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Sample records for arrow worms phylum

  1. 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

  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.

  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. 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.

  5. Molecular phylogeny of echiuran worms (Phylum: Annelida) reveals evolutionary pattern of feeding mode and sexual dimorphism.

    PubMed

    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.

  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.

  7. 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

  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. 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.

  10. 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.

  11. Observations on some unusual cell types in the enigmatic worm Xenoturbella (phylum uncertain).

    PubMed

    Israelsson, O

    2006-08-01

    The inner epithelially organized gastrodermis of the enigmatic simple worms of the genus Xenoturbella contains numerous partly phagocytized cells of two kinds, ciliated cells (PCCs) and muscle cells (PMCs). PCCs and PMCs have features of undifferentiated cells and do not derive from differentiated adult cells. Homology of phagocytized cells to pulsatile bodies in acoel and nemertodermatid flatworms is therefore rejected. The phagocytized cells might represent an hitherto unknown process of regeneration in Xenoturbella. The phagocytized material contains as much DNA as in all mitochondria and nuclei of the living cells. This is probably caused by lack of digestion of nucleic acids. The genome size of Xenoturbella bocki was determined. It has a C-value of about 0.55 pg.

  12. 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.

  13. 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

  14. 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.

  15. 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

  16. 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.

  17. 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

  18. Organization and nucleotide sequence of the cluster of five histone genes in the polichaete worm Chaetopterus variopedatus: first record of a H1 histone gene in the phylum Annelida.

    PubMed

    del Gaudio, R; Potenza, N; Stefanoni, P; Chiusano, M L; Geraci, G

    1998-01-01

    Histone genes were identified and their nucleotide sequences were determined in the polychaete marine worm Chaetopterus variopedatus. The genes are organized in about 390 clusters of 7.3 kbp. Each cluster contains one copy of the five histone genes. The H1 histone gene present in the clusters is the first ever isolated in the phylum Annelida. The cluster has the unique peculiarity that all genes contain both the replication-dependent and the replication-independent 3' mRNA termination signals. Despite the differences in cluster organization and transcription polarity of the individual histone genes between C. variopedatus and Platynereis dumerilii, the other annelid in which histone genes have been studied, phylogenetic analysis of the encoded amino acid sequences clearly groups together those two organisms in a tree in which the other studied worms find closely related positions on the same evolutionary branch.

  19. 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.

  20. 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

  1. 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.

  2. 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)

  3. Biology of the phylum nematomorpha.

    PubMed

    Hanelt, B; Thomas, F; Schmidt-Rhaesa, A

    2005-01-01

    Compared with most animal phyla, the Nematomorpha, also known as hair worms, is a relatively understudied metazoan phylum. Although nematomorphs make up only 1 of 3 animal phyla specializing solely on a parasitic life style, little attention has been focused on this enigmatic group scientifically. The phylum contains two main groups. The nectonematids are parasites of marine invertebrates such as hermit crabs. The gordiids are parasites of terrestrial arthropods, such as mantids, beetles, and crickets. Members of both of these groups are free-living as adults in marine and freshwaters respectively. In recent years, large strides have been made to understand this group more fully. New information has come from collection efforts, new approaches in organismal biology, modern techniques in microscopy and molecular biology. This review will focus on the advances made in four main areas of research: (1) morphology, (2) taxonomy and systematics, (3) life cycle and ecology and (4) host behavioural alterations. Recent research focus on the structure of both nectonematids and gordiids has added new insights on the morphology of adult worms and juveniles. The nervous system of gordiids is now well described, including the documentation of sensory cells. In addition, the availability of material from the juvenile of several species of gordiids has made it possible to document the development of the parasitic stage. New collections and reinvestigations of museum specimens have allowed for a critical reevaluation of the validity of established genera and species. However, traditional taxonomic work on this group continues to be hampered by two impeding factors: first is the lack of species-specific characters; and second is the problem of intraspecific variation, which has likely led to the description of numerous synonyms. Modern molecular techniques have been used recently to support independently the broad relationships among gordiids. During the turn of the millennium, the

  4. 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.

  5. 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…

  6. Aiming ARROW at Learning Targets.

    ERIC Educational Resources Information Center

    Lane, Colin

    1987-01-01

    ARROW (Aural-Read-Respond-Oral-Written) is a multisensory teaching approach where children listen to their own voices on tape recorders. Advantages of the ARROW program as demonstrated at four sites in Blackford, Somerset (England), with elementary/secondary students presenting moderate to severe learning difficulties, reading/spelling/vocabulary…

  7. 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.

  8. 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.

  9. 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…

  10. 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.

  11. A phylogenetic analysis of the phylum Fibrobacteres.

    PubMed

    Jewell, Kelsea A; Scott, Jarrod J; Adams, Sandra M; Suen, Garret

    2013-09-01

    Members of the phylum Fibrobacteres are highly efficient cellulolytic bacteria, best known for their role in rumen function and as potential sources of novel enzymes for bioenergy applications. Despite being key members of ruminants and other digestive microbial communities, our knowledge of this phylum remains incomplete, as much of our understanding is focused on two recognized species, Fibrobacter succinogenes and F. intestinalis. As a result, we lack insights regarding the environmental niche, host range, and phylogenetic organization of this phylum. Here, we analyzed over 1000 16S rRNA Fibrobacteres sequences available from public databases to establish a phylogenetic framework for this phylum. We identify both species- and genus-level clades that are suggestive of previously unknown taxonomic relationships between Fibrobacteres in addition to their putative lifestyles as host-associated or free-living. Our results shed light on this poorly understood phylum and will be useful for elucidating the function, distribution, and diversity of these bacteria in their niches.

  12. 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)

  13. Serotonin receptors in parasitic worms.

    PubMed

    Mansour, T E

    1984-01-01

    It is evident from the above review that during the last two decades a great deal of interest in investigating the action of serotonin in parasitic worms has been shown by parasitologists as well as by scientists from several other disciplines. What we have initially reported concerning the effect of serotonin on motility and carbohydrate metabolism of F. hepatica has been pursued on several other parasitic worms. The studies so far indicate that serotonin stimulates motility of every species tested among the phylum Platyhelminthes. The indoleamine also stimulates glycogenolysis in the few flatworm parasites that have been investigated. The information in nematodes is scanty and the role of serotonin in these parasites is still open for experimentation. Recent biochemical investigations on F. hepatica and S. mansoni demonstrated that serotonin and related compounds utilize a common class of receptors in plasma membrane particles which I designate as 'serotonin receptors'. These receptors are linked to an adenylate cyclase that catalyses the synthesis of the second messenger, cyclic 3',5'-AMP. Serotonin and its congeners increase the concentration of cyclic AMP in intact parasites whereas antagonists inhibit such an effect. Cyclic AMP stimulates glycogenolysis, glycolysis and some rate-limiting glycolytic enzymes. It activates a protein kinase that may be involved in activation of glycogen phosphorylase and phosphofructokinase. Serotonin-activated adenylate cyclase in S. mansoni is activated early in the life of the schistosomule. The possibility is discussed that the availability of cyclic AMP through serotonin activation in these parasites may be a prelude to the development processes that take place in the parasite. The different components of the serotonin-activated adenylate cyclase in the parasite are the same as those that have been previously described for the host. Binding characteristics of the receptors indicate that the receptors in F. hepatica appear to

  14. 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;"…

  15. Dracunculiasis (guinea worm disease).

    PubMed

    Greenaway, Chris

    2004-02-17

    Dracunculiasis (guinea worm disease) is a parasitic disease that is limited to remote, rural villages in 13 sub-Saharan African countries that do not have access to safe drinking water. It is one the next diseases targeted for eradication by the World Health Organization. Guinea worm disease is transmitted by drinking water containing copepods (water fleas) that are infected with Dracunculiasis medinensis larvae. One year after human ingestion of infected water a female adult worm emerges, typically from a lower extremity, producing painful ulcers that can impair mobility for up to several weeks. This disease occurs annually when agricultural activities are at their peak. Large proportions of economically productive individuals of a village are usually affected simultaneously, resulting in decreased agricultural productivity and economic hardship. Eradication of guinea worm disease depends on prevention, as there is no effective treatment or vaccine. Since 1986, there has been a 98% reduction in guinea worm disease worldwide, achieved primarily through community-based programs. These programs have educated local populations on how to filter drinking water to remove the parasite and how to prevent those with ulcers from infecting drinking-water sources. Complete eradication will require sustained high-level political, financial and community support.

  16. Illustrating cerebral function: the iconography of arrows.

    PubMed Central

    Schott, G D

    2000-01-01

    For over a century the arrow has appeared in illustrations of cerebral function, yet the implications of using such symbols have not been previously considered. This review seeks to outline the nature, evolution, applications and limitations of this deceptively simple graphic device when it is used to picture functions of the brain. The arrow is found to have been used in several different ways: as a means of endowing anatomical structures with functional properties; as a method of displaying neural function either in free-standing form or in a structural or spatial framework; as a device for correlating functional data with underlying brain topography; and as a technique for linking functions of the brain with the world outside and with various philosophical concepts. For many of these uses the essential feature of the arrow is its directional characteristic. In contrast to the line, it is direction that enables the arrow to display information about time, which in turn can be exploited to depict functional rather than structural data. However, the use of the arrow is fraught with difficulties. It is often unclear whether an arrow has been used to illustrate fact, hypothesis, impression or possibility, or merely to provide a decorative flourish. Furthermore, the powerful symbolic nature of the arrow can so easily confer a spurious validity on the conjectural. Increasingly now there are insuperable difficulties when attempting to illustrate complex mechanisms of brain function. In the iconography of cerebral function, therefore, arrows with all their ambiguities may in certain circumstances become superseded by more non-representational symbols such as the abstract devices of the computational neuroscientist. PMID:11205341

  17. 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.

  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. 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)

  1. WormBase 2007

    PubMed Central

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

    2008-01-01

    WormBase (www.wormbase.org) is the major publicly available database of information about Caenorhabditis elegans, an important system for basic biological and biomedical research. Derived from the initial ACeDB database of C. elegans genetic and sequence information, WormBase now includes the genomic, anatomical and functional information about C. elegans, other Caenorhabditis species and other nematodes. As such, it is a crucial resource not only for C. elegans biologists but the larger biomedical and bioinformatics communities. Coverage of core areas of C. elegans biology will allow the biomedical community to make full use of the results of intensive molecular genetic analysis and functional genomic studies of this organism. Improved search and display tools, wider cross-species comparisons and extended ontologies are some of the features that will help scientists extend their research and take advantage of other nematode species genome sequences. PMID:17991679

  2. 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

  3. Decision Making in the Arrow of Time.

    PubMed

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

    2015-12-18

    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.

  4. 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.

  5. Guinea worm disease outcomes in Ghana: determinants of broken worms.

    PubMed

    Glenshaw, Mary T; Roy, Sharon; Ruiz-Tiben, Ernesto; Downs, Philip; Williamson, John; Eberhard, Mark

    2009-08-01

    In 2006, Ghana ranked second in Guinea worm disease (GWD) incidence and reported a previously undocumented 20% prevalence of worm breakage. A prospective study was conducted in 2007 to validate and describe worm breakage and determinants. Among 221 patients with known outcomes, the worm breakage rate observed was 46%. After controlling for demographics, worm and wound presentation, and treatment course and provision, worm breakage was associated with narrow-diameter worms (< 2 mm) (adjusted odds ratio [AOR] 2.79; 95% confidence interval [CI] = 1.03-7.53). Protective factors against worm breakage included antibiotic ointment use (AOR 0.31; 95% CI = 0.14-0.70), bandage protocol compliance (AOR: 0.38; 95% CI = 0.16-0.89), intact bandages (AOR 0.27; 95% CI = 0.09-0.82), and bloody compared with dry wounds (AOR 0.09; 95% CI = 0.01-0.7). The high worm breakage rate observed warrants improvement in case management and patient care. Adherence to established treatment protocols should be facilitated through improved provider training and supervision to reduce the disabling consequences of broken worms.

  6. Zeno's arrow and classical phase space logics

    NASA Astrophysics Data System (ADS)

    Westmoreland, Michael D.; Schumacher, Benjamin W.

    1994-06-01

    We analyze the Zeno's familiar paradox of the arrow using recently developed non-Boolean derived logics for classical systems. We show that the paradox depends upon a premise that is identically false in such logics, so that the language of experimental propositions is immune to the paradox.

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. 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.

  12. 77 FR 35082 - Arrow Investment Advisers, LLC and Arrow Investments Trust; Notice of Application

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-06-12

    ... the delivery cycles present in foreign markets in which those Funds invest. Applicants have been...''); (b) secondary market transactions in Shares to occur at negotiated market prices; (c) certain series... seek to preserve and grow capital, independent of market direction. 2. Arrow, a Delaware...

  13. GreenArrow version 1.0

    SciTech Connect

    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, and allows the user to zoom, pan and rotate a graph, as well as manipulate the individual nodes.

  14. GreenArrow version 1.0

    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

  15. 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.

  16. 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

  17. 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.

  18. 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…

  19. 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,…

  20. 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

  1. 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

  2. Experimental taphonomy of velvet worms (Onychophora) and implications for the Cambrian "explosion, disparity and decimation" model.

    PubMed

    Monge-Nájera, Julián; Hou, Xianguang

    2002-01-01

    Experimental preservation of velvet worms (phylum Onychophora), a very rare but evolutionarily important group that has existed for more than 500 million years, showed that the absence of bucal parts, adhesive-expelling organs, gonopore, eyes, legs, claws, annulation and papillation in fossils may not represent absence in the living animals. In fossils, leg thickness and claw orientation can be unreliable. The experiments indicate that not only absence, but even presence of certain structures can simply be the result of tissue decomposition. Computer-aided photorealistic reconstructions of fossi onychophorans are presented. We recommend future researchers to conduct taphonomy experiments specially before analysing unusual fossils.

  3. ARROW-PAK Macroencapsulation. Innovative Technology Summary Report

    SciTech Connect

    2002-04-01

    An ARROW-PAK is a high density polyethylene (HDPE) tube, about 21 feet long and 30 inches wide. Each ARROW-PAK can hold the equivalent of 21 55-gallon drums of mixed waste debris. Each tube is fused to HDPE endcaps using localized heating and high pressure contact. The sleeves and encaps form a tube for macroencapsulating mixed waste debris. The ARROW-PAK may achieve a mixed waste debris volume one-fourth that of the conventional macroencapsulation approach. The mixed waste debris is loaded into 55-gallon drums. Once filled a 'supercompactor' crushes the drums into 12-inch thick pucks. Three pucks can be loaded into a standard 85-gallon metal drum known as an 'overpack'. Seven overpacks fit into each ARROW-PAK.

  4. 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)

  5. 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.

  6. The bow and arrow in northern North America.

    PubMed

    Maschner, Herbert; Mason, Owen K

    2013-01-01

    There were at least four waves of bow and arrow use in northern North America. These occurred at 12000, 4500, 2400, and after about 1300 years ago. But to understand the role of the bow and arrow in the north, one must begin in the eighteenth century, when the Russians first arrived in the Aleutian Islands. At that time, the Aleut were using both the atlatl and dart and the bow and arrow (Fig. ). This is significant for two particular and important reasons. First, there are few historic cases in which both technologies were used concurrently; second, the bow and arrow in the Aleutian Islands were used almost exclusively in warfare. The atlatl was a critical technology because the bow and arrow are useless for hunting sea mammals. One cannot launch an arrow from a kayak because it is too unstable and requires that both hands remain on a paddle. To use an atlatl, it is necessary only to stabilize the kayak with a paddle on one side and launch the atlatl dart with the opposite hand. The Aleut on the Alaska Peninsula did indeed use the bow and arrow to hunt caribou there. However, in the 1,400 km of the Aleutian Islands, there are no terrestrial mammals except humans and the bow was reserved almost exclusively for conflicts among them. The most significant event in the history of the bow and arrow is not its early introduction, but rather the Asian War Complex 1300 years ago, when the recurve and backed bows first entered the region, altering regional and hemispheric political dynamics forever. [Figure: see text].

  7. A Phylogenomic Analysis of the Bacterial Phylum Fibrobacteres.

    PubMed

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

    2015-01-01

    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.

  8. 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

  9. 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

  10. Low dimensional worm-holes

    NASA Astrophysics Data System (ADS)

    Samardzija, Nikola

    1995-01-01

    A simple three dimensional physical model is proposed to qualitatively address a particular type of dynamics evolving on toroidal structures. In the phase space this dynamics creates appearance of a worm-hole through which a chaotic, quasiperiodic and periodic behaviors are formed. An intriguing topological property of such a system is that it possesses no steady state solutions. As such, it opens some interesting questions in the bifurcation theory. The model also offers a novel qualitative tool for explaining some recently reported experimental and simulation results observed in physics, chemistry and biology.

  11. Maxwell's demons everywhere: evolving design as the arrow of time.

    PubMed

    Bejan, Adrian

    2014-02-10

    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.

  12. Worms--a "license to kill".

    PubMed

    Kaminsky, Ronald; Rufener, Lucien; Bouvier, Jacques; Lizundia, Regina; Schorderet Weber, Sandra; Sager, Heinz

    2013-08-01

    Worm infections can cause severe harm and death to both humans and numerous domestic and wild animals. Despite the fact that there are many beneficial worm species, veterinarians, physicians and parasitologists have multiple reasons to combat parasitic worms. The pros and cons of various approaches for the discovery of new control methods are discussed, including novel anthelmintics, vaccines and genetic approaches to identify novel drug and vaccine targets. Currently, the mainstay of worm control remains chemotherapy and prophylaxis. The importance of knowledgeable and wise use of the available anthelmintics is highlighted.

  13. Environment induced time arrow and the Closed Time Path method

    NASA Astrophysics Data System (ADS)

    Polonyi, Janos

    2013-06-01

    It is shown in the framework of a harmonic system that the thermodynamical time arrow is induced by the environmental initial conditions in a manner similar to spontaneous symmetry breaking. The Closed Time Path formalism is introduced in classical mechanics to handle Green functions for initial condition problems by the action principle, in a systematic manner. The application of this scheme for quantum systems shows the common dynamical origin of the thermodynamical and the quantum time arrows. It is furthermore conjectured that the quantum-classical transition is strongly coupled.

  14. FMRFamide and related peptides in the phylum mollusca.

    PubMed

    López-Vera, Estuardo; Aguilar, Manuel B; Heimer de la Cotera, Edgar P

    2008-02-01

    FMRFamide is one of the well-known peptides studied within the phylum Mollusca. It was first isolated from the clam Macrocallista nimbosa during the end of the 1960s. Since then, a number of reports related to FMRFamide have been published from different experimental approaches, revealing that it and its related peptides (FaRPs) are implicated in a variety of physiological processes. As this year is the 30th anniversary since its discovery, this review focuses on diverse findings related to both FMRFamide and FaRPs in the phylum Mollusca.

  15. 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...

  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. 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]…

  18. Accumulated span loadings of an arrow wing having vortex flow

    NASA Technical Reports Server (NTRS)

    Reddy, C. Subba

    1989-01-01

    The vortex flow over an arrow wing is theoretically investigated using the free-vortex-sheet method. The sectional lift coefficient and accumulated span loadings, which are important in determining the root bending moment, are calculated. The longitudinal stability variation is also estimated.

  19. 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…

  20. 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…

  1. 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

  2. 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

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. Internet worms and global routing instabilities

    NASA Astrophysics Data System (ADS)

    Cowie, James; Ogielski, Andy T.; Premore, B. J.; Yuan, Yougu

    2002-07-01

    We analyze the global BGP routing instabilities observed during the Code Red II and Nimda worm attacks in July and September 2001, respectively. Compelling analysis is shown on the correlation between the observed instabilities and the worm attacks. We analyze router failure modes that can be triggered by the abnormal traffic during the worm attack and how they can lead to global routing instability. Independent research has partially confirmed that such failure modes can and likely do occur in practice. Highly detailed large-scale simulations help close the loop, indicating that such failure modes do in fact trigger the kind of widespread BGP instabilities that were observed empirically.

  8. 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

  9. 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.

