Science.gov

Sample records for arrow worms phylum

  1. Barcoding of arrow worms (Phylum Chaetognatha) from three oceans: genetic diversity and evolution within an enigmatic phylum.

    PubMed

    Jennings, Robert M; Bucklin, Ann; Pierrot-Bults, Annelies

    2010-01-01

    Arrow worms (Phylum Chaetognatha) are abundant planktonic organisms and important predators in many food webs; yet, the classification and evolutionary relationships among chaetognath species remain poorly understood. A seemingly simple body plan is underlain by subtle variation in morphological details, obscuring the affinities of species within the phylum. Many species achieve near global distributions, spanning the same latitudinal bands in all ocean basins, while others present disjunct ranges, in some cases with the same species apparently found at both poles. To better understand how these complex evolutionary and geographic variables are reflected in the species makeup of chaetognaths, we analyze DNA barcodes of the mitochondrial cytochrome oxidase c subunit I (COI) gene, from 52 specimens of 14 species of chaetognaths collected mainly from the Atlantic Ocean. Barcoding analysis was highly successful at discriminating described species of chaetognaths across the phylum, and revealed little geographical structure. This barcode analysis reveals hitherto unseen genetic variation among species of arrow worms, and provides insight into some species relationships of this enigmatic group. PMID:20376348

  2. Expression pattern of the Brachyury gene in the arrow worm paraspadella gotoi (chaetognatha).

    PubMed

    Takada, Norio; Goto, Taichiro; Satoh, Nori

    2002-03-01

    Arrow worms (the phylum Chaetognatha), which are among the major marine planktonic animals, are direct developers and exhibit features characteristic of both deuterostomes and protostomes. In particular, the embryonic development of arrow worms appears to be of the deuterostome type. Brachyury functions critically in the formation of the notochord in chordates, whereas the gene is expressed in both the blastopore and stomodeum invagination regions in embryos of hemichordates and echinoderms. Here we analyzed the expression of Brachyury (Pg-Bra) in the arrow worm Paraspadella gotoi and showed that Pg-Bra is expressed in the blastopore region and the stomodeum region in the embryo and then around the mouth opening region at the time of hatching. The expression of Pg-Bra in the embryo resembles that of Brachyury in embryos of hemichordates and echinoderms, whereas that in the mouth opening region in the hatchling appears to be novel. PMID:11892013

  3. Expression of actin genes in the arrow worm Paraspadella gotoi (Chaetognatha).

    PubMed

    Yasuda, E; Goto, T; Makabe, K W; Satoh, N

    1997-12-01

    Arrow worms (the phylum Chaetognatha), one of the major marine planktonic animals, exhibit features characteristic to both deuterostomes and protostomes, and their ancestry therefore remains unknown. As the first step to elucidate the molecular bases of arrow worm phylogeny, physiology and embryology, we isolated cDNA clones for three different actin genes (PgAct1, PgAct2 and PgAct3) from the benthic species Paraspadella gotoi, and examined their expression patterns in adults and juveniles. The amino acid sequences of the three actins resembled each other, with identities ranging from 86% to 92%. However, the patterns of the spatial expression of the genes were independent. The PgAct1 gene might encode a cytoplasmic actin and was expressed in oogenic cells, spermatogenic cells, and cells in the ventral ganglion. The PgAct2 and PgAct3 genes encoded actins of divergent types. The former was expressed in well-developed muscle of the head (gnathic) region and trunk muscle cells, whereas the latter was expressed in muscle of the trunk and tail regions and oogenic cells. These results suggest that, similarly to other metazoans, the chaetognath contains multiple forms of actins, which are expressed in various manners in the adult and juvenile arrow worm. PMID:9520638

  4. Molecular Phylogeny of Echiuran Worms (Phylum: Annelida) Reveals Evolutionary Pattern of Feeding Mode and Sexual Dimorphism

    PubMed Central

    Goto, Ryutaro; Okamoto, Tomoko; Ishikawa, Hiroshi; Hamamura, Yoichi; Kato, Makoto

    2013-01-01

    The Echiura, or spoon worms, are a group of marine worms, most of which live in burrows in soft sediments. This annelid-like animal group was once considered as a separate phylum because of the absence of segmentation, although recent molecular analyses have placed it within the annelids. In this study, we elucidate the interfamily relationships of echiuran worms and their evolutionary pattern of feeding mode and sexual dimorphism, by performing molecular phylogenetic analyses using four genes (18S, 28S, H3, and COI) of representatives of all extant echiuran families. Our results suggest that Echiura is monophyletic and comprises two unexpected groups: [Echiuridae+Urechidae+Thalassematidae] and [Bonelliidae+Ikedidae]. This grouping agrees with the presence/absence of marked sexual dimorphism involving dwarf males and the paired/non-paired configuration of the gonoducts (genital sacs). Furthermore, the data supports the sister group relationship of Echiuridae and Urechidae. These two families share the character of having anal chaetae rings around the posterior trunk as a synapomorphy. The analyses also suggest that deposit feeding is a basal feeding mode in echiurans and that filter feeding originated once in the common ancestor of Urechidae. Overall, our results contradict the currently accepted order-level classification, especially in that Echiuroinea is polyphyletic, and provide novel insights into the evolution of echiuran worms. PMID:23457618

  5. Evaluating the Utility of Single-Locus DNA Barcoding for the Identification of Ribbon Worms (Phylum Nemertea)

    PubMed Central

    Sundberg, Per; Strand, Malin

    2016-01-01

    Whereas many nemerteans (ribbon worms; phylum Nemertea) can be identified from external characters if observed alive, many are still problematic. When it comes to preserved specimens (as in e.g. marine inventories), there is a particular need for specimen identifier alternatives. Here, we evaluate the utility of COI (cytochrome c oxidase subunit I) as a single-locus barcoding gene. We sequenced, data mined, and compared gene fragments of COI for 915 individuals representing 161 unique taxonomic labels for 71 genera, and subjected different constellations of these to both distance-based and character-based DNA barcoding approaches, as well as species delimitation analyses. We searched for the presence or absence of a barcoding gap at different taxonomic levels (phylum, subclass, family and genus) in an attempt to understand at what level a putative barcoding gap presents itself. This was performed both using the taxonomic labels as species predictors and using objectively inferred species boundaries recovered from our species delimitation analyses. Our data suggest that COI works as a species identifier for most groups within the phylum, but also that COI data are obscured by misidentifications in sequence databases. Further, our results suggest that the number of predicted species within the dataset is (in some cases substantially) higher than the number of unique taxonomic labels—this highlights the presence of several cryptic lineages within well-established taxa and underscores the urgency of an updated taxonomic backbone for the phylum. PMID:27171471

  6. Evaluating the Utility of Single-Locus DNA Barcoding for the Identification of Ribbon Worms (Phylum Nemertea).

    PubMed

    Sundberg, Per; Kvist, Sebastian; Strand, Malin

    2016-01-01

    Whereas many nemerteans (ribbon worms; phylum Nemertea) can be identified from external characters if observed alive, many are still problematic. When it comes to preserved specimens (as in e.g. marine inventories), there is a particular need for specimen identifier alternatives. Here, we evaluate the utility of COI (cytochrome c oxidase subunit I) as a single-locus barcoding gene. We sequenced, data mined, and compared gene fragments of COI for 915 individuals representing 161 unique taxonomic labels for 71 genera, and subjected different constellations of these to both distance-based and character-based DNA barcoding approaches, as well as species delimitation analyses. We searched for the presence or absence of a barcoding gap at different taxonomic levels (phylum, subclass, family and genus) in an attempt to understand at what level a putative barcoding gap presents itself. This was performed both using the taxonomic labels as species predictors and using objectively inferred species boundaries recovered from our species delimitation analyses. Our data suggest that COI works as a species identifier for most groups within the phylum, but also that COI data are obscured by misidentifications in sequence databases. Further, our results suggest that the number of predicted species within the dataset is (in some cases substantially) higher than the number of unique taxonomic labels-this highlights the presence of several cryptic lineages within well-established taxa and underscores the urgency of an updated taxonomic backbone for the phylum. PMID:27171471

  7. Calcium signaling and endoplasmic reticulum dynamics during fertilization in marine protostome worms belonging to the phylum Nemertea.

    PubMed

    Stricker, Stephen A

    2014-08-01

    Metaphase-I-arrested eggs of marine protostome worms in the phylum Nemertea generate a series of point-source calcium waves during fertilization. Such calcium oscillations depend on inositol-1,4,5-trisphosphate-mediated calcium release from endoplasmic reticulum (ER) stores that undergo structural reorganizations prior to and after fertilization. This article reviews fertilization-induced calcium transients and ER dynamics in nemertean eggs and compares these topics to what has been reported for other animals in order to identify unifying characteristics and distinguishing features of calcium responses during fertilization across the animal kingdom. PMID:24721427

  8. Histochemical demonstration of a rhodopsin-like substance in the eye of the arrow-worm, Spadella schizoptera (Chaetognatha).

    PubMed

    Goto, T; Yoshida, M

    1988-01-01

    The presumed photoreceptive region of the arrow-worms of the species Sagitta crassa and Spadella schizoptera consists of perforated lamellae which are unique as the photoreceptive structure. The existence of a visual pigment in this region was demonstrated by a histofluorescent technique using Spadella schizoptera, whose presumed photoreceptive region was much larger than in Sagitta crassa. A specific fluorescence, indicative of the presence of retinal-based proteins, appeared only in the perforated lamellar region. The result suggests that the perforated lamellae contain a rhodopsin-like substance and could be the primary photoreceptive site. PMID:3268423

  9. Peanut worms of the phylum Sipuncula from the Sea of Japan with a key to species

    NASA Astrophysics Data System (ADS)

    Maiorova, Anastassya S.; Adrianov, Andrey V.

    2013-02-01

    Sipunculan worms from the Russian waters of the Sea of Japan are still poorly investigated while they are much better known from the Japanese coast. The aim of this paper is to describe sipunculans from the Russian coast and from the deepest part of the Sea of Japan near the Primorye Province collected by SoJaBio expedition, and to provide keys for identification of sipunculan species from the Sea of Japan. At the Russian coast of the Sea of Japan only 8 valid species of sipunculans were found and identified: Golfingia margaritacea, G. vulgaris, Nephasoma capilleforme, N. wodjanizkii, Phascolion strombus, Thysanocardia nigra, Themiste hexadactyla (=T. pyroides), Phascolosoma agassizii. Taking into account 4 other valid species noted for this area, Nephasoma eremite, Thysanocardia catharinae, Themiste blanda and Phascolosoma scolops, which were not found, the sipunculan fauna of the Russian waters of the Sea of Japan now comprises 12 valid species. Nephasoma capilleforme and Nephasoma wodjanizkii are the first records for the North-West Pacific and the Sea of Japan. Species accounts include the most important taxonomic characters and specific biotope data. Accordingly, a key up to species level is provided. Totally, the fauna of the Sea of Japan is now estimated as having 31 valid species of sipunculans.

  10. Extensive and evolutionarily persistent mitochondrial tRNA editing in Velvet Worms (phylum Onychophora).

    PubMed

    Segovia, Romulo; Pett, Walker; Trewick, Steve; Lavrov, Dennis V

    2011-10-01

    Mitochondrial genomes of onychophorans (velvet worms) present an interesting problem: Some previous studies reported them lacking several transfer RNA (tRNA) genes, whereas others found that all their tRNA genes were present but severely reduced. To resolve this discrepancy, we determined complete mitochondrial DNA (mtDNA) sequences of the onychophorans Oroperipatus sp. and Peripatoides sympatrica as well as cDNA sequences from 14 and 10 of their tRNAs, respectively. We show that tRNA genes in these genomes are indeed highly reduced and encode truncated molecules, which are restored to more conventional structures by extensive tRNA editing. During this editing process, up to 34 nucleotides are added to the tRNA sequences encoded in Oroperipatus sp. mtDNA, rebuilding the aminoacyl acceptor stem, the TΨC arm, and in some extreme cases, the variable arm and even a part of the anticodon stem. The editing is less extreme in P. sympatrica in which at least a part of the TΨC arm is always encoded in mtDNA. When the entire TΨC arm is added de novo in Oroperipatus sp., the sequence of this arm is either identical or similar among different tRNA species, yet the sequences show substantial variation for each tRNA. These observations suggest that the arm is rebuilt, at least in part, by a template-independent mechanism and argue against the alternative possibility that tRNA genes or their parts are imported from the nucleus. By contrast, the 3' end of the aminoacyl acceptor stem is likely restored by a template-dependent mechanism. The extreme tRNA editing reported here has been preserved for >140 My as it was found in both extant families of onychophorans. Furthermore, a similar type of tRNA editing may be present in several other groups of arthropods, which show a high degree of tRNA gene reduction in their mtDNA. PMID:21546355

  11. The primary body-wall musculature in the arrow-worm Sagitta setosa (Chaetognatha): an ultrastructural study.

    PubMed

    Duvert, M; Salat, C

    1980-01-01

    The primary musculature of Sagitta is mainly made up of two kinds of alternating fibers, A and B. These fibers differ markedly in their localization in the muscular tissue, by the development of their SR and their mitochondria, and the shape of their myofibrils. Their contractile apparatus is similar and possesses myofibrils of regular thickness with very short I bands, flanked by invaginations which are large compartments communicating with the extracellular space. This fiber diversity appears and is maintained in the presence of an apparent common innervation. Nerve ending-like structures are scattered in the epidermis against the basement membrane and there are no nerve beneath this. The presence of at least two kinds of fibers in the primary musculature and the presence of the secondary musculature would suggest that the displacements of sagitta may be more complex than is generally admitted. The specializations of the trunk musculature underline the degree of specialization in the Chaetognatha phylum. PMID:7209960

  12. A new look at the ventral nerve centre of Sagitta: implications for the phylogenetic position of Chaetognatha (arrow worms) and the evolution of the bilaterian nervous system

    PubMed Central

    Harzsch, Steffen; Müller, Carsten HG

    2007-01-01

    Background The Chaetognatha (arrow worms) are a group of marine carnivores whose phylogenetic relationships are still vigorously debated. Molecular studies have as yet failed to come up with a stable hypothesis on their phylogenetic position. In a wide range of metazoans, the nervous system has proven to provide a wealth of characters for analysing phylogenetic relationships (neurophylogeny). Therefore, in the present study we explored the structure of the ventral nerve centre ("ventral ganglion") in Sagitta setosa with a set of histochemical and immunohistochemical markers. Results In specimens that were immunolabeled for acetylated-alpha tubulin the ventral nerve centre appeared to be a condensed continuation of the peripheral intraepidermal nerve plexus. Yet, synapsin immunolocalization showed that the ventral nerve centre is organized into a highly ordered array of ca. 80 serially arranged microcompartments. Immunohistochemistry against RFamide revealed a set of serially arranged individually identifiable neurons in the ventral nerve centre that we charted in detail. Conclusion The new information on the structure of the chaetognath nervous system is compared to previous descriptions of the ventral nerve centre which are critically evaluated. Our findings are discussed with regard to the debate on nervous system organisation in the last common bilaterian ancestor and with regard to the phylogenetic affinities of this Chaetognatha. We suggest to place the Chaetognatha within the Protostomia and argue against hypotheses which propose a deuterostome affinity of Chaetognatha or a sister-group relationship to all other Bilateria. PMID:17511857

  13. Morphology of a new deep-sea acorn worm (class Enteropneusta, phylum Hemichordata): a part-time demersal drifter with externalized ovaries.

    PubMed

    Holland, Nicholas D; Kuhnz, Linda A; Osborn, Karen J

    2012-07-01

    Ten individuals of an enteropneust in the family Torquaratoridae were videotaped between 2,900 and 3,500 m in the Eastern Pacific--one drifting a few centimeters above the bottom, two exposed on the substrate, and seven partly burrowed, reflecting a bentho-pelagic life style. Here, we describe a captured specimen (26 cm living length) as the holotype of Allapasus aurantiacus n. gen., n. sp. The small proboscis is dome-shaped, and the collar is only slightly wider than deep; both of these body regions are more muscular than in other torquaratorids, which presumably facilitates burrowing. The proboscis complex, in contrast to that of shallow-living enteropneusts, lacks a pericardial sac and is located relatively posteriorly in the proboscis stalk. The stomochord is separated from the main course of the gut by the intervention of a small, plate-like proboscis skeleton lacking posterior horns. The most anterior region of the trunk houses the pharynx, in which the pharyngeal skeletal bars are not connected by synapticles. The postpharyngeal trunk comprises three intestinal regions: prehepatic, hepatic (with conspicuous sacculations), and posthepatic. On either side of the worm, a flap of body wall (lateral wing) runs the entire length of the trunk. The two lateral wings can wrap the body so their edges meet in the dorsal midline, although they often gape open along the pharyngeal region. The holotype is a female (presumably the species is gonochoric) with numerous ovaries located in the lateral wings along the pharyngeal region. Each larger ovary contains a single primary oocyte (up to 1,500 μm in diameter) and bulges outwards in an epidermal pouch attached to the rest of the body by a slender stalk. Such externalized ovaries are unprecedented in any animal, and nothing is yet known of their role in the reproductive biology of A. aurantiacus. PMID:22419131

  14. Zoology: War of the Worms.

    PubMed

    Telford, Maximilian J; Copley, Richard R

    2016-04-25

    The phylogenetic affinities of Xenacoelomorpha - the phylum comprising Xenoturbella bocki and acoelomorph worms - are debated. Two recent studies conclude they represent the earliest branching bilaterally symmetrical animals, but additional tests may be needed to confirm this notion. PMID:27115693

  15. Programmed Worms.

    ERIC Educational Resources Information Center

    Piele, Donald T.

    1982-01-01

    A hungry worm is looking for something to eat according to very specific rules, and the path he takes is a graph. The problem is detailed in Applesoft BASIC using low resolution graphics for worms that turn 90 degrees and high resolution for worms that can turn 45 degrees. (MP)

  16. Time's Arrows Today

    NASA Astrophysics Data System (ADS)

    Savitt, Steven F.

    1997-06-01

    Introduction; Part I. Cosmology and Time's Arrow: 1. Time, gravity, and quantum mechanics W. Unruh; 2. Cosmology, time's arrow, and that old double standard H. Price; Part II. Quantum Theory and Time's Arrow: 3. Time's arrow and the quantum measurement problem A. Leggett; 4. Time, decoherence, and 'reversible' measurements P. Stamp; 5. Time flows, non-locality, and measurement in quantum mechanics S. McCall; 6. Stochastically branching spacetime topology R. Douglas; Part III. Thermodynamics and Time's Arrow: 7. The elusive object of desire: in pursuit of the kinetic equations and the second law L. Sklar; 8. Time in experience and in theoretical description of the world L. Sklar; 9. When and why does entropy increase? M. Barrett and E. Sober; Part IV. Time Travel and Time's Arrow: 10. Closed causal chains P Horwich; 11. Recent work on time travel J. Earman.

  17. Ribbon worm relationships: a phylogeny of the phylum Nemertea.

    PubMed

    Thollesson, Mikael; Norenburg, Jon L

    2003-02-22

    We present the most extensive phylogenetic analysis to date, to our knowledge, of higher-level nemertean relationships, based on sequence data from four different genes (the nuclear genes for nuclear large subunit rRNA (28S rRNA) and histone H3 (H3), and the mitochondrial genes for mitochondrial large subunit rRNA (16S rRNA) and cytochrome c oxidase subunit I (COI)). Well-supported clades are, in general, compatible with earlier, more limited, analyses, and current classification is largely in agreement with our results, although there are some notable exceptions. Bdellonemertea (represented by Malacobdella) is found to be a part of Monostilifera, and Polystilifera is the monophyletic sister group to Monostilifera. Cratenemertidae is the sister group to the remaining monostiliferans (including Malacobdella), a group to which we apply the new name Distromatonemertea. Heteronemertea is monophyletic and forms a clade with Hubrechtella; for this clade we introduce the name Pilidiophora. Finally, Pilidiophora and Hoplonemertea (with Malacobdella) form a monophyletic group, and we introduce the name Neonemertea to refer to this group. Palaeonemertea is found to be non-monophyletic and basal among nemerteans. PMID:12639321

  18. A Computer's Arrow of Time

    NASA Astrophysics Data System (ADS)

    Schulman, L. S.

    2005-12-01

    Some researchers believe that the psychological or consciousness arrow of time is a consequence of the thermodynamic arrow. Some don't. As for many issues in this area, the disagreement revolves about fundamental and undebatable assumptions. As a contribution to this standoff I consider the extent to which a computer---presumably governed by nothing more than the thermodynamic arrow---can be said to possess a psychological arrow. My contention is that the parallels are sufficiently strong as to leave little room for an independent psychological arrow. Reservations are nevertheless expressed on the complete objectivity of the thermodynamic arrow.

  19. Arrows: A Special Case of Graphic Communication.

    ERIC Educational Resources Information Center

    Hardin, Pris

    The purpose of this paper is to examine arrow design in relation to the type of pointing, connecting, or processing involved. Three possible approaches to the investigation of arrows as graphic communication include research: by arrow function, relating message structure to arrow design, and linking user expectations to arrow design. The following…

  20. Mini-hemoglobins from nemertean worms.

    PubMed

    Vandergon, Thomas L; Riggs, Austen F

    2008-01-01

    Hemoglobins (Hbs) found in members of the phylum Nemertea are smaller than any other known Hb molecules. These mini-Hbs have been of great interest because of their unique three-dimensional structure and their stable ligand-binding properties. Also of interest is the expression of mini-Hb in neural tissue, body wall muscle tissue, and red blood cells. This chapter outlines methods that may be used to isolate and purify functional mini-Hbs from all three tissue types in nemertean worms. PMID:18237651

  1. Worm-stars and half-worms

    PubMed Central

    Hodgkin, Jonathan; Clark, Laura C; Gravato-Nobre, Maria J

    2014-01-01

    In a recent paper, we reported the isolation and surprising effects of two new bacterial pathogens for Caenorhabditis and related nematodes. These two pathogens belong to the genus Leucobacter and were discovered co-infecting a wild isolate of Caenorhabditis that had been collected in Cape Verde. The interactions of these bacteria with C. elegans revealed both unusual mechanisms of pathogenic attack, and an unexpected defense mechanism on the part of the worm. One pathogen, known as Verde1, is able to trap swimming nematodes by sticking their tails together, resulting in the formation of “worm-star” aggregates, within which worms are killed and degraded. Trapped larval worms, but not adults, can sometimes escape by undergoing whole-body autotomy into half-worms. The other pathogen, Verde2, kills worms by a different mechanism associated with rectal infection. Many C. elegans mutants with alterations in surface glycosylation are resistant to Verde2 infection, but hypersensitive to Verde1, being rapidly killed without worm-star formation. Conversely, surface infection of wild-type worms with Verde1 is mildly protective against Verde2. Thus, there are trade-offs in susceptibility to the two bacteria. The Leucobacter pathogens reveal novel nematode biology and provide powerful tools for exploring nematode surface properties and bacterial susceptibility. PMID:25254146

  2. 50 CFR Appendix A to Part 622 - Species Tables

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... duster Family Serpulidae Spirobranchus giganteus, Christmas tree worm IV. Mollusks—Phylum Mollusca A... clinging Stenorhynchus seticornis, Yellowline arrow Family Palaemonida Periclimenes spp., Cleaner...

  3. 50 CFR Appendix A to Part 622 - Species Tables

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ..., Magnificent duster Family Serpulidae Spirobranchus giganteus, Christmas tree worm IV. Mollusks—Phylum Mollusca.... sculptus, Green clinging Stenorhynchus seticornis, Yellowline arrow Family Palaemonida Periclimenes...

  4. 50 CFR Appendix A to Part 622 - Species Tables

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ..., Magnificent duster Family Serpulidae Spirobranchus giganteus, Christmas tree worm IV. Mollusks—Phylum Mollusca.... sculptus, Green clinging Stenorhynchus seticornis, Yellowline arrow Family Palaemonida Periclimenes...

  5. The WORM site: worm.csirc.net

    SciTech Connect

    Jones, T.

    2000-07-01

    The Write One, Run Many (WORM) site (worm.csirc.net) is the on-line home of the WORM language and is hosted by the Criticality Safety Information Resource Center (CSIRC) (www.csirc.net). The purpose of this web site is to create an on-line community for WORM users to gather, share, and archive WORM-related information. WORM is an embedded, functional, programming language designed to facilitate the creation of input decks for computer codes that take standard ASCII text files as input. A functional programming language is one that emphasizes the evaluation of expressions, rather than execution of commands. The simplest and perhaps most common example of a functional language is a spreadsheet such as Microsoft Excel. The spreadsheet user specifies expressions to be evaluated, while the spreadsheet itself determines the commands to execute, as well as the order of execution/evaluation. WORM functions in a similar fashion and, as a result, is very simple to use and easy to learn. WORM improves the efficiency of today's criticality safety analyst by allowing: (1) input decks for parameter studies to be created quickly and easily; (2) calculations and variables to be embedded into any input deck, thus allowing for meaningful parameter specifications; (3) problems to be specified using any combination of units; and (4) complex mathematically defined models to be created. WORM is completely written in Perl. Running on all variants of UNIX, Windows, MS-DOS, MacOS, and many other operating systems, Perl is one of the most portable programming languages available. As such, WORM works on practically any computer platform.

  6. Gummy Worm Measurements.

    ERIC Educational Resources Information Center

    Callison, Priscilla L.; Anshutz, Ramona J.; Wright, Emmett L.

    1997-01-01

    Describes a science activity using gummy worms to help primary students develop the mathematical skills of measurement concepts, units of measure, estimation, and graphing needed for science learning. Groups of two begin by estimating the number of gummy worms in their package and identifying the colors they expect to find. Individual worms are…

  7. The Father Christmas worm

    NASA Technical Reports Server (NTRS)

    Green, James L.; Sisson, Patricia L.

    1989-01-01

    Given here is an overview analysis of the Father Christmas Worm, a computer worm that was released onto the DECnet Internet three days before Christmas 1988. The purpose behind the worm was to send an electronic mail message to all users on the computer system running the worm. The message was a Christmas greeting and was signed 'Father Christmas'. From the investigation, it was determined that the worm was released from a computer (node number 20597::) at a university in Switzerland. The worm was designed to travel quickly. Estimates are that it was copied to over 6,000 computer nodes. However, it was believed to have executed on only a fraction of those computers. Within ten minutes after it was released, the worm was detected at the Space Physics Analysis Network (SPAN), NASA's largest space and Earth science network. Once the source program was captured, a procedural cure, using the existing functionality of the computer operating systems, was quickly devised and distributed. A combination of existing computer security measures, the quick and accurate procedures devised to stop copies of the worm from executing, and the network itself, were used to rapidly provide the cure. These were the main reasons why the worm executed on such a small percentage of nodes. This overview of the analysis of the events concerning the worm is based on an investigation made by the SPAN Security Team and provides some insight into future security measures that will be taken to handle computer worms and viruses that may hit similar networks.

  8. The Length of Time's Arrow

    SciTech Connect

    Feng, Edward H.; Crooks, Gavin E.

    2008-08-21

    An unresolved problem in physics is how the thermodynamic arrow of time arises from an underlying time reversible dynamics. We contribute to this issue by developing a measure of time-symmetry breaking, and by using the work fluctuation relations, we determine the time asymmetry of recent single molecule RNA unfolding experiments. We define time asymmetry as the Jensen-Shannon divergencebetween trajectory probability distributions of an experiment and its time-reversed conjugate. Among other interesting properties, the length of time's arrow bounds the average dissipation and determines the difficulty of accurately estimating free energy differences in nonequilibrium experiments.

  9. MAINE MARINE WORM HABITAT

    EPA Science Inventory

    WORM provides a generalized representation at 1:24,000 scale of commercially harvested marine worm habitat in Maine, based on Maine Department of Marine Resources data from 1970's. Original maps were created by MDMR and published by USF&WS as part of the ""&quo...

  10. A subquantum arrow of time

    NASA Astrophysics Data System (ADS)

    Nieuwenhuizen, Theo M.

    2014-04-01

    The outcome of a single quantum experiment is unpredictable, except in a pure-state limit. The definite process that takes place in the apparatus may either be intrinsically random or be explainable from a deeper theory. While the first scenario is the standard lore, the latter implies that quantum mechanics is emergent. In that case, it is likely that one has to reconsider radiation by accelerated charges as a physical effect, which thus must be compensated by an energy input. Stochastic electrodynamics, for example, asserts that the vacuum energy arises from classical fluctuations with energy 1/2hslashω per mode. In such theories the stability of the hydrogen ground state will arise from energy input from fluctuations and output by radiation, hence due to an energy throughput. That flux of energy constitutes an arrow of time, which we call the "subquantum arrow of time". It is related to the stability of matter and it is more fundamental than, e.g., the thermodynamic and cosmological arrows.

  11. Celebrate Worm Week!

    ERIC Educational Resources Information Center

    Crocker, Betty; Garrett, Sandra; Trammell, Laura Z.

    1998-01-01

    Focuses on an extended learning experience with worms as the main topic in which students collect and organize information and choose an experimental question. Based on the constructivist theory of learning. Contains 17 references. (DDR)

  12. Worms, Worms, and Even More Worms: A Vermicomposting Guide for Teachers.

    ERIC Educational Resources Information Center

    California Integrated Waste Management Board, Sacramento.

    This guide is designed to help teachers gain a better understanding of how to get a worm vermicomposting system started. It provides reference curricula materials for using worms in the classroom. Chapters include: (1) "Why Worm Vermicomposting;" (2) "Basics of Vermicomposting;" (3) "Worm Facts;" (4) "Classroom Activities;" (5) "Lab Activities;"…

  13. Arrows in Comprehending and Producing Mechanical Diagrams

    ERIC Educational Resources Information Center

    Heiser, Julie; Tversky, Barbara

    2006-01-01

    Mechanical systems have structural organizations--parts, and their relations--and functional organizations--temporal, dynamic, and causal processes--which can be explained using text or diagrams. Two experiments illustrate the role of arrows in diagrams of mechanical systems. In Experiment 1, people described diagrams with or without arrows,…

  14. Worm Infections in Children.

    PubMed

    Weatherhead, Jill E; Hotez, Peter J

    2015-08-01

    • On the basis of research evidence, worm infections are important global child health conditions causing chronic disability that lasts from childhood into adulthood (Table 1). (2)(3) Evidence Quality: B • On the basis of research evidence, the major worm infections found in developing countries include ascariasis, trichuriasis, hookworm infection, and schistosomiasis; toxocariasis, enterobiasis, and cysticercosis are also found in poor regions of North America and Europe. (4)(9)(13) Evidence Quality: B • On the basis of expert consensus, children and adolescents are often vulnerable to acquiring large numbers of worms, ie, high-intensity infections (Fig 1)(21)(22)(23) Evidence Quality: D • On the basis of expert consensus and research evidence, moderate and heavy worm burdens cause increased morbidity because of growth and intellectual stunting in children and adolescents. Many of these effects may result from helminth-induced malnutrition. (21)(22)(23) Evidence Quality: C • On the basis of expert consensus and research evidence, worm infections are also commonly associated with eosinophilia. (48) (49) Evidence Quality: B • On the basis of research evidence as well as consensus, helminthes can cause inflammation in the lung (asthma), gastrointestinal tract (enteritis and colitis), liver (hepatitis and fibrosis), and urogenital tract. (7)(21)(22)(23)(27)(28)(40)(41)(43) Evidence Quality: B • On the basis of research evidence, microscopy techniques for diagnosis of worm infections in children often exhibit suboptimal sensitivities and specificities, necessitating new or improved diagnostic modalities such as polymerase chain reaction. (54)(55) Evidence Quality: A • On the basis of research evidence and expert consensus, mass drug administration (“preventive chemotherapy”) has becomea standard practice for ministries of health in low- and middle-income countries to control intestinal helminth infections and schistosomiasis. (67)(68) Evidence

  15. Concept, Characteristics and Defending Mechanism of Worms

    NASA Astrophysics Data System (ADS)

    Tang, Yong; Luo, Jiaqing; Xiao, Bin; Wei, Guiyi

    Worms are a common phenomenon in today's Internet and cause tens of billions of dollars in damages to businesses around the world each year. This article first presents various concepts related to worms, and then classifies the existing worms into four types- Internet worms, P2P worms, email worms and IM (Instant Messaging) worms, based on the space in which a worm finds a victim target. The Internet worm is the focus of this article. We identify the characteristics of Internet worms in terms of their target finding strategy, propagation method and anti-detection capability. Then, we explore state-of-the-art worm detection and worm containment schemes. This article also briefly presents the characteristics, defense methods and related research work of P2P worms, email worms and IM worms. Nowadays, defense against worms remains largely an open problem. In the end of this article, we outline some future directions on the worm research.

  16. A transcriptomic analysis of the phylum Nematoda.

    PubMed

    Parkinson, John; Mitreva, Makedonka; Whitton, Claire; Thomson, Marian; Daub, Jennifer; Martin, John; Schmid, Ralf; Hall, Neil; Barrell, Bart; Waterston, Robert H; McCarter, James P; Blaxter, Mark L

    2004-12-01

    The phylum Nematoda occupies a huge range of ecological niches, from free-living microbivores to human parasites. We analyzed the genomic biology of the phylum using 265,494 expressed-sequence tag sequences, corresponding to 93,645 putative genes, from 30 species, including 28 parasites. From 35% to 70% of each species' genes had significant similarity to proteins from the model nematode Caenorhabditis elegans. More than half of the putative genes were unique to the phylum, and 23% were unique to the species from which they were derived. We have not yet come close to exhausting the genomic diversity of the phylum. We identified more than 2,600 different known protein domains, some of which had differential abundances between major taxonomic groups of nematodes. We also defined 4,228 nematode-specific protein families from nematode-restricted genes: this class of genes probably underpins species- and higher-level taxonomic disparity. Nematode-specific families are particularly interesting as drug and vaccine targets. PMID:15543149

  17. A Can of Sea Worms

    ERIC Educational Resources Information Center

    Zinn, Donald J.

    1977-01-01

    A comprehensive discussion of the free-living worms that inhabit the beaches and subtidal bottoms of the Cape Cod shoreline is presented. Methods for the location, collection, preservation, and identification of sea worms are identified. (BT)

  18. Welcome to Worm Central

    ERIC Educational Resources Information Center

    Madison, Lisa; Rydant, A. L.; Jobin, Raymond A.; Sterling, Cindy

    2006-01-01

    This article describes a vermicomposting program at Epping Elementary School in New Hampshire. The "Feed It to the Worms: A Vermicomposting Geographic Curriculum," developed by the New Hampshire Geographic Alliance and led by fourth grade teacher, Lisa Madison, fits perfectly into the school's ongoing Artist-in-Residence program, where students…

  19. "Mighty Worm" Piezoelectric Actuator

    NASA Technical Reports Server (NTRS)

    Bamford, Robert M.; Wada, Ben K.; Moore, Donald M.

    1994-01-01

    "Mighty Worm" piezoelectric actuator used as adjustable-length structural member, active vibrator or vibration suppressor, and acts as simple (fixed-length) structural member when inactive. Load force not applied to piezoelectric element in simple-structural-member mode. Piezoelectric element removed from load path when not in use.

  20. Metagenomics of the Methane Ice Worm, Hesiocaeca methanicola

    NASA Astrophysics Data System (ADS)

    Goodwin, K. D.; Edsall, L.; Xin, W.; Head, S. R.; Gelbart, T.; Wood, A. M.; Gaasterland, T.

    2012-12-01

    The methane ice worm (Hesiocaeca methanicola) is a polychaete found on methane hydrate deposits for which there appears to be no publically available genomic or metagenomic data. Methane ice worms were collected in 2009 by the Johnson-Sea-Link submersible (543m depth; N 27:44.7526 W 91:13.3168). Next-generation sequencing (HiSeq2000) was applied to samples of tissue and gut contents. A subset of the assembled data (40M reads, randomly selected) was run through MG-RAST. Preliminary results for the gut content (1,269,153 sequences, average length 202 bp) indicated that 0.1% of the sequences contained ribosomal RNA genes with the majority (67%) classified as Bacteria, a relatively small per cent (1.4%) as Archae, and 31% as Eukaryota. Campylobacterales was the predominant order (14%), with unclassified (7.5%) and Desulfobacterales (4%) being the next dominant. Preliminary results for the worm tissue (2,716,461 sequences, average length 241 bp) indicated that the majority of sequences were Eukaryota (73%), with 256 sequences classified as phylum Annelida and 58% of those belonging to class Polychaeta. For the bacterial sequences obtained from the tissue samples, the predominant order was Actinomycetales (2.7%). For both the tissue and gut content samples, the majority of proteins were classified as clustering-based subsystems. This preliminary analysis will be compared to an assembly consisting of 40M of the highest quality reads.; methane ice worms on methane hydrate

  1. Galactic worms. I - Catalog of worm candidates

    NASA Technical Reports Server (NTRS)

    Koo, Bon-Chul; Heiles, Carl; Reach, William T.

    1992-01-01

    A catalog of candidates for the Galactic worms that are possibly the walls surrounding the superbubbles is compiled; 118 isolated structures that appear both in H I and in IR (60 and 100 microns). Fifty-two are possibly associated with H II regions. It is found that the 100-micron emissivity increases systematically toward the Galactic interior, which is consistent with the increase of the general interstellar radiation field. The 100-micron emissivity of the structures associated with the H II regions is larger than that of the structures without associated H II regions. The 60-100-micron ratio is large, 0.28 +/- 0.03, which may indicate that the grains associated with the atomic gas have a relatively large population of small grains. Thirty-five structures appear in the 408-MHz continuum. The IR and the radio continuum properties suggest that the 408-MHz continuum emission in those structures is very likely thermal. The implications of these results on the ionization of gas far from the Galactic plane are discussed.

  2. The design of worm gear sets

    NASA Technical Reports Server (NTRS)

    Razzaghi, Andrea I.

    1987-01-01

    A method is presented for designing worm gear sets to meet torque multiplication requirements. First, the fundamentals of worm gear design are discussed, covering worm gear set nomenclature, kinematics and proportions, force analysis, and stress analysis. Then, a suggested design method is discussed, explaining how to take a worm gear set application, and specify a complete worm gear set design. The discussions are limited to cylindrical worm gear sets that have a 90 deg shaft angle between the worm and the mating gear.

  3. Arrow injuries in North East Nigeria.

    PubMed

    Madziga, A G

    2003-06-01

    Arrow injuries are an extinct form of injury in most parts of the developed world but constitute 0.1% of emergency admissions in the University of Maiduguri Teaching Hospital annually. This is a retrospective study of arrow injuries carried out over a ten-year period (1989-1999) in order to study the reasons for its continued incidence the presentation and the experiences in the management of these injuries. There were 73 cases of arrow injuries and were all males with a peak age incidence of 31-40 years of age. Majority were farmers, cattle herdsmen and traders from the northeast region of Nigeria and the neighbouring republic of Cameroon, Chad and Niger. The various reasons for the injuries were armed robbery in 41%, communal clashes 20.5%, dispute between farmers and cattle herdsmen 13%, and cattle theft 8%. Majority were clinically stable on presentation with arrows in the head, neck, chest and abdomen this resulted in various surgical procedures in order to remove the arrows and repair damaged viscera. Unstable presentations resulted in mortalities (4.1%) preoperatively. Wound infection was the most common complication in patients who presented late. Improvements in the socio-economic conditions in the region and legislation on the use of these weapons would reduce the incidence of these injuries. PMID:14529215

  4. Worm Gear With Hydrostatic Engagement

    NASA Technical Reports Server (NTRS)

    Chaiko, Lev I.

    1994-01-01

    In proposed worm-gear transmission, oil pumped at high pressure through meshes between teeth of gear and worm coil. Pressure in oil separates meshing surfaces slightly, and oil reduces friction between surfaces. Conceived for use in drive train between gas-turbine engine and rotor of helicopter. Useful in other applications in which weight critical. Test apparatus simulates and measures some loading conditions of proposed worm gear with hydrostatic engagement.

  5. Decision Making in the Arrow of Time

    NASA Astrophysics Data System (ADS)

    Roldán, Édgar; Neri, Izaak; Dörpinghaus, Meik; Meyr, Heinrich; Jülicher, Frank

    2015-12-01

    We show that the steady-state entropy production rate of a stochastic process is inversely proportional to the minimal time needed to decide on the direction of the arrow of time. Here we apply Wald's sequential probability ratio test to optimally decide on the direction of time's arrow in stationary Markov processes. Furthermore, the steady-state entropy production rate can be estimated using mean first-passage times of suitable physical variables. We derive a first-passage time fluctuation theorem which implies that the decision time distributions for correct and wrong decisions are equal. Our results are illustrated by numerical simulations of two simple examples of nonequilibrium processes.

  6. The internet worm

    NASA Technical Reports Server (NTRS)

    Denning, Peter J.

    1989-01-01

    In November 1988 a worm program invaded several thousand UNIX-operated Sun workstations and VAX computers attached to the Research Internet, seriously disrupting service for several days but damaging no files. An analysis of the work's decompiled code revealed a battery of attacks by a knowledgeable insider, and demonstrated a number of security weaknesses. The attack occurred in an open network, and little can be inferred about the vulnerabilities of closed networks used for critical operations. The attack showed that passwork protection procedures need review and strengthening. It showed that sets of mutually trusting computers need to be carefully controlled. Sharp public reaction crystalized into a demand for user awareness and accountability in a networked world.

  7. Molecular determinants archetypical to the phylum Nematoda

    PubMed Central

    2009-01-01

    Background Nematoda diverged from other animals between 600–1,200 million years ago and has become one of the most diverse animal phyla on earth. Most nematodes are free-living animals, but many are parasites of plants and animals including humans, posing major ecological and economical challenges around the world. Results We investigated phylum-specific molecular characteristics in Nematoda by exploring over 214,000 polypeptides from 32 nematode species including 27 parasites. Over 50,000 nematode protein families were identified based on primary sequence, including ~10% with members from at least three different species. Nearly 1,600 of the multi-species families did not share homology to Pfam domains, including a total of 758 restricted to Nematoda. Majority of the 462 families that were conserved among both free-living and parasitic species contained members from multiple nematode clades, yet ~90% of the 296 parasite-specific families originated only from a single clade. Features of these protein families were revealed through extrapolation of essential functions from observed RNAi phenotypes in C. elegans, bioinformatics-based functional annotations, identification of distant homology based on protein folds, and prediction of expression at accessible nematode surfaces. In addition, we identified a group of nematode-restricted sequence features in energy-generating electron transfer complexes as potential targets for new chemicals with minimal or no toxicity to the host. Conclusion This study identified and characterized the molecular determinants that help in defining the phylum Nematoda, and therefore improved our understanding of nematode protein evolution and provided novel insights for the development of next generation parasite control strategies. PMID:19296854

  8. Early Cambrian origin of modern food webs: evidence from predator arrow worms

    PubMed Central

    Vannier, J; Steiner, M; Renvoisé, E; Hu, S.-X; Casanova, J.-P

    2006-01-01

    Although palaeontological evidence from exceptional biota demonstrates the existence of diverse marine communities in the Early Cambrian (approx. 540–520 Myr ago), little is known concerning the functioning of the marine ecosystem, especially its trophic structure and the full range of ecological niches colonized by the fauna. The presence of a diverse zooplankton in Early Cambrian oceans is still an open issue. Here we provide compelling evidence that chaetognaths, an important element of modern zooplankton, were present in the Early Cambrian Chengjiang biota with morphologies almost identical to Recent forms. New information obtained from the lowermost Cambrian of China added to previous studies provide convincing evidence that protoconodont-bearing animals also belonged to chaetognaths. Chaetognaths were probably widespread and diverse in the earliest Cambrian. The obvious raptorial function of their circumoral apparatuses (grasping spines) places them among the earliest active predator metazoans. Morphology, body ratios and distribution suggest that the ancestral chaetognaths were planktonic with possible ecological preferences for hyperbenthic niches close to the sea bottom. Our results point to the early introduction of prey–predator relationships into the pelagic realm, and to the increase of trophic complexity (three-level structure) during the Precambrian–Cambrian transition, thus laying the foundations of present-day marine food chains. PMID:17254986

  9. Early Cambrian origin of modern food webs: evidence from predator arrow worms.

    PubMed

    Vannier, J; Steiner, M; Renvoisé, E; Hu, S-X; Casanova, J-P

    2007-03-01

    Although palaeontological evidence from exceptional biota demonstrates the existence of diverse marine communities in the Early Cambrian (approx. 540-520 Myr ago), little is known concerning the functioning of the marine ecosystem, especially its trophic structure and the full range of ecological niches colonized by the fauna. The presence of a diverse zooplankton in Early Cambrian oceans is still an open issue. Here we provide compelling evidence that chaetognaths, an important element of modern zooplankton, were present in the Early Cambrian Chengjiang biota with morphologies almost identical to Recent forms. New information obtained from the lowermost Cambrian of China added to previous studies provide convincing evidence that protoconodont-bearing animals also belonged to chaetognaths. Chaetognaths were probably widespread and diverse in the earliest Cambrian. The obvious raptorial function of their circumoral apparatuses (grasping spines) places them among the earliest active predator metazoans. Morphology, body ratios and distribution suggest that the ancestral chaetognaths were planktonic with possible ecological preferences for hyperbenthic niches close to the sea bottom. Our results point to the early introduction of prey-predator relationships into the pelagic realm, and to the increase of trophic complexity (three-level structure) during the Precambrian-Cambrian transition, thus laying the foundations of present-day marine food chains. PMID:17254986

  10. Distribution and biomass of arrow worms (Chaetognatha) in Golfo de Nicoya and Golfo Dulce, Costa Rica.

    PubMed

    Hossfeld, B

    1996-12-01

    The chaetognath species guild was analyzed from samples collected during the cruise of the German RV Victor Hensen to the Pacific coast of Costa Rica in December 1993 and February, 1994, finding the following ten species of the genera Sagitta and Krohnitta: S. enflata, S. hexaptera, S. pacifica, S. neglecta, S. regularis, S. bedoti, S. friderici, S. popovicii, S. pulchra and K. pacifica. Because of their distributional patterns in the study area these species were ascribed to the following ecological groups: neritic, semi-neritic and oceanic. A strong gradient in species richness from offshore to inshore waters (8 to one respectively) was found in both gulf systems. Inshore chaetognaths were dominated by juveniles and adults of S. friderici in Golfo de Nicoya and by S. popovicii in Golfo Dulce. Biomass spectra were more continuous and of wider range in the Golfo Dulce area showing a dominance of larger chaetognaths, suggesting a more general developed pelagic system in Golfo Dulce, where larger chaetognaths might structure the plankton community by strong grazing pressure from above. PMID:9393651

  11. Entomophthoromycota: a new phylum and reclassification for entomophthoroid fungi

    Technology Transfer Automated Retrieval System (TEKTRAN)

    One result of the recent phylogenetically based rejection of the phylum Zygomycota was the description of the subphylum Entomophthoromycotina (not assigned to any phylum) for fungi traditionally treated in the order Entomophthorales. More extensive gene-based analyses of these fungi suggest that the...

  12. The worm that lived

    PubMed Central

    Chen, Hwei-yen; Maklakov, Alexei A

    2013-01-01

    Organisms age because of the “selection shadow”—the decline of the force of natural selection with age. Seemingly straightforward corollary of this theory is the Medawar-Williams prediction, which maintains that increased extrinsic (non-aging) mortality will result in the evolution of accelerated aging and decreased longevity. Despite its centrality to modern thinking about the ultimate causes of aging, this prediction ignores the fact that mortality is often a non-random process depending on individual condition. Increased condition-dependent mortality inescapably results in increased selection for resistance against the agent of mortality. Provided that resistance to various stressors is commonly associated with increased longevity, the evolutionary outcome is no longer certain. We recently documented this experimentally by showing that populations of Caenorhabditis remanei evolved to live shorter under high extrinsic mortality, but only when mortality was applied haphazardly. On the contrary, when extrinsic mortality was caused by heat-shock, populations experiencing the same rate of increased mortality evolved greater longevities, notwithstanding increased “selection shadow.” Intriguingly, stress-resistant and long-lived worms were also more fecund. We discuss these results in the light of recent theoretical developments, such as condition-environment interactions and hyperfunction theory of aging. PMID:24778930

  13. Arrow 227: Air transport system design simulation

    NASA Technical Reports Server (NTRS)

    Bontempi, Michael; Bose, Dave; Brophy, Georgeann; Cashin, Timothy; Kanarios, Michael; Ryan, Steve; Peterson, Timothy

    1992-01-01

    The Arrow 227 is a student-designed commercial transport for use in a overnight package delivery network. The major goal of the concept was to provide the delivery service with the greatest potential return on investment. The design objectives of the Arrow 227 were based on three parameters; production cost, payload weight, and aerodynamic efficiency. Low production cost helps to reduce initial investment. Increased payload weight allows for a decrease in flight cycles and, therefore, less fuel consumption than an aircraft carrying less payload weight and requiring more flight cycles. In addition, fewer flight cycles will allow a fleet to last longer. Finally, increased aerodynamic efficiency in the form of high L/D will decrease fuel consumption.

  14. Phylogeny and classification of phylum Cercozoa (Protozoa).

    PubMed

    Cavalier-Smith, Thomas; Chao, Ema E Y

    2003-10-01

    The protozoan phylum Cercozoa embraces numerous ancestrally biciliate zooflagellates, euglyphid and other filose testate amoebae, chlorarachnean algae, phytomyxean plant parasites (e.g. Plasmodiophora, Phagomyxa), the animal-parasitic Ascetosporea, and Gromia. We report 18S rRNA sequences of 27 culturable zooflagellates, many previously of unknown taxonomic position. Phylogenetic analysis shows that all belong to Cercozoa. We revise cercozoan classification in the light of our analysis and ultrastructure, adopting two subphyla: Filosa subphyl. nov. a clade comprising Monadofilosa and Reticulofilosa, ranked as superclasses, ancestrally having the same very rare base-pair substitution as all opisthokonts; and subphylum Endomyxa emend. comprising classes Phytomyxea (Plasmodiophorida, Phagomyxida), Ascetosporea (Haplosporidia, Paramyxida, Claustrosporida ord. nov.) and Gromiidea cl. nov., which did not. Monadofilosa comprise Sarcomonadea, zooflagellates with a propensity to glide on their posterior cilium and/or generate filopodia (e.g. Metopion; Cercomonas; Heteromitidae - Heteromita, Bodomorpha, Proleptomonas and Allantion) and two new classes: Imbricatea (with silica scales: Euglyphida; Thaumatomonadida, including Alias, Thaumatomastix) and Thecofilosea (Cryomonadida; Tectofilosida ord. nov. - non-scaly filose amoebae, e.g. Pseudodifflugia). Reticulofilosa comprise classes Chlorarachnea, Spongomonadea and Proteomyxidea (e.g. Massisteria, Gymnophrys, a Dimorpha-like protozoan). Cercozoa, now with nine classes and 17 orders (four new), will probably include many, possibly most, other filose and reticulose amoebae and zooflagellates not yet assigned to phyla. PMID:14658494

  15. A Phylogenomic Analysis of the Bacterial Phylum Fibrobacteres

    PubMed Central

    Abdul Rahman, Nurdyana; Parks, Donovan H.; Vanwonterghem, Inka; Morrison, Mark; Tyson, Gene W.; Hugenholtz, Philip

    2016-01-01

    The Fibrobacteres has been recognized as a bacterial phylum for over a decade, but little is known about the group beyond its environmental distribution, and characterization of its sole cultured representative genus, Fibrobacter, after which the phylum was named. Based on these incomplete data, it is thought that cellulose hydrolysis, anaerobic metabolism, and lack of motility are unifying features of the phylum. There are also contradicting views as to whether an uncultured sister lineage, candidate phylum TG3, should be included in the Fibrobacteres. Recently, chitin-degrading cultured representatives of TG3 were isolated from a hypersaline soda lake, and the genome of one species, Chitinivibrio alkaliphilus, sequenced and described in detail. Here, we performed a comparative analysis of Fibrobacter succinogenes, C. alkaliphilus and eight near or substantially complete Fibrobacteres/TG3 genomes of environmental populations recovered from termite gut, anaerobic digester, and sheep rumen metagenomes. We propose that TG3 should be amalgamated with the Fibrobacteres phylum based on robust monophyly of the two lineages and shared character traits. Polymer hydrolysis, using a distinctive set of glycoside hydrolases and binding domains, appears to be a prominent feature of members of the Fibrobacteres. Not all members of this phylum are strictly anaerobic as some termite gut Fibrobacteres have respiratory chains adapted to the microaerophilic conditions found in this habitat. Contrary to expectations, flagella-based motility is predicted to be an ancestral and common trait in this phylum and has only recently been lost in F. succinogenes and its relatives based on phylogenetic distribution of flagellar genes. Our findings extend current understanding of the Fibrobacteres and provide an improved basis for further investigation of this phylum. PMID:26779135

  16. Arrow poisons in south Asia. Part 1. Arrow poisons in ancient India.

    PubMed

    Bisset, N G; Mazars, G

    1984-10-01

    The use of arrow poisons in ancient India is discussed. While it is possible that Mesolithic hunting communities may have applied poison to their arrows, passages in the Rg Veda and Atharva Veda indicate its use in warfare. The meaning of the word -ala, used in the Rg Veda to denote the poison smeared on the arrowheads, is examined; but the available evidence, while almost certainly excluding a mineral (arsenical) source, does not allow a conclusion to be drawn between an animal and/or plant origin. Certain hymns in the Atharva Veda point to aconite tubers as one source. Later Sanskrit (and Buddhist) literature shows that poisoned arrows continued to be used and that a second source of poison was (putrefying) snakes--a source confirmed by an account in the classical literature of Alexander the Great's campaign in western India. Detailed descriptions of the symptoms and methods of treatment of wounds caused by poisoned arrows are to be found in the Sanskrit medical literature. PMID:6394907

  17. GreenArrow version 1.0

    Energy Science and Technology Software Center (ESTSC)

    2006-03-29

    GreenArrow is a visualization program for displaying directed graphs that can use text in place of lines to represent the edges between nodes. This text can be animated to show the link direction, and allow for more text to be displayed then would normally be allowed. The text is also tapered and arced to show direction. The node labels can be wrapped around the node to avoid label crossing as well. The program is interactive,more » and allows the user to zoom, pan and rotate a graph, as well as manipulate the individual nodes.« less

  18. Arrow of time in string theory

    NASA Astrophysics Data System (ADS)

    McInnes, Brett

    2007-10-01

    Inflation allows the problem of the arrow of time to be understood as a question about the structure of spacetime: why was the intrinsic curvature of the earliest spatial sections so much better behaved than it might have been? This is really just the complement of a more familiar problem: what mechanism prevents the extrinsic curvature of the earliest spatial sections from diverging, as classical general relativity suggests? We argue that the stringy version of “creation from nothing”, sketched by Ooguri, Vafa, and Verlinde, solves both of these problems at once. The argument, while very simple, hinges on some of the deepest theorems in global differential geometry. These results imply that when a spatially toral spacetime is created from nothing, the earliest spatial sections are forced to be [quasi-classically] exactly locally isotropic. This local isotropy, in turn, forces the inflaton into its minimal-entropy state. The theory explains why the arrow does not reverse in black holes or in a cosmic contraction, if any.

  19. Of FOXes and Forgetful Worms.

    PubMed

    Alic, Nazif

    2016-03-01

    Age-related cognitive decline is one of the most haunting aspects of human aging. In a recent publication, Coleen Murphy and colleagues (Kaletsky et al., 2016) describe the transcriptional program that maintains youthful function of aging neurons in the nematode worm. PMID:26959183

  20. Critical Considerations for WORM Software Development.

    ERIC Educational Resources Information Center

    Berg, Brian A.

    1987-01-01

    Addresses advantages and disadvantages of write-once read-many (WORM) optical disks and other software considerations resulting from the write-once nature of WORM media to provide guidelines for determining whether this technology is appropriate for an application. Three brief case studies describe WORM software development efforts. (MES)

  1. Subretinal Worm and Repeat Laser Photocoagulation

    PubMed Central

    Natesh, Sribhargava; K, Harsha; Nair, Unnikrishna; Nair, KGR

    2010-01-01

    Diffuse unilateral subacute neuroretinitis (DUSN) can be a diagnostic dilemma. Laser photocoagulation of the subretinal worm is an effective treatment for eradication. Early laser photocoagulation has been advocated. We report a case of a middle aged man who presented with decreased vision and a sub retinal macular worm that required two laser sessions for complete eradication of the worm. PMID:20616929

  2. Arrows as anchors: Conceptual blending and student use of electric field vector arrows

    NASA Astrophysics Data System (ADS)

    Gire, Elizabeth; Price, Edward

    2013-01-01

    We use the theory of conceptual blending with material anchors to describe how people make meaning of the vector arrows representation of electric fields. We describe this representation as a conceptual blend of a spatial (coordinate) input space and an electric-field-as-arrows space (which itself is a blend of electric field concept with arrows). This representation possesses material features including the use of spatial extent (e.g., distance on paper) to represent the coordinate space and to represent the magnitude of electric field vectors. As a result, this representation supports a geometric interpretation of the electric field, breaking the field into components, and the addition of two fields at a point. The material features also emphasize the spatial relationships between the source(s) and points where the field is represented. However, the material features also necessitate sampling and do not generally support the rapid superposition of two fields at all points. We illustrate this analysis with examples from clinical problem-solving interviews with upper-division physics majors, and interpret students' errors in using this representation as resulting from conflict between the input spaces in the blend.

  3. Avatars and arrows in the brain.

    PubMed

    Catmur, Caroline; Santiesteban, Idalmis; Conway, Jane R; Heyes, Cecilia; Bird, Geoffrey

    2016-05-15

    In this Commentary article we critically assess the claims made by Schurz, Kronbichler, Weissengrubler, Surtees, Samson and Perner (2015) relating to the neural processes underlying theory of mind and visual perspective taking. They attempt to integrate research findings in these two areas of social neuroscience using a perspective taking task contrasting mentalistic agents ('avatars'), with non-mentalistic control stimuli ('arrows'), during functional Magnetic Resonance Imaging. We support this endeavour whole-heartedly, agreeing that the integration of findings in these areas has been neglected in research on the social brain. However, we cannot find among the behavioural or neuroimaging data presented by Schurz et al. evidence supporting their claim of 'implicit mentalizing'-the automatic ascription of mental states to another representing what they can see. Indeed, we suggest that neuroimaging methods may be ill-suited to address the existence of implicit mentalizing, and suggest that approaches utilizing neurostimulation methods are likely to be more successful. PMID:26883064

  4. [World Collections of Parasitic Worms].

    PubMed

    Zinovieva, S V; Butorina, N N; Udalova, Zh V; Khasanova, S; Filimonova, L V; Petrosyan, V G; Pel'gunov, A N

    2015-01-01

    This article provides information about the depositories of parasitic worms in the scientific institutes and museums in the United States, Japan, and Europe (the total number of samples and the availability of types of helminths from various classes), as well as information on the availability of electronic catalogues of the collections in the continental, national, and regional centers for collective use. The extent of this material has determined the necessity of creating digital collections and libraries that would represent a new form of storing, displaying, and exchanging information for scientific research. An analysis was performed of the current state of approaches and methods of development of the specialized information retrieval system (IRS) and databases (DBs) on the parasitic worms in Russia on the basis of a common conceptual data model, taking into account their local use (as desktop systems of database management) and access by scientists worldwide via the Internet. PMID:26852482

  5. Adding and subtracting vectors: The problem with the arrow representation

    NASA Astrophysics Data System (ADS)

    Heckler, Andrew F.; Scaife, Thomas M.

    2015-06-01

    A small number of studies have investigated student understanding of vector addition and subtraction in generic or introductory physics contexts, but in almost all cases the questions posed were in the vector arrow representation. In a series of experiments involving over 1000 students and several semesters, we investigated student understanding of vector addition and subtraction in both the arrow and algebraic notation (using i ^, j ^, k ^) in generic mathematical and physics contexts. First, we replicated a number of previous findings of student difficulties in the arrow format and discovered several additional difficulties, including the finding that different relative arrow orientations can prompt different solution paths and different kinds of mistakes, which suggests that students need to practice with a variety of relative orientations. Most importantly, we found that average performance in the i j k format was typically excellent and often much better than performance in the arrow format in either the generic or physics contexts. Further, while we find that the arrow format tends to prompt students to a more physically intuitive solution path, we also find that, when prompted, student solutions in the i j k format also display significant physical insights into the problem. We also find a hierarchy in correct answering between the two formats, with correct answering in the i j k format being more fundamental than for the arrow format. Overall, the results suggest that many student difficulties with these simple vector problems lie with the arrow representation itself. For instruction, these results imply that introducing the i j k notation (or some equivalent) with the arrow notation concurrently may be a very useful way to improve student performance as well as help students to learn physics concepts involving vector addition and subtraction.

  6. Learning about Locomotion Patterns: Effective Use of Multiple Pictures and Motion-Indicating Arrows

    ERIC Educational Resources Information Center

    Imhof, Birgit; Scheiter, Katharina; Edelmann, Jorg; Gerjets, Peter

    2013-01-01

    This study investigated how enriching visualizations with arrows indicating the motion of objects may help in conveying dynamic information: Multiple static-simultaneous visualizations with motion-indicating arrows were compared with either multiple visualizations without arrows or a single visualization with arrows. Seventy-one students were…

  7. Visuospatial Attention Is Guided by Both the Symbolic Value and the Spatial Proximity of Selected Arrows

    ERIC Educational Resources Information Center

    Pratt, Jay; Radulescu, Petre; Guo, Ruo Mu; Hommel, Bernhard

    2010-01-01

    There is considerable evidence that overlearned symbols, especially arrows, can orient attention to peripheral locations. In 2003, Pratt and Hommel showed that when 1 arrow is selected from a set of arrows, based on an attentional control setting for a specific target color, the selected arrow determines the orientation of attention. Recently,…

  8. Relation between the psychological and thermodynamic arrows of time

    NASA Astrophysics Data System (ADS)

    Mlodinow, Leonard; Brun, Todd A.

    2014-05-01

    In this paper we lay out an argument that generically the psychological arrow of time should align with the thermodynamic arrow of time where that arrow is well defined. This argument applies to any physical system that can act as a memory, in the sense of preserving a record of the state of some other system. This result follows from two principles: the robustness of the thermodynamic arrow of time to small perturbations in the state, and the principle that a memory should not have to be fine-tuned to match the state of the system being recorded. This argument applies even if the memory system itself is completely reversible and nondissipative. We make the argument with a paradigmatic system, and then formulate it more broadly for any system that can be considered a memory. We illustrate these principles for a few other example systems and compare our criteria to earlier treatments of this problem.

  9. ARROW (Version 2) Commercial Software Validation and Configuration Control

    SciTech Connect

    HEARD, F.J.

    2000-02-10

    ARROW (Version 2), a compressible flow piping network modeling and analysis computer program from Applied Flow Technology, was installed for use at the U.S. Department of Energy Hanford Site near Richland, Washington.

  10. Charming penguin contributions to B{r_arrow}K{pi}

    SciTech Connect

    Isola, C.; Ladisa, M.; Nardulli, G.; Pham, T. N.; Santorelli, P.

    2001-07-01

    We present calculations of the charming-penguin long-distance contributions to B{r_arrow}K{pi} decays due to intermediate charmed meson states. Our calculation is based on the chiral effective Lagrangian for light and heavy mesons, corrected for the hard pion and kaon momenta. We find that the charming-penguin contributions increase significantly the B{r_arrow}K{pi} decay rates in comparison with the short-distance contributions, giving results in better agreement with experimental data.

  11. Identification of a Gravitational Arrow of Time

    NASA Astrophysics Data System (ADS)

    Barbour, Julian; Koslowski, Tim; Mercati, Flavio

    2014-10-01

    It is widely believed that special initial conditions must be imposed on any time-symmetric law if its solutions are to exhibit behavior of any kind that defines an "arrow of time." We show that this is not so. The simplest nontrivial time-symmetric law that can be used to model a dynamically closed universe is the Newtonian N -body problem with vanishing total energy and angular momentum. Because of special properties of this system (likely to be shared by any law of the Universe), its typical solutions all divide at a uniquely defined point into two halves. In each, a well-defined measure of shape complexity fluctuates but grows irreversibly between rising bounds from that point. Structures that store dynamical information are created as the complexity grows and act as "records." Each solution can be viewed as having a single past and two distinct futures emerging from it. Any internal observer must be in one half of the solution and will only be aware of the records of one branch and deduce a unique past and future direction from inspection of the available records.

  12. Identification of a gravitational arrow of time.

    PubMed

    Barbour, Julian; Koslowski, Tim; Mercati, Flavio

    2014-10-31

    It is widely believed that special initial conditions must be imposed on any time-symmetric law if its solutions are to exhibit behavior of any kind that defines an "arrow of time." We show that this is not so. The simplest nontrivial time-symmetric law that can be used to model a dynamically closed universe is the Newtonian N-body problem with vanishing total energy and angular momentum. Because of special properties of this system (likely to be shared by any law of the Universe), its typical solutions all divide at a uniquely defined point into two halves. In each, a well-defined measure of shape complexity fluctuates but grows irreversibly between rising bounds from that point. Structures that store dynamical information are created as the complexity grows and act as "records." Each solution can be viewed as having a single past and two distinct futures emerging from it. Any internal observer must be in one half of the solution and will only be aware of the records of one branch and deduce a unique past and future direction from inspection of the available records. PMID:25396357

  13. Keeping track of worm trackers.

    PubMed

    Husson, Steven J; Costa, Wagner Steuer; Schmitt, Cornelia; Gottschalk, Alexander

    2012-01-01

    C. elegans is used extensively as a model system in the neurosciences due to its well defined nervous system. However, the seeming simplicity of this nervous system in anatomical structure and neuronal connectivity, at least compared to higher animals, underlies a rich diversity of behaviors. The usefulness of the worm in genome-wide mutagenesis or RNAi screens, where thousands of strains are assessed for phenotype, emphasizes the need for computational methods for automated parameterization of generated behaviors. In addition, behaviors can be modulated upon external cues like temperature, O(subscript)2(/subscript) and CO(subscript)2(/subscript) concentrations, mechanosensory and chemosensory inputs. Different machine vision tools have been developed to aid researchers in their efforts to inventory and characterize defined behavioral "outputs". Here we aim at providing an overview of different worm-tracking packages or video analysis tools designed to quantify different aspects of locomotion such as the occurrence of directional changes (turns, omega bends), curvature of the sinusoidal shape (amplitude, body bend angles) and velocity (speed, backward or forward movement). PMID:23436808

  14. An Expanded Genomic Representation of the Phylum Cyanobacteria

    PubMed Central

    Soo, Rochelle M.; Skennerton, Connor T.; Sekiguchi, Yuji; Imelfort, Michael; Paech, Samuel J.; Dennis, Paul G.; Steen, Jason A.; Parks, Donovan H.; Tyson, Gene W.; Hugenholtz, Philip

    2014-01-01

    Molecular surveys of aphotic habitats have indicated the presence of major uncultured lineages phylogenetically classified as members of the Cyanobacteria. One of these lineages has recently been proposed as a nonphotosynthetic sister phylum to the Cyanobacteria, the Melainabacteria, based on recovery of population genomes from human gut and groundwater samples. Here, we expand the phylogenomic representation of the Melainabacteria through sequencing of six diverse population genomes from gut and bioreactor samples supporting the inference that this lineage is nonphotosynthetic, but not the assertion that they are strictly fermentative. We propose that the Melainabacteria is a class within the phylogenetically defined Cyanobacteria based on robust monophyly and shared ancestral traits with photosynthetic representatives. Our findings are consistent with theories that photosynthesis occurred late in the Cyanobacteria and involved extensive lateral gene transfer and extends the recognized functionality of members of this phylum. PMID:24709563

  15. Validation and justification of the phylum name Cryptomycota phyl. nov.

    PubMed

    Jones, Meredith D M; Richards, Thomas A; Hawksworth, David L; Bass, David

    2011-12-01

    The recently proposed new phylum name Cryptomycota phyl. nov. is validly published in order to facilitate its use in future discussions of the ecology, biology, and phylogenetic relationships of the constituent organisms. This name is preferred over the previously tentatively proposed "Rozellida" as new data suggest that the life-style and morphology of Rozella is not representative of the large radiation to which it and other Cryptomycota belong. Furthermore, taxa at higher ranks such as phylum are considered better not based on individual names of included genera, but rather on some special characteristics - in this case the cryptic nature of this group and that they were initially revealed by molecular methods rather than morphological discovery. If the group were later viewed as a member of a different kingdom, the name should be retained to indicate its fungal affinities, as is the practice for other fungal-like protist groups. PMID:22679602

  16. From Flowers to Worms: Understanding Nature's Cycle.

    ERIC Educational Resources Information Center

    Texas Child Care, 1995

    1995-01-01

    Gardening helps children learn how plants sprout, grow, bloom, and then wither away, leaving seeds behind. Participating in this natural process allows children to experience the stages of life. Suggested gardening activities include studying dandelions, focusing on culture for garden plant selection, and constructing a worm box or worm terrarium…

  17. Dew Worms in the White Nights

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Lumbricus terrestris L. (the dew worm) forages, mates and migrates on the soil surface during the night. Its distribution covers a broad latitudinal gradient and variation in day length conditions. Since soil-surface activity is crucial for the survival and reproduction of dew worms, it is conceivab...

  18. Maxwell's Demons Everywhere: Evolving Design as the Arrow of Time

    PubMed Central

    Bejan, Adrian

    2014-01-01

    Science holds that the arrow of time in nature is imprinted on one-way (irreversible) phenomena, and is accounted for by the second law of thermodynamics. Here I show that the arrow of time is painted much more visibly on another self-standing phenomenon: the occurrence and change (evolution in time) of flow organization throughout nature, animate and inanimate. This other time arrow has been present in science but not recognized as such since the birth of thermodynamics. It is Maxwell's demon. Translated in macroscopic terms, this is the physics of the phenomenon of design, which is the universal natural tendency of flow systems to evolve into configurations that provide progressively greater access over time, and is summarized as the constructal law of design and evolution in nature. Knowledge is the ability to effect design changes that facilitate human flows on the landscape. Knowledge too flows. PMID:24510201

  19. Time's arrows today. Recent physical and philosophical work on the direction of time.

    NASA Astrophysics Data System (ADS)

    Savitt, S. F.

