter for human use management in Canadian Rocky Mountain national parks

    Science.gov (United States)

    Derek Petersen

    2000-01-01

    Canadian National Parks within the Rocky Mountains recognize that human use must be managed if the integrity and health of the ecosystems are to be preserved. Parks Canada is being challenged to ensure that these management actions are based on credible scientific principles and understanding. Grizzly bears provide one of only a few ecological tools that can be used to...

  6. Radiological/Health physics program assessement at Rocky Flats, the process

    International Nuclear Information System (INIS)

    Psomas, P.O.

    1996-01-01

    The Department of Energy, Rocky Flats Office, Safety and Health Group, Health Physics Team (HPT) is responsible for oversight of the Radiation Protection and Health Physics Program (RPHP) of the Integrating Management Contractor (IMC), Kaiser-Hill (K-H) operations at the Rocky Flats Environmental Technology Site (RFETS). As of 1 January 1996 the Rocky Flats Plant employed 300 DOE and 4,300 contractor personnel (K-H and their subcontractors). WSI is a subcontractor and provides plant security. To accomplish the RPHP program oversight HPT personnel developed a systematic methodology for performing a functional RPHP Assessment. The initial process included development of a flow diagram identifying all programmatic elements and assessment criteria documents. Formulation of plans for conducting interviews and performance of assessments constituted the second major effort. The generation of assessment reports was the final step, based on the results of this process. This assessment will be a 6 person-year effort, over the next three years. This process is the most comprehensive assessment of any Radiation Protection and Health Physics (RPHP) Program ever performed at Rocky Flats. The results of these efforts will establish a baseline for future RPHP Program assessments at RFETS. This methodology has been well-received by contractor personnel and creates no Privacy Act violations or other misunderstandings

  7. Here today, here tomorrow: Managing forests for fisher habitat in the Northern Rockies

    Science.gov (United States)

    Sue Miller; Michael Schwartz; Lucretia E. Olson

    2016-01-01

    The fisher is a unique member of the weasel family and a sensitive species in the northern Rockies. They were almost extirpated by trapping in the early twentieth century, but these animals (a mix between a native and introduced population) now inhabit a swath of mesic coniferous forests in Idaho and Montana. Forest managers need information on fisher distribution and...

  8. Effects of fuel treatments on carbon-disturbance relationships in forests of the northern Rocky Mountains

    Science.gov (United States)

    Elizabeth Reinhardt; Lisa Holsinger

    2010-01-01

    Fuel treatments alter conditions in forested stands at the time of the treatment and subsequently. Fuel treatments reduce on-site carbon and also change the fire potential and expected outcome of future wildfires, including their carbon emissions. We simulated effects of fuel treatments on 140 stands representing seven major habitat type groups of the northern Rocky...

  9. High organic carbon export precludes eutrophication responses in experimental rocky shore communities

    NARCIS (Netherlands)

    Barrón, C.; Marbu, N.; Duarte, C.M.; Pedersen, M.F.; Lindblad, C.; Kersting, K.; Moy, F.; Bokn, T.

    2003-01-01

    We studied the effect of nutrient inputs on the carbon (C) budget of rocky shore communities using a set of eight large experimental mesocosms. The mesocosms received a range of inorganic nitrogen (N) and phosphorus (P) additions, at an N:P ratio of 16. These additions were designed to elevate the

  10. [Rocky Mountain regional low-level waste compact development and establishment of disposals

    International Nuclear Information System (INIS)

    1986-01-01

    This Compact Issue Study was intended to determine if state institutions in the Rocky Mountain region could reduce low-level radioactive waste shipping and disposal costs through jointly shipping their low-level radioactive wastes. Public institutions in the state of Colorado were used as a test case for this study

  11. Vitrification of plutonium at Rocky Flats the argument for a pilot plant

    Energy Technology Data Exchange (ETDEWEB)

    Moore, L. [Rocky Mountain Peace Center, Boulder, CO (United States)

    1996-05-01

    Current plans for stabilizing and storing the plutonium at Rocky Flats Plant fail to put the material in a form suitable for disposition and resistant to proliferation. Vitrification should be considered as an alternate technology. The vitrification should begin with a small-scale pilot plant.

  12. Climate vulnerability of native cold-water salmonids in the Northern Rockies Region [Chapter 5

    Science.gov (United States)

    Michael K. Young; Daniel J. Isaak; Scott Spaulding; Cameron A. Thomas; Scott A. Barndt; Matthew C. Groce; Dona Horan; David E. Nagel

    2018-01-01

    During the 21st century, climate change is expected to alter aquatic habitats throughout the Northern Rocky Mountains, intermountain basins, and western Great Plains. Particularly in montane watersheds, direct changes are likely to include warmer water temperatures, earlier snowmelt-driven runoff, earlier declines to summer baseflow, downhill movement of perennial...

  13. Book Review :The Essential Guide to Rocky Mountain Mushrooms by Habitat

    Science.gov (United States)

    A mushroom guide book, 'The Essential Guide to Rocky Mountain Mushrooms by Habitat' by Cathy L. Cripps, Vera S. Evenson, and Michael Kou (University of Illinois Press, 260 pages), is reviewed in non-technical fashion from the standpoints of format, comprehensiveness, and clarity. Postive features (...

  14. Why replication is important in landscape genetics: American black bear in the Rocky Mountains

    Science.gov (United States)

    R. A. Short Bull; Samuel Cushman; R. Mace; T. Chilton; K. C. Kendall; E. L. Landguth; Michael Schwartz; Kevin McKelvey; Fred W. Allendorf; G. Luikart

    2011-01-01

    We investigated how landscape features influence gene flow of black bears by testing the relative support for 36 alternative landscape resistance hypotheses, including isolation by distance (IBD) in each of 12 study areas in the north central U.S. Rocky Mountains. The study areas all contained the same basic elements, but differed in extent of forest fragmentation,...

  15. Patterns of resistance to Cronartium ribicola in Pinus aristata, Rocky Mountain bristlecone pine

    Science.gov (United States)

    A. W. Schoettle; R. A. Sniezko; A. Kegley; R. Danchok; K. S. Burns

    2012-01-01

    The core distribution of Rocky Mountain bristlecone pine, Pinus aristata Engelm., extends from central Colorado into northern New Mexico, with a disjunct population on the San Francisco Peaks in northern Arizona. Populations are primarily at high elevations and often define the alpine treeline; however, the species can also be found in open mixed conifer stands with...