  10. Genomewide analysis of phytochrome proteins in the phylum Basidiomycota.

    PubMed

    Lavín, José L; Ramírez, Lucía; Pisabarro, Antonio G; Oguiza, José A

    2015-09-01

    Phytochromes are photoreceptor proteins involved in the detection of the red and far-red regions of the visible light spectrum. Fungal phytochromes are hybrid histidine kinases with a conserved domain architecture composed of an N-terminal photosensory module and a C-terminal regulatory output module that includes the histidine kinase and response regulator receiver domains. In this study, we have analyzed the distribution, domain architecture, and phylogenetic analysis of phytochrome proteins in 47 published genome sequences among the phylum Basidiomycota. Genome analysis revealed that almost every genome of basidiomycetes contained at least one gene encoding a phytochrome protein. Domain architecture of fungal phytochromes was completely conserved in the identified phytochromes of basidiomycetes, and phylogenetic analysis clustered these proteins into clades related with the phylogenetic classification of this fungal phylum. PMID:25847700

  11. An expanded genomic representation of the phylum cyanobacteria.

    PubMed

    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

    2014-05-01

    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.

  12. 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

  13. Genomewide analysis of phytochrome proteins in the phylum Basidiomycota.

    PubMed

    Lavín, José L; Ramírez, Lucía; Pisabarro, Antonio G; Oguiza, José A

    2015-09-01

    Phytochromes are photoreceptor proteins involved in the detection of the red and far-red regions of the visible light spectrum. Fungal phytochromes are hybrid histidine kinases with a conserved domain architecture composed of an N-terminal photosensory module and a C-terminal regulatory output module that includes the histidine kinase and response regulator receiver domains. In this study, we have analyzed the distribution, domain architecture, and phylogenetic analysis of phytochrome proteins in 47 published genome sequences among the phylum Basidiomycota. Genome analysis revealed that almost every genome of basidiomycetes contained at least one gene encoding a phytochrome protein. Domain architecture of fungal phytochromes was completely conserved in the identified phytochromes of basidiomycetes, and phylogenetic analysis clustered these proteins into clades related with the phylogenetic classification of this fungal phylum.

  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. 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.

  16. 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.

  17. 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.

  18. Of water and worms: Guinea worm re-emergence in Niger.

    PubMed

    Royal, Nathaniel

    2014-03-01

    This paper aims to provide a better understanding of the re-emergence of Guinea worm into the water bodies of the Tillabéri region of the Niger Sahel. It examines the period of re-emergence and subsequent decline from 2002 until 2006. Using a geographic information system combined with a statistical approach to examine the location data of lakes with Guinea worm-associated cases, it is shown that the locations of population centers with cases of Guinea worm disease, the locations of lakes infected with Guinea worm larva, and features of the built environment are correlated in space.

  19. 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

  20. The phylum Synergistetes in gingivitis and necrotizing ulcerative gingivitis.

    PubMed

    Baumgartner, Angelica; Thurnheer, Thomas; Lüthi-Schaller, Helga; Gmür, Rudolf; Belibasakis, Georgios N

    2012-11-01

    The clinical manifestation of necrotizing ulcerative gingivitis (NUG) is distinct from that of common gingivitis in that it is characterized by local necrosis of the gingival tissues, rapid onset, pain and extensive bleeding. The phylum Synergistetes is a novel bacterial phylum consisting of Gram-negative anaerobes, with evidence of presence in biofilms associated with periodontal and endodontic infections. To date, the involvement of members of this phylum in NUG has not been investigated. This study aimed to evaluate the presence and levels of known human oral Synergistetes bacterial clusters in dental plaque from patients with NUG and compare them with those found in gingivitis. Marginal dental plaque samples from 21 NUG and 21 gingivitis patients were analysed quantitatively by fluorescent in situ hybridization and microscopy for members of two oral Synergistetes clusters (A and B) and for Jonquetella anthropi. Synergistetes cluster A bacteria were detected in all samples but at higher levels (9.4-fold) and proportions (2.5-fold) in NUG patients than in gingivitis patients. However, with regard to Synergistetes cluster B bacteria, there were no differences between NUG and gingivitis patients. J. anthropi was detected in only half of the samples and at lower levels than the other taxa. In conclusion, these data demonstrate that Synergistetes cluster A bacteria, but not cluster B bacteria or J. anthropi, are more strongly associated with NUG than with gingivitis.

  1. 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

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

    NASA Astrophysics Data System (ADS)

    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.

  3. 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

  4. 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.

  5. [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.

  6. Worm-stars and half-worms: Novel dangers and novel defense.

    PubMed

    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

  7. 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

  8. Measuring effects of voluntary attention: a comparison among predictive arrow, colour, and number cues.

    PubMed

    Olk, Bettina; Tsankova, Elena; Petca, A Raisa; Wilhelm, Adalbert F X

    2014-10-01

    The Posner cueing paradigm is one of the most widely used paradigms in attention research. Importantly, when employing it, it is critical to understand which type of orienting a cue triggers. It has been suggested that large effects elicited by predictive arrow cues reflect an interaction of involuntary and voluntary orienting. This conclusion is based on comparisons of cueing effects of predictive arrows, nonpredictive arrows (involuntary orienting), and predictive numbers (voluntary orienting). Experiment 1 investigated whether this conclusion is restricted to comparisons with number cues and showed similar results to those of previous studies, but now for comparisons to predictive colour cues, indicating that the earlier conclusion can be generalized. Experiment 2 assessed whether the size of a cueing effect is related to the ease of deriving direction information from a cue, based on the rationale that effects for arrows may be larger, because it may be easier to process direction information given by symbols such as arrows than that given by other cues. Indeed, direction information is derived faster and more accurately from arrows than from colour and number cues in a direction judgement task, and cueing effects are larger for arrows than for the other cues. Importantly though, performance in the two tasks is not correlated. Hence, the large cueing effects of arrows are not a result of the ease of information processing, but of the types of orienting that the arrows elicit. PMID:24697668

  9. 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

  10. B[sup +] [r arrow] D[sub s][sup *+][gamma] and B[sup +] [r arrow] D[sup *+][gamma] as probes of Vub

    SciTech Connect

    Grinstein, B.; Lebed, R.F.

    1999-02-01

    The decays B[sup +] [r arrow] D[sub s][sup *+][gamma] and B[sup +] [r arrow] D[sup *+]gamma can be used for an extraction of [vert bar]Vub[vert bar]. When the b and c quarks are nearly degenerate the rate for these modes can be determined in terms of other observed rates, namely B[anti B] mixing and D[sup *] [r arrow] D[gamma] decay. To this end the authors introduce a novel application of heavy quark and flavor symmetries. Although somewhat unrealistic, this limit provides one with a first estimate of these rates.

  11. Misidentification of Onchocerca volvulus as guinea worm.

    PubMed

    Eberhard, M L; Melemoko, G; Zee, A K; Weisskopf, M G; Ruiz-Tiben, E

    2001-12-01

    Over the past 10 years, the status of human infection with guinea worm (Dracunculus medinensis) in the Central African Republic (CAR) has been difficult to ascertain. It is unclear if indigenous cases are occurring and whether cases are migrating into the CAR from surrounding countries. A team of investigators visited the CAR in July-August 2000, to attempt to ascertain the presence of indigenous transmission. No cases of true guinea-worm infection (i.e. dracunculiasis) were detected, but three cases of human infection with Onchocerca volvulus, each of which had been misidentified as dracunculiasis, were detected. The unusual presentation of skin blisters and extraction of an intact female O. volvulus are described. As a result of this investigation, and the confusion of onchocerciasis being misidentified as dracunculiasis, the presence of endemic transmission of guinea worm in the CAR remains in question.

  12. 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

  13. 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.

  14. 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

  15. 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

  16. 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

  17. 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.

  18. 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

  19. 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

  20. 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

  1. 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.

  2. 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.

  3. 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.

  4. 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.…

  5. 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,…

  6. 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

  7. 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.

  8. Worms clear the smoke surrounding nicotine addiction.

    PubMed

    Kelley, Ann E

    2006-11-01

    In this issue of Cell, Feng et al. report a worm model of nicotine dependence that shows behavioral adaptations surprisingly similar to those in humans. These authors show a critical link between nicotinic receptors and TRP channels, which may represent a new therapeutic target for treating nicotine addiction.

  9. 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.

  10. Elastic mesh braided worm robot for locomotive endoscopy.

    PubMed

    Manwell, Thomas; Vítek, Tomáš; Ranzani, Tommaso; Menciassi, Arianna; Althoefer, Kaspar; Liu, Hongbin

    2014-01-01

    This paper presents a new design of worm robot whose body is constructed using a novel crimped elastic mesh braid inspired by the earthworm. The proposed worm robot is intended for inspection within the human body via natural orifices. The design and fabrication procedure of the worm robot are given in the paper. The imitation of peristalsis, used by natural worms, is used to control the worm robot for the purpose of producing motion while causing minimal trauma to biological tissue. The forward locomotive function of the worm robot has been tested on both a flat surface and in a rubber tube. It is shown that the worm robot is capable of propagating forwards for both test conditions in a form similar to the earthworm. The test results indicate the proposed worm robot design has promising application for natural tube inspection, like the colon and the esophagus.

  11. 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

  12. The WORM in Research (Write Once Read Many Optical Storage)

    PubMed Central

    Campbell, David; Marciniak, Thomas A.; Srivastava, Sudhir

    1988-01-01

    Write once, read many (WORM) optical storage is an available technology for storing inexpensively large amounts of data on a personal computer system. We summarize the technical tradeoffs of WORM drives and other forms of optical storage and discuss the use of WORM storage for typical medical data base applications: (1) flat files; (2) complex databases; and (3) text files.

  13. 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.

  14. Evolution of plant parasitism in the phylum Nematoda.

    PubMed

    Quist, Casper W; Smant, Geert; Helder, Johannes

    2015-01-01

    Within the species-rich and trophically diverse phylum Nematoda, at least four independent major lineages of plant parasites have evolved, and in at least one of these major lineages plant parasitism arose independently multiple times. Ribosomal DNA data, sequence information from nematode-produced, plant cell wall-modifying enzymes, and the morphology and origin of the style(t), a protrusible piercing device used to penetrate the plant cell wall, all suggest that facultative and obligate plant parasites originate from fungivorous ancestors. Data on the nature and diversification of plant cell wall-modifying enzymes point at multiple horizontal gene transfer events from soil bacteria to bacterivorous nematodes resulting in several distinct lineages of fungal or oomycete-feeding nematodes. Ribosomal DNA frameworks with sequence data from more than 2,700 nematode taxa combined with detailed morphological information allow for explicit hypotheses on the origin of agronomically important plant parasites, such as root-knot, cyst, and lesion nematodes.

  15. A photoactivatable green-fluorescent protein from the phylum Ctenophora.

    PubMed

    Haddock, Steven H D; Mastroianni, Nadia; Christianson, Lynne M

    2010-04-22

    Genes for the family of green-fluorescent proteins (GFPs) have been found in more than 100 species of animals, with some species containing six or more copies producing a variety of colours. Thus far, however, these species have all been within three phyla: Cnidaria, Arthropoda and Chordata. We have discovered GFP-type fluorescent proteins in the phylum Ctenophora, the comb jellies. The ctenophore proteins share the xYG chromophore motif of all other characterized GFP-type proteins. These proteins exhibit the uncommon property of reversible photoactivation, in which fluorescent emission becomes brighter upon exposure to light, then gradually decays to a non-fluorescent state. In addition to providing potentially useful optical probes with novel properties, finding a fluorescent protein in one of the earliest diverging metazoans adds further support to the possibility that these genes are likely to occur throughout animals.

  16. A photoactivatable green-fluorescent protein from the phylum Ctenophora

    PubMed Central

    Haddock, Steven H. D.; Mastroianni, Nadia; Christianson, Lynne M.

    2010-01-01

    Genes for the family of green-fluorescent proteins (GFPs) have been found in more than 100 species of animals, with some species containing six or more copies producing a variety of colours. Thus far, however, these species have all been within three phyla: Cnidaria, Arthropoda and Chordata. We have discovered GFP-type fluorescent proteins in the phylum Ctenophora, the comb jellies. The ctenophore proteins share the xYG chromophore motif of all other characterized GFP-type proteins. These proteins exhibit the uncommon property of reversible photoactivation, in which fluorescent emission becomes brighter upon exposure to light, then gradually decays to a non-fluorescent state. In addition to providing potentially useful optical probes with novel properties, finding a fluorescent protein in one of the earliest diverging metazoans adds further support to the possibility that these genes are likely to occur throughout animals. PMID:20018790

  17. 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 ...

  18. 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.

  19. Quantum Solution to the Arrow-of-Time Dilemma

    NASA Astrophysics Data System (ADS)

    Maccone, Lorenzo

    2009-08-01

    The arrow-of-time dilemma states that the laws of physics are invariant for time inversion, whereas the familiar phenomena we see everyday are not (i.e., entropy increases). I show that, within a quantum mechanical framework, all phenomena which leave a trail of information behind (and hence can be studied by physics) are those where entropy necessarily increases or remains constant. All phenomena where the entropy decreases must not leave any information of their having happened. This situation is completely indistinguishable from their not having happened at all. In the light of this observation, the second law of thermodynamics is reduced to a mere tautology: physics cannot study those processes where entropy has decreased, even if they were commonplace.

  20. Quantum solution to the arrow-of-time dilemma.

    PubMed

    Maccone, Lorenzo

    2009-08-21

    The arrow-of-time dilemma states that the laws of physics are invariant for time inversion, whereas the familiar phenomena we see everyday are not (i.e., entropy increases). I show that, within a quantum mechanical framework, all phenomena which leave a trail of information behind (and hence can be studied by physics) are those where entropy necessarily increases or remains constant. All phenomena where the entropy decreases must not leave any information of their having happened. This situation is completely indistinguishable from their not having happened at all. In the light of this observation, the second law of thermodynamics is reduced to a mere tautology: physics cannot study those processes where entropy has decreased, even if they were commonplace.

  1. Structural design studies of a supersonic cruise arrow wing configuration

    NASA Technical Reports Server (NTRS)

    Sobieszczanski, J.; Mccullers, L. A.; Ricketts, R. H.; Santoro, N. J.; Beskenis, S. D.; Kurtze, W. L.

    1976-01-01

    Structural member cross sections were sized with a system of integrated computer programs to satisfy strength and flutter design requirements for several variants of the arrow wing supersonic cruise vehicle. The resulting structural weights provide a measure of the structural efficiency of the planform geometry, structural layout, type of construction, and type of material including composites. The material distribution was determined for a baseline metallic structure and the results indicate that an approximate fatigue constraint has an important effect on the structural weight required for strength but, in all cases, additional material had to be added to satisfy flutter requirements with lighter mass engines with minimum fuel onboard. The use of composite materials on the baseline configuration was explored and indicated increased structural efficiency. In the strength sizing, the all-composite construction provided a lower weight design than the hybrid construction which contained composites only in the wing cover skins. Subsequent flutter analyses indicated a corresponding lower flutter speed.

  2. Worms to the rescue: can worm glycans protect from autoimmune diseases?

    PubMed

    Kuijk, Loes M; van Die, Irma

    2010-04-01

    Autoimmune and autoinflammatory diseases represent a significant health burden, especially in Western societies. For the majority of these diseases, no cure exists. Recently, research on parasitic worms (helminths) has demonstrated great potential for whole worms, their eggs or their excretory/secretory proteins in down-regulating inflammatory responses both in vitro and in vivo, in various disease models and, in some cases, even in clinical trials. The worms are thought to induce Th2 and regulatory T cells, interfere with Toll-like receptor (TLR) signaling and to down-regulate Th17 and Th1 responses. The molecular mechanisms underlying the worms' ability to modulate the host immune response are not well understood, and many hypotheses have been proposed to explain the observed immune modulation. Increasing evidence suggests that carbohydrate structures (glycans), for example, phosphorylcholine-modified glycans or Galbeta1-4(Fucalpha1-3)GlcNAc- (Lewis X, Le(X)) containing glycans, expressed by the worms contribute to these modulating properties by their interaction with antigen presenting cells. Helminths express a broad variety of protein- and lipid-linked glycans on their surface and on secretory products. These glycans differ in amount and composition and several of these structures are species specific. However, worms also express glycan antigens that are found in a wide variety of different species. Some of these "common" worm glycans are particularly interesting with regard to regulating host responses, because they have the potential to interact with C-type lectins on dendritic cells and thereby may interfere with T-cell polarization. Helminths and helminth-derived molecules form a novel and promising group of therapeutics for autoinflammatory diseases. However, much has to be learned about the molecular mechanisms behind the helminth-mediated antiinflammatory properties. This review will describe some of the emerging evidence in selected disease areas as

  3. 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

  4. 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

  5. WormBase: better software, richer content

    PubMed Central

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

    2006-01-01

    WormBase (), the public database for genomics and biology of Caenorhabditis elegans, has been restructured for stronger performance and expanded for richer biological content. Performance was improved by accelerating the loading of central data pages such as the omnibus Gene page, by rationalizing internal data structures and software for greater portability, and by making the Genome Browser highly customizable in how it views and exports genomic subsequences. Arbitrarily complex, user-specified queries are now possible through Textpresso (for all available literature) and through WormMart (for most genomic data). Biological content was enriched by reconciling all available cDNA and expressed sequence tag data with gene predictions, clarifying single nucleotide polymorphism and RNAi sites, and summarizing known functions for most genes studied in this organism. PMID:16381915

  6. 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.

  7. 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

  8. 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.

  9. 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

  10. 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

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

    PubMed

    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.

  12. Design parameters for sludge reduction in an aquatic worm reactor.

    PubMed

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

    2010-02-01

    Reduction and compaction of biological waste sludge from waste water treatment plants (WWTPs) can be achieved with the aquatic worm Lumbriculus variegatus. In our reactor concept for a worm reactor, the worms are immobilised in a carrier material. The size of a worm reactor will therefore mainly be determined by the sludge consumption rate per unit of surface area. This design parameter was determined in sequencing batch experiments using sludge from a municipal WWTP. Long-term experiments using carrier materials with 300 and 350 microm mesh sizes showed surface specific consumption rates of 45 and 58 g TSS/(m(2)d), respectively. Using a 350 microm mesh will therefore result in a 29% smaller reactor compared to using a 300 microm mesh. Large differences in consumption rates were found between different sludge types, although it was not clear what caused these differences. Worm biomass growth and decay rate were determined in sequencing batch experiments. The decay rate of 0.023 d(-1) for worms in a carrier material was considerably higher than the decay rate of 0.018 d(-1) for free worms. As a result, the net worm biomass growth rate for free worms of 0.026 d(-1) was much higher than the 0.009-0.011 d(-1) for immobilised worms. Finally, the specific oxygen uptake rate of the worms was determined at 4.9 mg O(2)/(gwwd), which needs to be supplied to the worms by aeration of the water compartment in the worm reactor.