    Most of the work in this volume, the paperback version of the 1995 edition, was presented at a conference, Vancouver, B.C. (Canada), Jun 1992. The eleven contributions are arranged under the following subject headings: 1. Cosmology and time's arrow (W. Unruh, H. Price). 2. Quantum theory and time's arrow (A. Leggett, P. Stamp, S. McCall, R. Douglas). 3. Thermodynamics and time's arrow (L. Sklar, M. Barrett, E. Sober). 4. Time travel and time's arrow (P. Horwich, J. Earman).

  20. A Common Worm in a Rare Place.

    PubMed

    Sheikhian, Mohammed Reza

    2013-11-01

    A case of a 40-year-old female, in whom a 6-meter long worm (Taenia saginata) was found in stomach, is reported here. In this patient, T. saginata upward migration of the worm to the stomach, its rare phenomenon, worm mostly seen in the small intestine. This is mainly because of the high gastric acidity. In this patient, we believe proton pump inhibitor (PPI) use caused hypochlorhydria and coexistence H. pylori infection caused chronic atrophic gastritis, which resulted in the retrograde migration of the tapeworm to the stomach in our patient. PMID:26171346

  1. Deep phylogeny and evolution of sponges (phylum Porifera).

    PubMed

    Wörheide, G; Dohrmann, M; Erpenbeck, D; Larroux, C; Maldonado, M; Voigt, O; Borchiellini, C; Lavrov, D V

    2012-01-01

    Sponges (phylum Porifera) are a diverse taxon of benthic aquatic animals of great ecological, commercial, and biopharmaceutical importance. They are arguably the earliest-branching metazoan taxon, and therefore, they have great significance in the reconstruction of early metazoan evolution. Yet, the phylogeny and systematics of sponges are to some extent still unresolved, and there is an on-going debate about the exact branching pattern of their main clades and their relationships to the other non-bilaterian animals. Here, we review the current state of the deep phylogeny of sponges. Several studies have suggested that sponges are paraphyletic. However, based on recent phylogenomic analyses, we suggest that the phylum Porifera could well be monophyletic, in accordance with cladistic analyses based on morphology. This finding has many implications for the evolutionary interpretation of early animal traits and sponge development. We further review the contribution that mitochondrial genes and genomes have made to sponge phylogenetics and explore the current state of the molecular phylogenies of the four main sponge lineages (Classes), that is, Demospongiae, Hexactinellida, Calcarea, and Homoscleromorpha, in detail. While classical systematic systems are largely congruent with molecular phylogenies in the class Hexactinellida and in certain parts of Demospongiae and Homoscleromorpha, the high degree of incongruence in the class Calcarea still represents a challenge. We highlight future areas of research to fill existing gaps in our knowledge. By reviewing sponge development in an evolutionary and phylogenetic context, we support previous suggestions that sponge larvae share traits and complexity with eumetazoans and that the simple sedentary adult lifestyle of sponges probably reflects some degree of secondary simplification. In summary, while deep sponge phylogenetics has made many advances in the past years, considerable efforts are still required to achieve a

  2. WDDD: Worm Developmental Dynamics Database.

    PubMed

    Kyoda, Koji; Adachi, Eru; Masuda, Eriko; Nagai, Yoko; Suzuki, Yoko; Oguro, Taeko; Urai, Mitsuru; Arai, Ryoko; Furukawa, Mari; Shimada, Kumiko; Kuramochi, Junko; Nagai, Eriko; Onami, Shuichi

    2013-01-01

    During animal development, cells undergo dynamic changes in position and gene expression. A collection of quantitative information about morphological dynamics under a wide variety of gene perturbations would provide a rich resource for understanding the molecular mechanisms of development. Here, we created a database, the Worm Developmental Dynamics Database (http://so.qbic.riken.jp/wddd/), which stores a collection of quantitative information about cell division dynamics in early Caenorhabditis elegans embryos with single genes silenced by RNA-mediated interference. The information contains the three-dimensional coordinate values of the outlines of nuclear regions and the dynamics of the outlines over time. The database provides free access to 50 sets of quantitative data for wild-type embryos and 136 sets of quantitative data for RNA-mediated interference embryos corresponding to 72 of the 97 essential embryonic genes on chromosome III. The database also provides sets of four-dimensional differential interference contrast microscopy images on which the quantitative data were based. The database will provide a novel opportunity for the development of computational methods to obtain fresh insights into the mechanisms of development. The quantitative information and microscopy images can be synchronously viewed through a web browser, which is designed for easy access by experimental biologists. PMID:23172286

  3. Archeterokrohnia docrickettsae (Chaetognatha: Phragmophora: Heterokrohniidae), a new species of deep-sea arrow worm from the Gulf of California.

    PubMed

    Thuesen, Erik V; Haddock, Steven H D

    2013-01-01

    A new species of deep-sea chaetognath, Archeterokrohnia docrickettsae n. sp. is described from a single specimen captured by the ROV Doc Ricketts ~2 m above the sea floor at 3245 m depth in the Pescadero Basin of the Gulf of California, Mexico. This is the first record of a living specimen of Archeterokrohnia and the second known occurrence of Archeterokrohnia in the Pacific Ocean. In life, the head and trunk sections were orange, while the tail section was translucent, a unique colour pattern not before seen in chaetognaths. Observations of its swimming behaviour in situ are given. Comparisons are made with the three other species of Archeterokrohnia. At 28.5 mm in length, this is the largest known species of the genus. An artificial key to the four species of Archeterokrohnia is presented. PMID:26176108

  4. Ultrastructural studies of the junctional complex in the musculature of the arrow-worm (Sagitta setosa) (Chaetognatha).

    PubMed

    Duvert, M; Gros, D; Salat, C

    1980-01-01

    In the A fibres of the primary musculature of Sagitta, the junctional complex is made up of three kinds of junctions. From the apex to the base they occur in the following order: an apical zonula adherens, a columnar zonula then columnar maculae intermingled with gap junction. Each columnar junction joins two intracellular filament networks in adjacent cells; this cytoskeleton is largely developed around the nucleus of the A fibres and in close relation with the contractile apparatus, especially at the I band level. The B fibres, which never reach the general cavity, lack zonula adherens and columnar zonula. The columnar junction constitutes a new type of junction which seems to belong to the adherens kind. At their level fibrous columns cross the extracellular space, joining the membranes. Each column faces two cytoplasmic densities localized against the cytoplasmic leaflets of the membranes. A cytoskeleton composed of bunldes of cytoplasmic filaments is in close contact with these cytoplasmic densities. The great number of columnar junctions and associated cytoskeleton assure the cohesion of the tissue and the distribution of contractile forces in the absence of connective tissue. The abundance of gap junctions can account for the metabolic and ionic coupling of the fibres. PMID:7189067

  5. Worm epidemics in wireless ad hoc networks

    NASA Astrophysics Data System (ADS)

    Nekovee, Maziar

    2007-06-01

    A dramatic increase in the number of computing devices with wireless communication capability has resulted in the emergence of a new class of computer worms which specifically target such devices. The most striking feature of these worms is that they do not require Internet connectivity for their propagation but can spread directly from device to device using a short-range radio communication technology, such as WiFi or Bluetooth. In this paper, we develop a new model for epidemic spreading of these worms and investigate their spreading in wireless ad hoc networks via extensive Monte Carlo simulations. Our studies show that the threshold behaviour and dynamics of worm epidemics in these networks are greatly affected by a combination of spatial and temporal correlations which characterize these networks, and are significantly different from the previously studied epidemics in the Internet.

  6. Symbol-and-Arrow Diagrams in Teaching Pharmacokinetics.

    ERIC Educational Resources Information Center

    Hayton, William L.

    1990-01-01

    Symbol-and-arrow diagrams are helpful adjuncts to equations derived from pharmacokinetic models. Both show relationships among dependent and independent variables. Diagrams show only qualitative relationships, but clearly show which variables are dependent and which are independent, helping students understand complex but important functional…

  7. Elliptical Orbit [arrow right] 1/r[superscript 2] Force

    ERIC Educational Resources Information Center

    Prentis, Jeffrey; Fulton, Bryan; Hesse, Carol; Mazzino, Laura

    2007-01-01

    Newton's proof of the connection between elliptical orbits and inverse-square forces ranks among the "top ten" calculations in the history of science. This time-honored calculation is a highlight in an upper-level mechanics course. It would be worthwhile if students in introductory physics could prove the relation "elliptical orbit" [arrow right]…

  8. Adding and Subtracting Vectors: The Problem with the Arrow Representation

    ERIC Educational Resources Information Center

    Heckler, Andrew F.; Scaife, Thomas M.

    2015-01-01

    A small number of studies have investigated student understanding of vector addition and subtraction in generic or introductory physics contexts, but in almost all cases the questions posed were in the vector arrow representation. In a series of experiments involving over 1000 students and several semesters, we investigated student understanding…

  9. Assessment of worm gearing for helicopter transmissions

    NASA Technical Reports Server (NTRS)

    Chaiko, Lev

    1990-01-01

    A high-efficiency hydrostatic worm gear drive for helicopter transmissions is assessed. The example given is for a large cargo helicopter with three 4000-kW engines and transmission reduction ratio of 110. Also contained are: an efficiency calculation, a description of the test stand for evaluating the feasibility of worm gear hydrostatic mesh, a weight calculation, and a comparison with conventional helicopter transmissions of the same power and transmission reduction ratio.

  10. Annulonemertes (phylum Nemertea): when segments do not count.

    PubMed

    Sundberg, Per; Strand, Malin

    2007-10-22

    We estimated the phylogenetic position of the pseudosegmented ribbon worm Annulonemertes minusculus to test proposed evolutionary hypotheses to explain these body constrictions. The analysis is based on 18S rDNA sequences and shows that the species belongs to an apomorphic clade of hoplonemertean species. The segmentation has no phylogenetic bearing as previously discussed, but is a derived character probably coupled to the species' interstitial habitat. PMID:17686756

  11. Arrow Lakes Reservoir Fertilization Experiment, Technical Report 1999-2004.

    SciTech Connect

    Schindler, E.

    2007-02-01

    The Arrow Lakes food web has been influenced by several anthropogenic stressors during the past 45 years. These include the introduction of mysid shrimp (Mysis relicta) in 1968 and 1974 and the construction of large hydroelectric impoundments in 1969, 1973 and 1983. The construction of the impoundments affected the fish stocks in Upper and Lower Arrow lakes in several ways. The construction of Hugh Keenleyside Dam (1969) resulted in flooding that eliminated an estimated 30% of the available kokanee spawning habitat in Lower Arrow tributaries and at least 20% of spawning habitat in Upper Arrow tributaries. The Mica Dam (1973) contributed to water level fluctuations and blocked upstream migration of all fish species including kokanee. The Revelstoke Dam (1983) flooded 150 km of the mainstem Columbia River and 80 km of tributary streams which were used by kokanee, bull trout, rainbow trout and other species. The construction of upstream dams also resulted in nutrient retention which ultimately reduced reservoir productivity. In Arrow Lakes Reservoir (ALR), nutrients settled out in the Revelstoke and Mica reservoirs, resulting in decreased productivity, a process known as oligotrophication. Kokanee are typically the first species to respond to oligotrophication resulting from aging impoundments. To address the ultra-oligotrophic status of ALR, a bottom-up approach was taken with the addition of nutrients (nitrogen and phosphorus in the form of liquid fertilizer from 1999 to 2004). Two of the main objectives of the experiment were to replace lost nutrients as a result of upstream impoundments and restore productivity in Upper Arrow and to restore kokanee and other sport fish abundance in the reservoir. The bottom-up approach to restoring kokanee in ALR has been successful by replacing nutrients lost as a result of upstream impoundments and has successfully restored the productivity of Upper Arrow. Primary production rates increased, the phytoplankton community responded

  12. Chordate evolution and the three-phylum system

    PubMed Central

    Satoh, Noriyuki; Rokhsar, Daniel; Nishikawa, Teruaki

    2014-01-01

    Traditional metazoan phylogeny classifies the Vertebrata as a subphylum of the phylum Chordata, together with two other subphyla, the Urochordata (Tunicata) and the Cephalochordata. The Chordata, together with the phyla Echinodermata and Hemichordata, comprise a major group, the Deuterostomia. Chordates invariably possess a notochord and a dorsal neural tube. Although the origin and evolution of chordates has been studied for more than a century, few authors have intimately discussed taxonomic ranking of the three chordate groups themselves. Accumulating evidence shows that echinoderms and hemichordates form a clade (the Ambulacraria), and that within the Chordata, cephalochordates diverged first, with tunicates and vertebrates forming a sister group. Chordates share tadpole-type larvae containing a notochord and hollow nerve cord, whereas ambulacrarians have dipleurula-type larvae containing a hydrocoel. We propose that an evolutionary occurrence of tadpole-type larvae is fundamental to understanding mechanisms of chordate origin. Protostomes have now been reclassified into two major taxa, the Ecdysozoa and Lophotrochozoa, whose developmental pathways are characterized by ecdysis and trochophore larvae, respectively. Consistent with this classification, the profound dipleurula versus tadpole larval differences merit a category higher than the phylum. Thus, it is recommended that the Ecdysozoa, Lophotrochozoa, Ambulacraria and Chordata be classified at the superphylum level, with the Chordata further subdivided into three phyla, on the basis of their distinctive characteristics. PMID:25232138

  13. Is there a plastid in Perkinsus atlanticus (Phylum Perkinsozoa)?

    PubMed

    Teles-Grilo, M Leonor; Tato-Costa, Joana; Duarte, Sérgio M; Maia, Alexandre; Casal, Graça; Azevedo, Carlos

    2007-06-01

    Perkinsus atlanticus is a pathogenic protist that infects the clam Ruditapes decussatus. The recent proposal for the inclusion of the genus Perkinsus in a new phylum, Perkinsozoa, in the infra-kingdom Alveolata, gave rise to controversies whether this genus should form a phylum on its own. Molecular analysis of some conserved nuclear genes shows a closer proximity of the genus Perkinsus to the dinoflagellates than to the apicomplexans. Studies on extranuclear genomes, however, could also be very helpful for a more precise definition of those phyla. In Perkinsozoa, there have been until now no reports about the isolation of mitochondria as well as no conclusive results about the presence of any plastids, therefore a comparison with the data already obtained in Apicomplexa and Dinoflagellata has not yet been possible. In this work, we identify a plastid in Perkinsus atlanticus, using ultrastructural techniques and inhibition growth tests. It will be important to analyze the plastid genome at a molecular level, in order to confirm if the plastid in Perkinsus is more similar to those of Dinoflagellata or Apicomplexa. Such information will doubtless contribute to a more precise determination of the phylogenetic position of the genus Perkinsus. PMID:17498932

  14. Chordate evolution and the three-phylum system.

    PubMed

    Satoh, Noriyuki; Rokhsar, Daniel; Nishikawa, Teruaki

    2014-11-01

    Traditional metazoan phylogeny classifies the Vertebrata as a subphylum of the phylum Chordata, together with two other subphyla, the Urochordata (Tunicata) and the Cephalochordata. The Chordata, together with the phyla Echinodermata and Hemichordata, comprise a major group, the Deuterostomia. Chordates invariably possess a notochord and a dorsal neural tube. Although the origin and evolution of chordates has been studied for more than a century, few authors have intimately discussed taxonomic ranking of the three chordate groups themselves. Accumulating evidence shows that echinoderms and hemichordates form a clade (the Ambulacraria), and that within the Chordata, cephalochordates diverged first, with tunicates and vertebrates forming a sister group. Chordates share tadpole-type larvae containing a notochord and hollow nerve cord, whereas ambulacrarians have dipleurula-type larvae containing a hydrocoel. We propose that an evolutionary occurrence of tadpole-type larvae is fundamental to understanding mechanisms of chordate origin. Protostomes have now been reclassified into two major taxa, the Ecdysozoa and Lophotrochozoa, whose developmental pathways are characterized by ecdysis and trochophore larvae, respectively. Consistent with this classification, the profound dipleurula versus tadpole larval differences merit a category higher than the phylum. Thus, it is recommended that the Ecdysozoa, Lophotrochozoa, Ambulacraria and Chordata be classified at the superphylum level, with the Chordata further subdivided into three phyla, on the basis of their distinctive characteristics. PMID:25232138

  15. The Fibrobacteres: an important phylum of cellulose-degrading bacteria.

    PubMed

    Ransom-Jones, Emma; Jones, David L; McCarthy, Alan J; McDonald, James E

    2012-02-01

    The phylum Fibrobacteres currently comprises one formal genus, Fibrobacter, and two cultured species, Fibrobacter succinogenes and Fibrobacter intestinalis, that are recognised as major bacterial degraders of lignocellulosic material in the herbivore gut. Historically, members of the genus Fibrobacter were thought to only occupy mammalian intestinal tracts. However, recent 16S rRNA gene-targeted molecular approaches have demonstrated that novel centres of variation within the genus Fibrobacter are present in landfill sites and freshwater lakes, and their relative abundance suggests a potential role for fibrobacters in cellulose degradation beyond the herbivore gut. Furthermore, a novel subphylum within the Fibrobacteres has been detected in the gut of wood-feeding termites, and proteomic analyses have confirmed their involvement in cellulose hydrolysis. The genome sequence of F. succinogenes rumen strain S85 has recently suggested that within this group of organisms a "third" way of attacking the most abundant form of organic carbon in the biosphere, cellulose, has evolved. This observation not only has evolutionary significance, but the superior efficiency of anaerobic cellulose hydrolysis by Fibrobacter spp., in comparison to other cellulolytic rumen bacteria that typically utilise membrane-bound enzyme complexes (cellulosomes), may be explained by this novel cellulase system. There are few bacterial phyla with potential functional importance for which there is such a paucity of phenotypic and functional data. In this review, we highlight current knowledge of the Fibrobacteres phylum, its taxonomy, phylogeny, ecology and potential as a source of novel glycosyl hydrolases of biotechnological importance. PMID:22213055

  16. Arrows as anchors: An analysis of the material features of electric field vector arrows

    NASA Astrophysics Data System (ADS)

    Gire, Elizabeth; Price, Edward

    2014-12-01

    Representations in physics possess both physical and conceptual aspects that are fundamentally intertwined and can interact to support or hinder sense making and computation. We use distributed cognition and the theory of conceptual blending with material anchors to interpret the roles of conceptual and material features of representations in students' use of representations for computation. We focus on the vector-arrows representation of electric fields and describe this representation as a conceptual blend of electric field concepts, physical space, and the material features of the representation (i.e., the physical writing and the surface upon which it is drawn). In this representation, spatial extent (e.g., distance on paper) is used to represent both distances in coordinate space and magnitudes of electric field vectors. In conceptual blending theory, this conflation is described as a clash between the input spaces in the blend. We explore the benefits and drawbacks of this clash, as well as other features of this representation. This analysis is illustrated with examples from clinical problem-solving interviews with upper-division physics majors. We see that while these intermediate physics students make a variety of errors using this representation, they also use the geometric features of the representation to add electric field contributions and to organize the problem situation productively.

  17. WORM - WINDOWED OBSERVATION OF RELATIVE MOTION

    NASA Technical Reports Server (NTRS)

    Bauer, F.

    1994-01-01

    The Windowed Observation of Relative Motion, WORM, program is primarily intended for the generation of simple X-Y plots from data created by other programs. It allows the user to label, zoom, and change the scale of various plots. Three dimensional contour and line plots are provided, although with more limited capabilities. The input data can be in binary or ASCII format, although all data must be in the same format. A great deal of control over the details of the plot is provided, such as gridding, size of tick marks, colors, log/semilog capability, time tagging, and multiple and phase plane plots. Many color and monochrome graphics terminals and hard copy printer/plotters are supported. The WORM executive commands, menu selections and macro files can be used to develop plots and tabular data, query the WORM Help library, retrieve data from input files, and invoke VAX DCL commands. WORM generated plots are displayed on local graphics terminals and can be copied using standard hard copy capabilities. Some of the graphics features of WORM include: zooming and dezooming various portions of the plot; plot documentation including curve labeling and function listing; multiple curves on the same plot; windowing of multiple plots and insets of the same plot; displaying a specific on a curve; and spinning the curve left, right, up, and down. WORM is written in PASCAL for interactive execution and has been implemented on a DEC VAX computer operating under VMS 4.7 with a virtual memory requirement of approximately 392K of 8 bit bytes. It uses the QPLOT device independent graphics library included with WORM. It was developed in 1988.

  18. Aquatic worms eat sludge: mass balances and processing of worm faeces.

    PubMed

    Hendrickx, T L G; Temmink, H; Elissen, H J H; Buisman, C J N

    2010-05-15

    Reduction of the amount of waste sludge from waste water treatment plants (WWTPs) can be achieved with the aquatic worm Lumbriculus variegatus in a new reactor concept. In addition to reducing the amount of waste sludge, further processing of produced worm faeces and released nutrients should also be considered. This study gives the mass balances for sludge consumed by L. variegatus, showing the fate of the consumed organic material, nutrients and heavy metals associated with the sludge. A distinction is made between conversion into worm biomass, release as dissolved metabolites and what remains in the worm faeces. The results showed that 39% of the nitrogen and 12% of the phosphorus in the sludge digested by the worms are used in the formation of new worm biomass, which has potential for reuse. Experiments showed that settling of the worm faeces leads to a factor 2.5 higher solids concentration, compared to settling of waste sludge. This could lead to a 67% reduction of the volumetric load on thickening equipment. The worm reactor is expected to be most interesting for smaller WWTPs where a decrease on the volumetric load on sludge handling operations will have most impact. PMID:20060212

  19. Diversity and Habitat Niche Modeling of Candidate Archaeal Phylum Aigarchaeota

    NASA Astrophysics Data System (ADS)

    Alba, T. W.; Goertz, G.; Williams, A. J.; Cole, J. K.; Murugapiran, S. K.; Dodsworth, J. A.; Hedlund, B. P.

    2013-12-01

    ';Aigarchaeota' (formerly known as pSL4 and Hot Water Crenarchaeotic Group I (HWCGI)) is a candidate phylum of Archaea known only by 16S rRNA gene fragments from cultivation-independent microbial surveys and a single composite genome from Candidatus ';Caldiarchaeum subterraneum', an inhabitant of a subterranean gold mine in Japan. Sequences reported in various publications are found exclusively in geothermal settings, but a comprehensive assessment has not yet been performed. We mined public databases for 16S rRNA gene sequences related to known ';Aigarchaeota' and used a combination of approaches to rigorously define the phylogenetic boundaries of the phylum. The analyses supported the proposed relationship between ';Aigarchaeota', Thaumarchaeota, Crenarchaeota, and Korarchaeota in the so-called 'TACK superphylum' and identified ~200 16S rRNA genes and gene fragments belonging to ';Aigarchaeota', including those recovered from terrestrial geothermal systems on several continents (North America, Asia, Africa, Europe, and Oceania) and marine geothermal and subsurface samples in both the Atlantic and Pacific. ';Aigarchaeota' belonged to at least three family- to order-level groups and at least seven genus-level groups. All genus-level groups were recovered from geographically distant locations, suggesting a global distribution within amenable habitats. ';Aigarchaeota'-specific primers for the polymerase chain reaction (PCR) amplification of 16S rRNA genes were designed using SP-Designer and reviewed using the Ribosomal Database Project Probe Match tool. The primers will be used to determine the presence and abundance of ';Aigarchaeota' in a wide variety of samples from terrestrial geothermal systems in the western U.S. and Asia. These phylogenetic data, along with a large geochemical database, will be analyzed using multivariate statistics to develop biogeographic and habitat niche models for ';Aigarchaeota'. This study offers the first coherent view of the

  20. Disulfide-Functionalized Diblock Copolymer Worm Gels.

    PubMed

    Warren, Nicholas J; Rosselgong, Julien; Madsen, Jeppe; Armes, Steven P

    2015-08-10

    Two strategies for introducing disulfide groups at the outer surface of RAFT-synthesized poly(glycerol monomethacrylate)-poly(2-hydroxypropyl methacrylate) (PGMA-PHPMA, or Gx-Hy for brevity) diblock copolymer worms are investigated. The first approach involved statistical copolymerization of GMA with a small amount of disulfide dimethacrylate (DSDMA, or D) comonomer to afford a G54-D0.50 macromolecular chain transfer agent (macro-CTA); this synthesis was conducted in relatively dilute solution in order to ensure mainly intramolecular cyclization and hence the formation of linear chains. Alternatively, a new disulfide-based bifunctional RAFT agent (DSDB) was used to prepare a G45-S-S-G45 (or (G45-S)2) macro-CTA. A binary mixture of a non-functionalized G55 macro-CTA was utilized with each of these two disulfide-based macro-CTAs in turn for the RAFT aqueous dispersion polymerization of 2-hydroxypropyl methacrylate (HPMA). By targeting a PHPMA DP of 130 and systematically varying the molar ratio of the two macro-CTAs, a series of disulfide-functionalized diblock copolymer worm gels were obtained. For both formulations, oscillatory rheology studies confirmed that higher disulfide contents led to stronger gels, presumably as a result of inter-worm covalent bond formation via disulfide/thiol exchange. Using the DSDB-based macro-CTA led to the strongest worm gels, and this formulation also proved to be more effective in suppressing the thermosensitive behavior that is observed for the nondisulfide-functionalized control worm gel. However, macroscopic precipitation occurred when the proportion of DSDB-based macro-CTA was increased to 50 mol %, whereas the DSDMA-based macro-CTA could be utilized at up to 80 mol %. Finally, the worm gel modulus could be reduced to that of a nondisulfide-containing worm gel by reductive cleavage of the inter-worm disulfide bonds using excess tris(2-carboxyethyl)phosphine (TCEP) to yield thiol groups. These new biomimetic worm gels are

  1. A taxonomic catalogue of Japanese nemerteans (phylum Nemertea).

    PubMed

    Kajihara, Hiroshi

    2007-04-01

    A literature-based taxonomic catalogue of the nemertean species (Phylum Nemertea) reported from Japanese waters is provided, listing 19 families, 45 genera, and 120 species as valid. Applications of the following species names to forms previously recorded from Japanese waters are regarded as uncertain: Amphiporus cervicalis, Amphiporus depressus, Amphiporus lactifloreus, Cephalothrix filiformis, Cephalothrix linearis, Cerebratulus fuscus, Lineus vegetus, Lineus bilineatus, Lineus gesserensis, Lineus grubei, Lineus longifissus, Lineus mcintoshii, Nipponnemertes pulchra, Oerstedia venusta, Prostoma graecense, and Prostoma grande. The identities of the taxa referred to by the following four nominal species require clarification through future investigations: Cosmocephala japonica, Dicelis rubra, Dichilus obscurus, and Nareda serpentina. The nominal species established from Japanese waters are tabulated. In addition, a brief history of taxonomic research on Japanese nemerteans is reviewed. PMID:17867829

  2. Comparative analysis of 35 basidiomycete genomes reveals diversity and uniqueness of the phylum

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Fungi of the phylum Basidiomycota (basidiomycetes), make up some 37% of the described fungi, and are important in forestry, agriculture, medicine, and bioenergy. This diverse phylum includes symbionts, pathogens, and saprobes including wood decaying fungi. To better understand the diversity of this ...

  3. Overview of the Cranked-Arrow Wing Aerodynamics Project International

    NASA Technical Reports Server (NTRS)

    Obara, Clifford J.; Lamar, John E.

    2008-01-01

    This paper provides a brief history of the F-16XL-1 aircraft, its role in the High Speed Research program and how it was morphed into the Cranked Arrow Wing Aerodynamics Project. Various flight, wind-tunnel and Computational Fluid Dynamics data sets were generated as part of the project. These unique and open flight datasets for surface pressures, boundary-layer profiles and skin-friction distributions, along with surface flow data, are described and sample data comparisons given. This is followed by a description of how the project became internationalized to be known as Cranked Arrow Wing Aerodynamics Project International and is concluded by an introduction to the results of a four year computational predictive study of data collected at flight conditions by participating researchers.

  4. Parity Violation in Exclusive B arrow γ Kππ

    NASA Astrophysics Data System (ADS)

    Bornheim, Adolf

    2003-04-01

    We present a study of radiative B meson decays into Kππγ using 13.4 fb-1 of e^+e^- data taken with the CLEO detector near the Υ(4S) resonance. By constructing a parity odd observable from the Kππ we are able to study the polarization of the photon from the radiative B decay. According to the standard model the photon from b arrow sγ (barb arrow barsγ) decays should have left-handed (right-handed) polarization, a prediction untested to date. We employ a maximum likelihood fit method to search for all possible charge combinations of the Kππγ final state in charged and neutral B meson decays and to investigate the photon polarization.

  5. Marine worms (genus Osedax) colonize cow bones

    PubMed Central

    Jones, William J; Johnson, Shannon B; Rouse, Greg W; Vrijenhoek, Robert C

    2007-01-01

    Bone-eating worms of the genus Osedax colonized and grew on cow bones deployed at depths ranging from 385 to 2893 m in Monterey Bay, California. Colonization occurred as rapidly as two months following deployment of the cow bones, similar to the time it takes to colonize exposed whalebones. Some Osedax females found on the cow bones were producing eggs and some hosted dwarf males in their tubes. Morphological and molecular examinations of these worms confirmed the presence of six Osedax species, out of the eight species presently known from Monterey Bay. The ability of Osedax species to colonize, grow and reproduce on cow bones challenges previous notions that these worms are ‘whale-fall specialists.’ PMID:18077256

  6. Arthropod larvae misidentified as parasitic worm infection.

    PubMed

    Munisamy, Sreetharan; Kilner, Rachael

    2011-01-01

    A healthy, asymptomatic man living in London, presented with seeing 'worms' in his toilet for two successive summer seasons. Repeated microscopic examination and cultures of both his faeces and urine were normal. He was empirically treated with multiple courses of antihelminthics without resolution of this problem. A sample of the worms was obtained, and positively identified as arthropod larvae under microscopic examination. These larvae do not parasitically colonise humans. It was subsequently deduced that a flying arthropod (most likely Culex pipiens mosquito) had laid eggs in standing toilet water, and the hatched larvae had been mistaken for parasitic worms. The patient was declared free of parasites and remains healthy. This case illustrates the dangers of starting empirical treatment without positive confirmation of causative organisms, which can result in unnecessary and potentially harmful treatment. PMID:22675109

  7. 32. Lighted arrows installed on the handrails, one on the ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    32. Lighted arrows installed on the handrails, one on the south span and one on the north span, used by the bridge operator to visually tell when the both of the spans are down. The walkways are on the western side of the bridge, view is facing southwest. - Henry Ford Bridge, Spanning Cerritos Channel, Los Angeles-Long Beach Harbor, Los Angeles, Los Angeles County, CA

  8. Transfer entropy in physical systems and the arrow of time.

    PubMed

    Spinney, Richard E; Lizier, Joseph T; Prokopenko, Mikhail

    2016-08-01

    Recent developments have cemented the realization that many concepts and quantities in thermodynamics and information theory are shared. In this paper, we consider a highly relevant quantity in information theory and complex systems, the transfer entropy, and explore its thermodynamic role by considering the implications of time reversal upon it. By doing so we highlight the role of information dynamics on the nuanced question of observer perspective within thermodynamics by relating the temporal irreversibility in the information dynamics to the configurational (or spatial) resolution of the thermodynamics. We then highlight its role in perhaps the most enduring paradox in modern physics, the manifestation of a (thermodynamic) arrow of time. We find that for systems that process information such as those undergoing feedback, a robust arrow of time can be formulated by considering both the apparent physical behavior which leads to conventional entropy production and the information dynamics which leads to a quantity we call the information theoretic arrow of time. We also offer an interpretation in terms of optimal encoding of observed physical behavior. PMID:27627274

  9. Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum

    PubMed Central

    McLean, Jeffrey S.; Lombardo, Mary-Jane; Badger, Jonathan H.; Edlund, Anna; Novotny, Mark; Yee-Greenbaum, Joyclyn; Vyahhi, Nikolay; Hall, Adam P.; Yang, Youngik; Dupont, Christopher L.; Ziegler, Michael G.; Chitsaz, Hamidreza; Allen, Andrew E.; Yooseph, Shibu; Tesler, Glenn; Pevzner, Pavel A.; Friedman, Robert M.; Nealson, Kenneth H.; Venter, J. Craig; Lasken, Roger S.

    2013-01-01

    The “dark matter of life” describes microbes and even entire divisions of bacterial phyla that have evaded cultivation and have yet to be sequenced. We present a genome from the globally distributed but elusive candidate phylum TM6 and uncover its metabolic potential. TM6 was detected in a biofilm from a sink drain within a hospital restroom by analyzing cells using a highly automated single-cell genomics platform. We developed an approach for increasing throughput and effectively improving the likelihood of sampling rare events based on forming small random pools of single-flow–sorted cells, amplifying their DNA by multiple displacement amplification and sequencing all cells in the pool, creating a “mini-metagenome.” A recently developed single-cell assembler, SPAdes, in combination with contig binning methods, allowed the reconstruction of genomes from these mini-metagenomes. A total of 1.07 Mb was recovered in seven contigs for this member of TM6 (JCVI TM6SC1), estimated to represent 90% of its genome. High nucleotide identity between a total of three TM6 genome drafts generated from pools that were independently captured, amplified, and assembled provided strong confirmation of a correct genomic sequence. TM6 is likely a Gram-negative organism and possibly a symbiont of an unknown host (nonfree living) in part based on its small genome, low-GC content, and lack of biosynthesis pathways for most amino acids and vitamins. Phylogenomic analysis of conserved single-copy genes confirms that TM6SC1 is a deeply branching phylum. PMID:23754396

  10. Live Worms Found Amid STS-107 Debris

    NASA Technical Reports Server (NTRS)

    2003-01-01

    NASA Project Manager Fred Ahmay holds a Biological Research in Canisters (BRIC) container in which C. elegans nemotodes (round worms) were found. The container was part of a middeck experiment that was among Columbia's debris recovered in East Texas. The worms were found alive after flying on Columbia's last mission, STS-107. The experiment was designed to verify a new synthetic nutrient solution for an International Space Station 'model' specimen planned to be used extensively for ISS gene expression studies and was sponsored by the NASA Ames Research Center. For more information on STS-107, please see GRIN Columbia General Explanation

  11. Battling Arrow's Paradox to Discover Robust Water Management Alternatives

    NASA Astrophysics Data System (ADS)

    Kasprzyk, J. R.; Reed, P. M.; Hadka, D.

    2013-12-01

    This study explores whether or not Arrow's Impossibility Theorem, a theory of social choice, affects the formulation of water resources systems planning problems. The theorem discusses creating an aggregation function for voters choosing from more than three alternatives for society. The Impossibility Theorem is also called Arrow's Paradox, because when trying to add more voters, a single individual's preference will dictate the optimal group decision. In the context of water resources planning, our study is motivated by recent theoretical work that has generalized the insights for Arrow's Paradox to the design of complex engineered systems. In this framing of the paradox, states of society are equivalent to water planning or design alternatives, and the voters are equivalent to multiple planning objectives (e.g. minimizing cost or maximizing performance). Seen from this point of view, multi-objective water planning problems are functionally equivalent to the social choice problem described above. Traditional solutions to such multi-objective problems aggregate multiple performance measures into a single mathematical objective. The Theorem implies that a subset of performance concerns will inadvertently dictate the overall design evaluations in unpredictable ways using such an aggregation. We suggest that instead of aggregation, an explicit many-objective approach to water planning can help overcome the challenges posed by Arrow's Paradox. Many-objective planning explicitly disaggregates measures of performance while supporting the discovery of the planning tradeoffs, employing multiobjective evolutionary algorithms (MOEAs) to find solutions. Using MOEA-based search to address Arrow's Paradox requires that the MOEAs perform robustly with increasing problem complexity, such as adding additional objectives and/or decisions. This study uses comprehensive diagnostic evaluation of MOEA search performance across multiple problem formulations (both aggregated and many

  12. Pan-phylum Comparison of Nematode Metabolic Potential

    PubMed Central

    Tyagi, Rahul; Rosa, Bruce A.; Lewis, Warren G.; Mitreva, Makedonka

    2015-01-01

    C. elegans and the human hookworm Necator americanus. We illustrate how analyzing and comparing metabolism at the level of pathway modules can improve existing knowledge of nematode metabolic potential and can provide parasitism related insights. Our reconstruction and comparison of nematode metabolic pathways at a pan-phylum and inter-phylum level enabled determination of phylogenetic restrictions and differential expression of pathways. A visualization of our results is available at http://nematode.net and the program for identification of module completeness (modDFS) is freely available at SourceForge. The methods reported will help biologists to predict biochemical potential of any organism with available deduced proteome, to direct experiments and test hypotheses. PMID:26000881

  13. Pan-phylum Comparison of Nematode Metabolic Potential.

    PubMed

    Tyagi, Rahul; Rosa, Bruce A; Lewis, Warren G; Mitreva, Makedonka

    2015-05-01

    C. elegans and the human hookworm Necator americanus. We illustrate how analyzing and comparing metabolism at the level of pathway modules can improve existing knowledge of nematode metabolic potential and can provide parasitism related insights. Our reconstruction and comparison of nematode metabolic pathways at a pan-phylum and inter-phylum level enabled determination of phylogenetic restrictions and differential expression of pathways. A visualization of our results is available at http://nematode.net and the program for identification of module completeness (modDFS) is freely available at SourceForge. The methods reported will help biologists to predict biochemical potential of any organism with available deduced proteome, to direct experiments and test hypotheses. PMID:26000881

  14. Practical experiences with worm gearing for spacecraft power transmission applications

    NASA Technical Reports Server (NTRS)

    Purdy, William; Mccown, William

    1989-01-01

    Experiences of several organizations using worm gearing for spacecraft are discussed. Practical aspects and subtleties of using worm gearing for design and operation is included. Knowledge gained from these applications is analyzed, and guidelines for usage are proposed.

  15. [Forensic medical assessment of injuries to the human body and clothes caused by a crossbow arrow].

    PubMed

    2011-01-01

    Analysis of the data published in the special literature revealed the lack of information for the objective comprehensive forensic medical evaluation of injuries to the human body and clothes caused by the arrows from different models of crossbows. Morphological characteristics of injuries were shown to strongly depend on the design features of the arrows. This fact can be used to differentiate between injuries inflicted by crossbow arrows and other types of missile weapons. PMID:21866845

  16. Of arrows and flows. Causality, determination, and specificity in the Central Dogma of molecular biology.

    PubMed

    Fantini, Bernardino

    2006-01-01

    From its first proposal, the Central Dogma had a graphical form, complete with arrows of different types, and this form quickly became its standard presentation. In different scientific contexts, arrows have different meanings and in this particular case the arrows indicated the flow of information among different macromolecules. A deeper analysis illustrates that the arrows also imply a causal statement, directly connected to the causal role of genetic information. The author suggests a distinction between two different kinds of causal links, defined as 'physical causality' and 'biological determination', both implied in the production of biological specificity. PMID:18351053

  17. Telonemia, a new protist phylum with affinity to chromist lineages.

    PubMed

    Shalchian-Tabrizi, K; Eikrem, W; Klaveness, D; Vaulot, D; Minge, M A; Le Gall, F; Romari, K; Throndsen, J; Botnen, A; Massana, R; Thomsen, H A; Jakobsen, K S

    2006-07-22

    Recent molecular investigations of marine samples taken from different environments, including tropical, temperate and polar areas, as well as deep thermal vents, have revealed an unexpectedly high diversity of protists, some of them forming deep-branching clades within important lineages, such as the alveolates and heterokonts. Using the same approach on coastal samples, we have identified a novel group of protist small subunit (SSU) rDNA sequences that do not correspond to any phylogenetic group previously identified. Comparison with other sequences obtained from cultures of heterotrophic protists showed that the environmental sequences grouped together with Telonema, a genus known since 1913 but of uncertain taxonomic affinity. Phylogenetic analyses using four genes (SSU, Hsp90, alpha-tubulin and beta-tubulin), and accounting for gamma- and covarion-distributed substitution rates, revealed Telonema as a distinct group of species branching off close to chromist lineages. Consistent with these gene trees, Telonema possesses ultrastructures revealing both the distinctness of the group and the evolutionary affinity to chromist groups. Altogether, the data suggest that Telonema constitutes a new eukaryotic phylum, here defined as Telonemia, possibly representing a key clade for the understanding of the early evolution of bikont protist groups, such as the proposed chromalveolate supergroup. PMID:16790418

  18. Telonemia, a new protist phylum with affinity to chromist lineages

    PubMed Central

    Shalchian-Tabrizi, K; Eikrem, W; Klaveness, D; Vaulot, D; Minge, M.A; Le Gall, F; Romari, K; Throndsen, J; Botnen, A; Massana, R; Thomsen, H.A; Jakobsen, K.S

    2006-01-01

    Recent molecular investigations of marine samples taken from different environments, including tropical, temperate and polar areas, as well as deep thermal vents, have revealed an unexpectedly high diversity of protists, some of them forming deep-branching clades within important lineages, such as the alveolates and heterokonts. Using the same approach on coastal samples, we have identified a novel group of protist small subunit (SSU) rDNA sequences that do not correspond to any phylogenetic group previously identified. Comparison with other sequences obtained from cultures of heterotrophic protists showed that the environmental sequences grouped together with Telonema, a genus known since 1913 but of uncertain taxonomic affinity. Phylogenetic analyses using four genes (SSU, Hsp90, alpha-tubulin and beta-tubulin), and accounting for gamma- and covarion-distributed substitution rates, revealed Telonema as a distinct group of species branching off close to chromist lineages. Consistent with these gene trees, Telonema possesses ultrastructures revealing both the distinctness of the group and the evolutionary affinity to chromist groups. Altogether, the data suggest that Telonema constitutes a new eukaryotic phylum, here defined as Telonemia, possibly representing a key clade for the understanding of the early evolution of bikont protist groups, such as the proposed chromalveolate supergroup. PMID:16790418

  19. SCAR arrow-wing active flutter suppression system

    NASA Technical Reports Server (NTRS)

    Gordon, C. K.; Visor, O. E.

    1977-01-01

    The potential performance and direct operating cost benefits of an active flutter suppression system (FSS) for the NASA arrow-wing supersonic cruise configuration were determined. A FSS designed to increase the flutter speed of the baseline airplane 20 percent. A comparison was made of the performance and direct operating cost between the FSS equipped aircraft and a previously defined configuration with structural modifications to provide the same flutter speed. Control system synthesis and evaluation indicated that a FSS could provide the increase in flutter speed without degrading airplane reliability, safety, handling qualities, or ride quality, and without increasing repeated loads or hydraulic and electrical power capacity requirements.

  20. Time arrow is influenced by the dark energy.

    PubMed

    Allahverdyan, A E; Gurzadyan, V G

    2016-05-01

    The arrow of time and the accelerated expansion are two fundamental empirical facts of the universe. We advance the viewpoint that the dark energy (positive cosmological constant) accelerating the expansion of the universe also supports the time asymmetry. It is related to the decay of metastable states under generic perturbations, as we show on example of a microcanonical ensemble. These states will not be metastable without dark energy. The latter also ensures a hyperbolic motion leading to dynamic entropy production with the rate determined by the cosmological constant. PMID:27300848

  1. Fundamental Aerodynamic Investigations for Development of Arrow-Stabilized Projectiles

    NASA Technical Reports Server (NTRS)

    Kurzweg, Hermann

    1947-01-01

    The numerous patent applications on arrow-stabilized projectiles indicate that the idea of projectiles without spin is not new, but has appeared in various proposals throughout the last decades. As far as projectiles for subsonic speeds are concerned, suitable shapes have been developed for sometime, for example, numerous grenades. Most of the patent applications, though, are not practicable particularly for projectiles with supersonic speed. This is because the inventor usually does not have any knowledge of aerodynamic flow around the projectile nor any particular understanding of the practical solution. The lack of wind tunnels for the development of projectiles made it necessary to use firing tests for development. These are obviously extremely tedious or expensive and lead almost always to failures. The often expressed opinion that arrow-stabilized projectiles cannot fly supersonically can be traced to this condition. That this is not the case has been shown for the first time by Roechling on long projectiles with foldable fins. Since no aerodynamic investigations were made for the development of these projectiles, only tedious series of firing tests with systematic variation of the fins could lead to satisfactory results. These particular projectiles though have a disadvantage which lies in the nature cf foldable fins. They occasionally do not open uniformly in flight, thus causing unsymmetry in flow and greater scatter. The junctions of fins and body are very bad aerodynamically and increase the drag. It must be possible to develop high-performance arrow-stabilized projectiles based on the aerodynamic research conducted during the last few years at Peenemuende and new construction ideas. Thus the final shape, ready for operational use, could be developed in the wind tunnel without loss of expensive time in firing tests. The principle of arrow-stabilized performance has been applied to a large number of caliburs which were stabilized by various means Most

  2. Emergence of Species-Specific Transporters During Evolution of the Hemiascomycete Phylum

    PubMed Central

    De Hertogh, Benoît; Hancy, Frédéric; Goffeau, André; Baret, Philippe V.

    2006-01-01

    We have traced the evolution patterns of 2480 transmembrane transporters from five complete genome sequences spanning the entire Hemiascomycete phylum: Saccharomyces cerevisiae, Candida glabrata, Kluyveromyces lactis, Debaryomyces hansenii, and Yarrowia lipolytica. The use of nonambiguous functional and phylogenetic criteria derived from the TCDB classification system has allowed the identification within the Hemiascomycete phylum of 97 small phylogenetic transporter subfamilies comprising a total of 355 transporters submitted to four distinct evolution patterns named “ubiquitous,” “species specific,” “phylum gains and losses,” or “homoplasic.” This analysis identifies the transporters that contribute to the emergence of species during the evolution of the Hemiascomycete phylum and may aid in establishing novel phylogenetic criteria for species classification. PMID:16118182

  3. The onchocercal nodule: interrelationship of adult worms and blood vessels.

    PubMed

    George, G H; Palmieri, J R; Connor, D H

    1985-11-01

    This study of onchocercal nodules reveals an intimate relationship between the cuticle of Onchocerca volvulus and the capillaries of the host. Perfusion of blood vessels with India ink and other special techniques reveal a proliferation of capillaries around the worms and communication between small vessels and the spaces around the worms. The space around the worm is continuous with the central fibrin lake. These findings, together with the fact that the worm's gut contains hemosiderin, suggest that the worm subverts the vascular reaction and causes within the nodule a controlled hemorrhage that serves the worm's nutritional needs. We believe this explains, in part, how worms survive in fibrous nodules for many years. PMID:3834800

  4. Measurement of the ratio fracl B(Υ(4S)arrow B^+B^-)l B(Υ(4S)arrow B^0 barB^0)

    NASA Astrophysics Data System (ADS)

    Hadavand, Haleh

    2003-04-01

    The ratio R^+/0=fracl B(Υ(4S) arrow B^+B^-)l B(Υ(4S) arrow B^0 barB^0) is measured with fully reconstructed candidates for B^± arrow J/ψ K^± and B^0 arrow J/ψ K^0S decays. Results are based on a data sample collected with the BaBar detector from 1999 to 2002.

  5. Measurement of the B^+/ B^0 Production Ratio from the Υ(4S) Meson using B^± arrow J/ψ K^± and B^0 arrow J/ψ K^0S decays.

    NASA Astrophysics Data System (ADS)

    Hadavand, Haleh

    2004-05-01

    The ratio R^+/0=fracl B(Υ(4S) arrow B^+ B^-)l B(Υ(4S) arrow B^0 barB^0) is measured with fully reconstructed candidates for B^± arrow J/ψ K^± and B^0 arrow J/ψ K^0S decays. Results are based on a data sample collected with the BaBar detector from 1999 to 2002.

  6. Monosomy 9p24{r_arrow}pter and trisomy 5q31{r_arrow}qter: Case report and review of two cases

    SciTech Connect

    Schimmenti, L.A.; Steinberger, J.; Mammel, M.C.

    1995-05-22

    Partial deletion of the short arm of chromosome 9 (p24{r_arrow}pter) and partial duplication of the long arm of chromosome 5 (q32{r_arrow}qter) were observed in an abnormal boy who died at age 8 weeks of a complex cyanotic cardiac defect. He also had minor anomalies, sagittal craniosynostosis, triphalangeal thumbs, hypospadias, and a bifid scrotum. Two other infants with similar cytogenetic abnormalities were described previously. These patients had severe congenital heart defect, genitourinary anomalies, broad nasal bridge, low hairline, apparently low-set ears, short neck, and triphalangeal thumbs, in common with our patient. We suggest that combined monosomy 9q23,24{r_arrow}pter and trisomy 5q31,32{r_arrow}qter may constitute a clinically recognizable syndrome. 13 refs., 2 figs., 2 tabs.

  7. Search for the flavor changing neutral current B-meson decays B^+arrow μ^+ μ^- K^+ and B^0arrow μ^+ μ^-K^*0 at CDF.

    NASA Astrophysics Data System (ADS)

    Erdmann, Wolfram; Speer, Thomas

    1997-04-01

    We present a search for rare B-meson decays B^+arrow μ^+ μ^- K^+ and B^0arrow μ^+ μ^-K^*0 using data from pbarp collisions at √s = 1.8 TeV recorded with CDF during the 1994 to 95 running period. We set upper limits on BR(B^+arrow μ^+ μ^- K^+) and BR(B^0arrow μ^+ μ^-K^*0). ^ Supported by U.S. DOE DE-AC02-76CH03000. ^*We thank the Fermilab staff and the technical staffs of the participating institutions for their vital contributions. This work was supported by the U.S. Department of Energy and National Science Foundation; the Italian Instituto Nazionale di Fisica Nucleare; the Ministry of Education, Science and Culture of Japan; the Natural Sciences and Engineering Research Council of Canada; the National Science Council of the Republic of China; and the A. P. Sloan Foundation.

  8. Parametric analysis of the end face engagement worm gear

    NASA Astrophysics Data System (ADS)

    Deng, Xingqiao; Wang, Jueling; Wang, Jinge; Chen, Shouan; Yang, Jie

    2015-11-01

    A novel specific type of worm drive, so-called end face engagement worm gear(EFEWD), is originally presented to minimize or overcome the gear backlash. Different factors, including the three different types, contact curves, tooth profile, lubrication angle and the induced normal curvature are taken into account to investigate the meshing characteristics and create the profile of a novel specific type of worm drive through mathematical models and theoretical analysis. The tooth of the worm wheel is very specific with the sine-shaped tooth which is located at the alveolus of the worm and the tooth profile of a worm is generated by the meshing movement of the worm wheel with the sine-shaped tooth, but just the end face of the worm(with three different typical meshing types) is adapted to meshing, and therefore an extraordinary manufacturing methods is used to generate the profile of the end face engagement worm. The research results indicates that the bearing contacts of the generated conjugate hourglass worm gear set are in line contacts, with certain advantages of no-backlash, high precision and high operating efficiency over other gears and gear systems besides the end face engagement worm gear drive may improve bearing contact, reduce the level of transmission errors and lessen the sensitivity to errors of alignment. Also, the end face engagement worm can be easily made with superior meshing and lubrication performance compared with the conventional techniques. In particular, the meshing and lubrication performance of the end face engagement worm gear by using the end face to meshing can be increased over 10% and 7%, respectively. This investigate is expect to provide a new insight on the design of the future no-backlash worm drive for industry.

  9. Qualitative Differences Between Conscious and Nonconscious Processing? On Inverse Priming Induced by Masked Arrows

    ERIC Educational Resources Information Center

    Verleger, Rolf; Jaskowski, Piotr; Aydemir, Aytac; van der Lubbe, Rob H. J.; Groen, Margriet

    2004-01-01

    In general, both consciously and unconsciously perceived stimuli facilitate responses to following similar stimuli. However, masked arrows delay responses to following arrows. This inverse priming has been ascribed to inhibition of premature motor activation, more recently even to special processing of nonconsciously perceived material. Here,…

  10. New Bouncing Curved Arrow Technique for the Depiction of Organic Mechanisms

    ERIC Educational Resources Information Center

    Straumanis, Andrei R.; Ruder, Suzanne M.

    2009-01-01

    Many students fail to develop a conceptual understanding of organic chemistry. Evidence suggests this failure goes hand-in-hand with a failure to grasp the techniques, meaning, and usefulness of curved arrow notation. Use of curved arrow notation to illustrate electrophilic addition appears to be a critical juncture in student understanding.…

  11. Atypical Visual Orienting to Gaze- and Arrow-Cues in Adults with High Functioning Autism

    ERIC Educational Resources Information Center

    Vlamings, Petra H. J. M.; Stauder, Johannes E. A.; van Son, Ilona A. M.; Mottron, Laurent

    2005-01-01

    The present study investigates visual orienting to directional cues (arrow or eyes) in adults with high functioning autism (n = 19) and age matched controls (n = 19). A choice reaction time paradigm is used in which eye-or arrow direction correctly (congruent) or incorrectly (incongruent) cues target location. In typically developing participants,…

  12. Avatars and arrows: implicit mentalizing or domain-general processing?

    PubMed

    Santiesteban, Idalmis; Catmur, Caroline; Hopkins, Senan Coughlan; Bird, Geoffrey; Heyes, Cecilia

    2014-06-01

    Previous studies using the dot perspective task have shown that adults are slower to verify the number of dots they can see in a picture when a human figure in the picture, an avatar, can see a different number of dots. This "self-consistency effect," which occurs even when the avatar's perspective is formally task-irrelevant, has been interpreted as evidence of implicit mentalizing; that humans can think about the mental states of others via dedicated, automatic processes. We tested this interpretation by giving participants 2 versions of the dot perspective task. In some trials, the avatar was presented as in previous experiments, and in other trials the avatar was replaced by an arrow with similar low-level features. We found self-consistency effects of comparable size in the avatar and arrow conditions, suggesting that self-consistency effects in the dot perspective task are due to domain-general processes such as those that mediate automatic attentional orienting. PMID:24377486

  13. A Novel Extracellular Gut Symbiont in the Marine Worm Priapulus caudatus (Priapulida) Reveals an Alphaproteobacterial Symbiont Clade of the Ecdysozoa

    PubMed Central

    Kroer, Paul; Kjeldsen, Kasper U.; Nyengaard, Jens R.; Schramm, Andreas; Funch, Peter

    2016-01-01

    Priapulus caudatus (phylum Priapulida) is a benthic marine predatory worm with a cosmopolitan distribution. In its digestive tract we detected symbiotic bacteria that were consistently present in specimens collected over 8 years from three sites at the Swedish west coast. Based on their 16S rRNA gene sequence, these symbionts comprise a novel genus of the order Rickettsiales (Alphaproteobacteria). Electron microscopy and fluorescence in situ hybridization (FISH) identified them as extracellular, elongate bacteria closely associated with the microvilli, for which we propose the name “Candidatus Tenuibacter priapulorum”. Within Rickettsiales, they form a phylogenetically well-defined, family-level clade with uncultured symbionts of marine, terrestrial, and freshwater arthropods. Cand. Tenuibacter priapulorum expands the host range of this candidate family from Arthropoda to the entire Ecdysozoa, which may indicate an evolutionary adaptation of this bacterial group to the microvilli-lined guts of the Ecdysozoa. PMID:27199899

  14. Bell's theorem and the causal arrow of time

    NASA Astrophysics Data System (ADS)

    Argaman, Nathan

    2010-10-01

    Einstein held that the formalism of quantum mechanics involves "spooky actions at a distance." In the 1960s, Bell amplified this by showing that the predictions of quantum mechanics disagree with the results of any locally causal description. It should be appreciated that accepting nonlocal descriptions while retaining causality leads to a clash with relativity. Furthermore, the causal arrow of time by definition contradicts time-reversal symmetry. For these reasons, Wheeler and Feynman, Costa de Beauregard, Cramer, Price, and others have advocated abandoning microscopic causality. In this paper, a simplistic but concrete example of this line of thought is presented, in the form of a retro-causal toy model that is stochastic and provides an appealing description of the quantum correlations discussed by Bell. It is concluded that Einstein's "spooky actions" may occur "in the past" rather than "at a distance," resolving the tension between quantum mechanics and relativity and opening unexplored possibilities for future reformulations of quantum mechanics.

  15. Time's arrow in nephrology: the discovery of the kidney.

    PubMed

    Cameron, J Stewart

    2005-01-01

    Time is a unique dimension of the universe, along with perhaps 10 dimensions of space, according to superstring theory. Our brain and its associated consciousness perceive time as a continuous unidirectional stream. Even though we appear to be able to move freely in three dimensions of space; time's arrow for us points only one way, the present eroding into the future to leave the past behind. For two millennia, time has been likened to a stream or river. In the West, for the past two centuries, time and change have been equated almost automatically with the idea of progress. However, change always brings with it loss as well as gain, and progress is far from inevitable. This remains true in the history of medicine. The history of any subject is full of blind alleys, which, although important at the time, generally become edited out in retrospect. PMID:16180549

  16. Arrow physicians: are economics and medicine philosophically incompatible?

    PubMed

    Tsang, Sandro

    2015-06-01

    Economics is en route to its further expansion in medicine, but many in the medical community remain unconvinced that its impact will be positive. Thus, a philosophical enquiry into the compatibility of economics and medicine is necessary to resolve the disagreements. The fundamental mission of medicine obliges physicians to practise science and compassion to serve the patient's best interests. Conventional (neoclassical) economics assumes that individuals are self-interested and that competitive markets will emerge optimal states. Economics is seemingly incompatible with the emphasis of putting patients' interests first. This idea is refuted by Professor Kenneth Arrow's health economics seminal paper. Arrow emphasizes that medical practice involves agency, knowledge, trust and professionalism, and physician-patient relation critically affects care quality. The term Arrow Physician is used to mean a humanistic carer who has a concern for the patient and acts on the best available evidence with health equity in mind. To make this practice sustainable, implementing appropriate motivations, constitutions and institutions to enable altruistic agency is critical. There is substantial evidence that polycentric governance can encourage building trust and reciprocity, so as to avoid depletion of communal resources. This paper proposes building trusting institutions through granting altruistic physicians adequate autonomy to direct resources based on patients' technical needs. It also summarizes the philosophy bases of medicine and economics. It, therefore, contributes to developing a shared language to facilitate intellectual dialogues, and will encourage trans-disciplinary research into medical practice. This should lead to medicine being reoriented to care for whole persons again. PMID:25850973

  17. Worms Eat My Garbage. How To Set Up and Maintain a Worm Composting System. First Edition.

    ERIC Educational Resources Information Center

    Appelhof, Mary

    This book is a resource for parents and teachers who want to teach about recycling and composting by setting up and maintaining a worm composting system. It is designed to be a detailed yet simple manual of vermicomposting. The manual covers the basics of vermicomposting and answers such questions as where to store a composting container, what…

  18. Sampling of general correlators in worm-algorithm based simulations

    NASA Astrophysics Data System (ADS)

    Rindlisbacher, Tobias; Åkerlund, Oscar; de Forcrand, Philippe

    2016-08-01

    Using the complex ϕ4-model as a prototype for a system which is simulated by a worm algorithm, we show that not only the charged correlator <ϕ* (x) ϕ (y) >, but also more general correlators such as < | ϕ (x) | | ϕ (y) | > or < arg ⁡ (ϕ (x)) arg ⁡ (ϕ (y)) >, as well as condensates like < | ϕ | >, can be measured at every step of the Monte Carlo evolution of the worm instead of on closed-worm configurations only. The method generalizes straightforwardly to other systems simulated by worms, such as spin or sigma models.

  19. A novel denitrifying methanotroph of the NC10 phylum and its microcolony

    PubMed Central

    He, Zhanfei; Cai, Chaoyang; Wang, Jiaqi; Xu, Xinhua; Zheng, Ping; Jetten, Mike S. M.; Hu, Baolan

    2016-01-01

    The NC10 phylum is a candidate phylum of prokaryotes and is considered important in biogeochemical cycles and evolutionary history. NC10 members are as-yet-uncultured and are difficult to enrich, and our knowledge regarding this phylum is largely limited to the first species ‘Candidatus Methylomirabilis oxyfera’ (M. oxyfera). Here, we enriched NC10 members from paddy soil and obtained a novel species of the NC10 phylum that mediates the anaerobic oxidation of methane (AOM) coupled to nitrite reduction. By comparing the new 16S rRNA gene sequences with those already in the database, this new species was found to be widely distributed in various habitats in China. Therefore, we tentatively named it ‘Candidatus Methylomirabilis sinica’ (M. sinica). Cells of M. sinica are roughly coccus-shaped (0.7–1.2 μm), distinct from M. oxyfera (rod-shaped; 0.25–0.5 × 0.8–1.1 μm). Notably, microscopic inspections revealed that M. sinica grew in honeycomb-shaped microcolonies, which was the first discovery of microcolony of the NC10 phylum. This finding opens the possibility to isolate NC10 members using microcolony-dependent isolation strategies. PMID:27582299

  20. Quorum Sensing: An Under-Explored Phenomenon in the Phylum Actinobacteria

    PubMed Central

    Polkade, Ashish V.; Mantri, Shailesh S.; Patwekar, Umera J.; Jangid, Kamlesh

    2016-01-01

    Quorum sensing is known to play a major role in the regulation of secondary metabolite production, especially, antibiotics, and morphogenesis in the phylum Actinobacteria. Although it is one of the largest bacterial phylum, only 25 of the 342 genera have been reported to use quorum sensing. Of these, only nine have accompanying experimental evidence; the rest are only known through bioinformatic analysis of gene/genome sequences. It is evident that this important communication mechanism is not extensively explored in Actinobacteria. In this review, we summarize the different quorum sensing systems while identifying the limitations of the existing screening strategies and addressing the improvements that have taken place in this field in recent years. The γ-butyrolactone system turned out to be almost exclusively limited to this phylum. In addition, methylenomycin furans, AI-2 and other putative AHL-like signaling molecules are also reported in Actinobacteria. The lack of existing screening systems in detecting minute quantities and of a wider range of signaling molecules was a major reason behind the limited information available on quorum sensing in this phylum. However, recent improvements in screening strategies hold a promising future and are likely to increase the discovery of new signaling molecules. Further, the quorum quenching ability in many Actinobacteria has a great potential in controlling the spread of plant and animal pathogens. A systematic and coordinated effort is required to screen and exploit the enormous potential that quorum sensing in the phylum Actinobacteria has to offer for human benefit. PMID:26904007

  1. A novel denitrifying methanotroph of the NC10 phylum and its microcolony.

    PubMed

    He, Zhanfei; Cai, Chaoyang; Wang, Jiaqi; Xu, Xinhua; Zheng, Ping; Jetten, Mike S M; Hu, Baolan

    2016-01-01

    The NC10 phylum is a candidate phylum of prokaryotes and is considered important in biogeochemical cycles and evolutionary history. NC10 members are as-yet-uncultured and are difficult to enrich, and our knowledge regarding this phylum is largely limited to the first species 'Candidatus Methylomirabilis oxyfera' (M. oxyfera). Here, we enriched NC10 members from paddy soil and obtained a novel species of the NC10 phylum that mediates the anaerobic oxidation of methane (AOM) coupled to nitrite reduction. By comparing the new 16S rRNA gene sequences with those already in the database, this new species was found to be widely distributed in various habitats in China. Therefore, we tentatively named it 'Candidatus Methylomirabilis sinica' (M. sinica). Cells of M. sinica are roughly coccus-shaped (0.7-1.2 μm), distinct from M. oxyfera (rod-shaped; 0.25-0.5 × 0.8-1.1 μm). Notably, microscopic inspections revealed that M. sinica grew in honeycomb-shaped microcolonies, which was the first discovery of microcolony of the NC10 phylum. This finding opens the possibility to isolate NC10 members using microcolony-dependent isolation strategies. PMID:27582299

  2. Electing a candidate: a speculative history of the bacterial phylum OP10.

    PubMed

    Dunfield, Peter F; Tamas, Ivica; Lee, Kevin C; Morgan, Xochitl C; McDonald, Ian R; Stott, Matthew B

    2012-12-01

    In 1998, a cultivation-independent survey of the microbial community in Obsidian Pool, Yellowstone National Park, detected 12 new phyla within the Domain Bacteria. These were dubbed 'candidate divisions' OP1 to OP12. Since that time the OP10 candidate division has been commonly detected in various environments, usually as part of the rare biosphere, but occasionally as a predominant community component. Based on 16S rRNA gene phylogeny, OP10 comprises at least 12 class-level subdivisions. However, despite this broad ecological and evolutionary diversity, all OP10 bacteria have eluded cultivation until recently. In 2011, two reference species of OP10 were taxonomically validated, removing the phylum from its 'candidate' status. Construction of a highly resolved phylogeny based on 29 universally conserved genes verifies its standing as a unique bacterial phylum. In the following paper we summarize what is known and what is suspected about the newest described bacterial phylum, the Armatimonadetes. PMID:22497633

  3. Evidence for the widespread distribution of CRISPR-Cas system in the Phylum Cyanobacteria

    PubMed Central

    Cai, Fei; Axen, Seth D.; Kerfeld, Cheryl A.

    2013-01-01

    Members of the phylum Cyanobacteria inhabit ecologically diverse environments. However, the CRISPR-Cas (clustered regularly interspaced short palindromic repeats, CRISPR associated genes), an extremely adaptable defense system, has not been surveyed in this phylum. We analyzed 126 cyanobacterial genomes and, surprisingly, found CRISPR-Cas in the majority except the marine subclade (Synechococcus and Prochlorococcus), in which cyanophages are a known force shaping their evolution. Multiple observations of CRISPR loci in the absence of cas1/cas2 genes may represent an early stage of losing a CRISPR-Cas locus. Our findings reveal the widespread distribution of their role in the phylum Cyanobacteria and provide a first step to systematically understanding CRISPR-Cas systems in cyanobacteria. PMID:23628889

  4. Metagenomic Analysis Reveals Unexpected Subgenomic Diversity of Magnetotactic Bacteria within the Phylum Nitrospirae ▿ †

    PubMed Central

    Lin, Wei; Jogler, Christian; Schüler, Dirk; Pan, Yongxin

    2011-01-01

    A targeted metagenomic approach was applied to investigate magnetotactic bacteria (MTB) within the phylum Nitrospirae in Lake Miyun near Beijing, China. Five fosmids containing rRNA operons were identified. Comparative sequence analysis of a total of 172 kb provided new insights into their genome organization and revealed unexpected subgenomic diversity of uncultivated MTB in the phylum Nitrospirae. In addition, affiliation of two novel MTB with the phylum Nitrospirae was verified by fluorescence in situ hybridization. One of them was morphologically similar to “Candidatus Magnetobacterium bavaricum,” but the other differed substantially in cell shape and magnetosome organization from all previously described “Ca. Magnetobacterium bavaricum”-like bacteria. PMID:21057016

  5. A transcriptomic approach to ribbon worm systematics (nemertea): resolving the pilidiophora problem.

    PubMed

    Andrade, Sónia C S; Montenegro, Horácio; Strand, Malin; Schwartz, Megan L; Kajihara, Hiroshi; Norenburg, Jon L; Turbeville, James M; Sundberg, Per; Giribet, Gonzalo

    2014-12-01

    Resolving the deep relationships of ancient animal lineages has proven difficult using standard Sanger-sequencing approaches with a handful of markers. We thus reassess the relatively well-studied phylogeny of the phylum Nemertea (ribbon worms)-for which the targeted gene approaches had resolved many clades but had left key phylogenetic gaps-by using a phylogenomic approach using Illumina-based de novo assembled transcriptomes and automatic orthology prediction methods. The analysis of a concatenated data set of 2,779 genes (411,138 amino acids) with about 78% gene occupancy and a reduced version with 95% gene occupancy, under evolutionary models accounting or not for site-specific amino acid replacement patterns results in a well-supported phylogeny that recovers all major accepted nemertean clades with the monophyly of Heteronemertea, Hoplonemertea, Monostilifera, being well supported. Significantly, all the ambiguous patterns inferred from Sanger-based approaches were resolved, namely the monophyly of Palaeonemertea and Pilidiophora. By testing for possible conflict in the analyzed supermatrix, we observed that concatenation was the best solution, and the results of the analyses should settle prior debates on nemertean phylogeny. The study highlights the importance, feasibility, and completeness of Illumina-based phylogenomic data matrices. PMID:25169929

  6. Phylogeny of sipunculan worms: A combined analysis of four gene regions and morphology.

    PubMed

    Schulze, Anja; Cutler, Edward B; Giribet, Gonzalo

    2007-01-01

    The intra-phyletic relationships of sipunculan worms were analyzed based on DNA sequence data from four gene regions and 58 morphological characters. Initially we analyzed the data under direct optimization using parsimony as optimality criterion. An implied alignment resulting from the direct optimization analysis was subsequently utilized to perform a Bayesian analysis with mixed models for the different data partitions. For this we applied a doublet model for the stem regions of the 18S rRNA. Both analyses support monophyly of Sipuncula and most of the same clades within the phylum. The analyses differ with respect to the relationships among the major groups but whereas the deep nodes in the direct optimization analysis generally show low jackknife support, they are supported by 100% posterior probability in the Bayesian analysis. Direct optimization has been useful for handling sequences of unequal length and generating conservative phylogenetic hypotheses whereas the Bayesian analysis under mixed models provided high resolution in the basal nodes of the tree. PMID:16919974

  7. Molecular karyotype analysis of Perkinsus atlanticus (Phylum Perkinsozoa) by pulsed field gel electrophoresis.

    PubMed

    Leonor Teles-Grilo, M; Duarte, Sérgio M; Tato-Costa, Joana; Gaspar-Maia, Alexandre; Oliveira, Carla; Rocha, António A; Marques, Américo; Cordeiro-da-Silva, Anabela; Azevedo, Carlos

    2007-11-01

    Perkinsus atlanticus is a pathogenic protist that infects the clam Ruditapes decussatus. Although it was recently proposed that the genus Perkinsus belongs to a new phylum, Perkinsozoa, in the infra-kingdom Alveolata, there remain different opinions about whether this genus should form a phylum on its own and consequently divergent views about its taxonomic characterization. In this work, we have identified nine chromosomes by pulsed field gel electrophoresis (PFGE) combined with densitometry analysis. The obtained karyotype of Perkinsus atlanticus, like that of other early branches of the dinoflagellate lineage, displays a more conventional chromosome organization, different from that of most dinoflagellates. PMID:17822886

  8. A Taxonomic Catalogue of the Nemerteans (Phylum Nemertea) of Spain and Portugal.

    PubMed

    Herrera-Bachiller, Alfonso; Fernández-Álvarez, Fernando Ángel; Junoy, Juan

    2015-12-01

    A literature-based taxonomic catalogue of nemerteans (phylum Nemertea) from Spain and Portugal is provided, listing 75 species (12 Palaeonemertea, 24 Pilidiophora, and 39 Hoplonemertea) belonging to 34 genera. This is a low species number compared with the approximately 400 species listed in Europe. This lack of knowledge is mainly due to the low number of researchers interested in the phylum and the well-known taxonomic difficulties of its study. Geographic records are indicated for each species, and for some, comments are included on certain biological and taxonomic aspects. PMID:26654034

  9. Arrow Lakes Reservoir Fertilization Experiment; Years 4 and 5, Technical Report 2002-2003.

    SciTech Connect

    Schindler, E.