  16. Faunal characteristics of the Southern Rocky Mountains of New Mexico: implications for biodiversity analysis and assessment

    Science.gov (United States)

    Rosamonde R. Cook; Curtis H. Flather; Kenneth R. Wilson

    2000-01-01

    To define the faunal context within which local and regional resource management decisions are made, conservation of biological diversity requires an understanding of regional species occurrence patterns. Our study focused on the Southern Rocky Mountains of New Mexico and included the San Juan, the Sangre de Cristo, and the Jemez Mountains. Across this region, we...

  17. A Long, Winding (and Rocky) Road to Environmental Education for Sustainability in 2006

    Science.gov (United States)

    Gough, Annette

    2006-01-01

    This article charts the history of environmental education over four decades--from the 1960s to 2006--as a rocky road of determined chocolate with the possibilities of rocks (nuts) and easy passage (marshmallow). There were distractions such as suggestions of changing names and new directions (add fruit?) along the way but the road has continued…

  18. Movements and habitat use of rocky mountain elk and mule deer.

    Science.gov (United States)

    Alan A. Ager; Haiganoush K. Preisler; Bruce K. Johnson; John G. Kie

    2004-01-01

    Understanding how ungulates use large landscapes to meet their daily needs for food, security and other resources is critical to wildlife management and conservation practices (Johnson et al. 2002). For ungulates like Rocky Mountain elk (Gems elaphui) and mule deer (Odocoileus hemionus), landscapes are a mosaic of different...

  19. Effects of climate change on forest vegetation in the northern Rockies [Chapter 5

    Science.gov (United States)

    Robert E. Keane; Mary Frances Mahalovich; Barry L. Bollenbacher; Mary E. Manning; Rachel A. Loehman; Terrie B. Jain; Lisa M. Holsinger; Andrew J. Larson

    2018-01-01

    Increasing air temperature, through its influence on soil moisture, is expected to cause gradual changes in the abundance and distribution of tree, shrub, and grass species throughout the Northern Rockies, with drought tolerant species becoming more competitive. The earliest changes will be at ecotones between lifeforms (e.g., upper and lower treelines). Ecological...

  20. Biochar effects on the nursery propagation of 4 northern Rocky Mountain native plant species

    Science.gov (United States)

    Clarice P. Matt; Christopher R. Keyes; R. Kasten Dumroese

    2018-01-01

    Biochar has emerged as a promising potential amendment of soilless nursery media for plant propagation. With this greenhouse study we used biochar to displace standard soilless nursery media at 4 rates (0, 15, 30, and 45% [v:v]) and then examined media chemistry, irrigation frequency, and the growth of 4 northern Rocky Mountain native plant species: Clarkia pulchella...

  1. 78 FR 48183 - Rocky Mountain Arsenal National Wildlife Refuge, Commerce City, CO; Comprehensive Conservation...

    Science.gov (United States)

    2013-08-07

    ... Plan and Environmental Impact Statement; Two Ponds National Wildlife Refuge, Arvada, CO; Comprehensive... prepare a Comprehensive Conservation Plan (CCP) and an Environmental Impact Statement (EIS) for the Rocky..., including more than 120 species of birds, coyote and red fox, muskrat, raccoon, and beaver, deer, several...

  2. Carbon pools along headwater streams with differing valley geometry in Rocky Mountain National Park, Colorado (Abstract)

    Science.gov (United States)

    Kathleen A. Dwire; Ellen E. Wohl; Nicholas A. Sutfin; Roberto A. Bazan; Lina Polvi-Pilgrim

    2012-01-01

    Headwaters are known to be important in the global carbon cycle, yet few studies have investigated carbon (C) pools along stream-riparian corridors. To better understand the spatial distribution of C storage in headwater fluvial networks, we estimated above- and below-ground C pools in 100-m-long reaches in six different valley types in Rocky Mountain National Park,...

  3. Low-level radioactive waste facility siting in the Rocky Mountain compact region

    International Nuclear Information System (INIS)

    Whitman, M.

    1983-09-01

    The puprose of the Rocky Mountain Low-Level Radioactive Waste Compact is to develop a regional management system for low-level waste (LLW) generated in the six states eligible for membership: Arizona, Colorado, Nevada, New Mexico, Utah and Wyoming. Under the terms of the compact, any party state generating at least 20% of the region's waste becomes responsible for hosting a regional LLW management facility. However, the compact prescribes no system which the host state must follow to develop a facility, but rather calls on the state to fulfill its responsibility through reliance on its own laws and regulations. Few of the Rocky Mountain compact states have legislation dealing specifically with LLW facility siting. Authority for LLW facility siting is usually obtained from radiation control statutes and solid or hazardous waste statutes. A state-by-state analysis of the siting authorities of each of the Rock Mountain compact states as they pertain to LLW disposal facility siting is presented. Siting authority for LLW disposal facilities in the Rocky Mountain compact region runs from no authority, as in Wyoming, to general statutory authority for which regulations would have to be promulgated, as in Arizona and Nevada, to more detailed siting laws, as in Colorado and New Mexico. Barring an amendment to, or different interpretation of, the Utah Hazardous Waste Facility Siting Act, none of the Rocky Mountain States' LLW facility siting authorities preempt local veto authorities

  4. Outbreak of Rocky Mountain spotted fever in Córdoba, Colombia

    Directory of Open Access Journals (Sweden)

    Marylin Hidalgo

    2011-02-01

    Full Text Available Rocky Mountain spotted fever (RMSF is a tick-borne disease caused by the obligate intracellular bacterium Rickettsia rickettsii. Although RMSF was first reported in Colombia in 1937, it remains a neglected disease. Herein, we describe the investigation of a large cluster of cases of spotted fever rickettsiosis in a new area of Colombia.

  5. [Complications and cause of death in mexican children with rocky mountain spotted fever].