  13. 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

  14. Literary Translation: The Experience of Translating Chinua Achebe's "Arrow of God" into French.

    ERIC Educational Resources Information Center

    d'Almeida, Irene

    1981-01-01

    Uses Achebe's "Arrow of God" as example of difficulty in translating English into French when author and translators are not native speakers of these languages. Suggests inventing French gibberish or use of translator's notes to translate Pidgin English. (BK)

  15. Discovery of multiple neuropeptide families in the phylum Platyhelminthes.

    PubMed

    McVeigh, Paul; Mair, Gunnar R; Atkinson, Louise; Ladurner, Peter; Zamanian, Mostafa; Novozhilova, Ekaterina; Marks, Nikki J; Day, Tim A; Maule, Aaron G

    2009-09-01

    Available evidence shows that short amidated neuropeptides are widespread and have important functions within the nervous systems of all flatworms (phylum Platyhelminthes) examined, and could therefore represent a starting point for new lead drug compounds with which to combat parasitic helminth infections. However, only a handful of these peptides have been characterised, the rigorous exploration of the flatworm peptide signalling repertoire having been hindered by the dearth of flatworm genomic data. Through searches of both expressed sequence tags and genomic resources using the basic local alignment search tool (BLAST), we describe 96 neuropeptides on 60 precursors from 10 flatworm species. Most of these (51 predicted peptides on 14 precursors) are novel and are apparently restricted to flatworms; the remainder comprise nine recognised peptide families including FMRFamide-like (FLPs), neuropeptide F (NPF)-like, myomodulin-like, buccalin-like and neuropeptide FF (NPFF)-like peptides; notably, the latter have only previously been reported in vertebrates. Selected peptides were localised immunocytochemically to the Schistosoma mansoni nervous system. We also describe several novel flatworm NPFs with structural features characteristic of the vertebrate neuropeptide Y (NPY) superfamily, previously unreported characteristics which support the common ancestry of flatworm NPFs with the NPY-superfamily. Our dataset provides a springboard for investigation of the functional biology and therapeutic potential of neuropeptides in flatworms, simultaneously launching flatworm neurobiology into the post-genomic era. PMID:19361512

  16. 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

  17. Discovery of multiple neuropeptide families in the phylum Platyhelminthes.

    PubMed

    McVeigh, Paul; Mair, Gunnar R; Atkinson, Louise; Ladurner, Peter; Zamanian, Mostafa; Novozhilova, Ekaterina; Marks, Nikki J; Day, Tim A; Maule, Aaron G

    2009-09-01

    Available evidence shows that short amidated neuropeptides are widespread and have important functions within the nervous systems of all flatworms (phylum Platyhelminthes) examined, and could therefore represent a starting point for new lead drug compounds with which to combat parasitic helminth infections. However, only a handful of these peptides have been characterised, the rigorous exploration of the flatworm peptide signalling repertoire having been hindered by the dearth of flatworm genomic data. Through searches of both expressed sequence tags and genomic resources using the basic local alignment search tool (BLAST), we describe 96 neuropeptides on 60 precursors from 10 flatworm species. Most of these (51 predicted peptides on 14 precursors) are novel and are apparently restricted to flatworms; the remainder comprise nine recognised peptide families including FMRFamide-like (FLPs), neuropeptide F (NPF)-like, myomodulin-like, buccalin-like and neuropeptide FF (NPFF)-like peptides; notably, the latter have only previously been reported in vertebrates. Selected peptides were localised immunocytochemically to the Schistosoma mansoni nervous system. We also describe several novel flatworm NPFs with structural features characteristic of the vertebrate neuropeptide Y (NPY) superfamily, previously unreported characteristics which support the common ancestry of flatworm NPFs with the NPY-superfamily. Our dataset provides a springboard for investigation of the functional biology and therapeutic potential of neuropeptides in flatworms, simultaneously launching flatworm neurobiology into the post-genomic era.

  18. 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.

  19. A novel report of hatching plasticity in the phylum Echinodermata.

    PubMed

    Armstrong, A Frances; Blackburn, Holly N; Allen, Jonathan D

    2013-02-01

    Hatching plasticity occurs in response to a wide range of stimuli across many animal taxa, including annelids, arthropods, mollusks, and chordates. Despite the prominence of echinoderms in developmental biology and more than 100 years of detailed examination of their development under a variety of conditions, environmentally cued hatching plasticity has never been reported in the phylum Echinodermata. Here we report plasticity in the timing and stage of hatching of embryos of the sand dollar Echinarachnius parma in response to reductions in salinity. Embryos of E. parma increased their time to hatching more than twofold in response to ecologically relevant salinity reductions, while maintaining an otherwise normal developmental schedule. Embryos that experienced the greatest delay in hatching time emerged from the fertilization envelope as four-arm pluteus larvae rather than hatching as blastulae or early gastrulae. Salinity manipulations across multiple male-female pairs indicated high variability in hatching time both within and among clutches, suggesting significant intraspecific variation in developmental responses to salinity.

  20. 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.

  1. 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.}

  2. The termite group I phylum is highly diverse and widespread in the environment.

    PubMed

    Herlemann, Daniel P R; Geissinger, Oliver; Brune, Andreas

    2007-10-01

    The bacterial candidate phylum Termite Group I (TG-1) presently consists mostly of "Endomicrobia," which are endosymbionts of flagellate protists occurring exclusively in the hindguts of termites and wood-feeding cockroaches. Here, we show that public databases contain many, mostly undocumented 16S rRNA gene sequences from other habitats that are affiliated with the TG-1 phylum but are only distantly related to "Endomicrobia." Phylogenetic analysis of the expanded data set revealed several diverse and deeply branching lineages comprising clones from many different habitats. In addition, we designed specific primers to explore the diversity and environmental distribution of bacteria in the TG-1 phylum.

  3. 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.

  4. 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.

  5. Impact of guinea worm disease on children in Nigeria.

    PubMed

    Ilegbodu, V A; Kale, O O; Wise, R A; Christensen, B L; Steele, J H; Chambers, L A

    1986-09-01

    School attendance records of all primary schools in a guinea worm-endemic village in southwestern Nigeria were examined to determine the cause of missed school days and school drop-outs. At the time of the survey, 1,495 pupils (768 boys and 727 girls were registered in the 4 primary schools in the village, of which 21% of the pupils were infected with guinea worm disease (GWD). Female pupils had a higher infection rate than their male counterparts. Guinea worm-infected pupils missed up to 25% of school year days compared to a non-guinea worm-infected absence of 2.5%. At the height of guinea worm season in the study area, guinea worm-related absences contributed virtually all of the absenteeism recorded in the schools. Implications of the findings within the context of educational attainment of the pupils are discussed.

  6. 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…

  7. 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.

  8. 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

  9. Moving Single Dots as Primes for Static Arrow Targets.

    PubMed

    Bermeitinger, Christina; Wentura, Dirk

    2016-03-01

    In response priming, responses are typically faster and more accurate if the prime calls for the same response as the target (i.e., compatible trials) than when primes and targets trigger different responses (i.e., incompatible trials). With moving rows-of-dots as primes for static arrow targets, participants instead responded faster to incompatible targets with longer SOAs (stimulus onset asynchrony, > 200 ms). Until now, it is unclear whether this effect is specific to the material. In the present research, a single moving dot was used as a prime. Further, we analyzed compatibility effects depending on reaction times (RTs). Positive compatibility effects in reaction times were found with an SOA of 147 ms and even with a relatively long SOA of 360 ms; for very long SOAs (800-1,200 ms), negative effects were found. We interpreted this as evidence that the specific type of motion is irrelevant for the occurrence of a negative compatibility effect.

  10. Moving Single Dots as Primes for Static Arrow Targets.

    PubMed

    Bermeitinger, Christina; Wentura, Dirk

    2016-03-01

    In response priming, responses are typically faster and more accurate if the prime calls for the same response as the target (i.e., compatible trials) than when primes and targets trigger different responses (i.e., incompatible trials). With moving rows-of-dots as primes for static arrow targets, participants instead responded faster to incompatible targets with longer SOAs (stimulus onset asynchrony, > 200 ms). Until now, it is unclear whether this effect is specific to the material. In the present research, a single moving dot was used as a prime. Further, we analyzed compatibility effects depending on reaction times (RTs). Positive compatibility effects in reaction times were found with an SOA of 147 ms and even with a relatively long SOA of 360 ms; for very long SOAs (800-1,200 ms), negative effects were found. We interpreted this as evidence that the specific type of motion is irrelevant for the occurrence of a negative compatibility effect. PMID:27221603

  11. Correction: Phylogenetic placement of the enigmatic parasite, Polypodium hydriforme, within the Phylum Cnidaria.

    PubMed

    Evans, Nathaniel M; Lindner, Alberto; Raikova, Ekaterina V; Collins, Allen G; Cartwright, Paulyn

    2009-07-15

    Correction to Evans, N.M., Lindner, A., Raikova, E.V., Collins, A.G. and Cartwright, P. Phylogenetic placement of the enigmatic parasite, Polypodium hydriforme, within the phylum Cnidaria. BMC Evol Biol, 2008, 8:139.

  12. 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

  13. N-terminal amino acid sequence of the deep-sea tube worm haemoglobin remarkably resembles that of annelid haemoglobin.

    PubMed Central

    Suzuki, T; Takagi, T; Ohta, S

    1988-01-01

    The deep-sea giant tube worm Lamellibrachia, belonging to the phylum Vestimentifera, contains two extracellular haemoglobins, an Mr 3,000,000 haemoglobin and an Mr 440,000 haemoglobin. The former has a hexagonal bilayer structure and consists of six polypeptide chains (AI-VI); a study of its haem content shows that not all of the chains contain haem. The Mr 440,000 haemoglobin consists of four haem-containing chains (BI-IV). We isolated most of the chains by reverse-phase chromatography and determined the amino acid sequences of the 21-45 N-terminal residues. Eight chains (AI-IV and BI-IV) showed significant homology with haem-containing chains of annelid giant haemoglobin. The highest homology was found between Lamellibrachia chain AI and Tylorrhynchus chain I; surprisingly, 18 out of the 20 N-terminal residues are identical. On the other hand, chain AV, with an unusual Mr of 32,000, showed a rather different sequence and is likely to be a non-haem chain which might act as a linker protein in the assembly of the haem-containing chains. From these results, we conclude that the tube worm Mr 3,000,000 haemoglobin is highly homologous with annelid haemoglobin. Images Fig. 2. PMID:3202832

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

    PubMed

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

    2006-01-01

    Research into arthropod evolution is hampered by the derived nature and rapid evolution of the best-studied out-group: the nematodes. We consider priapulids as an alternative out-group. Priapulids are a small phylum of bottom-dwelling marine worms; their tubular body with spiny proboscis or introvert has changed little over 520 million years and recognizable priapulids are common among exceptionally preserved Cambrian fossils. Using the complete mitochondrial genome and 42 nuclear genes from Priapulus caudatus, we show that priapulids are slowly evolving ecdysozoans; almost all these priapulid genes have evolved more slowly than nematode orthologs and the priapulid mitochondrial gene order may be unchanged since the Cambrian. Considering their primitive bodyplan and embryology and the great conservation of both nuclear and mitochondrial genomes, priapulids may deserve the popular epithet of "living fossil." Their study is likely to yield significant new insights into the early evolution of the Ecdysozoa and the origins of the arthropods and their kin as well as aiding inference of the morphology of ancestral Ecdysozoa and Bilateria and their genomes. PMID:17073934

  15. 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.

  16. Structure and membrane actions of a marine worm protein cytolysin, Cerebratulus toxin A-III.

    PubMed

    Kem, W R

    1994-02-28

    Four homologous Cerebratulus lacteus A toxins are the first and as yet only protein cytolysins to be isolated from an ancient phylum of marine worms, the nemertines. The most abundant and toxic variant, toxin A-III, has been sequenced and its mechanisms of action studied in the most detail. It consists of a single basic polypeptide chain of 95 amino acid residues cross-linked by three disulfide bonds, and possesses a predominantly alpha-helical secondary structure. The C-terminal third of the toxin sequence is postulated to be a helical 'hairpin' structure involved in pore formation. Toxin A-III permeabilizes a variety of cells as well as liposomes made from a variety of phospholipids; apparently large pores are formed, as large proteins are released almost as rapidly as small organic molecules and inorganic ions. At sublytic concentrations, the toxin also inhibits protein kinase C and endogenous voltage-gated cation selective (sodium, calcium) channels occurring in the nervous and cardiovascular systems. A curious observation, also reported for colicins and some other protein cytolysins, was the conservation of toxin secondary structure upon insertion into phospholipid liposomes, despite the strong likelihood that significant changes in tertiary structure occur to provide a hydrophobic surface for interaction with membrane lipids. Because of its small size and presumed single helical hairpin secondary structure, Cl toxin A-III is an excellent molecular subject for investigating protein insertion into biological membranes and mechanisms of pore formation.

  17. The Arrow of Time through the Lens of Computing

    NASA Astrophysics Data System (ADS)

    Palem, Krishna V.

    The concepts of temporal logic were introduced by Amir Pnueli [1] into the realm of computer science in general and programs in particular, to great effect. Given a program specification, a crucial element of reasoning through temporal logic is our ability to assert that one program event occurs before or after the other, with an order intuitively rooted in our notion of "time". In the realm of temporal logic, such assertions are abstracted as pure mathematical facts. An alternative is to consider the physical realization by executing the specified program through, for example, a microprocessor-based system. In such a case, a mechanism is used to ensure that the desired temporal relationships from the program specification are obeyed, and quite often this mechanism takes the form of a clock. In physical instantiations however clocks and similar mechanisms have an associated energy cost. They are guided by the laws of physics in general and thermodynamics in particular, with which the arrow of time and the associated irreversibility are intimately intertwined. Viewed through this lens, a key question arises of whether the need for ensuring that the temporal norms needed for program correctness accrue an inevitable energy cost. In this paper, I sketch some of the intricacies underlying this question. I will hint at the subtle interactions between models of computing, time as it is represented in them, and the associated thermodynamic cost. In his early work, Amir relied as much on the philosophy of reasoning about time [2-4] as on the technical intricacies of mathematical logic. In recognition of the richness of his intellectual endeavor, I have developed this exposition in a philosophical style mimicking that of the ancient greek philosopher Zeno [5,6].

  18. 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

  19. Local structure of numerically generated worm hole spacetime.

    NASA Astrophysics Data System (ADS)

    Siino, M.

    The author investigates the evolution of the apparent horizons in a numerically gererated worm hole spacetime. The behavior of the apparent horizons is affected by the dynamics of the matter field. By using the local mass of the system, he interprets the evolution of the worm hole structure.

  20. Two new septate junctions in the phylum Coelenterata.

    PubMed

    Green, C R; Flower, N E

    1980-04-01

    Freeze-fracture of fixed and unfixed tissue, lanthanum tracer and conventional thin-section studies have revealed 2 new types of septate junction in the class Anthozoa, phylum Coelenterata. These new junctions have the 15-18-nm intercellular spacing of all other described septate junctions and are found around the apical circumference of cells lining a lumen or outside edge. However, in freeze-fracture replicas and tangential views of lanthanum-impregnated tissue, they are seen to be quite different from other known septate junction types. One of the new junctions is found in endothelial tissue such as that lining the gut or the inside of the tentacles. In tangential view it is seen to consist of relatively short, straight, double septa, again with lateral projections. In feeeze-fracture of unfixed tissue, the junction consists of double rows of particles on the P face, the particles of one row being rounded, those of the other being elongated at right angles to the line of the septum. This dichotomy in particle size is unexpected, as the 2 halves of the septa as seen in tangential view are symmetrical. In freeze-fracture of fixed material the particle arrays remain on the P face and appear similar to those of unfixed material, but never as clear. In fixed tissue, some distortion had occurred and in extreme cases septa appear as a single broad jumbled row of particles. In this double septa junction, the rows of particles seen in freeze-fracture are occasionally seen to anastomose with a septum dividing into 2 and a third row of particles aligning with the 2 new septa to form their double particle rows. In both fixed and unfixed tissues, the E face of the junction consists of wide, shallow grooves. The second of the new junctions occurs in epithelial tissue, such as around the outer edge of sea-anemone tentacles, and consists of long wavy septa with lateral projections. In views where these projections appear longest, they arise predominantly from one side of the

  1. 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

  2. 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.

  3. 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.

  4. Early Cambrian sipunculan worms from southwest China.

    PubMed

    Huang, Di-Ying; Chen, Jun-Yuan; Vannier, Jean; Saiz Salinas, J I

    2004-08-22

    We report the discovery of sipunculan worms from the Lower Cambrian Maotianshan Shale, near Kunming (southwest China). Their sipunculan identity is evidenced by the general morphology of the animals (sausage-shaped body with a slender retractable introvert and a wider trunk) and by other features, both external (e.g. perioral crown of tentacles, and hooks, papillae and wrinkle rings on the body surface) and internal (U-shaped gut, and the anus opening near the introvert-trunk junction). The three fossil forms (Archaeogolfingia caudata gen. et sp. nov., Cambrosipunculus tentaculatus gen. et sp. nov. and Cambrosipunculus sp.) have striking similarities to modern sipunculans, especially the Golfingiidae to which their evolutionary relationships are discussed. This study suggests that most typical features of extant sipunculans have undergone only limited changes since the Early Cambrian, thus indicating a possible evolutionary stasis over the past 520 Myr. PMID:15306286

  5. Tropical aquarium aquatic dermatoses: bristle worm envenomation.

    PubMed

    Kay, Martin H; Bak, Rachel D; Kay, David N

    2010-01-01

    A 55-year-old high school science teacher with diabetes presented with severe pain and swelling of his left hand. He reported receiving a "shock" 2 days earlier while cleaning out his classroom's aquarium with a bare left hand. Thinking it was a "short" in the electrical connections to the aquarium's pump, he disconnected the electrical cord and continued to clean behind the pump mechanism. After a few more such shocks he put on a glove and retrieved 10 foot-long worms. Antibiotics were started. It took more than 2 weeks for the hand to return to its normal size. On presentation to our office, the patient's left hand was moderately swollen, with blistering and purpura seen on his distal fingers. He reported pain, itching, and numbness in the hand, which was getting worse. No systemic symptoms were reported. The patient was a non-insulin-dependent diabetic who was also taking warfarin for a carotid vascular problem. He brought to our office a bucket with coiled aquatic worms at the bottom (Figure 1). When extended, they measured about 1 foot and their morphology could be better seen (Figure 2). No spicules could be seen in the patient's hand on magnification, but taping was performed to remove any possible residual spicules. The patient was given oral antibiotics, a Medrol dose pack, oral antihistamines, and topical corticosteroids. Within 1 day of starting treatment his symptoms and hand swelling began to abate, by 1 week his hand skin peeled, and by 2 weeks the swelling and skin appearance was almost back to normal. Bacterial cultures of the hand's wounds showed no growth.

  6. Measurement of the ratio [ital scrB]([ital D][sup +][r arrow][pi][sup 0][ital l+][nu])/[ital scrB]([ital D][sup +][r arrow][ital [bar K

    SciTech Connect

    Alam, M.S.; Kim, I.J.; Nemati, B.; O'Neill, J.; Severini, H.; Sun, C.R.; Zoeller, M.M.; Crawford, G.; Daubenmier, C.M.; Fulton, R.; Fujino, D.; Gan, K.K.; Honscheid, K.; Kagan, H.; Kass, R.; Lee, J.; Malchow, R.; Morrow, F.; Skovpen, Y.; Sung, M.; White, C.; Whitmore, J.; Wilson, P.; Butler, F.; Fu, X.; Kalbfleisch, G.; Lambrecht, M.; Ross, W.R.; Skubic, P.; Snow, J.; Wang, P.L.; Wood, M.; Bortoletto, D.; Brown, D.N.; Fast, J.; McIlwain, R.L.; Miao, T.; Miller, D.H.; Modesitt, M.; Schaffner, S.F.; Shibata, E.I.; Shipsey, I.P.J.; Wang, P.N.; Battle, M.; Ernst, J.; Kroha, H.; Roberts, S.; Sparks, K.; Thorndike, E.H.; Wang, C.H.; Dominick, J.; Sanghera, S.; Skwarnicki, T.; Stroynowski, R.; Artuso, M.; He, D.; Goldberg, M.; Horwitz, N.; Kennett, R.; Moneti, G.C.; Muheim, F.; Mukhin, Y.; Playfer, S.; Rozen, Y.; Stone, S.; Thulasidas, M.; Vasseur, G.; Zhu, G.; Bartelt, J.; Csorna, S.E.; Egyed, Z.; Jain, V.; Sheldon, P.; Akerib, D.S.; Barish, B.; Chadha, M.; Chan, S.; Cowen, D.F.; Eigen, G.

    1993-08-30

    Using the CLEO-II detector, the branching ratio of the Cabibbo suppressed decay [ital D][sup +][r arrow][pi][sup 0][ital l+][nu], relative to the branching ratio of the Cabibbo favored decay [ital D][sup +][r arrow][ital [bar K

  7. The conflict adaptation is affected by attentional strategies: evidence from the arrow flanker task.

    PubMed

    Chen, Jia; Li, Chang; He, ChunHong; Chen, AnTao

    2009-10-01

    Recently, several studies have considered factors affecting the occurrence of congruency sequence effect (CSE) in the arrow flanker task. In the present study, the influence of the following factors was examined: the presentation of a fixation and the intertrial interval (ITI) were considered. Results of the study showed that the CSE was significant when there was no fixation and when the ITI was long for response repetitions and response changes, but disappeared for response change trials in other conditions. These results showed that, even in the arrow flanker task, the conflict adaptation effect did contribute to the CSE. The current results suggested that the conflict adaptation effect in the arrow flanker task was based on the appropriate application of attention strategies.