    2007-02-01

    This report presents the fourth and fifth year (2002 and 2003, respectively) of a five-year fertilization experiment on the Arrow Lakes Reservoir. The goal of the experiment was to increase kokanee populations impacted from hydroelectric development on the Arrow Lakes Reservoir. The impacts resulted in declining stocks of kokanee, a native land-locked sockeye salmon (Oncorhynchus nerka), a key species of the ecosystem. Arrow Lakes Reservoir, located in southeastern British Columbia, has undergone experimental fertilization since 1999. It is modeled after the successful Kootenay Lake fertilization experiment. The amount of fertilizer added in 2002 and 2003 was similar to the previous three years. Phosphorus loading from fertilizer was 52.8 metric tons and nitrogen loading from fertilizer was 268 metric tons. As in previous years, fertilizer additions occurred between the end of April and the beginning of September. Surface temperatures were generally warmer in 2003 than in 2002 in the Arrow Lakes Reservoir from May to September. Local tributary flows to Arrow Lakes Reservoir in 2002 and 2003 were generally less than average, however not as low as had occurred in 2001. Water chemistry parameters in select rivers and streams were similar to previous years results, except for dissolved inorganic nitrogen (DIN) concentrations which were significantly less in 2001, 2002 and 2003. The reduced snow pack in 2001 and 2003 would explain the lower concentrations of DIN. The natural load of DIN to the Arrow system ranged from 7200 tonnes in 1997 to 4500 tonnes in 2003; these results coincide with the decrease in DIN measurements from water samples taken in the reservoir during this period. Water chemistry parameters in the reservoir were similar to previous years of study except for a few exceptions. Seasonal averages of total phosphorus ranged from 2.11 to 7.42 {micro}g/L from 1997 through 2003 in the entire reservoir which were indicative of oligo-mesotrophic conditions

  10. The African eye worm: a case report and review.

    PubMed

    Ali, Sadia; Fisher, Melanie; Juckett, Gregory

    2008-01-01

    Loiasis, caused by the filarial nematode Loa loa, is often asymptomatic but frequently manifests as episodic angioedema and periocular migration of adult worms. Hence also known as the eye worm.(1) It is rarely encountered in the United States among travelers and immigrants. This report describes a case of loiasis in a Cameroonian student seen at a US university clinic. PMID:18217870

  11. Characterization of two exon-skipping mutations (3120G{r_arrow}A, 3600G{r_arrow}A) in the CFTR gene

    SciTech Connect

    Zielendki, J.; Markiewicz, D.; Ainsworth, P.J.

    1994-09-01

    Many different types of mutations have been identified in the CFTR gene in patients with cystic fibrosis. Due to the large size of the gene (230 kb), CF mutations have been primarily detected by genomic DNA analysis. While some of the sequence alterations, such as nonsense and frameshift mutations, provide immediate clues to possible molecular consequence, others such as missense mutations are less apparent in their involvement in the disease. In our systematic scanning of the entire coding regions of the CFTR gene for a group of CF patients carrying unknown mutations, two different G to A substitutions located at the last nucleotide position of an exon were identified in two patients. The first one, 3120G{r_arrow}A, is located in exon 16 and the other one, 3600G{r_arrow}A, in exon 18 of the CFTR gene. Both of them are also located at the third position of the corresponding amino acid codon (CAG and TTC, respectively). As a result, the changes would not affect the encoded amino acids (Glu and Leu, respectively). To demonstrate that these are in fact pathologic mutations, we have investigated the CFTR transcripts in these two patients. The results of RT-PCR analysis revealed that aberrant splicing occurred in both cases: transcripts missing exon 16 and 18 were present in the 2 patients, respectively. No normal product was detectable from the 3120G{r_arrow}A and 3600G{r_arrow}A alleles, suggesting that the normal-sized products were exclusively derived from the {triangle}F508 mutant alleles in both of these patients. Hence, we conclude that both 3120G{r_arrow}A and 3600G{r_arrow}A mutations cause exon-skipping leading to premature termination and truncation of CFTR and that the altered G residue in each of these exons is probably part of the splice donor sequence important for efficient mRNA splicing.

  12. Rare decay {eta}{r_arrow}{pi}{pi}{gamma}{gamma} in chiral perturbation theory

    SciTech Connect

    Knoechlein, G.; Scherer, S.; Drechsel, D.

    1996-04-01

    We investigate the rare radiative {eta} decay modes {eta}{r_arrow}{pi}{sup +}{pi}{sup {minus}}{gamma}{gamma} and {eta}{r_arrow}{pi}{sup 0}{pi}{sup 0}{gamma}{gamma} within the framework of chiral perturbation theory at {ital O}({ital p}{sup 4}). We present photon spectra and partial decay rates for both processes as well as a Dalitz contour plot for the charged decay. {copyright} {ital 1996 The American Physical Society.}

  13. Notions and treatment of guinea worm in northern Ghana.

    PubMed

    Bierlich, B

    1995-08-01

    Dracunculiasis, infection with Dracunculus medinensis or guinea worm, is widespread in the Northern Region of Ghana, where rural people drink from unprotected water sources such as ponds and small-scale dams. This paper discusses the results of an anthropological study of beliefs and practices concerning commonly occurring illnesses, such as infection with guinea worm (nierifu), in two rural Dagomba communities in the Northern Region of Ghana. The importance of knowing about local perceptions and treatment of guinea worm is stressed. Guinea worm is not attributed to water. The general understanding is that guinea worm is an innate part of human anatomy. It is not seen as an alien presence in the body. Guinea worm is rather said to be 'in people's blood', and sooner or later to 'stand up'. Guinea worm is considered an 'inevitable' feature of living. After a description of the background to the study, the methods are characterized. Brief background information on the people, their environment and their water sources are given. The central portion of the paper focuses on local perceptions of illness and notions of guinea worm ('guinea worm is in the human blood'), which are very different from those of biomedicine ('guinea worm is a disease'). Attention is also given to perceptions of water ('bitter' vs 'sweet') and the prevention of guinea worm. The social limitations to the filter technology are addressed. People's choice of therapy and the role of medicines (herbs and Western pharmaceuticals) in treatment of guinea worm are also considered. The paper concludes with a discussion of health education and stresses the importance of showing respect for the local view of guinea worm, which is said to be 'in the blood'. It is suggested that, since people are not adverse to the use of Western pharmaceuticals, the use of Western medicines to treat guinea worm should be further promoted. The social constraints on filtering must also be appreciated. These relate to the

  14. The occurrence of gizzard worms in Canada geese

    USGS Publications Warehouse

    Herman, C.M.; Wehr, E.E.

    1954-01-01

    Amidostomum anseris, a roundworm which occurs under the horny lining of the gizzard in birds, is a widely distributed parasite in Canada geese. It is also reported from snow geese (Chen hyperborea). Although the extent of erosion of the gizzard wall by these worms is not precisely correlated with the number of worms present, it is usually severe in Canada geese when 150 or more worms are present. Gizzard worm infection is considered a contributing factor to low weights, poor condition and to losses among the Canada geese which winter at the Pea Island National Wildlife Refuge in North Carolina. The mean number of gizzard worms per bird is considerably higher for Pea Island than for areas where winter losses have not been reported.

  15. Can aquatic worms enhance methane production from waste activated sludge?

    PubMed

    Serrano, Antonio; Hendrickx, Tim L G; Elissen, Hellen H J; Laarhoven, Bob; Buisman, Cees J N; Temmink, Hardy

    2016-07-01

    Although literature suggests that aquatic worms can help to enhance the methane production from excess activated sludge, clear evidence for this is missing. Therefore, anaerobic digestion tests were performed at 20 and at 30°C with sludge from a high-loaded membrane bioreactor, the aquatic worm Lumbriculus variegatus, feces from these worms and with mixtures of these substrates. A significant synergistic effect of the worms or their feces on methane production from the high-loaded sludge or on its digestion rate was not observed. However, a positive effect on low-loaded activated sludge, which generally has a lower anaerobic biodegradability, cannot be excluded. The results furthermore showed that the high-loaded sludge provides an excellent feed for L. variegatus, which is promising for concepts where worm biomass is considered a resource for technical grade products such as coatings and glues. PMID:26998797

  16. "Qupirruit": insects and worms in Inuit traditions.

    PubMed

    Laugrand, Frédéric; Oosten, Jarich

    2010-01-01

    Although small beings such as the "qupirruit" (insects and worms) appear in many different contexts in Inuit culture, they have not received much attention from scholars. In this paper we examine the symbolism associated with these small animals. We show that their small size makes them suitable to operate on the level of the "tarniq," a miniature image of a being. We discuss how insects often connect different scales and easily transform into other beings. We first deal with the perceptions of insects as they take shape in narratives and practices, and their roles in the manufacture and use of amulets. Then we move to a more specific analysis of the distinctive features of the various "qupirruit". PMID:20648981

  17. Arrows of time in the bouncing universes of the no-boundary quantum state

    NASA Astrophysics Data System (ADS)

    Hartle, James; Hertog, Thomas

    2012-05-01

    We derive the arrows of time of our universe that follow from the no-boundary theory of its quantum state (NBWF) in a minisuperspace model. Arrows of time are viewed four-dimensionally as properties of the four-dimensional Lorentzian histories of the universe. Probabilities for these histories are predicted by the NBWF. For histories with a regular “bounce” at a minimum radius fluctuations are small at the bounce and grow in the direction of expansion on either side. For recollapsing classical histories with big bang and big crunch singularities the fluctuations are small near one singularity and grow through the expansion and recontraction to the other singularity. The arrow of time defined by the growth in fluctuations thus points in one direction over the whole of a recollapsing spacetime but is bidirectional in a bouncing spacetime. We argue that the electromagnetic, thermodynamic, and psychological arrows of time are aligned with the fluctuation arrow. The implications of a bidirectional arrow of time for causality are discussed.

  18. Application of HQET to B {r_arrow} K{sup *} transitions

    SciTech Connect

    W. Roberts; F. Ledroit

    1995-10-01

    The authors examine the measured rates for the decays D {r_arrow} K{sup *}l{nu}, B {r_arrow} K{sup *}{psi}{prime} and B {r_arrow} K{sup *}{gamma} in a number of scenarios, in the framework of the heavy quark effective theory. They attempt to find a scenario in which all of these decays are described by a single set of form factors. Once such a scenario is found, they make predictions for the rare decays B {r_arrow} K{sup *}l{sup +}l{sup {minus}}. While they find that many scenarios can provide adequate descriptions of all the data, somewhat surprisingly, they observe that two popular choices of form factors, namely monopolar forms and exponential forms, exhibit some shortcomings, especially when confronted with polarization observables. They predict Br({anti B}{sup 0} {r_arrow} {anti K}{sup 0}{mu}{sup +}{mu}{sup {minus}}) = 6.4 {+-} 1.0 x 10{sup {minus}7} and Br({anti B}{sup 0} {r_arrow} {anti K}{sup *0}{mu}{sup +}{mu}{sup {minus}}) = 3.8 {+-} 1.3 x 10{sup {minus}6}. They also make predictions for polarization observables in these decays.

  19. Acidobacteria Phylum Sequences in Uranium-Contaminated Subsurface Sediments Greatly Expand the Known Diversity within the Phylum▿ †

    PubMed Central

    Barns, Susan M.; Cain, Elizabeth C.; Sommerville, Leslie; Kuske, Cheryl R.

    2007-01-01

    The abundance and composition of bacteria of the phylum Acidobacteria were surveyed in subsurface sediments from uranium-contaminated sites using amplification of 16S rRNA genes followed by clone/sequence analysis. Analysis of sequences from this study and public databases produced a revised and greatly expanded phylogeny of the Acidobacteria phylum consisting of 26 subgroups. PMID:17337544

  20. DNA → RNA: What Do Students Think the Arrow Means?

    PubMed Central

    Fisk, J. Nick; Newman, Dina L.

    2014-01-01

    The central dogma of molecular biology, a model that has remained intact for decades, describes the transfer of genetic information from DNA to protein though an RNA intermediate. While recent work has illustrated many exceptions to the central dogma, it is still a common model used to describe and study the relationship between genes and protein products. We investigated understanding of central dogma concepts and found that students are not primed to think about information when presented with the canonical figure of the central dogma. We also uncovered conceptual errors in student interpretation of the meaning of the transcription arrow in the central dogma representation; 36% of students (n = 128; all undergraduate levels) described transcription as a chemical conversion of DNA into RNA or suggested that RNA existed before the process of transcription began. Interviews confirm that students with weak conceptual understanding of information flow find inappropriate meaning in the canonical representation of central dogma. Therefore, we suggest that use of this representation during instruction can be counterproductive unless educators are explicit about the underlying meaning. PMID:26086664

  1. Draft Genome Sequence of Bacillus vietnamensis Strain UCD-SED5 (Phylum Firmicutes)

    PubMed Central

    Lee, Ruth D.; Jospin, Guillaume; Lang, Jenna M.; Coil, David A.

    2015-01-01

    Here, we present the draft genome sequence of Bacillus vietnamensis UCD-SED5 (phylum Firmicutes). This strain was isolated from sediment surrounding Zostera marina roots near the UC Davis Bodega Marine Laboratory (Bodega, Bay, California) and represents the second genome of this species. The assembly consists of 4,325,707 bp, in 108 contigs. PMID:26586901

  2. Draft Genome Sequence of Bacillus vietnamensis Strain UCD-SED5 (Phylum Firmicutes).

    PubMed

    Lee, Ruth D; Jospin, Guillaume; Lang, Jenna M; Eisen, Jonathan A; Coil, David A

    2015-01-01

    Here, we present the draft genome sequence of Bacillus vietnamensis UCD-SED5 (phylum Firmicutes). This strain was isolated from sediment surrounding Zostera marina roots near the UC Davis Bodega Marine Laboratory (Bodega Bay, California) and represents the second genome of this species. The assembly consists of 4,325,707 bp, in 108 contigs. PMID:26586901

  3. A putative greigite-type magnetosome gene cluster from the candidate phylum Latescibacteria.

    PubMed

    Lin, Wei; Pan, Yongxin

    2015-04-01

    The intracellular biomineralization of magnetite and/or greigite magnetosomes in magnetotactic bacteria (MTB) is strictly controlled by a group of conserved genes, termed magnetosome genes, which are organized as clusters (or islands) in MTB genomes. So far, all reported MTB are affiliated within the Proteobacteria phylum, the Nitrospirae phylum and the candidate division OP3. Here, we report the discovery of a putative magnetosome gene cluster structure from the draft genome of an uncultivated bacterium belonging to the candidate phylum Latescibacteria (formerly candidate division WS3) recently recovered by Rinke and colleagues, which contains 10 genes with homology to magnetosome mam genes of magnetotactic Proteobacteria and Nitrospirae. Moreover, these genes are phylogenetically closely related to greigite-type magnetosome genes that were only found from the Deltaproteobacteria MTB before, suggesting that the greigite genes may originate earlier than previously imagined. These findings indicate that some members of Latescibacteria may be capable of forming greigite magnetosomes, and thus may play previously unrecognized roles in environmental iron and sulfur cycles. The conserved genomic structure of magnetosome gene cluster in Latescibacteria phylum supports the hypothesis of horizontal transfer of these genes among distantly related bacterial groups in nature. PMID:25382584

  4. Insights into the distribution and abundance of the ubiquitous candidatus Saccharibacteria phylum following tag pyrosequencing.

    PubMed

    Ferrari, Belinda; Winsley, Tristrom; Ji, Mukan; Neilan, Brett

    2014-01-01

    The phylum candidatus Saccharibacteria formerly known as Candidate Division TM7 is a highly ubiquitous phylum with 16S rRNA gene sequences reported in soils, sediments, wastewater and animals, as well as a host of clinical environments. Here, the application of two taxon-specific primers on environmental and human-associated samples using bar-coded tag pyrosequencing revealed two new clades for this phylum to exist and we propose that the division consists of 2 monophyletic and 2 polyphyletic clades. Investigation into TM7 ecology revealed that a high proportion (58%) of phylotypes were sample specific, few were widely distributed and of those most widely distributed all belonged to subdivision 3. Additionally, 50% of the most relatively abundant phylotypes observed were also subdivision 3 members. Community analysis showed that despite the presence of a high proportion of unique phylotypes, specific groups of samples still harbor similar TM7 communities with samples clustering together. The lack of relatively abundant phylotypes from subdivisions 1, 2 and 4 and the presence of very few cosmopolitan members' highlights not only the site specific nature of this phylum but provides insight into why the majority of studies into TM7 have been biased towards subdivision 3. PMID:24492458

  5. Newly isolated but uncultivated magnetotactic bacterium of the phylum Nitrospirae from Beijing, China.

    PubMed

    Lin, Wei; Li, Jinhua; Pan, Yongxin

    2012-02-01

    Magnetotactic bacteria (MTB) in the phylum Nitrospirae synthesize up to hundreds of intracellular bullet-shaped magnetite magnetosomes. In the present study, a watermelon-shaped magnetotactic bacterium (designated MWB-1) from Lake Beihai in Beijing, China, was characterized. This uncultivated microbe was identified as a member of the phylum Nitrospirae and represents a novel phylogenetic lineage with ≥6% 16S rRNA gene sequence divergence from all currently described MTB. MWB-1 contained 200 to 300 intracellular bullet-shaped magnetite magnetosomes and showed a helical swimming trajectory under homogeneous magnetic fields; its magnetotactic velocity decreased with increasing field strength, and vice versa. A robust phylogenetic framework for MWB-1 and all currently known MTB in the phylum Nitrospirae was constructed utilizing maximum-likelihood and Bayesian algorithms, which yielded strong evidence that the Nitrospirae MTB could be divided into four well-supported groups. Considering its population densities in sediment and its high numbers of magnetosomes, MWB-1 was estimated to account for more than 10% of the natural remanent magnetization of the surface sediment. Taken together, the results of this study suggest that MTB in the phylum Nitrospirae are more diverse than previously realized and can make important contributions to the sedimentary magnetization in particular environments. PMID:22113917

  6. Newly Isolated but Uncultivated Magnetotactic Bacterium of the Phylum Nitrospirae from Beijing, China

    PubMed Central

    Li, Jinhua; Pan, Yongxin

    2012-01-01

    Magnetotactic bacteria (MTB) in the phylum Nitrospirae synthesize up to hundreds of intracellular bullet-shaped magnetite magnetosomes. In the present study, a watermelon-shaped magnetotactic bacterium (designated MWB-1) from Lake Beihai in Beijing, China, was characterized. This uncultivated microbe was identified as a member of the phylum Nitrospirae and represents a novel phylogenetic lineage with ≥6% 16S rRNA gene sequence divergence from all currently described MTB. MWB-1 contained 200 to 300 intracellular bullet-shaped magnetite magnetosomes and showed a helical swimming trajectory under homogeneous magnetic fields; its magnetotactic velocity decreased with increasing field strength, and vice versa. A robust phylogenetic framework for MWB-1 and all currently known MTB in the phylum Nitrospirae was constructed utilizing maximum-likelihood and Bayesian algorithms, which yielded strong evidence that the Nitrospirae MTB could be divided into four well-supported groups. Considering its population densities in sediment and its high numbers of magnetosomes, MWB-1 was estimated to account for more than 10% of the natural remanent magnetization of the surface sediment. Taken together, the results of this study suggest that MTB in the phylum Nitrospirae are more diverse than previously realized and can make important contributions to the sedimentary magnetization in particular environments. PMID:22113917

  7. Comparative Analysis of 35 Basidiomycete Genomes Reveals Diversity and Uniqueness of the Phylum

    SciTech Connect

    Riley, Robert; Salamov, Asaf; Otillar, Robert; Fagnan, Kirsten; Boussau, Bastien; Brown, Daren; Henrissat, Bernard; Levasseur, Anthony; Held, Benjamin; Nagy, Laszlo; Floudas, Dimitris; Morin, Emmanuelle; Manning, Gerard; Baker, Scott; Martin, Francis; Blanchette, Robert; Hibbett, David; Grigoriev, Igor V.

    2013-03-11

    Fungi of the phylum Basidiomycota (basidiomycetes), make up some 37percent of the described fungi, and are important in forestry, agriculture, medicine, and bioenergy. This diverse phylum includes symbionts, pathogens, and saprobes including wood decaying fungi. To better understand the diversity of this phylum we compared the genomes of 35 basidiomycete fungi including 6 newly sequenced genomes. The genomes of basidiomycetes span extremes of genome size, gene number, and repeat content. A phylogenetic tree of Basidiomycota was generated using the Phyldog software, which uses all available protein sequence data to simultaneously infer gene and species trees. Analysis of core genes reveals that some 48percent of basidiomycete proteins are unique to the phylum with nearly half of those (22percent) comprising proteins found in only one organism. Phylogenetic patterns of plant biomass-degrading genes suggest a continuum rather than a sharp dichotomy between the white rot and brown rot modes of wood decay among the members of Agaricomycotina subphylum. There is a correlation of the profile of certain gene families to nutritional mode in Agaricomycotina. Based on phylogenetically-informed PCA analysis of such profiles, we predict that that Botryobasidium botryosum and Jaapia argillacea have properties similar to white rot species, although neither has liginolytic class II fungal peroxidases. Furthermore, we find that both fungi exhibit wood decay with white rot-like characteristics in growth assays. Analysis of the rate of discovery of proteins with no or few homologs suggests the high value of continued sequencing of basidiomycete fungi.

  8. Draft Genome Sequence of Kocuria sp. Strain UCD-OTCP (Phylum Actinobacteria)

    PubMed Central

    Coil, David A.; Doctor, Jessica I.; Lang, Jenna M.; Darling, Aaron E.

    2013-01-01

    Here, we present the draft genome of Kocuria sp. strain UCD-OTCP, a member of the phylum Actinobacteria, isolated from a restaurant chair cushion. The assembly contains 3,791,485 bp (G+C content of 73%) and is contained in 68 scaffolds. PMID:23661474

  9. Draft Genome Sequence of Planomicrobium glaciei UCD-HAM (Phylum Firmicutes)

    PubMed Central

    Betts, Makayla N.; Jospin, Guillaume; Coil, David A.

    2015-01-01

    Here, we present the draft genome of Planomicrobium glaciei, a member of the phylum Firmicutes, found at the University of California Davis. Paired-end, 300-bp reads were generated on an Illumina MiSeq. The assembly consists of 3,925,122 bp, contained in 109 contigs, with a G+C content of 46.7%. PMID:26472846

  10. Stability analysis of an e-SEIAR model with point-to-group worm propagation

    NASA Astrophysics Data System (ADS)

    Wang, Fangwei; Zhang, Yunkai; Wang, Changguang; Ma, Jianfeng

    2015-03-01

    Internet worms have drawn significant attention due to their enormous threats to the Internet. The main goal of this paper is to explore the interaction dynamics between a malicious worm and an benign worm, using a mathematical model, namely e-SEIAR. The e-SEIAR model takes two important network environment factors into consideration: point-to-group worm propagation mode and benign worms. Furthermore, some related dynamics properties are studied, along with the analysis of how to combat the worm prevalence based on the stability of equilibria. Simulation results show that the performance of our proposed models is effective in combating such worms, in terms of decreasing the number of hosts infected by the malicious worm and reducing the malicious worm propagation speed. Based on our simulations, we believe there is great potential for an effective method to use benign worms to combat malicious worms in some point-to-group applications.

  11. Preparation of Samples for Single-Worm Tracking

    PubMed Central

    Yemini, Eviatar; Kerr, Rex A.; Schafer, William R.

    2016-01-01

    Neurobiological research in genetically tractable organisms relies heavily on robust assays for behavioral phenotypes. The simple body plan of the nematode Caenorhabditis elegans makes it particularly amenable to the use of automated microscopy and image analysis to describe behavioral patterns quantitatively. This protocol first describes the preparation and use of media for growing and maintaining worms for tracking. The second part of the protocol describes how to prepare a single young adult worm for recording during video analysis. Although the protocol was developed for use in a single-worm tracker, it addresses factors important for the generation of reproducible, standardized images in all systems. PMID:22135667

  12. Fossilization of an ancient (devonian) soft-bodied worm.

    PubMed

    Cameron, B

    1967-03-10

    A shell-boring polychaete worm was found replaced by the min eral limonite-goethite; this fossil is probably a limonite-goethite pseudo morph after pyrite, suggesting that the soft-bodied worm was originally re placed by pyrite. External structures such as a prostomium, anterior tentacle like palps, peristomial cirri, parapodia, setae bundles of the parapodia, and dorsal cirri of the parapodia are pre served. This worm resembles living members of the family Spionidae in form and habit. This discovery extends the known range of this family (Cre taceous?, Miocene to Recent) back about 365 million years to the Devo nian period. PMID:17847539

  13. High-resolution {upsilon}{sub OH} = 3{l_arrow}0 and {upsilon}{sub OH} = 4{l_arrow}0 overtone spectroscopy of HOD

    SciTech Connect

    Fair, J.R.; Votava, O.; Nesbitt, D.J.

    1996-12-31

    High-resolution (0.005 cm{sup -1}) IR overtone excitation with an injection seeded optical parametric oscillator (OPO) is used to investigate the spectroscopy of HOD in the {upsilon}{sub OH} = 3{l_arrow}0 region via room temperature photoacoustic detection methods. Comparison of the photoacoustic spectra from an H{sub 2}O/D{sub 2}O/HOD mixture and from pure H{sub 2}O determines the lines corresponding to {upsilon}{sub OH} = 3{l_arrow}0 absorptions in HOD. A prediction of the HOD spectrum in this region is generated from an extrapolation of {upsilon}{sub OH} = 0 and 1 rotational constants and from the {upsilon}{sub OH} = 3{l_arrow}0 band origin calculated by Tennyson and coworkers [private communication]. This predicted spectrum enables the HOD {upsilon}{sub OH} = 3{l_arrow}0 photoacoustic spectrum to be assigned; a fit of the experimental data produces the low-order rotational constants for this transition as well as a Birge-Sponer analysis of the overtone series. The vibrational dependence of the HOD rotational constants is demonstrated to be quite linear in {upsilon}{sub OH}, permitting reliable extrapolation to the {upsilon}{sub OH} = 4 manifold. As a result, the {upsilon}{sub OH} = 0, 1 and 3 constants can be used to predict the spectrum of HOD {upsilon}{sub OH} = 4{l_arrow}0, which now enables the assignment of the vibrationally mediated photodissociation spectrum measured by Crim and coworkers. The overtone spectroscopic data for HOD is further confirmed in double resonance IR and UV photolysis of HOD and HOD-containing clusters in slit supersonic expansions.

  14. Velvet worm development links myriapods with chelicerates.

    PubMed

    Mayer, Georg; Whitington, Paul M

    2009-10-22

    Despite the advent of modern molecular and computational methods, the phylogeny of the four major arthropod groups (Chelicerata, Myriapoda, Crustacea and Hexapoda, including the insects) remains enigmatic. One particular challenge is the position of myriapods as either the closest relatives to chelicerates (Paradoxopoda/Myriochelata hypothesis), or to crustaceans and hexapods (Mandibulata hypothesis). While neither hypothesis receives conclusive support from molecular analyses, most morphological studies favour the Mandibulata concept, with the mandible being the most prominent feature of this group. Although no morphological evidence was initially available to support the Paradoxopoda hypothesis, a putative synapomorphy of chelicerates and myriapods has recently been put forward based on studies of neurogenesis. However, this and other morphological characters remain of limited use for phylogenetic systematics owing to the lack of data from an appropriate outgroup. Here, we show that several embryonic characters are synapomorphies uniting the chelicerates and myriapods, as revealed by an outgroup comparison with the Onychophora or velvet worms. Our findings, thus provide, to our knowledge, first morphological/embryological support for the monophyly of the Paradoxopoda and suggest that the mandible might have evolved twice within the arthropods. PMID:19640885

  15. Spectrum of the elimination of loops and multiple arrows in coupled cell networks

    NASA Astrophysics Data System (ADS)

    Dias, A. P. S.; Moreira, C. S.

    2012-11-01

    A uniform lift of a given network is a network with no loops and no multiple arrows that admits the first network as quotient. Given a regular network (in which all cells have the same type and receive the same number of inputs and all arrows have the same type) with loops or multiple arrows, we prove that it is always possible to construct a uniform lift whose adjacency matrix has only two possible eigenvalues, namely, 0 and -1, in addition to all eigenvalues of the initial network adjacency matrix. Moreover, this uniform lift has the minimal number of cells over all uniform lifts. We also prove that if a non-vanishing eigenvalue of the initial adjacency matrix is fixed then it is always possible to construct a uniform lift that preserves the number of eigenvalues with the same real part of that eigenvalue. Finally, for the eigenvalue zero we show that such a construction is not always possible proving that there are networks with multiple arrows whose uniform lifts all have the eigenvalue 0, in addition to all eigenvalues of the initial network adjacency matrix. Using the concept of ODE-equivalence, we prove then that it is always possible to study a degenerate bifurcation arising in a system whose regular network has multiple arrows as a bifurcation of a bigger system associated with a regular uniform network.

  16. 19. WORM AND SPUR GEARS FOR CONTROLLING THE PADDLE VALVE ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    19. WORM AND SPUR GEARS FOR CONTROLLING THE PADDLE VALVE IN ONE OF THE LOCK GATES WHICH SEPARATES UPPER AND LOWER CHAMBERS: 1976 - Pawtucket Canal, Swamp Locks, Pawtucket & Merrimack Canals, Lowell, Middlesex County, MA

  17. 20. WORM AND SPUR GEARS FOR CONTROLLING THE PADDLE VALVE ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    20. WORM AND SPUR GEARS FOR CONTROLLING THE PADDLE VALVE IN ONE OF THE GATES BETWEEN THE UPPER AND LOWER CHAMBERS: 1976 - Pawtucket Canal, Swamp Locks, Pawtucket & Merrimack Canals, Lowell, Middlesex County, MA

  18. 2. Big Creek Road, worm fence and road at trailhead. ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    2. Big Creek Road, worm fence and road at trailhead. - Great Smoky Mountains National Park Roads & Bridges, Big Creek Road, Between State Route 284 & Big Creek Campground, Gatlinburg, Sevier County, TN

  19. Detail, terra cotta, ironwork, and painted wood "worm gear" carved ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Detail, terra cotta, ironwork, and painted wood "worm gear" carved columns, north rear. - San Bernardino Valley College, Library, 701 South Mount Vernon Avenue, San Bernardino, San Bernardino County, CA

  20. 18. WORM AND SPUR GEARS FOR CONTROLLING THE PADDLE VALVE ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    18. WORM AND SPUR GEARS FOR CONTROLLING THE PADDLE VALVE IN ONE OF THE GATES BETWEEN THE UPPER AND LOWER CHAMBERS: 1976 - Pawtucket Canal, Swamp Locks, Pawtucket & Merrimack Canals, Lowell, Middlesex County, MA

  1. Worm drive detail, roller hoist mechanism, rolling crest roller gate ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Worm drive detail, roller hoist mechanism, rolling crest roller gate - plan and sections - Grand Valley Diversion Dam, Half a mile north of intersection of I-70 & Colorado State Route 65, Cameo, Mesa County, CO

  2. 6. VIEW OF DRIFT SHAFT, HOIST MOTOR, WORM WHEEL GEAR ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    6. VIEW OF DRIFT SHAFT, HOIST MOTOR, WORM WHEEL GEAR ASSEMBLY, CROSS SHAFT, AND INTERMEDIATE GEAR HOIST ASSEMBLY FOR CONTROL GATE NO. 6, LOOKING WEST - Long Lake Hydroelectric Plant, Spillway Dam, Spanning Spokane River, Ford, Stevens County, WA

  3. Metagenomic Analysis of Microbial Symbionts in a Gutless Worm

    SciTech Connect

    Woyke, Tanja; Teeling, Hanno; Ivanova, Natalia N.; Hunteman, Marcel; Richter, Michael; Gloeckner, Frank Oliver; Boeffelli, Dario; Barry, Kerrie W.; Shapiro, Harris J.; Anderson, Iain J.; Szeto, Ernest; Kyrpides, Nikos C.; Mussmann, Marc; Amann, Rudolf; Bergin, Claudia; Ruehland, Caroline; Rubin, Edward M.; Dubilier, Nicole

    2006-05-01

    Symbioses between bacteria and eukaryotes are ubiquitous, yet our understanding of the interactions driving these associations is hampered by our inability to cultivate most host-associated microbes. Here we use a metagenomic approach to describe four co-occurring symbionts from the marine oligochaete Olavius algarvensis, a worm lacking a mouth, gut and nephridia. Shotgun sequencing and metabolic pathway reconstruction revealed that the symbionts are sulphur-oxidizing and sulphate-reducing bacteria, all of which are capable of carbon fixation, thus providing the host with multiple sources of nutrition. Molecular evidence for the uptake and recycling of worm waste products by the symbionts suggests how the worm could eliminate its excretory system, an adaptation unique among annelid worms. We propose a model that describes how the versatile metabolism within this symbiotic consortium provides the host with an optimal energy supply as it shuttles between the upper oxic and lower anoxic coastal sediments that it inhabits.

  4. WormBase: methods for data mining and comparative genomics.

    PubMed

    Harris, Todd W; Stein, Lincoln D

    2006-01-01

    WormBase is a comprehensive repository for information on Caenorhabditis elegans and related nematodes. Although the primary web-based interface of WormBase (http:// www.wormbase.org/) is familiar to most C. elegans researchers, WormBase also offers powerful data-mining features for addressing questions of comparative genomics, genome structure, and evolution. In this chapter, we focus on data mining at WormBase through the use of flexible web interfaces, custom queries, and scripts. The intended audience includes users wishing to query the database beyond the confines of the web interface or fetch data en masse. No knowledge of programming is necessary or assumed, although users with intermediate skills in the Perl scripting language will be able to utilize additional data-mining approaches. PMID:16988424

  5. Improved Gear Shapes for Face Worm Gear Drives

    NASA Technical Reports Server (NTRS)

    Litvin, Faydor L.; Nava, Alessandro; Fan, Qi; Fuentes, Alfonso

    2005-01-01

    Shapes different from the traditional ones have been proposed for face worm gears and for conical and cylindrical worms that mesh with them. The proposed shapes are based on the concept of generating a face worm gear surface by use of a tilted head cutter instead of by the traditional use of a hob. (As used here, head cutter is also meant to signify, alternatively, a head grinding tool.) The gear-surface-generation equipment would be similar to that used for generation of spiral bevel and hypoid gears. In comparison with the corresponding traditional hob, a tilted head cutter according to the proposal would be larger, could be fabricated with greater precision, and would enable the generation of gear surfaces with greater precision and greater productivity. A face worm gear would be generated (see figure) by use of a tilted head cutter, the blades or grinding surfaces of which would have straight-line profiles. The tilt of the head cutter would prevent interference with teeth adjacent to the groove being cut or ground. A worm to mesh with the face worm gear would be generated by use of a tilted head cutter mounted on the cradle of a generating machine. The blades or grinding surfaces of the head cutter would have a parabolic profile and would deviate from the straight-line profiles of the head cutter for the face worm gear. The shortest distance between the worm and the cradle would follow a parabolic function during the cycle of meshing in the generating process to provide a parabolic function of transmission errors to the gear drive. The small mismatch between the profiles of the face-worm-gear and worm head cutters would make it possible to localize the bearing contact in the worm gear drive. The parabolic function of transmission errors could absorb discontinuous linear functions of transmission errors caused by errors of alignment; this could afford a significant benefit, in that such errors are main sources of noise and vibration in gear drives. The main

  6. In Vitro Maintenance of Clonorchis sinensis Adult Worms

    PubMed Central

    Uddin, Md. Hafiz; Li, Shunyu; Bae, Young Mee; Choi, Min-Ho

    2012-01-01

    Clonorchis sinensis is a biological carcinogen inducing human cholangiocarcinoma, and clonorchiasis is one of the important endemic infectious diseases in East Asia. The present study investigated survival longevity of C. sinensis adult worms in various in vitro conditions to find the best way of keeping the worms longer. The worms were maintained in 0.85% NaCl, 1×PBS, 1×Locke's solution, RPMI-1640, DMEM, and IMDM media, and in 1×Locke's solution with different supplements. All of the worms died within 3 and 7 days in 0.85% NaCl and 1×PBS, respectively, but survived up to 57 days in 1×Locke's solution. The worms lived for 106 days in DMEM, and 114 days in both RPMI-1640 and IMDM media. The survival rate in RPMI-1640 medium was the highest (50%) compared to that in DMEM (20±10%) and in IMDM (33.3±25.2%) after 3 months. The 1×Locke's solution with 0.005% bovine bile supplement showed increased duration of maximum survival from 42 days to 70 days. Higher concentration of bile supplements than 0.005% or addition of glucose were disadvantageous for the worm survival. The worms died rapidly in solutions containing L-aspartic acid, L-glutamic acid, and adenine compared to L-arginine, L-serine, and L-tryptophan. In conclusion, the 1×Locke's solution best supports the worms alive among inorganic solutions for 57 days, and the RPMI-1640 medium maintains living C. sinensis adults better and longer up to 114 days in vitro than other media. PMID:23230328

  7. Using Lateral Coupled Snakes for Modeling the Contours of Worms

    NASA Astrophysics Data System (ADS)

    Wang, Qing; Ronneberger, Olaf; Schulze, Ekkehard; Baumeister, Ralf; Burkhardt, Hans

    A model called lateral coupled snakes is proposed to describe the contours of moving C. elegans worms on 2D images with high accuracy. The model comprises two curves with point correspondence between them. The line linking a corresponding pair is approximately perpendicular to the curves at the two points, which is ensured by shear restoring forces. Experimental proofs reveal that the model is a promising tool for locating and segmenting worms or objects with similar shapes.

  8. Partial purification and characterization of Ascaridia galli diagnostic worm antigen.

    PubMed

    Abdel Rahman, Eman H; Khalil, Fathia A M

    2005-08-01

    Partial purification of Ascaridia galli whole worm extract was conducted by Cyanogen bromide Sepharose 4B immunoaffinity column chromatography. The resulted fraction was characterized by sodium dodecyle sulphate polyacrylamide gel electrophoresis (SDS-PAGE) and isoelectric focusing. The fraction was found to be consisted of six bands of 207 KDa, 157 KDa. 110 KDa, 103 KDa, 76 KDa and 41 KDa. This profile was compared with that of whole worm and excretory-secretory antigens. Both antigens were resolved into multiple bands in both high and low molecular weight ranges. The isoelectric focusing of the fraction displayed 8 bands of isoelectric points 7.5, 7.0, 6.8, 6.5, 6.2, 5.8. 5.3 and 4.6. The potency of this fraction in the diagnosis of natural ascaridiosis in chickens was assessed by ELISA compared with that of whole worm and ES antigens. The affinity purified fraction showed higher potentials in the diagnosis of A. galli infection in chickens than whole worm antigen at any sera dilution and than ES antigen at high sera dilutions. While ES antigen of the worms revealed higher diagnostic capabilities than whole worm extract. The current research recommends utilization of the affinity isolated fraction in the diagnosis of natural ascaridiosis in chickens. PMID:16083065

  9. Social behaviour and collective motion in plant-animal worms.

    PubMed

    Franks, Nigel R; Worley, Alan; Grant, Katherine A J; Gorman, Alice R; Vizard, Victoria; Plackett, Harriet; Doran, Carolina; Gamble, Margaret L; Stumpe, Martin C; Sendova-Franks, Ana B

    2016-02-24

    Social behaviour may enable organisms to occupy ecological niches that would otherwise be unavailable to them. Here, we test this major evolutionary principle by demonstrating self-organizing social behaviour in the plant-animal, Symsagittifera roscoffensis. These marine aceol flat worms rely for all of their nutrition on the algae within their bodies: hence their common name. We show that individual worms interact with one another to coordinate their movements so that even at low densities they begin to swim in small polarized groups and at increasing densities such flotillas turn into circular mills. We use computer simulations to: (i) determine if real worms interact socially by comparing them with virtual worms that do not interact and (ii) show that the social phase transitions of the real worms can occur based only on local interactions between and among them. We hypothesize that such social behaviour helps the worms to form the dense biofilms or mats observed on certain sun-exposed sandy beaches in the upper intertidal of the East Atlantic and to become in effect a super-organismic seaweed in a habitat where macro-algal seaweeds cannot anchor themselves. Symsagittifera roscoffensis, a model organism in many other areas in biology (including stem cell regeneration), also seems to be an ideal model for understanding how individual behaviours can lead, through collective movement, to social assemblages. PMID:26911961

  10. A partial phylogenetic analysis of the "flavobacter-bacteroides" phylum: basis for taxonomic restructuring

    NASA Technical Reports Server (NTRS)

    Gherna, R.; Woese, C. R.

    1992-01-01

    On the basis of small subunit rRNA sequence analyses five major subgroups within the flavobacteria-bacteroides phylum have been defined. These are tentatively designated the cytophaga subgroup (comprising largely Cytophaga species), the flavobacter subgroup (comprising the true flavobacteria and the polyphyletic genus Weeksella), the bacteroides subgroup (comprising the bacteroides and certain cytophaga-like bacteria), the sphingobacter subgroup (which contains the known sphingolipid-producing members of the phylum), and the saprospira subgroup (comprising particular species of Flexibacter, Flavobacterium, Haliscomenobacter, and, of course, the genus Saprospira). These groupings are given not only by evolutionary distance analysis, but can be defined and distinguished on the basis of a simple small subunit rRNA signatures.

  11. New Geometry of Worm Face Gear Drives with Conical and Cylindrical Worms: Generation, Simulation of Meshing, and Stress Analysis

    NASA Technical Reports Server (NTRS)

    Litvin, Faydor L.; Nava, Alessandro; Fan, Qi; Fuentes, Alfonso

    2002-01-01

    New geometry of face worm gear drives with conical and cylindrical worms is proposed. The generation of the face worm-gear is based on application of a tilted head-cutter (grinding tool) instead of application of a hob applied at present. The generation of a conjugated worm is based on application of a tilted head-cutter (grinding tool) as well. The bearing contact of the gear drive is localized and is oriented longitudinally. A predesigned parabolic function of transmission errors for reduction of noise and vibration is provided. The stress analysis of the gear drive is performed using a three-dimensional finite element analysis. The contacting model is automatically generated. The developed theory is illustrated with numerical examples.

  12. Electrophysiological responses to violations of expectation from eye gaze and arrow cues.

    PubMed

    Tipples, Jason; Johnston, Pat; Mayes, Angela

    2013-06-01

    Isolating processes within the brain that are specific to human behavior is a key goal for social neuroscience. The current research was an attempt to test whether recent findings of enhanced negative ERPs in response to unexpected human gaze are unique to eye gaze stimuli by comparing the effects of gaze cues with the effects of an arrow cue. ERPs were recorded while participants (N = 30) observed a virtual actor or an arrow that gazed (or pointed) either toward (object congruent) or away from (object incongruent) a flashing checkerboard. An enhanced negative ERP (N300) in response to object incongruent compared to object congruent trials was recorded for both eye gaze and arrow stimuli. The findings are interpreted as reflecting a domain general mechanism for detecting unexpected events. PMID:22345367

  13. Navigating molecular worms inside chemical labyrinths.

    PubMed

    Haranczyk, M; Sethian, J A

    2009-12-22

    Predicting whether a molecule can traverse chemical labyrinths of channels, tunnels, and buried cavities usually requires performing computationally intensive molecular dynamics simulations. Often one wants to screen molecules to identify ones that can pass through a given chemical labyrinth or screen chemical labyrinths to identify those that allow a given molecule to pass. Because it is impractical to test each molecule/labyrinth pair using computationally expensive methods, faster, approximate methods are used to prune possibilities, "triaging" the ability of a proposed molecule to pass through the given chemical labyrinth. Most pruning methods estimate chemical accessibility solely on geometry, treating atoms or groups of atoms as hard spheres with appropriate radii. Here, we explore geometric configurations for a moving "molecular worm," which replaces spherical probes and is assembled from solid blocks connected by flexible links. The key is to extend the fast marching method, which is an ordered upwind one-pass Dijkstra-like method to compute optimal paths by efficiently solving an associated Eikonal equation for the cost function. First, we build a suitable cost function associated with each possible configuration, and second, we construct an algorithm that works in ensuing high-dimensional configuration space: at least seven dimensions are required to account for translational, rotational, and internal degrees of freedom. We demonstrate the algorithm to study shortest paths, compute accessible volume, and derive information on topology of the accessible part of a chemical labyrinth. As a model example, we consider an alkane molecule in a porous material, which is relevant to designing catalysts for oil processing. PMID:20018716

  14. Navigating molecular worms inside chemical labyrinths

    PubMed Central

    Haranczyk, M.; Sethian, J. A.

    2009-01-01

    Predicting whether a molecule can traverse chemical labyrinths of channels, tunnels, and buried cavities usually requires performing computationally intensive molecular dynamics simulations. Often one wants to screen molecules to identify ones that can pass through a given chemical labyrinth or screen chemical labyrinths to identify those that allow a given molecule to pass. Because it is impractical to test each molecule/labyrinth pair using computationally expensive methods, faster, approximate methods are used to prune possibilities, “triaging” the ability of a proposed molecule to pass through the given chemical labyrinth. Most pruning methods estimate chemical accessibility solely on geometry, treating atoms or groups of atoms as hard spheres with appropriate radii. Here, we explore geometric configurations for a moving “molecular worm,” which replaces spherical probes and is assembled from solid blocks connected by flexible links. The key is to extend the fast marching method, which is an ordered upwind one-pass Dijkstra-like method to compute optimal paths by efficiently solving an associated Eikonal equation for the cost function. First, we build a suitable cost function associated with each possible configuration, and second, we construct an algorithm that works in ensuing high-dimensional configuration space: at least seven dimensions are required to account for translational, rotational, and internal degrees of freedom. We demonstrate the algorithm to study shortest paths, compute accessible volume, and derive information on topology of the accessible part of a chemical labyrinth. As a model example, we consider an alkane molecule in a porous material, which is relevant to designing catalysts for oil processing. PMID:20018716

  15. Phylogenetic Framework and Molecular Signatures for the Main Clades of the Phylum Actinobacteria

    PubMed Central

    Gao, Beile

    2012-01-01

    Summary: The phylum Actinobacteria harbors many important human pathogens and also provides one of the richest sources of natural products, including numerous antibiotics and other compounds of biotechnological interest. Thus, a reliable phylogeny of this large phylum and the means to accurately identify its different constituent groups are of much interest. Detailed phylogenetic and comparative analyses of >150 actinobacterial genomes reported here form the basis for achieving these objectives. In phylogenetic trees based upon 35 conserved proteins, most of the main groups of Actinobacteria as well as a number of their superageneric clades are resolved. We also describe large numbers of molecular markers consisting of conserved signature indels in protein sequences and whole proteins that are specific for either all Actinobacteria or their different clades (viz., orders, families, genera, and subgenera) at various taxonomic levels. These signatures independently support the existence of different phylogenetic clades, and based upon them, it is now possible to delimit the phylum Actinobacteria (excluding Coriobacteriia) and most of its major groups in clear molecular terms. The species distribution patterns of these markers also provide important information regarding the interrelationships among different main orders of Actinobacteria. The identified molecular markers, in addition to enabling the development of a stable and reliable phylogenetic framework for this phylum, also provide novel and powerful means for the identification of different groups of Actinobacteria in diverse environments. Genetic and biochemical studies on these Actinobacteria-specific markers should lead to the discovery of novel biochemical and/or other properties that are unique to different groups of Actinobacteria. PMID:22390973

  16. Cytosine methylation is a conserved epigenetic feature found throughout the phylum Platyhelminthes

    PubMed Central

    2013-01-01

    Background The phylum Platyhelminthes (flatworms) contains an important group of bilaterian organisms responsible for many debilitating and chronic infectious diseases of human and animal populations inhabiting the planet today. In addition to their biomedical and veterinary relevance, some platyhelminths are also frequently used models for understanding tissue regeneration and stem cell biology. Therefore, the molecular (genetic and epigenetic) characteristics that underlie trophic specialism, pathogenicity or developmental maturation are likely to be pivotal in our continued studies of this important metazoan group. Indeed, in contrast to earlier studies that failed to detect evidence of cytosine or adenine methylation in parasitic flatworm taxa, our laboratory has recently defined a critical role for cytosine methylation in Schistosoma mansoni oviposition, egg maturation and ovarian development. Thus, in order to identify whether this epigenetic modification features in other platyhelminth species or is a novelty of S. mansoni, we conducted a study simultaneously surveying for DNA methylation machinery components and DNA methylation marks throughout the phylum using both parasitic and non-parasitic representatives. Results Firstly, using both S. mansoni DNA methyltransferase 2 (SmDNMT2) and methyl-CpG binding domain protein (SmMBD) as query sequences, we illustrate that essential DNA methylation machinery components are well conserved throughout the phylum. Secondly, using both molecular (methylation specific amplification polymorphism, MSAP) and immunological (enzyme-linked immunoabsorbent assay, ELISA) methodologies, we demonstrate that representative species (Echinococcus multilocularis, Protopolystoma xenopodis, Schistosoma haematobium, Schistosoma japonicum, Fasciola hepatica and Polycelis nigra) within all four platyhelminth classes (Cestoda, Monogenea, Trematoda and ‘Turbellaria’) contain methylated cytosines within their genome compartments

  17. Widespread vertical transmission and associated host sex-ratio distortion within the eukaryotic phylum Microspora.

    PubMed Central

    Terry, Rebecca S.; Smith, Judith E.; Sharpe, Rosie G.; Rigaud, Thierry; Littlewood, D. Timothy J.; Ironside, Joseph E.; Rollinson, David; Bouchon, Didier; MacNeil, Calum; Dick, Jaimie T. A.; Dunn, Alison M.

    2004-01-01

    Vertical transmission (VT) and associated manipulation of host reproduction are widely reported among prokaryotic endosymbionts. Here, we present evidence for widespread use of VT and associated sex-ratio distortion in a eukaryotic phylum. The Microspora are an unusual and diverse group of eukaryotic parasites that infect all animal phyla. Following our initial description of a microsporidian that feminizes its crustacean host, we survey the diversity and distribution of VT within the Microspora. We find that vertically transmitted microsporidia are ubiquitous in the amphipod hosts sampled and that they are also diverse, with 11 species of microsporidia detected within 16 host species. We found that infections were more common in females than males, suggesting that host sex-ratio distortion occurs in five out of eight parasite species tested. Phylogenetic reconstruction demonstrates that VT occurs in all major lineages of the phylum Microspora and that sex-ratio distorters are found on multiple branches of the phylogenetic tree. We propose that VT is either an ancestral trait or evolves with peculiar frequency in this phylum. If the association observed here between VT and host sex-ratio distortion holds true across other host taxa, these eukaryotic parasites may join the bacterial endosymbionts in their importance as sex-ratio distorters. PMID:15315893

  18. Crystal growth of bullet-shaped magnetite in magnetotactic bacteria of the Nitrospirae phylum.

    PubMed

    Li, Jinhua; Menguy, Nicolas; Gatel, Christophe; Boureau, Victor; Snoeck, Etienne; Patriarche, Gilles; Leroy, Eric; Pan, Yongxin

    2015-02-01

    Magnetotactic bacteria (MTB) are known to produce single-domain magnetite or greigite crystals within intracellular membrane organelles and to navigate along the Earth's magnetic field lines. MTB have been suggested as being one of the most ancient biomineralizing metabolisms on the Earth and they represent a fundamental model of intracellular biomineralization. Moreover, the determination of their specific crystallographic signature (e.g. structure and morphology) is essential for palaeoenvironmental and ancient-life studies. Yet, the mechanisms of MTB biomineralization remain poorly understood, although this process has been extensively studied in several cultured MTB strains in the Proteobacteria phylum. Here, we show a comprehensive transmission electron microscopy (TEM) study of magnetic and structural properties down to atomic scales on bullet-shaped magnetites produced by the uncultured strain MYR-1 belonging to the Nitrospirae phylum, a deeply branching phylogenetic MTB group. We observed a multiple-step crystal growth of MYR-1 magnetite: initial isotropic growth forming cubo-octahedral particles (less than approx. 40 nm), subsequent anisotropic growth and a systematic final elongation along [001] direction. During the crystal growth, one major {111} face is well developed and preserved at the larger basal end of the crystal. The basal {111} face appears to be terminated by a tetrahedral-octahedral-mixed iron surface, suggesting dimensional advantages for binding protein(s), which may template the crystallization of magnetite. This study offers new insights for understanding magnetite biomineralization within the Nitrospirae phylum. PMID:25566884

  19. Crystal growth of bullet-shaped magnetite in magnetotactic bacteria of the Nitrospirae phylum

    PubMed Central

    Li, Jinhua; Menguy, Nicolas; Gatel, Christophe; Boureau, Victor; Snoeck, Etienne; Patriarche, Gilles; Leroy, Eric; Pan, Yongxin

    2015-01-01

    Magnetotactic bacteria (MTB) are known to produce single-domain magnetite or greigite crystals within intracellular membrane organelles and to navigate along the Earth's magnetic field lines. MTB have been suggested as being one of the most ancient biomineralizing metabolisms on the Earth and they represent a fundamental model of intracellular biomineralization. Moreover, the determination of their specific crystallographic signature (e.g. structure and morphology) is essential for palaeoenvironmental and ancient-life studies. Yet, the mechanisms of MTB biomineralization remain poorly understood, although this process has been extensively studied in several cultured MTB strains in the Proteobacteria phylum. Here, we show a comprehensive transmission electron microscopy (TEM) study of magnetic and structural properties down to atomic scales on bullet-shaped magnetites produced by the uncultured strain MYR-1 belonging to the Nitrospirae phylum, a deeply branching phylogenetic MTB group. We observed a multiple-step crystal growth of MYR-1 magnetite: initial isotropic growth forming cubo-octahedral particles (less than approx. 40 nm), subsequent anisotropic growth and a systematic final elongation along [001] direction. During the crystal growth, one major {111} face is well developed and preserved at the larger basal end of the crystal. The basal {111} face appears to be terminated by a tetrahedral–octahedral-mixed iron surface, suggesting dimensional advantages for binding protein(s), which may template the crystallization of magnetite. This study offers new insights for understanding magnetite biomineralization within the Nitrospirae phylum. PMID:25566884

  20. Assessing the global phylum level diversity within the bacterial domain: A review

    PubMed Central

    Youssef, Noha H.; Couger, M.B.; McCully, Alexandra L.; Criado, Andrés Eduardo Guerrero; Elshahed, Mostafa S.

    2014-01-01

    Microbial ecology is the study of microbes in the natural environment and their interactions with each other. Investigating the nature of microorganisms residing within a specific habitat is an extremely important component of microbial ecology. Such microbial diversity surveys aim to determine the identity, physiological preferences, metabolic capabilities, and genomic features of microbial taxa within a specific ecosystem. A comprehensive review of various aspects of microbial diversity (phylogenetic, functional, and genomic diversities) in the microbial (bacterial, archaeal, and microeukaryotic) world is clearly a daunting task that could not be aptly summarized in a single review. Here, we focus on one aspect of diversity (phylogenetic diversity) in one microbial domain (the Bacteria). We restrict our analysis to the highest taxonomic rank (phylum) and attempt to investigate the extent of global phylum level diversity within the Bacteria. We present a brief historical perspective on the subject and highlight how the adaptation of molecular biological and phylogenetic approaches has greatly expanded our view of global bacterial diversity. We also summarize recent progress toward the discovery of novel bacterial phyla, present evidences that the scope of phylum level diversity in nature has hardly been exhausted, and propose novel approaches that could greatly facilitate the discovery process of novel bacterial phyla within various ecosystems. PMID:26257925

  1. Arrow-Elicited Cueing Effects at Short Intervals: Rapid Attentional Orienting or Cue-Target Stimulus Conflict?

    ERIC Educational Resources Information Center

    Green, Jessica J.; Woldorff, Marty G.

    2012-01-01

    The observation of cueing effects (faster responses for cued than uncued targets) rapidly following centrally-presented arrows has led to the suggestion that arrows trigger rapid automatic shifts of spatial attention. However, these effects have primarily been observed during easy target-detection tasks when both cue and target remain on the…

  2. Parametric flutter studies of an arrow-wing configuration: Some early results

    NASA Technical Reports Server (NTRS)

    Durham, Michael H.; Cole, Stanley R.; Cazier, F. W., Jr.; Keller, Donald F.; Parker, Ellen C.; Wilkie, W. Keats

    1988-01-01

    Some early experimental results from a combined experimental and analytical study being conducted at NASA-Langley of the transonic flutter characterisitics of a generic arrow wing configuration are presented. The planned study includes the parametric variation of a variety of structural and geometric characteristics. Presented here are flutter results of the basic arrow wing, for the basic wing with the addition of two simulated lower-surface-mounted engine nacelles, and for the basic wing with the addition of both the fin and the engine nacelles.

  3. Evidence for the Decay K{sup +}{r_arrow}{pi}{sup +}{nu}{bar v}

    SciTech Connect

    Adler, S.; Atiya, M.S.; Chiang, I.; Diwan, M.V.; Frank, J.S.; Haggerty, J.S.; Kettell, S.H.; Kycia, T.F.; Li, K.K.; Littenberg, L.S.; Ng, C.; Sambamurti, A.; Stevens, A.; Strand, R.C.; Witzig, C.; Komatsubara, T.K.; Kuriki, M.; Muramatsu, N.; Sugimoto, S.; Inagaki, T.; Kabe, S.; Kobayashi, M.; Kuno, Y.; Sato, T.; Shinkawa, T.; Yoshimura, Y.; Kishi, Y.; Nakano, T.; Ardebili, M.; Bazarko, A.O.; Convery, M.R.; Ito, M.M.; Marlow, D.R.; McPherson, R.A.; Meyers, P.D.; Shoemaker, F.C.; Smith, A.J.; Stone, J.R.; Aoki, M.; Blackmore, E.W.; Bergbusch, P.C.; Bryman, D.A.; Konaka, A.; Macdonald, J.A.; Mildenberger, J.; Numao, T.; Padley, P.; Poutissou, J.; Poutissou, R.; Redlinger, G.; Roy, J.; Turcot, A.S.; Kitching, P.; Soluk, R.

    1997-09-01

    An event consistent with the signature expected for the rare kaon decay K{sup +}{r_arrow}{pi}{sup +}{nu}{bar {nu}} has been observed. In the pion momentum region examined, 211{lt}P{lt}230 MeV/c , the backgrounds are estimated to contribute 0.08{plus_minus}0.03 events. If the event is due to K{sup +}{r_arrow}{pi}{sup +}{nu}{bar {nu}} , the branching ratio is 4.2{sup +9.7}{sub {minus}3.5}{times}10{sup {minus}10} . {copyright} {ital 1997} {ital The American Physical Society}

  4. Penetrating neck injury by an arrow: a paradigm of age old assault.

    PubMed

    Nepal, A; Joshi, R R; Bhandary, S; Mathur, N N; Roka, Y B; Yadav, R

    2010-03-01

    Penetrating neck injuries by traditional weapons are rare entity in the modern era of sophisticated weapons. We report an unusual case of penetrating neck injury by a metallic arrow entering anterior neck in zone II and its tip coming out of neck posteriorly causing difficulty for patient to lie down as well as posing challenge to intubate. Arrows are low velocity projectile and from a close proximity they can cause penetrating trauma similar to a low powered handgun. Management of the case was discussed. PMID:20677615

  5. t {r_arrow} cWW and WW {r_arrow} {anti t}c + t{anti c} in extended models

    SciTech Connect

    David Atwood; Marc Sher

    1997-07-01

    Jenkins has pointed out that the process t {r_arrow} cW{sup +}W{sup {minus}}is GIM suppressed in the standard model. In this note, the authors calculate the branching ratio for a wide range of models, in which the decay occurs at tree level through exchange of a scalar, fermion or vector. In the case of scalar exchange, a scalar mass between 2m{sub W} and 200 GeV leads to a resonant enhancement, giving a branching ratio as high as a few tenths of a percent. They then note that all of these models will also allow W{sup +}W{sup {minus}} {r_arrow} {anti t}c + t{anti c}, and they calculate the single-top/single-charm production rate at the LHC. The rates aren't negligibly small, but the background from single-top/single-bottom production will probably swamp the signal.

  6. Complete Genome Sequence of the Bacterium Aalborg_AAW-1, Representing a Novel Family within the Candidate Phylum SR1

    PubMed Central

    Dueholm, Morten Simonsen; Albertsen, Mads; Stokholm-Bjerregaard, Mikkel; McIlroy, Simon J.; Karst, Søren M.

    2015-01-01

    Here, we present the complete genome sequence of the candidate phylum SR1 bacterium Aalborg_AAW-1. Its 16S rRNA gene is only 85.5% similar to that of the closest relative, RAAC1_SR1, and the genome of Aalborg_AAW-1 consequently represents the first of a novel family within the candidate phylum SR1. PMID:26067967

  7. Hollywood Addresses Postwar Assimilation: Indian/White Attitudes in "Broken Arrow."

    ERIC Educational Resources Information Center

    Aleiss, Angela

    1987-01-01

    Examines Western films in context of post-World War II attitudes regarding racial equality. Film "Broken Arrow" and Eliott Arnold's novel "Blood Brother," both recounting story of Apache chief Cochise, examined as benchmark works in national racial attitudes. Films generally seen as supporting Indian assimilation into White culture. (TES)

  8. How Do Selected Arrows Guide Visuospatial Attention? Dissociating Symbolic Value and Spatial Proximity

    ERIC Educational Resources Information Center

    Leblanc, Emilie; Jolicoeur, Pierre

    2010-01-01

    Previous research on the control of visuospatial attention showed that overlearned symbols like arrows have the potential to induce involuntary shifts of attention. Following work on the role of attentional control settings and of the content of working memory in the involuntary deployment of visuospatial attention, Pratt and Hommel (2003) found…

  9. Making Sense of the Arrow-Pushing Formalism among Chemistry Majors Enrolled in Organic Chemistry

    ERIC Educational Resources Information Center

    Ferguson, Robert; Bodner, George M.

    2008-01-01

    This paper reports results of a qualitative study of sixteen students enrolled in a second year organic chemistry course for chemistry and chemical engineering majors. The focus of the study was student use of the arrow-pushing formalism that plays a central role in both the teaching and practice of organic chemistry. The goal of the study was to…

  10. The Effect of Arrow Diagrams on Achievement in Applying the Chain Rule

    ERIC Educational Resources Information Center

    Uygur, Tangul; Ozdas, Aynur

    2007-01-01

    In this study the effectiveness of an arrow diagram which can help students apply the Chain Rule was investigated. Different variations of this diagram were used as mnemonic devices for applying the Chain Rule. For the investigation two instruments were developed, diagnostic test and post-test. The diagnostic test was developed to determine the…

  11. Six Impossible Mechanisms before Breakfast: Arrow Pushing as an Instructional Device in Inorganic Chemistry

    ERIC Educational Resources Information Center

    Berg, Steffen; Ghosh, Abhik

    2013-01-01

    In a recent article by the authors, the suggestion was made that arrow pushing, a widely used tool in organic chemistry, could also be profitably employed in the teaching of introductory inorganic chemistry. A number of relatively simple reactions were used to illustrate this thesis, raising the question whether the same approach might rationalize…

  12. Decorating with Arrows: Toward the Development of Representational Competence in Organic Chemistry

    ERIC Educational Resources Information Center

    Grove, Nathaniel P.; Cooper, Melanie M.; Rush, Kelli M.

    2012-01-01

    Much effort has been expended in developing improved methods for presenting mechanistic thinking and the curved-arrow notation to organic chemistry students; however, most of these techniques are not research-based. The little research that has been conducted has mainly focused on understanding the meaning that students associate with the…

  13. Reflexive Orienting in Response to Eye Gaze and an Arrow in Children with and without Autism

    ERIC Educational Resources Information Center

    Senju, Atsushi; Tojo, Yoshikuni; Dairoku, Hitoshi; Hasegawa, Toshikazu

    2004-01-01

    Background: This study investigated whether another person's social attention, specifically the direction of their eye gaze, and a non-social directional cue, an arrow, triggered reflexive orienting in children with and without autism in an experimental situation. Methods: Children with autism and typically developed children participated in one…

  14. A Couple of "Lim (h[right arrow]0)-Is-Missing" Problems

    ERIC Educational Resources Information Center

    Lau, Ko Hin

    2007-01-01

    Since most students "hate" the concept of limit, in order to make them "happier," this article suggests a couple of naive "lim (h[right arrow]0)-is-missing" problems for them to try for fun. Indeed, differential functional equations that are related to difference quotients in calculus are studied in this paper. In particular, two interesting…

  15. Inhibitory cueing effects following manual and saccadic responses to arrow cues.

    PubMed

    Ding, Yun; He, Tao; Satel, Jason; Wang, Zhiguo

    2016-05-01

    With two cueing tasks, in the present study we examined output-based inhibitory cueing effects (ICEs) with manual responses to arrow targets following manual or saccadic responses to arrow cues. In all experiments, ICEs were observed when manual localization responses were required to both the cues and targets, but only when the cue-target onset asynchrony (CTOA) was 2,000 ms or longer. In contrast, when saccadic responses were made in response to the cues, ICEs were only observed with CTOAs of 2,000 ms or less-and only when an auditory cue-back signal was used. The present study also showed that the magnitude of ICEs following saccadic responses to arrow cues decreased with time, much like traditional inhibition-of-return effects. The magnitude of ICEs following manual responses to arrow cues, however, appeared later in time and had no sign of decreasing even 3 s after cue onset. These findings suggest that ICEs linked to skeletomotor activation do exist and that the ICEs evoked by oculomotor activation can carry over to the skeletomotor system. PMID:26956560

  16. Design, fabrication, and characterization of Si-based ARROW photonic crystal bend waveguides and power splitters.

    PubMed

    Chen, Jian-Hua; Huang, Yang-Tung; Yang, Yu-Lin; Lu, Ming-Feng; Shieh, Jia-Min

    2012-08-20

    Silicon-based (Si-based) photonic crystal waveguide based on antiresonant reflecting optical waveguide (ARROW PCW) structures consisting of 60° bends and Y-branch power splitters were designed and first efficiently fabricated and characterized. The ARROW structure has a relatively large core size suitable for efficient coupling with a single-mode fiber. Simple capsule-shaped topography defects at 60° photonic crystal (PC) bend corners and Y-branch PC power splitters were used for increasing the broadband light transmission. In the preliminary measurements, the propagation losses of the ARROW PC straight waveguides lower than 2 dB/mm with a long length of 1500 μm were achieved. The average bend loss of 60° PC bend waveguides was lower than 3 dB/bend. For the Y-branch PC power splitters, the average power imbalance was lower than 0.6 dB. The results show that our fabricated Si-based ARROW PCWs with 60° bends and Y-branch structures can provide good light transmission and power-splitting ability. PMID:22907016

  17. Ballistic parameters and trauma potential of carbon dioxide-actuated arrow pistols.

    PubMed

    Nguyen, Tien Thanh; Grossjohann, Rico; Ekkernkamp, Axel; Bockholdt, Britta; Frank, Matthias

    2015-05-01

    Medical literature abounds with reports of injuries and fatalities caused by arrows and crossbow bolts. Crossbows are of particular forensic and traumatological interest, because their mode of construction allows for temporary mechanical storage of energy. A newly developed type of pistol (Arcus Arrowstar), which belongs to the category of air and carbon dioxide weapons, discharges arrow-shaped bolts actuated by carbon dioxide cylinders. As, to the best of the authors' knowledge, literature contains no information on this uncommon subclass of weapons it is the aim of this work to provide the experimental data and to assess the trauma potential of these projectiles based on the ascertained physical parameters. Basic kinetic parameters of these carbon dioxide-actuated bolts (velocity v = 39 m/s, energy E = 7.2 J, energy density E' = 0.26 J/mm(2)) are similar to bolts discharged by pistol crossbows. Subsequent firing resulted in a continuous and fast decrease in kinetic energy of the arrows. Test shots into ballistic soap blocks reveal a high penetration capacity, especially when compared to conventional projectiles of equal kinetic energy values (like, e.g., airgun pellets). To conclude, these data demonstrate the high efficiency of arrow-shaped projectiles, which are also characterized by a high cross-sectional density (ratio of mass to cross-sectional area of a projectile). PMID:25246008

  18. Eye Gaze versus Arrows as Spatial Cues: Two Qualitatively Different Modes of Attentional Selection

    ERIC Educational Resources Information Center

    Marotta, Andrea; Lupianez, Juan; Martella, Diana; Casagrande, Maria

    2012-01-01

    This study aimed to evaluate the type of attentional selection (location- and/or object-based) triggered by two different types of central noninformative cues: eye gaze and arrows. Two rectangular objects were presented in the visual field, and subjects' attention was directed to the end of a rectangle via the observation of noninformative…

  19. Diet of Worms Emended: An Update of Polychaete Feeding Guilds

    NASA Astrophysics Data System (ADS)

    Jumars, Peter A.; Dorgan, Kelly M.; Lindsay, Sara M.