    Science.gov (United States)

    Martínez-Medina, Miguel Ángel; Rascón-Alcantar, Adela

    Rocky Mountain spotted fever is a life threatening disease caused by Rickettsia rickettsia, characterized by multisystem involvement. We studied 19 dead children with Rocky Mountain spotted fever. All children who were suspected of having rickettsial infections were defined as having Rocky Mountain spotted fever by serology test and clinical features. Through the analysis of each case, we identified the clinical profile and complications associated to the death of a patient. In nine (69.2%) of 13 cases that died in the first three days of admission, the associated condition was septic shock. Others complications included respiratory distress causes by non-cardiogenic pulmonary edema, renal impairment, and multiple organ damage. The main cause of death in this study was septic shock. The fatality rate from Rocky Mountain spotted fever can be related to the severity of the infection, delay in diagnosis, and delay in initiation of antibiotic therapy. Pulmonary edema and cerebral edema can be usually precipitated by administration of excess intravenous fluids.

  6. Studies on ’Macaca mulatta’ Infected with Rocky Mountain Spotted Fever

    Science.gov (United States)

    1976-09-10

    Mountain spotted fever (RMSF) rickettsiae. The LD50 in monkeys of the yolk-sac-grown seed stock was 10 to the 1.35th power plaque-forming units. Blood...acid glycoprotein, haptoglobin and albumin) were measured during a study in 16 male rhesus monkeys to determine the median lethal dose (LD50) of Rocky

  7. New assay of protective activity of Rocky Mountain spotted fever vaccines.

    Science.gov (United States)

    Anacker, R L; Smith, R F; Mann, R E; Hamilton, M A

    1976-01-01

    Areas under the fever curves of guinea pigs inoculated with Rocky Mountain spotted fever vaccine over a restricted dose range and infected with a standardized dose of Rickettsia rickettsii varied linearly with log10 dose of vaccine. A calculator was programmed to plot fever curves and calculate the vaccine dose that reduced the fever of infected animals by 50%. PMID:823177

  8. Outbreak of Rocky Mountain spotted fever in Córdoba, Colombia.

    Science.gov (United States)

    Hidalgo, Marylin; Miranda, Jorge; Heredia, Damaris; Zambrano, Pilar; Vesga, Juan Fernando; Lizarazo, Diana; Mattar, Salim; Valbuena, Gustavo

    2011-02-01

    Rocky Mountain spotted fever (RMSF) is a tick-borne disease caused by the obligate intracellular bacterium Rickettsia rickettsii. Although RMSF was first reported in Colombia in 1937, it remains a neglected disease. Herein, we describe the investigation of a large cluster of cases of spotted fever rickettsiosis in a new area of Colombia.

  9. Comparative risk analysis for the Rocky Flats Plant integrated project planning

    International Nuclear Information System (INIS)

    Jones, M.E.; Shain, D.I.

    1994-01-01

    The Rocky Flats Plant is developing, with active stakeholder participation, a comprehensive planning strategy that will support transition of the Rocky Flats Plant from a nuclear weapons production facility to site cleanup and final disposition. Consideration of the interrelated nature of sitewide problems, such as material movement and disposition, facility and land use endstates, costs, relative risks to workers and the public, and waste disposition are all needed. Comparative Risk Analysis employs both incremental risk and cumulative risk evaluations to compare risks from postulated options or endstates and is an analytical tool for the Rocky Flats Plant Integrated Project Planning which can assist a decision-maker in evaluating relative risks among proposed remediation activity. However, risks from all of the remediation activities, decontamination and decommissioning activities, and normal ongoing operations are imposed upon the Rocky Flats workers, the surrounding public, and the environment. Comparative Risk Analysis will provide risk information, both human health and ecological, to aid in reducing unnecessary resource and monetary expenditures by focusing these resources on the largest risks first. Comparative Risk Analysis has been developed to aggregate various incremental risk estimates to develop a site cumulative risk estimate. The Comparative Risk Analysis methodology Group, consisting of community stakeholders, was established. Early stakeholder involvement in the risk analysis methodology development provides an opportunity for stakeholders to influence the risk information delivered to a decision-maker. This paper discusses development of the Comparative Risk Analysis methodology, stakeholder participation and lessons learned from these challenges

  10. William L. Baker: Fire ecology in Rocky Mountain landscapes [book review

    Science.gov (United States)

    Daniel. Yaussy

    2010-01-01

    Every so often, we need something to make us question our beliefs and views of the natural order of things, to open our minds to different versions of reality so that we become better informed and open to new avenues of thought. The author comes across as slightly antagonistic in his attempt to set the record straight concerning fires in the Rocky Mountains.

  11. A preliminary survey of the cichlid fishes of rocky habitats in Lake ...

    African Journals Online (AJOL)

    given on some of the other rocky shore fishes particularly in the genus Cyrtocara. ... biology, numerical abundance and distribution. Indeed, ... some species have very limited distributions. Exporters of ..... Fishelson (1974) to describe the diversity of fishes at par- ..... zooplankton, phytoplankton, benthic Invertebrata, fish fry.

  12. Effects of climate change and wildfire on soil loss in the Southern Rockies Ecoregion

    Science.gov (United States)

    S. E. Litschert; D. M. Theobald; T. C. Brown

    2014-01-01

    Forests in the Southern Rockies Ecoregion surround the headwaters of several major rivers in the western and central US. Future climatic changes will increase the incidence of wildfire in those forests, and will likely lead to changes in downstream water quality, including sediment loads.We estimated soil loss under the historic climate and two IPCC climate change...