  8. 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

  9. 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

  10. 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

  11. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

    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.

  13. 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

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

    PubMed

    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.

  15. 78 FR 21345 - In the Matter of: Liem Duc Huynh, a/k/a Duc Huynh, 2905 South Elm, Broken Arrow, OK 74012; Order...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-10

    ... Arrow, OK 74012; Order Denying Export Privileges On April 17, 2012, in the U.S. District Court, Central... last known address at: 2905 South Elm, Broken Arrow, OK 74012, and when acting for or on behalf...

  16. 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…

  17. Complications after meniscal repair with bioabsorbable arrows: two cases and analysis of literature.

    PubMed

    Otte, Stephanie; Klinger, Hans-Michael; Beyer, Juergen; Baums, Mike H

    2002-07-01

    Biodegradable implants were introduced in the middle 1990s as a new technique for the arthroscopic treatment of reparable meniscal tears. We have used these implants since 1999 and present two cases of failure of biodegradable meniscal repair implants. One foreign-body reaction with granuloma and one fresh meniscus tear after renewed trauma in the case of receding meniscus arrows with a chondral lesion. We also performed a review of the literature with the Medline database. Meniscus refixation with bioabsorbable arrows is considered reliable but shows various other complications that must be borne in mind.

  18. Time reversal invariance and the arrow of time in classical electrodynamics.

    PubMed

    Rohrlich, Fritz

    2005-11-01

    Time reversal invariance, T, is well known to hold in quantum electrodynamics. However, it has caused difficulties in classical electrodynamics (CED). These are shown to be conceptual misunderstandings. When corrected: (1) the classical equations of motion of a charge are T invariant despite the explicit occurrence of retarded fields in the equations of motion. (2) Advanced fields violate causality and occur neither in nature nor in the CED that describes it. (3) The nonexistence of advanced fields in nature implies an "arrow of time" for electromagnetic radiation: radiation emission is an overall dissipative phenomenon. This electromagnetic "arrow of time" does not contradict time reversal invariance.

  19. Sex ratios of Dirofilaria immitis in naturally infected dogs show female bias at low worm intensities.

    PubMed

    Rishniw, Mark; Schukken, Ynte; Greiner, Ellis

    2012-12-01

    Sex ratios in invertebrates commonly deviate from parity (1:1). Various genetic and epigenetic factors distort sex ratios to favor males or females. We examined sex ratios in Dirofilaria immitis (heartworms) obtained from naturally-infected dogs. Dirofilaria from 84 naturally-infected pound-source dogs were extracted at necropsy, counted and sexed. Dogs had a median worm intensity of 15 filariae. Overall, sex ratios equaled 1. However, at low worm intensities, dogs were more likely to have female than male worms. Of eight unisex infections, seven were all-female (range 1-11 worms), while only one dog had a single male worm. Similarly, in mixed-sex infection at worm intensities<20 worms, dogs were more likely to have more female worms than male worms. Our results suggest that sex disequilibrium exists in D. immitis at lower worm intensities, but disappears with higher worm intensities. Reasons for this disequilibrium are unknown, but presumably confer a species survival advantage.

  20. 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.

  1. 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.

  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. 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.

  4. 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

  5. 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

  6. 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.

  7. Velvet worm development links myriapods with chelicerates

    PubMed Central

    Mayer, Georg; Whitington, Paul M.

    2009-01-01

    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

  8. RNAi pathways in parasitic protists and worms.

    PubMed

    Batista, Thiago Mafra; Marques, João Trindade

    2011-08-24

    Tropical diseases caused by parasitic worms and protists are of major public health concern affecting millions of people worldwide. New therapeutic and diagnostic tools would be of great help in dealing with the public health and economic impact of these diseases. RNA interference (RNAi) pathways utilize small non-coding RNAs to regulate gene expression in a sequence-specific manner. In recent years, a wealth of data about the mechanisms and biological functions of RNAi pathways in distinct groups of eukaryotes has been described. Often, RNAi pathways have unique features that are restricted to groups of eukaryotes. The focus of this review will be on RNAi pathways in specific groups of parasitic eukaryotes that include Trypanosoma cruzi, Plasmodium and Schistosoma mansoni. These parasites are the causative agents of Chagas disease, Malaria, and Schistosomiasis, respectively, all of which are tropical diseases that would greatly benefit from the development of new diagnostic and therapeutic tools. In this context, we will describe specific features of RNAi pathways in each of these parasitic eukaryotic groups and discuss how they could be exploited for the treatment of tropical diseases.

  9. Class-level relationships in the phylum Cnidaria: evidence from mitochondrial genome structure.

    PubMed Central

    Bridge, D; Cunningham, C W; Schierwater, B; DeSalle, R; Buss, L W

    1992-01-01

    The phylogenetic relationships of the Recent cnidarian classes remain one of the classic problems in invertebrate zoology. We survey the structure of the mitochondrial genome in representatives of the four extant cnidarian classes and in the phylum Ctenophora. We find that all anthozoan species tested possess mtDNA in the form of circular molecules, whereas all scyphozoan, cubozoan, and hydrozoan species tested display mtDNA in the form of linear molecules. Because ctenophore and all other known metazoan mtDNA is circular, the shared occurrence of linear mtDNA in three of the four cnidarian classes suggests a basal position for the Anthozoa within the phylum. Images PMID:1356268

  10. 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

  11. 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.

  12. 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

  13. 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

  14. 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

  15. 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.

  16. 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

  17. 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

  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. 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

  20. 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.

  1. WormBase: a comprehensive resource for nematode research

    PubMed Central

    Harris, Todd W.; Antoshechkin, Igor; Bieri, Tamberlyn; Blasiar, Darin; Chan, Juancarlos; Chen, Wen J.; De La Cruz, Norie; Davis, Paul; Duesbury, Margaret; Fang, Ruihua; Fernandes, Jolene; Han, Michael; Kishore, Ranjana; Lee, Raymond; Müller, Hans-Michael; Nakamura, Cecilia; Ozersky, Philip; Petcherski, Andrei; Rangarajan, Arun; Rogers, Anthony; Schindelman, Gary; Schwarz, Erich M.; Tuli, Mary Ann; Van Auken, Kimberly; Wang, Daniel; Wang, Xiaodong; Williams, Gary; Yook, Karen; Durbin, Richard; Stein, Lincoln D.; Spieth, John; Sternberg, Paul W.

    2010-01-01

    WormBase (http://www.wormbase.org) is a central data repository for nematode biology. Initially created as a service to the Caenorhabditis elegans research field, WormBase has evolved into a powerful research tool in its own right. In the past 2 years, we expanded WormBase to include the complete genomic sequence, gene predictions and orthology assignments from a range of related nematodes. This comparative data enrich the C. elegans data with improved gene predictions and a better understanding of gene function. In turn, they bring the wealth of experimental knowledge of C. elegans to other systems of medical and agricultural importance. Here, we describe new species and data types now available at WormBase. In addition, we detail enhancements to our curatorial pipeline and website infrastructure to accommodate new genomes and an extensive user base. PMID:19910365

  2. 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

  3. 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).

  4. 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)

  5. 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…

  6. Sociopolitical effects of bow and arrow technology in prehistoric coastal California.

    PubMed

    Kennett, Douglas J; Lambert, Patricia M; Johnson, John R; Culleton, Brendan J

    2013-01-01

    Bow and arrow technology spread across California between ∼AD 250 and 1200, first appearing in the intermountain deserts of the Great Basin and later spreading to the coast. We critically evaluate the available data for the initial spread in bow and arrow technology and examine its societal effects on the well-studied Northern Channel Islands off the coast of Southern California. The introduction of this technology to these islands between AD 650 and 900 appears to predate the appearance of hereditary inequality between AD 900 and 1300. We conclude, based on the available data, that this technology did not immediately trigger intergroup warfare. We argue that the introduction of the bow and arrow contributed to sociopolitical instabilities that were on the rise within the context of increasing population levels and unstable climatic conditions, which stimulated intergroup conflict and favored the development of hereditary inequality. Population aggregation and economic intensification did occur with the introduction of the bow and arrow. This observation is consistent with the hypothesis that social coercion via intra-group "law enforcement" contributed to changes in societal scale that ultimately resulted in larger groups that were favored in inter-group conflict. We argue that the interplay between intra-group "law enforcement" and inter-group warfare were both essential for the ultimate emergence of social inequality between AD 900 and 1300.

  7. 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…

  8. 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…

  9. 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…

  10. 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

  11. 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…

  12. 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…

  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. Javelin, Arrow, Dart and Pin Games of Native American Women of the Plains.

    ERIC Educational Resources Information Center

    Pesavento, Wilma J.; Pesavento, Lisa C.

    This study was designed to determine (1) the arrow, dart, javelin, and pin games of Native American girls and women of the Great Plains, (2) the geographical spread of the games within the culture area, and (3) the characteristics of the various games. Data for this investigation were researched from "Annual Reports of the Bureau of American…

  15. Investigating Hemispheric Lateralization of Reflexive Attention to Gaze and Arrow Cues

    ERIC Educational Resources Information Center

    Marotta, Andrea; Lupianez, Juan; Casagrande, Maria

    2012-01-01

    Recent studies have demonstrated that central cues, such as eyes and arrows, reflexively trigger attentional shifts. However, it is not clear whether the attentional mechanisms induced by these two cues are similar or rather differ in some important way. We investigated hemispheric lateralization of the orienting effects induced by the two cue…

  16. 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.

  17. 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

  18. 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.

  19. Mosquito Infection Responses to Developing Filarial Worms

    PubMed Central

    Erickson, Sara M.; Xi, Zhiyong; Mayhew, George F.; Ramirez, Jose L.; Aliota, Matthew T.; Christensen, Bruce M.; Dimopoulos, George

    2009-01-01

    Human lymphatic filariasis is a mosquito-vectored disease caused by the nematode parasites Wuchereria bancrofti, Brugia malayi and Brugia timori. These are relatively large roundworms that can cause considerable damage in compatible mosquito vectors. In order to assess how mosquitoes respond to infection in compatible mosquito-filarial worm associations, microarray analysis was used to evaluate transcriptome changes in Aedes aegypti at various times during B. malayi development. Changes in transcript abundance in response to the different stages of B. malayi infection were diverse. At the early stages of midgut and thoracic muscle cell penetration, a greater number of genes were repressed compared to those that were induced (20 vs. 8). The non-feeding, intracellular first-stage larvae elicited few differences, with 4 transcripts showing an increased and 9 a decreased abundance relative to controls. Several cecropin transcripts increased in abundance after parasites molted to second-stage larvae. However, the greatest number of transcripts changed in abundance after larvae molted to third-stage larvae and migrated to the head and proboscis (120 induced, 38 repressed), including a large number of putative, immunity-related genes (∼13% of genes with predicted functions). To test whether the innate immune system of mosquitoes was capable of modulating permissiveness to the parasite, we activated the Toll and Imd pathway controlled rel family transcription factors Rel1 and Rel2 (by RNA interference knockdown of the pathway's negative regulators Cactus and Caspar) during the early stages of infection with B. malayi. The activation of either of these immune signaling pathways, or knockdown of the Toll pathway, did not affect B. malayi in Ae. aegypti. The possibility of LF parasites evading mosquito immune responses during successful development is discussed. PMID:19823571

  20. 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

  1. Mosquito infection responses to developing filarial worms.

    PubMed

    Erickson, Sara M; Xi, Zhiyong; Mayhew, George F; Ramirez, Jose L; Aliota, Matthew T; Christensen, Bruce M; Dimopoulos, George

    2009-01-01

    Human lymphatic filariasis is a mosquito-vectored disease caused by the nematode parasites Wuchereria bancrofti, Brugia malayi and Brugia timori. These are relatively large roundworms that can cause considerable damage in compatible mosquito vectors. In order to assess how mosquitoes respond to infection in compatible mosquito-filarial worm associations, microarray analysis was used to evaluate transcriptome changes in Aedes aegypti at various times during B. malayi development. Changes in transcript abundance in response to the different stages of B. malayi infection were diverse. At the early stages of midgut and thoracic muscle cell penetration, a greater number of genes were repressed compared to those that were induced (20 vs. 8). The non-feeding, intracellular first-stage larvae elicited few differences, with 4 transcripts showing an increased and 9 a decreased abundance relative to controls. Several cecropin transcripts increased in abundance after parasites molted to second-stage larvae. However, the greatest number of transcripts changed in abundance after larvae molted to third-stage larvae and migrated to the head and proboscis (120 induced, 38 repressed), including a large number of putative, immunity-related genes (approximately 13% of genes with predicted functions). To test whether the innate immune system of mosquitoes was capable of modulating permissiveness to the parasite, we activated the Toll and Imd pathway controlled rel family transcription factors Rel1 and Rel2 (by RNA interference knockdown of the pathway's negative regulators Cactus and Caspar) during the early stages of infection with B. malayi. The activation of either of these immune signaling pathways, or knockdown of the Toll pathway, did not affect B. malayi in Ae. aegypti. The possibility of LF parasites evading mosquito immune responses during successful development is discussed. PMID:19823571

  2. 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

  3. 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

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

    PubMed

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

    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.

  5. Proposal to include the rank of phylum in the International Code of Nomenclature of Prokaryotes.

    PubMed

    Oren, Aharon; da Costa, Milton S; Garrity, George M; Rainey, Fred A; Rosselló-Móra, Ramon; Schink, Bernhard; Sutcliffe, Iain; Trujillo, Martha E; Whitman, William B

    2015-11-01

    The International Code of Nomenclature of Prokaryotes covers the nomenclature of prokaryotes up to the rank of class. We propose here modifying the Code to include the rank of phylum so that names of phyla that fulfil the rules of the Code will obtain standing in the nomenclature. PMID:26654112

  6. 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.

  7. Proposal to include the rank of phylum in the International Code of Nomenclature of Prokaryotes.

    PubMed

    Oren, Aharon; da Costa, Milton S; Garrity, George M; Rainey, Fred A; Rosselló-Móra, Ramon; Schink, Bernhard; Sutcliffe, Iain; Trujillo, Martha E; Whitman, William B

    2015-11-01

    The International Code of Nomenclature of Prokaryotes covers the nomenclature of prokaryotes up to the rank of class. We propose here modifying the Code to include the rank of phylum so that names of phyla that fulfil the rules of the Code will obtain standing in the nomenclature.

  8. 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.

  9. 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.

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

    PubMed

    Betts, Makayla N; Jospin, Guillaume; Eisen, Jonathan A; 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%.

  11. 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.

  12. Draft Genome Sequence of the Endosymbiont "Candidatus Ruthia magnifica" UCD-CM (Phylum Proteobacteria).

    PubMed

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

    2014-07-17

    Here, we present the draft genome of the endosymbiont "Candidatus Ruthia magnifica" UCD-CM, a member of the phylum Proteobacteria, found from the gills of a deep-sea giant clam, Calyptogena magnifica. The assembly consists of 1,160,249 bp contained in 18 contigs.

  13. 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

  14. Phylogeny and molecular signatures for the phylum Fusobacteria and its distinct subclades.

    PubMed

    Gupta, Radhey S; Sethi, Mohit

    2014-08-01

    The members of the phylum Fusobacteria and its two families, Fusobacteriaceae and Leptotrichiaceae, are distinguished at present mainly on the basis of their branching in the 16S rRNA gene trees and analysis of the internal transcribed spacer sequences in the 16S-23S rDNA. However, no biochemical or molecular characteristics are known that are uniquely shared by all of most members of these groups of bacteria. We report here detailed phylogenetic and comparative analyses on 45 sequenced Fusobacteria genomes to examine their evolutionary relationships and to identify molecular markers that are specific for the members of this phylum. In phylogenetic trees based on 16S rRNA gene sequences or concatenated sequences for 17 conserved proteins, members of the families Fusobacteriaceae and Leptotrichiaceae formed strongly supported clades and were clearly distinguished. In these trees, the species from the genus Fusobacterium also formed a number of well-supported clades. In parallel, comparative analyses on Fusobacteria genomes have identified 44 conserved signature indels (CSIs) in proteins involved in a broad range of functions that are either specific for the phylum Fusobacteria or a number of distinct subclades within this phylum. Seven of these CSIs in important proteins are uniquely present in the protein homologs of all sequenced Fusobacteria and they provide potential molecular markers for this phylum. Six and three other CSIs in other protein sequences are specific for members of the families Fusobacteriaceae and Leptotrichiaceae, respectively, and they provide novel molecular means for distinguishing members of these two families. Fourteen additional CSIs in different proteins, which are specific for either members of the genera Fusobacterium or Leptotrichia, or a number of other well-supported clades of Fusobacteria at multiple phylogenetic levels, provide molecular markers for these groups and information regarding the evolutionary relationships among the

  15. Study of long distance contributions to {ital K}{r_arrow}{ital n}{pi}{nu}{bar {nu}}

    SciTech Connect

    Geng, C.Q.; Hsu, I.J.; Lin, Y.C.

    1996-07-01

    We calculate the long distance contributions to {ital K}{r_arrow}{pi}{nu}{bar {nu}},{pi}{pi}{nu}{bar {nu}}, and {pi}{pi}{pi}{nu}{bar {nu}} modes within the framework of chiral perturbation theory. We find that these contributions to decay rates of {ital K}{r_arrow}{pi}{nu}{bar {nu}} and {ital K}{r_arrow}{pi}{pi}{nu}{bar {nu}} in the chiral logarithmic approximation are at least seven orders of magnitude suppressed relative to those from the short distance parts. The long distance effects in this class of decays are, therefore, negligible. {copyright} {ital 1996 The American Physical Society.}

  16. Improved upper limits on B(K{sub L}{sup 0} {r_arrow} {mu}e) and B(K{sub L}{sup 0} {r_arrow} ee) and a new value for B(K{sub L}{sup 0} {r_arrow} {mu}{mu})

    SciTech Connect

    Molzon, W.R.

    1998-09-01

    The author gives recent results from E791 at BNL with improved upper limits on the branching fractions B(K{sub L}{sup 0} {r_arrow} {mu}e) and B(K{sub L}{sup 0} {r_arrow} ee) of 8.5 {times} 10{sup {minus}11} and 11.6 {times} 10{sup {minus}11} at 90% C.L. He also gives a preliminary result of a new measurement B(K{sub L}{sup 0} {r_arrow} {mu}{mu}) = 7.6 {+-} 0.5(stat) {+-} 0.4(syst) {times} 10{sup {minus}9}.

  17. Electroweak Penguins, Final State Interaction Phases, and {ital CP} Violation in B {r_arrow} K {pi} Decays

    SciTech Connect

    Deshpande, N.G.; He, X.; Hou, W.; He, X.; Hou, W.; Pakvasa, S.

    1999-03-01

    The recently observed B{sup {minus}} {r_arrow} K{sup {minus}} {pi} {sup 0}, {bar K}{sup 0} {pi} {sup {minus}} and {bar B} {sup 0} {r_arrow} K{sup {minus}} {pi} {sup +} decay modes appear to have nearly equal branching ratios. This suggests that tree and electroweak penguins play an important role, and inclusion of the latter improves agreement between factorization calculation and experimental data. The value of {gamma} in the range of 90{degree} {endash} 130{degree} and 220{degree} {endash} 260{degree} is favored, while the {bar B} {sup 0} {r_arrow} {bar K} {sup 0} {pi} {sup 0} rate is suppressed. Direct CP violation for B{r_arrow} K{pi} modes can be large if final state interaction phases are large. {copyright} {ital 1999} {ital The American Physical Society}

  18. Extracting B({omega}{r_arrow}{pi}{sup +}{pi}{sup {minus}}) from the timelike pion form factor

    SciTech Connect

    Gardner, S.; OConnell, H.B.