    2015-01-01

    Polychaetes are common in most marine habitats and dominate many infaunal communities. Functional guild classification based on taxonomic identity and morphology has linked community structure to ecological function. The functional guilds now include osmotrophic siboglinids as well as sipunculans, echiurans, and myzostomes, which molecular genetic analyses have placed within Annelida. Advances in understanding of encounter mechanisms explicitly relate motility to feeding mode. New analyses of burrowing mechanics explain the prevalence of bilateral symmetry and blur the boundary between surface and subsurface feeding. The dichotomy between microphagous deposit and suspension feeders and macrophagous carnivores, herbivores, and omnivores is further supported by divergent digestive strategies. Deposit feeding appears to be limited largely to worms longer than 1 cm, with juveniles and small worms in general restricted to ingesting highly digestible organic material and larger, rich food items, blurring the macrophage-microphage dichotomy that applies well to larger worms.

  20. Logistics of Guinea Worm Disease Eradication in South Sudan

    PubMed Central

    Jones, Alexander H.; Becknell, Steven; Withers, P. Craig; Ruiz-Tiben, Ernesto; Hopkins, Donald R.; Stobbelaar, David; Makoy, Samuel Yibi

    2014-01-01

    From 2006 to 2012, the South Sudan Guinea Worm Eradication Program reduced new Guinea worm disease (dracunculiasis) cases by over 90%, despite substantial programmatic challenges. Program logistics have played a key role in program achievements to date. The program uses disease surveillance and program performance data and integrated technical–logistical staffing to maintain flexible and effective logistical support for active community-based surveillance and intervention delivery in thousands of remote communities. Lessons learned from logistical design and management can resonate across similar complex surveillance and public health intervention delivery programs, such as mass drug administration for the control of neglected tropical diseases and other disease eradication programs. Logistical challenges in various public health scenarios and the pivotal contribution of logistics to Guinea worm case reductions in South Sudan underscore the need for additional inquiry into the role of logistics in public health programming in low-income countries. PMID:24445199

  1. Higher throughput high resolution multi-worm tracker

    NASA Astrophysics Data System (ADS)

    Javer, Avelino; Li, Kezhi; Gyenes, Bertalan; Brown, Andre; Behavioural Genomics Team

    2015-03-01

    We have developed a high throughput imaging system for tracking multiple nematode worms at high resolution. The tracker consists of 6 cameras mounted on a motorized gantry so that up to 48 plates (each with approximately 30 worms) can be imaged without user intervention. To deal with the high data rate of the cameras we use real time processing to find worms and only save the immediately surrounding pixels. The system is also equipped with automatic oxygen and carbon dioxide control for observing stimulus response behaviour. We will describe the design and performance of the new system, some of the challenges of truly high throughput behaviour recording, and report preliminary results on inter-individual variation in behaviour as well as a quantitative analysis of C. elegans response to hypoxia, oxygen reperfusion, and carbon dioxide. Funding provided by the Medical Research Council.

  2. Hybrid epidemics--a case study on computer worm conficker.

    PubMed

    Zhang, Changwang; Zhou, Shi; Chain, Benjamin M

    2015-01-01

    Conficker is a computer worm that erupted on the Internet in 2008. It is unique in combining three different spreading strategies: local probing, neighbourhood probing, and global probing. We propose a mathematical model that combines three modes of spreading: local, neighbourhood, and global, to capture the worm's spreading behaviour. The parameters of the model are inferred directly from network data obtained during the first day of the Conficker epidemic. The model is then used to explore the tradeoff between spreading modes in determining the worm's effectiveness. Our results show that the Conficker epidemic is an example of a critically hybrid epidemic, in which the different modes of spreading in isolation do not lead to successful epidemics. Such hybrid spreading strategies may be used beneficially to provide the most effective strategies for promulgating information across a large population. When used maliciously, however, they can present a dangerous challenge to current internet security protocols. PMID:25978309

  3. WormBase: new content and better access

    PubMed Central

    Bieri, Tamberlyn; Blasiar, Darin; Ozersky, Philip; Antoshechkin, Igor; Bastiani, Carol; Canaran, Payan; Chan, Juancarlos; Chen, Nansheng; Chen, Wen J.; Davis, Paul; Fiedler, Tristan J.; Girard, Lisa; Han, Michael; Harris, Todd W.; Kishore, Ranjana; Lee, Raymond; McKay, Sheldon; Müller, Hans-Michael; Nakamura, Cecilia; Petcherski, Andrei; Rangarajan, Arun; Rogers, Anthony; Schindelman, Gary; Schwarz, Erich M.; Spooner, Will; Tuli, Mary Ann; Auken, Kimberly Van; Wang, Daniel; Wang, Xiaodong; Williams, Gary; Durbin, Richard; Stein, Lincoln D.; Sternberg, Paul W.; Spieth, John

    2007-01-01

    WormBase (), a model organism database for Caenorhabditis elegans and other related nematodes, continues to evolve and expand. Over the past year WormBase has added new data on C.elegans, including data on classical genetics, cell biology and functional genomics; expanded the annotation of closely related nematodes with a new genome browser for Caenorhabditis remanei; and deployed new hardware for stronger performance. Several existing datasets including phenotype descriptions and RNAi experiments have seen a large increase in new content. New datasets such as the C.remanei draft assembly and annotations, the Vancouver Fosmid library and TEC-RED 5′ end sites are now available as well. Access to and searching WormBase has become more dependable and flexible via multiple mirror sites and indexing through Google. PMID:17099234

  4. Continuous-time quantum Monte Carlo using worm sampling

    NASA Astrophysics Data System (ADS)

    Gunacker, P.; Wallerberger, M.; Gull, E.; Hausoel, A.; Sangiovanni, G.; Held, K.

    2015-10-01

    We present a worm sampling method for calculating one- and two-particle Green's functions using continuous-time quantum Monte Carlo simulations in the hybridization expansion (CT-HYB). Instead of measuring Green's functions by removing hybridization lines from partition function configurations, as in conventional CT-HYB, the worm algorithm directly samples the Green's function. We show that worm sampling is necessary to obtain general two-particle Green's functions which are not of density-density type and that it improves the sampling efficiency when approaching the atomic limit. Such two-particle Green's functions are needed to compute off-diagonal elements of susceptibilities and occur in diagrammatic extensions of the dynamical mean-field theory and in efficient estimators for the single-particle self-energy.

  5. Diet of worms emended: an update of polychaete feeding guilds.

    PubMed

    Jumars, Peter A; Dorgan, Kelly M; Lindsay, Sara M

    2015-01-01

    Polychaetes are common in most marine habitats and dominate many infaunal communities. Functional guild classification based on taxonomic identity and morphology has linked community structure to ecological function. The functional guilds now include osmotrophic siboglinids as well as sipunculans, echiurans, and myzostomes, which molecular genetic analyses have placed within Annelida. Advances in understanding of encounter mechanisms explicitly relate motility to feeding mode. New analyses of burrowing mechanics explain the prevalence of bilateral symmetry and blur the boundary between surface and subsurface feeding. The dichotomy between microphagous deposit and suspension feeders and macrophagous carnivores, herbivores, and omnivores is further supported by divergent digestive strategies. Deposit feeding appears to be limited largely to worms longer than 1 cm, with juveniles and small worms in general restricted to ingesting highly digestible organic material and larger, rich food items, blurring the macrophage-microphage dichotomy that applies well to larger worms. PMID:25251269

  6. Shai-Hulud: The quest for worm sign

    NASA Astrophysics Data System (ADS)

    Jaenisch, Holger M.; Handley, James W.; Faucheux, Jeffery P.; Lamkin, Ken

    2005-03-01

    Successful worm detection at real-time OC-48 and OC-192 speed requires hardware to extract web based binary sequences at faster than these speeds, and software to process the incoming sequences to identify worms. Computer hardware advancement in the form of field programmable gate arrays (FPGAs) makes real-time extraction of these sequences possible. Lacking are mathematical algorithms for worm detection in the real time data sequence, and the ability to convert these algorithms into lookup tables (LUTs) that can be compiled into FPGAs. Data Modeling provides the theory and algorithms for an effective mathematical framework for real-time worm detection and conversion of algorithms into LUTs. Detection methods currently available such as pattern recognition algorithms are limited both by the amount of time to compare the current data sequence with a historical database of potential candidates, and by the inability to accurately classify information that was unseen in the training process. Data Modeling eliminates these limitations by training only on examples of nominal behavior. This results in a highly tuned and fast running equation model that is compiled in a FPGA as a LUT and used at real-time OC-48 and OC-192 speeds to detect worms and other anomalies. This paper provides an overview of our approach for generating these Data Change Models for detecting worms, and their subsequent conversion into LUTs. A proof of concept is given using binary data from a WEBDAV, SLAMMER packet, and RED PROBE attack, with BASIC source code for the detector and LUT provided.

  7. Preparation of Pickering double emulsions using block copolymer worms.

    PubMed

    Thompson, Kate L; Mable, Charlotte J; Lane, Jacob A; Derry, Mathew J; Fielding, Lee A; Armes, Steven P

    2015-04-14

    The rational formulation of Pickering double emulsions is described using a judicious combination of hydrophilic and hydrophobic block copolymer worms as highly anisotropic emulsifiers. More specifically, RAFT dispersion polymerization was utilized to prepare poly(lauryl methacrylate)-poly(benzyl methacrylate) worms at 20% w/w solids in n-dodecane and poly(glycerol monomethacrylate)-poly(2-hydroxypropyl methacrylate)-poly(benzyl methacrylate) worms at 13% w/w solids in water by polymerization-induced self-assembly (PISA). Water-in-oil-in-water (w/o/w) double emulsions can be readily prepared with mean droplet diameters ranging from 30 to 80 μm using a two-stage approach. First, a w/o precursor emulsion comprising 25 μm aqueous droplets is prepared using the hydrophobic worms, followed by encapsulation within oil droplets stabilized by the hydrophilic worms. The double emulsion droplet diameter and number of encapsulated water droplets can be readily varied by adjusting the stirring rate employed during the second stage. For each stage, the droplet volume fraction is relatively high at 0.50. The double emulsion nature of the final formulation was confirmed by optical and fluorescence microscopy studies. Such double emulsions are highly stable to coalescence, with little or no change in droplet diameter being detected over storage at 20 °C for 10 weeks as judged by laser diffraction. Preliminary experiments indicate that the complementary o/w/o emulsions can also be prepared using the same pair of worms by changing the order of homogenization, although somewhat lower droplet volume fractions were required in this case. Finally, we demonstrate that triple and even quadruple emulsions can be formulated using these new highly anisotropic Pickering emulsifiers. PMID:25834923

  8. Preparation of Pickering Double Emulsions Using Block Copolymer Worms

    PubMed Central

    2015-01-01

    The rational formulation of Pickering double emulsions is described using a judicious combination of hydrophilic and hydrophobic block copolymer worms as highly anisotropic emulsifiers. More specifically, RAFT dispersion polymerization was utilized to prepare poly(lauryl methacrylate)–poly(benzyl methacrylate) worms at 20% w/w solids in n-dodecane and poly(glycerol monomethacrylate)–poly(2-hydroxypropyl methacrylate)–poly(benzyl methacrylate) worms at 13% w/w solids in water by polymerization-induced self-assembly (PISA). Water-in-oil-in-water (w/o/w) double emulsions can be readily prepared with mean droplet diameters ranging from 30 to 80 μm using a two-stage approach. First, a w/o precursor emulsion comprising 25 μm aqueous droplets is prepared using the hydrophobic worms, followed by encapsulation within oil droplets stabilized by the hydrophilic worms. The double emulsion droplet diameter and number of encapsulated water droplets can be readily varied by adjusting the stirring rate employed during the second stage. For each stage, the droplet volume fraction is relatively high at 0.50. The double emulsion nature of the final formulation was confirmed by optical and fluorescence microscopy studies. Such double emulsions are highly stable to coalescence, with little or no change in droplet diameter being detected over storage at 20 °C for 10 weeks as judged by laser diffraction. Preliminary experiments indicate that the complementary o/w/o emulsions can also be prepared using the same pair of worms by changing the order of homogenization, although somewhat lower droplet volume fractions were required in this case. Finally, we demonstrate that triple and even quadruple emulsions can be formulated using these new highly anisotropic Pickering emulsifiers. PMID:25834923

  9. Got worms? Perinatal exposure to helminths prevents persistent immune sensitization and cognitive dysfunction induced by early-life infection.

    PubMed

    Williamson, Lauren L; McKenney, Erin A; Holzknecht, Zoie E; Belliveau, Christine; Rawls, John F; Poulton, Susan; Parker, William; Bilbo, Staci D

    2016-01-01

    The incidence of autoimmune and inflammatory diseases has risen dramatically in post-industrial societies. "Biome depletion" - loss of commensal microbial and multicellular organisms such as helminths (intestinal worms) that profoundly modulate the immune system - may contribute to these increases. Hyperimmune-associated disorders also affect the brain, especially neurodevelopment, and increasing evidence links early-life infection to cognitive and neurodevelopmental disorders. We have demonstrated previously that rats infected with bacteria as newborns display life-long vulnerabilities to cognitive dysfunction, a vulnerability that is specifically linked to long-term hypersensitivity of microglial cell function, the resident immune cells of the brain. Here, we demonstrate that helminth colonization of pregnant dams attenuated the exaggerated brain cytokine response of their offspring to bacterial infection, and that combined with post-weaning colonization of offspring with helminths (consistent with their mothers treatment) completely prevented enduring microglial sensitization and cognitive dysfunction in adulthood. Importantly, helminths had no overt impact on adaptive immune cell subsets, whereas exaggerated innate inflammatory responses in splenic macrophages were prevented. Finally, helminths altered the effect of neonatal infection on the gut microbiome; neonatal infection with Escherichia coli caused a shift from genera within the Actinobacteria and Tenericutes phyla to genera in the Bacteroidetes phylum in rats not colonized with helminths, but helminths attenuated this effect. In sum, these data point toward an inter-relatedness of various components of the biome, and suggest potential mechanisms by which this helminth might exert therapeutic benefits in the treatment of neuroinflammatory and cognitive disorders. PMID:26162711

  10. Localization of Waves without Bistability: Worms in Nematic Electroconvection

    SciTech Connect

    Riecke, H.; Granzow, G.D.

    1998-07-01

    A general localization mechanism for waves in dissipative systems is identified that does not require the bistability of the basic state and the nonlinear plane-wave state. We conjecture that the mechanism explains the two-dimensional localized wave structures ({open_quotes}worms{close_quotes}) that recently have been observed in experiments on electroconvection in nematic liquid crystals where the transition to extended waves is supercritical. The mechanism accounts for the shape of the worms, their propagation direction, and certain aspects of their interaction. The dynamics of the localized waves can be steady or irregular. {copyright} {ital 1998} {ital The American Physical Society}

  11. Microbubble array for on-chip worm processing

    NASA Astrophysics Data System (ADS)

    Xu, Yuhao; Hashmi, Ali; Yu, Gan; Lu, Xiaonan; Kwon, Hyuck-Jin; Chen, Xiaolin; Xu, Jie

    2013-01-01

    We present an acoustic non-contact technique for achieving trapping, enrichment, and manipulation of Caenorhabditis elegans using an array of oscillating microbubbles. We characterize the trapping efficiency and enrichment ratio under various flow conditions, and demonstrate a single-worm manipulation mechanism through temporal actuation of bubbles. The reason for oscillating bubbles being versatile in processing worms in a microfluidic environment is due to the complex interactions among acoustic field, microbubbles, fluid flow, and live animals. We explain the operating mechanisms used in our device by the interplay among secondary acoustic radiation force, drag force, and the propulsive force of C. elegans.

  12. Gliding Motility and Por Secretion System Genes Are Widespread among Members of the Phylum Bacteroidetes

    PubMed Central

    Zhu, Yongtao

    2013-01-01

    The phylum Bacteroidetes is large and diverse, with rapid gliding motility and the ability to digest macromolecules associated with many genera and species. Recently, a novel protein secretion system, the Por secretion system (PorSS), was identified in two members of the phylum, the gliding bacterium Flavobacterium johnsoniae and the nonmotile oral pathogen Porphyromonas gingivalis. The components of the PorSS are not similar in sequence to those of other well-studied bacterial secretion systems. The F. johnsoniae PorSS genes are a subset of the gliding motility genes, suggesting a role for the secretion system in motility. The F. johnsoniae PorSS is needed for assembly of the gliding motility apparatus and for secretion of a chitinase, and the P. gingivalis PorSS is involved in secretion of gingipain protease virulence factors. Comparative analysis of 37 genomes of members of the phylum Bacteroidetes revealed the widespread occurrence of gliding motility genes and PorSS genes. Genes associated with other bacterial protein secretion systems were less common. The results suggest that gliding motility is more common than previously reported. Microscopic observations confirmed that organisms previously described as nonmotile, including Croceibacter atlanticus, “Gramella forsetii,” Paludibacter propionicigenes, Riemerella anatipestifer, and Robiginitalea biformata, exhibit gliding motility. Three genes (gldA, gldF, and gldG) that encode an apparent ATP-binding cassette transporter required for F. johnsoniae gliding were absent from two related gliding bacteria, suggesting that the transporter may not be central to gliding motility. PMID:23123910

  13. Mitochondrial genome of Micrura bella (Nemertea: Heteronemertea), the largest mitochondrial genome known to phylum Nemertea.

    PubMed

    Shen, Chunyang; Shi-Chun, Sun

    2016-07-01

    The complete mitochondrial genome (mitogenome) of Micrura bella was sequenced and analyzed. Being the largest mitogenome known to phylum Nemertea, the genome is 16 847 bp in length. It encodes 37 genes typical to metazoan mitogenomes and has the same gene arrangement with the other Heteronemertea mitogenomes sequenced to date. The genome has the maximal number of non-coding nucleotides (2037 bp at 25 sites) in Nemertea mitogenomes, among which two large non-coding regions were found (507 and 508 bp, respectively). PMID:26155969

  14. Potential Conservation of Circadian Clock Proteins in the phylum Nematoda as Revealed by Bioinformatic Searches

    PubMed Central

    Romanowski, Andrés; Garavaglia, Matías Javier; Goya, María Eugenia; Ghiringhelli, Pablo Daniel; Golombek, Diego Andrés

    2014-01-01

    Although several circadian rhythms have been described in C. elegans, its molecular clock remains elusive. In this work we employed a novel bioinformatic approach, applying probabilistic methodologies, to search for circadian clock proteins of several of the best studied circadian model organisms of different taxa (Mus musculus, Drosophila melanogaster, Neurospora crassa, Arabidopsis thaliana and Synechoccocus elongatus) in the proteomes of C. elegans and other members of the phylum Nematoda. With this approach we found that the Nematoda contain proteins most related to the core and accessory proteins of the insect and mammalian clocks, which provide new insights into the nematode clock and the evolution of the circadian system. PMID:25396739

  15. Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylum

    DOE PAGESBeta

    Anantharaman, Karthik; Brown, Christopher T.; Burstein, David; Castelle, Cindy J.; Probst, Alexander J.; Thomas, Brian C.; Williams, Kenneth H.; Banfield, Jillian F.

    2016-01-28

    Five closely related populations of bacteria from the Candidate Phylum (CP) Peregrinibacteria, part of the bacterial Candidate Phyla Radiation (CPR), were sampled from filtered groundwater obtained from an aquifer adjacent to the Colorado River near the town of Rifle, CO, USA. Here, we present the first complete genome sequences for organisms from this phylum. These bacteria have small genomes and, unlike most organisms from other lineages in the CPR, have the capacity for nucleotide synthesis. They invest significantly in biosynthesis of cell wall and cell envelope components, including peptidoglycan, isoprenoids via the mevalonate pathway, and a variety of amino sugarsmore » including perosamine and rhamnose. The genomes encode an intriguing set of large extracellular proteins, some of which are very cysteine-rich and may function in attachment, possibly to other cells. Strain variation in these proteins is an important source of genotypic variety. Overall, the cell envelope features, combined with the lack of biosynthesis capacities for many required cofactors, fatty acids, and most amino acids point to a symbiotic lifestyle. Furthermore, phylogenetic analyses indicate that these bacteria likely represent a new class within the Peregrinibacteria phylum, although they ultimately may be recognized as members of a separate phylum. In conclusion, we propose the provisional taxonomic assignment as ‘Candidatus Peribacter riflensis’, Genus Peribacter, Family Peribacteraceae, Order Peribacterales, Class Peribacteria in the phylum Peregrinibacteria.« less

  16. Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylum

    PubMed Central

    Anantharaman, Karthik; Burstein, David; Castelle, Cindy J.; Probst, Alexander J.; Thomas, Brian C.; Williams, Kenneth H.

    2016-01-01

    Five closely related populations of bacteria from the Candidate Phylum (CP) Peregrinibacteria, part of the bacterial Candidate Phyla Radiation (CPR), were sampled from filtered groundwater obtained from an aquifer adjacent to the Colorado River near the town of Rifle, CO, USA. Here, we present the first complete genome sequences for organisms from this phylum. These bacteria have small genomes and, unlike most organisms from other lineages in the CPR, have the capacity for nucleotide synthesis. They invest significantly in biosynthesis of cell wall and cell envelope components, including peptidoglycan, isoprenoids via the mevalonate pathway, and a variety of amino sugars including perosamine and rhamnose. The genomes encode an intriguing set of large extracellular proteins, some of which are very cysteine-rich and may function in attachment, possibly to other cells. Strain variation in these proteins is an important source of genotypic variety. Overall, the cell envelope features, combined with the lack of biosynthesis capacities for many required cofactors, fatty acids, and most amino acids point to a symbiotic lifestyle. Phylogenetic analyses indicate that these bacteria likely represent a new class within the Peregrinibacteria phylum, although they ultimately may be recognized as members of a separate phylum. We propose the provisional taxonomic assignment as ‘Candidatus Peribacter riflensis’, Genus Peribacter, Family Peribacteraceae, Order Peribacterales, Class Peribacteria in the phylum Peregrinibacteria. PMID:26844018

  17. Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylum.

    PubMed

    Anantharaman, Karthik; Brown, Christopher T; Burstein, David; Castelle, Cindy J; Probst, Alexander J; Thomas, Brian C; Williams, Kenneth H; Banfield, Jillian F

    2016-01-01

    Five closely related populations of bacteria from the Candidate Phylum (CP) Peregrinibacteria, part of the bacterial Candidate Phyla Radiation (CPR), were sampled from filtered groundwater obtained from an aquifer adjacent to the Colorado River near the town of Rifle, CO, USA. Here, we present the first complete genome sequences for organisms from this phylum. These bacteria have small genomes and, unlike most organisms from other lineages in the CPR, have the capacity for nucleotide synthesis. They invest significantly in biosynthesis of cell wall and cell envelope components, including peptidoglycan, isoprenoids via the mevalonate pathway, and a variety of amino sugars including perosamine and rhamnose. The genomes encode an intriguing set of large extracellular proteins, some of which are very cysteine-rich and may function in attachment, possibly to other cells. Strain variation in these proteins is an important source of genotypic variety. Overall, the cell envelope features, combined with the lack of biosynthesis capacities for many required cofactors, fatty acids, and most amino acids point to a symbiotic lifestyle. Phylogenetic analyses indicate that these bacteria likely represent a new class within the Peregrinibacteria phylum, although they ultimately may be recognized as members of a separate phylum. We propose the provisional taxonomic assignment as 'Candidatus Peribacter riflensis', Genus Peribacter, Family Peribacteraceae, Order Peribacterales, Class Peribacteria in the phylum Peregrinibacteria. PMID:26844018

  18. 11. INTERIOR VIEW OF OPERATING HOUSE NO. 4, SHOWING WORM ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    11. INTERIOR VIEW OF OPERATING HOUSE NO. 4, SHOWING WORM WHEEL GEAR ASSEMBLY, ORIGINAL 20 HP EAST HOIST MOTOR, AND CONTROL GATES 7 AND 8 HAND BRAKES, WITH MOTOR SELECTOR SWITCH, MOTOR STARTING SWITCH, AND OIL CIRCUIT BREAKER IN BACKGROUND - Long Lake Hydroelectric Plant, Spillway Dam, Spanning Spokane River, Ford, Stevens County, WA

  19. Opinion Dynamics Driven by Leaders, Media, Viruses and Worms

    NASA Astrophysics Data System (ADS)

    Tuncay, Çağlar

    A model on the effects of leader, media, viruses, worms, and other agents on the opinion of individuals is developed and utilized to simulate the formation of consensus in society and price in market via excess between supply and demand. The effects of some time varying drives (harmonic and hyperbolic) are also investigated.

  20. CHROMOSOME COMPLEMENT OF THE MARINE WORM 'NEANTHES ARENACEODENTATA' (POLYCHAETA: ANNELIDA)

    EPA Science Inventory

    The chromosome complement for the marine worm, Neanthes arenaceodentata, consists of nine pairs; one pair has a median centromere, seven pairs have submedian centromeres, and one pair is polymorphic with either a subterminal or terminal centromere. A technique for studying polych...

  1. The Worm Process for the Ising Model is Rapidly Mixing

    NASA Astrophysics Data System (ADS)

    Collevecchio, Andrea; Garoni, Timothy M.; Hyndman, Timothy; Tokarev, Daniel

    2016-07-01

    We prove rapid mixing of the worm process for the zero-field ferromagnetic Ising model, on all finite connected graphs, and at all temperatures. As a corollary, we obtain a fully-polynomial randomized approximation scheme for the Ising susceptibility, and for a certain restriction of the two-point correlation function.

  2. The Worm Guide: A Vericomposting Guide for Teachers.

    ERIC Educational Resources Information Center

    California Integrated Waste Management Board, Sacramento.

    This guide focuses on vermicomposting of food waste. Contents include: (1) "Integrated Waste Management"; (2) "Basics of Vermicomposting"; (3) "Other Worm Bin Residents"; (4) "The Garden Connection"; (5) "Closing the Food Loop at Your School"; (6) "Fundraising"; (7) "Activities for Classroom"; and (8) "Case Studies". Appendices include educational…

  3. The opportunistic transmission of wireless worms between mobile devices

    NASA Astrophysics Data System (ADS)

    Rhodes, C. J.; Nekovee, M.

    2008-12-01

    The ubiquity of portable wireless-enabled computing and communications devices has stimulated the emergence of malicious codes (wireless worms) that are capable of spreading between spatially proximal devices. The potential exists for worms to be opportunistically transmitted between devices as they move around, so human mobility patterns will have an impact on epidemic spread. The scenario we address in this paper is proximity attacks from fleetingly in-contact wireless devices with short-range communication range, such as Bluetooth-enabled smart phones. An individual-based model of mobile devices is introduced and the effect of population characteristics and device behaviour on the outbreak dynamics is investigated. The model uses straight-line motion to achieve population, though it is recognised that this is a highly simplified representation of human mobility patterns. We show that the contact rate can be derived from the underlying mobility model and, through extensive simulation, that mass-action epidemic models remain applicable to worm spreading in the low density regime studied here. The model gives useful analytical expressions against which more refined simulations of worm spread can be developed and tested.

  4. WormBase 2014: new views of curated biology

    PubMed Central

    Harris, Todd W.; Baran, Joachim; Bieri, Tamberlyn; Cabunoc, Abigail; Chan, Juancarlos; Chen, Wen J.; Davis, Paul; Done, James; Grove, Christian; Howe, Kevin; Kishore, Ranjana; Lee, Raymond; Li, Yuling; Muller, Hans-Michael; Nakamura, Cecilia; Ozersky, Philip; Paulini, Michael; Raciti, Daniela; Schindelman, Gary; Tuli, Mary Ann; Auken, Kimberly Van; Wang, Daniel; Wang, Xiaodong; Williams, Gary; Wong, J. D.; Yook, Karen; Schedl, Tim; Hodgkin, Jonathan; Berriman, Matthew; Kersey, Paul; Spieth, John; Stein, Lincoln; Sternberg, Paul W.

    2014-01-01

    WormBase (http://www.wormbase.org/) is a highly curated resource dedicated to supporting research using the model organism Caenorhabditis elegans. With an electronic history predating the World Wide Web, WormBase contains information ranging from the sequence and phenotype of individual alleles to genome-wide studies generated using next-generation sequencing technologies. In recent years, we have expanded the contents to include data on additional nematodes of agricultural and medical significance, bringing the knowledge of C. elegans to bear on these systems and providing support for underserved research communities. Manual curation of the primary literature remains a central focus of the WormBase project, providing users with reliable, up-to-date and highly cross-linked information. In this update, we describe efforts to organize the original atomized and highly contextualized curated data into integrated syntheses of discrete biological topics. Next, we discuss our experiences coping with the vast increase in available genome sequences made possible through next-generation sequencing platforms. Finally, we describe some of the features and tools of the new WormBase Web site that help users better find and explore data of interest. PMID:24194605

  5. The Worm Process for the Ising Model is Rapidly Mixing

    NASA Astrophysics Data System (ADS)

    Collevecchio, Andrea; Garoni, Timothy M.; Hyndman, Timothy; Tokarev, Daniel

    2016-09-01

    We prove rapid mixing of the worm process for the zero-field ferromagnetic Ising model, on all finite connected graphs, and at all temperatures. As a corollary, we obtain a fully-polynomial randomized approximation scheme for the Ising susceptibility, and for a certain restriction of the two-point correlation function.

  6. Making sense of genomes of parasitic worms: Tackling bioinformatic challenges.

    PubMed

    Korhonen, Pasi K; Young, Neil D; Gasser, Robin B

    2016-01-01

    Billions of people and animals are infected with parasitic worms (helminths). Many of these worms cause diseases that have a major socioeconomic impact worldwide, and are challenging to control because existing treatment methods are often inadequate. There is, therefore, a need to work toward developing new intervention methods, built on a sound understanding of parasitic worms at molecular level, the relationships that they have with their animal hosts and/or the diseases that they cause. Decoding the genomes and transcriptomes of these parasites brings us a step closer to this goal. The key focus of this article is to critically review and discuss bioinformatic tools used for the assembly and annotation of these genomes and transcriptomes, as well as various post-genomic analyses of transcription profiles, biological pathways, synteny, phylogeny, biogeography and the prediction and prioritisation of drug target candidates. Bioinformatic pipelines implemented and established recently provide practical and efficient tools for the assembly and annotation of genomes of parasitic worms, and will be applicable to a wide range of other parasites and eukaryotic organisms. Future research will need to assess the utility of long-read sequence data sets for enhanced genomic assemblies, and develop improved algorithms for gene prediction and post-genomic analyses, to enable comprehensive systems biology explorations of parasitic organisms. PMID:26956711

  7. Analysis of environmental 18S ribosomal RNA sequences reveals unknown diversity of the cosmopolitan phylum Telonemia.

    PubMed

    Shalchian-Tabrizi, Kamran; Kauserud, Håvard; Massana, Ramon; Klaveness, Dag; Jakobsen, Kjetill S

    2007-04-01

    Telonemia has recently been described as a new eukaryotic phylum with uncertain evolutionary origin. So far, only two Telonemia species, Telonema subtilis and Telonema antarcticum, have been described, but there are substantial variations in size and morphology among Telonema isolates and field observations, indicating a hidden diversity of Telonemia-like species and populations. In this study, we investigated the diversity and the global distribution of this group by analyzing 18S rDNA sequences from marine environmental clone libraries published in GenBank as well as several unpublished sequences from the Indian Ocean. Phylogenetic analyses of the identified sequences suggest that the Telonemia phylum includes several undescribed 18S rDNA phylotypes, probably corresponding to a number of different species and/or populations. The Telonemia phylotypes form two main groups, here referred to as Telonemia Groups 1 and 2. Some of the closely related sequences originate from separate oceans, indicating worldwide distributions of various Telonemia phylotypes, while other phylotypes seem to have limited geographical distribution. Further investigations of the evolutionary relationships within Telonemia should be conducted on isolated cultures of Telonema-like strains using multi-locus sequencing and morphological data. PMID:17196879

  8. The First Complete Genome Sequence of the Class Fimbriimonadia in the Phylum Armatimonadetes

    PubMed Central

    Im, Wan-Taek; Wang, Sheng-Yue; Zhao, Guo-Ping; Zheng, Hua-Jun; Quan, Zhe-Xue

    2014-01-01

    In this study, we present the complete genome of Fimbriimonas ginsengisoli Gsoil 348T belonging to the class Fimbriimonadia of the phylum Armatimonadetes, formerly called as candidate phylum OP10. The complete genome contains a single circular chromosome of 5.23 Mb including a 45.5 kb prophage. Of the 4820 open reading frames (ORFs), 3,000 (62.2%) genes could be classified into Clusters of Orthologous Groups (COG) families. With the split of rRNA genes, strain Gsoil 348T had no typical 16S-23S-5S ribosomal RNA operon. In this genome, the GC skew inversion which was usually observed in archaea was found. The predicted gene functions suggest that the organism lacks the ability to synthesize histidine, and the TCA cycle is incomplete. Phylogenetic analyses based on ribosomal proteins indicated that strain Gsoil 348T represents a deeply branching lineage of sufficient divergence with other phyla, but also strongly involved in superphylum Terrabacteria. PMID:24967843

  9. FROM INCIPIENT TO SUBSTANTIAL: EVOLUTION OF PLACENTOTROPHY IN A PHYLUM OF AQUATIC COLONIAL INVERTEBRATES

    PubMed Central

    Ostrovsky, Andrew N; Fairbairn, D

    2013-01-01

    Matrotrophy has long been known in invertebrates, but it is still poorly understood and has never been reviewed. A striking example of matrotrophy (namely, placentotrophy) is provided by the Bryozoa, a medium-sized phylum of the aquatic colonial filter feeders. Here I report on an extensive anatomical study of placental analogues in 21 species of the bryozoan order Cheilostomata, offering the first review on matrotrophy among aquatic invertebrates. The first anatomical description of incipient placentotrophy in invertebrates is presented together with the evidence for multiple independent origins of placental analogues in this order. The combinations of contrasting oocytic types (macrolecithal or microlecithal) and various degrees of placental development and embryonic enlargement during incubation, found in different bryozoan species, are suggestive of a transitional series from the incipient to the substantial placentotrophy accompanied by an inverse change in oogenesis, a situation reminiscent of some vertebrates. It seems that matrotrophy could trigger the evolution of sexual zooidal polymorphism in some clades. The results of this study show that this phylum, with its wide variety of reproductive patterns, incubation devices, and types of the simple placenta-like systems, offers a promising model for studying parallel evolution of placentotrophy in particular, and matrotrophy in general. PMID:23617914

  10. Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs.

    PubMed

    Eloe-Fadrosh, Emiley A; Paez-Espino, David; Jarett, Jessica; Dunfield, Peter F; Hedlund, Brian P; Dekas, Anne E; Grasby, Stephen E; Brady, Allyson L; Dong, Hailiang; Briggs, Brandon R; Li, Wen-Jun; Goudeau, Danielle; Malmstrom, Rex; Pati, Amrita; Pett-Ridge, Jennifer; Rubin, Edward M; Woyke, Tanja; Kyrpides, Nikos C; Ivanova, Natalia N

    2016-01-01

    Analysis of the increasing wealth of metagenomic data collected from diverse environments can lead to the discovery of novel branches on the tree of life. Here we analyse 5.2 Tb of metagenomic data collected globally to discover a novel bacterial phylum ('Candidatus Kryptonia') found exclusively in high-temperature pH-neutral geothermal springs. This lineage had remained hidden as a taxonomic 'blind spot' because of mismatches in the primers commonly used for ribosomal gene surveys. Genome reconstruction from metagenomic data combined with single-cell genomics results in several high-quality genomes representing four genera from the new phylum. Metabolic reconstruction indicates a heterotrophic lifestyle with conspicuous nutritional deficiencies, suggesting the need for metabolic complementarity with other microbes. Co-occurrence patterns identifies a number of putative partners, including an uncultured Armatimonadetes lineage. The discovery of Kryptonia within previously studied geothermal springs underscores the importance of globally sampled metagenomic data in detection of microbial novelty, and highlights the extraordinary diversity of microbial life still awaiting discovery. PMID:26814032

  11. Distribution and Evolution of Nitrogen Fixation Genes in the Phylum Bacteroidetes

    PubMed Central

    Inoue, Jun-ichi; Oshima, Kenshiro; Suda, Wataru; Sakamoto, Mitsuo; Iino, Takao; Noda, Satoko; Hongoh, Yuichi; Hattori, Masahira; Ohkuma, Moriya

    2015-01-01

    Diazotrophs had not previously been identified among bacterial species in the phylum Bacteroidetes until the rapid expansion of bacterial genome sequences, which revealed the presence of nitrogen fixation (nif) genes in this phylum. We herein determined the draft genome sequences of Bacteroides graminisolvens JCM 15093T and Geofilum rubicundum JCM 15548T. In addition to these and previously reported ‘Candidatus Azobacteroides pseudotrichonymphae’ and Paludibacter propionicigenes, an extensive survey of the genome sequences of diverse Bacteroidetes members revealed the presence of a set of nif genes (nifHDKENB) in strains of Dysgonomonas gadei, Dysgonomonas capnocytophagoides, Saccharicrinis fermentans, and Alkaliflexus imshenetskii. These eight species belonged to and were distributed sporadically within the order Bacteroidales. Acetylene reduction activity was detected in the five species examined, strongly suggesting their diazotrophic nature. Phylogenetic analyses showed monophyletic clustering of the six Nif protein sequences in the eight Bacteroidales species, implying that nitrogen fixation is ancestral to Bacteroidales and has been retained in these species, but lost in many other lineages. The identification of nif genes in Bacteroidales facilitates the prediction of the organismal origins of related sequences directly obtained from various environments. PMID:25736980

  12. Molecular phylogeny of the phylum Gastrotricha: new data brings together molecules and morphology.

    PubMed

    Paps, Jordi; Riutort, Marta

    2012-04-01

    Gastrotricha is a species-rich phylum of microscopical animals that contains two main orders, Chaetonotida and Macrodasyida. Gastrotrichs are important members of the aquatic environment and significant players in the study of animal evolution. In spite of their ecological and evolutionary importance, their internal relationships are not yet well understood. We have produced new sequences for the 18S rDNA gene to improve both the quality and quantity of taxon sampling for the gastrotrichs. Our phylogeny recovers the monophyly of the two main Gastrotricha clades, in contrast to recent studies with similar sampling, but in agreement with morphology based analyses. However, our topology is not able to resolve the first branches of the macrodasyidans or settle the position of the puzzling Neodasys, a controversial genus classified as a chaetonotidan on morphological grounds but placed within macrodasyidans by molecular studies. This analysis is the most exhaustive molecular phylogeny of the phylum to date, and significantly increases our knowledge of gastrotrich evolution. PMID:22198640

  13. Phylum-Level Conservation of Regulatory Information in Nematodes despite Extensive Non-coding Sequence Divergence

    PubMed Central

    Gordon, Kacy L.; Arthur, Robert K.; Ruvinsky, Ilya

    2015-01-01

    Gene regulatory information guides development and shapes the course of evolution. To test conservation of gene regulation within the phylum Nematoda, we compared the functions of putative cis-regulatory sequences of four sets of orthologs (unc-47, unc-25, mec-3 and elt-2) from distantly-related nematode species. These species, Caenorhabditis elegans, its congeneric C. briggsae, and three parasitic species Meloidogyne hapla, Brugia malayi, and Trichinella spiralis, represent four of the five major clades in the phylum Nematoda. Despite the great phylogenetic distances sampled and the extensive sequence divergence of nematode genomes, all but one of the regulatory elements we tested are able to drive at least a subset of the expected gene expression patterns. We show that functionally conserved cis-regulatory elements have no more extended sequence similarity to their C. elegans orthologs than would be expected by chance, but they do harbor motifs that are important for proper expression of the C. elegans genes. These motifs are too short to be distinguished from the background level of sequence similarity, and while identical in sequence they are not conserved in orientation or position. Functional tests reveal that some of these motifs contribute to proper expression. Our results suggest that conserved regulatory circuitry can persist despite considerable turnover within cis elements. PMID:26020930

  14. Phylum-wide comparative genomics unravel the diversity of secondary metabolism in Cyanobacteria

    SciTech Connect

    Calteau, Alexandra; Fewer, David P.; Latifi, Amel; Coursin, Thérèse; Laurent, Thierry; Jokela, Jouni; Kerfeld, Cheryl A.; Sivonen, Kaarina; Piel, Jörn; Gugger, Muriel

    2014-11-18

    Cyanobacteria are an ancient lineage of photosynthetic bacteria from which hundreds of natural products have been described, including many notorious toxins but also potent natural products of interest to the pharmaceutical and biotechnological industries. Many of these compounds are the products of non-ribosomal peptide synthetase (NRPS) or polyketide synthase (PKS) pathways. However, current understanding of the diversification of these pathways is largely based on the chemical structure of the bioactive compounds, while the evolutionary forces driving their remarkable chemical diversity are poorly understood. We carried out a phylum-wide investigation of genetic diversification of the cyanobacterial NRPS and PKS pathways for the production of bioactive compounds. 452 NRPS and PKS gene clusters were identified from 89 cyanobacterial genomes, revealing a clear burst in late-branching lineages. Our genomic analysis further grouped the clusters into 286 highly diversified cluster families (CF) of pathways. Some CFs appeared vertically inherited, while others presented a more complex evolutionary history. Only a few horizontal gene transfers were evidenced amongst strongly conserved CFs in the phylum, while several others have undergone drastic gene shuffling events, which could result in the observed diversification of the pathways. In addition to toxin production, several NRPS and PKS gene clusters are devoted to important cellular processes of these bacteria such as nitrogen fixation and iron uptake. The majority of the biosynthetic clusters identified here have unknown end products, highlighting the power of genome mining for the discovery of new natural products.

  15. Phylum-wide comparative genomics unravel the diversity of secondary metabolism in Cyanobacteria

    DOE PAGESBeta

    Calteau, Alexandra; Fewer, David P.; Latifi, Amel; Coursin, Thérèse; Laurent, Thierry; Jokela, Jouni; Kerfeld, Cheryl A.; Sivonen, Kaarina; Piel, Jörn; Gugger, Muriel

    2014-11-18

    Cyanobacteria are an ancient lineage of photosynthetic bacteria from which hundreds of natural products have been described, including many notorious toxins but also potent natural products of interest to the pharmaceutical and biotechnological industries. Many of these compounds are the products of non-ribosomal peptide synthetase (NRPS) or polyketide synthase (PKS) pathways. However, current understanding of the diversification of these pathways is largely based on the chemical structure of the bioactive compounds, while the evolutionary forces driving their remarkable chemical diversity are poorly understood. We carried out a phylum-wide investigation of genetic diversification of the cyanobacterial NRPS and PKS pathways formore » the production of bioactive compounds. 452 NRPS and PKS gene clusters were identified from 89 cyanobacterial genomes, revealing a clear burst in late-branching lineages. Our genomic analysis further grouped the clusters into 286 highly diversified cluster families (CF) of pathways. Some CFs appeared vertically inherited, while others presented a more complex evolutionary history. Only a few horizontal gene transfers were evidenced amongst strongly conserved CFs in the phylum, while several others have undergone drastic gene shuffling events, which could result in the observed diversification of the pathways. In addition to toxin production, several NRPS and PKS gene clusters are devoted to important cellular processes of these bacteria such as nitrogen fixation and iron uptake. The majority of the biosynthetic clusters identified here have unknown end products, highlighting the power of genome mining for the discovery of new natural products.« less

  16. Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs

    PubMed Central

    Eloe-Fadrosh, Emiley A.; Paez-Espino, David; Jarett, Jessica; Dunfield, Peter F.; Hedlund, Brian P.; Dekas, Anne E.; Grasby, Stephen E.; Brady, Allyson L.; Dong, Hailiang; Briggs, Brandon R.; Li, Wen-Jun; Goudeau, Danielle; Malmstrom, Rex; Pati, Amrita; Pett-Ridge, Jennifer; Rubin, Edward M.; Woyke, Tanja; Kyrpides, Nikos C.; Ivanova, Natalia N.

    2016-01-01

    Analysis of the increasing wealth of metagenomic data collected from diverse environments can lead to the discovery of novel branches on the tree of life. Here we analyse 5.2 Tb of metagenomic data collected globally to discover a novel bacterial phylum (‘Candidatus Kryptonia') found exclusively in high-temperature pH-neutral geothermal springs. This lineage had remained hidden as a taxonomic ‘blind spot' because of mismatches in the primers commonly used for ribosomal gene surveys. Genome reconstruction from metagenomic data combined with single-cell genomics results in several high-quality genomes representing four genera from the new phylum. Metabolic reconstruction indicates a heterotrophic lifestyle with conspicuous nutritional deficiencies, suggesting the need for metabolic complementarity with other microbes. Co-occurrence patterns identifies a number of putative partners, including an uncultured Armatimonadetes lineage. The discovery of Kryptonia within previously studied geothermal springs underscores the importance of globally sampled metagenomic data in detection of microbial novelty, and highlights the extraordinary diversity of microbial life still awaiting discovery. PMID:26814032

  17. Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs

    DOE PAGESBeta

    Eloe-Fadrosh, Emiley A.; Paez-Espino, David; Jarett, Jessica; Dunfield, Peter F.; Hedlund, Brian P.; Dekas, Anne E.; Grasby, Stephen E.; Brady, Allyson L.; Dong, Hailiang; Briggs, Brandon R.; et al

    2016-01-27

    We analyse the increasing wealth of metagenomic data collected from diverse environments can lead to the discovery of novel branches on the tree of life. Here we analyse 5.2 Tb of metagenomic data collected globally to discover a novel bacterial phylum (‘Candidatus Kryptonia’) found exclusively in high-temperature pH-neutral geothermal springs. This lineage had remained hidden as a taxonomic ‘blind spot’ because of mismatches in the primers commonly used for ribosomal gene surveys. Genome reconstruction from metagenomic data combined with single-cell genomics results in several high-quality genomes representing four genera from the new phylum. Metabolic reconstruction indicates a heterotrophic lifestyle withmore » conspicuous nutritional deficiencies, suggesting the need for metabolic complementarity with other microbes. Co-occurrence patterns identifies a number of putative partners, including an uncultured Armatimonadetes lineage. The discovery of Kryptonia within previously studied geothermal springs underscores the importance of globally sampled metagenomic data in detection of microbial novelty, and highlights the extraordinary diversity of microbial life still awaiting discovery.« less

  18. A molecular phylogeny of the flagellated fungi (Chytridiomycota) and description of a new phylum (Blastocladiomycota).

    PubMed

    James, Timothy Y; Letcher, Peter M; Longcore, Joyce E; Mozley-Standridge, Sharon E; Porter, David; Powell, Martha J; Griffith, Gareth W; Vilgalys, Rytas

    2006-01-01

    Chytridiomycota (chytrids) is the only phylum of true Fungi that reproduces with motile spores (zoospores). Chytrids currently are classified into five orders based on habitat, zoospore characters and life cycles. In this paper we estimate the phylogeny of the chytrids with DNA sequences from the ribosomal RNA operon (18S+5.8S+28S subunits). To our surprise the morphologically reduced parasites Olpidium and Rozella comprise two entirely new, and separate, lineages on the fungal tree. Olpidium brassicae groups among the Zygomycota, and Rozella spp. are the earliest branch to diverge in the fungal kingdom. The phylogeny also suggests that Chytridiomycota is not monophyletic and there are four major lineages of chytrids: Rozella spp., Olpidium brassicae, the Blastocladiales and a "core chytrid clade" containing the remaining orders and families and the majority of flagellated fungi. Within the core chytrid group 11 subclades can be identified, each of which correlates well with zoospore ultrastructure or morphology. We provide a synopsis of each clade and its morphological circumscription. The Blastocladiales appears to be the sister taxon of most nonflagellated fungi. Based on molecular phylogenetic and ultrastructural characters this order is elevated to a phylum, the Blastocladiomycota. PMID:17486963

  19. From incipient to substantial: evolution of placentotrophy in a phylum of aquatic colonial invertebrates.

    PubMed

    Ostrovsky, Andrew N

    2013-05-01

    Matrotrophy has long been known in invertebrates, but it is still poorly understood and has never been reviewed. A striking example of matrotrophy (namely, placentotrophy) is provided by the Bryozoa, a medium-sized phylum of the aquatic colonial filter feeders. Here I report on an extensive anatomical study of placental analogues in 21 species of the bryozoan order Cheilostomata, offering the first review on matrotrophy among aquatic invertebrates. The first anatomical description of incipient placentotrophy in invertebrates is presented together with the evidence for multiple independent origins of placental analogues in this order. The combinations of contrasting oocytic types (macrolecithal or microlecithal) and various degrees of placental development and embryonic enlargement during incubation, found in different bryozoan species, are suggestive of a transitional series from the incipient to the substantial placentotrophy accompanied by an inverse change in oogenesis, a situation reminiscent of some vertebrates. It seems that matrotrophy could trigger the evolution of sexual zooidal polymorphism in some clades. The results of this study show that this phylum, with its wide variety of reproductive patterns, incubation devices, and types of the simple placenta-like systems, offers a promising model for studying parallel evolution of placentotrophy in particular, and matrotrophy in general. PMID:23617914

  20. The first complete genome sequence of the class Fimbriimonadia in the phylum Armatimonadetes.

    PubMed

    Hu, Zi-Ye; Wang, Yue-Zhu; Im, Wan-Taek; Wang, Sheng-Yue; Zhao, Guo-Ping; Zheng, Hua-Jun; Quan, Zhe-Xue

    2014-01-01

    In this study, we present the complete genome of Fimbriimonas ginsengisoli Gsoil 348T belonging to the class Fimbriimonadia of the phylum Armatimonadetes, formerly called as candidate phylum OP10. The complete genome contains a single circular chromosome of 5.23 Mb including a 45.5 kb prophage. Of the 4820 open reading frames (ORFs), 3,000 (62.2%) genes could be classified into Clusters of Orthologous Groups (COG) families. With the split of rRNA genes, strain Gsoil 348T had no typical 16S-23S-5S ribosomal RNA operon. In this genome, the GC skew inversion which was usually observed in archaea was found. The predicted gene functions suggest that the organism lacks the ability to synthesize histidine, and the TCA cycle is incomplete. Phylogenetic analyses based on ribosomal proteins indicated that strain Gsoil 348T represents a deeply branching lineage of sufficient divergence with other phyla, but also strongly involved in superphylum Terrabacteria. PMID:24967843

  1. Review of Cranked-Arrow Wing Aerodynamics Project: Its International Aeronautical Community Role

    NASA Technical Reports Server (NTRS)

    Lamar, John E.; Obara, Clifford J.

    2007-01-01

    This paper provides a brief history of the F-16XL-1 aircraft, its role in the High Speed Research (HSR) program and how it was morphed into the Cranked Arrow Wing Aerodynamics Project (CAWAP). Various flight, wind-tunnel and Computational Fluid Dynamics (CFD) data sets were generated during the CAWAP. These unique and open flight datasets for surface pressures, boundary-layer profiles and skinfriction distributions, along with surface flow data, are described and sample data comparisons given. This is followed by a description of how the project became internationalized to be known as Cranked Arrow Wing Aerodynamics Project International (CAWAPI) and is concluded by an introduction to the results of a 4 year CFD predictive study of data collected at flight conditions by participating researchers.

  2. From the Dynamics of Coupled Map Lattices to the Psychological Arrow of Time

    NASA Astrophysics Data System (ADS)

    Atmanspacher, Harald; Filk, Thomas; Scheingraber, Herbert

    2006-10-01

    Stable neuronal assemblies are generally regarded as neural correlates of mental representations. Their temporal sequence corresponds to the experience of a direction of time, sometimes called the psychological time arrow. We show that the stability of particular, biophysically motivated models of neuronal assemblies, called coupled map lattices, is supported by causal interactions among neurons and obstructed by non-causal or anti-causal interactions among neurons. This surprising relation between causality and stability suggests that those neuronal assemblies that are stable due to causal neuronal interactions, and thus correlated with mental representations, generate a psychological time arrow. Yet this impact of causal interactions among neurons on the directed sequence of mental representations does not rule out the possibility of mentally less efficacious non-causal or anti-causal interactions among neurons.

  3. The Significance of Causally Coupled, Stable Neuronal Assemblies for the Psychological Time Arrow

    NASA Astrophysics Data System (ADS)

    Atmanspacher, Harald; Filk, Thomas; Scheingraber, Herbert

    2005-10-01

    Stable neuronal assemblies are generally regarded as neural correlates of mental representations. Their temporal sequence corresponds to the experience of a direction of time, sometimes called the psychological time arrow. We show that the stability of particular, biophysically motivated models of neuronal assemblies, called coupled map lattices, is supported by causal interactions among neurons and obstructed by non-causal or anti-causal interactions among neurons. This surprising relation between causality and stability suggests that those neuronal assemblies that are stable due to causal neuronal interactions, and thus correlated with mental representations, generate a psychological time arrow. Yet this impact of causal interactions among neurons on the directed sequence of mental representations does not rule out the possibility of mentally less efficacious non-causal or anti-causal interactions among neurons.

  4. Poor vigilance affects attentional orienting triggered by central uninformative gaze and arrow cues.

    PubMed

    Marotta, Andrea; Martella, Diana; Maccari, Lisa; Sebastiani, Mara; Casagrande, Maria

    2014-11-01

    Behaviour and neuroimaging studies have shown that poor vigilance (PV) due to sleep deprivation (SD) negatively affects exogenously cued selective attention. In the current study, we assessed the impact of PV due to both partial SD and night-time hours on reflexive attentional orienting triggered by central un-informative eye-gaze and arrow cues. Subjective mood and interference performance in emotional Stroop task were also investigated. Twenty healthy participants performed spatial cueing tasks using central directional arrow and eye-gaze as a cue to orient attention. The target was a word written in different coloured inks. The participant's task was to identify the colour of the ink while ignoring the semantic content of the word (with negative or neutral emotional valence). The experiment took place on 2 days. On the first day, each participant performed a 10-min training session of the spatial cueing task. On the second day, half of participants performed the task once at 4:30 p.m. (BSL) and once at 6:30 a.m. (PV), whereas the other half performed the task in the reversed order. Results showed that mean reaction times on the spatial cueing tasks were worsened by PV, although gaze paradigm was more resistant to this effect as compared to the arrow paradigm. Moreover, PV negatively affects attentional orienting triggered by both central un-informative gaze and arrow cues. Finally, prolonged wakefulness affects self-reported mood but does not influence interference control in emotional Stroop task. PMID:24718933

  5. Effects of vortex flaps on the low-speed aerodynamic characteristics of an arrow wing

    NASA Technical Reports Server (NTRS)

    Yip, L. P.; Murri, D. G.

    1981-01-01

    Tests were conducted in the Langley 12-foot low-speed wind-tunnel to determine the longitudinal and lateral-directional aerodynamic effects of plain and tabbed vortex flaps on a flat-plate, highly swept arrow-wing model. Flow-visualization studies were made using a helium-bubble technique. Static forces and moments were measured over an angle-of-attack range from 0 deg to 50deg for sideslip angles of 0 deg and + or - 4 deg.

  6. Attentional orienting induced by arrows and eye-gaze compared with an endogenous cue.

    PubMed

    Brignani, D; Guzzon, D; Marzi, C A; Miniussi, C

    2009-01-01

    Exogenous orienting has been widely studied by using peripheral cues whereas endogenous orienting has been studied with directional central cues. However, recent evidence has shown that centrally presented eye-gaze and arrows may produce an automatic rather than voluntary orienting of attention. Therefore, the aim of the present study was to investigate the behavioural and electrophysiological (event-related potentials-ERP) correlates of the attentional shift induced by arrows and eye-gaze. In order to have a control condition, we compared arrows and eye-gaze with a purely endogenous cue, i.e., a texture arbitrarily coding one direction. We analyzed the ERP components (P1, N1, P2a, P2p, P3) elicited by the cue stimuli and the early lateralised attentional effect (early directing attention negativity-EDAN). In addition, in order to investigate the topography of the neural mechanisms underlying the cortical activity in each cueing condition, we applied a temporal segmentation procedure. The results showed that the three cueing conditions induced a different strength of activation within the same cortical network. Occipito-parietal regions were involved in the early processing of visual information, followed by an involvement of frontal areas, likely implicated in learning associations. These data confirm the assumption that, in contrast to purely endogenous cues, arrows and eye-gaze induce a very fast attentional shift. However, the similarity of the ERP components and of the topographical cortical maps among conditions suggest that this early orienting of attention is more likely related to an overlearned association mechanism rather than to a real exogenous attentional process. PMID:18926835

  7. QuantWorm: a comprehensive software package for Caenorhabditis elegans phenotypic assays.

    PubMed

    Jung, Sang-Kyu; Aleman-Meza, Boanerges; Riepe, Celeste; Zhong, Weiwei

    2014-01-01

    Phenotypic assays are crucial in genetics; however, traditional methods that rely on human observation are unsuitable for quantitative, large-scale experiments. Furthermore, there is an increasing need for comprehensive analyses of multiple phenotypes to provide multidimensional information. Here we developed an automated, high-throughput computer imaging system for quantifying multiple Caenorhabditis elegans phenotypes. Our imaging system is composed of a microscope equipped with a digital camera and a motorized stage connected to a computer running the QuantWorm software package. Currently, the software package contains one data acquisition module and four image analysis programs: WormLifespan, WormLocomotion, WormLength, and WormEgg. The data acquisition module collects images and videos. The WormLifespan software counts the number of moving worms by using two time-lapse images; the WormLocomotion software computes the velocity of moving worms; the WormLength software measures worm body size; and the WormEgg software counts the number of eggs. To evaluate the performance of our software, we compared the results of our software with manual measurements. We then demonstrated the application of the QuantWorm software in a drug assay and a genetic assay. Overall, the QuantWorm software provided accurate measurements at a high speed. Software source code, executable programs, and sample images are available at www.quantworm.org. Our software package has several advantages over current imaging systems for C. elegans. It is an all-in-one package for quantifying multiple phenotypes. The QuantWorm software is written in Java and its source code is freely available, so it does not require use of commercial software or libraries. It can be run on multiple platforms and easily customized to cope with new methods and requirements. PMID:24416295

  8. Molecular signatures for the phylum Synergistetes and some of its subclades.

    PubMed

    Bhandari, Vaibhav; Gupta, Radhey S

    2012-11-01

    Species belonging to the phylum Synergistetes are poorly characterized. Though the known species display Gram-negative characteristics and the ability to ferment amino acids, no single characteristic is known which can define this group. For eight Synergistetes species, complete genome sequences or draft genomes have become available. We have used these genomes to construct detailed phylogenetic trees for the Synergistetes species and carried out comprehensive analysis to identify molecular markers consisting of conserved signature indels (CSIs) in protein sequences that are specific for either all Synergistetes or some of their sub-groups. We report here identification of 32 CSIs in widely distributed proteins such as RpoB, RpoC, UvrD, GyrA, PolA, PolC, MraW, NadD, PyrE, RpsA, RpsH, FtsA, RadA, etc., including a large >300 aa insert within the RpoC protein, that are present in various Synergistetes species, but except for isolated bacteria, these CSIs are not found in the protein homologues from any other organisms. These CSIs provide novel molecular markers that distinguish the species of the phylum Synergistetes from all other bacteria. The large numbers of other CSIs discovered in this work provide valuable information that supports and consolidates evolutionary relationships amongst the sequenced Synergistetes species. Of these CSIs, seven are specifically present in Jonquetella, Pyramidobacter and Dethiosulfovibrio species indicating a cladal relationship among them, which is also strongly supported by phylogenetic trees. A further 15 CSIs that are only present in Jonquetella and Pyramidobacter indicate a close association between these two species. Additionally, a previously described phylogenetic relationship between the Aminomonas and Thermanaerovibrio species was also supported by 9 CSIs. The strong relationships indicated by the indel analysis provide incentives for the grouping of species from these clades into higher taxonomic groups such as families

  9. Sociopolitical complexity and the bow and arrow in the American Southwest.

    PubMed

    VanPool, Todd L; O'Brien, Michael J

    2013-01-01

    The evolution of sociopolitical complexity, including heightened relations of cooperation and competition among large nonkin groups, has long been a central focus of anthropological research. Anthropologists suggest any number of variables that affect the waxing and waning of complexity and define the precise trajectories that groups take, including population density, subsistence strategies, warfare, the distribution of resources, and trade relationships. Changes in weaponry, here the introduction of the bow and arrow, can have profound implications for population aggregation and density, subsistence and settlement strategies, and access to resources, trade, and warfare.Bingham and Souza provide a general conceptual model for the relationship between complexity and the bow and arrow, arguing that this compound weapon system, whereby smaller projectiles travel at higher speed and are capable of hitting targets more accurately and at greater distances than hand-thrown darts, fundamentally favors the formation of larger groups because it allows for cost-effective means of dealing with conflicts of interest through social coercion, thereby dramatically transforming kin-based social relations. Here we consider the impacts the introduction of the bow and arrow had on sociopolitical complexity in the North American Southwest. PMID:23776047

  10. Biostratigraphy and paleoenvironment of Morrowan (Zone 2) brachiopoda, Bird Spring Group, Arrow Canyon, Clark County, Nevada

    SciTech Connect

    Vaiden, R.C.; Langenheim, R.L.

    1985-02-01

    Comprehensive study of the Morrowan brachiopod faunas of the Bird Spring Group at Arrow Canyon, Clark County, Nevada, is important because the section has been suggested as a stratotype for the base and top of the Pennsylvanian Subsystem and for the Atoka Series. Twenty-three species of brachiopods belonging to 17 genera occur in zone 20 at Arrow Canyon. Many of these also occur in described Morrowan faunas in Wyoming, Colorado, Utah, and New Mexico; but similarities with the Mid-Continent and Appalachian assemblages are less. However, no striking regional differences are evident, and it appears that the North American Morrowan fauna is more or less homogeneous. In contrast to the exotic South American and Arctic elements known from Atokan, Missourian, and Virgilian rocks at Arrow Canyon, no foreign taxa have been noted in zone 20. Microfacies and faunal association indicate four distinct brachiopod-bearing environments; (1) relatively deep water below turbulence with few brachiopods on a soft substrate; (2) somewhat shallower, more turbulent water with many species, of which only a few are represented by large populations, living on a more firm substrate; (3) environments just below the zone of turbulence in which many species of brachiopods are represented by substantial populations on a calcarenitic substrate; and (4) crinoidal bars in the zone of turbulence with a few species represented by relatively few individuals.

  11. Evidence for K{sup +} {r_arrow} {pi}{sup +} {nu}{bar {nu}}

    SciTech Connect

    KETTELL,S.

    1998-12-18

    The first observation of the decay K{sup +} {r_arrow} {pi}{sup +} {nu}{bar {nu}} has been reported. The E787 experiment presented evidence for the K{sup +} {r_arrow} {pi}{sup +} {nu}{bar {nu}} decay, based on the observation of a single clean event from data collected during the 1995 run of the AGS (Alternating Gradient Synchrotron at Brookhaven National Laboratory). The branching ratio indicated by this observation, B(K{sup +} {r_arrow} {pi}{sup +} {nu}{bar {nu}}) = 4.2{sub {minus}3.5}{sup +9.7} x 10{sup {minus}10}, is consistent with the Standard Model expectation although the central experimental value is four times larger. The final E787 data sample, from the 1995--98 runs, should reach a sensitivity of about five times that of the 1995 run alone. A new experiment, E949, has been given scientific approval and should start data collection in 2001. It is expected to achieve a sensitivity of more than an order of magnitude below the prediction of the Standard Model.

  12. Evidence for {Kappa}{sup +} {r_arrow} {pi}{sup +}{nu}{anti {nu}}

    SciTech Connect

    Kettell, S.

    1998-12-31

    The first observation of the decay {Kappa}{sup +} {r_arrow} {pi}{sup +}{nu}{anti {nu}} has been reported. The E787 experiment presented evidence for the {Kappa}{sup +} {r_arrow} {pi}{sup +}{nu}{anti {nu}} decay, based on the observation of a single clean event from data collected during the 1995 run of the AGS (Alternating Gradient Synchrotron at Brookhaven National Laboratory). The branching ratio indicated by this observation, {Beta}({Kappa}{sup +} {r_arrow} {pi}{sup +}{nu}{anti {nu}}) = 4.2{sub {minus}3.5}{sup +9.7} {times} 10{sup {minus}10}, is consistent with the Standard Model expectation although the central experimental value is four times larger. The final E787 data sample, from the 1995--98 runs, should reach a sensitivity of about five times that of the 1995 run alone. A new experiment, E949, has been given scientific approval and should start data collection in 2001. It is expected to achieve a sensitivity of more than an order of magnitude below the prediction of the Standard Model.

  13. Evidence for K{sup +} {r_arrow} {pi}{sup +} {nu}{anti {nu}}

    SciTech Connect

    Kettell, S.; E787 Collaboration; E949 Collaboration

    1998-12-31

    The decay K{sup +} {r_arrow} {pi}{sup +}{nu}{anti {nu}} has been observed for the first time. The E787 experiment has presented evidence for the K{sup +} {r_arrow} {pi}{sup +}{nu}{anti {nu}} decay, based on the observation of a single clean event from data collected during the 1995 run of the AGS (Alternating Gradient Synchrotron at Brookhaven National Laboratory). The branching ratio indicated by this observation, B(K{sup +} {r_arrow} {pi}{sup +}{nu}{anti {nu}}) = 4.2{sub {minus}3.5}{sup +9.7} {times} 10{sup {minus}10}, is consistent with the Standard Model expectation although the central experimental value is four times larger. The final E787 data sample, from the 1995--99 runs, should reach a sensitivity of about eight times that of the 1995 run alone. A new experiment, E949, has been approved to run, starting in the year 2000, and is expected to achieve a sensitivity of more than an order of magnitude below the prediction of the Standard Model.

  14. CP violation in the exclusive decays B{r_arrow}{pi}e{sup +}e{sup {minus}} and B{r_arrow}{rho}e{sup +}e{sup {minus}}

    SciTech Connect

    Krueger, F.; Sehgal, L.M.