  13. Rocky Flats Plant Site, Golden, Colorado. Volume I. Draft environmental impact statement

    International Nuclear Information System (INIS)

    1977-09-01

    Two previous environmental statements have been issued for the Rocky Flats Plant site. One concerned a new plutonium recovery facility (WASH-1517, USAEC, January 1972); the second concerned land acquisition (WASH-1518, USAEC, April 1972). This document responds to those who indicated concerns and also ERDA's anticipated concerns about activities associated with the Rocky Flats Plant. Most concerns focus on two points including the Plant's involvement in the production of nuclear weapons and the Plant's handling of hazardous materials, particularly the radioactive element plutonium. The production of nuclear weapons, in which the Rocky Flats Plant maintains a vital role, will probably continue for as long as the world situation suggests that this country must have a strong defense. Operations at the Rocky Flats Plant have resulted in some plutonium being released to the environment, but evidence does not indicate that the amounts involved have presented any measurable hazard to human health. Ongoing improvements to the Plant's facilities and operational procedures are intended to preclude any recurrence of past releases. Despite these improvements, some public concern has resulted from past releases and the potential adverse effects from any possible future releases. This DEIS addresses that concern. It comments on past mishaps along with their causes and effects. It discusses current operations plus related costs and benefits to the region. Various alternatives to continuing present operations are explored, and the costs and benefits of the different options are compared

  14. Biogeographic, cultural, and historical setting of the Northern Rocky Mountains [Chapter 2

    Science.gov (United States)

    S. Karen. Dante-Wood

    2018-01-01

    The Northern Rockies Adaptation Partnership (NRAP) includes diverse landscapes, ranging from high mountains to grasslands, from alpine glaciers to broad rivers (fig. 1.1). This region, once inhabited solely by Native Americans, has been altered by two centuries of settlement by Euro- Americans through extractive practices such as timber harvest, grazing, and mining,...

  15. Management of spruce-fir in even-aged stands in the central Rocky Mountains

    Science.gov (United States)

    Robert R. Alexander; Carleton B. Edminster

    1980-01-01

    Potential production of Engelmann spruce and subalpine fir in the central Rocky Mountains is simulated for vario.us combinations of stand density, site quality, ages, and thinning schedules. Such estimates are needed to project future development of stands managed in different ways for various uses.

  16. Diseases of whooping cranes seen during annual migration of the Rocky Mountain flock

    Science.gov (United States)

    Snyder, S. Bret; Richard, Michael J.; Drewien, Roderick C.; Thomas, Nancy J.; Thilsted, John P.; Junge, Randall E.

    1991-01-01

    Diagnosis and treatment of ill whooping cranes of the Rocky Mountain flock was provided by a zoological facility. Cases of avian cholera, lead poisoning and avian tuberculosis were encountered. The zoo efforts were an adjunct to the U.S. Fish and Wildlife Service, Whooping Crane Recovery Plan.

  17. Portrait of a Cult Film Audience: "The Rocky Horror Picture Show."

    Science.gov (United States)

    Austin, Bruce A.

    1981-01-01

    Examines the phenomenon of the cult film and the characteristics of the audiences of the "Rocky Horror Picture Show." Suggests that the preparation, waiting, and finally the active participation in the viewing of the film itself appear to be part of a group ritual which characterizes the cult film as an event. (JMF)

  18. Long-term effects of Exxon Valdez oiling and shoreline treatments on rocky intertidal epibiota

    International Nuclear Information System (INIS)

    Houghton, J.P.; Fukuyama, A.K.; Lees, D.C.; Driskell, W.B.; Shigenaka, G.; Mearns, A.J.

    1993-01-01

    Hot-water treatments used to remove Exxon Valdez oil from rocky beaches of Prince William Sound in 1989 were shown to have severe short-term impacts on intertidal epibenthos. Quantitative sampling was conducted from 1989 through 1993 to evaluate recovery of littoral habitats from the effects of oiling and hotwater washing. Effects of hot-water treatments applied in 1989 remained visible in intertidal assemblages through 1993. Some hot-water treated rocky shores that had been stripped of biota showed little colonization by 1991; significant differences remained between epibiota on unoiled shores and that on oiled shores that were hot-water washed. On other oiled rocky shores that were not hot-water washed, the majority of the community dominants, including rockweed, mussels, barnacles, limpets, drills, and littorines, survived the oiling; by July 1991 these shores did not differ in most respects from unoiled shores. By July 1993 hot-water-washed rocky shores had been colonized by opportunistic species as well as by most of the original biota. Algal assemblages were heavily dominated by rockweed, but red algae reminded depressed, especially at lower elevations; otherwise, few significant differences remained in 1993 between the epibiota on unoiled and hot-water-washed shores. Full recovery appears to be several years away in many areas, however

  19. [A fatal case series of Rocky Mountain spotted fever in Sonora, México].

    Science.gov (United States)

    Delgado-De la Mora, Jesús; Licona-Enríquez, Jesús David; Leyva-Gastélum, Marcia; Delgado-De la Mora, David; Rascón-Alcantar, Adela; Álvarez-Hernández, Gerardo

    2018-03-15

    Rocky Mountain spotted fever is a highly lethal infectious disease, particularly if specific treatment with doxycycline is given belatedly. To describe the clinical profile of fatal Rocky Mountain spotted fever cases in hospitalized patients in the state of Sonora, México. We conducted a cross-sectional study on a series of 47 deaths caused by Rickettsia rickettsii from 2013 to 2016. The diagnosis of Rocky Mountain spotted fever was confirmed in a single blood sample by polymerase chain reaction (PCR) or by a four-fold increase in immunoglobulin G measured in paired samples analyzed by indirect immunofluorescence. Clinical and laboratory characteristics were compared stratifying subjects into two groups: pediatric and adult. There were no differences in clinical characteristics between groups; petechial rash was the most frequent sign (96%), followed by headache (70%) and myalgia (67%). Although that doxycycline was administered before the fifth day from the onset of symptoms, death occurred in 55% of patients. In clinical laboratory, thrombocytopenia, and biomarkers of liver acute failure and acute kidney failure were the most frequent. Rocky Mountain spotted fever remains as one of the most lethal infectious diseases, which may be related not only to the lack of diagnostic suspicion and delayed administration of doxycycline, but to genotypic characteristics of Rickettsia rickettsii that may play a role in the variability of the fatality rate that has been reported in other geographical regions where the disease is endemic.

  20. Tools for Closure Project and Contract Management: Development of the Rocky Flats Integrated Closure Project Baseline

    International Nuclear Information System (INIS)

    Gelles, C. M.; Sheppard, F. R.