    1999-04-01

    We extract the {ital G}-parity-violating branching ratio B({omega}{r_arrow}{pi}{sup +}{pi}{sup {minus}}) from the effective {rho}{sup 0}-{omega} mixing matrix element {tilde {Pi}}{sub {rho}{omega}}(s), determined from e{sup +}e{sup {minus}}{r_arrow}{pi}{sup +}{pi}{sup {minus}} data. The {omega}{r_arrow}{pi}{sup +}{pi}{sup {minus}} partial width can be determined either from the timelike pion form factor or through the constraint that the mixed physical propagator D{sub {rho}{omega}}{sup {mu}{nu}}(s) possesses no poles. The two procedures are inequivalent in practice, and we show why the first is preferred, to find finally B({omega}{r_arrow}{pi}{sup +}{pi}{sup {minus}})=1.9{plus_minus}0.3{percent}. {copyright} {ital 1999} {ital The American Physical Society}

  19. 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

  20. Farmers' loss due to Guinea worm disease: a pilot study.

    PubMed

    Brieger, W R; Guyer, J

    1990-04-01

    Guinea worm disease has been blamed for much disability and loss of productivity among farmers in Africa and South Asia. Many studies have tried to equate days lost in illness to monetary values. These attempts often overlook the process of disability in relation to farming patterns. This pilot effort uses a qualitative case study approach to learn about how Guinea worm can cause loss to farmers. Twenty in-depth interviews with affected farmers showed that their losses are related to the time of year they are affected by Guinea worm. Some crops with flexible planting times, e.g. cassava, may not be as affected. Duration of disability is another determining factor. Insights from this pilot study can be used to design more appropriate large-scale survey instruments and guide development of longitudinal research.

  1. 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.

  2. 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.

  3. Logistics of Guinea worm disease eradication in South Sudan.

    PubMed

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

    2014-03-01

    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.

  4. 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.

  5. 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

  6. [Specific features of the injuries inflicted by the arrows for a universal crossbow depending on its constructional features].

    PubMed

    Makarov, I Iu; Lorents, A S

    2012-01-01

    There is scarce information in forensic medical practice allowing to reliably diagnose injuries inflicted by arrows from a universal crossbow. The arrows with specific constructional properties cause characteristic morphological changes in non-biological targets, such as mock clothing (coarse calico and plasticine) and homogeneous tissues of the human body. It is concluded that the data obtained in the present study can be used for objective differential diagnostics of crossbow wounds. PMID:23405460

  7. Some applications of the NASTRAN level 16 subsonic flutter analysis capability. [to transport wing and arrow wing

    NASA Technical Reports Server (NTRS)

    Doggett, R. V., Jr.; Cunningham, H. J.

    1976-01-01

    The Level 16 flutter analysis capability was applied to an aspect-ratio-6.8 subsonic transport type wing, an aspect-ratio-1.7 arrow wing, and an aspect-ratio-1.3 all movable horizontal tail with a geared elevator. The transport wing and arrow wing results are compared with experimental results obtained in the Langley transonic dynamic tunnel and with other calculated results obtained using subsonic lifting surface (kernel function) unsteady aerodynamic theory.

  8. The B {r{underscore}arrow} D*{ell}{nu} form factor at zero recoil

    SciTech Connect

    Simone, J.N.; Hashimoto, S.; El-Khadra, A.X.; Kronfeld, A.S.; Mackenzie, P.B.; Ryan, S.M.

    2000-01-26

    The authors describe a model independent lattice QCD method for determining the deviation from unity for h{sub A{sub 1}}, the B {r{underscore}arrow} D*{ell}{nu} form factor at zero recoil. They extend the double ratio method previously used to determine the B {r{underscore}arrow} D{ell}{nu} form factor. The bulk of statistical and systematic errors cancel in the double ratios they consider, yielding form factors which promise to reduce present theoretical uncertainties in the determination of {vert{underscore}bar}V{sub cb}{vert{underscore}bar}. They present results from a prototype calculation at a single lattice spacing corresponding to {beta} = 5.7.

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. WORM: A general-purpose input deck specification language

    SciTech Connect

    Jones, T.

    1999-07-01

    Using computer codes to perform criticality safety calculations has become common practice in the industry. The vast majority of these codes use simple text-based input decks to represent the geometry, materials, and other parameters that describe the problem. However, the data specified in input files are usually processed results themselves. For example, input decks tend to require the geometry specification in linear dimensions and materials in atom or weight fractions, while the parameter of interest might be mass or concentration. The calculations needed to convert from the item of interest to the required parameter in the input deck are usually performed separately and then incorporated into the input deck. This process of calculating, editing, and renaming files to perform a simple parameter study is tedious at best. In addition, most computer codes require dimensions to be specified in centimeters, while drawings or other materials used to create the input decks might be in other units. This also requires additional calculation or conversion prior to composition of the input deck. These additional calculations, while extremely simple, introduce a source for error in both the calculations and transcriptions. To overcome these difficulties, WORM (Write One, Run Many) was created. It is an easy-to-use programming language to describe input decks and can be used with any computer code that uses standard text files for input. WORM is available, via the Internet, at worm.lanl.gov. A user's guide, tutorials, example models, and other WORM-related materials are also available at this Web site. Questions regarding WORM should be directed to worm{at}lanl.gov.

  14. 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.

  15. Failure of thiabendazole and metronidazole in the treatment and suppression of guinea worm disease.

    PubMed

    Belcher, D W; Wunapa, F K; Ward, W B

    1975-05-01

    Guinea worm disease is endemic in West Africa. In 1973 a field drug trial was conducted to compare effectiveness, cost, and side-effects of thiabendazole and metronidazole in treating active guinea worm disease and preventing latent worms from emerging. A mass chemotherapy campaign was planned to follow the drug trial. Only 15.5% of the treated patients expelled the worm completely, and in 28.4% of the cases worms continued to appear. Both drugs were equally unsatisfactory in their anti-helminthic effect. Consequently, our efforts to control guinea worm have shifted from chemotherapy to chemical control of cyclops and improvement of rural water supplies.

  16. 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.

  17. 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.

  18. 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}

  19. [Common tropical infections with protozoans, worms and ectoparasites].

    PubMed

    Schliemann, S

    2014-10-01

    Infectious diseases of the skin have become rarer in industrialized nations, but they still affect a considerable part of the population in tropical regions. Skin diseases induced by protozoa, worms and ectoparasites are among the 17 "neglected tropical diseases" defined by the WHO (leishmaniasis, dracunculiasis, lymphatic filariasis, onchocerciasis). Skin symptoms in travellers returning from the tropics may challenge dermatologists in Germany regarding differential diagnostic assessment and therapy. Among the 12 most frequent skin diseases in travellers are cutaneous larva migrans, leishmaniasis and myiasis. In this review, diagnosis, treatment and prevention of some the most relevant tropical dermatoses due to protozoa, worms and ectoparasites are discussed.

  20. Utilizing Genomics to Study Entomopathogenicity in the Fungal Phylum Entomophthoromycota: A Review of Current Genetic Resources.

    PubMed

    De Fine Licht, H H; Hajek, A E; Eilenberg, J; Jensen, A B

    2016-01-01

    The order Entomophthorales, which formerly contained c.280 species, has recently been recognized as a separate phylum, Entomophthoromycota, consisting of three recognized classes and six families. Many genera in this group contain obligate insect-pathogenic species with narrow host ranges, capable of producing epizootics in natural insect populations. Available sequence information from the phylum Entomophthoromycota can be classified into three main categories: first, partial gene regions (exons+introns) used for phylogenetic inference; second, protein coding gene regions obtained using degenerate primers, expressed sequence tag methodology or de novo transcriptome sequencing with molecular function inferred by homology analysis; and third, primarily forthcoming whole-genome sequencing data sets. Here we summarize the current genetic resources for Entomophthoromycota and identify research areas that are likely to be significantly advanced from the availability of new whole-genome resources.

  1. 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.

  2. Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics.

    PubMed

    Evans, Paul N; Parks, Donovan H; Chadwick, Grayson L; Robbins, Steven J; Orphan, Victoria J; Golding, Suzanne D; Tyson, Gene W

    2015-10-23

    Methanogenic and methanotrophic archaea play important roles in the global flux of methane. Culture-independent approaches are providing deeper insight into the diversity and evolution of methane-metabolizing microorganisms, but, until now, no compelling evidence has existed for methane metabolism in archaea outside the phylum Euryarchaeota. We performed metagenomic sequencing of a deep aquifer, recovering two near-complete genomes belonging to the archaeal phylum Bathyarchaeota (formerly known as the Miscellaneous Crenarchaeotal Group). These genomes contain divergent homologs of the genes necessary for methane metabolism, including those that encode the methyl-coenzyme M reductase (MCR) complex. Additional non-euryarchaeotal MCR-encoding genes identified in a range of environments suggest that unrecognized archaeal lineages may also contribute to global methane cycling. These findings indicate that methane metabolism arose before the last common ancestor of the Euryarchaeota and Bathyarchaeota.

  3. New light on the enigmatic Xenoturbella (phylum uncertain): ontogeny and phylogeny

    PubMed Central

    Israelsson, O.

    1999-01-01

    Xenoturbella is an enigmatic animal that is merely a ciliated bag with epithelial epidermis and gastrodermis, a subepidermal nerve plexus and a ventral mouth, but without an anus or any distinct organs. It is marine, free living, and up to 4 cm long. Its simplicity in organization has led to diverse interpretations during the last 50 years: as an acoelomorph flatworm, a paedomorphic holothurian or enteropneust, or a unique representative of a plesiomorphic phylum. I report here the previously unknown embryology of Xenoturbella that unequivocally corroborates a bivalve relationship and thus once and for all dismisses the potential new phylum. The simplicity of the adult Xenoturbella is due to neither plesiomorphy nor paedomorphy. It is caused by metamorphosis from a trochophore larva of molluscan type with a defined organ system, including a concentrated nervous system with ganglia, to an adult without any defined organs.

  4. 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.

  5. 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.

  6. The decay b r arrow s + H sup 0 in sypersymmetric theories

    SciTech Connect

    Iogansen, A.A.; Ural'tsev, N.G.; Khoze, V.A. )

    1989-04-01

    The probability of production of {ital H}{sup 0} in decays of {ital B} mesons is calculated in the framework of supersymmetric models, in which a light {ital H}{sup 0} boson can appear in a natural manner. It is shown that the quantity Br({ital b}{r arrow}{ital s}+{ital H}) is strongly suppressed in comparison with the prediction of the standard model. The principal cancellation of the standard contribution is due to {ital H}-boson exchange, and the higgsino--wino has a somewhat smaller role. The contributions of the neutral superparticles, including the gluinos, are found to be negligibly small. Because of the small value of the {ital b}{r arrow}{ital s}+{ital H}{sup 0} amplitude the available experimental data on the decays of {ital B} mesons cannot rule out the existence of a light {ital H}{sup 0} boson in supersymmetric schemes. At the same time, the probabilities of radiative quarkonium decays of the type {Upsilon}{r arrow}{ital H}{sup 0}+{gamma} remain the same as in the standard model.

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. 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

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

    PubMed

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

    2015-05-01

    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.

  13. Phylogenomic evaluation of members above the species level within the phylum Firmicutes based on conserved proteins.

    PubMed

    Zhang, Weiwei; Lu, Zhitang

    2015-04-01

    Currently, numerous taxonomic units above species level of the phylum Firmicutes are ambiguously placed in the phylogeny determined by 16S rRNA gene. Here, we evaluated the use of 16S rRNA gene compared with 81 conserved proteins (CPs) or 41 ribosomal proteins (RPs) as phylogenetic markers and applied this to the analysis of the phylum Firmicutes. Results show that the phylogenetic trees constructed are in good agreement with each other; however, the protein-based trees are able to resolve the relationships between several branches where so far only ambiguous classifications are possible. Thus, the phylogeny deduced based on concatenated proteins provides significant basis for re-classifying members in this phylum. It indicates that the genera Coprothermobacter and Thermodesulfobium represent two new phyla; the families Paenibacillaceae and Alicyclobacillaceae should be elevated to order level; and the families Bacillaceae and Thermodesulfobiaceae should be separated to 2 and 3 families respectively. We also suggest that four novel families should be proposed in the orders Clostridiales and Bacillales, and 11 genera should be moved to other existing families different from the current classification status. Moreover, notably, RPs are a well-suited subset of CPs that could be applied to Firmicutes phylogenetic analysis instead of the 16S rRNA gene.

  14. 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.

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

    PubMed

    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

    2004-09-01

    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.

  16. The demise of a phylum of protists: phylogeny of Myxozoa and other parasitic cnidaria.

    PubMed

    Siddall, M E; Martin, D S; Bridge, D; Desser, S S; Cone, D K

    1995-12-01

    The notion that members of the phylum Myxozoa Grassé, 1970 do not properly belong in classifications of protists has frequently been suggested because the infective spores of these parasites are not unicellular. Systematists have failed to be decisive about myxozoan phylogenetic affinities, either finding the suggestion of a cnidarian connection to be preposterous or considering the recent suggestion of a relationship with nematodes to be an obvious failure of molecular phylogenetics. Thus, the group has remained in classifications as a protistan phylum in its own right. The ultrastructure of the development of myxozoans was critically re-examined in order to more fully explore the possibility of morphological synapomorphies with metazoan taxa. These morphological characters, in combination with small ribosomal subunit gene sequences, were used in a phylogenetic analysis in order to assess myxozoan origins. The results unequivocally support the inclusion of myxozoans as a clade of highly derived parasitic cnidarians, and as sister taxon to the narcomedusan Polypodium hydriforme. Reassessment of myxozoans as metazoans reveals terminal differentiation, typical metazoan cellular junctions, and collagen production. Their "polar capsules" are redescribed as typical nematocysts bearing atrichous isorhiza. Insofar as taxa cannot be contained within other taxa of equal rank, the phylum Myxozoa is abandoned and it is recommended that the group as a whole be removed from all protistan classifications and placed in a more comprehensive cnidarian system.

  17. Molecular phylogenetic evidence that the phylum Haplosporidia has an alveolate ancestry.

    PubMed

    Siddall, M E; Stokes, N A; Burreson, E M

    1995-07-01

    The phylogenetic position of the phylum Haplosporidia among other protists was investigated with the complete 16S-like rRNA gene sequences from two species in the phylum: Haplosporidium nelsoni, a parasite of oysters, and Minchinia teredinis, a parasite of shipworms. Because the lack of obvious morphological homologies with other protists hampered decisions regarding taxonomic composition for sequence alignment and phylogenetic analysis, the complete sequences for these two haplosporidians were directed as search queries to the blast/ncbi.nlm.nih.gov electronic mail server. The results of this heuristic similarity search provided a basis for constructing a preliminary higher-taxonomic-level analysis comparing the haplosporidians with species from the slime molds, fungi, algae, amoebae, ciliates, dinoflagellates, and apicomplexans. Maximum parsimony yielded equivocal results, whereas transversionally weighted parsimony suggested an affinity with the alveolates (i.e., the ciliates, dinoflagellates, and apicomplexans). Multiple alignment of the two haplosporidian sequences against 17 taxa in a secondary analysis focusing on the alveolates and subsequent parsimony analysis placed the phylum Haplosporidia as a monophyletic group within the Alveolata and as a taxon of equal rank with the other three alveolate phyla. The precise placement within the Alveolata was sensitive to weighting.

  18. 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…

  19. 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.

  20. 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.

  1. Worm infestation among the school children of Dhankuta District.

    PubMed

    Sah, R B; Yadav, S; Jha, P K; Yadav, B K; Pokharel, P K

    2013-03-01

    Intestinal parasitic infections (IPI) cause serious public health problem in Nepal. They are more prevalent in the poor segments of the population with low household income, poor handling of personal and environmental sanitation, overcrowding and limited access to clean water. The objective of the study is to assess knowledge and practice about worm infestation and to find out the relation of knowledge and practice with the selected variables. A cross-sectional study was conducted in 200 students of Grade 9 and 10 in Government and private schools of Dhankuta. The chi-square test was used to measure the association of knowledge and practice about worm infestation. The knowledge regarding risk factors of worm infestation due to unhygienic pig farming practices is significantly higher in female (66.4%) than male (44.8%). All the risk factors were found to be significantly higher in knowledge among the private school as compared to Government school. Regarding Fathers occupation, unemployed (100.0%) believe it is due to poor personal hygiene and very less of labor (50%) which is significantly associated. Regarding Mother Group, students never eat raw meat and vender food whose mothers have skilled worker. The school going students of Dhankuta were aware of the knowledge regarding the worm infestation but had less knowledge among the school children of Government as compared to private.

  2. 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

  3. 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

  4. 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

  5. Guinea worm infection of urinary bladder manifesting as obstructive uropathy in rural Maharashtra.

    PubMed

    Birare, Shivaji D; Kamble, M H; Lanjewar, D N; Parija, S C; Girji, D D; Kulkarni, P V; Gupta, Rashmi S; Abdul Jabbar, A M

    2005-10-01

    Guinea worm or Dracunculus medinensis is a well-documented helminthic infestation in many areas of Asia. In this report, we describe a rare case of guinea worm infestation in a 25-year-old woman who had developed symptoms of obstructive uropathy, in whom fragments of guinea worm were removed after urethral catheterization. To the best of our knowledge, adult guinea worm occurring in the urinary bladder has not been previously described.

  6. Prenatal diagnosis of QT prolongation by fetal magnetocardiogram--use of QRS and T-wave current-arrow maps.

    PubMed

    Kandori, A; Miyashita, T; Tsukada, K; Hosono, T; Miyashita, S; Chiba, Y; Horigome, H; Shigemitsu, S; Asaka, M

    2001-05-01

    To determine the T wave of a fetal magnetocardiogram (FMCG), we have evaluated the T/QRS ratio and obtained current-arrow maps that indicate weak currents. We measured FMCG signals for 52 normal fetuses and two abnormal fetuses with prolonged QT waves by using three superconducting quantum interference device (SQUID) systems: a nine-channel system, a 12-channel vector system and a 64-channel system. The T/QRS ratio was calculated for all the normal fetuses from the maximum magnitudes of the QRS complex and the T wave. Current-arrow maps of the QRS complex (R wave) and T wave were obtained by using the 64-channel system, and the phase differences of the total-current vectors were calculated by using the current-arrow maps. The results showed that the T/QRS ratio had a wide variability of 0.35 for the normal fetuses. However, the magnitude of the prolonged T wave was as weak as the detection limit of the SQUID magnetometer. Although the T/QRS ratios for the fetuses with QT prolongation were within the normal range (< 0.35), the weak magnitude of the prolonged T wave could be evaluated. On the other hand, by comparing the current-arrow maps of the R and T waves for the normal fetuses, we found that the maximum-current arrows were indicated as either in the same direction or in opposite directions. These patterns could be identified clearly by the phase differences. Very weak prolonged T waves for the two abnormal fetuses could be determined by using these current-arrow maps and phase differences. Consequently, although the T/QRS ratios of FMCG signals have a wide distribution, we have concluded that the current-arrow map and phase difference can be used to determine the T wave of an FMCG signal. PMID:11411247

  7. 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.

  8. 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.

  9. 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.

  10. Distribution and diversity of members of the bacterial phylum Fibrobacteres in environments where cellulose degradation occurs.

    PubMed

    Ransom-Jones, Emma; Jones, David L; Edwards, Arwyn; McDonald, James E

    2014-10-01

    The Fibrobacteres phylum contains two described species, Fibrobacter succinogenes and Fibrobacter intestinalis, both of which are prolific degraders of cellulosic plant biomass in the herbivore gut. However, recent 16S rRNA gene sequencing studies have identified novel Fibrobacteres in landfill sites, freshwater lakes and the termite hindgut, suggesting that members of the Fibrobacteres occupy a broader ecological range than previously appreciated. In this study, the ecology and diversity of Fibrobacteres was evaluated in 64 samples from contrasting environments where cellulose degradation occurred. Fibrobacters were detected in 23 of the 64 samples using Fibrobacter genus-specific 16S rRNA gene PCR, which provided their first targeted detection in marine and estuarine sediments, cryoconite from Arctic glaciers, as well as a broader range of environmental samples. To determine the phylogenetic diversity of the Fibrobacteres phylum, Fibrobacter-specific 16S rRNA gene clone libraries derived from 17 samples were sequenced (384 clones) and compared with all available Fibrobacteres sequences in the Ribosomal Database Project repository. Phylogenetic analysis revealed 63 lineages of Fibrobacteres (95% OTUs), with many representing as yet unclassified species. Of these, 24 OTUs were exclusively comprised of fibrobacters derived from environmental (non-gut) samples, 17 were exclusive to the mammalian gut, 15 to the termite hindgut, and 7 comprised both environmental and mammalian strains, thus establishing Fibrobacter spp. as indigenous members of microbial communities beyond the gut ecosystem. The data highlighted significant taxonomic and ecological diversity within the Fibrobacteres, a phylum circumscribed by potent cellulolytic activity, suggesting considerable functional importance in the conversion of lignocellulosic biomass in the biosphere.