    1997-11-01

    As a sequel to the calculation of the CP-violating asymmetry in the decay rates of b{r_arrow}dl{sup +}l{sup {minus}} and {bar b}{r_arrow}{bar d}l{sup +}l{sup {minus}}, we address in this paper the asymmetry in exclusive channels {bar B}{r_arrow}{pi}e{sup +}e{sup {minus}} and {bar B}{r_arrow}{rho}e{sup +}e{sup {minus}}, using form factors from two different models. In the invariant mass region 1GeV{lt}{radical} (s) {lt}M{sub J/{psi}}, the partial width asymmetry in the channel {bar B}{r_arrow}{pi} is {minus}6{percent} ({minus}2{percent}), and that in the channel {bar B}{r_arrow}{rho}, for one choice of form factors, is {minus}5{percent} ({minus}2{percent}), assuming Cabibbo-Kobayashi-Maskawa parameters {eta}=0.34, {rho}=0.3 ({minus}0.3). We also calculate the forward-backward asymmetry A{sub FB} of the e{sup {minus}} in the e{sup +}e{sup {minus}} center-of-mass system, and find average values {l_angle}A{sub FB}{r_angle}{sub {bar B}{r_arrow}{pi}}{equivalent_to}0, {l_angle}A{sub FB}{r_angle}{sub {bar B}{r_arrow}{rho}}={minus}17{percent}, to be compared with the inclusive result {l_angle}A{sub FB}{r_angle}{sub b{r_arrow}d}={minus}9{percent}. There is a CP-violating difference between A{sub FB} and the corresponding asymmetry in the antiparticle channel {bar A}{sub FB}. Formulas are given that are applicable to any flavor-changing neutral current channel {bar B}{r_arrow}P{sub q}(V{sub q})l{sup +}l{sup {minus}}, q=s,d, with m{sub l}{ne}0, including lepton spin effects. An approximate procedure is used to incorporate the {rho}, {omega}, and J/{psi} resonances. {copyright} {ital 1997} {ital The American Physical Society}

  15. From the Flavobacterium genus to the phylum Bacteroidetes: genomic analysis of dnd gene clusters.

    PubMed

    Barbier, Paul; Lunazzi, Aurélie; Fujiwara-Nagata, Erina; Avendaño-Herrera, Ruben; Bernardet, Jean-François; Touchon, Marie; Duchaud, Eric

    2013-11-01

    Phosphorothioate modification of DNA and the corresponding DNA degradation (Dnd) phenotype that occurs during gel electrophoresis are caused by dnd genes. Although widely distributed among Bacteria and Archaea, dnd genes have been found in only very few, taxonomically unrelated, bacterial species so far. Here, we report the presence of dnd genes and their associated Dnd phenotype in two Flavobacterium species. Comparison with dnd gene clusters previously described led us to report a noncanonical genetic organization and to identify a gene likely encoding a hybrid DndE protein. Hence, we showed that dnd genes are also present in members of the family Flavobacteriaceae, a bacterial group occurring in a variety of habitats with an interesting diversity of lifestyle. Two main types of genomic organization of dnd loci were uncovered probably denoting their spreading in the phylum Bacteroidetes via distinct genetic transfer events. PMID:23965156

  16. Microfluidic platform integrated with worm-counting setup for assessing manganese toxicity.

    PubMed

    Zhang, Beibei; Li, Yinbao; He, Qidi; Qin, Jun; Yu, Yanyan; Li, Xinchun; Zhang, Lin; Yao, Meicun; Liu, Junshan; Chen, Zuanguang

    2014-09-01

    We reported a new microfluidic system integrated with worm responders for evaluating the environmental manganese toxicity. The micro device consists of worm loading units, worm observing chambers, and a radial concentration gradient generator (CGG). Eight T-shape worm loading units of the micro device were used to load the exact number of worms into the corresponding eight chambers with the assistance of worm responders and doorsills. The worm responder, as a key component, was employed for performing automated worm-counting assay through electric impedance sensing. This label-free and non-invasive worm-counting technique was applied to the microsystem for the first time. In addition, the disk-shaped CGG can generate a range of stepwise concentrations of the appointed chemical automatically and simultaneously. Due to the scalable architecture of radial CGG, it has the potential to increase the throughput of the assay. Dopaminergic (DAergic) neurotoxicity of manganese on C. elegans was quantitatively assessed via the observation of green fluorescence protein-tagged DAergic neurons of the strain BZ555 on-chip. In addition, oxidative stress triggered by manganese was evaluated by the quantitative fluorescence intensity of the strain CL2166. By scoring the survival ratio and stroke frequency of worms, we characterized the dose- and time-dependent mobility defects of the manganese-exposed worms. Furthermore, we applied the microsystem to investigate the effect of natural antioxidants to protect manganese-induced toxicity. PMID:25538805

  17. Microfluidic platform integrated with worm-counting setup for assessing manganese toxicity

    PubMed Central

    Zhang, Beibei; Li, Yinbao; He, Qidi; Qin, Jun; Yu, Yanyan; Li, Xinchun; Zhang, Lin; Yao, Meicun; Liu, Junshan; Chen, Zuanguang

    2014-01-01

    We reported a new microfluidic system integrated with worm responders for evaluating the environmental manganese toxicity. The micro device consists of worm loading units, worm observing chambers, and a radial concentration gradient generator (CGG). Eight T-shape worm loading units of the micro device were used to load the exact number of worms into the corresponding eight chambers with the assistance of worm responders and doorsills. The worm responder, as a key component, was employed for performing automated worm-counting assay through electric impedance sensing. This label-free and non-invasive worm-counting technique was applied to the microsystem for the first time. In addition, the disk-shaped CGG can generate a range of stepwise concentrations of the appointed chemical automatically and simultaneously. Due to the scalable architecture of radial CGG, it has the potential to increase the throughput of the assay. Dopaminergic (DAergic) neurotoxicity of manganese on C. elegans was quantitatively assessed via the observation of green fluorescence protein-tagged DAergic neurons of the strain BZ555 on-chip. In addition, oxidative stress triggered by manganese was evaluated by the quantitative fluorescence intensity of the strain CL2166. By scoring the survival ratio and stroke frequency of worms, we characterized the dose- and time-dependent mobility defects of the manganese-exposed worms. Furthermore, we applied the microsystem to investigate the effect of natural antioxidants to protect manganese-induced toxicity. PMID:25538805

  18. Diaspore bank of bryophytes in tropical rain forests: the importance of breeding system, phylum and microhabitat.

    PubMed

    Maciel-Silva, Adaíses S; Válio, Ivany Ferraz Marques; Rydin, Håkan

    2012-02-01

    Diaspore banks are crucial for the maintenance and resilience of plant communities, but diaspore banks of bryophytes remain poorly known, especially from tropical ecosystems. This is the first study to focus on the role of diaspore banks of bryophytes in tropical rain forests. Our aim was to test whether microhabitat (substrate type) and species traits (breeding system, phylum) are important in explaining the diaspore bank composition. Using samples cultivated in the laboratory, we assessed the number of species and shoots emerging from bark, decaying wood and soil from two sites of the Atlantic rain forest (montane and sea level) in Brazil by comparing the contribution of species by phylum (mosses, liverworts) and breeding system (monoicous, dioicous). More species emerged from bark (68) and decaying wood (55) than from soil (22). Similar numbers of species were found at both sites. Mosses were more numerous in terms of number of species and shoots, and monoicous species dominated over dioicous species. Substrate pH had only weak effects on shoot emergence. Species commonly producing sporophytes and gemmae had a high contribution to the diaspore banks. These superficial diaspore banks represented the extant vegetation rather well, but held more monoicous species (probably short-lived species) compared to dioicous ones. We propose that diaspore bank dynamics are driven by species traits and microhabitat characteristics, and that short-term diaspore banks of bryophytes in tropical rain forests contribute to fast (re)establishment of species after disturbances and during succession, particularly dioicous mosses investing in asexual reproduction and monoicous mosses investing in sexual reproduction. PMID:21842162

  19. Genomic analysis of Chthonomonas calidirosea, the first sequenced isolate of the phylum Armatimonadetes.

    PubMed

    Lee, Kevin C-Y; Morgan, Xochitl C; Dunfield, Peter F; Tamas, Ivica; McDonald, Ian R; Stott, Matthew B

    2014-07-01

    Most of the lineages of bacteria have remained unknown beyond environmental surveys using molecular markers. Until the recent characterisation of several strains, the phylum Armatimonadetes (formerly known as 'candidate division OP10') was a dominant and globally-distributed lineage within this 'uncultured majority'. Here we report the first Armatimonadetes genome from the thermophile Chthonomonas calidirosea T49(T) and its role as a saccharide scavenger in a geothermal steam-affected soil environment. Phylogenomic analysis indicates T49(T) to be related closely to the phylum Chloroflexi. The predicted genes encoding for carbohydrate transporters (27 carbohydrate ATP-binding cassette transporter-related genes) and carbohydrate-metabolising enzymes (including at least 55 putative enzymes with glycosyl hydrolase domains) within the 3.43 Mb genome help explain its ability to utilise a wide range of carbohydrates as well as its inability to break down extracellular cellulose. The presence of only a single class of branched amino acid transporter appears to be the causative step for the requirement of isoleucine for growth. The genome lacks many commonly conserved operons (for example, lac and trp). Potential causes for this, such as dispersion of functionally related genes via horizontal gene transfer from distant taxa or recent genome recombination, were rejected. Evidence suggests T49(T) relies on the relatively abundant σ-factors, instead of operonic organisation, as the primary means of transcriptional regulation. Examination of the genome with physiological data and environmental dynamics (including interspecific interactions) reveals ecological factors behind the apparent elusiveness of T49(T) to cultivation and, by extension, the remaining 'uncultured majority' that have so far evaded conventional microbiological techniques. PMID:24477196

  20. Plastic parasites: extreme dimorphism creates a taxonomic conundrum in the phylum Microsporidia.

    PubMed

    Stentiford, G D; Bateman, K S; Feist, S W; Chambers, E; Stone, D M

    2013-04-01

    In this paper, we combine field observations of highly statistically significant co-occurrence with histopathological, ultrastructural and molecular phylogenetic analyses, to provide evidence for extreme morphological plasticity in a microsporidium parasite infecting the musculature of marine crabs. The parasite appears to alternate between lineages that culminate in production of either bizarre needle-like spores in the peripheral sarcoplasm of heart and skeletal muscle fibres (reminiscent of Nadelspora canceri infecting Cancer magister) or alternatively, Ameson-like spores with pronounced surface projections, in the skeletal muscles (as for Ameson pulvis, previously described infecting Carcinus maenas). Both lineages occur in direct contact with the cytoplasm of host muscle cells and can exist simultaneously within the same cell. Pathological data appears to reveal a remarkable shift in morphology during pathogenic remodelling of host tissues. Sequence analysis of multiple clones derived from amplification of the ssrRNA gene from infected regions of the heart and skeletal muscles appear to confirm the genetic identity of the two lineages. Furthermore, derived ssrRNA gene sequences are more similar (>99%) to N. canceri than to the coparasite Ameson michaelis infecting Callinectes sapidus (93%). Although molecular phylogenetic data support transfer of A. pulvis into the genus Nadelspora, the expansion in the generic description required to include such widely divergent characteristics is so significant as to be unfeasible within the current taxonomic framework of the phylum Microsporidia. At present, it is preferable to propose that the parasite infecting C. maenas forms a clade with other morphologically diverse but phylogenetically and ecologically similar muscle-infecting microsporidians from marine crustacean hosts. Given the strong evidence for significant plasticity in morphology amongst members of the phylum Microsporidia, novel approaches to phylogeny

  1. Genomic analysis of Chthonomonas calidirosea, the first sequenced isolate of the phylum Armatimonadetes

    PubMed Central

    Lee, Kevin C-Y; Morgan, Xochitl C; Dunfield, Peter F; Tamas, Ivica; McDonald, Ian R; Stott, Matthew B

    2014-01-01

    Most of the lineages of bacteria have remained unknown beyond environmental surveys using molecular markers. Until the recent characterisation of several strains, the phylum Armatimonadetes (formerly known as ‘candidate division OP10') was a dominant and globally-distributed lineage within this ‘uncultured majority'. Here we report the first Armatimonadetes genome from the thermophile Chthonomonas calidirosea T49T and its role as a saccharide scavenger in a geothermal steam-affected soil environment. Phylogenomic analysis indicates T49T to be related closely to the phylum Chloroflexi. The predicted genes encoding for carbohydrate transporters (27 carbohydrate ATP-binding cassette transporter-related genes) and carbohydrate-metabolising enzymes (including at least 55 putative enzymes with glycosyl hydrolase domains) within the 3.43 Mb genome help explain its ability to utilise a wide range of carbohydrates as well as its inability to break down extracellular cellulose. The presence of only a single class of branched amino acid transporter appears to be the causative step for the requirement of isoleucine for growth. The genome lacks many commonly conserved operons (for example, lac and trp). Potential causes for this, such as dispersion of functionally related genes via horizontal gene transfer from distant taxa or recent genome recombination, were rejected. Evidence suggests T49T relies on the relatively abundant σ-factors, instead of operonic organisation, as the primary means of transcriptional regulation. Examination of the genome with physiological data and environmental dynamics (including interspecific interactions) reveals ecological factors behind the apparent elusiveness of T49T to cultivation and, by extension, the remaining ‘uncultured majority' that have so far evaded conventional microbiological techniques. PMID:24477196

  2. Effects of PAHs on the feeding activity of tubificid worms

    SciTech Connect

    Lotufo, G.R.

    1994-12-31

    Sediment collected from a clean site in LA was sieved through a 125{mu}m screen and contaminated with individual PAHs (pyrene, phenanthrene and dibenzofuran) at increasing concentrations using spiking procedure and with a mixture of the 3 PAHs at a single concentration by shell coating. Feeding activity was estimated by defecation rate. Groups of 15 worms were assigned to defecation chambers in 4 replicates per treatment. Feces were collected daily for 10 days, filtered through a 8{mu}m membrane filter and dry weight measured. Results obtained with phenanthrene and mixture of 3 PAHs indicate that PHA bulk concentration of 100 mg/dry kg and higher significantly reduce tubificid ingestion of sediment. Total recovery to control levels occurred when worms exposed to high concentration of PAH were transferred to clean sediment. Total OC was determined to be 3.2 %.

  3. Hi shells, supershells, shell-like objects, and ''worms''

    SciTech Connect

    Heiles, C.

    1984-08-01

    We present photographic representations of the combination of two Hi surveys, so as to eliminate the survey boundaries at Vertical BarbVertical Bar = 10/sup 0/. We also present high-contrast photographs for particular velocities to exhibit weak Hi features. All of these photographs were used to prepare a new list of Hi shells, supershells, and shell-like objects. We discuss the structure of three shell-like objects that are associated with high-velocity gas, and with gas at all velocities that is associated with radio continuum loops I, II, and III. We use spatial filtering to find wiggly gas filaments: ''worms'': crawling away from the galactic plane in the inner Galaxy. The ''worms'' are probably parts of shells that are open at the top; such shells should be good sources of hot gas for the galactic halo.

  4. A worm algorithm for the fully-packed loop model

    NASA Astrophysics Data System (ADS)

    Zhang, Wei; Garoni, Timothy M.; Deng, Youjin

    2009-06-01

    We present a Markov-chain Monte Carlo algorithm of worm type that correctly simulates the fully-packed loop model with n=1 on the honeycomb lattice, and we prove that it is ergodic and has uniform stationary distribution. The honeycomb-lattice fully-packed loop model with n=1 is equivalent to the zero-temperature triangular-lattice antiferromagnetic Ising model, which is fully frustrated and notoriously difficult to simulate. We test this worm algorithm numerically and estimate the dynamic exponent z=0.515(8). We also measure several static quantities of interest, including loop-length and face-size moments. It appears numerically that the face-size moments are governed by the magnetic dimension for percolation.

  5. Genome size and chromosome number in velvet worms (Onychophora).

    PubMed

    Jeffery, Nicholas W; Oliveira, Ivo S; Gregory, T Ryan; Rowell, David M; Mayer, Georg

    2012-12-01

    The Onychophora (velvet worms) represents a small group of invertebrates (~180 valid species), which is commonly united with Tardigrada and Arthropoda in a clade called Panarthropoda. As with the majority of invertebrate taxa, genome size data are very limited for the Onychophora, with only one previously published estimate. Here we use both flow cytometry and Feulgen image analysis densitometry to provide genome size estimates for seven species of velvet worms from both major subgroups, Peripatidae and Peripatopsidae, along with karyotype data for each species. Genome sizes in these species range from roughly 5-19 pg, with densitometric estimates being slightly larger than those obtained by flow cytometry for all species. Chromosome numbers range from 2n = 8 to 2n = 54. No relationship is evident between genome size, chromosome number, or reproductive mode. Various avenues for future genomic research are presented based on these results. PMID:23307271

  6. Genome sequence of Victivallis vadensis ATCC BAA-548, an anaerobic bacterium from the phylum Lentisphaerae, isolated from the human gastro-intestinal tract

    SciTech Connect

    Van Passel, Mark W.J.; Kant, Ravi; Palva, Airi; Lucas, Susan; Copeland, A; Lapidus, Alla L.; Glavina Del Rio, Tijana; Dalin, Eileen; Tice, Hope; Bruce, David; Goodwin, Lynne A.; Pitluck, Sam; Davenport, Karen W.; Sims, David; Detter, J. Chris; Han, Cliff; Larimer, Frank W; Land, Miriam L; Hauser, Loren John; Kyrpides, Nikos C; Ovchinnikova, Galina; Richardson, Paul; De Vos, Willem M.; Smidt, Hauke; Zoetendal, Erwin G.

    2011-01-01

    Victivallis vadensis ATCC BAA-548 represents the first cultured representative from the novel phylum Lentisphaerae, a deep-branching bacterial lineage. Few cultured bacteria from this phylum are known, and V. vadensis therefore represents an important organism for evolutionary studies. V. vadensis is a strictly anaerobic sugar-fermenting isolate from the human gastro-intestinal tract.

  7. WormBase 2012: more genomes, more data, new website.

    PubMed

    Yook, Karen; Harris, Todd W; Bieri, Tamberlyn; Cabunoc, Abigail; Chan, Juancarlos; Chen, Wen J; Davis, Paul; de la Cruz, Norie; Duong, Adrian; Fang, Ruihua; Ganesan, Uma; Grove, Christian; Howe, Kevin; Kadam, Snehalata; Kishore, Ranjana; Lee, Raymond; Li, Yuling; Muller, Hans-Michael; Nakamura, Cecilia; Nash, Bill; Ozersky, Philip; Paulini, Michael; Raciti, Daniela; Rangarajan, Arun; Schindelman, Gary; Shi, Xiaoqi; Schwarz, Erich M; Ann Tuli, Mary; Van Auken, Kimberly; Wang, Daniel; Wang, Xiaodong; Williams, Gary; Hodgkin, Jonathan; Berriman, Matthew; Durbin, Richard; Kersey, Paul; Spieth, John; Stein, Lincoln; Sternberg, Paul W

    2012-01-01

    Since its release in 2000, WormBase (http://www.wormbase.org) has grown from a small resource focusing on a single species and serving a dedicated research community, to one now spanning 15 species essential to the broader biomedical and agricultural research fields. To enhance the rate of curation, we have automated the identification of key data in the scientific literature and use similar methodology for data extraction. To ease access to the data, we are collaborating with journals to link entities in research publications to their report pages at WormBase. To facilitate discovery, we have added new views of the data, integrated large-scale datasets and expanded descriptions of models for human disease. Finally, we have introduced a dramatic overhaul of the WormBase website for public beta testing. Designed to balance complexity and usability, the new site is species-agnostic, highly customizable, and interactive. Casual users and developers alike will be able to leverage the public RESTful application programming interface (API) to generate custom data mining solutions and extensions to the site. We report on the growth of our database and on our work in keeping pace with the growing demand for data, efforts to anticipate the requirements of users and new collaborations with the larger science community. PMID:22067452

  8. Polyanhydride Nanoparticle Delivery Platform Dramatically Enhances Killing of Filarial Worms

    PubMed Central

    Binnebose, Andrea M.; Haughney, Shannon L.; Martin, Richard; Imerman, Paula M.; Narasimhan, Balaji; Bellaire, Bryan H.

    2015-01-01

    Filarial diseases represent a significant social and economic burden to over 120 million people worldwide and are caused by endoparasites that require the presence of symbiotic bacteria of the genus Wolbachia for fertility and viability of the host parasite. Targeting Wolbachia for elimination is a therapeutic approach that shows promise in the treatment of onchocerciasis and lymphatic filariasis. Here we demonstrate the use of a biodegradable polyanhydride nanoparticle-based platform for the co-delivery of the antibiotic doxycycline with the antiparasitic drug, ivermectin, to reduce microfilarial burden and rapidly kill adult worms. When doxycycline and ivermectin were co-delivered within polyanhydride nanoparticles, effective killing of adult female Brugia malayi filarial worms was achieved with approximately 4,000-fold reduction in the amount of drug used. Additionally the time to death of the macrofilaria was also significantly reduced (five-fold) when the anti-filarial drug cocktail was delivered within polyanhydride nanoparticles. We hypothesize that the mechanism behind this dramatically enhanced killing of the macrofilaria is the ability of the polyanhydride nanoparticles to behave as a Trojan horse and penetrate the cuticle, bypassing excretory pumps of B. malayi, and effectively deliver drug directly to both the worm and Wolbachia at high enough microenvironmental concentrations to cause death. These provocative findings may have significant consequences for the reduction in the amount of drug and the length of treatment required for filarial infections in terms of patient compliance and reduced cost of treatment. PMID:26496201

  9. Polyanhydride Nanoparticle Delivery Platform Dramatically Enhances Killing of Filarial Worms.

    PubMed

    Binnebose, Andrea M; Haughney, Shannon L; Martin, Richard; Imerman, Paula M; Narasimhan, Balaji; Bellaire, Bryan H

    2015-01-01

    Filarial diseases represent a significant social and economic burden to over 120 million people worldwide and are caused by endoparasites that require the presence of symbiotic bacteria of the genus Wolbachia for fertility and viability of the host parasite. Targeting Wolbachia for elimination is a therapeutic approach that shows promise in the treatment of onchocerciasis and lymphatic filariasis. Here we demonstrate the use of a biodegradable polyanhydride nanoparticle-based platform for the co-delivery of the antibiotic doxycycline with the antiparasitic drug, ivermectin, to reduce microfilarial burden and rapidly kill adult worms. When doxycycline and ivermectin were co-delivered within polyanhydride nanoparticles, effective killing of adult female Brugia malayi filarial worms was achieved with approximately 4,000-fold reduction in the amount of drug used. Additionally the time to death of the macrofilaria was also significantly reduced (five-fold) when the anti-filarial drug cocktail was delivered within polyanhydride nanoparticles. We hypothesize that the mechanism behind this dramatically enhanced killing of the macrofilaria is the ability of the polyanhydride nanoparticles to behave as a Trojan horse and penetrate the cuticle, bypassing excretory pumps of B. malayi, and effectively deliver drug directly to both the worm and Wolbachia at high enough microenvironmental concentrations to cause death. These provocative findings may have significant consequences for the reduction in the amount of drug and the length of treatment required for filarial infections in terms of patient compliance and reduced cost of treatment. PMID:26496201

  10. WormBase 2016: expanding to enable helminth genomic research

    PubMed Central

    Howe, Kevin L.; Bolt, Bruce J.; Cain, Scott; Chan, Juancarlos; Chen, Wen J.; Davis, Paul; Done, James; Down, Thomas; Gao, Sibyl; Grove, Christian; Harris, Todd W.; Kishore, Ranjana; Lee, Raymond; Lomax, Jane; Li, Yuling; Muller, Hans-Michael; Nakamura, Cecilia; Nuin, Paulo; Paulini, Michael; Raciti, Daniela; Schindelman, Gary; Stanley, Eleanor; Tuli, Mary Ann; Van Auken, Kimberly; Wang, Daniel; Wang, Xiaodong; Williams, Gary; Wright, Adam; Yook, Karen; Berriman, Matthew; Kersey, Paul; Schedl, Tim; Stein, Lincoln; Sternberg, Paul W.

    2016-01-01

    WormBase (www.wormbase.org) is a central repository for research data on the biology, genetics and genomics of Caenorhabditis elegans and other nematodes. The project has evolved from its original remit to collect and integrate all data for a single species, and now extends to numerous nematodes, ranging from evolutionary comparators of C. elegans to parasitic species that threaten plant, animal and human health. Research activity using C. elegans as a model system is as vibrant as ever, and we have created new tools for community curation in response to the ever-increasing volume and complexity of data. To better allow users to navigate their way through these data, we have made a number of improvements to our main website, including new tools for browsing genomic features and ontology annotations. Finally, we have developed a new portal for parasitic worm genomes. WormBase ParaSite (parasite.wormbase.org) contains all publicly available nematode and platyhelminth annotated genome sequences, and is designed specifically to support helminth genomic research. PMID:26578572

  11. Comparative Genomics of Candidate Phylum TM6 Suggests That Parasitism Is Widespread and Ancestral in This Lineage

    PubMed Central

    Yeoh, Yun Kit; Sekiguchi, Yuji; Parks, Donovan H.; Hugenholtz, Philip

    2016-01-01

    Candidate phylum TM6 is a major bacterial lineage recognized through culture-independent rRNA surveys to be low abundance members in a wide range of habitats; however, they are poorly characterized due to a lack of pure culture representatives. Two recent genomic studies of TM6 bacteria revealed small genomes and limited gene repertoire, consistent with known or inferred dependence on eukaryotic hosts for their metabolic needs. Here, we obtained additional near-complete genomes of TM6 populations from agricultural soil and upflow anaerobic sludge blanket reactor metagenomes which, together with the two publicly available TM6 genomes, represent seven distinct family level lineages in the TM6 phylum. Genome-based phylogenetic analysis confirms that TM6 is an independent phylum level lineage in the bacterial domain, possibly affiliated with the Patescibacteria superphylum. All seven genomes are small (1.0–1.5 Mb) and lack complete biosynthetic pathways for various essential cellular building blocks including amino acids, lipids, and nucleotides. These and other features identified in the TM6 genomes such as a degenerated cell envelope, ATP/ADP translocases for parasitizing host ATP pools, and protein motifs to facilitate eukaryotic host interactions indicate that parasitism is widespread in this phylum. Phylogenetic analysis of ATP/ADP translocase genes suggests that the ancestral TM6 lineage was also parasitic. We propose the name Dependentiae (phyl. nov.) to reflect dependence of TM6 bacteria on host organisms. PMID:26615204

  12. Comparative Genomics of Candidate Phylum TM6 Suggests That Parasitism Is Widespread and Ancestral in This Lineage.

    PubMed

    Yeoh, Yun Kit; Sekiguchi, Yuji; Parks, Donovan H; Hugenholtz, Philip

    2016-04-01

    Candidate phylum TM6 is a major bacterial lineage recognized through culture-independent rRNA surveys to be low abundance members in a wide range of habitats; however, they are poorly characterized due to a lack of pure culture representatives. Two recent genomic studies of TM6 bacteria revealed small genomes and limited gene repertoire, consistent with known or inferred dependence on eukaryotic hosts for their metabolic needs. Here, we obtained additional near-complete genomes of TM6 populations from agricultural soil and upflow anaerobic sludge blanket reactor metagenomes which, together with the two publicly available TM6 genomes, represent seven distinct family level lineages in the TM6 phylum. Genome-based phylogenetic analysis confirms that TM6 is an independent phylum level lineage in the bacterial domain, possibly affiliated with the Patescibacteria superphylum. All seven genomes are small (1.0-1.5 Mb) and lack complete biosynthetic pathways for various essential cellular building blocks including amino acids, lipids, and nucleotides. These and other features identified in the TM6 genomes such as a degenerated cell envelope, ATP/ADP translocases for parasitizing host ATP pools, and protein motifs to facilitate eukaryotic host interactions indicate that parasitism is widespread in this phylum. Phylogenetic analysis of ATP/ADP translocase genes suggests that the ancestral TM6 lineage was also parasitic. We propose the name Dependentiae (phyl. nov.) to reflect dependence of TM6 bacteria on host organisms. PMID:26615204

  13. Clinical assessment of coded Unani formulation D-worm and mebandazole for the treatment of hook worm, roundworm and whip worm.

    PubMed

    Ahmad, Khalil; Usmanghani, Khan; Akhtar, Naveed; Nazar, Halima

    2015-11-01

    A case control, multicenter, prospective randomized two arm parallel group clinical trials was conducted on 190 patients. The main objective of this study is to provide comparative efficacy results of both trialed medicines. The comparison was done in between herbal medicine D-Worm and Mebandazole allopathic drug for the treatment of helminthiasis. All the rules of GCP (Good Clinical Practices) were followed including clinical history, clinical presentation, examination findings and stool tests. Stool D/R and Parasite antigen tests were performed before and after treatment. The comparison of symptoms were also done including the improvement in abdominal pain, worms in stool, anal itching, nausea and vomiting, loss of appetite, and fatigue etc. The data on clinical proforma was gathered and subjected to statistical analysis. Parasite specific antigen test and stool D/R is considered as gold standard test for the diagnosis and confirmation of helminthes infection. Different parameter i.e. age, sex, and other clinical sign and symptoms were studied and compared between two treatment groups (Control and Test groups) at baseline and end of therapeutic application. Consent of patient was taken at first before the start of examination. Majority of the patients (90%) included in this study group get cured after herbal treatment. The statistical analysis used for the assessment of the effect of the treatment also showed significant improvement after treatment. PMID:26639505

  14. Form factors of the transitions {gamma}{sup *}{pi}{sup 0} {r_arrow} {gamma} and {gamma}{sup *}{eta}{r_arrow}{gamma}

    SciTech Connect

    Afanasev, A.

    1994-04-01

    The author discusses possibilities to study {gamma}*{pi}{sup 0} and {gamma}*{eta} {r_arrow} {gamma} transition form factors at CEBAF energies. The author shows that for 4 GeV electron beam, these form factors can be measured at CEBAF for the 4-momentum transfers Q{sup 2} {le} 2.5 (GeV/c){sup 2} using virtual Compton scattering on the proton and nuclear target in the kinematic regime of low momentum transfers to the target. These measurements can be extended to Q{sup 2} {le} 4.0 (GeV/c){sup 2} using the electron beam with the energy 6 GeV.

  15. Refining the phylum Chlorobi by resolving the phylogeny and metabolic potential of the representative of a deeply branching, uncultivated lineage.

    PubMed

    Hiras, Jennifer; Wu, Yu-Wei; Eichorst, Stephanie A; Simmons, Blake A; Singer, Steven W

    2016-04-01

    Recent studies have expanded the phylum Chlorobi, demonstrating that the green sulfur bacteria (GSB), the original cultured representatives of the phylum, are a part of a broader lineage whose members have more diverse metabolic capabilities that overlap with members of the phylum Bacteroidetes. The 16S rRNA gene of an uncultivated clone, OPB56, distantly related to the phyla Chlorobi and Bacteroidetes, was recovered from Obsidian Pool in Yellowstone National Park; however, the detailed phylogeny and function of OPB56 and related clones have remained unknown. Culturing of thermophilic bacterial consortia from compost by adaptation to grow on ionic-liquid pretreated switchgrass provided a consortium in which one of the most abundant members, NICIL-2, clustered with OPB56-related clones. Phylogenetic analysis using the full-length 16S rRNA gene from NICIL-2 demonstrated that it was part of a monophyletic clade, referred to as OPB56, distinct from the Bacteroidetes and Chlorobi. A near complete draft genome (>95% complete) was recovered from metagenomic data from the culture adapted to grow on ionic-liquid pretreated switchgrass using an automated binning algorithm, and this genome was used for marker gene-based phylogenetic analysis and metabolic reconstruction. Six additional genomes related to NICIL-2 were reconstructed from metagenomic data sets obtained from thermal springs at Yellowstone National Park and Nevada Great Boiling Spring. In contrast to the 16S rRNA gene phylogenetic analysis, protein phylogenetic analysis was most consistent with the clustering of the Chlorobea, Ignavibacteria and OPB56 into a single phylum level clade. Metabolic reconstruction of NICIL-2 demonstrated a close linkage with the class Ignavibacteria and the family Rhodothermaceae, a deeply branching Bacteroidetes lineage. The combined phylogenetic and functional analysis of the NICIL-2 genome has refined the membership in the phylum Chlorobi and emphasized the close evolutionary and

  16. Complete leading order analysis in Chiral Perturbation Theory of the decays K{sub L}{r_arrow}{gamma}{gamma} and K{sub L}{r_arrow}l{sub +}l{sub {minus}}{gamma}

    SciTech Connect

    J. L. Goity; Longzhe Zhang

    1997-02-01

    The decays K{sub L}{r_arrow}{gamma}{gamma} and K{sub L}{r_arrow}l{sup +}l{sup {minus}}{gamma} are studied at the leading order p{sup 6} in Chiral Perturbation Theory. One-loop contributions stemming from the odd intrinsic parity {vert_bar}{Delta}S{vert_bar}=1 effective Lagrangian of order p{sup 4} are included and shown to be of possible relevance. They affect the decay K{sub L}{r_arrow}{gamma}{gamma} adding to the usual pole terms a piece free of counterterm uncertainties. In the case of the K{sub L}{r_arrow}l{sup +}l{sup {minus}}{gamma} decays the dependence of the form factor on the dilepton invariant mass requires a counterterm. The form factor may receive a sizeable contribution from chiral logarithms. Including considerations from the K{sub L}{r_arrow}{pi}{sup +}{pi}{sup {minus}}{gamma} direct emission amplitude, the authors obtain two consistent scenarios. In one scenario the long distance contributions from the one-loop terms are important, while in the other they are marginal. In both cases the counterterm is shown to be significant.

  17. A 170 J electron beam pumped XeF(C{r_arrow}A) laser

    SciTech Connect

    Litzenberger, L.N.; Smith, M.J.

    1995-03-01

    A pulse output energy of 170 J has been achieved from an XeF (C{r_arrow}A) laser system, pumped by a pair of counterpropagating, three-meter-long electron beams. This represents a record for all types of pumping, for this excimer system. Energy was extracted from a volume of {approximately}100 L, using a free-running stable oscillator. No evidence of laser oscillations on the competing XeF(B{r_arrow}X) transition was observed. Within the extraction volume the laser gas was pumped at a rate of 140 kW/cm{sup 3} (time average value), for a period of 1.7 {mu}s. The optical cavity was folded, giving a gain length of 6 m. The optical pulse duration was 0.8 {mu}s (full width at half maximum), and the observed flux buildup time of {approximately}1 {mu}s was consistent with modeling and a measurement of the net gain. The specific output energy was 1.7 J/L which is comparable to that achieved in previous, small scale experiments at somewhat higher pump rate. The results confirm the volumetric scalability of the electron beam pumped XeF(C{r_arrow}A) laser system to high output energy per pulse, and the feasibility of operating this system at a low electron beam pump rate which relaxes constraints on the design of the electron gun and pulse power subsystems in a high output energy device. Means for extending the laser pulse duration and increasing the output energy of the specific test device are discussed. An output energy of {approximately}1,000 J is projected for an optimized gas cell width, for full size resonator mirrors, and with injection.

  18. Analysis of trace elements in the giant panda and arrow bamboo

    NASA Astrophysics Data System (ADS)

    Wang, Nengming; Chen, Suqing; Chen, Jianxuan; Zhang, Dazhong; Feng, Wenhe

    1987-04-01

    Trace elements from the giant panda including hair, liver, kidney, ovary and testis, were determined by PIXE. Comparative studies of the elemental contents in hair, liver and kidney from epileptic and normal giant pandas were performed respectively. The differences in the elemental contents of leaf, stalk, and bamboo shoots from normal and withered arrows were determined. For this research work a Van de Graaff electrostatic accelerator and a Si(Li) semiconductor spectrometer at the Institute of Nuclear Science and Technology of Sichuan University were employed.

  19. Target asymmetry measurements of {gamma} p{r_arrow}{pi} {sup +}n with Phoenics at ELSA

    SciTech Connect

    Althoff, K.; Anton, G.; Arends, J.; Beulertz, W.; Bock, A.; Breuer, M.; Detemple, P.; Dutz, H.; Gehring, R.; Gemander, M.; Goertz, S.; Helbing, K.; Hey, J.; Kraemer, D.; Meyer, W.; Noeldeke, G.; Reicherz, G.; Thomas, A.; Zucht, B.

    1995-05-10

    The target asymmetry T of the reaction {gamma} p{r_arrow}{pi} {sup +}n has been measured with the Phoenics detector in combination with the Bonn frozen spin target at ELSA. For the first time the polarization observable T has been determined simultaneously over a large photon energy range (E{sub {gamma}}=220--800 MeV) and pion angles ({Theta}{sub {pi}}{sup m}=35{degree}--135{degree}) with a tagged photon facility. {copyright} {ital 1995} {ital American} {ital Institute} {ital of} {ital Physics}.

  20. Arrow-wing supersonic cruise aircraft structural design concepts evaluation. Volume 1: Sections 1 through 6

    NASA Technical Reports Server (NTRS)

    Sakata, I. F.; Davis, G. W.

    1975-01-01

    The structural approach best suited for the design of a Mach 2.7 arrow-wing supersonic cruise aircraft was investigated. Results, procedures, and principal justification of results are presented. Detailed substantiation data are given. In general, each major analysis is presented sequentially in separate sections to provide continuity in the flow of the design concepts analysis effort. In addition to the design concepts evaluation and the detailed engineering design analyses, supporting tasks encompassing: (1) the controls system development; (2) the propulsion-airframe integration study; and (3) the advanced technology assessment are presented.

  1. Advanced structures technology applied to a supersonic cruise arrow-wing configuration

    NASA Technical Reports Server (NTRS)

    Sakata, I. F.; Davis, G. W.

    1976-01-01

    The application of advanced technology to a promising aerodynamic configuration was explored to investigate the improved payload range characteristics over the configuration postulated during the National SST Program. The results of an analytical study performed to determine the best structural approach for design of a Mach number 2.7 arrow-wing supersonic cruise aircraft are highlighted. The data conducted under the auspices of the Structures Directorate of the National Aeronautics and Space Administration, Langley Research Center, established firm technical bases from which further trend studies were conducted to quantitatively assess the benefits and feasibility of using advanced structures technology to arrive at a viable advanced supersonic cruise aircraft.

  2. Arrow-wing supersonic cruise aircraft structural design concepts evaluation. Volume 3: Sections 12 through 14

    NASA Technical Reports Server (NTRS)

    Sakata, I. F.; Davis, G. W.

    1975-01-01

    The design of an economically viable supersonic cruise aircraft requires the lowest attainable structural-mass fraction commensurate with the selected near-term structural material technology. To achieve this goal of minimum structural-mass fraction, various combinations of promising wing and fuselage primary structure were analyzed for the load-temperature environment applicable to the arrow wing configuration. This analysis was conducted in accordance with the design criteria specified and included extensive use of computer-aided analytical methods to screen the candidate concepts and select the most promising concepts for the in-depth structural analysis.

  3. Transonic pressure measurements and comparison of theory to experiment for three arrow-wing configurations

    NASA Technical Reports Server (NTRS)

    Manro, M. E.

    1982-01-01

    Wind tunnel tests of arrow-wing body configurations consisting of flat, twisted, and cambered twisted wings, as well as a variety of leading and trailing edge control surface deflections, were conducted at Mach numbers from 0.4 to 1.05 to provide an experimental pressure data base for comparison with theoretical methods. Theory to experiment comparisons of detailed pressure distributions were made using state of the art attached flow methods. Conditions under which these theories are valid for these wings are presented.

  4. Arrow-wing supersonic cruise aircraft structural design concepts evaluation. Volume 4: Sections 15 through 21

    NASA Technical Reports Server (NTRS)

    Sakata, I. F.; Davis, G. W.

    1975-01-01

    The analyses performed to provide structural mass estimates for the arrow wing supersonic cruise aircraft are presented. To realize the full potential for structural mass reduction, a spectrum of approaches for the wing and fuselage primary structure design were investigated. The objective was: (1) to assess the relative merits of various structural arrangements, concepts, and materials; (2) to select the structural approach best suited for the Mach 2.7 environment; and (3) to provide construction details and structural mass estimates based on in-depth structural design studies. Production costs, propulsion-airframe integration, and advanced technology assessment are included.

  5. Irreversibility and the Arrow of Time in a Quenched Quantum System

    NASA Astrophysics Data System (ADS)

    Batalhão, T. B.; Souza, A. M.; Sarthour, R. S.; Oliveira, I. S.; Paternostro, M.; Lutz, E.; Serra, R. M.

    2015-11-01

    Irreversibility is one of the most intriguing concepts in physics. While microscopic physical laws are perfectly reversible, macroscopic average behavior has a preferred direction of time. According to the second law of thermodynamics, this arrow of time is associated with a positive mean entropy production. Using a nuclear magnetic resonance setup, we measure the nonequilibrium entropy produced in an isolated spin-1 /2 system following fast quenches of an external magnetic field. We experimentally demonstrate that it is equal to the entropic distance, expressed by the Kullback-Leibler divergence, between a microscopic process and its time reversal. Our result addresses the concept of irreversibility from a microscopic quantum standpoint.

  6. Cellerator: extending a computer algebra system to include biochemical arrows for signal transduction simulations

    NASA Technical Reports Server (NTRS)

    Shapiro, Bruce E.; Levchenko, Andre; Meyerowitz, Elliot M.; Wold, Barbara J.; Mjolsness, Eric D.

    2003-01-01

    Cellerator describes single and multi-cellular signal transduction networks (STN) with a compact, optionally palette-driven, arrow-based notation to represent biochemical reactions and transcriptional activation. Multi-compartment systems are represented as graphs with STNs embedded in each node. Interactions include mass-action, enzymatic, allosteric and connectionist models. Reactions are translated into differential equations and can be solved numerically to generate predictive time courses or output as systems of equations that can be read by other programs. Cellerator simulations are fully extensible and portable to any operating system that supports Mathematica, and can be indefinitely nested within larger data structures to produce highly scaleable models.

  7. Irreversibility and the Arrow of Time in a Quenched Quantum System.

    PubMed

    Batalhão, T B; Souza, A M; Sarthour, R S; Oliveira, I S; Paternostro, M; Lutz, E; Serra, R M

    2015-11-01

    Irreversibility is one of the most intriguing concepts in physics. While microscopic physical laws are perfectly reversible, macroscopic average behavior has a preferred direction of time. According to the second law of thermodynamics, this arrow of time is associated with a positive mean entropy production. Using a nuclear magnetic resonance setup, we measure the nonequilibrium entropy produced in an isolated spin-1/2 system following fast quenches of an external magnetic field. We experimentally demonstrate that it is equal to the entropic distance, expressed by the Kullback-Leibler divergence, between a microscopic process and its time reversal. Our result addresses the concept of irreversibility from a microscopic quantum standpoint. PMID:26588367

  8. Supersonic pressure measurements and comparison of theory to experiment for an arrow-wing configuration

    NASA Technical Reports Server (NTRS)

    Manro, M. E.

    1976-01-01

    A wind tunnel test of an arrow-wing-body configuration consisting of flat and twisted wings, as well as leading- and trailing-edge control surface deflections, was conducted at Mach numbers from 1.54 to 2.50 to provide an experimental pressure data base for comparison with theoretical methods. Theory-to-experiment comparisons of detailed pressure distributions were made using a state-of-the-art inviscid flow, constant-pressure-panel method. Emphasis was on conditions under which this theory is valid for both flat and twisted wings.

  9. Search for the Rare Decay barB^0 arrow D^*0γ

    NASA Astrophysics Data System (ADS)

    Bauer, Johannes

    2003-04-01

    We report on the search for the rare decay barB^0 arrow D^*0γ, which is dominated by a W-exchange and has not yet been observed. This analysis is based on a data sample comprised of 88.9× 10^6 B\\overline B pairs collected with the BABAR detector at the PEP-II asymmetric B Factory at SLAC. ^* Work supported by U.S. Dept. of Energy grant DE-FG05-91ER40622.

  10. Oocyte maturation and fertilization in marine nemertean worms: using similar sorts of signaling pathways as in mammals, but often with differing results.

    PubMed

    Stricker, Stephen A; Cline, Cory; Goodrich, David

    2013-08-01

    In marine worms belonging to the phylum Nemertea, oocyte maturation and fertilization are regulated by the same general kinds of signals that control such processes in mammals. However, unlike mammalian oocytes that develop within follicles, nemertean oocytes characteristically lack a surrounding sheath of follicle cells and often respond differently to maturation-related cues than do mammalian oocytes. For example, elevators of cyclic adenosine monophosphate (cAMP) or cyclic guanosine monophosphate (cGMP) levels promote the resumption of meiotic maturation (=germinal vesicle breakdown, GVBD) in nemertean oocytes, whereas increasing intraoocytic cAMP and cGMP typically blocks GVBD in mammals. Similarly, AMP-activated kinase (AMPK) signaling keeps nemertean oocytes from maturing, but in mouse oocytes, AMPK activation triggers GVBD. In addition, protein kinase C (PKC) activity is required for seawater-induced GVBD in nemerteans, whereas some PKCs have been shown to inhibit GVBD in mammals. Furthermore, although fertilization causes both types of oocytes to reorganize their endoplasmic reticulum and generate calcium oscillations that can involve soluble sperm factor activity and inositol 1,4,5-trisphosphate signaling, some discrepancies in the spatiotemporal patterns and underlying mechanisms of fertilization are also evident in nemerteans versus mammals. Thus, to characterize differences and similarities in gamete biology more fully, aspects of oocyte maturation and fertilization in marine nemertean worms are reviewed and briefly compared with related findings that have been published for mammalian oocytes. In addition, possible causes of the alternative responses displayed by oocytes in these two animal groups are addressed. PMID:23995739

  11. Spatially resolved X-ray diffraction phase mapping and {alpha} {r_arrow} {beta} {r_arrow} {alpha} transformation kinetics in the heat-affected zone of commercially pure titanium arc welds

    SciTech Connect

    Elmer, J.W.; Wong, J.; Ressler, T.

    1998-11-01

    Spatially resolved X-ray diffraction (SRXRD) is used to map the {alpha} {r_arrow} {beta} {r_arrow} {alpha} phase transformation in the heat-affected zone (HAZ) of commercially pure titanium gas tungsten arc welds. In situ SRXRD experiments were conducted using a 180-{micro}m-diameter X-ray beam at the Stanford Synchrotron Radiation Laboratory (SSRL) (Stanford, CA) to probe the phases present in the HAZ of a 1.9 kW weld moving at 1.1 mm/s. Results of sequential linear X-ray diffraction scans made perpendicular to the weld direction were combined to construct a phase transformation map around the liquid weld pool. This map identifies six HAZ microstructural regions between the liquid weld pool and the base metal: (1) {alpha}-Ti that is undergoing annealing and recrystallization; (2) completely recrystallized {alpha}-Ti; (3) partially transformed {alpha}-Ti, where {alpha}-Ti and {beta}-Ti coexist; (4) single-phase {beta}-Ti; (5) back-transformed {alpha}Ti; and (6) recrystallized {alpha}-Ti plus back-transformed {alpha}-Ti. Although the microstructure consisted predominantly of {alpha}-Ti, both prior to and after the weld, the crystallographically textured starting material was altered during welding to produce different {alpha}-Ti textures within the resulting HAZ. Based on the travel speed of the weld, the {alpha} {r_arrow} {beta} transformation was measured to take 1.83 seconds during heat, while the {beta} {r_arrow} {alpha} transformation was measured to take 0.91 seconds during cooling. The {alpha} {r_arrow} {beta} transformation was characterized to be dominated by long-range diffusion growth on the leading (heating) side of the weld, while the {beta} {r_arrow} {alpha} transformation was characterized to be predominantly massive on the trailing (cooling) side of the weld, with a massive growth rate on the order of 100 {micro}m/s.

  12. A Horsehair Worm, Gordius sp. (Nematomorpha: Gordiida), Passed in a Canine Feces

    PubMed Central

    Hong, Eui-Ju; Sim, Cheolho; Chae, Joon-Seok; Kim, Hyeon-Cheol; Park, Jinho; Choi, Kyoung-Seong; Yu, Do-Hyeon; Yoo, Jae-Gyu; Park, Bae-Keun

    2015-01-01

    Nematomorpha, horsehair or Gordian worms, include about 300 freshwater species in 22 genera (Gordiida) and 5 marine species in 1 marine genus (Nectonema). They are parasitic in arthropods during their juvenile stage. In the present study, the used gordian worm was found in the feces of a dog (5-month old, male) in July 2014. Following the worm analysis using light and scanning electron microscopes, the morphological classification was re-evaluated with molecular analysis. The worm was determined to be a male worm having a bi-lobed tail and had male gonads in cross sections. It was identified as Gordius sp. (Nematomorpha: Gordiidae) based on the characteristic morphologies of cross sections and areole on the cuticle. DNA analysis on 18S rRNA partial sequence arrangements was also carried out, and the gordiid worm was assumed to be close to the genus Gordius based on a phylogenic tree analysis. PMID:26797439

  13. A Comparison Study of the Exclusive Decays barB^0 arrow D^*+ l^- barνl and B^- arrow D^*0 l^- barνl Using Partial Reconstruction.

    NASA Astrophysics Data System (ADS)

    Godang, Romulus; Kinoshita, Kay

    2000-04-01

    Using 2.81 fb-1 of Υ(4S) data collected with the CLEO II detector at the Cornell Electron Storage Ring, we compare the exclusive decays barB^0 arrow D^*+ l^- barνl and B^- arrow D^*0 l^- barν_l. We use a partial reconstruction method, where only a lepton and soft pion are detected and the D is not reconstructed. The method yields sufficient statistics to allow a reasonable comparison as a function of pion momentum. A preliminary result of the charged to neutral B production ratio at the Υ(4S) will be presented.

  14. Towards global Guinea worm eradication in 2015: the experience of South Sudan.

    PubMed

    Awofeso, Niyi

    2013-08-01

    For centuries, the Guinea worm parasite (Dracunculus medinensis) has caused disabling misery, infecting people who drink stagnant water contaminated with the worm's larvae. In 2012, there were 542 cases of Guinea worm reported globally, of which 521 (96.1%) were reported in South Sudan. Protracted civil wars, an inadequate workforce, neglect of potable water provision programs, suboptimal Guinea worm surveillance and case containment, and fragmented health systems account for many of the structural and operational factors encumbering South Sudan's Guinea worm eradication efforts. This article reviews the impacts of six established Guinea worm control strategies in South Sudan: (1) surveillance to determine actual caseload distribution and trends in response to control measures; (2) educating community members from whom worms are emerging to avoid immersing affected parts in sources of drinking water; (3) filtering potentially contaminated drinking water using cloth filters or filtered drinking straws; (4) treating potentially contaminated surface water with the copepod larvicide temephos (Abate); (5) providing safe drinking water from boreholes or hand-dug wells; and (6) containment of transmission through voluntary isolation of each patient to prevent contamination of drinking water sources, provision of first aid, and manual extraction of the worm. Surveillance, community education, potable water provision, and case containment remain weak facets of the program. Abate pesticide is not a viable option for Guinea worm control in South Sudan. In light of current case detection and containment trends, as well as capacity building efforts for Guinea worm eradication, South Sudan is more likely to eradicate Guinea worm by 2020, rather than by 2015. The author highlights areas in which substantial improvements are required in South Sudan's Guinea worm eradication program, and suggests improvement strategies. PMID:23623648

  15. Experiences in the development of the Mighty Worm. [development of actuator for space applications

    NASA Technical Reports Server (NTRS)

    Bamford, R.; Moore, D.; Mon, G.; Wada, B.

    1993-01-01

    A 'Mighty Worm' actuator with the active member capable of carrying large loads during the launch phase was developed for adaptive structures applications. Two types of Mighty Worm performance are characterized, namely, long-stroke motion and incremental positioning at 0, 25, 50, 75, and 100 lb. Long-stroke motion involves successive translations of all Mighty Worm moving elements, and incremental positioning involves only in-place stack expansion.

  16. VizieR Online Data Catalog: Galactic Worms (Koo+, 1992)

    NASA Astrophysics Data System (ADS)

    Koo, B.-C.; Heiles, C.; Reach, W. T.

    2016-02-01

    118 structures catalogued as "worm candidates" are found on the basis of the maps in HI-21cm, IRAS 100 and 60μm. The 21cm maps of the Galactic Plane (b < 10°) result from available surveys (Kerr et al. 1986A&AS...66..373K; Weaver & Williams 1973A&AS....8....1W, Cat. VIII/11) and from new observations near the Galactic center during 1989 and 1990 using the Hat Creek 26m telescope. (3 data files).

  17. Pet roundworms and hookworms: A continuing need for global worming

    PubMed Central

    2012-01-01

    Ascarids and ancylostomatids are the most important parasites affecting dogs and cats worldwide, in terms of diffusion and risk for animal and human health. Different misconceptions have led the general public and pet owners to minimize the importance of these intestinal worms. A low grade of interest is also registered among veterinary professions, although there is a significant merit in keeping our guard up against these parasites. This article reviews current knowledge of ascarids and ancylostomatids, with a special focus on pathogenicity, epidemiology and control methods in veterinary and human medicine. PMID:22574783

  18. Genomic insights into the uncultured genus ‘Candidatus Magnetobacterium' in the phylum Nitrospirae

    PubMed Central

    Lin, Wei; Deng, Aihua; Wang, Zhang; Li, Ying; Wen, Tingyi; Wu, Long-Fei; Wu, Martin; Pan, Yongxin

    2014-01-01

    Magnetotactic bacteria (MTB) of the genus ‘Candidatus Magnetobacterium' in phylum Nitrospirae are of great interest because of the formation of hundreds of bullet-shaped magnetite magnetosomes in multiple bundles of chains per cell. These bacteria are worldwide distributed in aquatic environments and have important roles in the biogeochemical cycles of iron and sulfur. However, except for a few short genomic fragments, no genome data are available for this ecologically important genus, and little is known about their metabolic capacity owing to the lack of pure cultures. Here we report the first draft genome sequence of 3.42 Mb from an uncultivated strain tentatively named ‘Ca. Magnetobacterium casensis' isolated from Lake Miyun, China. The genome sequence indicates an autotrophic lifestyle using the Wood–Ljungdahl pathway for CO2 fixation, which has not been described in any previously known MTB or Nitrospirae organisms. Pathways involved in the denitrification, sulfur oxidation and sulfate reduction have been predicted, indicating its considerable capacity for adaptation to variable geochemical conditions and roles in local biogeochemical cycles. Moreover, we have identified a complete magnetosome gene island containing mam, mad and a set of novel genes (named as man genes) putatively responsible for the formation of bullet-shaped magnetite magnetosomes and the arrangement of multiple magnetosome chains. This first comprehensive genomic analysis sheds light on the physiology, ecology and biomineralization of the poorly understood ‘Ca. Magnetobacterium' genus. PMID:24914800

  19. Apibacter adventoris gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from honey bees.

    PubMed

    Kwong, Waldan K; Moran, Nancy A

    2016-03-01

    Honey bees and bumble bees harbour a small, defined set of gut bacterial associates. Strains matching sequences from 16S rRNA gene surveys of bee gut microbiotas were isolated from two honey bee species from East Asia. These isolates were mesophlic, non-pigmented, catalase-positive and oxidase-negative. The major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 0 and C16 : 0 3-OH. The DNA G+C content was 29-31 mol%. They had ∼87 % 16S rRNA gene sequence identity to the closest relatives described. Phylogenetic reconstruction using 20 protein-coding genes showed that these bee-derived strains formed a highly supported monophyletic clade, sister to the clade containing species of the genera Chryseobacterium and Elizabethkingia within the family Flavobacteriaceae of the phylum Bacteroidetes. On the basis of phenotypic and genotypic characteristics, we propose placing these strains in a novel genus and species: Apibacter adventoris gen. nov., sp. nov. The type strain of Apibacter adventoris is wkB301T ( = NRRL B-65307T = NCIMB 14986T). PMID:26743158

  20. Persistence of the dominant soil phylum Acidobacteria by trace gas scavenging

    PubMed Central

    Greening, Chris; Carere, Carlo R.; Rushton-Green, Rowena; Harold, Liam K.; Hards, Kiel; Taylor, Matthew C.; Morales, Sergio E.; Stott, Matthew B.; Cook, Gregory M.

    2015-01-01

    The majority of microbial cells in global soils exist in a spectrum of dormant states. However, the metabolic processes that enable them to survive environmental challenges, such as nutrient-limitation, remain to be elucidated. In this work, we demonstrate that energy-starved cultures of Pyrinomonas methylaliphatogenes, an aerobic heterotrophic acidobacterium isolated from New Zealand volcanic soils, persist by scavenging the picomolar concentrations of H2 distributed throughout the atmosphere. Following the transition from exponential to stationary phase due to glucose limitation, the bacterium up-regulates by fourfold the expression of an eight-gene operon encoding an actinobacteria-type H2-uptake [NiFe]-hydrogenase. Whole-cells of the organism consume atmospheric H2 in a first-order kinetic process. Hydrogen oxidation occurred most rapidly under oxic conditions and was weakly associated with the cell membrane. We propose that atmospheric H2 scavenging serves as a mechanism to sustain the respiratory chain of P. methylaliphatogenes when organic electron donors are scarce. As the first observation of H2 oxidation to our knowledge in the Acidobacteria, the second most dominant soil phylum, this work identifies new sinks in the biogeochemical H2 cycle and suggests that trace gas oxidation may be a general mechanism for microbial persistence. PMID:26240343

  1. Global Habitat Suitability and Ecological Niche Separation in the Phylum Placozoa.

    PubMed

    Paknia, Omid; Schierwater, Bernd

    2015-01-01

    The enigmatic placozoans, which hold a key position in the metazoan Tree of Life, have attracted substantial attention in many areas of biological and biomedical research. While placozoans have become an emerging model system, their ecology and particularly biogeography remain widely unknown. In this study, we use modelling approaches to explore habitat preferences, and distribution pattern of the placozoans phylum. We provide hypotheses for discrete ecological niche separation between genetic placozoan lineages, which may also help to understand biogeography patterns in other small marine invertebrates. We, here, used maximum entropy modelling to predict placozoan distribution using 20 environmental grids of 9.2 km2 resolution. In addition, we used recently developed metrics of niche overlap to compare habitat suitability models of three genetic clades. The predicted distributions range from 55°N to 44°S and are restricted to regions of intermediate to warm sea surface temperatures. High concentrations of salinity and low nutrient concentrations appear as secondary factors. Tests of niche equivalency reveal the largest differences between placozoan clades I and III. Interestingly, the genetically well-separated clades I and V appear to be ecologically very similar. Our habitat suitability models predict a wider latitudinal distribution for placozoans, than currently described, especially in the northern hemisphere. With respect to biogeography modelling, placozoans show patterns somewhere between higher metazoan taxa and marine microorganisms, with the first group usually showing complex biogeographies and the second usually showing "no biogeography." PMID:26580806

  2. Forest-to-pasture conversion increases the diversity of the phylum Verrucomicrobia in Amazon rainforest soils.

    PubMed

    Ranjan, Kshitij; Paula, Fabiana S; Mueller, Rebecca C; Jesus, Ederson da C; Cenciani, Karina; Bohannan, Brendan J M; Nüsslein, Klaus; Rodrigues, Jorge L M

    2015-01-01

    The Amazon rainforest is well known for its rich plant and animal diversity, but its bacterial diversity is virtually unexplored. Due to ongoing and widespread deforestation followed by conversion to agriculture, there is an urgent need to quantify the soil biological diversity within this tropical ecosystem. Given the abundance of the phylum Verrucomicrobia in soils, we targeted this group to examine its response to forest-to-pasture conversion. Both taxonomic and phylogenetic diversities were higher for pasture in comparison to primary and secondary forests. The community composition of Verrucomicrobia in pasture soils was significantly different from those of forests, with a 11.6% increase in the number of sequences belonging to subphylum 3 and a proportional decrease in sequences belonging to the class Spartobacteria. Based on 99% operational taxonomic unit identity, 40% of the sequences have not been detected in previous studies, underscoring the limited knowledge regarding the diversity of microorganisms in tropical ecosystems. The abundance of Verrucomicrobia, measured with quantitative PCR, was strongly correlated with soil C content (r = 0.80, P = 0.0016), indicating their importance in metabolizing plant-derived carbon compounds in soils. PMID:26284056

  3. A history of the taxonomy and systematics of arbuscular mycorrhizal fungi belonging to the phylum Glomeromycota.

    PubMed

    Stürmer, Sidney Luiz

    2012-05-01

    Arbuscular mycorrhizal fungi (AMF) are grouped in a monophyletic group, the phylum Glomeromycota. In this review, the history and complexity of the taxonomy and systematics of these obligate biotrophs is addressed by recognizing four periods. The initial discovery period (1845-1974) is characterized by description mainly of sporocarp-forming species and the proposal of a classification for these fungi. The following alpha taxonomy period (1975-1989) established a solid morphological basis for species identification and classification, resulting in a profuse description of new species and a need to standardize the nomenclature of spore subcellular structures. The cladistics period from 1990 to 2000 saw the first cladistic classification of AMF based on phenotypic characters only. At the end of this period, genetic characters played a role in defining taxa and elucidating evolutionary relationships within the group. The most recent phylogenetic synthesis period (2001 to present) started with the proposal of a new classification based on genetic characters using sequences of the multicopy rRNA genes. PMID:22391803

  4. Phylogenetic diversity and ecophysiology of Candidate phylum Saccharibacteria in activated sludge.

    PubMed

    Kindaichi, Tomonori; Yamaoka, Shiro; Uehara, Ryohei; Ozaki, Noriatsu; Ohashi, Akiyoshi; Albertsen, Mads; Nielsen, Per Halkjær; Nielsen, Jeppe Lund

    2016-06-01

    Candidate phylum Saccharibacteria (former TM7) are abundant and widespread in nature, but little is known about their ecophysiology and detailed phylogeny. In this study phylogeny, morphology and ecophysiology of Saccharibacteria were investigated in activated sludge from nine wastewater treatment plants (WWTPs) from Japan and Denmark using the full-cycle 16S rRNA approach in combination with microautoradiography (MAR) and fluorescence in situ hybridization (FISH). Phylogenetic analysis showed that Saccharibacteria from all WWTPs were evenly distributed within subdivision 1 and 3 and in a distinct phylogenetic clade. Three probes were designed for the distinct saccharibacterial groups, and revealed morphotypes representing thin filaments, thick filaments and rods/cocci. MAR-FISH results showed that most probe-defined Saccharibacteria utilized glucose under aerobic-, nitrate reducing- and anaerobic conditions. Some Saccharibacteria also utilized N-acetylglucosamine, oleic acid, amino acids and butyrate, which are not predicted from available genomes so far. In addition, some filamentous Saccharibacteria exhibited β-galactosidase and lipase activities determined using a combination of enzyme-labeled fluorescence and FISH (ELF-FISH). No uptake of acetate, propionate, pyruvate, glycerol and ethanol was observed. These results indicate that Saccharibacteria is a phylogenetically diverse group and play a role in the degradation of various organic compounds as well as sugar compounds under aerobic-, nitrate reducing- and anaerobic conditions. PMID:27090759

  5. Global Habitat Suitability and Ecological Niche Separation in the Phylum Placozoa

    PubMed Central

    Paknia, Omid; Schierwater, Bernd

    2015-01-01

    The enigmatic placozoans, which hold a key position in the metazoan Tree of Life, have attracted substantial attention in many areas of biological and biomedical research. While placozoans have become an emerging model system, their ecology and particularly biogeography remain widely unknown. In this study, we use modelling approaches to explore habitat preferences, and distribution pattern of the placozoans phylum. We provide hypotheses for discrete ecological niche separation between genetic placozoan lineages, which may also help to understand biogeography patterns in other small marine invertebrates. We, here, used maximum entropy modelling to predict placozoan distribution using 20 environmental grids of 9.2 km2 resolution. In addition, we used recently developed metrics of niche overlap to compare habitat suitability models of three genetic clades. The predicted distributions range from 55°N to 44°S and are restricted to regions of intermediate to warm sea surface temperatures. High concentrations of salinity and low nutrient concentrations appear as secondary factors. Tests of niche equivalency reveal the largest differences between placozoan clades I and III. Interestingly, the genetically well-separated clades I and V appear to be ecologically very similar. Our habitat suitability models predict a wider latitudinal distribution for placozoans, than currently described, especially in the northern hemisphere. With respect to biogeography modelling, placozoans show patterns somewhere between higher metazoan taxa and marine microorganisms, with the first group usually showing complex biogeographies and the second usually showing “no biogeography.” PMID:26580806

  6. Entorrhizomycota: A New Fungal Phylum Reveals New Perspectives on the Evolution of Fungi

    PubMed Central

    Garnica, Sigisfredo; Oberwinkler, Franz; Riess, Kai; Weiß, Michael; Begerow, Dominik

    2015-01-01

    Entorrhiza is a small fungal genus comprising 14 species that all cause galls on roots of Cyperaceae and Juncaceae. Although this genus was established 130 years ago, crucial questions on the phylogenetic relationships and biology of this enigmatic taxon are still unanswered. In order to infer a robust hypothesis about the phylogenetic position of Entorrhiza and to evaluate evolutionary trends, multiple gene sequences and morphological characteristics of Entorrhiza were analyzed and compared with respective findings in Fungi. In our comprehensive five-gene analyses Entorrhiza appeared as a highly supported monophyletic lineage representing the sister group to the rest of the Dikarya, a phylogenetic placement that received but moderate maximum likelihood and maximum parsimony bootstrap support. An alternative maximum likelihood tree with the constraint that Entorrhiza forms a monophyletic group with Basidiomycota could not be rejected. According to the first phylogenetic hypothesis, the teliospore tetrads of Entorrhiza represent the prototype of the dikaryan meiosporangium. The alternative hypothesis is supported by similarities in septal pore structure, cell wall and spindle pole bodies. Based on the isolated phylogenetic position of Entorrhiza and its peculiar combination of features related to ultrastructure and reproduction mode, we propose a new phylum Entorrhizomycota, for the genus Entorrhiza, which represents an apparently widespread group of inconspicuous fungi. PMID:26200112

  7. First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking

    PubMed Central

    Ohashi, Akiko; Parks, Donovan H.; Yamauchi, Toshihiro; Tyson, Gene W.

    2015-01-01

    Filamentous cells belonging to the candidate bacterial phylum KSB3 were previously identified as the causative agent of fatal filament overgrowth (bulking) in a high-rate industrial anaerobic wastewater treatment bioreactor. Here, we obtained near complete genomes from two KSB3 populations in the bioreactor, including the dominant bulking filament, using differential coverage binning of metagenomic data. Fluorescence in situ hybridization with 16S rRNA-targeted probes specific for the two populations confirmed that both are filamentous organisms. Genome-based metabolic reconstruction and microscopic observation of the KSB3 filaments in the presence of sugar gradients indicate that both filament types are Gram-negative, strictly anaerobic fermenters capable of non-flagellar based gliding motility, and have a strikingly large number of sensory and response regulator genes. We propose that the KSB3 filaments are highly sensitive to their surroundings and that cellular processes, including those causing bulking, are controlled by external stimuli. The obtained genomes lay the foundation for a more detailed understanding of environmental cues used by KSB3 filaments, which may lead to more robust treatment options to prevent bulking. PMID:25650158

  8. Genome Analysis of Thermosulfurimonas dismutans, the First Thermophilic Sulfur-Disproportionating Bacterium of the Phylum Thermodesulfobacteria.

    PubMed

    Mardanov, Andrey V; Beletsky, Alexey V; Kadnikov, Vitaly V; Slobodkin, Alexander I; Ravin, Nikolai V

    2016-01-01

    Thermosulfurimonas dismutans S95(T), isolated from a deep-sea hydrothermal vent is the first bacterium of the phylum Thermodesulfobacteria reported to grow by the disproportionation of elemental sulfur, sulfite, or thiosulfate with carbon dioxide as the sole carbon source. In contrast to its phylogenetically close relatives, which are dissimilatory sulfate-reducers, T. dismutans is unable to grow by sulfate respiration. The features of this organism and its 2,1 Mb draft genome sequence are described in this report. Genome analysis revealed that the T. dismutans genome contains the set of genes for dissimilatory sulfate reduction including ATP sulfurylase, the AprA and B subunits of adenosine-5'-phosphosulfate reductase, and dissimilatory sulfite reductase. The oxidation of elemental sulfur to sulfite could be enabled by APS reductase-associated electron transfer complex QmoABC and heterodisulfide reductase. The genome also contains several membrane-linked molybdopterin oxidoreductases that are thought to be involved in sulfur metabolism as subunits of thiosulfate, polysulfide, or tetrathionate reductases. Nitrate could be used as an electron acceptor and reduced to ammonium, as indicated by the presence of periplasmic nitrate and nitrite reductases. Autotrophic carbon fixation is enabled by the Wood-Ljungdahl pathway, and the complete set of genes that is required for nitrogen fixation is also present in T. dismutans. Overall, our results provide genomic insights into energy and carbon metabolism of chemolithoautotrophic sulfur-disproportionating bacterium that could be important primary producer in microbial communities of deep-sea hydrothermal vents. PMID:27379079

  9. Bacteria of the Candidate Phylum TM7 are Prevalent in Acidophilic Nitrifying Sequencing-Batch Reactors

    PubMed Central

    Hanada, Akiko; Kurogi, Takashi; Giang, Nguyen Minh; Yamada, Takeshi; Kamimoto, Yuki; Kiso, Yoshiaki; Hiraishi, Akira

    2014-01-01

    Laboratory-scale acidophilic nitrifying sequencing-batch reactors (ANSBRs) were constructed by seeding with sewage-activated sludge and cultivating with ammonium-containing acidic mineral medium (pH 4.0) with or without a trace amount of yeast extract. In every batch cycle, the pH varied between 2.7 and 4.0, and ammonium was completely converted to nitrate. Attempts to detect nitrifying functional genes in the fully acclimated ANSBRs by PCR with previously designed primers mostly gave negative results. 16S rRNA gene-targeted PCR and a subsequent denaturating gradient gel electrophoresis analysis revealed that a marked change occurred in the bacterial community during the overall period of operation, in which members of the candidate phylum TM7 and the class Gammaproteobacteria became predominant at the fully acclimated stage. This result was fully supported by a 16S rRNA gene clone library analysis, as the major phylogenetic groups of clones detected (>5% of the total) were TM7 (33%), Gammaproteobacteria (37%), Actinobacteria (10%), and Alphaproteobacteria (8%). Fluorescence in situ hybridization with specific probes also demonstrated the prevalence of TM7 bacteria and Gammaproteobacteria. These results suggest that previously unknown nitrifying microorganisms may play a major role in ANSBRs; however, the ecophysiological significance of the TM7 bacteria predominating in this process remains unclear. PMID:25241805

  10. Genomic insights into the uncultured genus 'Candidatus Magnetobacterium' in the phylum Nitrospirae.

    PubMed

    Lin, Wei; Deng, Aihua; Wang, Zhang; Li, Ying; Wen, Tingyi; Wu, Long-Fei; Wu, Martin; Pan, Yongxin

    2014-12-01

    Magnetotactic bacteria (MTB) of the genus 'Candidatus Magnetobacterium' in phylum Nitrospirae are of great interest because of the formation of hundreds of bullet-shaped magnetite magnetosomes in multiple bundles of chains per cell. These bacteria are worldwide distributed in aquatic environments and have important roles in the biogeochemical cycles of iron and sulfur. However, except for a few short genomic fragments, no genome data are available for this ecologically important genus, and little is known about their metabolic capacity owing to the lack of pure cultures. Here we report the first draft genome sequence of 3.42 Mb from an uncultivated strain tentatively named 'Ca. Magnetobacterium casensis' isolated from Lake Miyun, China. The genome sequence indicates an autotrophic lifestyle using the Wood-Ljungdahl pathway for CO2 fixation, which has not been described in any previously known MTB or Nitrospirae organisms. Pathways involved in the denitrification, sulfur oxidation and sulfate reduction have been predicted, indicating its considerable capacity for adaptation to variable geochemical conditions and roles in local biogeochemical cycles. Moreover, we have identified a complete magnetosome gene island containing mam, mad and a set of novel genes (named as man genes) putatively responsible for the formation of bullet-shaped magnetite magnetosomes and the arrangement of multiple magnetosome chains. This first comprehensive genomic analysis sheds light on the physiology, ecology and biomineralization of the poorly understood 'Ca. Magnetobacterium' genus. PMID:24914800

  11. Persistence of the dominant soil phylum Acidobacteria by trace gas scavenging.

    PubMed

    Greening, Chris; Carere, Carlo R; Rushton-Green, Rowena; Harold, Liam K; Hards, Kiel; Taylor, Matthew C; Morales, Sergio E; Stott, Matthew B; Cook, Gregory M

    2015-08-18

    The majority of microbial cells in global soils exist in a spectrum of dormant states. However, the metabolic processes that enable them to survive environmental challenges, such as nutrient-limitation, remain to be elucidated. In this work, we demonstrate that energy-starved cultures of Pyrinomonas methylaliphatogenes, an aerobic heterotrophic acidobacterium isolated from New Zealand volcanic soils, persist by scavenging the picomolar concentrations of H2 distributed throughout the atmosphere. Following the transition from exponential to stationary phase due to glucose limitation, the bacterium up-regulates by fourfold the expression of an eight-gene operon encoding an actinobacteria-type H2-uptake [NiFe]-hydrogenase. Whole-cells of the organism consume atmospheric H2 in a first-order kinetic process. Hydrogen oxidation occurred most rapidly under oxic conditions and was weakly associated with the cell membrane. We propose that atmospheric H2 scavenging serves as a mechanism to sustain the respiratory chain of P. methylaliphatogenes when organic electron donors are scarce. As the first observation of H2 oxidation to our knowledge in the Acidobacteria, the second most dominant soil phylum, this work identifies new sinks in the biogeochemical H2 cycle and suggests that trace gas oxidation may be a general mechanism for microbial persistence. PMID:26240343

  12. Isolation and survey of novel fluoroacetate-degrading bacteria belonging to the phylum Synergistetes.

    PubMed

    Davis, Carl K; Webb, Richard I; Sly, Lindsay I; Denman, Stuart E; McSweeney, Chris S

    2012-06-01

    Microbial dehalogenation of chlorinated compounds in anaerobic environments is well known, but the degradation of fluorinated compounds under similar conditions has rarely been described. Here, we report on the isolation of a bovine rumen bacterium that metabolizes fluoroacetate under anaerobic conditions, the mode of degradation and its presence in gut ecosystems. The bacterium was identified using 16S rRNA gene sequence analysis as belonging to the phylum Synergistetes and was designated strain MFA1. Growth was stimulated by amino acids with greater quantities of amino acids metabolized in the presence of fluoroacetate, but sugars were not fermented. Acetate, formate, propionate, isobutryate, isovalerate, ornithine and H(2) were end products of amino acid metabolism. Acetate was the primary end product of fluoroacetate dehalogenation, and the amount produced correlated with the stoichiometric release of fluoride which was confirmed using fluorine nuclear magnetic resonance ((19) F NMR) spectroscopy. Hydrogen and formate produced in situ were consumed during dehalogenation. The growth characteristics of strain MFA1 indicated that the bacterium may gain energy via reductive dehalogenation. This is the first study to identify a bacterium that can anaerobically dehalogenate fluoroacetate. Nested 16S rRNA gene-specific PCR assays detected the bacterium at low numbers in the gut of several herbivore species. PMID:22372434

  13. Forest-to-pasture conversion increases the diversity of the phylum Verrucomicrobia in Amazon rainforest soils

    PubMed Central

    Ranjan, Kshitij; Paula, Fabiana S.; Mueller, Rebecca C.; Jesus, Ederson da C.; Cenciani, Karina; Bohannan, Brendan J. M.; Nüsslein, Klaus; Rodrigues, Jorge L. M.