    2002-01-01

    This paper details the development of the Rocky Flats Integrated Closure Project Baseline - an innovative project management effort undertaken to ensure proactive management of the Rocky Flats Closure Contract in support of the Department's goal for achieving the safe closure of the Rocky Flats Environmental Technology Site (RFETS) in December 2006. The accelerated closure of RFETS is one of the most prominent projects within the Department of Energy (DOE) Environmental Management program. As the first major former weapons plant to be remediated and closed, it is a first-of-kind effort requiring the resolution of multiple complex technical and institutional challenges. Most significantly, the closure of RFETS is dependent upon the shipment of all special nuclear material and wastes to other DOE sites. The Department is actively working to strengthen project management across programs, and there is increasing external interest in this progress. The development of the Rocky Flats Integrated Closure Project Baseline represents a groundbreaking and cooperative effort to formalize the management of such a complex project across multiple sites and organizations. It is original in both scope and process, however it provides a useful precedent for the other ongoing project management efforts within the Environmental Management program

  1. Evaluation of episodic acidification and amphibian declines in the Rocky Mountains

    Science.gov (United States)

    Frank A. Vertucci; Paul Stephen Corn

    1996-01-01

    We define criteria for documenting episodic acidification of amphibian breeding habitats and examine whether episodic acidification is responsible for observed declines of amphibian populations in the Rocky Mountains. Anthropogenic episodic acidification, caused by atmospheric deposition of sulfate and nitrate, occurs when the concentration of acid anions increases...

  2. Logging residues in principal forest types of the Northern Rocky Mountains

    Science.gov (United States)

    Robert E. Benson; Joyce A. Schlieter

    1980-01-01

    An estimated 466 million ft 3 of forest residue material (nonmerchantable, 3 inches diameter and larger) is generated annually in the Northern Rocky Mountains (Montana, Idaho, Wyoming). Extensive studies of residues in the major forest types show a considerable portion is suited for various products. The lodgepole pine type has the greatest potential for increased...

  3. Rocky Mountain Research Station 2008-2012 National Fire Plan Investments

    Science.gov (United States)

    Erika Gallegos

    2013-01-01

    This report highlights selected accomplishments by the USDA Forest Service Rocky Mountain Research Station's Wildland Fire and Fuels Research & Development projects in support of the National Fire Plan from 2008 through 2012. These projects are examples of the broad range of knowledge and tools developed by National Fire Plan funding beginning in 2008.

  4. Small cities face greater impact from automation.

    Science.gov (United States)

    Frank, Morgan R; Sun, Lijun; Cebrian, Manuel; Youn, Hyejin; Rahwan, Iyad

    2018-02-01

    The city has proved to be the most successful form of human agglomeration and provides wide employment opportunities for its dwellers. As advances in robotics and artificial intelligence revive concerns about the impact of automation on jobs, a question looms: how will automation affect employment in cities? Here, we provide a comparative picture of the impact of automation across US urban areas. Small cities will undertake greater adjustments, such as worker displacement and job content substitutions. We demonstrate that large cities exhibit increased occupational and skill specialization due to increased abundance of managerial and technical professions. These occupations are not easily automatable, and, thus, reduce the potential impact of automation in large cities. Our results pass several robustness checks including potential errors in the estimation of occupational automation and subsampling of occupations. Our study provides the first empirical law connecting two societal forces: urban agglomeration and automation's impact on employment. © 2018 The Authors.

  5. Small cities face greater impact from automation

    Science.gov (United States)

    Sun, Lijun; Cebrian, Manuel; Rahwan, Iyad

    2018-01-01

    The city has proved to be the most successful form of human agglomeration and provides wide employment opportunities for its dwellers. As advances in robotics and artificial intelligence revive concerns about the impact of automation on jobs, a question looms: how will automation affect employment in cities? Here, we provide a comparative picture of the impact of automation across US urban areas. Small cities will undertake greater adjustments, such as worker displacement and job content substitutions. We demonstrate that large cities exhibit increased occupational and skill specialization due to increased abundance of managerial and technical professions. These occupations are not easily automatable, and, thus, reduce the potential impact of automation in large cities. Our results pass several robustness checks including potential errors in the estimation of occupational automation and subsampling of occupations. Our study provides the first empirical law connecting two societal forces: urban agglomeration and automation's impact on employment. PMID:29436514

  6. Planning for greater-confinement disposal

    International Nuclear Information System (INIS)

    Gilbert, T.L.; Luner, C.; Meshkov, N.K.; Trevorrow, L.E.; Yu, C.

    1984-01-01

    This contribution is a progress report for preparation of a document that will summarize procedures and technical information needed to plan for and implement greater-confinement disposal (GCD) of low-level radioactive waste. Selection of a site and a facility design (Phase I), and construction, operation, and extended care (Phase II) will be covered in the document. This progress report is limited to Phase I. Phase I includes determination of the need for GCD, design alternatives, and selection of a site and facility design. Alternative designs considered are augered shafts, deep trenches, engineered structures, high-integrity containers, hydrofracture, and improved waste form. Design considerations and specifications, performance elements, cost elements, and comparative advantages and disadvantages of the different designs are covered. Procedures are discussed for establishing overall performance objectives and waste-acceptance criteria, and for comparative assessment of the performance and cost of the different alternatives. 16 references

  7. Greater confinement disposal of radioactive wastes

    International Nuclear Information System (INIS)

    Trevorrow, L.E.; Gilbert, T.L.; Luner, C.; Merry-Libby, P.A.; Meshkov, N.K.; Yu, C.

    1985-01-01

    Low-level radioactive waste (LLW) includes a broad spectrum of different radionuclide concentrations, half-lives, and hazards. Standard shallow-land burial practice can provide adequate protection of public health and safety for most LLW. A small volume fraction (approx. 1%) containing most of the activity inventory (approx. 90%) requires specific measures known as greater-confinement disposal (GCD). Different site characteristics and different waste characteristics - such as high radionuclide concentrations, long radionuclide half-lives, high radionuclide mobility, and physical or chemical characteristics that present exceptional hazards - lead to different GCD facility design requirements. Facility design alternatives considered for GCD include the augered shaft, deep trench, engineered structure, hydrofracture, improved waste form, and high-integrity container. Selection of an appropriate design must also consider the interplay between basic risk limits for protection of public health and safety, performance characteristics and objectives, costs, waste-acceptance criteria, waste characteristics, and site characteristics

  8. Planning for greater-confinement disposal

    International Nuclear Information System (INIS)

    Gilbert, T.L.; Luner, C.; Meshkov, N.K.; Trevorrow, L.E.; Yu, C.