  11. 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.

  12. Some experimental and theoretical flutter characteristics of an arrow-wing configuration

    NASA Technical Reports Server (NTRS)

    Doggett, R. V., Jr.; Ricketts, R. H.

    1977-01-01

    Experimental and theoretical flutter results are presented for a simplified 1/50-size wind-tunnel model of an arrow-wing configuration. Transonic flutter characteristics are presented for three configurations - wing without engine nacelles, wing with flow-through nacelles, and wing with pencil nacelles (thin, streamline bodies). Experimental results are correlated with analytical results obtained from kernel-function and doublet-lattice unsteady aerodynamic theories. Theoretical results are presented that show the effects on flutter of systematic changes in structural stiffness and mass.

  13. Application of an advanced computerized structural design system to an arrow-wing supersonic cruise aircraft

    NASA Technical Reports Server (NTRS)

    Robinson, J. C.; Yates, E. C., Jr.; Turner, M. J.; Grande, D. L.

    1975-01-01

    A structural design study of an arrow-wing supersonic cruise aircraft has been made using the integrated design system, ATLAS, and a relatively large analytical finite-element model containing 8500 degrees of freedom. This paper focuses on structural design methods developed and used in support of the study with emphasis on aeroelasticity. The use of ATLAS permitted (1) automatic resizing of the wing structure for multiple load conditions, (2) rapid evaluation of aeroelastic effects, and (3) an iterative approach to the correction of flutter deficiencies. The significant results of the study are discussed along with the advantages derived from the use of an advanced structural design system in preliminary design studies.

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. 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.

  20. Exploratory subsonic investigation of vortex-flap concept on arrow wing configuration

    NASA Technical Reports Server (NTRS)

    Rao, D. M.

    1981-01-01

    The drag reduction potential of a vortex flap concept, utilizing the thrust contribution of separation vortices maintained over leading edge flap surfaces, was explored in subsonic wind tunnel tests on a highly swept arrow wing configuration. Several flap geometries were tested in comparison with a previous study on the same model with leading edges drooped for attached flow. The most promising vortex flap arrangements produced drag reductions comparable with leading edge droop over a range of lift coefficients from 0.3 to 0.6 (untrimmed), and also indicated beneficial effects in the longitudinal and lateral static stability characteristics.

  1. 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.

  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. 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.

  4. 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).

  5. 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

  6. Potential conservation of circadian clock proteins in the phylum Nematoda as revealed by bioinformatic searches.

    PubMed

    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.

  7. 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

  8. 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.

  9. The maturity of Nypa palm worm Namalycastis rhodochorde (Nereididae: Polychaeta)

    NASA Astrophysics Data System (ADS)

    Junardi, Anggraeni, Tjandra; Ridwan, Ahmad; Yuwono, Edy

    2014-03-01

    The Nypa Palm Worm Namalycastis rhodochorde has been used as bait for fishing and commercial species in Pontianak. Maturity is one important characteristic to learn the population dynamic and management. The Nypa Palm worm samples were collected from mangrove area in Kapuas Estuary, West Kalimantan. Fresh samples of gametes collected from the coelomic fluid were observed carefully under compound microscope for the initial determination of maturity. The presences of oocyte ≥120μm in diameter and lipid droplet are the indication of female maturity, while free swimming spermatozoon in the body fluid is the indication of male maturity. Morphologically, the maturity of N. rhodochorde was indicated by the change of body color, softer and fragile body, yet no modified chaetae and heteronereid form.

  10. 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

  11. 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.

  12. 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 %.

  13. Worms and malaria: blind men feeling the elephant?

    PubMed

    Nacher, M

    2008-06-01

    For thousands of years the deadliest human parasite, Plasmodium falciparum, has been evolving in populations also infected by the most prevalent parasites, worms. This is likely to have shaped the genome of all 3 protagonists--man, worms and malaria. Observational studies in Thailand have shown that although P. falciparum malaria incidence increased two-fold in helminth-infected patients, there was a 64% reduction of cerebral malaria and an 84% reduction of acute renal failure in helminth-infected patients relative to those without helminths. In addition, it was suggested that mixed infections, anaemia and gametocyte carriage were more frequent in helminth-infected patients. On the contrary, fever was lower in helminth-infected patients. The present hypotheses, their implications and the limitations of the results described and of those from studies in Africa are discussed.

  14. A Unified Theory For The WORM Sensitivity Function

    NASA Astrophysics Data System (ADS)

    Mendez, Antonio J.

    1988-02-01

    The sensitivity function ▵R of WORM media often is a function of the incident energy (E) and pulsewidth (t), as well as incident power (P), of the write laser. A unified theory is developed to include all variables. It models the sensitivity function as ▵R (E,P,t) = AR (Y,t) [1 - X at (Y,t)/X], where X is the dominant and Y the secondary variable which determines media performance. ▵R(Y,t) is the saturation and X at(Y t) is the threshold behavior. The theory is applied to five distinct types of organic,T 'inorganic, and textured WORM media. The results are discussed and recommendations for test planning are made.

  15. 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.

  16. Th9 Cells Drive Host Immunity against Gastrointestinal Worm Infection.

    PubMed

    Licona-Limón, Paula; Henao-Mejia, Jorge; Temann, Angela U; Gagliani, Nicola; Licona-Limón, Ileana; Ishigame, Harumichi; Hao, Liming; Herbert, De'broski R; Flavell, Richard A

    2013-10-17

    Type 2 inflammatory cytokines, including interleukin-4 (IL-4), IL-5, IL-9, and IL-13, drive the characteristic features of immunity against parasitic worms and allergens. Whether IL-9 serves an essential role in the initiation of host-protective responses is controversial, and the importance of IL-9- versus IL-4-producing CD4⁺ effector T cells in type 2 immunity is incompletely defined. Herein, we generated IL-9-deficient and IL-9-fluorescent reporter mice that demonstrated an essential role for this cytokine in the early type 2 immunity against Nippostrongylus brasiliensis. Whereas T helper 9 (Th9) cells and type 2 innate lymphoid cells (ILC2s) were major sources of infection-induced IL-9 production, the adoptive transfer of Th9 cells, but not Th2 cells, caused rapid worm expulsion, marked basophilia, and increased mast cell numbers in Rag2-deficient hosts. Taken together, our data show a critical and nonredundant role for Th9 cells and IL-9 in host-protective type 2 immunity against parasitic worm infection.

  17. 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

  18. 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

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

    PubMed Central

    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

  20. 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}}.

  1. 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

  2. Primary structure of a constituent polypeptide chain (AIII) of the giant haemoglobin from the deep-sea tube worm Lamellibrachia. A possible H2S-binding site.

    PubMed

    Suzuki, T; Takagi, T; Ohta, S

    1990-02-15

    The deep-sea tube worm Lamellibrachia, belonging to the Phylum Vestimentifera, contains two giant extracellular haemoglobins, a 3000 kDa haemoglobin and a 440 kDa haemoglobin. The former consists of four haem-containing chains (AI-AIV) and two linker chains (AV and AVI) for the assembly of the haem-containing chains [Suzuki, Takagi & Ohta (1988) Biochem. J. 255, 541-545]. The tube-worm haemoglobins are believed to have a function of transporting sulphide (H2S) to internal bacterial symbionts, as well as of facilitating O2 transport [Arp & Childress (1983) Science 219, 295-297]. We have determined the complete amino acid sequence of Lamellibrachia chain AIII by automated or manual Edman sequencing. The chain is composed of 144 amino acid residues, has three cysteine residues at positions 3, 74 and 133, and has a molecular mass of 16,620 Da, including a haem group. The sequence showed significant homology (30-50% identity) with those of haem-containing chains of annelid giant haemoglobins. Two of the three cysteine residues are located at the positions where an intrachain disulphide bridge is formed in all annelid chains, but the remaining one (Cys-74) was located at a unique position, compared with annelid chains. Since the chain AIII was shown to have a reactive thiol group in the intact 3000 kDa molecule by preliminary experiments, the cysteine residue at position 74 appears to be one of the most probable candidates for the sulphide-binding sites. A phylogenetic tree was constructed from nine chains of annelid giant haemoglobins and one chain of vestimentiferan tube-worm haemoglobin now determined. The tree clearly showed that Lamellibrachia chain AIII belongs to the family of strain A of annelid giant haemoglobins, and that the two classes of Annelida, polychaete and oligochaete, and the vestimentiferan tube worm diverged at almost the same time. H.p.l.c. patterns of peptides (Figs. 4-7), amino acid compositions of peptides (Table 2) and amino acid sequences of

  3. 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.

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

    DOE PAGES

    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

  5. Testing factorization in color-suppressed [ital b]-flavor decays with the [ital B][r arrow][eta][sub [ital c

    SciTech Connect

    Gourdin, M.; Keum, Y.Y.; Pham, X.Y. )

    1995-04-01

    The discrepancy recently observed between [ital B][r arrow][ital J]/[psi]+[ital K]([ital K][sup *]) data and commonly used hadronic form factor models might be due to a breakdown of the factorization assumption. By showing that the [ital B][r arrow][eta][sub [ital c

  6. 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.

  7. 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/.

  8. Functional type 2 photosynthetic reaction centers found in the rare bacterial phylum Gemmatimonadetes.

    PubMed

    Zeng, Yonghui; Feng, Fuying; Medová, Hana; Dean, Jason; Koblížek, Michal

    2014-05-27

    Photosynthetic bacteria emerged on Earth more than 3 Gyr ago. To date, despite a long evolutionary history, species containing (bacterio)chlorophyll-based reaction centers have been reported in only 6 out of more than 30 formally described bacterial phyla: Cyanobacteria, Proteobacteria, Chlorobi, Chloroflexi, Firmicutes, and Acidobacteria. Here we describe a bacteriochlorophyll a-producing isolate AP64 that belongs to the poorly characterized phylum Gemmatimonadetes. This red-pigmented semiaerobic strain was isolated from a freshwater lake in the western Gobi Desert. It contains fully functional type 2 (pheophytin-quinone) photosynthetic reaction centers but does not assimilate inorganic carbon, suggesting that it performs a photoheterotrophic lifestyle. Full genome sequencing revealed the presence of a 42.3-kb-long photosynthesis gene cluster (PGC) in its genome. The organization and phylogeny of its photosynthesis genes suggests an ancient acquisition of PGC via horizontal transfer from purple phototrophic bacteria. The data presented here document that Gemmatimonadetes is the seventh bacterial phylum containing (bacterio)chlorophyll-based phototrophic species. To our knowledge, these data provide the first evidence that (bacterio)chlorophyll-based phototrophy can be transferred between distant bacterial phyla, providing new insights into the evolution of bacterial photosynthesis. PMID:24821787

  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. The phylum Cnidaria and investigations of its toxins and venoms until 1990.

    PubMed

    Turk, Tom; Kem, William R

    2009-12-15

    Cnidarians are the largest phylum of generally toxic animals, yet their toxins and venoms have not received as much scientific attention as those of many terrestrial (snakes, scorpions, spiders, etc.) and even some marine animals (i.e. cone snails). Approximately 13,000 living cnidarian species have been described by systematists. A major rationale for their study in the past, besides scientific curiosity, was to better treat victims of their envenomation. While that goal remains a high priority, it is now appreciated that the toxins of these mostly marine animals can be very useful molecular probes for the analysis of ion channels involved in electrical signaling, immune responses and other signal transduction processes of biomedical interest. For instance, anaphylaxis was discovered by Richet (1905) during experiments with sea anemone and hydrozoan tentacular extracts. Similarly, it has recently been shown that a toxin from another sea anemone is able to potently inhibit T-lymphocyte proliferation in models of certain autoimmune diseases. Thus, these natural substances continue to be of relevance for understanding and treating human diseases. In addition to introducing phylum Cnidaria (Coelenterata), we provide a short history of early (until about 1990) research on cnidarian toxins and venoms, to provide a perspective for appreciating the scientific advances of the past two decades that are summarized in the ensuing 19 papers in this special Toxicon issue.

  11. 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

  12. Functional type 2 photosynthetic reaction centers found in the rare bacterial phylum Gemmatimonadetes

    PubMed Central

    Zeng, Yonghui; Feng, Fuying; Medová, Hana; Dean, Jason; Koblížek, Michal

    2014-01-01

    Photosynthetic bacteria emerged on Earth more than 3 Gyr ago. To date, despite a long evolutionary history, species containing (bacterio)chlorophyll-based reaction centers have been reported in only 6 out of more than 30 formally described bacterial phyla: Cyanobacteria, Proteobacteria, Chlorobi, Chloroflexi, Firmicutes, and Acidobacteria. Here we describe a bacteriochlorophyll a-producing isolate AP64 that belongs to the poorly characterized phylum Gemmatimonadetes. This red-pigmented semiaerobic strain was isolated from a freshwater lake in the western Gobi Desert. It contains fully functional type 2 (pheophytin-quinone) photosynthetic reaction centers but does not assimilate inorganic carbon, suggesting that it performs a photoheterotrophic lifestyle. Full genome sequencing revealed the presence of a 42.3-kb–long photosynthesis gene cluster (PGC) in its genome. The organization and phylogeny of its photosynthesis genes suggests an ancient acquisition of PGC via horizontal transfer from purple phototrophic bacteria. The data presented here document that Gemmatimonadetes is the seventh bacterial phylum containing (bacterio)chlorophyll-based phototrophic species. To our knowledge, these data provide the first evidence that (bacterio)chlorophyll-based phototrophy can be transferred between distant bacterial phyla, providing new insights into the evolution of bacterial photosynthesis. PMID:24821787

  13. 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

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

    DOE PAGES

    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

  15. 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

    2016-01-27

    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.

  16. Phylum-specific regulation of resistomycin production in a Streptomyces sp. via microbial coculture.

    PubMed

    Carlson, Skylar; Tanouye, Urszula; Omarsdottir, Sesselja; Murphy, Brian T

    2015-03-27

    Actinomycete genomes are encoded with immense potential to produce secondary metabolites, however standard laboratory culture experiments rarely provide the conditions under which associated biosynthetic pathways are expressed. Despite years of research attempting to access these pathways and aside from a few well-studied bacterial quorum sensing systems, little is known about the specificity of secondary metabolite regulation in bacteria, such as the conditions under which a bacterium produces an antibiotic and the extent to which it does so in recognition of a particular species in the immediate environment. In the current study, we observed that the cocultivation of a Streptomyces sp. (strain B033) with four pathogenic strains of the phylum Proteobacteria resulted in the production of the antibiotic resistomycin. After further coculture experiments, we determined that Proteobacteria induced the production of resistomycin in B033 at significantly higher rates (65%) than strains from the phyla Firmicutes (5.9%) and Actinobacteria (9.1%), supporting that the regulation of secondary metabolism in bacteria can be dependent on the species present in the immediate environment. These results suggest a lack of promiscuity of antibiotic biosynthetic pathway regulation and indicate that it is feasible to mine existing microbial strain libraries for antibiotics in a phylum-specific manner.

  17. Distribution and evolution of nitrogen fixation genes in the phylum Bacteroidetes.

    PubMed

    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 15093(T) and Geofilum rubicundum JCM 15548(T). 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.

  18. 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

  19. 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

  20. 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

  1. The first internal molecular phylogeny of the animal phylum Entoprocta (Kamptozoa).

    PubMed

    Fuchs, Judith; Iseto, Tohru; Hirose, Mamiko; Sundberg, Per; Obst, Matthias

    2010-07-01

    This article provides the first molecular phylogenetic study of the enigmatic invertebrate phylum Entoprocta and was designed to resolve the internal phylogenetic relationships of the taxon. The study is based on partial and combined analyses of the mitochondrial gene cytochrome c oxidase subunit I (COI), as well as the nuclear ribosomal genes 28S rDNA and 18S rDNA. A short morphological character matrix was constructed to trace character evolution along the combined molecular phylogenetic tree. The combined analyses of all three genes strongly support the monophyly of the phylum Entoprocta and a sister group relationship of Entoprocta and Cycliophora, a result which is consistent with a number of previous morphological and molecular assessments. We find evidence for two separate lineages within the Entoprocta, one lineage leading to all recent colonial taxa, Coloniales, another representing the clade of solitary entoprocts, Solitaria. Our study suggests that Loxosomella is a paraphyletic assembly with regard to the genera Loxomitra, Loxosoma, and Loxocorone. The results imply that the ancestral entoproct was a solitary, marine organism with an epizoic life style. The groundplan of the entoproct adult stage probably included a bilobed centralized nervous system, and the larva was assumedly planktonic, with a gut and a ciliated creeping sole.

  2. 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.

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

    DOE PAGES

    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

  4. 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.

  5. The hemimastigophora (Hemimastix amphikineta nov. gen., nov. spec.), a new protistan phylum from gondwanian soils.

    PubMed

    Foissner, W; Blatterer, H; Foissner, I

    1988-10-01

    The morphology, morphogenesis and ultrastructure of Hemimastix amphikineta nov. gen., nov. spec, are described. This species occurred in some Australian and in 1 Chilean soil, but was absent from more than 1000 soil samples from Laurasian localities. Thus, it has probably a restricted Gondwanian distribution. Hemimastix amphikineta is a small (14-20 × 7-10 μn), colourless organism that looks distinctly Ciliophora-like because of its posteriorly located contractile vacuole and its 2 longitudinal somatic kineties each composed of about 12 cilia-like flagella. These 2 kineties are interposed between 2 large plicated and microtubule-bearing pellicular plates which are arranged inversely mirror-image like ("diagonal symmetry"). Hemimastix amphikineta has saccular to tubular mitochondrial cristae and complex extrusomes. It has 2 microtubular systems and a membranous sac associated with each kinetid. The nucleolus persists throughout nuclear division. A permanent cytostome-cytopharyngeal complex, pharyngeal rods, striated fibres, mastigonemes, and a paraflagellar rod are absent. This unique combination of characters dictates a very separate position for H. amphikineta within the known protists. Thus, the phylum Hemimastigophora nov. phylum (Hemimastigea nov. cl. and Hemimastigida nov. ord.), is established to include H. amphikineta and possibly Spironema multiciliatum Klebs, 1892. The structure of the pellicle and the nuclear apparatus of H. amphikineta indicate some relationship with the Euglenophyta. However, clear evidence for a certain affinity is lacking. Thus, the Hemimastigophora are placed in an incertae sedis position within the kingdom Protista Haeckel, 1866.

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

    PubMed

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

    2015-05-01

    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.

  7. 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

  8. 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

  9. 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

  10. 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.

  11. 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).

  12. Routes of uptake of diclofenac, fluoxetine, and triclosan into sediment-dwelling worms.

    PubMed

    Karlsson, Maja V; Marshall, Stuart; Gouin, Todd; Boxall, Alistair B A

    2016-04-01

    The present study investigated the route and degree of uptake of 2 ionizable pharmaceuticals (diclofenac and fluoxetine) and 1 ionizable compound used in personal care products (triclosan) into the sediment-dwelling worm Lumbriculus variegatus. Studies were done on complete worms ("feeding") and worms where the head was absent ("nonfeeding") using (14) C-labeled ingredients. Biota sediment accumulation factors (BSAF), based on uptake of (14) C, for feeding worms increased in the order fluoxetine (0.3) < diclofenac (0.5) < triclosan (9), which is correlated with a corresponding increase in log octanol-water partition coefficient. Biota sediment accumulation factor estimates are representative of maximum values because the degree of biotransformation in the worms was not quantified. Although no significant differences were seen between the uptake of diclofenac and that of fluoxetine in feeding and nonfeeding worms, uptake of the more hydrophobic antimicrobial, triclosan, into the feeding worms was significantly greater than that in the nonfeeding worms, with the 48-h BSAF for feeding worms being 36% higher than that for the nonfeeding worms. The results imply that dietary uptake contributes to the uptake of triclosan, which may be a result of the high hydrophobicity of the compound. Models that estimate exposure of ionizable substances may need to consider uptake from both the water column and food, particularly when assessing risks from dynamic exposures to organic contaminants.