    2015-01-01

    The Amazon rainforest is well known for its rich plant and animal diversity, but its bacterial diversity is virtually unexplored. Due to ongoing and widespread deforestation followed by conversion to agriculture, there is an urgent need to quantify the soil biological diversity within this tropical ecosystem. Given the abundance of the phylum Verrucomicrobia in soils, we targeted this group to examine its response to forest-to-pasture conversion. Both taxonomic and phylogenetic diversities were higher for pasture in comparison to primary and secondary forests. The community composition of Verrucomicrobia in pasture soils was significantly different from those of forests, with a 11.6% increase in the number of sequences belonging to subphylum 3 and a proportional decrease in sequences belonging to the class Spartobacteria. Based on 99% operational taxonomic unit identity, 40% of the sequences have not been detected in previous studies, underscoring the limited knowledge regarding the diversity of microorganisms in tropical ecosystems. The abundance of Verrucomicrobia, measured with quantitative PCR, was strongly correlated with soil C content (r = 0.80, P = 0.0016), indicating their importance in metabolizing plant-derived carbon compounds in soils. PMID:26284056

  14. Global Patterns of Abundance, Diversity and Community Structure of the Aminicenantes (Candidate Phylum OP8)

    PubMed Central

    Farag, Ibrahim F.; Davis, James P.; Youssef, Noha H.; Elshahed, Mostafa S.

    2014-01-01

    We investigated the global patterns of abundance, diversity, and community structure of members of the Aminicenantes (candidate phylum OP8). Our aim was to identify the putative ecological role(s) played by members of this poorly characterized bacterial lineages in various ecosystems. Analysis of near full-length 16S rRNA genes identified four classes and eight orders within the Aminicenantes. Within 3,134 datasets comprising ∼1.8 billion high throughput-generated partial 16S rRNA genes, 47,351 Aminicenantes-affiliated sequences were identified in 913 datasets. The Aminicenantes exhibited the highest relative abundance in hydrocarbon-impacted environments, followed by marine habitats (especially hydrothermal vents and coral-associated microbiome samples), and aquatic, non-marine habitats (especially in terrestrial springs and groundwater samples). While the overall abundance of the Aminicenantes was higher in low oxygen tension as well as non-saline and low salinity habitats, it was encountered in a wide range of oxygen tension, salinities, and temperatures. Analysis of the community structure of the Aminicenantes showed distinct patterns across various datasets that appear to be, mostly, driven by habitat variations rather than prevalent environmental parameters. We argue that the detection of the Aminicenantes across environmental extremes and the observed distinct community structure patterns reflect a high level of intraphylum metabolic diversity and adaptive capabilities that enable its survival and growth in a wide range of habitats and environmental conditions. PMID:24637619

  15. Determination of the {ital b}{r_arrow}{ital c} handedness using nonleptonic {Lambda}{sub {ital c}} decays

    SciTech Connect

    Koenig, B.; Koerner, J.G.; Kraemer, M.

    1994-03-01

    We consider possibilities to determine the handedness of {ital b}{r_arrow}{ital c} current transitions using semileptonic baryonic {Lambda}{sub {ital b}}{r_arrow}{Lambda}{sub {ital c}} transitions. We propose to analyze the longitudinal polarization of the daughter baryon {Lambda}{sub {ital c}} by using momentum-spin correlation measurements in the form of forward-backward (FB) asymmetry measures involving its nonleptonic decay products. We use an explicit form factor model to determine the longitudinal polarization of {Lambda}{sub {ital c}} in the semileptonic decay {Lambda}{sub {ital b}}{r_arrow}{Lambda}{sub {ital c}}+{ital l}{sup {minus}}+{bar {nu}}{sub {ital l}}. The mean longitudinal polarization of {Lambda}{sub {ital c}} is negative (positive) for left-chiral (right-chiral) {ital b}{r_arrow}{ital c} current transitions. The frame-dependent longitudinal polarization of {Lambda}{sub {ital c}} is large ({congruent}80%) in the {Lambda}{sub {ital b}} rest frame and somewhat smaller (30%--40%) in the lab frame when the {Lambda}{sub {ital b}}`s are produced on the {ital Z}{sup 0} peak. We suggest to use nonleptonic decay modes of {Lambda}{sub {ital c}} to analyze its polarization and thereby to determine the chirality of the {ital b}{r_arrow}{ital c} transition. Since {Lambda}{sub {ital b}}`s produced on the {ital Z}{sup 0} are expected to be polarized we discuss issues of the polarization transfer in {Lambda}{sub {ital b}}{r_arrow}{Lambda}{sub {ital c}} transitions. We also investigate the {ital p}{sub {perpendicular}}- and {ital p}-cut sensitivity of our predictions for the polarization of {Lambda}{sub {ital c}}.

  16. Spatial and temporal differences in giant kidney worm, dictophyma renale, prevalence in Minnesota Mink, Mustela vison

    USGS Publications Warehouse

    Mech, L.D.

    2008-01-01

    Examination of 110 Mink (Mustela vison) carcasses from 1998 through 2007 indicated that the giant kidney worm, Dioctophyma renale, occurred in Pine and Kanabec Counties of eastern Minnesota with annual prevalences of 0-92%. Worm prevalence increased from 20% in 1999 to 92% in 2001 and decreased to 6% in 2005. During 2000 to 2007, no worms were found in Mink from Anoka and Chisago Counties (n = 54), and in 2000, none in 107 Mink from LeSeur, Freeborn, Redwood, Brown and Watonwan Counties. Changes in kidney worm prevalence were positively related to trapping success, considered an index of Mink density.

  17. Bose-Einstein correlations in e{sup +}e{sup {minus}} {r_arrow} W{sup +}W{sup {minus}} at a linear collider

    SciTech Connect

    Chekanov, S. V.; De Roeck, A.; De Wolf, E. A.

    2000-03-03

    The authors show that the most popular method to simulate Bose-Einstein (BE) interference effects predicts negligible correlations between identical pions originating from the hadronic decay of different W's produced in e{sup +}e{sup {minus}} {r_arrow} W{sup +}W{sup {minus}} {r_arrow} 4 jets at typical linear collider energies.

  18. Detailed study of the T = 0, NN interaction via N-italic-arrow-rightP- scattering at 68 MEV

    SciTech Connect

    Henneck, R.; Campbell, J.; Gysin, C.; Hammans, M.; Lorenzon, W.; Pickar, M.A.; Sick, I.; Konter, J.A.; Mango, S.; Van den Brandt, B.; and others

    1988-11-20

    We report on first results for a measurement of the spin correlation parameter A/sub z//sub z/ in n-italic-arrow-rightp-arrow-right scattering at 68 MeV, which is highly sensitive to the mixing parameter epsilon/sub 1/. A phase shift analysis of these data, together with forthcoming results of our measurements of /sup d//sup sigma//sub d//sub ..cap omega../ and A/sub y/ at the same energy is expected to allow a determination of epsilon/sub 1/ to within /similar to/ +- 0.3/sup 0/.

  19. Integration and characterization of SiN nanopores for single-molecule detection in liquid-core ARROW waveguides

    NASA Astrophysics Data System (ADS)

    Rudenko, M. I.; Yin, D.; Holmes, M.; Hawkins, A. R.; Schmidt, H.

    2007-02-01

    We demonstrate a method for integrating silicon nitride nanopores in liquid core Anti Resonant Reflecting Optical Waveguides (ARROW) for single molecule electrical detection and control. We use a two-step integration process when a micropore is fabricated first, paving the way for subsequent nanopore integration in the first silicon nitride layer of the ARROW structure. Nanopores with dimensions as small as 11 nm were fabricated using a Focused Ion Beam shrinking process commensurate with single particle gating of viruses, proteins, ribosomes and other biomolecules.

  20. The Pitch Imagery Arrow Task: effects of musical training, vividness, and mental control.

    PubMed

    Gelding, Rebecca W; Thompson, William Forde; Johnson, Blake W

    2015-01-01

    Musical imagery is a relatively unexplored area, partly because of deficiencies in existing experimental paradigms, which are often difficult, unreliable, or do not provide objective measures of performance. Here we describe a novel protocol, the Pitch Imagery Arrow Task (PIAT), which induces and trains pitch imagery in both musicians and non-musicians. Given a tonal context and an initial pitch sequence, arrows are displayed to elicit a scale-step sequence of imagined pitches, and participants indicate whether the final imagined tone matches an audible probe. It is a staircase design that accommodates individual differences in musical experience and imagery ability. This new protocol was used to investigate the roles that musical expertise, self-reported auditory vividness and mental control play in imagery performance. Performance on the task was significantly better for participants who employed a musical imagery strategy compared to participants who used an alternative cognitive strategy and positively correlated with scores on the Control subscale from the Bucknell Auditory Imagery Scale (BAIS). Multiple regression analysis revealed that Imagery performance accuracy was best predicted by a combination of strategy use and scores on the Vividness subscale of BAIS. These results confirm that competent performance on the PIAT requires active musical imagery and is very difficult to achieve using alternative cognitive strategies. Auditory vividness and mental control were more important than musical experience in the ability to perform manipulation of pitch imagery. PMID:25807078

  1. Radiative Recombination in the Terrestrial Nightglow: e + O^+ arrow O + hν

    NASA Astrophysics Data System (ADS)

    Slanger, T. G.; Cosby, P. C.; Sharpee, B. D.; Huestis, D. L.

    2003-10-01

    Large aperture telescopes have been equipped with superbly calibrated high-resolution spectrographs with performance comparable with the best laboratory instrumentation. From analysis of spectra of the ``empty sky" (really the Earth's atmosphere) we have made the first experimental determination of the relative strengths of 25 emission lines between 390 and 930 nm from Rydberg excited states following the reaction e + O^+ arrow O + hν in the terrestrial ionosphere. We observe ns,np,nd arrow 3s,3p orbital transitions, around the O^+(^4S) core, for n=3-11 and for triplet and quintet overall spin. Two modern calculations of cross sections for radiative recombination are in use by atmospheric scientists [1] and astronomers [2]. In general, the observed relative intensities agree rather well with theory, especially for the quintet states. Modeling the triplets is complicated by optical trapping. Supported by the NSF and NASA. [1] V. Escalante and G. A. Victor, Planet. Space Sci. 40, 1705 (1992). [2] D. Pequignot, P. Petitjean, and C. Boisson, Astron. Astrophys. 251, 680 (1991).

  2. Safety effects of traffic signing for left turn flashing yellow arrow signals.

    PubMed

    Schattler, Kerrie L; Gulla, Cody J; Wallenfang, Travis J; Burdett, Beau A; Lund, Jessica A

    2015-02-01

    In 2010, the left turn flashing yellow arrow (FYA) signal displays were installed at signalized intersections on state routes in the Peoria, Illinois, area. Supplemental traffic signs with text "Left Turn Yield on Flashing Yellow Arrow" were mounted on the mast arm adjacent to the left turn signal at over half of the FYA installations. The purpose of this paper is to present the results of the effectiveness evaluation of the FYA supplemental sign on safety. Analyses are presented on the effects of the FYA supplemental sign for all drivers and a subset of drivers age 65 and older. A crash-based comparison of 164 FYA approaches including 90 approaches with the sign and 74 approaches without the sign showed greater crash reductions when the supplemental FYA sign was present. The results also showed that crashes involving drivers age 65 and older did not experience the same magnitudes of crash reductions as compared to all drivers. The findings of this research indicate that supplemental FYA signs may help in improving safety for left-turning vehicles during the permissive interval. Thus, it is recommended that supplemental signs be used when initially implementing the FYA, and that effort to educate the driving public on new traffic control be made to further improve safety at signalized intersections. PMID:25528438

  3. The Pitch Imagery Arrow Task: Effects of Musical Training, Vividness, and Mental Control

    PubMed Central

    Gelding, Rebecca W.; Thompson, William Forde; Johnson, Blake W.

    2015-01-01

    Musical imagery is a relatively unexplored area, partly because of deficiencies in existing experimental paradigms, which are often difficult, unreliable, or do not provide objective measures of performance. Here we describe a novel protocol, the Pitch Imagery Arrow Task (PIAT), which induces and trains pitch imagery in both musicians and non-musicians. Given a tonal context and an initial pitch sequence, arrows are displayed to elicit a scale-step sequence of imagined pitches, and participants indicate whether the final imagined tone matches an audible probe. It is a staircase design that accommodates individual differences in musical experience and imagery ability. This new protocol was used to investigate the roles that musical expertise, self-reported auditory vividness and mental control play in imagery performance. Performance on the task was significantly better for participants who employed a musical imagery strategy compared to participants who used an alternative cognitive strategy and positively correlated with scores on the Control subscale from the Bucknell Auditory Imagery Scale (BAIS). Multiple regression analysis revealed that Imagery performance accuracy was best predicted by a combination of strategy use and scores on the Vividness subscale of BAIS. These results confirm that competent performance on the PIAT requires active musical imagery and is very difficult to achieve using alternative cognitive strategies. Auditory vividness and mental control were more important than musical experience in the ability to perform manipulation of pitch imagery. PMID:25807078

  4. Distribution of two triamines, spermidine and homospermidine, and an aromatic amine, 2-phenylethylamine, within the phylum Bacteroidetes.

    PubMed

    Hosoya, Ryuichi; Hamana, Koei

    2004-10-01

    Cellular polyamines of the newly additional 19 species belonging to the class Bacteroides of the phylum Bacteroidetes were analyzed by HPLC to display polyamine distribution as a chemotaxonomic marker within the total 41 species. Three profiles, the presence of spermidine, the presence of homospermidine and the absence of both triamines, corresponded to their phylogenetical positions within the four families of the class. The occurrence of an aromatic amine, 2-phenylethylamine, extracted into cellular polyamine fraction, was also determined within the 121 species distributed within the phylum. This aromatic amine was found in Cellulophaga lytica, Cytophaga latercula, Tenacibaculum amylolyticum, Tenacibaculum martimum, Tenacibaculum mesophilum and Psychroflexus torquis belonging to the family Flavobacteriaceae of the class Flavobacteria, and Flexibacter flexilis and Microscilla marina belonging to the family Flexibacteraceae of the class Sphingobacteria. PMID:15747230

  5. Complete mitochondrial genome of yellow meal worm(Tenebrio molitor)

    PubMed Central

    LIU, Li-Na; WANG, Cheng-Ye

    2014-01-01

    The yellow meal worm(Tenebrio molitor L.) is an important resource insect typically used as animal feed additive. It is also widely used for biological research. The first complete mitochondrial genome of T. molitor was determined for the first time by long PCR and conserved primer walking approaches. The results showed that the entire mitogenome of T. molitor was 15 785 bp long, with 72.35% A+T content [deposited in GenBank with accession number KF418153]. The gene order and orientation were the same as the most common type suggested as ancestral for insects. Two protein-coding genes used atypical start codons(CTA in ND2 and AAT in COX1), and the remaining 11 protein-coding genes started with a typical insect initiation codon ATN. All tRNAs showed standard clover-leaf structure, except for tRNASer(AGN), which lacked a dihydrouridine(DHU) arm. The newly added T. molitor mitogenome could provide information for future studies on yellow meal worm. PMID:25465087

  6. Meandering worms: mechanics of undulatory burrowing in muds.

    PubMed

    Dorgan, Kelly M; Law, Chris J; Rouse, Greg W

    2013-04-22

    Recent work has shown that muddy sediments are elastic solids through which animals extend burrows by fracture, whereas non-cohesive granular sands fluidize around some burrowers. These different mechanical responses are reflected in the morphologies and behaviours of their respective inhabitants. However, Armandia brevis, a mud-burrowing opheliid polychaete, lacks an expansible anterior consistent with fracturing mud, and instead uses undulatory movements similar to those of sandfish lizards that fluidize desert sands. Here, we show that A. brevis neither fractures nor fluidizes sediments, but instead uses a third mechanism, plastically rearranging sediment grains to create a burrow. The curvature of the undulating body fits meander geometry used to describe rivers, and changes in curvature driven by muscle contraction are similar for swimming and burrowing worms, indicating that the same gait is used in both sediments and water. Large calculated friction forces for undulatory burrowers suggest that sediment mechanics affect undulatory and peristaltic burrowers differently; undulatory burrowing may be more effective for small worms that live in sediments not compacted or cohesive enough to extend burrows by fracture. PMID:23446526

  7. Meandering worms: mechanics of undulatory burrowing in muds

    PubMed Central

    Dorgan, Kelly M.; Law, Chris J.; Rouse, Greg W.

    2013-01-01

    Recent work has shown that muddy sediments are elastic solids through which animals extend burrows by fracture, whereas non-cohesive granular sands fluidize around some burrowers. These different mechanical responses are reflected in the morphologies and behaviours of their respective inhabitants. However, Armandia brevis, a mud-burrowing opheliid polychaete, lacks an expansible anterior consistent with fracturing mud, and instead uses undulatory movements similar to those of sandfish lizards that fluidize desert sands. Here, we show that A. brevis neither fractures nor fluidizes sediments, but instead uses a third mechanism, plastically rearranging sediment grains to create a burrow. The curvature of the undulating body fits meander geometry used to describe rivers, and changes in curvature driven by muscle contraction are similar for swimming and burrowing worms, indicating that the same gait is used in both sediments and water. Large calculated friction forces for undulatory burrowers suggest that sediment mechanics affect undulatory and peristaltic burrowers differently; undulatory burrowing may be more effective for small worms that live in sediments not compacted or cohesive enough to extend burrows by fracture. PMID:23446526

  8. Distribution of meningeal worm (Parelaphostrongylus tenuis) in South Dakota.

    PubMed

    Jacques, Christopher N; Jenks, Jonathan A

    2004-01-01

    Heads of hunter-harvested deer (Odocoileus sp.) and elk (Cervus elaphus) were collected from meat processing plants throughout South Dakota (USA) from 1997 through 1999 to determine distribution of meningeal worm (Parelaphostrongylus tenuis) in eastern and western South Dakota. A total of 2,848 white-tailed deer (WTD) were examined for P. tenuis, of which 578 (20.3%) were infected with the parasite. Of 578 deer infected, 570 (98.6%) were harvested east of the Missouri River. Our results indicate that P. tenuis is widely distributed throughout eastern South Dakota and limited to the southcentral region of western South Dakota. Infected WTD were documented in 37 of 44 counties in eastern South Dakota and three of 22 counties in western South Dakota. No meningeal worms were found on the meninges or cranial surfaces of 215 mule deer ( Odocoileus hemionus) or 344 elk examined. These findings further define the distribution of the parasite throughout the state. We suggest that the Missouri River acts, in part, as a physical barrier to the westward expansion of P. tenuis to the grasslands of western South Dakota. PMID:15137501

  9. Bio-inspired microfluidics: The case of the velvet worm

    NASA Astrophysics Data System (ADS)

    Concha, Andres; Mellado, Paula; Morera-Brenes, Bernal; Sampaio-Costa, Cristiano; Mahadevan, L.; Monge-Najera, Julian

    The rapid squirt of a proteinaceous slime jet endow velvet worms (Onychophora) with a unique mechanism for defense from predators and for capturing prey by entangling them in a disordered web that immobilizes their target. However, to date neither qualitative nor quantitative descriptions have been provided for this unique adaptation. We have investigated the mechanism that allows velvet worms the fast oscillatory motion of their oral papillae and the exiting liquid jet that oscillates with frequencies f ~ 30 - 60 Hz. Using anatomical images and high speed videography, we show that even without fast muscular action of the papilla, a strong contraction of the slime reservoir and the geometry of the reservoir-papilla system suffices to accelerate the slime to speeds up to v ~ 5 m /s in about Δt ~ 60 ms. A theoretical analysis and a physical simulacrum allow us to infer that this fast oscillatory motion is the result of an elastohydrodynamic instability driven by the interplay between the elasticity of oral papillae and the fast unsteady flow during squirting. We propose several applications that can be implemented using this instability, ranging from high-throughput droplet production, printing, and micro-nanofiber production among others. A.C was partially supported by Fondecyt Grant 11130075.

  10. Genome analysis of Elusimicrobium minutum, the first cultivated representative of the Elusimicrobia phylum (formerly Termite Group 1)

    SciTech Connect

    Herlemann, D. P. R.; Geissinger, O.; Ikeda-Ohtsubo, W.; Kunin, V.; Sun, H.; Lapidus, A.; Hugenholtz, P.; Brune, A.

    2009-02-01

    The candidate phylum Termite group 1 (TG1), is regularly 1 encountered in termite hindguts but is present also in many other habitats. Here we report the complete genome sequence (1.64 Mbp) of Elusimicrobium minutum strain Pei191{sup T}, the first cultured representative of the TG1 phylum. We reconstructed the metabolism of this strictly anaerobic bacterium isolated from a beetle larva gut and discuss the findings in light of physiological data. E. minutum has all genes required for uptake and fermentation of sugars via the Embden-Meyerhof pathway, including several hydrogenases, and an unusual peptide degradation pathway comprising transamination reactions and leading to the formation of alanine, which is excreted in substantial amounts. The presence of genes encoding lipopolysaccharide biosynthesis and the presence of a pathway for peptidoglycan formation are consistent with ultrastructural evidence of a Gram-negative cell envelope. Even though electron micrographs showed no cell appendages, the genome encodes many genes putatively involved in pilus assembly. We assigned some to a type II secretion system, but the function of 60 pilE-like genes remains unknown. Numerous genes with hypothetical functions, e.g., polyketide synthesis, non-ribosomal peptide synthesis, antibiotic transport, and oxygen stress protection, indicate the presence of hitherto undiscovered physiological traits. Comparative analysis of 22 concatenated single-copy marker genes corroborated the status of Elusimicrobia (formerly TG1) as a separate phylum in the bacterial domain, which was so far based only on 16S rRNA sequence analysis.

  11. Bioaccumulation and food-chain analysis for evaluating ecological risks in terrestrial and wetland habitats: Availability-transfer factors (ATFs) in soil {r_arrow} soil macroinvertebrate {r_arrow} amphibian food chains

    SciTech Connect

    Linder, G.; Bollman, M.; Callahan, C.; Gillette, C.; Nebeker, A.; Wilborn, D.

    1998-12-31

    As part of the ecological risk assessment process for terrestrial and wetland habitats, the evaluation of bioaccumulative chemicals of concern (BCCs) is frequently pursued through food-chain analysis with a subsequent comparison of daily doses to benchmark toxicity reference values, when available. Food-chain analysis has frequently been applied to the analysis of exposure to BCCs identified as chemicals of potential ecological concern (COPECs) in the ecological risk assessment process. Here, designed studies focused on wetland food-chains such as hydric soil {r_arrow} soil macroinvertebrate {r_arrow} amphibian and terrestrial food-chains such as soil {r_arrow} plant {r_arrow} small mammal illustrate an approach for the derivation and validation of trophic transfer factors for metals considered as COPECs such as cadmium, chromium, copper, lead, and zinc. The results clearly indicate that the transfer of chemicals between trophic levels is critical in the bioaccumulation process in wetland and terrestrial food-chains and is influenced by numerous interacting abiotic and biotic factors, including physicochemical properties of soil, and the role, if any, that the metal has in the receptor as a required trace element.

  12. Genome Analysis of Thermosulfurimonas dismutans, the First Thermophilic Sulfur-Disproportionating Bacterium of the Phylum Thermodesulfobacteria

    PubMed Central

    Mardanov, Andrey V.; Beletsky, Alexey V.; Kadnikov, Vitaly V.; Slobodkin, Alexander I.; Ravin, Nikolai V.

    2016-01-01

    Thermosulfurimonas dismutans S95T, isolated from a deep-sea hydrothermal vent is the first bacterium of the phylum Thermodesulfobacteria reported to grow by the disproportionation of elemental sulfur, sulfite, or thiosulfate with carbon dioxide as the sole carbon source. In contrast to its phylogenetically close relatives, which are dissimilatory sulfate-reducers, T. dismutans is unable to grow by sulfate respiration. The features of this organism and its 2,1 Mb draft genome sequence are described in this report. Genome analysis revealed that the T. dismutans genome contains the set of genes for dissimilatory sulfate reduction including ATP sulfurylase, the AprA and B subunits of adenosine-5′-phosphosulfate reductase, and dissimilatory sulfite reductase. The oxidation of elemental sulfur to sulfite could be enabled by APS reductase-associated electron transfer complex QmoABC and heterodisulfide reductase. The genome also contains several membrane-linked molybdopterin oxidoreductases that are thought to be involved in sulfur metabolism as subunits of thiosulfate, polysulfide, or tetrathionate reductases. Nitrate could be used as an electron acceptor and reduced to ammonium, as indicated by the presence of periplasmic nitrate and nitrite reductases. Autotrophic carbon fixation is enabled by the Wood–Ljungdahl pathway, and the complete set of genes that is required for nitrogen fixation is also present in T. dismutans. Overall, our results provide genomic insights into energy and carbon metabolism of chemolithoautotrophic sulfur-disproportionating bacterium that could be important primary producer in microbial communities of deep-sea hydrothermal vents. PMID:27379079

  13. Isolation and Characterization of Soil Bacteria That Define Terriglobus gen. nov., in the Phylum Acidobacteria▿

    PubMed Central

    Eichorst, Stephanie A.; Breznak, John A.; Schmidt, Thomas M.

    2007-01-01

    Bacteria in the phylum Acidobacteria are widely distributed and abundant in soils, but their ecological roles are poorly understood, owing in part to a paucity of cultured representatives. In a molecular survey of acidobacterial diversity at the Michigan State University Kellogg Biological Station Long-Term Ecological Research site, 27% of acidobacterial 16S rRNA gene clones in a never-tilled, successional plant community belonged to subdivision 1, whose relative abundance varied inversely with soil pH. Strains of subdivision 1 were isolated from these never-tilled soils using low-nutrient medium incubated for 3 to 4 weeks under elevated levels of carbon dioxide, which resulted in a slightly acidified medium that matched the pH optima of the strains (between 5 and 6). Colonies were approximately 1 mm in diameter and either white or pink, the latter due to a carotenoid(s) that was synthesized preferentially under 20% instead of 2% oxygen. Strains were gram-negative, aerobic, chemo-organotrophic, nonmotile rods that produced an extracellular matrix. All strains contained either one or two copies of the 16S rRNA encoding gene, which along with a relatively slow doubling time (10 to 15 h at ca. 23°C) is suggestive of an oligotrophic lifestyle. Six of the strains are sufficiently similar to one another, but distinct from previously named Acidobacteria, to warrant creation of a new genus, Terriglobus, with Terriglobus roseus defined as the type species. The physiological and nutritional characteristics of Terriglobus are consistent with its potential widespread distribution in soil. PMID:17293520

  14. Phylogenetic placement of the enigmatic parasite, Polypodium hydriforme, within the Phylum Cnidaria

    PubMed Central

    2008-01-01

    Background Polypodium hydriforme is a parasite with an unusual life cycle and peculiar morphology, both of which have made its systematic position uncertain. Polypodium has traditionally been considered a cnidarian because it possesses nematocysts, the stinging structures characteristic of this phylum. However, recent molecular phylogenetic studies using 18S rDNA sequence data have challenged this interpretation, and have shown that Polypodium is a close relative to myxozoans and together they share a closer affinity to bilaterians than cnidarians. Due to the variable rates of 18S rDNA sequences, these results have been suggested to be an artifact of long-branch attraction (LBA). A recent study, using multiple protein coding markers, shows that the myxozoan Buddenbrockia, is nested within cnidarians. Polypodium was not included in this study. To further investigate the phylogenetic placement of Polypodium, we have performed phylogenetic analyses of metazoans with 18S and partial 28S rDNA sequences in a large dataset that includes Polypodium and a comprehensive sampling of cnidarian taxa. Results Analyses of a combined dataset of 18S and partial 28S sequences, and partial 28S alone, support the placement of Polypodium within Cnidaria. Removal of the long-branched myxozoans from the 18S dataset also results in Polypodium being nested within Cnidaria. These results suggest that previous reports showing that Polypodium and Myxozoa form a sister group to Bilateria were an artifact of long-branch attraction. Conclusion By including 28S rDNA sequences and a comprehensive sampling of cnidarian taxa, we demonstrate that previously conflicting hypotheses concerning the phylogenetic placement of Polypodium can be reconciled. Specifically, the data presented provide evidence that Polypodium is indeed a cnidarian and is either the sister taxon to Hydrozoa, or part of the hydrozoan clade, Leptothecata. The former hypothesis is consistent with the traditional view that Polypodium

  15. On the Extent and Origins of Genic Novelty in the Phylum Nematoda

    PubMed Central

    Wasmuth, James; Schmid, Ralf; Hedley, Ann; Blaxter, Mark

    2008-01-01

    Background The phylum Nematoda is biologically diverse, including parasites of plants and animals as well as free-living taxa. Underpinning this diversity will be commensurate diversity in expressed genes, including gene sets associated specifically with evolution of parasitism. Methods and Findings Here we have analyzed the extensive expressed sequence tag data (available for 37 nematode species, most of which are parasites) and define over 120,000 distinct putative genes from which we have derived robust protein translations. Combined with the complete proteomes of Caenorhabditis elegans and Caenorhabditis briggsae, these proteins have been grouped into 65,000 protein families that in turn contain 40,000 distinct protein domains. We have mapped the occurrence of domains and families across the Nematoda and compared the nematode data to that available for other phyla. Gene loss is common, and in particular we identify nearly 5,000 genes that may have been lost from the lineage leading to the model nematode C. elegans. We find a preponderance of novelty, including 56,000 nematode-restricted protein families and 26,000 nematode-restricted domains. Mapping of the latest time-of-origin of these new families and domains across the nematode phylogeny revealed ongoing evolution of novelty. A number of genes from parasitic species had signatures of horizontal transfer from their host organisms, and parasitic species had a greater proportion of novel, secreted proteins than did free-living ones. Conclusions These classes of genes may underpin parasitic phenotypes, and thus may be targets for development of effective control measures. PMID:18596977

  16. Analysis of the Na+/Ca2+ Exchanger Gene Family within the Phylum Nematoda

    PubMed Central

    He, Chao; O'Halloran, Damien M.

    2014-01-01

    Na+/Ca2+ exchangers are low affinity, high capacity transporters that rapidly transport calcium at the plasma membrane, mitochondrion, endoplasmic (and sarcoplasmic) reticulum, and the nucleus. Na+/Ca2+ exchangers are widely expressed in diverse cell types where they contribute homeostatic balance to calcium levels. In animals, Na+/Ca2+ exchangers are divided into three groups based upon stoichiometry: Na+/Ca2+ exchangers (NCX), Na+/Ca2+/K+ exchangers (NCKX), and Ca2+/Cation exchangers (CCX). In mammals there are three NCX genes, five NCKX genes and one CCX (NCLX) gene. The genome of the nematode Caenorhabditis elegans contains ten Na+/Ca2+ exchanger genes: three NCX; five CCX; and two NCKX genes. Here we set out to characterize structural and taxonomic specializations within the family of Na+/Ca2+ exchangers across the phylum Nematoda. In this analysis we identify Na+/Ca2+ exchanger genes from twelve species of nematodes and reconstruct their phylogenetic and evolutionary relationships. The most notable feature of the resulting phylogenies was the heterogeneous evolution observed within exchanger subtypes. Specifically, in the case of the CCX exchangers we did not detect members of this class in three Clade III nematodes. Within the Caenorhabditis and Pristionchus lineages we identify between three and five CCX representatives, whereas in other Clade V and also Clade IV nematode taxa we only observed a single CCX gene in each species, and in the Clade III nematode taxa that we sampled we identify NCX and NCKX encoding genes but no evidence of CCX representatives using our mining approach. We also provided re-annotation for predicted CCX gene structures from Heterorhabditis bacteriophora and Caenorhabditis japonica by RT-PCR and sequencing. Together, these findings reveal a complex picture of Na+/Ca2+ transporters in nematodes that suggest an incongruent evolutionary history of proteins that provide central control of calcium dynamics. PMID:25397810

  17. Analysis of the Na+/Ca2+ exchanger gene family within the phylum Nematoda.

    PubMed

    He, Chao; O'Halloran, Damien M

    2014-01-01

    Na+/Ca2+ exchangers are low affinity, high capacity transporters that rapidly transport calcium at the plasma membrane, mitochondrion, endoplasmic (and sarcoplasmic) reticulum, and the nucleus. Na+/Ca2+ exchangers are widely expressed in diverse cell types where they contribute homeostatic balance to calcium levels. In animals, Na+/Ca2+ exchangers are divided into three groups based upon stoichiometry: Na+/Ca2+ exchangers (NCX), Na+/Ca2+/K+ exchangers (NCKX), and Ca2+/Cation exchangers (CCX). In mammals there are three NCX genes, five NCKX genes and one CCX (NCLX) gene. The genome of the nematode Caenorhabditis elegans contains ten Na+/Ca2+ exchanger genes: three NCX; five CCX; and two NCKX genes. Here we set out to characterize structural and taxonomic specializations within the family of Na+/Ca2+ exchangers across the phylum Nematoda. In this analysis we identify Na+/Ca2+ exchanger genes from twelve species of nematodes and reconstruct their phylogenetic and evolutionary relationships. The most notable feature of the resulting phylogenies was the heterogeneous evolution observed within exchanger subtypes. Specifically, in the case of the CCX exchangers we did not detect members of this class in three Clade III nematodes. Within the Caenorhabditis and Pristionchus lineages we identify between three and five CCX representatives, whereas in other Clade V and also Clade IV nematode taxa we only observed a single CCX gene in each species, and in the Clade III nematode taxa that we sampled we identify NCX and NCKX encoding genes but no evidence of CCX representatives using our mining approach. We also provided re-annotation for predicted CCX gene structures from Heterorhabditis bacteriophora and Caenorhabditis japonica by RT-PCR and sequencing. Together, these findings reveal a complex picture of Na+/Ca2+ transporters in nematodes that suggest an incongruent evolutionary history of proteins that provide central control of calcium dynamics. PMID:25397810

  18. Description of a Riboflavin Biosynthetic Gene Variant Prevalent in the Phylum Proteobacteria

    PubMed Central

    Brutinel, Evan D.; Dean, Antony M.

    2013-01-01

    Riboflavin (vitamin B2) is the precursor of flavin mononucleotide and flavin adenine dinucleotide, which are cofactors essential for a host of intracellular redox reactions. Microorganisms synthesize flavins de novo to fulfill nutritional requirements, but it is becoming increasingly clear that flavins play a wider role in cellular physiology than was previously appreciated. Flavins mediate diverse processes beyond the cytoplasmic membrane, including iron acquisition, extracellular respiration, and interspecies interactions. While investigating the regulation of flavin electron shuttle biosynthesis in the Gram-negative gammaproteobacterium Shewanella oneidensis, we discovered that a riboflavin biosynthetic gene (ribBA) annotated as encoding a bifunctional 3,4-dihydroxy-2-butanone 4-phosphate (DHBP) synthase/GTP cyclohydrolase II does not possess both functions. The novel gene, renamed ribBX here, encodes an amino-terminal DHBP synthase domain. The carboxy-terminal end of RibBX not only lacks GTP cyclohydrolase II activity but also has evolved a different function altogether in S. oneidensis, regulating the activity of the DHBP synthase domain. Phylogenetic analysis revealed that the misannotation of ribBX as ribBA is rampant throughout the phylum Proteobacteria (40% of 2,173 annotated ribBA genes) and that ribBX emerged early in the evolution of this group of microorganisms. We examined the functionality of representative ribBX genes from Beta-, Gamma-, and Epsilonproteobacteria and found that, consistent with sequence-based predictions, the encoded GTP cyclohydrolase II domains lack catalytic activity. The persistence of ribBX in the genomes of so many phylogenetically divergent bacterial species lends weight to the argument that ribBX has evolved a function which lends a selective advantage to the host. PMID:24097946

  19. In Silico Analysis of the Metabolic Potential and Niche Specialization of Candidate Phylum "Latescibacteria" (WS3).

    PubMed

    Youssef, Noha H; Farag, Ibrahim F; Rinke, Christian; Hallam, Steven J; Woyke, Tanja; Elshahed, Mostafa S

    2015-01-01

    The "Latescibacteria" (formerly WS3), member of the Fibrobacteres-Chlorobi-Bacteroidetes (FCB) superphylum, represents a ubiquitous candidate phylum found in terrestrial, aquatic, and marine ecosystems. Recently, single-cell amplified genomes (SAGs) representing the "Latescibacteria" were obtained from the anoxic monimolimnion layers of Sakinaw Lake (British Columbia, Canada), and anoxic sediments of a coastal lagoon (Etoliko lagoon, Western Greece). Here, we present a detailed in-silico analysis of the four SAGs to gain some insights on their metabolic potential and apparent ecological roles. Metabolic reconstruction suggests an anaerobic fermentative mode of metabolism, as well as the capability to degrade multiple polysaccharides and glycoproteins that represent integral components of green (Charophyta and Chlorophyta) and brown (Phaeophycaea) algae cell walls (pectin, alginate, ulvan, fucan, hydroxyproline-rich glycoproteins), storage molecules (starch and trehalose), and extracellular polymeric substances (EPSs). The analyzed SAGs also encode dedicated transporters for the uptake of produced sugars and amino acids/oligopeptides, as well as an extensive machinery for the catabolism of all transported sugars, including the production of a bacterial microcompartment (BMC) to sequester propionaldehyde, a toxic intermediate produced during fucose and rhamnose metabolism. Finally, genes for the formation of gas vesicles, flagella, type IV pili, and oxidative stress response were found, features that could aid in cellular association with algal detritus. Collectively, these results indicate that the analyzed "Latescibacteria" mediate the turnover of multiple complex organic polymers of algal origin that reach deeper anoxic/microoxic habitats in lakes and lagoons. The implications of such process on our understanding of niche specialization in microbial communities mediating organic carbon turnover in stratified water bodies are discussed. PMID:26039074

  20. In Silico Analysis of the Metabolic Potential and Niche Specialization of Candidate Phylum "Latescibacteria" (WS3)

    PubMed Central

    Youssef, Noha H.; Farag, Ibrahim F.; Rinke, Christian; Hallam, Steven J.; Woyke, Tanja; Elshahed, Mostafa S.

    2015-01-01

    The “Latescibacteria” (formerly WS3), member of the Fibrobacteres–Chlorobi–Bacteroidetes (FCB) superphylum, represents a ubiquitous candidate phylum found in terrestrial, aquatic, and marine ecosystems. Recently, single-cell amplified genomes (SAGs) representing the “Latescibacteria” were obtained from the anoxic monimolimnion layers of Sakinaw Lake (British Columbia, Canada), and anoxic sediments of a coastal lagoon (Etoliko lagoon, Western Greece). Here, we present a detailed in-silico analysis of the four SAGs to gain some insights on their metabolic potential and apparent ecological roles. Metabolic reconstruction suggests an anaerobic fermentative mode of metabolism, as well as the capability to degrade multiple polysaccharides and glycoproteins that represent integral components of green (Charophyta and Chlorophyta) and brown (Phaeophycaea) algae cell walls (pectin, alginate, ulvan, fucan, hydroxyproline-rich glycoproteins), storage molecules (starch and trehalose), and extracellular polymeric substances (EPSs). The analyzed SAGs also encode dedicated transporters for the uptake of produced sugars and amino acids/oligopeptides, as well as an extensive machinery for the catabolism of all transported sugars, including the production of a bacterial microcompartment (BMC) to sequester propionaldehyde, a toxic intermediate produced during fucose and rhamnose metabolism. Finally, genes for the formation of gas vesicles, flagella, type IV pili, and oxidative stress response were found, features that could aid in cellular association with algal detritus. Collectively, these results indicate that the analyzed “Latescibacteria” mediate the turnover of multiple complex organic polymers of algal origin that reach deeper anoxic/microoxic habitats in lakes and lagoons. The implications of such process on our understanding of niche specialization in microbial communities mediating organic carbon turnover in stratified water bodies are discussed. PMID

  1. Defending against Internet worms using a phase space method from chaos theory

    NASA Astrophysics Data System (ADS)

    Hu, Jing; Gao, Jianbo; Rao, Nageswara S.

    2007-04-01

    Enterprise networks are facing ever-increasing security threats from Distributed Denial of Service (DDoS) attacks, worms, viruses, intrusions, Trojans, port scans, and network misuses, and thus effective monitoring approaches to quickly detect these activities are greatly needed. In this paper, we employ chaos theory and propose an interesting phase space method to detect Internet worms. An Internet worm is a self-propagating program that automatically replicates itself to vulnerable systems and spreads across the Internet. Most deployed worm-detection systems are signature-based. They look for specific byte sequences (called attack signatures) that are known to appear in the attack traffic. Conventionally, the signatures are manually identified by human experts through careful analysis of the byte sequence from captured attack traffic. We propose to embed the traffic sequence to a high-dimensional phase space using chaos theory. We have observed that the signature sequence of a specific worm will occupy specific regions in the phase space, which may be appropriately called the invariant subspace of the worm. The invariant subspace of the worm separates itself widely from the subspace of the normal traffic. This separation allows us to construct three simple metrics, each of which completely separates 100 normal traffic streams from 200 worm traffic streams, without training in the conventional sense. Therefore, the method is at least as accurate as any existing methods. More importantly, our method is much faster than existing methods, such as based on expectation maximization and hidden Markov models.

  2. Worms in the College Classroom: More than Just a Composting Demonstration

    ERIC Educational Resources Information Center

    Kelley, Rebecca L.

    2010-01-01

    Although worm bins have been used by K-12 and nonformal educators for decades, there is little evidence of their use in postsecondary education. The ease of use, maintenance, affordability, portability, and diversity of scientific concepts that can be demonstrated with a worm bin make it a valuable tool in college science classrooms. The purpose…

  3. Worms Expelled With the Urine From a Bosniak Cyst III of the Left Kidney.

    PubMed

    Yang, Jie; Li, Pu; Su, Chuan; Zhang, Jia-Yi; Gu, Min

    2016-07-01

    An old fishman presented with left lumbago and finding worms in his urine. Type-B ultrasonic inspection and computed tomography scan found a Bosniak cyst III, containing several wire-like elements, in the middle of the left kidney. Expelled worms were confirmed to be Dioctophyma renale. After two courses of albendazole, the man was cured. PMID:27015940

  4. New result on K{sup +} {r_arrow} {pi}{sup +} {nu}{bar {nu}} from BNL E787

    SciTech Connect

    REDLINGER,G.

    1999-06-21

    E787 at BNL has reported evidence for the rare decay K{sup +} {r_arrow} {pi}{sup +}{nu}{bar {nu}}, based on the observation of one candidate event. In this paper, we present the result of analyzing a new dataset of comparable sensitivity to the published result.

  5. Comparison of gunshot wounds and field-tipped arrow wounds using morphological criteria and chemical spot tests.

    PubMed

    Randall, B; Newby, P

    1989-05-01

    Arrow wounds represent an unusual class of wounds rarely seen by most death investigators. Although the edged, broadhead-tipped arrow produces a wound usually characteristic of archery/crossbow weapons, the plain, field-tipped arrow wound can be confused with gunshot injuries in those cases in which powder residue or firearm projectiles or fragments or both are not recovered. We present a case of a deer carcass with a wound of uncertain firearm or archery origin which initiated a comparison of firearm wounds and archery wounds on fresh road-killed deer. We found the following features to be valuable in the differentiation of gunshot wounds and field-tipped archery wounds: First, the majority of the gunshot wounds (but none of the arrow wounds) had identifiable, macroscopic, wipe-off material and chemically identifiable wipe-off residue by spot test. Second, the archery wound defects had very inconspicuous abrasion rings as compared to the often prominent abrasion rings of gunshot wounds. Third, the actual central defect in the archery wounds was more likely to be oblong or slit-like compared to the gunshot wound defects, which were more likely to be round. PMID:2738561

  6. The invention of the pilidium larva in an otherwise perfectly good spiralian phylum Nemertea.

    PubMed

    Maslakova, Svetlana A

    2010-11-01

    One of the most remarkable larval types among spiralians, and invertebrates in general, is the planktotrophic pilidium. The pilidium is found in a single clade of nemerteans, called the Pilidiophora, and appears to be an innovation of this group. All other nemerteans have either planktotrophic or lecithotrophic juvenile-like planuliform larvae or have direct development. The invention of the pilidium larva is associated with the formation of an extensive blastocoel that supports the delicate larval frame and elaborate ciliary band. Perhaps the most striking characteristic of the pilidium is the way the juvenile worm develops inside the larva from a series of isolated rudiments, called the imaginal discs. The paired cephalic discs, cerebral organ discs, and trunk discs originate as invaginations of larval epidermis and subsequently grow and fuse around the larval gut to form the juvenile. The fully formed juvenile ruptures the larval body and, more often than not, devours the larva during catastrophic metamorphosis. This review is an attempt to examine the pilidium in the context of recent data on development of non-pilidiophoran nemerteans, and speculate about the evolution of pilidial larval development. The author emphasizes the difference between the planuliform larvae of Palaeonemerteans and Hoplonemerteans, and suggest a new name for the hoplonemertean larvae--the decidula. PMID:21558236

  7. Global dynamics of a novel multi-group model for computer worms

    NASA Astrophysics Data System (ADS)

    Gong, Yong-Wang; Song, Yu-Rong; Jiang, Guo-Ping

    2013-04-01

    In this paper, we study worm dynamics in computer networks composed of many autonomous systems. A novel multi-group SIQR (susceptible-infected-quarantined-removed) model is proposed for computer worms by explicitly considering anti-virus measures and the network infrastructure. Then, the basic reproduction number of worm R0 is derived and the global dynamics of the model are established. It is shown that if R0 is less than or equal to 1, the disease-free equilibrium is globally asymptotically stable and the worm dies out eventually, whereas, if R0 is greater than 1, one unique endemic equilibrium exists and it is globally asymptotically stable, thus the worm persists in the network. Finally, numerical simulations are given to illustrate the theoretical results.

  8. Ethnophysiology and herbal treatments of intestinal worms in Dominica, West Indies.

    PubMed

    Quinlan, Marsha B; Quinlan, Robert J; Nolan, Justin M

    2002-04-01

    In rural Dominican ethnophysiology worms reside in a human organ called the 'worm bag'. Unchecked, worms can cause illness by growing in size and number, spreading out of the worm bag and into other organs. In this study of 'bush medicine', we use a measure of cognitive salience in free-listing tasks, which reveals five plants commonly used to treat intestinal worms. These were Ambrosia hispida (Asteraceae), Aristolochia trilobata (Aristlochiaceae), Chenopodium ambrosioides (Chenopodiaceae), Portulaca oleracea (Portulacaceae), and Artemisia absinthium (Asteraceae). Bioactive compounds appear to be present in all of these plants. The cognitive salience of these plant remedies coupled with evidence of biochemical properties suggest that they provide efficacious treatments for controlling intestinal parasite loads. PMID:11891089

  9. Graphical method for profiling hob mill that generate cycloid worms

    NASA Astrophysics Data System (ADS)

    Teodor, V.; Berbinschi, S.; Baroiu, N.; Oancea, N.

    2015-11-01

    The hob mill for generating ordered curls of cycloid surface with non involute profiles may be profiled based on the fundamental theorems of surface enveloping - Olivier - as surface reciprocally enveloping with point like contact. In this paper, is proposed a methodology based on a complementary theorem of the surface enveloping in a graphical expression developed in a graphical design environment - CATIA. The graphical method presented in this paper is developed in two stages: determining of the rack gear model based on the solid model of the surface to be generated, using an original algorithm, following this, based on 3D modelling is determined the solid model of the primary peripheral surface of the hob mill. An application for a cycloid worm is presented - a central screw of helical pumps. In order to prove the quality of method, the analytical and graphical solutions are comparatively presented.

  10. Not whale-fall specialists, Osedax worms also consume fishbones

    PubMed Central

    Rouse, Greg W.; Goffredi, Shana K.; Johnson, Shannon B.; Vrijenhoek, Robert C.

    2011-01-01

    Marine annelid worms of the genus Osedax exploit sunken vertebrate bones for food. To date, the named species occur on whale or other mammalian bones, and it is argued that Osedax is a whale-fall specialist. To assess whether extant Osedax species could obtain nutrition from non-mammalian resources, we deployed teleost bones and calcified shark cartilage at approximately 1000 m depth for five months. Although the evidence from shark cartilage was inconclusive, the teleost bones hosted three species of Osedax, each of which also lives off whalebones. This suggests that rather than being a whale-fall specialist, Osedax has exploited and continues to exploit a variety of food sources. The ability of Osedax to colonize and to grow on fishbone lends credibility to a hypothesis that it might have split from its siboglinid relatives to assume the bone-eating lifestyle during the Cretaceous, well before the origin of marine mammals. PMID:21490008

  11. Worm-like instability of a vibrated sessile drop

    NASA Astrophysics Data System (ADS)

    Hemmerle, A.; Froehlicher, G.; Bergeron, V.; Charitat, T.; Farago, J.

    2015-07-01

    We study the effects of vertical sinusoidal vibrations on a liquid droplet with a low surface tension (ethanol) deposited on a solid substrate. In a precise range of amplitudes and frequencies, the drop exhibits a dramatic worm-like shape instability with a strong symmetry breaking, comparable to the one observed by Pucci et al. (Phys. Rev. Lett., 106 (2011) 024503) on a vibrated floating lens. However, the geometry of our system is much simpler since it does not involve the oscillation and deformation of a liquid-liquid-air contact line. We show that the Faraday waves appearing on the surface of the droplet control its shape and we draw a systematic phase diagram of the instability. A simple theoretical model allows us to derive a relation between the elongation of the droplet and the amplitude of the Faraday wave, in good agreement with measurements of both quantities.

  12. Hybrid Epidemics—A Case Study on Computer Worm Conficker

    PubMed Central

    Zhang, Changwang; Zhou, Shi; Chain, Benjamin M.

    2015-01-01

    Conficker is a computer worm that erupted on the Internet in 2008. It is unique in combining three different spreading strategies: local probing, neighbourhood probing, and global probing. We propose a mathematical model that combines three modes of spreading: local, neighbourhood, and global, to capture the worm’s spreading behaviour. The parameters of the model are inferred directly from network data obtained during the first day of the Conficker epidemic. The model is then used to explore the tradeoff between spreading modes in determining the worm’s effectiveness. Our results show that the Conficker epidemic is an example of a critically hybrid epidemic, in which the different modes of spreading in isolation do not lead to successful epidemics. Such hybrid spreading strategies may be used beneficially to provide the most effective strategies for promulgating information across a large population. When used maliciously, however, they can present a dangerous challenge to current internet security protocols. PMID:25978309

  13. Wombs, Worms and Wolves: Constructing Cancer in Early Modern England

    PubMed Central

    Skuse, Alanna

    2014-01-01

    This essay examines medical and popular attitudes to cancer in the early modern period, c.1580–1720. Cancer, it is argued, was understood as a cruel and usually incurable disease, diagnosable by a well-defined set of symptoms understood to correspond to its etymological root, karkinos (the crab). It was primarily understood as produced by an imbalance of the humours, with women being particularly vulnerable. However, such explanations proved inadequate to make sense of the condition's malignancy, and medical writers frequently constructed cancer as quasi-sentient, zoomorphising the disease as an eating worm or wolf. In turn, these constructions materially influenced medical practice, in which practitioners swung between anxiety over ‘aggravating’ the disease and an adversarial approach which fostered the use of radical and dangerous ‘cures’ including caustics and surgery. PMID:25352720

  14. Not whale-fall specialists, Osedax worms also consume fishbones.

    PubMed

    Rouse, Greg W; Goffredi, Shana K; Johnson, Shannon B; Vrijenhoek, Robert C

    2011-10-23

    Marine annelid worms of the genus Osedax exploit sunken vertebrate bones for food. To date, the named species occur on whale or other mammalian bones, and it is argued that Osedax is a whale-fall specialist. To assess whether extant Osedax species could obtain nutrition from non-mammalian resources, we deployed teleost bones and calcified shark cartilage at approximately 1000 m depth for five months. Although the evidence from shark cartilage was inconclusive, the teleost bones hosted three species of Osedax, each of which also lives off whalebones. This suggests that rather than being a whale-fall specialist, Osedax has exploited and continues to exploit a variety of food sources. The ability of Osedax to colonize and to grow on fishbone lends credibility to a hypothesis that it might have split from its siboglinid relatives to assume the bone-eating lifestyle during the Cretaceous, well before the origin of marine mammals. PMID:21490008

  15. Postembryonic development of the bone-eating worm Osedax japonicus

    NASA Astrophysics Data System (ADS)

    Miyamoto, Norio; Yamamoto, Tomoko; Yusa, Yoichi; Fujiwara, Yoshihiro

    2013-03-01

    Bone-eating worms of the genus Osedax exclusively inhabit sunken vertebrate bones on the seafloor. The unique lifestyle and morphology of Osedax spp. have received much scientific attention, but the whole process of their development has not been observed. We herein report the postembryonic development and settlement of Osedax japonicus Fujikura et al. (Zool Sci 23:733-740, 2006). Fertilised eggs were spawned into the mucus of a female, and the larvae swam out from the mucus at the trochophore stage. Larvae survived for 10 days under laboratory conditions. The larvae settled on bones, elongated their bodies and crawled around on the bones. Then they secreted mucus to create a tube and the palps started to develop. The palps of O. japonicus arose from the prostomium, whereas the anterior appendages of other siboglinids arose from the peristomium. The recruitment of dwarf males was induced by rearing larvae with adult females. Females started to spawn eggs 6 weeks after settlement.

  16. An unusual and unsettling place for a worm.

    PubMed

    Samuel, M I; Taylor, C

    2010-07-01

    A 56-year-old man presented complaining of urinary frequency, passing urine eight times per day, urethral irritation and dysuria. Investigations showed no evidence of urinary tract infection or sexually transmitted infections. Three months later he presented, again complaining of increased urinary frequency and urethral irritation. He brought with him a urine specimen containing a small 'worm', 2 mm in length, identified as a drain fly (or moth fly) larva, of the genus Psychoda (dipterous flies). Psychoda lay eggs in organically polluted water such as sewage plants, sink drains or on decaying vegetables and fruits. Urogenital myiasis may arise from hatching of larvae near the urethral opening and ascending migration along the urethra with consequent urethritis. Following larval identification, ivermectin was prescribed and the man's symptoms improved after six weeks. PMID:20852207

  17. Trichuris suis: thiol protease activity from adult worms.

    PubMed

    Hill, D E; Sakanari, J A

    1997-01-01

    Trichuris suis, the whipworm of swine, causes anemia, weight loss, anorexia, mucohemorrhagic diarrhea, and death in heavy infections. A zinc metalloprotease has been suggested to play a role in the severe enteric pathology associated with infection and the infiltration of opportunistic bacteria into deeper tissues in the swine colon. In this study, a thiol protease from gut extracts of adult T. suis and from excretory/secretory components (E/S) of adult worms was characterized using fluorogenic peptide substrates and protein substrate gels. The protease cleaved the fluorogenic substrate Z-Phe-Arg-AMC, and this cleavage was completely inhibited by the thiol protease inhibitors E-64, leupeptin, Z-Phe-Ala-CH2F, and Z-Phe-Arg-CH2F. Gelatin substrate gels and fluorescence assays using both the gut and the stichosome extracts and E/S revealed enhanced activity when 2 mM dithiothreitol or 5 mM cysteine was included in the incubation buffer, and optimal activity was seen over a pH range of 5.5 to 8.5. Incubation of gut extracts or E/S material with inhibitors of aspartic, serine, or metalloproteases had no effect on the cleavage of Z-Phe-Arg-AMC. Thiol protease activity was found in extracts of gut tissue but not in the extracts of stichocytes of adult worms. N-terminal amino acid sequencing of the protease revealed sequence homologies with cathepsin B-like thiol protease identified from parasitic and free-living nematodes. PMID:9024202

  18. Two Leucobacter strains exert complementary virulence on Caenorhabditis including death by worm-star formation.

    PubMed

    Hodgkin, Jonathan; Félix, Marie-Anne; Clark, Laura C; Stroud, Dave; Gravato-Nobre, Maria J

    2013-11-01

    The nematode Caenorhabditis elegans has been much studied as a host for microbial infection. Some pathogens can infect its intestine, while others attack via its external surface. Cultures of Caenorhabditis isolated from natural environments have yielded new nematode pathogens, such as microsporidia and viruses. We report here a novel mechanism for bacterial attack on worms, discovered during investigation of a diseased and coinfected natural isolate of Caenorhabditis from Cape Verde. Two related coryneform pathogens (genus Leucobacter) were obtained from this isolate, which had complementary effects on C. elegans and related nematodes. One pathogen, Verde1, was able to cause swimming worms to stick together irreversibly by their tails, leading to the rapid formation of aggregated "worm-stars." Adult worms trapped in these aggregates were immobilized and subsequently died, with concomitant growth of bacteria. Trapped larval worms were sometimes able to escape from worm-stars by undergoing autotomy, separating their bodies into two parts. The other pathogen, Verde2, killed worms after rectal invasion, in a more virulent version of a previously studied infection. Resistance to killing by Verde2, by means of alterations in host surface glycosylation, resulted in hypersensitivity to Verde1, revealing a trade-off in bacterial susceptibility. Conversely, a sublethal surface infection of worms with Verde1 conferred partial protection against Verde2. The formation of worm-stars by Verde1 occurred only when worms were swimming in liquid but provides a striking example of asymmetric warfare as well as a bacterial equivalent to the trapping strategies used by nematophagous fungi. PMID:24206844

  19. Clinical results of meniscus repair with the meniscus arrow: a 4- to 8-year follow-up study.

    PubMed

    Koukoulias, Nikolaos; Papastergiou, Stergios; Kazakos, Konstantinos; Poulios, Georgios; Parisis, Konstantinos

    2007-02-01

    The short-term clinical results of meniscus repair with the meniscus arrow were promising. Unfavorable outcomes were reported in two studies, with longer follow-up, raising concerns about the efficacy of this device. We retrospectively reviewed 62 patients (mean age 23.7 years; range 14-37 years) that underwent all-inside meniscus repair, using the meniscus arrow. Seventeen patients had an isolated meniscus tear (ACL intact group) and 45 patients concomitant ACL rupture that was reconstructed at the same time with the meniscus repair (ACL reconstructed group). All patients followed a non-aggressive rehabilitation protocol. Follow-up was assessed by clinical examination, Lysholm and Tegner score, IKDC knee examination form and KT-2000 arthrometry for the anteroposterior laxity of the reconstructed knees. At an average follow-up of 73 months (range 49-96 months) there were three failures (4.8%), one from the ACL intact group and two from the ACL reconstructed group. One patient developed arthrofibrosis (ACL reconstructed group) that resolved conservatively. Soft tissue irritation at the repair site was noted in three patients. In two patients the symptoms were transient. In the third patient the arrow tip was cut off under local anaesthesia due to saphenous infrapatellar branch irritation and the symptoms resolved (inappropriate arrow size). KT-2000 arthrometry showed that sagittal knee laxity was less than 3 mm in all reconstructed knees. The mean Tegner activity score decreased from 6.7 (pretrauma) to 6.2 (postoperatively). The average Lysholm score was 96, with normal or nearly normal function of all success knees, according to the IKDC knee examination form. Our results show a high clinical success rate of meniscus repair with the meniscus arrow. We found this device both safe and effective. PMID:16858563

  20. Effect of a simulated engine jet blowing above an arrow wing at Mach 2.0

    NASA Technical Reports Server (NTRS)

    Shrout, B. L.; Hayes, C.

    1977-01-01

    The effects of a gas jet simulating a turbojet engine exhaust blowing above a cambered and twisted arrow wing were investigated. Tests were conducted in the Langley 4-foot supersonic pressure tunnel at a Mach number of 2.0. Nozzle pressure ratios from 1 to 64 were tested with both helium and air used as jet gases. The tests were conducted at angles of attack from -2 deg to 8 deg at a Reynolds number of 9,840,000 per meter. Only the forces and moments on the wing were measured. Results of the investigation indicated that the jet blowing over the wing caused reductions in maximum lift-drag ratio of about 4 percent for helium and 6 percent for air at their respective design nozzle pressure ratios, relative to jet-off data. Moderate changes in the longitudinal, vertical, or angular positions of the jet relative to the wing had little effect on the wing aerodynamic characteristics.

  1. Study of advanced composite structural design concepts for an arrow wing supersonic cruise configuration

    NASA Technical Reports Server (NTRS)

    Turner, M. J.; Grande, D. L.

    1978-01-01

    Based on estimated graphite and boron fiber properties, allowable stresses and strains were established for advanced composite materials. Stiffened panel and conventional sandwich panel concepts were designed and analyzed, using graphite/polyimide and boron/polyimide materials. The conventional sandwich panel was elected as the structural concept for the modified wing structure. Upper and lower surface panels of the arrow wing structure were then redesigned, using high strength graphite/polyimide sandwich panels, retaining the titanium spars and ribs from the prior study. The ATLAS integrated analysis and design system was used for stress analysis and automated resizing of surface panels. Flutter analysis of the hybrid structure showed a significant decrease in flutter speed relative to the titanium wing design. The flutter speed was increased to that of the titanium design by selective increase in laminate thickness and by using graphite fibers with properties intermediate between high strength and high modulus values.

  2. Evaluation of structural design concepts for an arrow-wing supersonic cruise aircraft

    NASA Technical Reports Server (NTRS)

    Sakata, I. F.; Davis, G. W.

    1977-01-01

    An analytical study was performed to determine the best structural approach for design of primary wing and fuselage structure of a Mach 2.7 arrow wing supersonic cruise aircraft. Concepts were evaluated considering near term start of design. Emphasis was placed on the complex interactions between thermal stress, static aeroelasticity, flutter, fatigue and fail safe design, static and dynamic loads, and the effects of variations in structural arrangements, concepts and materials on these interactions. Results indicate that a hybrid wing structure incorporating low profile convex beaded and honeycomb sandwich surface panels of titanium alloy 6Al-4V were the most efficient. The substructure includes titanium alloy spar caps reinforced with boron polyimide composites. The fuselage shell consists of hat stiffened skin and frame construction of titanium alloy 6Al-4V. A summary of the study effort is presented, and a discussion of the overall logic, design philosophy and interaction between the analytical methods for supersonic cruise aircraft design are included.

  3. Scan path entropy and arrow plots: capturing scanning behavior of multiple observers.

    PubMed

    Hooge, Ignace; Camps, Guido

    2013-01-01

    Designers of visual communication material want their material to attract and retain attention. In marketing research, heat maps, dwell time, and time to AOI first hit are often used as evaluation parameters. Here we present two additional measures (1) "scan path entropy" to quantify gaze guidance and (2) the "arrow plot" to visualize the average scan path. Both are based on string representations of scan paths. The latter also incorporates transition matrices and time required for 50% of the observers to first hit AOIs (T50). The new measures were tested in an eye tracking study (48 observers, 39 advertisements). Scan path entropy is a sensible measure for gaze guidance and the new visualization method reveals aspects of the average scan path and gives a better indication in what order global scanning takes place. PMID:24399993

  4. Titanium and advanced composite structures for a supersonic cruise arrow wing configuration

    NASA Technical Reports Server (NTRS)

    Turner, M. J.; Hoy, J. M.

    1976-01-01

    Structural design studies were made, based on current technology and on an estimate of technology to be available in the mid 1980's, to assess the relative merits of structural concepts and materials for an advanced arrow wing configuration cruising at Mach 2.7. Preliminary studies were made to insure compliance of the configuration with general design criteria, integrate the propulsion system with the airframe, and define an efficient structural arrangement. Material and concept selection, detailed structural analysis, structural design and airplane mass analysis were completed based on current technology. Based on estimated future technology, structural sizing for strength and a preliminary assessment of the flutter of a strength designed composite structure were completed. An advanced computerized structural design system was used, in conjunction with a relatively complex finite element model, for detailed analysis and sizing of structural members.

  5. The f0 Mesons in Processes pi][pi [right arrow] [pi][pi], KK

    NASA Astrophysics Data System (ADS)

    Surovtsev, Yu. S.; Krupa, D.; Nagy, M.

    2002-06-01

    Combined analysis the experimental data on the processes pi][pi [right arrow] pi][pi, KK in the channel with IGJPC = 0+0++ in a model-independent approach leads to the following results: 1) The f0(665) state with properties of the sigma-meson is proved to exist; 2) It is shown that the f0(980) and especially f0(1370) (if exists) have a dominant ss component; 3) Indications for the glueball nature of the f0(1500) and for the considerable ss component in the f0(1710) are obtained; 4) Conclusion on the linear realization of chiral symmetry (chiS) is drawn.

  6. Scan path entropy and arrow plots: capturing scanning behavior of multiple observers

    PubMed Central

    Hooge, Ignace; Camps, Guido

    2013-01-01

    Designers of visual communication material want their material to attract and retain attention. In marketing research, heat maps, dwell time, and time to AOI first hit are often used as evaluation parameters. Here we present two additional measures (1) “scan path entropy” to quantify gaze guidance and (2) the “arrow plot” to visualize the average scan path. Both are based on string representations of scan paths. The latter also incorporates transition matrices and time required for 50% of the observers to first hit AOIs (T50). The new measures were tested in an eye tracking study (48 observers, 39 advertisements). Scan path entropy is a sensible measure for gaze guidance and the new visualization method reveals aspects of the average scan path and gives a better indication in what order global scanning takes place. PMID:24399993

  7. Low-speed wind tunnel investigation of an advanced supersonic cruise arrow-wing configuration

    NASA Technical Reports Server (NTRS)

    Coe, P. L., Jr.; Smith, P. M.; Parlett, L. P.

    1977-01-01

    A preliminary assessment of possible means for improving the low speed aerodynamic characteristics of advanced supersonic cruise arrow wing configurations and to extend the existing data base of such configurations has been made. Principle configuration variables included wing-leading and trailing-edge flap deflection, fuselage nose strakes, and engine exhaust nozzle deflection. Results showed that deflecting the wing leading edge apex flaps downward provided improved longitudinal stability but resulted in reduced directional stability. The model exhibited relatively low values of directional stability over the operational angle of attack range and experienced large asymmetric yawing moments at high angles of attack. The use of nose strakes was found to be effective in increasing the directional stability and eliminating the asymmetric yawing moment.

  8. Time asymmetry of probabilities versus relativistic causal structure: an arrow of time.

    PubMed

    Coecke, Bob; Lal, Raymond

    2012-05-18

    There is an incompatibility between the symmetries of causal structure in relativity theory and the signaling abilities of probabilistic devices with inputs and outputs: while time reversal in relativity will not introduce the ability to signal between spacelike separated regions, this is not the case for probabilistic devices with spacelike separated input-output pairs. We explicitly describe a nonsignaling device which becomes a perfect signaling device under time reversal, where time reversal can be conceptualized as playing backwards a videotape of an agent manipulating the device. This leads to an arrow of time that is identifiable when studying the correlations of events for spacelike separated regions. Somewhat surprisingly, although the time reversal of Popescu-Rohrlich boxes also allows agents to signal, it does not yield a perfect signaling device. Finally, we realize time reversal using postselection, which could to lead experimental implementation. PMID:23003129

  9. Nonstandard. gamma. gamma. r arrow l sup + l minus processes in relativistic heavy-ion collisions

    SciTech Connect

    Almeida, L.D.; Natale, A.A.; Novaes, S.F. ); Eboli, O.J.P. )

    1991-07-01

    We study lepton pair production in heavy-ion collisions with emphasis on nonstandard contributions to the QED subprocess {gamma}{gamma}{r arrow}{ital l}{sup +}{ital l{minus}}. The existence of compositeness of fermions and/or bosons can be tested in this reaction up to the TeV mass scale. We show that for some processes the capabilities of relativistic heavy-ion colliders to disclose new physics surpass the possibilities of {ital e}{sup +}{ital e{minus}} or {ital p{bar p}} machines. In particular, spin-zero composite particles which couple predominantly to two photons, predicted in composite models, can be studied in a broad range of masses.