    1984-01-01

    This contribution is a progress report for preparation of a document that will summarize procedures and technical information needed to plan for and implement greater-confinement disposal (GCD) of low-level radioactive waste. Selection of a site and a facility design (Phase I), and construction, operation, and extended care (Phase II) will be covered in the document. This progress report is limited to Phase I. Phase I includes determination of the need for GCD, design alternatives, and selection of a site and facility design. Alternative designs considered are augered shafts, deep trenches, engineered structures, high-integrity containers, hydrofracture, and improved waste form. Design considerations and specifications, performance elements, cost elements, and comparative advantages and disadvantages of the different designs are covered. Procedures are discussed for establishing overall performance objecties and waste-acceptance criteria, and for comparative assessment of the performance and cost of the different alternatives. 16 refs

  9. Association analysis of PRNP gene region with chronic wasting disease in Rocky Mountain elk

    Directory of Open Access Journals (Sweden)

    Spraker Terry R

    2010-11-01

    Full Text Available Abstract Background Chronic wasting disease (CWD is a transmissible spongiform encephalopathy (TSE of cervids including white-tailed (Odocoileus virginianus and mule deer (Odocoileus hemionus, Rocky Mountain elk (Cervus elaphus nelsoni, and moose (Alces alces. A leucine variant at position 132 (132L in prion protein of Rocky Mountain elk confers a long incubation time with CWD, but not complete resistance. However, variants in regulatory regions outside the open reading frame of PRNP have been associated with varying degrees of susceptibility to prion disease in other species, and some variants have been observed in similar regions of Rocky Mountain elk PRNP. Thus, additional genetic variants might provide increased protection, either alone or in combination with 132L. Findings This study provided genomic sequence of all exons for PRNP of Rocky Mountain elk. Many functional sites in and around the PRNP gene region were sequenced, and this report approximately doubled (to 75 the number of known variants in this region. A haplotype-tagging approach was used to reduce the number of genetic variants required to survey this variation in the PRNP gene region of 559 Rocky Mountain elk. Eight haplotypes were observed with frequencies over 1.0%, and one haplotype was present at 71.2% frequency, reflecting limited genetic diversity in the PRNP gene region. Conclusions The presence of 132L cut odds of CWD by more than half (Odds Ratio = 0.43; P = 0.0031, which was similar to a previous report. However after accounting for 132L, no association with CWD was found for any additional variants in the PRNP region (P > 0.05.

  10. Atmospheric dispersion modeling at the Rocky Flats Plant. Progress report, December 1981-December 1985

    International Nuclear Information System (INIS)

    Hodgin, C.R.

    1986-01-01

    The Rocky Flats Plant applies atmospheric dispersion modeling as a tool for Emergency Response, Risk Assessment, and Regulatory Compliance. Extreme variations in terrain around the facility have necessitated the development of an advanced modeling approach. The Terrain-Responsive Atmospheric Code (TRAC) was developed to treat realistically the changing wind, stability, dispersion, and deposition patterns that are experienced in mountainous areas. The result is a detailed picture of dose and deposition patterns associated with postulated or actual releases. A unified approach was taken to modeling needs at Rocky Flats. This produces consistent dose projections for all applications. A Risk Assessment version of TRAC is now operational. A high-speed version of the code is being implemented for Emergency Response, and development of a regulatory version is under way. Public, scientific, and governmental acceptance of TRAC is critical to successful applications at the Rocky Flats Plant. A program of peer review and regulatory approval was initiated to provide a full outside evaluation of our techniques. Full field validation (tracer testing) is key to demonstrating reliability of the TRAC model. A validation study was planned for implementation beginning in early CY-1986. The necessary funding ($500,000) is being sought. Although the TRAC model development and approval program was developed for site-specific needs at the Rocky Flats Plant, potential exists for wider application within the Department of Energy (DOE). The TRAC model can be easily applied at other sites in complex terrain. A coordinated approach to model validation throughout the Albquerque Operations Office (AL) or DOE complexes could prove more cost effective than site-by-site evaluations. Finally, the model approval procedure developed jointly by Rocky Flats and the Environmental Protection Agency (EPA) is general and could be applied to other models or as the basis for a DOE-wide program

  11. A high resolution complex terrain dispersion study in the Rocky Flats, Colorado vicinity

    International Nuclear Information System (INIS)

    Poulos, G.S.; Bossert, J.E.

    1992-01-01

    In January/February, 1991 an intensive set of measurements was taken around Rocky Flats near Denver, CO under the auspices of the Department of Energy Atmospheric Studies over Complex Terrain (ASCOT) program. This region of the country is known as the Front Range, and is characterized by a transition from the relatively flat terrain of the Great Plains to the highly varied terrain of the Rocky Mountains. One goal of the ASCOT 1991 program was to gain insight into multi-scale meteorological interaction by observing wintertime drainage conditions at the mountain-valley-plains interface. ASCOT data included surface and upper air measurements on approximately a 50km 2 scale. Simultaneously, an SF 6 tracer release study was being conducted around Rocky Flats, a nuclear materials production facility. Detailed surface concentration measurements were completed for the SF 6 plume. This combination of meteorological and tracer concentration data provided a unique data set for comparisons of mesoscale and dispersion modeling results with observations and for evaluating our capability to predict pollutant transport. Our approach is to use the Regional Atmospheric Modeling System (RAMS) mesoscale model to simulate atmospheric conditions and the Lagrangian Particle Dispersion Model (LPDM), a component of the RAMS system, to model the dispersion of the SF 6 . We have chosen the 4--5 February, 1991 overnight period as our case study. This night was characterized by strong drainage flows from the Rocky Mountains to the west of Rocky Flats, southerly winds in a layer about lkm thick above the drainage flows, and northwesterly winds above that layer extending to the tropopause

  12. FY 1992 Annual report: Mediated electrochemical oxidation treatment for Rocky Flats combustible low-level mixed waste

    International Nuclear Information System (INIS)

    Chiba, Z.; Lewis, P.R.; Kahle, R.W.