  13. The effect of operating conditions on aquatic worms eating waste sludge.

    PubMed

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

    2009-03-01

    Several techniques are available for dealing with the waste sludge produced in biological waste water treatment. A biological approach uses aquatic worms to consume and partially digest the waste sludge. In our concept for a worm reactor, the worms (Lumbriculus variegatus) are immobilised in a carrier material. For correct sizing and operation of such a worm reactor, the effect of changes in dissolved oxygen (DO) concentration, ammonia concentration, temperature and light exposure were studied in sequencing batch experiments. DO concentration had an effect on both sludge consumption rate and sludge reduction efficiency. Sludge consumption rate was four times higher at DO concentrations above 8.1 mg/L, when compared to DO concentrations below 2.5 mg/L. Sludge reduction was 36 and 77% at these respective DO concentrations. The effect is most likely the result of a difference in gut residence time. An increase in unionised ammonia concentration drastically decreased the consumption rate. Ammonia is released by the worms at a rate of 0.02 mg N/mg TSS digested; therefore, replacing the effluent in the worm reactor is required to maintain a low ammonia concentration. The highest sludge consumption rates were measured at a temperature around 15 degrees C, whilst the highest TSS reduction was achieved at 10 degrees C. Not exposing the worms to light did not affect consumption or digestion rates. High temperatures (above 25 degrees C) as well as low DO concentrations (below 1 mg/L) in the worm reactor should be avoided as these lead to significant decreases in the number of worms. The main challenges for applying the worm reactor at a larger scale are the supply of oxygen to the worms and maintaining a low ammonia concentration in the worm reactor. Applying a worm reactor at a waste water treatment plant was estimated to increase the oxygen consumption and the ammonia load by 15-20% and 5% respectively. PMID:19081597

  14. 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.

  15. Controlling Attention to Gaze and Arrows in Childhood: An fMRI Study of Typical Development and Autism Spectrum Disorders

    ERIC Educational Resources Information Center

    Vaidya, Chandan J.; Foss-Feig, Jennifer; Shook, Devon; Kaplan, Lauren; Kenworthy, Lauren; Gaillard, William D.

    2011-01-01

    Functional magnetic resonance imaging was used to examine functional anatomy of attention to social (eye gaze) and nonsocial (arrow) communicative stimuli in late childhood and in a disorder defined by atypical processing of social stimuli, Autism Spectrum Disorders (ASD). Children responded to a target word ("LEFT"/"RIGHT") in the context of a…

  16. Gender and Spatial Ability and the Use of Specific Labels and Diagrammatic Arrows in a Micro-Level Chemistry Animation

    ERIC Educational Resources Information Center

    Falvo, David A.; Suits, Jerry P.

    2009-01-01

    This study investigates the effects of using both specific labels and diagrammatic arrows in the animation of salt dissolution. Four different versions of the animation served as treatments that were developed based upon principles of educational technology and cognitive psychology. The researchers studied the effects of spatial ability (high or…

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

    PubMed

    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

    2015-12-01

    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.

  18. 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

  19. 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).

  20. Ecdysone receptor homologs from mollusks, leeches and a polychaete worm.

    PubMed

    Laguerre, Michel; Veenstra, Jan A

    2010-11-01

    The genomes of the mollusk Lottia gigantea, the leech Helobdella robusta and the polychaete worm Capitella teleta each have a gene encoding an ecdysone receptor homolog. Publicly available genomic and EST sequences also contain evidence for ecdysone receptors in the seahare Aplysia californica, the bobtail squid Euprymna scolopes and the medicinal leech Hirudo medicinalis. Three-dimensional models of the ligand binding domains of these predicted ecdysone receptor homologs suggest that each of them could potentially bind an ecdysone-related steroid. Thus, ecdysone receptors are not limited to arthropods and nematodes.

  1. 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

  2. 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.

  3. 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.

  4. 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

  5. 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

  6. 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.

  7. 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

  8. "Endomicrobia": cytoplasmic symbionts of termite gut protozoa form a separate phylum of prokaryotes.

    PubMed

    Stingl, Ulrich; Radek, Renate; Yang, Hong; Brune, Andreas

    2005-03-01

    Lignocellulose digestion by wood-feeding termites depends on the mutualistic interaction of unusual, flagellate protists located in their hindgut. Most of the flagellates harbor numerous prokaryotic endosymbionts of so-far-unknown identity and function. Using a full-cycle molecular approach, we show here that the endosymbionts of the larger gut flagellates of Reticulitermes santonensis belong to the so-called termite group 1 (TG-1) bacteria, a group of clones previously obtained exclusively from gut homogenates of Reticulitermes speratus that are only distantly related to other bacteria and are considered a novel bacterial phylum based on their 16S rRNA gene sequences. Fluorescence in situ hybridization with specifically designed oligonucleotide probes confirmed that TG-1 bacteria are indeed located within the flagellate cells and demonstrated that Trichonympha agilis (Hypermastigida) and Pyrsonympha vertens (Oxymonadida) harbor phylogenetically distinct populations of symbionts (<95% sequence similarity). Transmission electron microscopy revealed that the symbionts are small, spindle-shaped cells (0.6 microm in length and 0.3 microm in diameter) surrounded by two membranes and located within the cytoplasm of their hosts. The symbionts of the two flagellates are described as candidate species in the candidate genus "Endomicrobium." Moreover, we provide evidence that the members of the TG-1 phylum, for which we propose the candidate name "Endomicrobia," are phylogenetically extremely diverse and are present in and also restricted to the guts of all lower termites and wood-feeding cockroaches of the genus Cryptocercus, the only insects that are in an exclusive, obligately mutualistic association with such unique cellulose-fermenting protists.

  9. A broad molecular phylogeny of ciliates: identification of major evolutionary trends and radiations within the phylum.

    PubMed Central

    Baroin-Tourancheau, A; Delgado, P; Perasso, R; Adoutte, A

    1992-01-01

    The cellular architecture of ciliates is one of the most complex known within eukaryotes. Detailed systematic schemes have thus been constructed through extensive comparative morphological and ultrastructural analysis of the ciliature and of its internal cytoskeletal derivatives (the infraciliature), as well as of the architecture of the oral apparatus. In recent years, a consensus was reached in which the phylum was divided in eight classes as defined by Lynn and Corliss [Lynn, D. H. & Corliss, J. O. (1991) in Microscopic Anatomy of Invertebrates: Protozoa (Wiley-Liss, New York), Vol. 1, pp. 333-467]. By comparing partial sequences of the large subunit rRNA molecule, and by using both distance-matrix and maximum-parsimony-tree construction methods (checked by boot-strapping), we examine the phylogenetic relationships of 22 species belonging to seven of these eight classes. At low taxonomic levels, the traditional grouping of the species is generally confirmed. At higher taxonomic levels, the branching pattern of these seven classes is resolved in several deeply separated major branches. Surprisingly, the first emerging one contains the heterotrichs and is strongly associated with a karyorelictid but deeply separated from hypotrichs. The litostomes, the oligohymenophorans, and the hypotrichs separate later in a bush-like topology hindering the resolution of their order of diversification. These results show a much more ancient origin of heterotrichs than was classically assumed, indicating that asymmetric, abundantly ciliated oral apparatuses do not correspond to "highly evolved" traits as previously thought. They also suggest the occurrence of a major radiative explosion in the evolutionary history of the ciliates, yielding five of the eight classes of the phylum. These classes appear to differ essentially according to the cytoskeletal architecture used to shape and sustain the cellular cortex (a process of essential adaptative and morphogenetic importance in

  10. 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.

  11. 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

  12. Surgical extraction of guinea worm: disability reduction and contribution to disease control.

    PubMed

    Rohde, J E; Sharma, B L; Patton, H; Deegan, C; Sherry, J M

    1993-01-01

    Surgical extraction of Guinea worm prior to eruption through the skin has long been performed by traditional healers in India. Using modern aseptic techniques under local anesthesia, unerupted worms can be completely and painlessly removed in several minutes. As a result, the average number of working days lost due to a single worm is reduced from three weeks or more to three days. In the field, the procedure results not only in a dramatic decrease in Guinea worm associated disability, but also in an improvement in detecting cases, and appears to reduce disease transmission.

  13. 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.

  14. Temperature effects on tubificid worms and their relation to sediment oxygen demand.

    PubMed

    Otubu, John E; Hunter, Joseph V; Francisco, Kelly L; Uchrin, Christopher G

    2006-01-01

    Sediment samples were collected from the Dead River in New Jersey and tested in the laboratory under two temperature conditions, 4 degrees C and 20 degrees C. The study was conducted to determine the effect of worm density on the sediment oxygen demand (SOD) rate and if temperature affects the ability for tubificid worms to deplete dissolved oxygen (DO) from the overlying stream water. The study showed that the DO concentration was affected by tubificid worm density and that higher temperature increased the metabolic activity of the worms. PMID:16835114

  15. 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.

  16. Membrane Bound GSK-3 Activates Wnt Signaling through Disheveled and Arrow

    PubMed Central

    Mannava, Anirudh G.; Tolwinski, Nicholas S.

    2015-01-01

    Wnt ligands and their downstream pathway components coordinate many developmental and cellular processes. In adults, they regulate tissue homeostasis through regulation of stem cells. Mechanistically, signal transduction through this pathway is complicated by pathway components having both positive and negative roles in signal propagation. Here we examine the positive role of GSK-3/Zw3 in promoting signal transduction at the plasma membrane. We find that targeting GSK-3 to the plasma membrane activates signaling in Drosophila embryos. This activation requires the presence of the co-receptor Arrow-LRP5/6 and the pathway activating protein Disheveled. Our results provide genetic evidence for evolutionarily conserved, separable roles for GSK-3 at the membrane and in the cytosol, and are consistent with a model where the complex cycles from cytosol to membrane in order to promote signaling at the membrane and to prevent it in the cytosol. PMID:25848770

  17. A search for B arrow γ e \\overlineν_e

    NASA Astrophysics Data System (ADS)

    Chen, Edward

    2003-04-01

    We present the results of a search for the radiative leptonic decay B arrow γ e \\overlineνe using a sample of (88.85 ± 0.98) × 10^6 B\\overlineB pairs collected with the BABAR detector at the PEP-II asymmetric B Factory at SLAC. We report a 90% confidence level upper limit on the branching fraction. This decay mode is related to the theoretically clean purely leptonic decay, but with a larger branching fraction due to the lack of helicity supression. An observation of this decay could be used either to evaluate the B meson pseudoscalar decay constant fB or, with an independent determination of f_B, to test theoretical models of charmless B decays.

  18. 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

  19. 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.

  20. Entanglement versus Stosszahlansatz: disappearance of the thermodynamic arrow in a high-correlation environment.

    PubMed

    Partovi, M Hossein

    2008-02-01

    The crucial role of ambient correlations in determining thermodynamic behavior is established. A class of entangled states of two macroscopic systems is constructed such that each component is in a state of thermal equilibrium at a given temperature, and when the two are allowed to interact heat can flow from the colder to the hotter system. A dilute gas model exhibiting this behavior is presented. This reversal of the thermodynamic arrow is a consequence of the entanglement between the two systems, a condition that is opposite to molecular chaos and shown to be unlikely in a low-entropy environment. By contrast, the second law is established by proving Clausius' inequality in a low-entropy environment. These general results strongly support the expectation, first expressed by Boltzmann and subsequently elaborated by others, that the second law is an emergent phenomenon which requires a low-entropy cosmological environment, one that can effectively function as an ideal information sink. PMID:18351990

  1. 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

  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. 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.

  4. 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.

  5. The emergence of time's arrows and special science laws from physics.

    PubMed

    Loewer, Barry

    2012-02-01

    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.

  6. 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

  7. Solid phase microextraction Arrow for the sampling of volatile amines in wastewater and atmosphere.

    PubMed

    Helin, Aku; Rönkkö, Tuukka; Parshintsev, Jevgeni; Hartonen, Kari; Schilling, Beat; Läubli, Thomas; Riekkola, Marja-Liisa

    2015-12-24

    A new method is introduced for the sampling of volatile low molecular weight alkylamines in ambient air and wastewater by utilizing a novel SPME Arrow system, which contains a larger volume of sorbent compared to a standard SPME fiber. Parameters affecting the extraction, such as coating material, need for preconcentration, sample volume, pH, stirring rate, salt addition, extraction time and temperature were carefully optimized. In addition, analysis conditions, including desorption temperature and time as well as gas chromatographic parameters, were optimized. Compared to conventional SPME fiber, the SPME Arrow had better robustness and sensitivity. Average intermediate reproducibility of the method expressed as relative standard deviation was 12% for dimethylamine and 14% for trimethylamine, and their limit of quantification 10μg/L and 0.13μg/L respectively. Working range was from limits of quantification to 500μg/L for dimethylamine and to 130μg/L for trimethylamine. Several alkylamines were qualitatively analyzed in real samples, while target compounds dimethyl- and trimethylamines were quantified. The concentrations in influent and effluent wastewater samples were almost the same (∼80μg/L for dimethylamine, 120μg/L for trimethylamine) meaning that amines pass the water purification process unchanged or they are produced at the same rate as they are removed. For the air samples, preconcentration with phosphoric acid coated denuder was required and the concentration of trimethylamine was found to be around 1ng/m(3). The developed method was compared with optimized method based on conventional SPME and advantages and disadvantages of both approaches are discussed.

  8. 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

  9. 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.

  10. 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.

  11. 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

  12. Complete mitochondrial genome of yellow meal worm (Tenebrio molitor).

    PubMed

    Liu, Li-Na; Wang, Cheng-Ye

    2014-11-18

    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 tRNA(Ser) (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

  13. 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

  14. 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

  15. Epidemiological studies on guinea-worm in some newly discovered villages of Jhabua District (M.P.) and test of carica papaya leaves of guinea worm infection.

    PubMed

    Sanghvi, P K

    1989-05-01

    Epidemiological survey was carried out for prevalence of guinea worm infection in 12 villages having a total population of 10281 persons in Jhabua district of M.P. The prevalence of 2.85 percent. Infection was more common in males. A paste of leaves of carica papya with opium and common salt applied for 3 days was helpful in relief of symptoms and easy extraction of worm from the body.

  16. 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.

  17. Bancroftian filariasis in Egypt: visualization of adult worms and subclinical lymphatic pathology by scrotal ultrasound.

    PubMed

    Faris, R; Hussain, O; El Setouhy, M; Ramzy, R M; Weil, G J

    1998-12-01

    The purpose of this study was to explore the value of scrotal ultrasound as a means of evaluating Bancroftian filariasis. Color Doppler ultrasound examinations were performed to look for subclinical hydroceles and motile adult filarial worms (dancing worms) in dilated lymphatics. Sixty-one male subjects from a filariasis-endemic area in Egypt were studied including 19 clinically normal microfilaria (MF) carriers (seven with dancing worms and eight with subclinical hydroceles), 13 MF-negative subjects with positive filarial antigen test results (three with dancing worms and seven with subclinical hydroceles), 22 exposed subjects with no MF and negative antigen test results (no dancing worms, four subclinical hydroceles), and seven subjects with clinical filariasis (no dancing worms, seven hydroceles). Thus, all men tested with clinical filariasis and most clinically normal subjects with either microfilaremia or filarial antigenemia had abnormal ultrasound examination results. Ultrasound findings often changed after therapy with diethylcarbamazine, with disappearance of dancing worms and development of new scrotal calcifications or hydroceles. This study confirms the value of scrotal ultrasound as a means of noninvasively visualizing adult filarial worms and assessing subclinical lymphatic damage in Bancroftian filariasis.

  18. 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…

  19. 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.

  20. 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.

  1. Worm recovery and precipitin antibody response in guinea pigs and rats infected with Clonorchis sinensis.

    PubMed

    Su, K E; Wang, F Y; Chi, P Y

    1998-12-01

    Guinea pigs (Hartley strain) and rats (Wistar strain) were each fed 200 and 100 Clonorchis sinensis metacercariae, respectively. Five animals from each species were sacrificed weekly between 1-8 weeks postinfection (WPI) and then at 12, 16, 20 and 30 WPI for collection of worms, bile and sera. The overall worm recovery rates for guinea pigs and rats were 18.7% and 12.4%, respectively. Only one of the five rats examined at 20 WPI still harbored one worm, while all were worm-free at 30 WPI. By a double diffusion test, no antibodies were detected against C. sinensis adult antigens in the bile juice. Serum antibodies were detected in at least 95% of the infected guinea pigs between 4-30 WPI and rats between 3-16 WPI. Precipitin antibodies seemed to be correlated with the presence of live worms in rats that had been infected for more than 12 weeks.

  2. 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.

  3. 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.

  4. Evolutionarily conserved, multitasking TRP channels: lessons from worms and flies.

    PubMed

    Venkatachalam, Kartik; Luo, Junjie; Montell, Craig

    2014-01-01

    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.

  5. 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

  6. Marriage shrines and worms impacting our understanding of mammalian fertilization

    PubMed Central

    Krauchunas, Amber R.; Singson, Andrew

    2016-01-01

    ABSTRACT Genetic approaches in C. elegans are complementing the biochemical and antibody based strategies traditionally used to study the molecular underpinnings of fertilization in other organisms. A pair of worm studies, one based on forward genetics and one based on reverse genetics, converge on the sperm immunoglobulin superfamily molecule SPE-45. Loss of spe-45 function leads to the production of sperm that cannot fertilize wild-type eggs. This is a strikingly similar phenotype as those seen in mice lacking the immunoglobulin superfamily protein Izumo1. This work sets the stage for leveraging the power of the C. elegans model system to learn more about Izumo-like molecular function but also for the discovery of additional deeply conserved components of fertility pathways. PMID:27695649

  7. 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.

  8. Microplastic ingestion decreases energy reserves in marine worms.

    PubMed

    Wright, Stephanie L; Rowe, Darren; Thompson, Richard C; Galloway, Tamara S

    2013-12-01

    The indiscriminate disposal of plastic to the environment is of concern. Microscopic plastic litter (<5 mm diameter; 'microplastic') is increasing in abundance in the marine environment, originating from the fragmentation of plastic items and from industry and personal-care products [1]. On highly impacted beaches, microplastic concentrations (<1mm) can reach 3% by weight, presenting a global conservation issue [2]. Microplastics are a novel substrate for the adherence of hydrophobic contaminants [1], deposition of eggs [3], and colonization by unique bacterial assemblages [4]. Ingestion by indiscriminate deposit-feeders has been reported, yet physical impacts remain understudied [1]. Here, we show that deposit-feeding marine worms maintained in sediments spiked with microscopic unplasticised polyvinylchloride (UPVC) at concentrations overlapping those in the environment had significantly depleted energy reserves by up to 50% (Figure 1). Our results suggest that depleted energy reserves arise from a combination of reduced feeding activity, longer gut residence times of ingested material and inflammation.

  9. 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

  10. 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.

  11. Giant kidney worm (Dioctophyma renale) infection mimicking retroperitoneal neoplasm.

    PubMed

    Sun, T; Turnbull, A; Lieberman, P H; Sternberg, S S

    1986-07-01

    A 50-year-old Chinese man was found by ultrasound and computed tomography to have a retroperitoneal mass in the right upper quadrant of the abdomen. At operation, a hemorrhagic cyst was detected at the upper pole of the right kidney adjacent to the adrenal gland. Microscopic examination revealed that the cyst wall was composed of granulomatous tissue loaded with eggs and cross-sections of parasites, identified as Dioctophyma renale. The eggs were characterized by a birefringent striated double wall. The presence of cross sections of adult worms of D. renale in human tissue has not been previously described. Another unique feature of this case was that the right kidney was intact, as examined grossly at laparotomy and by intravenous pyelography. Eggs were not detected in the urine.

  12. Helminthic therapy: using worms to treat immune-mediated disease.

    PubMed

    Elliott, David E; Weinstock, Joel V

    2009-01-01

    There is an epidemic of immune-mediated disease in highly-developed industrialized countries. Such diseases, like inflammatory bowel disease, multiple sclerosis and asthma increase in prevalence as populations adopt modern hygienic practices. These practices prevent exposure to parasitic worms (helminths). Epidemiologic studies suggest that people who carry helminths have less immune-mediated disease. Mice colonized with helminths are protected from disease in models of colitis, encephalitis, Type 1 diabetes and asthma. Clinical trials show that exposure to helminths reduce disease activity in patients with ulcerative colitis or Crohn's disease. This chapter reviews some of the work showing that colonization with helminths alters immune responses, against dysregulated inflammation. These helminth-host immune interactions have potentially important implications for the treatment of immune-mediated diseases.