  10. The emergence of time's arrows and special science laws from physics

    PubMed Central

    Loewer, Barry

    2012-01-01

    In this paper, I will argue that there is an important connection between two questions concerning how certain features of the macro world emerge from the laws and processes of fundamental microphysics and suggest an approach to answering these questions. The approach involves a kind of emergence but quite different from ‘top-down’ emergence discussed at the conference, for which an earlier version of this paper was written. The two questions are (i) How do ‘the arrows of time’ emerge from microphysics? (ii) How do macroscopic special science laws and causation emerge from microphysics? Answering these questions is especially urgent for those, who like myself, think that a certain version of physicalism, which I call ‘micro-physical completeness’ (MC), is true. According to MC, there are fundamental dynamical laws that completely govern (deterministically or probabilistically), the evolution of all micro-physical events and there are no additional ontologically independent dynamical or causal special science laws. In other words, there is no ontologically independent ‘top-down’ causation. Of course, MC does not imply that physicists now or ever will know or propose the complete laws of physics. Or even if the complete laws were known we would know how special science properties and laws reduce to laws and properties of fundamental physics. Rather, MC is a contingent metaphysical claim about the laws of our world. After a discussion of the two questions, I will argue the key to showing how it is possible for the arrows of time and the special science laws to emerge from microphysics and a certain account of how thermodynamics is related to fundamental dynamical laws. PMID:23386956

  11. Time's Arrow and Archimedes' Point - New Directions for the Physics of Time

    NASA Astrophysics Data System (ADS)

    Price, Huw

    1997-12-01

    Why is the future so different from the past? Why does the past affect the future and not the other way around? What does quantum mechanics really tell us about the world? In this important and accessible book, Huw Price throws fascinating new light these great mysteries of modern physics, and connects them in a wholly original way. Price begins with the mystery of the arrow of time. Price shows that, for over a century, most physicists have thought about problems of time in the wrong way. Misled by the human perspective from within time, which distorts and exaggerates the differences between past and future, they have fallen victim to what Price calls the "double standard fallacy": proposed explanations of the difference between the past and the future turn out to rely on a difference which has been slipped in at the beginning, when the physicists themselves treat the past and future in different ways. To avoid this fallacy, Price argues, we need to overcome our natural tendency to think about the past and the future differently. We need to imagine a point outside time--an Archimedean "view from nowhen"--from which to observe time in an unbiased way. Time's Arrow and Archimedes'Point presents an innovative and controversial view of time and contemporary physics. In this exciting book, Price urges physicists, philosophers, and anyone who has ever pondered the mysteries of time to look at the world from the fresh perspective of Archimedes' Point and gain a deeper understanding of ourselves, the universe around us, and our own place in time.

  12. Environmental Sensing in Actinobacteria: a Comprehensive Survey on the Signaling Capacity of This Phylum

    PubMed Central

    Huang, Xiaoluo; Pinto, Daniela; Fritz, Georg

    2015-01-01

    , classify, and describe numerous novel and conserved signaling devices. Hence, our work serves as an important resource for any researcher interested in signal transduction of this important bacterial phylum, which contains organisms of ecological, biotechnological, and medical relevance. PMID:25986905

  13. Measurement of Br({Kappa}{sub L} {r_arrow} {mu}{sup +} {mu}{sup {minus}}): New results from BNL E791

    SciTech Connect

    Schwartz, A.

    1991-12-31

    Using a sample of 349 {Kappa}{sub L} {r_arrow} {mu}{sup +}{mu}{sup {minus}} candidates collected during the 1990 data run, the author measures a branching fraction Br({Kappa}{sub L} {r_arrow} {mu}{sup +}{mu}{sup {minus}}) = (6.96 {+-} 0.40 {+-} 0.22) {times} 10{sup {minus}9}. The sample used is the largest to date of {Kappa}{sub L} {r_arrow} {mu}{sup +}{mu}{sup {minus}} events. The result is close to the unitarity bound 6.83 {times} 10{sup {minus}9} coming from an absorptive 2-{gamma} intermediate state.

  14. Biouptake of chlorinated hydrocarbons from laboratory-spiked and field sediments by oligochaete worms

    SciTech Connect

    Oliver, B.G.

    1987-08-01

    The uptake and depuration of 37 chemicals from spiked Lake Ontario sediments by oligochaete worms has been studied at 8 and 20/sup 0/C in laboratory aquaria. The worms were found to rapidly accumulate the chemicals and reach peak concentrations within 2 weeks. The concentration of chemical in the sediment pore water appeared to be the major factor controlling the bioconcentration of chemicals by worms. The worm bioconcentration factors increased with increasing octanol-water partition coefficient of the chemicals. The worm-mediated fluxes of the chemicals from the sediments have also been estimated. Depuration studies showed in the half-lives of the chemicals in the worms ranged from less than 5 days to several months. Field worms and associated sediments from Lake Ontario near the Niagara River were analyzed. The agreement between the field and laboratory results was good for the more persistent chemicals because of time differences for sorting the two samples types. 30 references, 3 figures, 5 tables.

  15. Aqueous worm gels can be reconstituted from freeze-dried diblock copolymer powder.

    PubMed

    Kocik, M K; Mykhaylyk, O O; Armes, S P

    2014-06-14

    Worm-like diblock copolymer nanoparticles comprising poly(glycerol monomethacrylate) (PGMA) as a stabilizer block and poly(2-hydroxypropyl methacrylate) (PHPMA) as a core-forming block were readily synthesized at 10% w/w solids via aqueous dispersion polymerization at 70 °C using Reversible Addition-Fragmentation chain Transfer (RAFT) chemistry. On cooling to 20 °C, soft transparent free-standing gels are formed due to multiple inter-worm interactions. These aqueous PGMA-PHPMA diblock copolymer worms were freeze-dried, then redispersed in water with cooling to 3-5 °C before warming up to 20 °C; this protocol ensures molecular dissolution of the copolymer chains, which aids formation of a transparent aqueous gel. Rheology, SAXS and TEM studies confirm that such reconstituted gels comprise formed PGMA-PHPMA copolymer worms and they possess essentially the same physical properties determined for the original worm gels prior to freeze-drying. Such worm gel reconstitution is expected to be highly beneficial in the context of various biomedical applications, since it enables worm gels to be readily prepared using a wide range of cell growth media as the continuous aqueous phase. PMID:24733440

  16. Viability of developmental stages of Schistosoma mansoni quantified with xCELLigence worm real-time motility assay (xWORM)

    PubMed Central

    Rinaldi, Gabriel; Loukas, Alex; Brindley, Paul J.; Irelan, Jeff T.; Smout, Michael J.

    2015-01-01

    Infection with helminth parasites causes morbidity and mortality in billions of people and livestock worldwide. Where anthelmintic drugs are available, drug resistance is a major problem in livestock parasites, and a looming threat to public health. Monitoring the efficacy of these medicines and screening for new drugs has been hindered by the lack of objective, high-throughput approaches. Several cell monitoring technologies have been adapted for parasitic worms, including video-, fluorescence-, metabolism enzyme- and impedance-based tools that minimize the screening bottleneck. Using the xCELLigence impedance-based system we previously developed a motility-viability assay that is applicable for a range of helminth parasites. Here we have improved substantially the assay by using diverse frequency settings, and have named it the xCELLigence worm real-time motility assay (xWORM). By utilizing strictly standardized mean difference analysis we compared the xWORM output measured with 10, 25 and 50 kHz frequencies to quantify the motility of schistosome adults (human blood flukes) and hatching of schistosome eggs. Furthermore, we have described a novel application of xWORM to monitor movement of schistosome cercariae, the developmental stage that is infectious to humans. For all three stages, 25 kHz was either optimal or near-optimal for monitoring and quantifying schistosome motility. These improvements in methodology sensitivity should enhance the capacity to screen small compound libraries for new drugs both for schistosomes and other helminth pathogens at large. PMID:26288742

  17. Viability of developmental stages of Schistosoma mansoni quantified with xCELLigence worm real-time motility assay (xWORM).

    PubMed

    Rinaldi, Gabriel; Loukas, Alex; Brindley, Paul J; Irelan, Jeff T; Smout, Michael J

    2015-12-01

    Infection with helminth parasites causes morbidity and mortality in billions of people and livestock worldwide. Where anthelmintic drugs are available, drug resistance is a major problem in livestock parasites, and a looming threat to public health. Monitoring the efficacy of these medicines and screening for new drugs has been hindered by the lack of objective, high-throughput approaches. Several cell monitoring technologies have been adapted for parasitic worms, including video-, fluorescence-, metabolism enzyme- and impedance-based tools that minimize the screening bottleneck. Using the xCELLigence impedance-based system we previously developed a motility-viability assay that is applicable for a range of helminth parasites. Here we have improved substantially the assay by using diverse frequency settings, and have named it the xCELLigence worm real-time motility assay (xWORM). By utilizing strictly standardized mean difference analysis we compared the xWORM output measured with 10, 25 and 50 kHz frequencies to quantify the motility of schistosome adults (human blood flukes) and hatching of schistosome eggs. Furthermore, we have described a novel application of xWORM to monitor movement of schistosome cercariae, the developmental stage that is infectious to humans. For all three stages, 25 kHz was either optimal or near-optimal for monitoring and quantifying schistosome motility. These improvements in methodology sensitivity should enhance the capacity to screen small compound libraries for new drugs both for schistosomes and other helminth pathogens at large. PMID:26288742

  18. Thermo-responsive Diblock Copolymer Worm Gels in Non-polar Solvents

    PubMed Central

    2014-01-01

    Benzyl methacrylate (BzMA) is polymerized using a poly(lauryl methacrylate) macromolecular chain transfer agent (PLMA macro-CTA) using reversible addition–fragmentation chain transfer (RAFT) polymerization at 70 °C in n-dodecane. This choice of solvent leads to an efficient dispersion polymerization, with polymerization-induced self-assembly (PISA) occurring via the growing PBzMA block to produce a range of PLMA–PBzMA diblock copolymer nano-objects, including spheres, worms, and vesicles. In the present study, particular attention is paid to the worm phase, which forms soft free-standing gels at 20 °C due to multiple inter-worm contacts. Such worm gels exhibit thermo-responsive behavior: heating above 50 °C causes degelation due to the onset of a worm-to-sphere transition. Degelation occurs because isotropic spheres interact with each other much less efficiently than the highly anisotropic worms. This worm-to-sphere thermal transition is essentially irreversible on heating a dilute solution (0.10% w/w) but is more or less reversible on heating a more concentrated dispersion (20% w/w). The relatively low volatility of n-dodecane facilitates variable-temperature rheological studies, which are consistent with eventual reconstitution of the worm phase on cooling to 20 °C. Variable-temperature 1H NMR studies conducted in d26-dodecane confirm partial solvation of the PBzMA block at elevated temperature: surface plasticization of the worm cores is invoked to account for the observed change in morphology, because this is sufficient to increase the copolymer curvature and hence induce a worm-to-sphere transition. Small-angle X-ray scattering and TEM are used to investigate the structural changes that occur during the worm-to-sphere-to-worm thermal cycle; experiments conducted at 1.0 and 5.0% w/w demonstrate the concentration-dependent (ir)reversibility of these morphological transitions. PMID:24678949

  19. The early bird catches the worm: new technologies for the Caenorhabditis elegans toolkit

    PubMed Central

    Xu, Xiao; Kim, Stuart K.

    2014-01-01

    The inherent simplicity of Caenorhabditis elegans and its extensive genetic toolkit make it ideal for studying complex biological processes. Recent developments further increase the usefulness of the worm, including new methods for: altering gene expression, altering physiology using optogenetics, manipulating large numbers of worms, automating laborious processes and processing high-resolution images. These developments both enhance the worm as a model for studying processes such as development and ageing and make it an attractive model in areas such as neurobiology and behaviour. PMID:21969037

  20. Simulation of worms transmission in computer network based on SIRS fuzzy epidemic model

    NASA Astrophysics Data System (ADS)

    Darti, I.; Suryanto, A.; Yustianingsih, M.

    2015-03-01

    In this paper we study numerically the behavior of worms transmission in a computer network. The model of worms transmission is derived by modifying a SIRS epidemic model. In this case, we consider that the transmission rate, recovery rate and rate of susceptible after recovery follows fuzzy membership functions, rather than constants. To study the transmission of worms in a computer network, we solve the model using the fourth order Runge-Kutta method. Our numerical results show that the fuzzy transmission rate and fuzzy recovery rate may lead to a changing of basic reproduction number which therefore also changes the stability properties of equilibrium points.

  1. How algae influence sessile marine organisms: The tube worms case of study

    NASA Astrophysics Data System (ADS)

    Casoli, Edoardo; Bonifazi, Andrea; Ardizzone, Giandomenico; Gravina, Maria Flavia

    2016-09-01

    Tube worms and phytobenthic assemblages in three infralittoral and shallow circalittoral Mediterranean benthic communities developed between 5 and 35 m depth at Punta del Lazzaretto (Giglio Island, Central Thyrrenian sea) were investigated. Despite being three algae-dominated habitats, these displayed different covering both in terms of algal layers and algal morphologies, reflecting different structural organizations. Twenty-eight serpulid taxa have been reported, increasing both diversity and density values from most photophilic to most sciaphilous habitats. Multivariate analyses showed how algal thalli and tube worm assemblages were strongly correlated; substrata are influenced both physically and biologically, providing different conditions for tube worm settlement.

  2. Thermo-responsive diblock copolymer worm gels in non-polar solvents.

    PubMed

    Fielding, Lee A; Lane, Jacob A; Derry, Matthew J; Mykhaylyk, Oleksandr O; Armes, Steven P

    2014-04-16

    Benzyl methacrylate (BzMA) is polymerized using a poly(lauryl methacrylate) macromolecular chain transfer agent (PLMA macro-CTA) using reversible addition-fragmentation chain transfer (RAFT) polymerization at 70 °C in n-dodecane. This choice of solvent leads to an efficient dispersion polymerization, with polymerization-induced self-assembly (PISA) occurring via the growing PBzMA block to produce a range of PLMA-PBzMA diblock copolymer nano-objects, including spheres, worms, and vesicles. In the present study, particular attention is paid to the worm phase, which forms soft free-standing gels at 20 °C due to multiple inter-worm contacts. Such worm gels exhibit thermo-responsive behavior: heating above 50 °C causes degelation due to the onset of a worm-to-sphere transition. Degelation occurs because isotropic spheres interact with each other much less efficiently than the highly anisotropic worms. This worm-to-sphere thermal transition is essentially irreversible on heating a dilute solution (0.10% w/w) but is more or less reversible on heating a more concentrated dispersion (20% w/w). The relatively low volatility of n-dodecane facilitates variable-temperature rheological studies, which are consistent with eventual reconstitution of the worm phase on cooling to 20 °C. Variable-temperature (1)H NMR studies conducted in d26-dodecane confirm partial solvation of the PBzMA block at elevated temperature: surface plasticization of the worm cores is invoked to account for the observed change in morphology, because this is sufficient to increase the copolymer curvature and hence induce a worm-to-sphere transition. Small-angle X-ray scattering and TEM are used to investigate the structural changes that occur during the worm-to-sphere-to-worm thermal cycle; experiments conducted at 1.0 and 5.0% w/w demonstrate the concentration-dependent (ir)reversibility of these morphological transitions. PMID:24678949

  3. Comparative Finite Element Method Analysis of Spiroid Worm Gear Drives Having Arched Profile and Having Linear Profile in Axial Section

    NASA Astrophysics Data System (ADS)

    Bodzás, Sándor; Dudás, Illés

    2014-12-01

    With the knowledge of the advantageous characteristics of the cylindrical worm gear drives having arched profile in axial section and the conical worm gear drives having linear profile in axial section, a new geometric type conical worm gear drive has been designed and then manufactured, that is the conical worm gear drive having arched profile in axial section. Beside similar charging and marginal conditions in case of the same geometric spiroid worm gear drives having arched profile and having linear profile in axial section we have done comparative finite element method analysis for awarding of the strains, deformations and stresses of this gear drives.

  4. Chromosomal localization of the genes encoding the kinetochore proteins CENPE and DENPF to human chromosomes 4q24{r_arrow}q25 and 1q32{r_arrow}q41, respectively, by fluorescence in situ hybridization

    SciTech Connect

    Testa, J.R.; Zhou, J.Y.; Bell, D.W.; Yen, T.J.

    1994-10-01

    CENPE and CENPF are human kinetochore proteins of 312 and {approximately}400 kDa, respectively. As part of an effort to characterize the functions of these two proteins, we have used their respective cDNAs to map their human chromosomal locations by fluorescence in situ hybridization. The gene that encodes CENPE, a kinetochore-associated motor protein that is postulated to segregate chromosomes during mitosis, maps to chromosome 4q24{r_arrow}q25. The CENPF gene, which encodes a structural protein of the kinetochore, maps to chromosome 1q32{r_arrow}q41 within close proximity to the genetic locus that is linked to Van der Woude syndrome. 8 refs., 1 fig.

  5. Trisomy 1q42{r_arrow}qter in a sister and brother: Further delineation of the {open_quotes}trisomy 1q42{r_arrow}qter syndrome{close_quotes}

    SciTech Connect

    Verschuuren-Bemelmans, C.C.; Leegte, B.; Hodenius, T.M.J.

    1995-07-31

    We report on a 22-year-old woman and her 21-year-old brother with mild mental retardation, long face, prominent forehead, retrognathia, and (relative) macrocephaly. At birth they were small for date, their length is now below the 10th centile. Chromosome analysis demonstrated a nearly pure trisomy 1q42{r_arrow}qter in both patients due to unbalanced segregation of a paternal reciprocal balanced translocation 46,XY,t(1;15) (q42;p11). This is the second report of a nearly pure trisomy 1q42{r_arrow}qter. When comparing the manifestations of our patients with those of other reported cases we conclude that the most characteristic clinical manifestations of this syndrome are macrocephaly, prominent forehead, micro/retrognathia, large fontanelle, intrauterine growth retardation, postnatal growth retardation, and mental retardation. 56 refs., 4 figs., 1 tab.

  6. Prospects for measuring K{sup +} {r_arrow} {pi}{sup +} {nu}{bar {nu}} and K{sub L}{sup 0} {r_arrow} {pi}{sup 0} {nu}{bar {nu}} at BNL

    SciTech Connect

    Bryman, D.A.; Littenberg, L.

    2000-09-18

    Rare kaon decay experiments underway or planned for the BNL AGS will yield new and independent determinations of V*{sub ts}V{sub td}. A measurement of B(K{sub L}{sup 0} {r_arrow} {pi}{sup 0} {nu}{bar {nu}}) allows a determination of the imaginary part of this quantity, which is the fundamental CP-violating parameter of the Standard Model, in a uniquely clean manner. Since the measurement of B(K{sup +} {r_arrow} {pi}{sup +} {nu}{bar {nu}}) determines {vert_bar}V*{sub ts}V{sub td}, a complete derivation of the unitarity triangle is facilitated. These results can be compared to high precision data expected to come from the B sector in a number of ways, allowing for unique tests of new physics.

  7. Coherent diffraction reactions p + C {r_arrow} ({Epsilon}(1385){sup O}K{sup +}) + C and p + C {r_arrow} ({Epsilon}{sup O}K{sup +}) + C: The search for exotic baryons

    SciTech Connect

    Vavilov, D.V.; Viktorov, V.A.; Golovkin, S.V.

    1995-08-01

    The coherent diffractive reactions p + C {r_arrow} ({Epsilon}(1385){sup O}K{sup +}) + C and p + C {r_arrow} ({Epsilon}{sup O}K{sup +}) + C are investigated in experiments with the SPHINX detector irradiated by 70-GeV protons. A structure X(2050) with M = 2052 {plus_minus} 6 MeV and {Gamma} = 91 {plus_minus} 17MeV in the {Epsilon}{sup O}K{sup +} mass spectrum are observed in the former and latter processes, respectively. The small decay widths of these states and the anomalously large branching ratios of their decays that involve the emission of strange particles make them serious candidates for cryptoexotic varyons with hidden strangeness. 18 refs., 6 figs., 2 tabs.

  8. The mechanism of synthesis of a mixed-linkage (1{r{underscore}arrow}3), (1{r{underscore}arrow}4) {beta}-D-glucan in maize. Evidence for multiple sites of glucosyl transfer in the synthase complex

    SciTech Connect

    Buckeridge, M.S.; Vergara, C.E.; Carpita, N.C.

    1999-08-01

    The authors examined the mechanism of synthesis in vitro of (1{r{underscore}arrow}3), (1{r{underscore}arrow}4){Beta}-D-glucan ({Beta}-glucan), a growth-specific cell wall polysaccharide round in grasses and cereals. {beta}-Glucan is composed primarily of cellotriosyl and cellotetraosyl units linked by single (1{r{underscore}arrow}3){beta}-linkages. The ratio of cellotriosyl and cellotetraosyl units in the native polymer is strictly controlled at between 2 and 3 in all grasses, whereas the ratios of these units in {Beta}-glucan formed in vitro vary from 1.5 with 5 {micro}M UDP-glucose (GLc) to over 11 with 30 nM substrate. These results support a model in which three sites of glycosyl transfer occur within the synthase complex to produce the cellobiosyl-(1{r{underscore}arrow}3)-D-glucosyl units. The authors propose that failure to fill one of the sites results in the iterative addition of one or more cellobiosyl units to produce the longer cellodextrin units in the polymer. Variations in the UDP-Glc concentration in excised maize (Zea mays) coleoptiles did not result in wide variations in the ratios of cellotriosyl and cellotetraosyl units in {beta}-glucan synthesized in vivo, indicating that other factors control delivery of UDP-Glc to the synthase. In maize sucrose synthase is enriched in Golgi membranes and plasma membranes and may be involved in the control of substrate delivery to {beta}-glucan synthase and cellulose synthase.

  9. Comparison of community structures of Candidatus Methylomirabilis oxyfera-like bacteria of NC10 phylum in different freshwater habitats.

    PubMed

    Shen, Li-Dong; Wu, Hong-Sheng; Gao, Zhi-Qiu; Liu, Xu; Li, Ji

    2016-01-01

    Methane oxidation coupled to nitrite reduction is mediated by 'Candidatus Methylomirabilis oxyfera' (M. oxyfera), which belongs to the NC10 phylum. In this study, the community composition and diversity of M. oxyfera-like bacteria of NC10 phylum were examined and compared in four different freshwater habitats, including reservoir sediments (RS), pond sediments (PS), wetland sediments (WS) and paddy soils (PAS), by using Illumina-based 16S rRNA gene sequencing. The recovered NC10-related sequences accounted for 0.4-2.5% of the 16S rRNA pool in the examined habitats, and the highest percentage was found in WS. The diversity of NC10 bacteria were the highest in RS, medium in WS, and lowest in PS and PAS. The observed number of OTUs (operational taxonomic unit; at 3% cut-off) were 97, 46, 61 and 40, respectively, in RS, PS, WS and PAS. A heterogeneous distribution of NC10 bacterial communities was observed in the examined habitats, though group B members were the dominant bacteria in each habitat. The copy numbers of NC10 bacterial 16S rRNA genes ranged between 5.8 × 10(6) and 3.2 × 10(7) copies g(-1) sediment/soil in the examined habitats. These results are helpful for a systematic understanding of NC10 bacterial communities in different types of freshwater habitats. PMID:27157928

  10. In vitro assembly of the bacterial actin protein MamK from ' Candidatus Magnetobacterium casensis' in the phylum Nitrospirae.

    PubMed

    Deng, Aihua; Lin, Wei; Shi, Nana; Wu, Jie; Sun, Zhaopeng; Sun, Qinyun; Bai, Hua; Pan, Yongxin; Wen, Tingyi

    2016-04-01

    Magnetotactic bacteria (MTB), a group of phylogenetically diverse organisms that use their unique intracellular magnetosome organelles to swim along the Earth's magnetic field, play important roles in the biogeochemical cycles of iron and sulfur. Previous studies have revealed that the bacterial actin protein MamK plays essential roles in the linear arrangement of magnetosomes in MTB cells belonging to the Proteobacteria phylum. However, the molecular mechanisms of multiple-magnetosome-chain arrangements in MTB remain largely unknown. Here, we report that the MamK filaments from the uncultivated 'Candidatus Magnetobacterium casensis' (Mcas) within the phylum Nitrospirae polymerized in the presence of ATP alone and were stable without obvious ATP hydrolysis-mediated disassembly. MamK in Mcas can convert NTP to NDP and NDP to NMP, showing the highest preference to ATP. Unlike its Magnetospirillum counterparts, which form a single magnetosome chain, or other bacterial actins such as MreB and ParM, the polymerized MamK from Mcas is independent of metal ions and nucleotides except for ATP, and is assembled into well-ordered filamentous bundles consisted of multiple filaments. Our results suggest a dynamically stable assembly of MamK from the uncultivated Nitrospirae MTB that synthesizes multiple magnetosome chains per cell. These findings further improve the current knowledge of biomineralization and organelle biogenesis in prokaryotic systems. PMID:26960409

  11. Symbiosis and insect diversification: an ancient symbiont of sap-feeding insects from the bacterial phylum Bacteroidetes.

    PubMed

    Moran, Nancy A; Tran, Phat; Gerardo, Nicole M

    2005-12-01

    Several insect groups have obligate, vertically transmitted bacterial symbionts that provision hosts with nutrients that are limiting in the diet. Some of these bacteria have been shown to descend from ancient infections. Here we show that the large group of related insects including cicadas, leafhoppers, treehoppers, spittlebugs, and planthoppers host a distinct clade of bacterial symbionts. This newly described symbiont lineage belongs to the phylum Bacteroidetes. Analyses of 16S rRNA genes indicate that the symbiont phylogeny is completely congruent with the phylogeny of insect hosts as currently known. These results support the ancient acquisition of a symbiont by a shared ancestor of these insects, dating the original infection to at least 260 million years ago. As visualized in a species of spittlebug (Cercopoidea) and in a species of sharpshooter (Cicadellinae), the symbionts have extraordinarily large cells with an elongate shape, often more than 30 mum in length; in situ hybridizations verify that these correspond to the phylum Bacteroidetes. "Candidatus Sulcia muelleri" is proposed as the name of the new symbiont. PMID:16332876

  12. Symbiosis and Insect Diversification: an Ancient Symbiont of Sap-Feeding Insects from the Bacterial Phylum Bacteroidetes

    PubMed Central

    Moran, Nancy A.; Tran, Phat; Gerardo, Nicole M.

    2005-01-01

    Several insect groups have obligate, vertically transmitted bacterial symbionts that provision hosts with nutrients that are limiting in the diet. Some of these bacteria have been shown to descend from ancient infections. Here we show that the large group of related insects including cicadas, leafhoppers, treehoppers, spittlebugs, and planthoppers host a distinct clade of bacterial symbionts. This newly described symbiont lineage belongs to the phylum Bacteroidetes. Analyses of 16S rRNA genes indicate that the symbiont phylogeny is completely congruent with the phylogeny of insect hosts as currently known. These results support the ancient acquisition of a symbiont by a shared ancestor of these insects, dating the original infection to at least 260 million years ago. As visualized in a species of spittlebug (Cercopoidea) and in a species of sharpshooter (Cicadellinae), the symbionts have extraordinarily large cells with an elongate shape, often more than 30 μm in length; in situ hybridizations verify that these correspond to the phylum Bacteroidetes. “Candidatus Sulcia muelleri” is proposed as the name of the new symbiont. PMID:16332876

  13. Comparison of community structures of Candidatus Methylomirabilis oxyfera-like bacteria of NC10 phylum in different freshwater habitats

    PubMed Central

    Shen, Li-dong; Wu, Hong-sheng; Gao, Zhi-qiu; Liu, Xu; Li, Ji

    2016-01-01

    Methane oxidation coupled to nitrite reduction is mediated by ‘Candidatus Methylomirabilis oxyfera’ (M. oxyfera), which belongs to the NC10 phylum. In this study, the community composition and diversity of M. oxyfera-like bacteria of NC10 phylum were examined and compared in four different freshwater habitats, including reservoir sediments (RS), pond sediments (PS), wetland sediments (WS) and paddy soils (PAS), by using Illumina-based 16S rRNA gene sequencing. The recovered NC10-related sequences accounted for 0.4–2.5% of the 16S rRNA pool in the examined habitats, and the highest percentage was found in WS. The diversity of NC10 bacteria were the highest in RS, medium in WS, and lowest in PS and PAS. The observed number of OTUs (operational taxonomic unit; at 3% cut-off) were 97, 46, 61 and 40, respectively, in RS, PS, WS and PAS. A heterogeneous distribution of NC10 bacterial communities was observed in the examined habitats, though group B members were the dominant bacteria in each habitat. The copy numbers of NC10 bacterial 16S rRNA genes ranged between 5.8 × 106 and 3.2 × 107 copies g−1 sediment/soil in the examined habitats. These results are helpful for a systematic understanding of NC10 bacterial communities in different types of freshwater habitats. PMID:27157928

  14. The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria

    PubMed Central

    Di Rienzi, Sara C; Sharon, Itai; Wrighton, Kelly C; Koren, Omry; Hug, Laura A; Thomas, Brian C; Goodrich, Julia K; Bell, Jordana T; Spector, Timothy D; Banfield, Jillian F; Ley, Ruth E

    2013-01-01

    Cyanobacteria were responsible for the oxygenation of the ancient atmosphere; however, the evolution of this phylum is enigmatic, as relatives have not been characterized. Here we use whole genome reconstruction of human fecal and subsurface aquifer metagenomic samples to obtain complete genomes for members of a new candidate phylum sibling to Cyanobacteria, for which we propose the designation ‘Melainabacteria’. Metabolic analysis suggests that the ancestors to both lineages were non-photosynthetic, anaerobic, motile, and obligately fermentative. Cyanobacterial light sensing may have been facilitated by regulators present in the ancestor of these lineages. The subsurface organism has the capacity for nitrogen fixation using a nitrogenase distinct from that in Cyanobacteria, suggesting nitrogen fixation evolved separately in the two lineages. We hypothesize that Cyanobacteria split from Melainabacteria prior or due to the acquisition of oxygenic photosynthesis. Melainabacteria remained in anoxic zones and differentiated by niche adaptation, including for symbiosis in the mammalian gut. DOI: http://dx.doi.org/10.7554/eLife.01102.001 PMID:24137540

  15. Dracunculiasis (Guinea Worm Disease) and the Eradication Initiative

    PubMed Central

    Cairncross, Sandy; Muller, Ralph; Zagaria, Nevio

    2002-01-01

    Dracunculiasis, also known as guinea worm disease, is caused by the large female of the nematode Dracunculus medinensis, which emerges painfully and slowly from the skin, usually on the lower limbs. The disease can infect animals, and sustainable animal cycles occur in North America and Central Asia but do not act as reservoirs of human infection. The disease is endemic across the Sahel belt of Africa from Mauritania to Ethiopia, having been eliminated from Asia and some African countries. It has a significant socioeconomic impact because of the temporary disability that it causes. Dracunculiasis is exclusively caught from drinking water, usually from ponds. A campaign to eradicate the disease was launched in the 1980s and has made significant progress. The strategy of the campaign is discussed, including water supply, health education, case management, and vector control. Current issues including the integration of the campaign into primary health care and the mapping of cases by using geographic information systems are also considered. Finally, some lessons for other disease control and eradication programs are outlined. PMID:11932231

  16. Subconjunctival Loa loa worm: first case report in Brazil.

    PubMed

    Passos, Renato Magalhães; Barbosa, Carolina Pelegrini; Almeida, Juliana de Souza; Ogawa, Guilherme Maerschner; Camargo, Luis Marcelo Aranha

    2012-01-01

    We report the first case of ocular infestation by Loa loa in Brazil. Loiasis is caused by infestation with Loa loa, a filarial parasite originally found in the rainforests of western and central Africa. It is transmitted by the bite of the fly Chrysops and has been recently described in other places other than Africa, in African immigrants or travellers. Our case is a 33 year-old woman from Cameroon who was living in São Paulo, Brazil, for 5 years. She was asymptomatic until one morning she started feeling "something moving" in the left eye. Under topical anesthesia, on the slit lamp, a moving worm was removed from the subconjunctival space, which later was confirmed to be a male Loa loa adult specimen. Blood tests revealed microfilaraemia of 129 mf/mL. The patient was treated with 400 mg oral albendazole for 3 weeks and 60 mg prednisone. This report illustrates an unusual ocular disease, which is extremely rare outside of Africa, but easily diagnosed and treated. Ophthalmologists should be aware of it, in face of an increasingly globalized world. PMID:22552423

  17. Serological Screening of the Schistosoma mansoni Adult Worm Proteome

    PubMed Central

    Ludolf, Fernanda; Patrocínio, Paola R.; Corrêa-Oliveira, Rodrigo; Gazzinelli, Andréa; Falcone, Franco H.; Teixeira-Ferreira, André; Perales, Jonas; Oliveira, Guilherme C.; Silva-Pereira, Rosiane A.

    2014-01-01

    Background New interventions tools are a priority for schistosomiasis control and elimination, as the disease is still highly prevalent. The identification of proteins associated with active infection and protective immune response may constitute the basis for the development of a successful vaccine and could also indicate new diagnostic candidates. In this context, post-genomic technologies have been progressing, resulting in a more rational discovery of new biomarkers of resistance and antigens for diagnosis. Methodology/Principal Findings Two-dimensional electrophoresed Schistosoma mansoni adult worm protein extracts were probed with pooled sera of infected and non-infected (naturally resistant) individuals from a S. mansoni endemic area. A total of 47 different immunoreactive proteins were identified by mass spectrometry. Although the different pooled sera shared most of the immunoreactive protein spots, nine protein spots reacted exclusively with the serum pool of infected individuals, which correspond to annexin, major egg antigen, troponin T, filamin, disulphide-isomerase ER-60 precursor, actin and reticulocalbin. One protein spot, corresponding to eukaryotic translation elongation factor, reacted exclusively with the pooled sera of non-infected individuals living in the endemic area. Western blotting of two selected recombinant proteins, major egg antigen and hemoglobinase, showed a similar recognition pattern of that of the native protein. Concluding/Significance Using a serological proteome analysis, a group of antigens related to the different infection status of the endemic area residents was identified and may be related to susceptibility or resistance to infection. PMID:24651847

  18. Methane Ice Worms: Hesiocaeca methanicola Colonizing Fossil Fuel Reserves

    NASA Astrophysics Data System (ADS)

    Fisher, C. R.; MacDonald, I. R.; Sassen, R.; Young, C. M.; Macko, S. A.; Hourdez, S.; Carney, R. S.; Joye, S.; McMullin, E.

    During a research cruise in July 1997 in the Gulf of Mexico we discovered a gas hydrate approximately 1m thick and over 2m in diameter which had recently breached the sea floor at a depth of 540m. The hydrate surface visible from the submarine was considerably greater than that of any other reported hydrate. Two distinct color bands of hydrate were present in the same mound, and the entire exposed surface of the hydrate was infested (2500 individuals/m2) with 2 to 4 cm-long worms, since described as a new species, Hesiocaecamethanicola, in the polychaete family Hesionidae (Desbruyères and Toulmond 1998). H.methanicola tissue stable isotope values are consistent with a chemoautotrophic food source. No evidence of chemoautotrophic symbionts was detected, but geochemical data support the presence of abundant free living bacteria on the hydrate. The activities of the polychaetes, grazing on the hydrate bacteria and supplying oxygen to their habitats, appears to contribute to the dissolution of hydrates in surface sediments.

  19. Methane ice worms: Hesiocaeca methanicola colonizing fossil fuel reserves.

    PubMed

    Fisher, C R; MacDonald, I R; Sassen, R; Young, C M; Macko, S A; Hourdez, S; Carney, R S; Joye, S; McMullin, E

    2000-04-01

    During a research cruise in July 1997 in the Gulf of Mexico we discovered a gas hydrate approximately 1 m thick and over 2 m in diameter which had recently breached the sea floor at a depth of 540 m. The hydrate surface visible from the submarine was considerably greater than that of any other reported hydrate. Two distinct color bands of hydrate were present in the same mound, and the entire exposed surface of the hydrate was infested (2500 individuals/m2) with 2 to 4 cm-long worms, since described as a new species, Hesiocaeca methanicola, in the polychaete family Hesionidae (Desbruyères and Toulmond 1998). H. methanicola tissue stable isotope values are consistent with a chemo-autotrophic food source. No evidence of chemo-autotrophic symbionts was detected, but geochemical data support the presence of abundant free living bacteria on the hydrate. The activities of the polychaetes, grazing on the hydrate bacteria and supplying oxygen to their habitats, appears to contribute to the dissolution of hydrates in surface sediments. PMID:10840806

  20. Functional brain regeneration in the acoel worm Symsagittifera roscoffensis

    PubMed Central

    Sprecher, Simon G.; Bernardo-Garcia, F. Javier; van Giesen, Lena; Hartenstein, Volker; Reichert, Heinrich; Neves, Ricardo; Bailly, Xavier; Martinez, Pedro; Brauchle, Michael

    2015-01-01

    ABSTRACT The ability of some animals to regrow their head and brain after decapitation provides a striking example of the regenerative capacity within the animal kingdom. The acoel worm Symsagittifera roscoffensis can regrow its head, brain and sensory head organs within only a few weeks after decapitation. How rapidly and to what degree it also reacquires its functionality to control behavior however remains unknown. We provide here a neuroanatomical map of the brain neuropils of the adult S. roscoffensis and show that after decapitation a normal neuroanatomical organization of the brain is restored in the majority of animals. By testing different behaviors we further show that functionality of both sensory perception and the underlying brain architecture are restored within weeks after decapitation. Interestingly not all behaviors are restored at the same speed and to the same extent. While we find that phototaxis recovered rapidly, geotaxis is not restored within 7 weeks. Our findings show that regeneration of the head, sensory organs and brain result in the restoration of directed navigation behavior, suggesting a tight coordination in the regeneration of certain sensory organs with that of their underlying neural circuits. Thus, at least in S. roscoffensis, the regenerative capacity of different sensory modalities follows distinct paths. PMID:26581588

  1. Functional brain regeneration in the acoel worm Symsagittifera roscoffensis.

    PubMed

    Sprecher, Simon G; Bernardo-Garcia, F Javier; van Giesen, Lena; Hartenstein, Volker; Reichert, Heinrich; Neves, Ricardo; Bailly, Xavier; Martinez, Pedro; Brauchle, Michael

    2015-01-01

    The ability of some animals to regrow their head and brain after decapitation provides a striking example of the regenerative capacity within the animal kingdom. The acoel worm Symsagittifera roscoffensis can regrow its head, brain and sensory head organs within only a few weeks after decapitation. How rapidly and to what degree it also reacquires its functionality to control behavior however remains unknown. We provide here a neuroanatomical map of the brain neuropils of the adult S. roscoffensis and show that after decapitation a normal neuroanatomical organization of the brain is restored in the majority of animals. By testing different behaviors we further show that functionality of both sensory perception and the underlying brain architecture are restored within weeks after decapitation. Interestingly not all behaviors are restored at the same speed and to the same extent. While we find that phototaxis recovered rapidly, geotaxis is not restored within 7 weeks. Our findings show that regeneration of the head, sensory organs and brain result in the restoration of directed navigation behavior, suggesting a tight coordination in the regeneration of certain sensory organs with that of their underlying neural circuits. Thus, at least in S. roscoffensis, the regenerative capacity of different sensory modalities follows distinct paths. PMID:26581588

  2. Bioaccumulation and biological effects of cigarette litter in marine worms.

    PubMed

    Wright, Stephanie L; Rowe, Darren; Reid, Malcolm J; Thomas, Kevin V; Galloway, Tamara S

    2015-01-01

    Marine debris is a global environmental issue. Smoked cigarette filters are the predominant coastal litter item; 4.5 trillion are littered annually, presenting a source of bioplastic microfibres (cellulose acetate) and harmful toxicants to marine environments. Despite the human health risks associated with smoking, little is known of the hazards cigarette filters present to marine life. Here we studied the impacts of smoked cigarette filter toxicants and microfibres on the polychaete worm Hediste diversicolor (ragworm), a widespread inhabitant of coastal sediments. Ragworms exposed to smoked cigarette filter toxicants in seawater at concentrations 60 fold lower than those reported for urban run-off exhibited significantly longer burrowing times, >30% weight loss, and >2-fold increase in DNA damage compared to ragworms maintained in control conditions. In contrast, ragworms exposed to smoked cigarette filter microfibres in marine sediment showed no significant effects. Bioconcentration factors for nicotine were 500 fold higher from seawater than from sediment. Our results illustrate the vulnerability of organisms in the water column to smoking debris and associated toxicants, and highlight the risks posed by smoked cigarette filter debris to aquatic life. PMID:26369692

  3. Evolutionarily Conserved, Multitasking TRP Channels: Lessons from Worms and Flies

    PubMed Central

    Venkatachalam, Kartik; Luo, Junjie; Montell, Craig

    2015-01-01

    The Transient Receptor Potential (TRP) channel family is comprised of a large group of cation-permeable channels, which display an extraordinary diversity of roles in sensory signaling. TRPs allow animals to detect chemicals, mechanical force, light, and changes in temperature. Consequently, these channels control a plethora of animal behaviors. Moreover, their functions are not limited to the classical senses, as they are cellular sensors, which are critical for ionic homeostasis and metabolism. Two genetically tractable invertebrate model organisms, Caenorhabditis elegans and Drosophila melanogaster, have led the way in revealing a wide array of sensory roles and behaviors that depend on TRP channels. Two overriding themes have emerged from these studies. First, TRPs are multitasking proteins, and second, many functions and modes of activation of these channels are evolutionarily conserved, including some that were formerly thought to be unique to invertebrates, such as phototransduction. Thus, worms and flies offer the potential to decipher roles for mammalian TRPs, which would otherwise not be suspected. PMID:24961975

  4. Do We Need Worms to Promote Immune Health?

    PubMed

    Weinstock, Joel V

    2015-10-01

    Many immune-mediated diseases like inflammatory bowel disease, multiple sclerosis, type 1 diabetes, asthma, and food allergy appeared to have increased in frequency in developed countries in the latter part of the twentieth century. Reports from less developed countries suggest that the "epidemic" of immune-mediated diseases now is spreading into these regions as well. The "hygiene hypothesis" was developed to partly explain this phenomenon. It has been proposed that modern-day sanitary living has altered our exposure to organisms that provided protection from these diseases in the past. Alternations in the composition of our intestinal flora and fauna could play a role. Helminths are a group of worm-like parasitic organisms that have adapted to live in various regions of their hosts. Epidemiological and some clinical data suggest that these organisms can protect people from developing immune-mediated diseases. Animal experimentation has shown that helminths stimulate the production of regulatory cytokines, activate regulatory T cells, and induce regulatory dendritic cells and macrophages. This could be the mechanism by which they protect the host from these diseases. Early clinical studies also suggest that helminths may prove useful for treating immunological diseases. More sophisticated clinical studies are underway, testing live helminth agents as therapeutic agents. Also, a strong effort is ongoing to discover the agents produced by helminths that modulate host immune responses with an eye on developing new, highly effective immune modulatory therapeutic agent. PMID:25326880

  5. Bioaccumulation and biological effects of cigarette litter in marine worms

    PubMed Central

    Wright, Stephanie L.; Rowe, Darren; Reid, Malcolm J.; Thomas, Kevin V.; Galloway, Tamara S.

    2015-01-01

    Marine debris is a global environmental issue. Smoked cigarette filters are the predominant coastal litter item; 4.5 trillion are littered annually, presenting a source of bioplastic microfibres (cellulose acetate) and harmful toxicants to marine environments. Despite the human health risks associated with smoking, little is known of the hazards cigarette filters present to marine life. Here we studied the impacts of smoked cigarette filter toxicants and microfibres on the polychaete worm Hediste diversicolor (ragworm), a widespread inhabitant of coastal sediments. Ragworms exposed to smoked cigarette filter toxicants in seawater at concentrations 60 fold lower than those reported for urban run-off exhibited significantly longer burrowing times, >30% weight loss, and >2-fold increase in DNA damage compared to ragworms maintained in control conditions. In contrast, ragworms exposed to smoked cigarette filter microfibres in marine sediment showed no significant effects. Bioconcentration factors for nicotine were 500 fold higher from seawater than from sediment. Our results illustrate the vulnerability of organisms in the water column to smoking debris and associated toxicants, and highlight the risks posed by smoked cigarette filter debris to aquatic life. PMID:26369692

  6. Beetle and plant arrow poisons of the Ju|’hoan and Hai||om San peoples of Namibia (Insecta, Coleoptera, Chrysomelidae; Plantae, Anacardiaceae, Apocynaceae, Burseraceae)

    PubMed Central

    Chaboo, Caroline S.; Biesele, Megan; Hitchcock, Robert K.; Weeks, Andrea

    2016-01-01

    Abstract The use of archery to hunt appears relatively late in human history. It is poorly understood but the application of poisons to arrows to increase lethality must have occurred shortly after developing bow hunting methods; these early multi-stage transitions represent cognitive shifts in human evolution. This paper is a synthesis of widely-scattered literature in anthropology, entomology, and chemistry, dealing with San (“Bushmen”) arrow poisons. The term San (or Khoisan) covers many indigenous groups using so-called ‘click languages’ in southern Africa. Beetles are used for arrow poison by at least eight San groups and one non-San group. Fieldwork and interviews with Ju|’hoan and Hai||om hunters in Namibia revealed major differences in the nature and preparation of arrow poisons, bow and arrow construction, and poison antidote. Ju|’hoan hunters use leaf-beetle larvae of Diamphidia Gerstaecker and Polyclada Chevrolat (Chrysomelidae: Galerucinae: Alticini) collected from soil around the host plants Commiphora africana (A. Rich.) Engl. and Commiphora angolensis Engl. (Burseracaeae). In the Nyae Nyae area of Namibia, Ju|’hoan hunters use larvae of Diamphidia nigroornata Ståhl. Larvae and adults live above-ground on the plants and eat leaves, but the San collect the underground cocoons to extract the mature larvae. Larval hemolymph is mixed with saliva and applied to arrows. Hai||om hunters boil the milky plant sap of Adenium bohemianum Schinz (Apocynaceae) to reduce it to a thick paste that is applied to their arrows. The socio-cultural, historical, and ecological contexts of the various San groups may determine differences in the sources and preparation of poisons, bow and arrow technology, hunting behaviors, poison potency, and perhaps antidotes. PMID:27006594

  7. Beetle and plant arrow poisons of the Ju|'hoan and Hai||om San peoples of Namibia (Insecta, Coleoptera, Chrysomelidae; Plantae, Anacardiaceae, Apocynaceae, Burseraceae).

    PubMed

    Chaboo, Caroline S; Biesele, Megan; Hitchcock, Robert K; Weeks, Andrea

    2016-01-01

    The use of archery to hunt appears relatively late in human history. It is poorly understood but the application of poisons to arrows to increase lethality must have occurred shortly after developing bow hunting methods; these early multi-stage transitions represent cognitive shifts in human evolution. This paper is a synthesis of widely-scattered literature in anthropology, entomology, and chemistry, dealing with San ("Bushmen") arrow poisons. The term San (or Khoisan) covers many indigenous groups using so-called 'click languages' in southern Africa. Beetles are used for arrow poison by at least eight San groups and one non-San group. Fieldwork and interviews with Ju|'hoan and Hai||om hunters in Namibia revealed major differences in the nature and preparation of arrow poisons, bow and arrow construction, and poison antidote. Ju|'hoan hunters use leaf-beetle larvae of Diamphidia Gerstaecker and Polyclada Chevrolat (Chrysomelidae: Galerucinae: Alticini) collected from soil around the host plants Commiphora africana (A. Rich.) Engl. and Commiphora angolensis Engl. (Burseracaeae). In the Nyae Nyae area of Namibia, Ju|'hoan hunters use larvae of Diamphidia nigroornata Ståhl. Larvae and adults live above-ground on the plants and eat leaves, but the San collect the underground cocoons to extract the mature larvae. Larval hemolymph is mixed with saliva and applied to arrows. Hai||om hunters boil the milky plant sap of Adenium bohemianum Schinz (Apocynaceae) to reduce it to a thick paste that is applied to their arrows. The socio-cultural, historical, and ecological contexts of the various San groups may determine differences in the sources and preparation of poisons, bow and arrow technology, hunting behaviors, poison potency, and perhaps antidotes. PMID:27006594

  8. The Cranked Arrow Wing Aerodynamics Project (CAWAP) and its Extension to the International Community as CAWAPI: Objectives and Overview

    NASA Technical Reports Server (NTRS)

    Lamar, John E.; Obara, Clifford J.

    2009-01-01

    This paper provides a brief history of the F-16XL-1 aircraft, its role in the High Speed Research (HSR) program and how it was morphed into the Cranked Arrow Wing Aerodynamics Project (CAWAP). Various flight, wind-tunnel and Computational Fluid Dynamics (CFD) data sets were generated during the CAWAP. These unique and open flight datasets for surface pressures, boundary-layer profiles and skin-friction distributions, along with surface flow data, are described and sample data comparisons given. This is followed by a description of how the project became internationalized to be known as Cranked Arrow Wing Aerodynamics Project International (CAWAPI) and is concluded by an introduction to the results of a 5-year CFD predictive study of data.

  9. CHRONIC EFFECTS OF THE HERBICIDE DIURON ON FRESHWATER CLADOCERANS,AMPHIPODS,MIDGES,MINNOWS,WORMS, AND SNAILS

    EPA Science Inventory

    The chronic effects of the herbicide diuron on survival and reproduction of Daphnia pulex, and survival and growth of the amphipod Hyalella azteca, the midge Chironomus tentans, juvenile and embro/larval fathead minnows, Pimephales promelas, annelid worms, Lumbriculus variegatus,...

  10. Toxicity of metals to a freshwater tubificid worm Tubifex tubifex (Muller)

    SciTech Connect

    Khangarot, B.S. )

    1991-06-01

    Salts of various metals are being released in ever increasing amounts into the aquatic environment from mining operations, metal processing facilities, chemical industries and other similar sources. Although there has been considerable study of the acute and chronic toxicities of metals to freshwater fishes, crustaceans and snails, little information is available on the effects of metals to tubificid worms which are widely distributed in the aquatic environment. Tubificid worms are useful indicators of varying degrees of aquatic pollution. It is suggested that tubificid worms are an important element in the aquatic environment and therefore their use as a bioassay organism is logical one. The present study was undertaken to determine the acute toxicities of various metals to a fresh-water tubificid worm, Tubifex tubifex (Muller), which form an important link in aquatic food chain(s).

  11. Effect of Worm Predation on Changes in Waste Activated Sludge Properties.

    PubMed

    Zhu, Xuefeng; Yuan, Wenyi; Wang, Zhiwei; Zhou, Mingyuan; Guan, Jie

    2016-05-01

    This study explored the effects of worm predation on changes in waste activated sludge properties. Results showed that the rate by which worm predation reduced mixed liquor volatile suspended solids (MLVSS) was approximately 23.7% ± 3.1%. Particle size distribution and extracellular polymeric substance (EPS) analyses indicated that the reduction of fine particles and EPS content in sludge predated by worms mainly increased dewaterability and reduced the ratio of MLVSS/mixed liquor suspended solids. Moreover, both mean particle size and protein/carbohydrate ratio increased. The results of three-dimensional excitation-emission matrix and gel filtration chromatogram analyses demonstrated the varied properties of soluble microbial products and EPS were attributed to the worms' selective predation of low molecular-weight organic matter, which facilitated the hydrolysis of macromolecular organic matter. PMID:27131302

  12. Comparison of the complete protein sets of worm and yeast: orthology and divergence.

    PubMed

    Chervitz, S A; Aravind, L; Sherlock, G; Ball, C A; Koonin, E V; Dwight, S S; Harris, M A; Dolinski, K; Mohr, S; Smith, T; Weng, S; Cherry, J M; Botstein, D

    1998-12-11

    Comparative analysis of predicted protein sequences encoded by the genomes of Caenorhabditis elegans and Saccharomyces cerevisiae suggests that most of the core biological functions are carried out by orthologous proteins (proteins of different species that can be traced back to a common ancestor) that occur in comparable numbers. The specialized processes of signal transduction and regulatory control that are unique to the multicellular worm appear to use novel proteins, many of which re-use conserved domains. Major expansion of the number of some of these domains seen in the worm may have contributed to the advent of multicellularity. The proteins conserved in yeast and worm are likely to have orthologs throughout eukaryotes; in contrast, the proteins unique to the worm may well define metazoans. PMID:9851918

  13. Methods and strategies for gene structure curation in WormBase

    PubMed Central

    Williams, G.W.; Davis, P.A.; Rogers, A.S.; Bieri, T.; Ozersky, P.; Spieth, J.

    2011-01-01

    The Caenorhabditis elegans genome sequence was published over a decade ago; this was the first published genome of a multi-cellular organism and now the WormBase project has had a decade of experience in curating this genome's sequence and gene structures. In one of its roles as a central repository for nematode biology, WormBase continues to refine the gene structure annotations using sequence similarity and other computational methods, as well as information from the literature- and community-submitted annotations. We describe the various methods of gene structure curation that have been tried by WormBase and the problems associated with each of them. We also describe the current strategy for gene structure curation, and introduce the WormBase ‘curation tool’, which integrates different data sources in order to identify new and correct gene structures. Database URL: http://www.wormbase.org/ PMID:21543339

  14. The polychaete worm Nereis diversicolor increases mercury lability and methylation in intertidal mudflats.

    PubMed

    Sizmur, Tom; Canário, João; Edmonds, Samuel; Godfrey, Adam; O'Driscoll, Nelson J

    2013-08-01

    The polychaete worm Nereis diversicolor engineers its environment by creating oxygenated burrows in anoxic intertidal sediments. The authors carried out a laboratory microcosm experiment to test the impact of polychaete burrowing and feeding activity on the lability and methylation of mercury in sediments from the Bay of Fundy, Canada. The concentration of labile inorganic mercury and methylmercury in burrow walls was elevated compared to worm-free sediments. Mucus secretions and organic detritus in worm burrows increased labile mercury concentrations. Worms decreased sulfide concentrations, which increased Hg bioavailability to sulfate-reducing bacteria and increased methylmercury concentrations in burrow linings. Because the walls of polychaete burrows have a greater interaction with organisms, and the overlying water, the concentrations of mercury and methylmercury they contain is more toxicologically relevant to the base of a coastal food web than bulk samples. The authors recommend that researchers examining Hg in marine environments account for sediment dwelling invertebrate activity to more fully assess mercury bioavailability. PMID:23633443

  15. Face Gear Drive with Spur Involute Pinion: Geometry, Generation by a Worm, Stress Analysis

    NASA Technical Reports Server (NTRS)

    Litvin, Faydor L.; Fuentes, Alfonso; Zanzi, Claudio; Pontiggia, Matteo; Handschuh, Robert F. (Technical Monitor)

    2002-01-01

    A face gear drive with a spur involute pinion is considered. The generation of the face gear is based on application of a grinding or cutting worm whereas the conventional method of generation is based on application of an involute shaper. An analytical approach is proposed for the determination of: (1) the worm thread surface; (2) avoidance of singularities of the worm thread surface, (air) dressing of the worm; and (3) determination of stresses of the face-gear drive. A computer program for simulation of meshing and contact of the pinion and face-gear has been developed. Correction of machine-tool settings is proposed for reduction of the shift of the bearing contact caused by misalignment. An automatic development of the model of five contacting teeth has been proposed for stress analysis. Numerical examples for illustration of the developed theory are provided.

  16. Terminal deletion of the long arm of chromosome 3 [46,XX,del(3)(q27{r_arrow}qter)

    SciTech Connect

    Chitayat, D.; Babul, R.; Silver, M.M.

    1996-01-02

    We report on a terminal deletion of the long arm of chromosome 3[46,XX,del(3)(q27{r_arrow}qter)] in a female newborn infant who died 45 hours after delivery and had multiple congenital abnormalities including bilateral anophthalmia, congenital heart disease, and abnormal genitalia. The findings are compared to those of four previously reported cases with terminal de (3q). 8 refs., 4 figs., 1 tab.

  17. PAL SPME Arrow--evaluation of a novel solid-phase microextraction device for freely dissolved PAHs in water.

    PubMed

    Kremser, Andreas; Jochmann, Maik A; Schmidt, Torsten C

    2016-01-01

    After more than 25 years, solid-phase microextraction (SPME) has gained widespread acceptance as a well-automatable and flexible microextraction technique, while its instrumental basis remained mostly unchanged. The novel PAL (Prep And Load solution) SPME Arrow combines the advantages of SPME with the benefits of extraction techniques providing larger sorption phase volumes such as stir bar sorptive extraction (SBSE). It thereby avoids the inherent drawbacks of both techniques such as limitations in method automation in the case of SBSE, as well as the small sorption phase volumes and the lacking fiber robustness of classical SPME fibers. This new design is based on a robust stainless steel backbone, carrying, the screw connection to the PAL sampler, the enlarged sorption phase, and an arrow-shaped tip for conservative penetration of septa (hence the name). An outer capillary encloses this phase apart from enrichment and desorption processes and rests against the tip during transfer and penetrations, resulting in a homogeneously closed device. Here, we present an evaluation and a comparison of the novel PAL SPME Arrow with classical SPME fibers, extracting polycyclic aromatic hydrocarbons (PAHs) as model analytes, from the freely dissolved fraction in lab water and groundwater via direct immersion using polydimethylsiloxane (PDMS) as common sorption phase material. Limits of detection, repeatabilities, and extraction yields were determined for the PAL SPME Arrow and compared to data of classical SPME fibers and SBSE bars. Results indicate a significant benefit in extraction efficiency due to the larger sorption phase volume. It is accompanied by faultless mechanical robustness and thus better reliability, especially in case of prolonged, unattended, and automated operation. As an exemplary application, the water-soluble fraction of PAHs and derivatives in a roofing felt sample was quantified. PMID:26677018

  18. Laparoscopic common bile duct exploration for extraction of a round worm.

    PubMed

    Moirangthem, G S; Singh, C Arunkumar; Lokendra, K; Singh, L Deban

    2006-01-01

    A 35 years old lady presented with fever, biliary colic, mild jaundice, indigestion and flatulence. The upper abdominal ultrasonography revealed cholecystitis with sludge and a round worm in the common bile duct. Laparoscopic cholecystectomy and exploration of the bile duct for the removal of round worm was performed. The post-operative period was uneventful and the patient was discharged fit on the 4th post-operative day. PMID:17542295

  19. Infestation of the clam Chione fluctifraga by the burrowing worm Polydora sp. nov. in laboratory conditions.

    PubMed

    Tinoco-Orta, Gissel Dalila; Cáceres-Martínez, Jorge

    2003-07-01

    Burrowing worms that belong to Polydora spp. infest marine mollusks cultured worldwide, causing problems for production and marketing. The clam Chione fluctifraga is semi-cultured in Bahía Falsa, Baja California, NW Mexico, and some clams harbor burrowing worms. The present study was carried out to determine the identity of the worm species infesting the clam, the infesting process by cohabitation of infested and non-infested clams in aquaria with a variety of substrates (fine sand, gross sand, plastic bag used for clam culture, and aquarium without substrate) and turbulence conditions, and the occurrence of architomy phenomena in connection with infestation of the clam. The burrowing worm was considered as a nova species due to its singular limbate neurosetae and notosetae in the setiger 5, hooks in the setiger 6, eyes not present, and general pigmentation, among other characteristics. Infestation was similar in all substrates and turbulence conditions, but it was more abundant on clams previously infested than on those free of worms, showing a preferential settlement of worm infesting stages on pre-infested clams. Regeneration was observed in all segments of the worm: anterior (metastomium), medium, and posterior (prostomium); the complete regeneration time occurred in 40 days. This is the first record of architomy in a species of Polydora and this phenomenon could account for the increase of infestation intensity in pre-infested clams at the end of the study period. Infestation of clams by settling polichaete in the conditions studied, and the architomy process in this worm species, shows its great infesting capacity. PMID:12877826

  20. Clinical evaluation of meniscus repair with a bioabsorbable arrow: a 2- to 3-year follow-up study.

    PubMed

    Ellermann, A; Siebold, R; Buelow, J U; Sobau, C

    2002-09-01

    In a clinical study with the bioabsorbable Bionx Meniscus Arrow we prospectively evaluated 113 consecutive patients (113 menisci) after all-inside meniscus repair. Repairs were performed in either the medial (80.5%) or lateral (19.5%) posterior horn in the red-red or red-white meniscal zone; 66% of patients underwent concomitant ACL reconstruction. Assessment was based on history, clinical examination, and Lysholm [37] and Cincinnati Knee Scores. After a mean follow-up was 33 months (range 24-43; n=105) 21 (20%) patients showed signs and symptoms consistent with a meniscus tear (16 medial, 5 lateral) and underwent partial meniscectomy. In 11 (52%) of the revised patients concomitant ACL reconstruction was performed; 4 (19%) of revised patients were older than 35 years. In the nonrevised the average Lysholm Score was 92.5 and the average Cincinnati Score 90.4. Two patients showed a distinct femoral cartilage damage. Patient's age did not significantly affect the revision rate. Meniscus repair with the bioabsorbable arrow leads to clinical results comparable to those of traditional suture techniques. When stabilized, patients with concomitant ACL reconstruction showed comparable results to patients without ACL rupture. The simple and time saving all-inside insertion obviates the need for additional incisions and avoids knot tying. A proper tear selection and arrow positioning is necessary and should avoid cartilage damage. PMID:12355303

  1. Contributions to the Dart versus Arrow Debate: New Data from Holocene Projectile Points from Southeastern and Southern Brazil.

    PubMed

    Okumura, Mercedes; Araujo, Astolfo G M

    2015-01-01

    Lithic bifacial points are very common in the southern and southeastern regions of the Brazilian territory. Dated from Early to Late Holocene, these artifacts have not been studied in terms of their propulsion system. Given the characteristics of the bow and arrow compared to the atlatl and dart, there are important differences in the size and weight of arrowheads and dart points. Applying the techniques proposed by Shott (1997), Bradbury (1997), Fenenga (1953), Hughes (1998), and Hildebrandt and King (2012) to specimens recovered from eight sites dating from the early to the late Holocene, this work aims to present preliminary results to better understand the potential presence of darts and arrows in southeastern and southern Brazil. There was a variation in the results according to the application of different techniques. At least one set of points, dated from the Early Holocene, presented quite a high proportion of specimens classified as arrows, indicating the presence of points that could be used as arrowheads. PMID:26648546

  2. Influence of ecologic factors on prevalence of meningeal worm (Parelaphostrongylus tenuis) infection in South Dakota, USA.

    PubMed

    Jacques, Christopher N; Jenks, Jonathan A; Grovenburg, Troy W; Klaver, Robert W; Dubay, Shelli A

    2015-04-01

    The meningeal worm (Parelaphostrongylus tenuis) is a nematode parasite that commonly infects white-tailed deer (Odocoileus virginianus; WTD) throughout the deciduous forest biome and deciduous-coniferous ecotone of eastern and central North America; the species is not known to occur west of the grassland biome of central North America. We used county-specific prevalence data to evaluate potential effects of landscape and climatologic factors on the spatial distribution of meningeal worm infection in South Dakota, US. Probability of infection increased 4-fold between eastern and western South Dakota and 1.3-fold for each 1-cm increase in summer precipitation. Sixty-three percent of WTD had only a single worm in the cranium. Expansion of meningeal worm infection across western South Dakota may be inherently low due to the combined effects of arid climate and potential attributes of the Missouri River that limit regional movements by infected WTD. Use of landscape genetic analyses to identify potential relationships between landscape features and population genetic structure of infected deer and parasites may contribute to a greater understanding of regional heterogeneity in meningeal worm infection rates across South Dakota, particularly in counties adjacent to the Missouri River. Future research evaluating heterogeneity in prevalence and intensity of infection between fawn and yearling deer, and the potential role of yearling male deer as dispersal agents of meningeal worms across the Missouri River, also is warranted. PMID:25588013

  3. Census of bacterial microbiota associated with the glacier ice worm Mesenchytraeus solifugus.

    PubMed

    Murakami, Takumi; Segawa, Takahiro; Bodington, Dylan; Dial, Roman; Takeuchi, Nozomu; Kohshima, Shiro; Hongoh, Yuichi

    2015-03-01

    The glacier ice worm, Mesenchytraeus solifugus, is a unique annelid, inhabiting only snow and ice in North American glaciers. Here, we analyzed the taxonomic composition of bacteria associated with M. solifugus based on the 16S rRNA gene. We analyzed four fixed-on-site and 10 starved ice worm individuals, along with glacier surface samples. In total, 1341 clones of 16S rRNA genes were analyzed for the ice worm samples, from which 65 bacterial phylotypes (99.0% cut-off) were identified. Of these, 35 phylotypes were closely related to sequences obtained from their habitat glacier and/or other components of cryosphere; whereas three dominant phylotypes were affiliated with animal-associated lineages of the class Mollicutes. Among the three, phylotype Ms-13 shared less than 89% similarity with database sequences and was closest to a gut symbiont of a terrestrial earthworm. Using fluorescence in situ hybridization, Ms-13 was located on the gut wall surface of the ice worms. We propose a novel genus and species, 'Candidatus Vermiplasma glacialis', for this bacterium. Our results raise the possibility that the ice worm has exploited indigenous glacier bacteria, while several symbiotic bacterial lineages have maintained their association with the ice worm during the course of adaptive evolution to the permanently cold environment. PMID:25764456

  4. Influence of ecological factors on prevalence of meningeal worm (Parelaphostrongylus tenuis infection in South Dakota, USA

    USGS Publications Warehouse

    Jacques, Christopher N.; Jenks, Jonathan A.; Grovenburg, Troy W.; Klaver, Robert W.; Dubay, Shelli A.

    2015-01-01

    The meningeal worm (Parelaphostrongylus tenuis) is a nematode parasite that commonly infects white-tailed deer (Odocoileus virginianus; WTD) throughout the deciduous forest biome and deciduous-coniferous ecotone of eastern and central North America; the species is not known to occur west of the grassland biome of central North America. We used county-specific prevalence data to evaluate potential effects of landscape and climatologic factors on the spatial distribution of meningeal worm infection in South Dakota, US. Probability of infection increased 4-fold between eastern and western South Dakota and 1.3-fold for each 1-cm increase in summer precipitation. Sixty-three percent of WTD had only a single worm in the cranium. Expansion of meningeal worm infection across western South Dakota may be inherently low due to the combined effects of arid climate and potential attributes of the Missouri River that limit regional movements by infected WTD. Use of landscape genetic analyses to identify potential relationships between landscape features and population genetic structure of infected deer and parasites may contribute to a greater understanding of regional heterogeneity in meningeal worm infection rates across South Dakota, particularly in counties adjacent to the Missouri River. Future research evaluating heterogeneity in prevalence and intensity of infection between fawn and yearling deer, and the potential role of yearling male deer as dispersal agents of meningeal worms across the Missouri River, also is warranted.