    1993-03-01

    The Mediated Electrochemical Oxidation (MEO) process was studied for destroying low-level combustible mixed wastes at Rocky Flats (RFP). Tests were performed with nonradioactive surrogate materials: Trimsol for the contaminated oils, and reagent-grade cellulose for the cellulosic wastes. Extensive testing was carried out on Trimsol in both small laboratory-scale apparatus and on a large-scale system incorporating an industrial-size electrochemical cell. Preliminary tests were also carried out in the small-scale system with cellulose. The following operating and system parameters were studied: use of a silver-nitric acid versus a cobalt-sulfuric acid system, effect of electrolyte temperature, effect of acid concentration, effect of current density, and use of ultrasonic agitation. Destruction and coulombic efficiencies were calculated using data obtained from continuous carbon dioxide monitors and total organic carbon (TOC) analysis of electrolyte samples. For Trimsol, the best performance was achieved with the silver-nitrate system at high acid concentrations, temperatures, and current densities. Destruction efficiencies of 98% or greater and coulombic efficiencies close to 50% were obtained in both small- and large-scale systems. For the cellulose, high destruction efficiencies and reasonable coulombic efficiencies were obtained for both silver-nitrate and cobalt-sulfate systems

  13. Interactive effects of historical logging and fire exclusion on ponderosa pine forest structure in the northern Rockies.

    Science.gov (United States)

    Naficy, Cameron; Sala, Anna; Keeling, Eric G; Graham, Jon; DeLuca, Thomas H

    2010-10-01

    Increased forest density resulting from decades of fire exclusion is often perceived as the leading cause of historically aberrant, severe, contemporary wildfires and insect outbreaks documented in some fire-prone forests of the western United States. Based on this notion, current U.S. forest policy directs managers to reduce stand density and restore historical conditions in fire-excluded forests to help minimize high-severity disturbances. Historical logging, however, has also caused widespread change in forest vegetation conditions, but its long-term effects on vegetation structure and composition have never been adequately quantified. We document that fire-excluded ponderosa pine forests of the northern Rocky Mountains logged prior to 1960 have much higher average stand density, greater homogeneity of stand structure, more standing dead trees and increased abundance of fire-intolerant trees than paired fire-excluded, unlogged counterparts. Notably, the magnitude of the interactive effect of fire exclusion and historical logging substantially exceeds the effects of fire exclusion alone. These differences suggest that historically logged sites are more prone to severe wildfires and insect outbreaks than unlogged, fire-excluded forests and should be considered a high priority for fuels reduction treatments. Furthermore, we propose that ponderosa pine forests with these distinct management histories likely require distinct restoration approaches. We also highlight potential long-term risks of mechanical stand manipulation in unlogged forests and emphasize the need for a long-term view of fuels management.

  14. Finding of no significant impact. Consolidation and interim storage of special nuclear material at Rocky Flats Environmental Technology Site

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-06-01

    The Department of Energy (DOE) has prepared an environmental assessment (EA), DOE/EA -- 1060, for the consolidation, processing, and interim storage of Category I and II special nuclear material (SNM) in Building 371 at the Rocky Flats Environmental Technology Site (hereinafter referred to as Rocky Flats or Site), Golden, Colorado. The scope of the EA included alternatives for interim storage including the no action alternative, the construction of a new facility for interim storage at Rocky Flats, and shipment to other DOE facilities for interim storage.

  15. Finding of no significant impact. Consolidation and interim storage of special nuclear material at Rocky Flats Environmental Technology Site

    International Nuclear Information System (INIS)

    1995-06-01

    The Department of Energy (DOE) has prepared an environmental assessment (EA), DOE/EA -- 1060, for the consolidation, processing, and interim storage of Category I and II special nuclear material (SNM) in Building 371 at the Rocky Flats Environmental Technology Site (hereinafter referred to as Rocky Flats or Site), Golden, Colorado. The scope of the EA included alternatives for interim storage including the no action alternative, the construction of a new facility for interim storage at Rocky Flats, and shipment to other DOE facilities for interim storage

  16. Land use planning: A potential force for retaining habitat connectivity in the Greater Yellowstone Ecosystem and Beyond

    Directory of Open Access Journals (Sweden)

    Craig L. Shafer

    2015-01-01

    Full Text Available The grizzly bear (Ursus arctos horribilis population in the Greater Yellowstone Ecosystem (GYE is perceived to have been isolated from the population in the Northern Continental Divide Ecosystem for a century. Better land use planning is needed to thwart progressive intra- and inter-ecosystem habitat fragmentation, especially due to private land development. The dilemma of private lands being intermixed in large landscapes is addressed. This review attempts to identify some land use planning levels and tools which might facilitate dispersal by the grizzly bear and other large mammals. The planning levels discussed include national, regional, state, county and municipal, and federal land management agency. Specific potential federal tools mentioned include zoning, Landscape Conservation Cooperatives, the Endangered Species Act, beyond boundary authority, land exchanges, less-than-fee acquisition and other incentives, the Northern Rockies Ecosystem Protection Act, and federal land annexation. Besides summarizing existing recommendations, some derived observations are offered.

  17. MADS goes genomic in conifers: towards determining the ancestral set of MADS-box genes in seed plants.

    Science.gov (United States)

    Gramzow, Lydia; Weilandt, Lisa; Theißen, Günter

    2014-11-01

    MADS-box genes comprise a gene family coding for transcription factors. This gene family expanded greatly during land plant evolution such that the number of MADS-box genes ranges from one or two in green algae to around 100 in angiosperms. Given the crucial functions of MADS-box genes for nearly all aspects of plant development, the expansion of this gene family probably contributed to the increasing complexity of plants. However, the expansion of MADS-box genes during one important step of land plant evolution, namely the origin of seed plants, remains poorly understood due to the previous lack of whole-genome data for gymnosperms. The newly available genome sequences of Picea abies, Picea glauca and Pinus taeda were used to identify the complete set of MADS-box genes in these conifers. In addition, MADS-box genes were identified in the growing number of transcriptomes available for gymnosperms. With these datasets, phylogenies were constructed to determine the ancestral set of MADS-box genes of seed plants and to infer the ancestral functions of these genes. Type I MADS-box genes are under-represented in gymnosperms and only a minimum of two Type I MADS-box genes have been present in the most recent common ancestor (MRCA) of seed plants. In contrast, a large number of Type II MADS-box genes were found in gymnosperms. The MRCA of extant seed plants probably possessed at least 11-14 Type II MADS-box genes. In gymnosperms two duplications of Type II MADS-box genes were found, such that the MRCA of extant gymnosperms had at least 14-16 Type II MADS-box genes. The implied ancestral set of MADS-box genes for seed plants shows simplicity for Type I MADS-box genes and remarkable complexity for Type II MADS-box genes in terms of phylogeny and putative functions. The analysis of transcriptome data reveals that gymnosperm MADS-box genes are expressed in a great variety of tissues, indicating diverse roles of MADS-box genes for the development of gymnosperms. This study is