  5. Culturing Caenorhabditis elegans in Axenic Liquid Media and Creation of Transgenic Worms by Microparticle Bombardment

    PubMed Central

    Samuel, Tamika K.; Sinclair, Jason W.; Pinter, Katherine L.; Hamza, Iqbal

    2014-01-01

    In this protocol, we present the required materials, and the procedure for making modified C. elegans Habituation and Reproduction media (mCeHR). Additionally, the steps for exposing and acclimatizing C. elegans grown on E. coli to axenic liquid media are described. Finally, downstream experiments that utilize axenic C. elegans illustrate the benefits of this procedure. The ability to analyze and determine C. elegans nutrient requirement was illustrated by growing N2 wild type worms in axenic liquid media with varying heme concentrations. This procedure can be replicated with other nutrients to determine the optimal concentration for worm growth and development or, to determine the toxicological effects of drug treatments. The effects of varied heme concentrations on the growth of wild type worms were determined through qualitative microscopic observation and by quantitating the number of worms that grew in each heme concentration. In addition, the effect of varied nutrient concentrations can be assayed by utilizing worms that express fluorescent sensors that respond to changes in the nutrient of interest. Furthermore, a large number of worms were easily produced for the generation of transgenic C. elegans using microparticle bombardment. PMID:25145601

  6. Viscoelastic properties of the nematode Caenorhabditis elegans, a self-similar, shear-thinning worm

    PubMed Central

    Backholm, Matilda; Ryu, William S.; Dalnoki-Veress, Kari

    2013-01-01

    Undulatory motion is common to many creatures across many scales, from sperm to snakes. These organisms must push off against their external environment, such as a viscous medium, grains of sand, or a high-friction surface; additionally they must work to bend their own body. A full understanding of undulatory motion, and locomotion in general, requires the characterization of the material properties of the animal itself. The material properties of the model organism Caenorhabditis elegans were studied with a micromechanical experiment used to carry out a three-point bending measurement of the worm. Worms at various developmental stages (including dauer) were measured and different positions along the worm were probed. From these experiments we calculated the viscoelastic properties of the worm, including the effective spring constant and damping coefficient of bending. C. elegans moves by propagating sinusoidal waves along its body. Whereas previous viscoelastic approaches to describe the undulatory motion have used a Kelvin–Voigt model, where the elastic and viscous components are connected in parallel, our measurements show that the Maxwell model, where the elastic and viscous components are in series, is more appropriate. The viscous component of the worm was shown to be consistent with a non-Newtonian, shear-thinning fluid. We find that as the worm matures it is well described as a self-similar elastic object with a shear-thinning damping term and a stiffness that becomes smaller as one approaches the tail. PMID:23460699

  7. Animal Models for Echinostoma malayanum Infection: Worm Recovery and Some Pathology.

    PubMed

    Songsri, Jiraporn; Aukkanimart, Ratchadawan; Boonmars, Thidarut; Ratanasuwan, Panaratana; Laummaunwai, Porntip; Sriraj, Pranee; Sripan, Panupan

    2016-02-01

    Echinostomes are intestinal trematodes that infect a wide range of vertebrate hosts, including humans, in their adult stage and also parasitize numerous invertebrate and cold-blooded vertebrate hosts in their larval stages. The purpose of this study was to compare Echinostoma malayanum parasite growth, including worm recovery, body size of adult worms, eggs per worm, eggs per gram of feces, and pathological changes in the small intestine of experimental animals. In this study, 6-8-week-old male hamsters, rats, mice, and gerbils were infected with echinostome metacercariae and then sacrificed at day 60 post-infection. The small intestine and feces of each infected animal were collected and then processed for analysis. The results showed that worm recovery, eggs per worm, and eggs per gram of feces from all infected hamsters were higher compared with infected rats and mice. However, in infected gerbils, no parasites were observed in the small intestine, and there were no parasite eggs in the feces. The volume of eggs per gram of feces and eggs per worm were related to parasite size. The results of histopathological changes in the small intestine of infected groups showed abnormal villi and goblet cells, as evidenced by short villi and an increase in the number and size of goblet cells compared with the normal control group. PMID:26951978

  8. Animal Models for Echinostoma malayanum Infection: Worm Recovery and Some Pathology

    PubMed Central

    Songsri, Jiraporn; Aukkanimart, Ratchadawan; Boonmars, Thidarut; Ratanasuwan, Panaratana; Laummaunwai, Porntip; Sriraj, Pranee; Sripan, Panupan

    2016-01-01

    Echinostomes are intestinal trematodes that infect a wide range of vertebrate hosts, including humans, in their adult stage and also parasitize numerous invertebrate and cold-blooded vertebrate hosts in their larval stages. The purpose of this study was to compare Echinostoma malayanum parasite growth, including worm recovery, body size of adult worms, eggs per worm, eggs per gram of feces, and pathological changes in the small intestine of experimental animals. In this study, 6-8-week-old male hamsters, rats, mice, and gerbils were infected with echinostome metacercariae and then sacrificed at day 60 post-infection. The small intestine and feces of each infected animal were collected and then processed for analysis. The results showed that worm recovery, eggs per worm, and eggs per gram of feces from all infected hamsters were higher compared with infected rats and mice. However, in infected gerbils, no parasites were observed in the small intestine, and there were no parasite eggs in the feces. The volume of eggs per gram of feces and eggs per worm were related to parasite size. The results of histopathological changes in the small intestine of infected groups showed abnormal villi and goblet cells, as evidenced by short villi and an increase in the number and size of goblet cells compared with the normal control group. PMID:26951978

  9. Study of advanced composite structural design concepts for an arrow wing supersonic cruise configuration, task 3

    NASA Technical Reports Server (NTRS)

    1978-01-01

    A structural design study was conducted to assess the relative merits of structural concepts using advanced composite materials for an advanced supersonic aircraft cruising at Mach 2.7. The configuration and structural arrangement developed during Task I and II of the study, was used as the baseline configuration. Allowable stresses and strains were established for boron and advanced graphite fibers based on projected fiber properties available in the next decade. Structural concepts were designed and analyzed using graphite polyimide and boron polyimide, applied to stiffened panels and conventional sandwich panels. The conventional sandwich panels were selected as the structural concept to be used on the wing structure. The upper and lower surface panels of the Task I arrow wing were redesigned using high-strength graphite polyimide sandwich panels over the titanium spars and ribs. The ATLAS computer system was used as the basis for stress analysis and resizing the surface panels using the loads from the Task II study, without adjustment for change in aeroelastic deformation. The flutter analysis indicated a decrease in the flutter speed compared to the baseline titanium wing design. The flutter analysis indicated a decrease in the flutter speed compared to the baseline titanium wing design. The flutter speed was increased to that of the titanium wing, with a weight penalty less than that of the metallic airplane.

  10. Phase Space Approach for S2 arrow S0 internal conversion in the benzene molecule.

    NASA Astrophysics Data System (ADS)

    Kallush, Shimshon; Segev, Bilha; Sergeev, Alexei; Heller, Eric J.

    2000-06-01

    The theoretical problem of finding propensity rules for the partition of energy between competing vibrations in a radiationless vibronic relaxation transition, is converted by the phase-space method of [1,2] to the simple mathematical problem of finding a maximum for a simple function under a constraint. The function is the Wigner function of the initial state and the constraint is energy conservation, defining an accepting energy surface in phase space. We apply this phase space method for finding propensity rules for vibronic transitions when the Frack-Condon factors are exponentially small to the classical example of the benzene molecule. We extend the method to forbidden transitions and include in the analysis non-harmonic force-field effects. Using the phase space analysis, we explain the non-classical behavior of the S_2arrow S0 relaxation of the benzene. Given the energy gap, reasonable displacements and recently calculated force fields [3] we show that almost all the energy must go to C-H stretching. Non-harmonic effects increase in this case the transition rate but do not change the partition of energy between the accepting vibrational modes. [1] E.J. Heller and D. Beck, Chem. Phys. Lett. 202, 350 (1993). [2] B. Segev and E.J. Heller, Journal of Chemical Physics, 112, 4004-4013 (2000). [3] A. Miani, E. Cane, P. Palmieri, A. Trombetti,N.C. Handy, J. Chem. Phys., 112, 248-259 (2000).

  11. Supersonic Aerodynamic Design Improvements of an Arrow-Wing HSCT Configuration Using Nonlinear Point Design Methods

    NASA Technical Reports Server (NTRS)

    Unger, Eric R.; Hager, James O.; Agrawal, Shreekant

    1999-01-01

    This paper is a discussion of the supersonic nonlinear point design optimization efforts at McDonnell Douglas Aerospace under the High-Speed Research (HSR) program. The baseline for these optimization efforts has been the M2.4-7A configuration which represents an arrow-wing technology for the High-Speed Civil Transport (HSCT). Optimization work on this configuration began in early 1994 and continued into 1996. Initial work focused on optimization of the wing camber and twist on a wing/body configuration and reductions of 3.5 drag counts (Euler) were realized. The next phase of the optimization effort included fuselage camber along with the wing and a drag reduction of 5.0 counts was achieved. Including the effects of the nacelles and diverters into the optimization problem became the next focus where a reduction of 6.6 counts (Euler W/B/N/D) was eventually realized. The final two phases of the effort included a large set of constraints designed to make the final optimized configuration more realistic and they were successful albeit with a loss of performance.

  12. ARGX-87: Accident Response Group Exercise, 1987: A Broken Arrow mini exercise. [Training

    SciTech Connect

    Schuld, E.P.; Cruff, D.F.

    1987-07-01

    A Broken Arrow mini exercise dubbed ''Accident Response Group Exercise - 1987'' (ARGX-87) was conducted on June 1, 1987 at the Lawrence Livermore National Laboratory (LLNL) and Sandia National Laboratories, Livermore (SNLL). The exercise started at 0445 PDT with a call from the Department of Energy (DOE) - EOC in Washington, DC, to the Albuquerque Operations (AL - ) - EOC. AL, in turn, called the Laboratory off-hour emergency number (Fire Dispatcher), who called the Laboratory Emergency Duty Officer (LEDO). The LEDO then contacted the Accident Response Group (ARG) Senior Scientific Advisor. Calls were placed to assemble appropriate members of the ARG in the ALERT Center. No phone number for SNLL was available at the Albuquerque Operations EOC, so a controller injected a message to SNLL to get them involved in the exercise. The messages received at the Laboratory identified the Air Force line item weapon system involved in the accident and the accident location. As people arrived at the ALERT Center they began discussing the details of the accident. They also started working the deployment logistics and other issues. Travel arrangements for the HOT SPOT equipment and ARG personnel were made for immediate deployment to the accident site in North Dakota. The exercise was terminated at 0840 as planned. While certain procedural deficiencies were noted, the exercise was considered a valuable learning experience. The results and observations from this experience will be used to refine the operating procedures and the training program.

  13. Threshold responses of Blackside Dace (Chrosomus cumberlandensis) and Kentucky Arrow Darter (Etheostoma spilotum) to stream conductivity

    USGS Publications Warehouse

    Hitt, Nathaniel P.; Floyd, Michael; Compton, Michael; McDonald, Kenneth

    2016-01-01

    Chrosomus cumberlandensis (Blackside Dace [BSD]) and Etheostoma spilotum (Kentucky Arrow Darter [KAD]) are fish species of conservation concern due to their fragmented distributions, their low population sizes, and threats from anthropogenic stressors in the southeastern United States. We evaluated the relationship between fish abundance and stream conductivity, an index of environmental quality and potential physiological stressor. We modeled occurrence and abundance of KAD in the upper Kentucky River basin (208 samples) and BSD in the upper Cumberland River basin (294 samples) for sites sampled between 2003 and 2013. Segmented regression indicated a conductivity change-point for BSD abundance at 343 μS/cm (95% CI: 123–563 μS/cm) and for KAD abundance at 261 μS/cm (95% CI: 151–370 μS/cm). In both cases, abundances were negligible above estimated conductivity change-points. Post-hoc randomizations accounted for variance in estimated change points due to unequal sample sizes across the conductivity gradients. Boosted regression-tree analysis indicated stronger effects of conductivity than other natural and anthropogenic factors known to influence stream fishes. Boosted regression trees further indicated threshold responses of BSD and KAD occurrence to conductivity gradients in support of segmented regression results. We suggest that the observed conductivity relationship may indicate energetic limitations for insectivorous fishes due to changes in benthic macroinvertebrate community composition.

  14. Design study of structural concepts for an arrow-wing supersonic-cruise aircraft

    NASA Technical Reports Server (NTRS)

    Sakata, I. F.; Davis, G. W.; Robinson, J. C.; Yates, E. C., Jr.

    1975-01-01

    An analytical study was performed to determine the best structural approach for design of primary wing and fuselage structure of a Mach number 2.7 arrow-wing supersonic cruise aircraft. Concepts were evaluated considering near-term start-of-design. Emphasis was placed on the complex interactions between thermal stress, static aeroelasticity, flutter, fatigue and fail-safe design, static and dynamic loads, and the effects of variations in structural arrangements, concepts and materials on these interactions. Results indicate that a hybrid wing structure incorporating low-profile convex-beaded and honeycomb sandwich surface panels of titanium alloy 6Al-4V were the most efficient. The substructure includes titanium alloy spar caps reinforced with Boron-polyimide composites. The fuselage shell is a closed-hat stiffened skin and frame construction of titanium alloy 6Al-4V. This paper presents an executive summary of the study effort, and includes a discussion of the overall study logic, design philosophy and interaction between the analytical methods for supersonic cruise aircraft design.

  15. Identification of a Novel Toluene-Degrading Bacterium from the Candidate Phylum TM7, as Determined by DNA Stable Isotope Probing▿

    PubMed Central

    Luo, Chunling; Xie, Shuguang; Sun, Weimin; Li, Xiangdong; Cupples, Alison M.

    2009-01-01

    The dominant bacterium responsible for carbon uptake from toluene in an agricultural soil was identified by stable isotope probing. Samples were amended with unlabeled toluene or labeled [ring-13C6]toluene, and DNA was extracted over time. Sequencing indicated that the organism involved belongs to the candidate phylum TM7. Microorganisms in this candidate phylum are of particular interest because although they have been found in a variety of habitats, no stable culture of any species exists, so their general metabolic capabilities are largely unknown. PMID:19447956

  16. An inconvenient truth: global worming and anthelmintic resistance.

    PubMed

    Kaplan, Ray M; Vidyashankar, Anand N

    2012-05-01

    Over the past 10-15 years, we have witnessed a rapid increase in both the prevalence and magnitude of anthelmintic resistance, and this increase appears to be a worldwide phenomenon. Reports of anthelmintic resistance to multiple drugs in individual parasite species, and in multiple parasite species across virtually all livestock hosts, are increasingly common. In addition, since the introduction of ivermectin in 1981, no novel anthelmintic classes were developed and introduced for use in livestock until recently with the launch of monepantel in New Zealand. Thus, livestock producers are often left with few options for effective treatment against many important parasite species. While new anthelmintic classes with novel mechanisms of action could potentially solve this problem, new drugs are extremely expensive to develop, and can be expected to be more expensive than older drugs. Thus, it seems clear that the "Global Worming" approach that has taken hold over the past 40-50 years must change, and livestock producers must develop a new vision for parasite control and sustainability of production. Furthermore, parasitologists must improve methods for study design and data analysis that are used for diagnosing anthelmintic resistance, especially for the fecal egg count reduction test (FECRT). Currently, standards for diagnosis of anthelmintic resistance using FECRT exist only for sheep. Lack of standards in horses and cattle and arbitrarily defined cutoffs for defining resistance, combined with inadequate analysis of the data, mean that errors in assigning resistance status are common. Similarly, the lack of standards makes it difficult to compare data among different studies. This problem needs to be addressed, because as new drugs are introduced now and in the future, the lack of alternative treatments will make early and accurate diagnosis of anthelmintic resistance increasingly important. PMID:22154968

  17. Sulfide:quinone oxidoreductase from echiuran worm Urechis unicinctus.

    PubMed

    Ma, Yu-Bin; Zhang, Zhi-Feng; Shao, Ming-Yu; Kang, Kyoung-Ho; Tan, Zhi; Li, Jin-Long

    2011-02-01

    Sulfide is a natural, widely distributed, poisonous substance, and sulfide:quinone oxidoreductase (SQR) has been identified to be responsible for the initial oxidation of sulfide in mitochondria. In this study, full-length SQR cDNA was cloned from the echiuran worm Urechis unicinctus, a benthic organism living in marine sediments. The protein consisted of 451 amino acids with a theoretical pI of 8.98 and molecular weight of 50.5 kDa. Subsequently, the SQR mRNA expression in different tissues was assessed by real-time reverse transcription and polymerase chain reaction and showed that the highest expression was in midgut, followed by anal sacs and coelomic fluid cells, and then body wall and hindgut. Furthermore, activated SQR was obtained by dilution refolding of recombinant SQR expression in E. coli, and the refolded product showed optimal activity at 37 °C and pH 8.5 and K (m) for ubiquinone and sulfide at 15.6 µM and 40.3 µM, respectively. EDTA and GSH had an activating effect on refolded SQR, while Zn(2+) caused decreased activity. Western blot showed that SQR in vivo was located in mitochondria and was ∼ 10 kDa heavier than the recombinant protein. In addition, SQR, detected by immunohistochemistry, was mainly located in the epithelium of all tissues examined. Ultrastructural observations of these tissues' epithelium by transmission electron microscopy provided indirect cytological evidence for its mitochondrial location. Interesting aspects of the U. unicinctus SQR amino acid sequence, its catalytic mechanism, and the different roles of these tissues in sulfide metabolic adaptation are also discussed. PMID:20419499

  18. Phylogenetic Diversity, Localization, and Cell Morphologies of Members of the Candidate Phylum TG3 and a Subphylum in the Phylum Fibrobacteres, Recently Discovered Bacterial Groups Dominant in Termite Guts▿ †

    PubMed Central

    Hongoh, Yuichi; Deevong, Pinsurang; Hattori, Satoshi; Inoue, Tetsushi; Noda, Satoko; Noparatnaraporn, Napavarn; Kudo, Toshiaki; Ohkuma, Moriya

    2006-01-01

    Recently we discovered two novel, deeply branching lineages in the domain Bacteria from termite guts by PCR-based analyses of 16S rRNA (Y. Hongoh, P. Deevong, T. Inoue, S. Moriya, S. Trakulnaleamsai, M. Ohkuma, C. Vongkaluang, N. Noparatnaraporn, and T. Kudo, Appl. Environ. Microbiol. 71:6590-6599, 2005). Here, we report on the specific detection of these bacteria, the candidate phylum TG3 (Termite Group 3) and a subphylum in the phylum Fibrobacteres, by fluorescence in situ hybridization in the guts of the wood-feeding termites Microcerotermes sp. and Nasutitermes takasagoensis. Both bacterial groups were detected almost exclusively from the luminal fluid of the dilated portion in the hindgut. Each accounted for approximately 10% of the total prokaryotic cells, constituting the second-most dominant groups in the whole-gut microbiota. The detected cells of both groups were in undulate or vibroid forms and apparently resembled small spirochetes. The cell sizes were 0.2 to 0.4 by 1.3 to 6.0 μm and 0.2 to 0.3 by 1.3 to 4.9 μm in the TG3 and Fibrobacteres, respectively. Using PCR screenings with specific primers, we found that both groups are distributed among various termites. The obtained clones formed monophyletic clusters that were delineated by the host genus rather than by the geographic distance, implying a robust association between these bacteria and host termites. TG3 clones were also obtained from a cockroach gut, lake sediment, rice paddy soil, and deep-sea sediments. Our results suggest that the TG3 and Fibrobacteres bacteria are autochthonous gut symbionts of various termites and that the TG3 members are also widely distributed among various other environments. PMID:17021231

  19. Endoplasmic reticulum reorganizations and Ca2+ signaling in maturing and fertilized oocytes of marine protostome worms: the roles of MAPKs and MPF.

    PubMed

    Stricker, Stephen A; Smythe, Toni L

    2003-07-01

    Before a proper Ca(2+) response is produced at fertilization, oocytes typically undergo a maturation process during which their endoplasmic reticulum (ER) is restructured. In marine protostome worms belonging to the phylum Nemertea, the ER of maturing oocytes forms numerous distinct clusters that are about 5 micro m in diameter. After fertilization, mature oocytes with such aggregates generate a normal series of Ca(2+) oscillations and eventually disassemble their ER clusters at around the time that the oscillations cease. Immature oocytes, however, lack prominent ER clusters and fail to exhibit repetitive Ca(2+) oscillations upon insemination, collectively suggesting that cell cycle-related changes in ER structure may play a role in Ca(2+) signaling. To assess the effects of meiotic regulators on the morphology of the ER and the type of Ca(2+) response that is produced at fertilization, nemertean oocytes were treated with pharmacological modulators of mitogen-activated protein kinases (MAPKs) or maturation-promoting factor (MPF) prior to confocal microscopic analyses. Based on such imaging studies and correlative assays of kinase activities, MAPKs of the ERK1/2 type (extracellular signal regulated kinases 1/2) do not seem to be essential for either structural reorganizations of the ER or repetitive Ca(2+) signaling at fertilization. Conversely, MPF levels appear to modulate both ER structure and the capacity to produce normal Ca(2+) oscillations. The significance of these findings is discussed with respect to other reports on ER structure, MPF cycling and Ca(2+) signaling in oocytes of deuterostome animals. PMID:12756171

  20. The Deinococcus-Thermus phylum and the effect of rRNA composition on phylogenetic tree construction

    NASA Technical Reports Server (NTRS)

    Weisburg, W. G.; Giovannoni, S. J.; Woese, C. R.

    1989-01-01

    Through comparative analysis of 16S ribosomal RNA sequences, it can be shown that two seemingly dissimilar types of eubacteria Deinococcus and the ubiquitous hot spring organism Thermus are distantly but specifically related to one another. This confirms an earlier report based upon 16S rRNA oligonucleotide cataloging studies (Hensel et al., 1986). Their two lineages form a distinctive grouping within the eubacteria that deserved the taxonomic status of a phylum. The (partial) sequence of T. aquaticus rRNA appears relatively close to those of other thermophilic eubacteria. e.g. Thermotoga maritima and Thermomicrobium roseum. However, this closeness does not reflect a true evolutionary closeness; rather it is due to a "thermophilic convergence", the result of unusually high G+C composition in the rRNAs of thermophilic bacteria. Unless such compositional biases are taken into account, the branching order and root of phylogenetic trees can be incorrectly inferred.

  1. Larkinella insperata gen. nov., sp. nov., a bacterium of the phylum 'Bacteroidetes' isolated from water of a steam generator.

    PubMed

    Vancanneyt, Marc; Nedashkovskaya, Olga I; Snauwaert, Cindy; Mortier, Stefanie; Vandemeulebroecke, Katrien; Hoste, Bart; Dawyndt, Peter; Frolova, Galina M; Janssens, Danielle; Swings, Jean

    2006-01-01

    A Gram-negative bacterium, designated strain LMG 22510T, was isolated from water of a pharmaceutical company steam generator. The cells had a ring-like and horseshoe-shaped morphology and possessed gliding motility. Phylogenetic analysis of the 16S rRNA gene sequence showed that the strain was a member of the Flexibacter group within the phylum 'Bacteroidetes'; its nearest neighbour was Spirosoma linguale (88.8 % sequence similarity). DNA base content, fatty acid composition and biochemical characteristics were determined. Genotypic and phenotypic data indicated that strain LMG 22510T could not be assigned to any recognized genus; therefore, a novel genus and species is proposed, Larkinella insperata gen. nov., sp. nov., with LMG 22510T (= NCIMB 14103T) as the type strain. PMID:16403892

  2. Evidence of K{sup +} {r_arrow} {pi}{sup +}{nu}{anti {nu}}: The BNL E787 1995 result (How did we get here)

    SciTech Connect

    Chiang, I.H.; E787 Collaboration

    1998-02-01

    The kaon was studied very thoroughly since its discovery some 50 years ago. In the study of charged kaon branching ratios, it was noticed that K{sup +} {r_arrow} {pi}{sup 0}e{sup +}{nu}{sub e} is allowed while K{sup +} {r_arrow} {pi}{sup +}{nu}{anti {nu}} is not. The latter was then empirically classified as a forbidden decay, leading to the so called strangeness changing current rule. The decay K{sup +} {r_arrow} {pi}{sup 0}e{sup +}{nu}{sub e} is mediated by the strangeness changing charged current and its branching ratio is 4.8%. By contrast K{sup +} {r_arrow} {pi}{sup +}{nu}{anti {nu}} is a strangeness changing neutral current, which is forbidden. In 1970, the GIM model was introduced to explain this effect and in 1974, Gaillard and Lee calculated the K{sup +} {r_arrow} {pi}{sup +}{nu}{anti {nu}} branching ratio to be on the order of 10{sup {minus}10}. In the current theory, the K{sup +} {r_arrow} {pi}{sup +}{nu}{anti {nu}} is mediated by a Flavor Changing Neutral Current (FCNC) in which the cancellation of the three quark generations should be complete down to second order except for the difference in the quark masses. The top quark is much heavier than the charm and up quarks, so that the cancellation is not complete. In other words, this decay is more dependent on the top sector. The measurement of K{sup +} {r_arrow}{pi}{sup +}{nu}{anti {nu}} branching ratio measures the modulus of the V{sub td} element of the CKM Matrix. The 1995 results of E787 were published in 1997. This report is focused on how the author achieved the goal of detecting events with such as small branching ratio.

  3. Phylogeny and physiology of candidate phylum 'Atribacteria' (OP9/JS1) inferred from cultivation-independent genomics.

    PubMed

    Nobu, Masaru K; Dodsworth, Jeremy A; Murugapiran, Senthil K; Rinke, Christian; Gies, Esther A; Webster, Gordon; Schwientek, Patrick; Kille, Peter; Parkes, R John; Sass, Henrik; Jørgensen, Bo B; Weightman, Andrew J; Liu, Wen-Tso; Hallam, Steven J; Tsiamis, George; Woyke, Tanja; Hedlund, Brian P

    2016-02-01

    The 'Atribacteria' is a candidate phylum in the Bacteria recently proposed to include members of the OP9 and JS1 lineages. OP9 and JS1 are globally distributed, and in some cases abundant, in anaerobic marine sediments, geothermal environments, anaerobic digesters and reactors and petroleum reservoirs. However, the monophyly of OP9 and JS1 has been questioned and their physiology and ecology remain largely enigmatic due to a lack of cultivated representatives. Here cultivation-independent genomic approaches were used to provide a first comprehensive view of the phylogeny, conserved genomic features and metabolic potential of members of this ubiquitous candidate phylum. Previously available and heretofore unpublished OP9 and JS1 single-cell genomic data sets were used as recruitment platforms for the reconstruction of atribacterial metagenome bins from a terephthalate-degrading reactor biofilm and from the monimolimnion of meromictic Sakinaw Lake. The single-cell genomes and metagenome bins together comprise six species- to genus-level groups that represent most major lineages within OP9 and JS1. Phylogenomic analyses of these combined data sets confirmed the monophyly of the 'Atribacteria' inclusive of OP9 and JS1. Additional conserved features within the 'Atribacteria' were identified, including a gene cluster encoding putative bacterial microcompartments that may be involved in aldehyde and sugar metabolism, energy conservation and carbon storage. Comparative analysis of the metabolic potential inferred from these data sets revealed that members of the 'Atribacteria' are likely to be heterotrophic anaerobes that lack respiratory capacity, with some lineages predicted to specialize in either primary fermentation of carbohydrates or secondary fermentation of organic acids, such as propionate. PMID:26090992

  4. Evidence of Carbon Fixation Pathway in a Bacterium from Candidate Phylum SBR1093 Revealed with Genomic Analysis

    PubMed Central

    Wang, Zhiping; Guo, Feng; Liu, Lili; Zhang, Tong

    2014-01-01

    Autotrophic CO2 fixation is the most important biotransformation process in the biosphere. Research focusing on the diversity and distribution of relevant autotrophs is significant to our comprehension of the biosphere. In this study, a draft genome of a bacterium from candidate phylum SBR1093 was reconstructed with the metagenome of an industrial activated sludge. Based on comparative genomics, this autotrophy may occur via a newly discovered carbon fixation path, the hydroxypropionate-hydroxybutyrate (HPHB) cycle, which was demonstrated in a previous work to be uniquely possessed by some genera from Archaea. This bacterium possesses all of the thirteen enzymes required for the HPHB cycle; these enzymes share 30∼50% identity with those in the autotrophic species of Archaea that undergo the HPHB cycle and 30∼80% identity with the corresponding enzymes of the mixotrophic species within Bradyrhizobiaceae. Thus, this bacterium might have an autotrophic growth mode in certain conditions. A phylogenetic analysis based on the 16S rRNA gene reveals that the phylotypes within candidate phylum SBR1093 are primarily clustered into 5 clades with a shallow branching pattern. This bacterium is clustered with phylotypes from organically contaminated environments, implying a demand for organics in heterotrophic metabolism. Considering the types of regulators, such as FnR, Fur, and ArsR, this bacterium might be a facultative aerobic mixotroph with potential multi-antibiotic and heavy metal resistances. This is the first report on Bacteria that may perform potential carbon fixation via the HPHB cycle, thus may expand our knowledge of the distribution and importance of the HPHB cycle in the biosphere. PMID:25310003

  5. Experimental Investigation of a Point Design Optimized Arrow Wing HSCT Configuration

    NASA Technical Reports Server (NTRS)

    Narducci, Robert P.; Sundaram, P.; Agrawal, Shreekant; Cheung, S.; Arslan, A. E.; Martin, G. L.

    1999-01-01

    The M2.4-7A Arrow Wing HSCT configuration was optimized for straight and level cruise at a Mach number of 2.4 and a lift coefficient of 0.10. A quasi-Newton optimization scheme maximized the lift-to-drag ratio (by minimizing drag-to-lift) using Euler solutions from FL067 to estimate the lift and drag forces. A 1.675% wind-tunnel model of the Opt5 HSCT configuration was built to validate the design methodology. Experimental data gathered at the NASA Langley Unitary Plan Wind Tunnel (UPWT) section #2 facility verified CFL3D Euler and Navier-Stokes predictions of the Opt5 performance at the design point. In turn, CFL3D confirmed the improvement in the lift-to-drag ratio obtained during the optimization, thus validating the design procedure. A data base at off-design conditions was obtained during three wind-tunnel tests. The entry into NASA Langley UPWT section #2 obtained data at a free stream Mach number, M(sub infinity), of 2.55 as well as the design Mach number, M(sub infinity)=2.4. Data from a Mach number range of 1.8 to 2.4 was taken at UPWT section #1. Transonic and low supersonic Mach numbers, M(sub infinity)=0.6 to 1.2, was gathered at the NASA Langley 16 ft. Transonic Wind Tunnel (TWT). In addition to good agreement between CFD and experimental data, highlights from the wind-tunnel tests include a trip dot study suggesting a linear relationship between trip dot drag and Mach number, an aeroelastic study that measured the outboard wing deflection and twist, and a flap scheduling study that identifies the possibility of only one leading-edge and trailing-edge flap setting for transonic cruise and another for low supersonic acceleration.

  6. [Fatal head injury caused by a crossbow arrow with unusually preserved posttraumatic volitional activity - case report].

    PubMed

    Řehulka, Hynek; Čechová, Eva; Mottlová, Jitka; Valenta, Martin; Mareška, Zdeněk

    2016-01-01

    The authors deal with a case of suicidal attempt resulting in a fatal head injury. A young man shot himself with a serially produced mechanical sports crossbow. The young man with a critical intracranial injury, a penetration, was nevertheless capable of basic locomotive activity, as well as of coherent communication with another people present at the scene. The critically injured patient was transported from the scene directly to medical centre where he subsequently underwent a neurologic surgery. On the eight day after the incident he died in the hospital as a result of sustained wounds. During the autopsy, a penetrating arrow-shot wound head injury was certified, occurring in the right and left temple area. Signs of a complex decompressive craniectomy were established too. The shooting channel was generally horizontally oriented, extending from the right to the left side, from behind in a 10 up to 15 degrees angle to the frontal plane, penetrating the brain from the right temple lobe and the frontal lobe, thereby pervading also frontal horns of lateral ventricles, and from the left afflicting the frontal lobe on the left side of the brain. In the course of the shooting channel, brain contusion occurred, accompanied by intraventricular haemorrhage. In addition, a heavy cerebral oedema, multiple secondary malacias, Durett haemorrhages and extensive thrombosis of cerebral sinuses were stated. In the course of police investigation, based mainly on the information given by the wounded man right after he had been found at the scene, it was revealed that another person might have been involved. The forensic autopsy, the investigation of the Police and the subsequent criminalist-ballistics expert investigation, supported by a series of experimental substitutive target shots, didnt, however, decidedly prove that any other culprit had been involved. PMID:27108656

  7. Box-and-arrow explanations need not be more abstract than neuroscientific mechanism descriptions

    PubMed Central

    Datteri, Edoardo; Laudisa, Federico

    2014-01-01

    The nature of the relationship between box-and-arrow (BA) explanations and neuroscientific mechanism descriptions (NMDs) is a key foundational issue for cognitive science. In this article we attempt to identify the nature of the constraints imposed by BA explanations on the formulation of NMDs. On the basis of a case study about motor control, we argue that BA explanations and NMDs both identify regularities that hold in the system, and that these regularities place constraints on the formulation of NMDs from BA analyses, and vice versa. The regularities identified in the two kinds of explanation play a crucial role in reasoning about the relationship between them, and in justifying the use of neuroscientific experimental techniques for the empirical testing of BA analyses of behavior. In addition, we make claims concerning the similarities and differences between BA analyses and NMDs. First, we argue that both types of explanation describe mechanisms. Second, we propose that they differ in terms of the theoretical vocabulary used to denote the entities and properties involved in the mechanism and engaging in regular, mutual interactions. On the contrary, the notion of abstractness, defined as omission of detail, does not help to distinguish BA analyses from NMDs: there is a sense in which BA analyses are more detailed than NMDs. In relation to this, we also focus on the nature of the extra detail included in NMDs and missing from BA analyses, arguing that such detail does not always concern how the system works. Finally, we propose reasons for doubting that BA analyses, unlike NMDs, may be considered “mechanism sketches.” We have developed these views by critically analyzing recent claims in the philosophical literature regarding the foundations of cognitive science. PMID:24904480

  8. Complete Genome Sequence of Endomicrobium proavitum, a Free-Living Relative of the Intracellular Symbionts of Termite Gut Flagellates (Phylum Elusimicrobia)

    PubMed Central

    Zheng, Hao

    2015-01-01

    We sequenced the complete genome of Endomicrobium proavitum strain Rsa215, the first isolate of the class Endomicrobia (phylum Elusimicrobia). It is the closest free-living relative of the endosymbionts of termite gut flagellates and thereby provides an excellent model for studying the evolutionary processes during the establishment of an intracellular symbiosis. PMID:26184928

  9. Draft Genome Sequence of "Candidatus Bacteroides periocalifornicus," a New Member of the Bacteriodetes Phylum Found within the Oral Microbiome of Periodontitis Patients.

    PubMed

    McLean, Jeffrey S; Liu, Quanhui; Thompson, John; Edlund, Anna; Kelley, Scott

    2015-01-01

    Here we present the draft genome of a distantly related member within the phylum Bacteriodetes, "Candidatus Bacteroides periocalifornicus." The draft genome sequence was assembled with metagenomic data from a patient with periodontitis. The closest relative has less than 68% average nucleic identity, supporting a novel family within Bacteriodetes. PMID:26701081

  10. Draft Genome Sequence of “Candidatus Bacteroides periocalifornicus,” a New Member of the Bacteriodetes Phylum Found within the Oral Microbiome of Periodontitis Patients

    PubMed Central

    Liu, Quanhui; Thompson, John; Edlund, Anna

    2015-01-01

    Here we present the draft genome of a distantly related member within the phylum Bacteriodetes, “Candidatus Bacteroides periocalifornicus.” The draft genome sequence was assembled with metagenomic data from a patient with periodontitis. The closest relative has less than 68% average nucleic identity, supporting a novel family within Bacteriodetes. PMID:26701081

  11. Zygomycete genealogy of life (ZyGoLife): A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Evolutionary relationships among zygomycete fungi have proven to be among the most difficult to resolve within Kingdom Fungi. Historically they were classified as a single phylum, Zygomycota, based on sexual reproduction by zygospores, frequent asexual reproduction by sporangia, absence of multicell...

  12. Search for anomalous WW/WZ {r_arrow} e{nu}jj production at D0; Busqueda de produccion anomala WW/WZ {r_arrow}e{nu}jj en D-Zero

    SciTech Connect

    Hernandez, A.S.

    1997-02-01

    A search for anomalous WW and WZ production in p{anti p} collisions at {radical}s = 1.8 TeV using the D0 detector at Fermilab is presented. With a data sample of p{anti p} {r_arrow} e{nu}jjX events corresponding to an integrated luminosity of 76.5 {+-} 4.1pb{sup {minus}1}. 399 candidate events were identified, from which 387.1 {+-} 39.8 events were estimated to be background. No deviations from the Standard Model were seen, which predicts 16.2 {+-} 2.7 events. The 95% CL limit on the cross section {sigma}(p{anti p} {r_arrow} W{sup +}W{sup {minus}}X) was calculated to be 93.8 pb. Limits on the CP-conserving anomalous WW{sub {gamma}} and WWZ coupling parameters were obtained from a binned likelihood fit to the transverse momentum spectrum of the W boson. Assuming that the WW{sub {gamma}} and WWZ coupling parameters are equal, the 95% CL limits on the CP-conserving couplings are {minus}0.56 < {Delta}{kappa} < 0.75 (with {lambda} = 0) and {minus}0.42 < {lambda} < 0.44 (with {Delta}{kappa} = 0), for a form factor scale {Lambda}{sub FF} = 1.5 TeV. Limits on other assumptions are also reported. These results were combined with the previous D0 WW, WZ {r_arrow} e{nu}jj published results (13.7 {+-} 0.7 pb{sup {minus}1}), and the limits on the anomalous coupling parameters were set to {minus}0.44 < {Delta}{kappa} < 0.60 (with {lambda} = 0) and {minus}0.34 < {lambda} 0.37 (with {Delta}{kappa} = 0), for a form factor scale {Lambda}{sub FF} = 2.0 TeV.

  13. Worm Grunting, Fiddling, and Charming—Humans Unknowingly Mimic a Predator to Harvest Bait

    PubMed Central

    Catania, Kenneth C.

    2008-01-01

    Background For generations many families in and around Florida's Apalachicola National Forest have supported themselves by collecting the large endemic earthworms (Diplocardia mississippiensis). This is accomplished by vibrating a wooden stake driven into the soil, a practice called “worm grunting”. In response to the vibrations, worms emerge to the surface where thousands can be gathered in a few hours. Why do these earthworms suddenly exit their burrows in response to vibrations, exposing themselves to predation? Principal Findings Here it is shown that a population of eastern American moles (Scalopus aquaticus) inhabits the area where worms are collected and that earthworms have a pronounced escape response from moles consisting of rapidly exiting their burrows to flee across the soil surface. Recordings of vibrations generated by bait collectors and moles suggest that “worm grunters” unknowingly mimic digging moles. An alternative possibility, that worms interpret vibrations as rain and surface to avoid drowning is not supported. Conclusions Previous investigations have revealed that both wood turtles and herring gulls vibrate the ground to elicit earthworm escapes, indicating that a range of predators may exploit the predator-prey relationship between earthworms and moles. In addition to revealing a novel escape response that may be widespread among soil fauna, the results show that humans have played the role of “rare predators” in exploiting the consequences of a sensory arms race. PMID:18852902

  14. WormFarm: a quantitative control and measurement device toward automated Caenorhabditis elegans aging analysis.

    PubMed

    Xian, Bo; Shen, Jie; Chen, Weiyang; Sun, Na; Qiao, Nan; Jiang, Dongqing; Yu, Tao; Men, Yongfan; Han, Zhijun; Pang, Yuhong; Kaeberlein, Matt; Huang, Yanyi; Han, Jing-Dong J

    2013-06-01

    Caenorhabditis elegans is a leading model organism for studying the basic mechanisms of aging. Progress has been limited, however, by the lack of an automated system for quantitative analysis of longevity and mean lifespan. To address this barrier, we developed 'WormFarm', an integrated microfluidic device for culturing nematodes. Cohorts of 30-50 animals are maintained throughout their lifespan in each of eight separate chambers on a single WormFarm polydimethylsiloxane chip. Design features allow for automated removal of progeny and efficient control of environmental conditions. In addition, we have developed computational algorithms for automated analysis of video footage to quantitate survival and other phenotypes, such as body size and motility. As proof-of-principle, we show here that WormFarm successfully recapitulates survival data obtained from a standard plate-based assay for both RNAi-mediated and dietary-induced changes in lifespan. Further, using a fluorescent reporter in conjunction with WormFarm, we report an age-associated decrease in fluorescent intensity of GFP in transgenic worms expressing GFP tagged with a mitochondrial import signal under the control of the myo-3 promoter. This marker may therefore serve as a useful biomarker of biological age and aging rate. PMID:23442149

  15. WormQTL--public archive and analysis web portal for natural variation data in Caenorhabditis spp.

    PubMed

    Snoek, L Basten; Van der Velde, K Joeri; Arends, Danny; Li, Yang; Beyer, Antje; Elvin, Mark; Fisher, Jasmin; Hajnal, Alex; Hengartner, Michael O; Poulin, Gino B; Rodriguez, Miriam; Schmid, Tobias; Schrimpf, Sabine; Xue, Feng; Jansen, Ritsert C; Kammenga, Jan E; Swertz, Morris A

    2013-01-01

    Here, we present WormQTL (http://www.wormqtl.org), an easily accessible database enabling search, comparative analysis and meta-analysis of all data on variation in Caenorhabditis spp. Over the past decade, Caenorhabditis elegans has become instrumental for molecular quantitative genetics and the systems biology of natural variation. These efforts have resulted in a valuable amount of phenotypic, high-throughput molecular and genotypic data across different developmental worm stages and environments in hundreds of C. elegans strains. WormQTL provides a workbench of analysis tools for genotype-phenotype linkage and association mapping based on but not limited to R/qtl (http://www.rqtl.org). All data can be uploaded and downloaded using simple delimited text or Excel formats and are accessible via a public web user interface for biologists and R statistic and web service interfaces for bioinformaticians, based on open source MOLGENIS and xQTL workbench software. WormQTL welcomes data submissions from other worm researchers. PMID:23180786

  16. CHARGE association in a child with de novo inverted duplication (14) (q22{r_arrow}q24.3)

    SciTech Connect

    North, K.N.; Wu, Bai Lin; Cao, B.N.

    1995-07-17

    We report on a 4-{1/2} year old girl with apparent CHARGE association who had a de novo inverted duplication (14) (q22{r_arrow}24.3), iris colobomas, ventricular septal defect, soft tissue choanal atresia, intellectual impairment, growth retardation, sensorineural deafness, apparently low set ears, and upslanting palpebral fissures. Family history was unremarkable and parental chromosomes were normal. Similarities between this and previously reported cases of 14q duplication suggest that a locus for a gene or genes causing some of the anomalies of CHARGE association may reside in the region 14q22 to 24.3. 26 refs., 2 figs., 1 tab.

  17. Ectopic Human Fasciola hepatica Infection by an Adult Worm in the Mesocolon

    PubMed Central

    Kim, Ah Jin; Choi, Chang Hwan; Choi, Sun Keun; Shin, Yong Woon; Park, Yun-Kyu; Kim, Lucia; Choi, Suk Jin; Han, Jee Young; Kim, Joon Mee; Chu, Young Chae; Park, In Suh

    2015-01-01

    We report here an ectopic case of Fasciola hepatica infection confirmed by recovery of an adult worm in the mesocolon. A 56-year-old female was admitted to our hospital with discomfort and pain in the left lower quadrant of the abdomen. Abdominal CT showed 3 abscesses in the left upper quadrant, mesentery, and pelvic cavity. On surgical exploration, abscess pockets were found in the mesocolon of the sigmoid colon and transverse colon. A leaf-like worm found in the abscess pocket of the mesocolon of the left colon was diagnosed as an adult fluke of F. hepatica. Histologically, numerous eggs of F. hepatica were noted with acute and chronic granulomatous inflammations in the subserosa and pericolic adipose tissues. Conclusively, a rare case of ectopic fascioliasis has been confirmed in this study by the adult worm recovery of F. hepatica in the mesocolon. PMID:26797440

  18. Ectopic Human Fasciola hepatica Infection by an Adult Worm in the Mesocolon.

    PubMed

    Kim, Ah Jin; Choi, Chang Hwan; Choi, Sun Keun; Shin, Yong Woon; Park, Yun-Kyu; Kim, Lucia; Choi, Suk Jin; Han, Jee Young; Kim, Joon Mee; Chu, Young Chae; Park, In Suh

    2015-12-01

    We report here an ectopic case of Fasciola hepatica infection confirmed by recovery of an adult worm in the mesocolon. A 56-year-old female was admitted to our hospital with discomfort and pain in the left lower quadrant of the abdomen. Abdominal CT showed 3 abscesses in the left upper quadrant, mesentery, and pelvic cavity. On surgical exploration, abscess pockets were found in the mesocolon of the sigmoid colon and transverse colon. A leaf-like worm found in the abscess pocket of the mesocolon of the left colon was diagnosed as an adult fluke of F. hepatica. Histologically, numerous eggs of F. hepatica were noted with acute and chronic granulomatous inflammations in the subserosa and pericolic adipose tissues. Conclusively, a rare case of ectopic fascioliasis has been confirmed in this study by the adult worm recovery of F. hepatica in the mesocolon. PMID:26797440

  19. Adult filarial worm from the breast aspirate of a young man.

    PubMed

    Fernandes, Hilda; Thomas, Beena Mary; Putran, Indira

    2016-06-01

    Microfilariae and adult filarial worm have been incidentally detected in fine needle aspirates of various lesions in clinically unsuspected cases. Here we report a male patient who presented with a tender breast nodule and single enlarged lymph node. Fine Needle Aspiration (FNA) yielded 1 ml of yellow coloured fluid and single thread like worm measuring 6 × 0.2 cm. A diagnosis of breast abscess with a worm morphologically consistent with filariasis was offered. A follow up visit after 2 months showed regression of the breast lesion and the lymph node. Filariasis of the breast is an uncommon condition and can cause a diagnostic dilemma at times. FNA cytology appears to be a more convenient and effective diagnostic tool in patients with mass lesions. Demonstration and identification of the parasite in smears helps in avoiding surgical excision and early institution of prompt therapy especially in young patients. PMID:27413335

  20. Chemo-paralysis for the removal of a live intraocular worm in ocular angiostrongyliasis.

    PubMed

    Mehta, Dinesh Kumar; Arora, Ritu; Chauhan, Deepender; Shroff, Daraius; Narula, Ritesh

    2006-07-01

    Angiostrongylus cantonensis is also called the rodent lung worm. It was first discovered in 1935 by Chen in Rattus rattus, in Canton, China. The rodent is the definitive host while infected mollusks, snails and crabs act as the intermediate hosts. Humans are infected by the 3rd stage larvae, either by eating undercooked intermediate hosts or by consuming vegetables.(1) It is a delicate nematode reported in Asia Pacific region most commonly in South-east Asia and has been reported from Taiwan, Thailand, Indonesia, Vietnam and Sri Lanka.(2) Anterior chamber angiostrogyliasis is extremely rare, and no previous case of ocular angiostrogyliasis from India could be found on Medline search. We report a new technique in the removal of the actively motile thread-like worm by paralysing it with intracameral preservative free lidocaine, which aids in the easy removal of the intact worm. PMID:16872350

  1. Species richness and macronutrient content of wawo worms (Polychaeta, Annelida) from Ambonese waters, Maluku, Indonesia

    PubMed Central

    2015-01-01

    Abstract The aims of this research were to: (1) investigate the species richness of wawo worms, and to (2) analyze macronutrient content of the worms. Wawo worms were sampled using a fishing net on March 18th-19th, 2014, from Ambonese waters, Maluku. As many as 26 wawo species belonging to 5 families were identified. Palola sp. was identified as the most abundant species of wawo, followed by Lysidice oele, Horst 1905, Eunice spp. and nereidids. Results of the proximate analysis reveal that female epitokes of Palola sp. contain 10.78 % ash, 10.71 % moisture, 11.67 % crude fat, 54.72 % crude protein and 12.12 % carbohydrate. PMID:25829856

  2. OpenWorm: an open-science approach to modeling Caenorhabditis elegans

    PubMed Central

    Szigeti, Balázs; Gleeson, Padraig; Vella, Michael; Khayrulin, Sergey; Palyanov, Andrey; Hokanson, Jim; Currie, Michael; Cantarelli, Matteo; Idili, Giovanni; Larson, Stephen

    2014-01-01

    OpenWorm is an international collaboration with the aim of understanding how the behavior of Caenorhabditis elegans (C. elegans) emerges from its underlying physiological processes. The project has developed a modular simulation engine to create computational models of the worm. The modularity of the engine makes it possible to easily modify the model, incorporate new experimental data and test hypotheses. The modeling framework incorporates both biophysical neuronal simulations and a novel fluid-dynamics-based soft-tissue simulation for physical environment-body interactions. The project's open-science approach is aimed at overcoming the difficulties of integrative modeling within a traditional academic environment. In this article the rationale is presented for creating the OpenWorm collaboration, the tools and resources developed thus far are outlined and the unique challenges associated with the project are discussed. PMID:25404913

  3. Mortality of rocky mountain elk in Michigan due to meningeal worm

    USGS Publications Warehouse

    Bender, L.C.; Schmitt, S.M.; Carlson, E.; Haufler, J.B.; Beyer, D.E., Jr.

    2005-01-01

    Mortality from cerebrospinal parelaphostrongylosis caused by the meningeal worm (Parelaphostrongylus tenuis) has been hypothesized to limit elk (Cervus elaphus nelsoni) populations in areas where elk are conspecific with white-tailed deer (Odocoileus virginianus). Elk were reintroduced into Michigan (USA) in the early 1900s and subsequently greatly increased population size and distribution despite sympatric high-density (???12/km2) white-tailed deer populations. We monitored 100 radio-collared elk of all age and sex classes from 1981-94, during which time we documented 76 mortalities. Meningeal worm was a minor mortality factor for elk in Michigan and accounted for only 3% of mortalities, fewer than legal harvest (58%), illegal kills (22%), other diseases (7%), and malnutrition (4%). Across years, annual cause-specific mortality rates due to cerebrospinal parelaphostrongylosis were 0.033 (SE=0.006), 0.029 (SE=0.005), 0.000 (SE=0.001), and 0.000 (SE=0.000) for calves, 1-yr-old, 2-yr-old, and ???3-yr-old, respectively. The overall population-level mortality rate due to cerebrospinal parelaphostrongylosis was 0.009 (SE=0.001). Thus, meningeal worm had little impact on elk in Michigan during our study despite greater than normal precipitation (favoring gastropods) and record (???14 km2) deer densities. Further, elk in Michigan have shown sustained population rates-of-increase of ???18%/yr and among the highest levels of juvenile production and survival recorded for elk in North America, indicating that elk can persist in areas with meningeal worm at high levels of population productivity. it is likely that local ecologic characteristics among elk, white-tailed deer, and gastropods, and degree of exposure, age of elk, individual and population experience with meningeal worm, overall population vigor, and moisture determine the effects of meningeal worm on elk populations. ?? Wildlife Disease Association 2005.

  4. Eradicating guinea worm without wells: unrealized hopes of the Water Decade.

    PubMed

    Brieger, W R; Otusanya, S; Adeniyi, J D; Tijani, J; Banjoko, M

    1997-12-01

    At the start of the United Nations International Drinking Water Supply and Sanitation Decade in the 1980s, guinea worm disease was targeted as the major indicator of the success of the Decade's efforts to promote safe water. By the late 1980s, most of the guinea worm endemic countries in Africa and South Asia had established guinea worm eradication programmes that included water supply as one of their main technical strategies. By surveying the water supply situation in Ifeloju Local Government Area (LGA) in Oyo State, Nigeria, in June 1996, as a case study, it was possible to determine the role that water supply has played in the eradication effort. Although two major agencies, the former Directorate for Food, Roads and Rural Infrastructure and UNICEF, provided hand dug and bore-hole wells respectively in many parts of the LGA, coverage of the smaller farm hamlets has been minor compared to efforts in the larger towns. This is ironic because the farm hamlets served as a reservoir for the disease in the 1980s, such that when the piped water system in the towns broke down, guinea worm was easily reintroduced into the towns. The survey of 188 ever-endemic hamlets with an estimated population of 23,556 found that 74.3% of the people still drink only pond water. Another 11.3% have wells that have become dysfunctional. Only 14.4% of this rural population has access' to functioning wells. Guinea worm was eliminated from 107 of the hamlets mainly by the use of cloth filters and chemical treatment of ponds. While this proves that it is possible to eradicate guinea worm, it fails to leave behind the legacy of reliable, safe water supplies that was the hope of the Water Decade. PMID:10176270

  5. Highly toxic ribbon worm Cephalothrix simula containing tetrodotoxin in Hiroshima Bay, Hiroshima Prefecture, Japan.

    PubMed

    Asakawa, Manabu; Ito, Katsutoshi; Kajihara, Hiroshi

    2013-02-01

    In 1998, during a toxicological surveillance of various marine fouling organisms in Hiroshima Bay, Japan, specimens of the ribbon worm, Cephalothrix simula (Nemertea: Palaeonemertea) were found. These ribbon worms contained toxins with extremely strong paralytic activity. The maximum toxicity in terms of tetrodotoxin (TTX) was 25,590 mouse units (MU) per gram for the whole worm throughout the monitoring period. The main toxic component was isolated and recrystallized from an acidified methanolic solution. The crystalline with a specific toxicity of 3520 MU/mg was obtained and identified as TTX by high performance liquid chromatography (HPLC)-fluorescent detection (FLD) (HPLC-FLD), electrospray ionization-mass spectrometry (ESI-MS), infrared (IR), nuclear magnetic resonance (NMR) and gas chromatography-mass spectrometry (GC-MS). The highest toxicity of C. simula exceeded the human lethal dose per a single worm. A toxicological surveillance of C. simula from 1998 to 2005 indicated approximately 80% of the individuals were ranked as "strongly toxic" (≥1000 MU/g). Forty-eight percent of the specimens possessed toxicity scores of more than 2000 MU/g. Seasonal variations were observed in the lethal potency of C. simula. Specimens collected on January 13, 2000 to December 26, 2000 showed mean toxicities of 665-5300 MU/g (n = 10). These data prompted a toxicological surveillance of ribbon worms from other localities with different habitats in Japan, including Akkeshi Bay (Hokkaido) under stones on rocky intertidal beaches, as well as Otsuchi (Iwate) among calcareous tubes of serpulid polychaetes on rocky shores. Within twelve species of ribbon worms examined, only C. simula possessed extremely high toxicity. Therefore, C. simula appears to show generally high toxicity irrespective of their locality and habitat. PMID:23430577

  6. Highly Toxic Ribbon Worm Cephalothrix simula Containing Tetrodotoxin in Hiroshima Bay, Hiroshima Prefecture, Japan

    PubMed Central

    Asakawa, Manabu; Ito, Katsutoshi; Kajihara, Hiroshi

    2013-01-01

    In 1998, during a toxicological surveillance of various marine fouling organisms in Hiroshima Bay, Japan, specimens of the ribbon worm, Cephalothrix simula (Nemertea: Palaeonemertea) were found. These ribbon worms contained toxins with extremely strong paralytic activity. The maximum toxicity in terms of tetrodotoxin (TTX) was 25,590 mouse units (MU) per gram for the whole worm throughout the monitoring period. The main toxic component was isolated and recrystallized from an acidified methanolic solution. The crystalline with a specific toxicity of 3520 MU/mg was obtained and identified as TTX by high performance liquid chromatography (HPLC)-fluorescent detection (FLD) (HPLC-FLD), electrospray ionization-mass spectrometry (ESI-MS), infrared (IR), nuclear magnetic resonance (NMR) and gas chromatography–mass spectrometry (GC-MS). The highest toxicity of C. simula exceeded the human lethal dose per a single worm. A toxicological surveillance of C. simula from 1998 to 2005 indicated approximately 80% of the individuals were ranked as “strongly toxic” (≥1000 MU/g). Forty-eight percent of the specimens possessed toxicity scores of more than 2000 MU/g. Seasonal variations were observed in the lethal potency of C. simula. Specimens collected on January 13, 2000 to December 26, 2000 showed mean toxicities of 665–5300 MU/g (n = 10). These data prompted a toxicological surveillance of ribbon worms from other localities with different habitats in Japan, including Akkeshi Bay (Hokkaido) under stones on rocky intertidal beaches, as well as Otsuchi (Iwate) among calcareous tubes of serpulid polychaetes on rocky shores. Within twelve species of ribbon worms examined, only C. simula possessed extremely high toxicity. Therefore, C. simula appears to show generally high toxicity irrespective of their locality and habitat. PMID:23430577

  7. Evaluation of existing EPRI and INEL test data to determine the worm to worm gear coefficient of friction in Limitorque actuators

    SciTech Connect

    Garza, I.A.

    1996-12-01

    About the last sizing parameter for motor operated valves which has not been determined by utility or NRC sponsored testing is actuator efficiency. A by-product of EPRI testing for valve factors is the measurement of the actuator efficiencies. Motor sizing in this testing provides efficiency testing for motors running near synchronous speed. INEL testing, sponsored by the NRC, for stem factors and rate of loading provides complimentary data for motors loaded down to zero speed. This paper analyzes the data from these two test programs to determine the coefficient of friction for the worm to worm gear interface. This allowed the development of an algorithm for determining the efficiency of actuators which have not been tested. This paper compares the results of this algorithm to the test data to provide a measure of the accuracy of this method for calculating actuator efficiency.

  8. The 5 f r arrow 6 d absorption spectrum of Pa sup 4+ /Cs sub 2 ZrCl sub 6

    SciTech Connect

    Edelstein, N.; Kot, W.K. ); Krupa, J. )

    1992-01-01

    The 5{ital f}{sup 1}{r arrow}6{ital d}{sup 1} absorption spectrum of {sup 231}Pa{sup 4+} diluted in a single crystal of Cs{sub 2}ZrCl{sub 6} has been measured at 4.2 K. Three bands corresponding to the 6{ital d}({Gamma}{sub 8{ital g}}, {Gamma}{sub 7{ital g}}, and {Gamma}{sup {prime}}{sub 8{ital g}} ) levels are assigned. Extensive vibronic structure has been observed for the lowest 5{ital f}{r arrow}6{ital d} transition and this structure is compared to that recently reported for the 6{ital d}{sup 1}{r arrow}5{ital f}{sup 1} emission spectra in the same system.

  9. Non-intentional but not automatic: reduction of word- and arrow-based compatibility effects by sound distractors in the same categorical domain.

    PubMed

    Miles, James D; Proctor, Robert W

    2009-10-01

    In the current study, we show that the non-intentional processing of visually presented words and symbols can be attenuated by sounds. Importantly, this attenuation is dependent on the similarity in categorical domain between the sounds and words or symbols. Participants performed a task in which left or right responses were made contingent on the color of a centrally presented target that was either a location word (LEFT or RIGHT) or a left or right arrow. Responses were faster when they were on the side congruent with the word or arrow. This bias was reduced for location words by a neutral spoken word and for arrows by a tone series, but not vice versa. We suggest that words and symbols are processed with minimal attentional requirements until they are categorized into specific knowledge domains, but then become sensitive to other information within the same domain regardless of the similarity between modalities. PMID:19688202

  10. Typical Meteoritic Worm-Like Forms Seen in the Polonnaruwa Meteorite

    NASA Astrophysics Data System (ADS)

    Wainwright, Milton; Rose, Christopher E.; Baker, Alexander J.; Briston, J. K.; Wickramasinghe, N. Chandra

    2013-03-01

    Fossilized "wormlike forms" were found in a putative new type of carbonaceous meteorite which recently fell on Polonnaruwa, Sri Lanka. Such worm-like forms have been found in other meteorites notably the Martian Allen Hills sample and a lunar meteorite. It has been claimed that such forms are fossilized bacteria, although this possibility is still disputed. The occurrence of worm-like forms in the Polonnaruwa sample adds weight to the view that it is a meteorite and not, as has been suggested, a fulgerite, formed by lightning striking the Earth's surface.

  11. Distribution, abundance and trail characteristics of acorn worms at Australian continental margins

    NASA Astrophysics Data System (ADS)

    Anderson, T. J.; Przeslawski, R.; Tran, M.

    2011-04-01

    Acorn worms (Enteropneusta), which were previously thought to be a missing link in understanding the evolution of chordates, are an unusual and potentially important component of many deep-sea benthic environments, particularly for nutrient cycling. Very little is known about their distribution, abundance, or behaviour in deep-sea environments around the world, and almost nothing is known about their distribution within Australian waters. In this study, we take advantage of two large-scale deep-sea mapping surveys along the eastern (northern Lord Howe Rise) and western continental margins of Australia to quantify the distribution, abundance and trail-forming behaviour of this highly unusual taxon. This is the first study to quantify the abundance and trail behaviour of acorn worms within Australian waters and provides the first evidence of strong depth-related distributions. Acorn worm densities and trail activity were concentrated between transect-averaged depths of 1600 and 3000 m in both eastern and western continental margins. The shallow limit of their depth distribution was 1600 m. The deeper limit was less well-defined, as individuals were found in small numbers below 3000 down to 4225 m. This distributional pattern may reflect a preference for these depths, possibly due to higher availability of nutrients, rather than a physiological constraint to greater depths. Sediment characteristics alone were poor predictors of acorn worm densities and trail activity. High densities of acorn worms and trails were associated with sandy-mud sediments, but similar sediment characteristics in either shallower or deeper areas did not support similar densities of acorn worms or trails. Trail shapes varied between eastern and western margins, with proportionally more meandering trails recorded in the east, while spiral and meandering trails were both common in the west. Trail shape varied by depth, with spiral-shaped trails dominant in areas of high acorn worm densities

  12. In vitro antifilarial effects of three plant species against adult worms of subperiodic Brugia malayi.

    PubMed

    Zaridah, M Z; Idid, S Z; Omar, A W; Khozirah, S

    2001-11-01

    Five aqueous extracts from three plant species, i.e., dried husks (HX), dried seeds (SX) and dried leaves (LX) of Xylocarpus granatum (Meliaceae), dried stems (ST) of Tinospora crispa (Menispermaceae) and dried leaves (LA) of Andrographis paniculata (Acanthaceae) were tested in vitro against adult worms of subperiodic Brugia malayi. The relative movability (RM) value of the adult worms over the 24-h observation period was used as a measure of the antifilarial activity of the aqueous extracts. SX extract of X. granatum demonstrated the strongest activity, followed by the LA extract of A. paniculata, ST extract of T. crispa, HX extract and LX extract of X. granatum. PMID:11585692

  13. A Concept Space Approach to Addressing the Vocabulary Problem in Scientific Information Retrieval: An Experiment on the Worm Community System.

    ERIC Educational Resources Information Center

    Chen, Hsinchun; Ng, Tobun D.; Martinez, Joanne; Schatz, Bruce R.

    1997-01-01

    Presents an algorithmic approach to addressing the vocabulary problem in scientific information retrieval and information sharing, using the molecular biology domain as an example. A cognitive study and a follow-up document retrieval study were conducted using first a conjoined fly-worm thesaurus and then an actual worm database and the conjoined…

  14. The politics of attention contextualized: gaze but not arrow cuing of attention is moderated by political temperament.

    PubMed

    Carraro, Luciana; Dalmaso, Mario; Castelli, Luigi; Galfano, Giovanni

    2015-08-01

    It is known that an averted gaze can trigger shifts of attention in an observer, a phenomenon known as gaze-cuing effect. Recently, Dodd et al. (Atten Percept Psychophys 73:24-29, 2011) have reported a reliable gaze-cuing effect for liberals but not for conservatives. The present study tested whether this result is gaze-specific or extends over nonsocial spatial signals. Conservatives and liberals took part in a spatial-cuing task in which centrally placed gaze and arrow cues, pointing rightward or leftward, were followed by a peripheral onset target requiring a simple detection response. Whereas a reliable cuing effect was present for both gaze and arrow cues in the case of liberals, conservatives showed a reduced cuing response only for gaze cues. These results provide further support for the pattern reported by Dodd et al. (2011) and are consistent with the view that conservatives are less susceptible to the influence of spatial cues provided by other individuals. PMID:26055660

  15. Development, integration, testing, and evaluation of the U.S. Army Buckeye System to the NAVAIR Arrow UAV

    NASA Astrophysics Data System (ADS)

    Fischer, Robert L.; Kennedy, Brian G.; Jones, Mitchell; Walker, Jeffrey; Muresan, Darian; Baxter, Gregory; Flood, Mark; Follmer, Brian; Sun, Xiuhong; Chen, William; Ruby, Jeffrey G.

    2008-04-01

    The Buckeye high-resolution geospatial collection system is currently supporting operations within both Iraq and Afghanistan. The Buckeye system, originally developed by the U.S. Army Corps of Engineers (USACE), Engineer Research and Development Center (ERDC), provides timely tactical high resolution geospatial information to field commanders. The Buckeye system is applicable in the following arenas: intelligence, surveillance, and reconnaissance (ISR), mapping, change detection, mission rehearsal, simulation, and battlefield visualization. Three distinct Buckeye systems hosted on multiple air platforms have provided continuous geospatial data delivery to U.S. Forces since November 2004. Further capability is to be provided by integrating next generation Buckeye components to an Unmanned Aerial Vehicle (UAV). The UAV selected for this effort is the experimental Arrow Unmanned Aerial System (UAS). This paper describes the physical and systems integration of the Buckeye Electro-Optical (EO) and Light Detection and Ranging (LIDAR) components to the Arrow platform. Engineering solutions for mass balancing, thermal dispersion, and component calibration are presented. The distributed on-board architecture which performs instrument control, image compression, and data downlink, is described and discussed. Finally theoretical, laboratory and flight testing results are presented with a discussion on implementation and data dissemination within a tactical environment.

  16. Contribution of extracellular polymeric substances (EPS) and their subfractions to the sludge aggregation in membrane bioreactor coupled with worm reactor.

    PubMed

    Li, Zhipeng; Tian, Yu; Ding, Yi; Wang, Haoyu; Chen, Lin

    2013-09-01

    This study focused on the effect of predated sludge recycle on the contribution of extracellular polymeric substances (EPSs) and their subfractions to sludge aggregation in combined MBR system. It was observed that aggregation abilities of sludge samples were decreased by worm predation. Furthermore, worm predation enhanced the energy barriers and weakened the secondary energy minimum in the interaction energy profiles of slime, loosely bound EPS (LB-EPS) and tightly bound EPS (TB-EPS). Further investigations demonstrated that the content decrease and structural change of different EPS fractions induced by worm predation may be the reason for the decreased aggregation of sludge. Concomitantly, the adsorption tests and atomic force microscopy observation confirmed that the worm predation decreased the adsorption of slime, LB-EPS and TB-EPS on membrane. This would indicate the worm predation could keep an optimum EPS level for which floc structure was maintained and the fouling propensity of mixed liquid was reduced. PMID:23891833

  17. Expression, purification, enzymatic characterization and crystallization of glyceraldehyde-3-phosphate dehydrogenase from Naegleria gruberi, the first one from phylum Percolozoa.

    PubMed

    Machado, Agnes Thiane Pereira; Silva, Marcio; Iulek, Jorge

    2016-11-01

    Naegleria gruberi had its genome sequenced by Fritz-Laylin and collaborators in 2010. It is not pathogenic, but has characteristics similar to those of Naegleria fowleri, opportunistic pathogen that can cause fatal encephalitis in humans. N. gruberi genome has contributed to a better understanding of the primitive eukaryotic metabolism and revealed the complexity of several metabolic pathways. In this paper we describe the expression, purification, enzyme characterization and crystallization of N. gruberi GAPDH, the first one for an organism belonging to phylum Percolozoa. The results indicated that 10 mM, 8.0 and 25 °C are the optimum arsenate concentration, pH and temperature, respectively. The enzyme presents allosteric positive cooperativity for substrates NAD(+) and G3P as indicated by the Hill coefficients. The phylogenetic proximity between N. fowleri and N. gruberi suggests that contributions from the study of the latter might provide information to assist the search for treatments of Primary Amebic Meningoencephalitis, especially, in this work, taking into account that GAPDH is identified as a therapeutic target. PMID:27426132

  18. The All-Data-Based Evolutionary Hypothesis of Ciliated Protists with a Revised Classification of the Phylum Ciliophora (Eukaryota, Alveolata)

    PubMed Central

    Gao, Feng; Warren, Alan; Zhang, Qianqian; Gong, Jun; Miao, Miao; Sun, Ping; Xu, Dapeng; Huang, Jie; Yi, Zhenzhen; Song, Weibo

    2016-01-01

    The phylum Ciliophora plays important roles in a wide range of biological studies. However, the evolutionary relationships of many groups remain unclear due to a lack of sufficient molecular data. In this study, molecular dataset was expanded with representatives from 55 orders and all major lineages. The main findings are: (1) 14 classes were recovered including one new class, Protocruziea n. cl.; (2) in addition to the two main branches, Postciliodesmatophora and Intramacronucleata, a third branch, the Mesodiniea, is identified as being basal to the other two subphyla; (3) the newly defined order Discocephalida is revealed to be a sister clade to the euplotids, strongly suggesting the separation of discocephalids from the hypotrichs; (4) the separation of mobilids from the peritrichs is not supported; (5) Loxocephalida is basal to the main scuticociliate assemblage, whereas the thigmotrichs are placed within the order Pleuronematida; (6) the monophyly of classes Phyllopharyngea, Karyorelictea, Armophorea, Prostomatea, Plagiopylea, Colpodea and Heterotrichea are confirmed; (7) ambiguous genera Askenasia, CyclotrichiumParaspathidium and Plagiocampa show close affiliation to the well known plagiopyleans; (8) validity of the subclass Rhynchostomatia is supported, and (9) the systematic positions of Halteriida and Linconophoria remain unresolved and are thus regarded as incertae sedis within Spirotrichea. PMID:27126745

  19. The All-Data-Based Evolutionary Hypothesis of Ciliated Protists with a Revised Classification of the Phylum Ciliophora (Eukaryota, Alveolata).

    PubMed

    Gao, Feng; Warren, Alan; Zhang, Qianqian; Gong, Jun; Miao, Miao; Sun, Ping; Xu, Dapeng; Huang, Jie; Yi, Zhenzhen; Song, Weibo

    2016-01-01

    The phylum Ciliophora plays important roles in a wide range of biological studies. However, the evolutionary relationships of many groups remain unclear due to a lack of sufficient molecular data. In this study, molecular dataset was expanded with representatives from 55 orders and all major lineages. The main findings are: (1) 14 classes were recovered including one new class, Protocruziea n. cl.; (2) in addition to the two main branches, Postciliodesmatophora and Intramacronucleata, a third branch, the Mesodiniea, is identified as being basal to the other two subphyla; (3) the newly defined order Discocephalida is revealed to be a sister clade to the euplotids, strongly suggesting the separation of discocephalids from the hypotrichs; (4) the separation of mobilids from the peritrichs is not supported; (5) Loxocephalida is basal to the main scuticociliate assemblage, whereas the thigmotrichs are placed within the order Pleuronematida; (6) the monophyly of classes Phyllopharyngea, Karyorelictea, Armophorea, Prostomatea, Plagiopylea, Colpodea and Heterotrichea are confirmed; (7) ambiguous genera Askenasia, CyclotrichiumParaspathidium and Plagiocampa show close affiliation to the well known plagiopyleans; (8) validity of the subclass Rhynchostomatia is supported, and (9) the systematic positions of Halteriida and Linconophoria remain unresolved and are thus regarded as incertae sedis within Spirotrichea. PMID:27126745

  20. The candidate phylum 'Termite Group 1' of bacteria: phylogenetic diversity, distribution, and endosymbiont members of various gut flagellated protists.

    PubMed

    Ohkuma, Moriya; Sato, Tomoyuki; Noda, Satoko; Ui, Sadaharu; Kudo, Toshiaki; Hongoh, Yuichi

    2007-06-01

    The candidate phylum 'Termite Group 1' (TG1) of bacteria, which is abundant in termite guts but has no culturable representative, was investigated with respect to the in situ localization, distribution, and diversity. Based on the 16S rRNA gene sequence analyses and FISH in termite guts, a number of lineages of TG1 members were identified as endosymbionts of a variety of gut flagellated protists from the orders Trichonymphida, Cristamonadida, and Oxymonadida that are mostly unique to termites. However, the survey in various environments using specific PCR primers revealed that TG1 members were also present in termites, a cockroach, and the bovine rumen that typically lack these protist orders. Most of the TG1 members from gut flagellates, termites, cockroaches, and the rumen formed a monophyletic subcluster that showed a shallow branching pattern in the phylogenetic tree, suggesting their recent diversification. Although endosymbionts of the same protist genera tended to be closely related, the endosymbiont lineages were often independent of the higher level classifications of their host protist and were dispersed in the phylogenetic tree. It appears that their cospeciation is not the sole rule for the diversification of TG1 members of endosymbionts. PMID:17391329