  18. Urban acid deposition in Greater Manchester

    Energy Technology Data Exchange (ETDEWEB)

    Lee, D.S.; Longhurst, J.W.S.; Gee, D.R.; Hare, S.E. (Manchester Polytechnic, Manchester (UK). Acid Rain Information Centre)

    1989-08-01

    Data are presented from a monitoring network of 18 bulk precipitation collectors and one wet-only collector in the urban area of Greater Manchester, in the north west of England. Weekly samples were analysed for all the major ions in precipitation along with gaseous nitrogen dioxide concentrations from diffusion tubes. Statistical analysis of the data shows significant spatial variation of non marine sulphate, nitrate, ammonium, acidity and calcium concentrations, and nitrogen dioxide concentrations. Calcium is thought to be responsible for the buffering of acidity and is of local origin. Wet deposition is the likely removal process for calcium in the atmosphere and probably by below cloud scavenging. Nitrate and ammonium concentrations and depositions show close spatial, temporal and statistical association. Examination of high simultaneous episodes of nitrate and ammonium deposition shows that these depositions cannot be explained in terms of trajectories and it is suggested that UK emissions of ammonia may be important. Statistical analysis of the relationships between nitrate and ammonium depositions, concentrations and precipitation amount suggest that ammonia from mesoscale sources reacts reversibly with nitric acid aerosol and is removed by below cloud scavenging. High episodes of the deposition of non marine sulphate are difficult to explain by trajectory analysis alone, perhaps suggesting local sources. In a comparison between wet deposition and bulk deposition, it was shown that only 15.2% of the non marine sulphur was dry deposited to the bulk precipitation collector. 63 refs., 86 figs., 31 tabs.

  19. Late Cenozoic Magmatic and Tectonic Evolution of the Ancestral Cascade Arc in the Bodie Hills, California and Nevada: Insights from Integrated Geologic, Geophysical, Geochemical and Geochronologic Studies

    Science.gov (United States)

    John, D. A.; du Bray, E. A.; Box, S. E.; Blakely, R. J.; Fleck, R. J.; Vikre, P. G.; Cousens, B.; Moring, B. C.

    2012-12-01

    Geologic mapping integrated with new geophysical, geochemical, and geochronologic data characterize the evolution of Bodie Hills volcanic field (BHVF), a long-lived eruptive center in the southern part of the ancestral Cascade arc. The ~700 km2 field was a locus of magmatic activity from ~15 to 8 Ma. It includes >25 basaltic andesite to trachyandesite stratovolcanoes and silicic trachyandesite to rhyolite dome complexes. The southeastern part of the BHVF is overlain by the ~3.9 to 0.1 Ma, post-arc Aurora Volcanic Field. Long-lived BHVF magmatism was localized by crustal-scale tectonic features, including the Precambrian continental margin, the Walker Lane, the Basin and Range Province, and the Mina deflection. BHVF eruptive activity occurred primarily during 3 stages: 1) dominantly trachyandesite stratovolcanoes (~15.0 to 12.9 Ma), 2) coalesced trachydacite and rhyolite lava domes and trachyandesite stratovolcanoes (~11.6 to 9.7 Ma), and 3) dominantly silicic trachyandesite to dacite lava dome complexes (~9.2 to 8.0 Ma). Small rhyolite domes were emplaced at ~6 Ma. Relatively mafic stratovolcanoes surrounded by debris flow aprons lie on the margins of the BHVF, whereas more silicic dome fields occupy its center. Detailed gravity and aeromagnetic data suggest the presence of unexposed cogenetic granitic plutons beneath the center of the BHVF. Isotopic compositions of BHVF rocks are generally more radiogenic with decreasing age (e.g., initial Sr isotope values increase from ~0.7049 to 0.7061), which suggests progressively greater magma contamination by crustal components during evolution of the BHVF. Approximately circular, polygenetic volcanoes and scarcity of dikes suggest a low differential horizontal stress field during BHVF formation. Extensive alluvial gravel deposits that grade laterally into fluvial gravels and finer grained lacustrine sediments and the westerly sourced Eureka Valley Tuff (EVT; ~9.4 Ma) blanket large parts of the BHVF. The earliest sediments

  20. A novel assessment of population structure and gene flow in grey wolf populations of the Northern Rocky Mountains of the United States.

    Science.gov (United States)

    vonHoldt, Bridgett M; Stahler, Daniel R; Bangs, Edward E; Smith, Douglas W; Jimenez, Mike D; Mack, Curt M; Niemeyer, Carter C; Pollinger, John P; Wayne, Robert K

    2010-10-01

    The successful re-introduction of grey wolves to the western United States is an impressive accomplishment for conservation science. However, the degree to which subpopulations are genetically structured and connected, along with the preservation of genetic variation, is an important concern for the continued viability of the metapopulation. We analysed DNA samples from 555 Northern Rocky Mountain wolves from the three recovery areas (Greater Yellowstone Area, Montana, and Idaho), including all 66 re-introduced founders, for variation in 26 microsatellite loci over the initial 10-year recovery period (1995-2004). The population maintained high levels of variation (H(O) = 0.64-0.72; allelic diversity k=7.0-10.3) with low levels of inbreeding (F(IS) wolves will rely on management decisions that promote natural dispersal dynamics and minimize anthropogenic factors that reduce genetic connectivity. © 2010 Blackwell Publishing Ltd.