  13. Worms, wisdom, and wealth: why deworming can make economic sense.

    PubMed

    Bundy, Donald A P; Walson, Judd L; Watkins, Kristie L

    2013-03-01

    For those of us who have had worms, getting rid of them seems a good idea, and multiple studies demonstrate the simplicity and benefit of deworming children. In the past decade or so, there has been a dramatic increase in efforts to provide inexpensive deworming medications, but at the same time there have been calls to re-evaluate the impact of deworming programs. In this review, we examine the history of deworming and explore the evidence for effects of deworming on health, on child development, and on economic returns. Important policy conclusions include that a paucity of randomized trial data suggesting benefit does not equate to a lack of benefit and that a greater emphasis on documenting such benefit should be pursued.

  14. 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.

  15. Comparative descriptions of non-adult stages of four genera of Gordiids (Phylum: Nematomorpha).

    PubMed

    Szmygiel, Cleo; Schmidt-Rhaesa, Andreas; Hanelt, Ben; Bolek, Matthew G

    2014-02-25

    Freshwater hairworms infect terrestrial arthropods as larvae but are free-living in aquatic habitats as adults. Estimates suggest that only 18% of hairworm species have been described globally and biodiversity studies on this group have been hindered by unreliable ways of collecting adult free living worms over large geographical areas. However, recent work indicates that non-adult cyst stages of hairworms may be the most commonly encountered stages of gordiids in the environment, and can be used for discovering the hidden diversity of this group. Unfortunately, little information is available on the morphological characteristics of non-adult stages of hairworms. To address this problem, we describe and compare morphological characteristics of non-adult stages for nine species of African and North American gordiids from four genera (Chordodes, Gordius, Paragordius, and Neochordodes). Observations were made on the oviposition behavior of adult worms and morphological characteristics were recorded for egg strings, larvae and cysts using light and differential interference contrast microscopy and/or scanning electron microscopy. Our study indicates that three distinct types of oviposition behaviors and three distinct morphological types of egg string, larva, and cysts were present among the four genera of gordiids. Although species identification based on cyst characteristics was not always possible among different species of gordiids, cyst morphology was conserved among some genera and all clades of gordiids. More importantly, our work indicates that gordiid larval morphology can be used for predicting cyst morphology among other gordiid genera. The capability to identify and predict gordiid genera and/or clades based on cyst morphology will be useful for culturing gordiids in the laboratory from field collected cysts and these new techniques will undoubtedly allow others to discover new species of gordiids from around the world.

  16. 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.

  17. 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

  18. 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

  19. 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.

  20. Is the hypothesis about a low entropy initial state of the Universe necessary for explaining the arrow of time?

    NASA Astrophysics Data System (ADS)

    Goldstein, Sheldon; Tumulka, Roderich; Zanghı, Nino

    2016-07-01

    According to statistical mechanics, microstates of an isolated physical system (say, a gas in a box) at time t0 in a given macrostate of less-than-maximal entropy typically evolve in such a way that the entropy at time t increases with |t -t0| in both time directions. In order to account for the observed entropy increase in only one time direction, the thermodynamic arrow of time, one usually appeals to the hypothesis that the initial state of the Universe was one of very low entropy. In certain recent models of cosmology, however, no hypothesis about the initial state of the Universe is invoked. We discuss how the emergence of a thermodynamic arrow of time in such models can nevertheless be compatible with the above-mentioned consequence of statistical mechanics, appearances to the contrary notwithstanding.

  1. Exploratory investigation of a spanwise blowing concept for tip-stall control on cranked-arrow wings

    NASA Technical Reports Server (NTRS)

    Rao, Dhanvada M.

    1992-01-01

    A novel blowing concept aimed at controlling the tip-panel stall of 'cranked-arrow' type wings was experimentally investigated. A spanwise-directed jet sheet tangential to the upper surface, blown from a chordwise slot located at the crank, interacts obliquely with the external flow to generate a powerful and highly controllable vortex, substantially covering the tip panel. The incremental suction due to this jet vortex, coupled with its flow stabilization effect improves the tip-panel maximum lift and stall characteristics, leading to pitch-up alleviation and lateral control augmentation. Low-speed wind tunnel flow visualizations, pressure measurements and force/moment results are presented validating the flow-control concept and illustrating its potential on a generic crank-arrow wing model.

  2. 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.

  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. The expression of tubulin and tektin genes in dicyemid mesozoans (Phylum: Dicyemida).

    PubMed

    Ogino, Kazutoyo; Tsuneki, Kazuhiko; Furuya, Hidetaka

    2007-06-01

    Dicyemid mesozoans (Phylum Dicyemida) are endoparasites (or endosymbionts) that typically are found in the renal sac of benthic cephalopod mollusks such as octopuses and cuttlefishes. Adult dicyemids likely adhere to the renal appendage of hosts via cilia of calotte peripheral cells. These cilia seem to be continuously worn away in the interaction between the dicyemids and the epidermal cells of host renal appendages. We cloned 4 cDNAs and genes, alpha-tubulin, beta-tubulin, tektin B, and tektin C, which are thought to play a key role in ciliogenesis, from Dicyema japonicum, and studied expression patterns of these genes by whole-mount in situ hybridization. We detected coexpression of these genes in the calotte peripheral cells, but not in the trunk peripheral cells. This suggests that regeneration and turnover of cilia continuously occur in the calotte. In vermiform and infusoriform embryos, we also detected coexpression patterns of these genes, which might correlate with ciliogenesis during the embryogenesis. We also predicted the secondary structure and the coiled-coil regions of dicyemid tektins.

  5. Bacteria of the candidate phylum TM7 are prevalent in acidophilic nitrifying sequencing-batch reactors.

    PubMed

    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.

  6. 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

  7. 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

  8. A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont.

    PubMed

    Huber, Harald; Hohn, Michael J; Rachel, Reinhard; Fuchs, Tanja; Wimmer, Verena C; Stetter, Karl O

    2002-05-01

    According to small subunit ribosomal RNA (ss rRNA) sequence comparisons all known Archaea belong to the phyla Crenarchaeota, Euryarchaeota, and--indicated only by environmental DNA sequences--to the 'Korarchaeota'. Here we report the cultivation of a new nanosized hyperthermophilic archaeon from a submarine hot vent. This archaeon cannot be attached to one of these groups and therefore must represent an unknown phylum which we name 'Nanoarchaeota' and species, which we name 'Nanoarchaeum equitans'. Cells of 'N. equitans' are spherical, and only about 400 nm in diameter. They grow attached to the surface of a specific archaeal host, a new member of the genus Ignicoccus. The distribution of the 'Nanoarchaeota' is so far unknown. Owing to their unusual ss rRNA sequence, members remained undetectable by commonly used ecological studies based on the polymerase chain reaction. 'N. equitans' harbours the smallest archaeal genome; it is only 0.5 megabases in size. This organism will provide insight into the evolution of thermophily, of tiny genomes and of interspecies communication. PMID:11986665

  9. 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.

  10. Phylogenetic reference data for systematics and phylotaxonomy of arbuscular mycorrhizal fungi from phylum to species level.

    PubMed

    Krüger, Manuela; Krüger, Claudia; Walker, Christopher; Stockinger, Herbert; Schüssler, Arthur

    2012-03-01

    Although the molecular phylogeny, evolution and biodiversity of arbuscular mycorrhizal fungi (AMF) are becoming clearer, phylotaxonomically reliable sequence data are still limited. To fill this gap, a data set allowing resolution and environmental tracing across all taxonomic levels is provided. Two overlapping nuclear DNA regions, totalling c. 3 kb, were analysed: the small subunit (SSU) rRNA gene (up to 1800 bp) and a fragment spanning c. 250 bp of the SSU rDNA, the internal transcribed spacer (ITS) region (c. 475-520 bp) and c. 800 bp of the large subunit (LSU) rRNA gene. Both DNA regions together could be analysed for 35 described species, the SSU rDNA for c. 76 named and 18 as yet undefined species, and the ITS region or LSU rDNA, or a combination of both, for c. 91 named and 16 as yet undefined species. Present phylogenetic analyses, based on the three rDNA markers, provide reliable and robust resolution from phylum to species level. Altogether, 109 named species and 27 cultures representing as yet undefined species were analysed. This study provides a reference data set for molecular systematics and environmental community analyses of AMF, including analyses based on deep sequencing.

  11. 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

  12. A unique mitovirus from Glomeromycota, the phylum of arbuscular mycorrhizal fungi.

    PubMed

    Kitahara, Ryoko; Ikeda, Yoji; Shimura, Hanako; Masuta, Chikara; Ezawa, Tatsuhiro

    2014-08-01

    Arbuscular mycorrhizal (AM) fungi that belong to the phylum Glomeromycota associate with most land plants and supply mineral nutrients to the host plants. One of the four viral segments found by deep-sequencing of dsRNA in the AM fungus Rhizophagus clarus strain RF1 showed similarity to mitoviruses and is characterized in this report. The genome segment is 2,895 nucleotides in length, and the largest ORF was predicted by applying either the mold mitochondrial or the universal genetic code. The ORF encodes a polypeptide of 820 amino acids with a molecular mass of 91.2 kDa and conserves the domain of the mitovirus RdRp superfamily. Accordingly, the dsRNA was designated as R. clarus mitovirus 1 strain RF1 (RcMV1-RF1). Mitoviruses are localized exclusively in mitochondria and thus generally employ the mold mitochondrial genetic code. The distinct codon usage of RcMV1-RF1, however, suggests that the virus is potentially able to replicate not only in mitochondria but also in the cytoplasm. RcMV1-RF1 RdRp showed the highest similarity to the putative RdRp of a mitovirus-like ssRNA found in another AM fungus, followed by RdRp of a mitovirus in an ascomycotan ectomycorrhizal fungus. The three mitoviruses found in the three mycorrhizal fungi formed a deeply branching clade that is distinct from the two major clades in the genus Mitovirus.

  13. 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

  14. 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.

  15. 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).

  16. 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.

  17. Insights into thermoadaptation and the evolution of mesophily from the bacterial phylum Thermotogae.

    PubMed

    Pollo, Stephen M J; Zhaxybayeva, Olga; Nesbø, Camilla L

    2015-09-01

    Thermophiles are extremophiles that grow optimally at temperatures >45 °C. To survive and maintain function of their biological molecules, they have a suite of characteristics not found in organisms that grow at moderate temperature (mesophiles). At the cellular level, thermophiles have mechanisms for maintaining their membranes, nucleic acids, and other cellular structures. At the protein level, each of their proteins remains stable and retains activity at temperatures that would denature their mesophilic homologs. Conversely, cellular structures and proteins from thermophiles may not function optimally at moderate temperatures. These differences between thermophiles and mesophiles presumably present a barrier for evolutionary transitioning between the 2 lifestyles. Therefore, studying closely related thermophiles and mesophiles can help us determine how such lifestyle transitions may happen. The bacterial phylum Thermotogae contains hyperthermophiles, thermophiles, mesophiles, and organisms with temperature ranges wide enough to span both thermophilic and mesophilic temperatures. Genomic, proteomic, and physiological differences noted between other bacterial thermophiles and mesophiles are evident within the Thermotogae. We argue that the Thermotogae is an ideal group of organisms for understanding of the response to fluctuating temperature and of long-term evolutionary adaptation to a different growth temperature range.

  18. 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.

  19. 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.

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

    PubMed

    Sekiguchi, Yuji; Ohashi, Akiko; Parks, Donovan H; Yamauchi, Toshihiro; Tyson, Gene W; Hugenholtz, Philip

    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.

  1. 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

  2. A phylogenetic test of the Red Queen Hypothesis: outcrossing and parasitism in the Nematode phylum.

    PubMed

    Gibson, Amanda Kyle; Fuentes, Jesualdo Arturo

    2015-02-01

    Sexual outcrossing is costly relative to selfing and asexuality, yet it is ubiquitous in nature, a paradox that has long puzzled evolutionary biologists. The Red Queen Hypothesis argues that outcrossing is maintained by antagonistic interactions between host and parasites. Most tests of this hypothesis focus on the maintenance of outcrossing in hosts. The Red Queen makes an additional prediction that parasitic taxa are more likely to be outcrossing than their free-living relatives. We test this prediction in the diverse Nematode phylum using phylogenetic comparative methods to evaluate trait correlations. In support of the Red Queen, we demonstrate a significant correlation between parasitism and outcrossing in this clade. We find that this correlation is driven by animal parasites, for which outcrossing is significantly enriched relative to both free-living and plant parasitic taxa. Finally, we test hypotheses for the evolutionary history underlying the correlation of outcrossing and animal parasitism. Our results demonstrate that selfing and asexuality are significantly less likely to arise on parasitic lineages than on free-living ones. The findings of this study are consistent with the Red Queen Hypothesis. Moreover, they suggest that the maintenance of genetic variation is an important factor in the persistence of parasitic lineages.

  3. 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

  4. 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

  5. Discovery of the Novel Candidate Phylum “Poribacteria” in Marine Sponges

    PubMed Central

    Fieseler, Lars; Horn, Matthias; Wagner, Michael; Hentschel, Ute

    2004-01-01

    Marine sponges (Porifera) harbor large amounts of commensal microbial communities within the sponge mesohyl. We employed 16S rRNA gene library construction using specific PCR primers to provide insights into the phylogenetic identity of an abundant sponge-associated bacterium that is morphologically characterized by the presence of a membrane-bound nucleoid. In this study, we report the presence of a previously unrecognized evolutionary lineage branching deeply in the domain Bacteria that is moderately related to the Planctomycetes, Verrucomicrobia, and Chlamydia lines of decent. Because members of this lineage showed <75% 16S rRNA gene sequence similarity to known bacterial phyla, we suggest the status of a new candidate phylum, named “Poribacteria”, to acknowledge the affiliation of the new bacterium with sponges. The affiliation of the morphologically conspicuous sponge bacterium with the novel phylogenetic lineage was confirmed by fluorescence in situ hybridization with newly designed probes targeting different sites of the poribacterial 16S rRNA. Consistent with electron microscopic observations of cell compartmentalization, the fluorescence signals appeared in a ring-shaped manner. PCR screening with “Poribacteria”-specific primers gave positive results for several other sponge species, while samples taken from the environment (seawater, sediments, and a filter-feeding tunicate) were PCR negative. In addition to a report for Planctomycetes, this is the second report of cell compartmentalization, a feature that was considered exclusive to the eukaryotic domain, in prokaryotes. PMID:15184179

  6. 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

  7. 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

  8. Porifera a reference phylum for evolution and bioprospecting: the power of marine genomics.

    PubMed

    Müller, Werner E G; Schwertner, Heiko; Müller, Isabel M

    2004-09-01

    The term Urmetazoa, as the hypothetical metazoan ancestor, was introduced to highlight the finding that all metazoan phyla including the Porifera [sponges] derived from one common ancestor. Analyses of sponge genomes, from Demospongiae, Calcarea and Hexactinellida have permitted the reconstruction of the evolutionary trail from Fungi to Metazoa. This has provided evidence that the characteristic evolutionary novelties of Metazoa existing in Porifera share high sequence similarities and in some aspects also functional similarities to related polypeptides found in other metazoan phyla. It is surprising that the genome of Porifera is large and comprises substantially more genes than Protostomia and Deuterostomia. On the basis of solid taxonomy and ecological data, the high value of this phylum for human application becomes obvious especially with regard to the field of chemical ecology and the hope to find novel potential drugs for clinical use. In addition, the benefit of efforts in understanding molecular biodiversity with focus on sponges can be seen in the fact that these animals as "living fossils" allow to stethoscope into the past of our globe especially with respect to the evolution of Metazoa.

  9. 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

  10. 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.

  11. 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.

  12. Nuclear receptors in nematode development: Natural experiments made by a phylum.

    PubMed

    Kostrouchova, Marta; Kostrouch, Zdenek

    2015-02-01

    The development of complex multicellular organisms is dependent on regulatory decisions that are necessary for the establishment of specific differentiation and metabolic cellular states. Nuclear receptors (NRs) form a large family of transcription factors that play critical roles in the regulation of development and metabolism of Metazoa. Based on their DNA binding and ligand binding domains, NRs are divided into eight NR subfamilies from which representatives of six subfamilies are present in both deuterostomes and protostomes indicating their early evolutionary origin. In some nematode species, especially in Caenorhabditis, the family of NRs expanded to a large number of genes strikingly exceeding the number of NR genes in vertebrates or insects. Nematode NRs, including the multiplied Caenorhabditis genes, show clear relation to vertebrate and insect homologues belonging to six of the eight main NR subfamilies. This review summarizes advances in research of nematode NRs and their developmental functions. Nematode NRs can reveal evolutionarily conserved mechanisms that regulate specific developmental and metabolic processes as well as new regulatory adaptations. They represent the results of a large number of natural experiments with structural and functional potential of NRs for the evolution of the phylum. The conserved and divergent character of nematode NRs adds a new dimension to our understanding of the general biology of regulation by NRs. This article is part of a Special Issue entitled: Nuclear receptors in animal development.

  13. 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

  14. 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.

  15. [Diversity of Cuproproteins and Copper Homeostasis Systems in Melioribacter roseus, a Facultatively Anaerobic Thermophilic Member of a New Phylum Ignavibacteriae].

    PubMed

    Karnachuk, O V; Gavrilov, S N; Avakyan, M R; Podosokorskaya, O A; Frank, Yu A; Bonch-Osmolovskaya, E A; Kublanov, I B

    2015-01-01

    The genome of Melioribacter roseus, one of two members of the recently described phylum Ignavibacteriae, was searched for the genes encoding proteins associated with copper transport or containing copper as cofactors, and the effect of Cu2+ concentration in the medium on M. roseus growth was investigated. Genomic analysis revealed a variety of copper-containing oxidoreductases in this facultative anaerobe. Three ATPases responsible for copper transport were identified. One of them (MROS_1511) was.probably involved in assembly of the copper-containing cytochrome c oxidase, while two others (MROS_0327 and MROS_0791) probably carried out a detoxification function. The presence of several copper-containing oxidoreductases and copper homeostasis systems in M. roseus is in agreement with the previously hypothesized origin of the phylum Ignavibacteriae from an aerobic ancestor common with those of Bacteroidetes and Chlorobi.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. Molecular signatures for the phylum Aquificae and its different clades: proposal for division of the phylum Aquificae into the emended order Aquificales, containing the families Aquificaceae and Hydrogenothermaceae, and a new order Desulfurobacteriales ord. nov., containing the family Desulfurobacteriaceae.

    PubMed

    Gupta, Radhey S; Lali, Ricky

    2013-09-01

    We report here detailed phylogenetic and comparative analyses on 11 sequenced genomes from the phylum Aquificae to identify molecular markers that are specific for the species from this phylum or its different families (viz. Aquificaceae, Hydrogenothermaceae and Desulfurobacteriaceae). In phylogenetic trees based on 16S rRNA gene or concatenated sequences for 32 conserved proteins, species from the three Aquificae families formed distinct clades. These trees also supported a strong relationship between the Aquificaceae and Hydrogenothermaceae families. In parallel, comparative analyses on protein sequences from Aquificae genomes have identified 46 conserved signature indels (CSIs) in broadly distributed proteins that are either exclusively or mainly found in members of the phylum Aquificae or its different families and subclades. Four of these CSIs, which are found in all sequenced Aquificae species, provide potential molecular markers for this phylum. Twelve, six and thirteen other CSIs that respectively are specific for the sequenced Aquificaceae, Hydrogenothermaceae and Desulfurobacteriaceae species provide molecular markers and novel tools for the identification of members of these families and for genetic and biochemical studies on them. Lastly, these studies have identified 11 CSIs in divergent proteins that are uniquely shared by members of the Aquificaceae and Hydrogenothermaceae families providing strong evidence that these two groups of bacteria shared a common ancestor exclusive of all other Aquificae (bacteria). The species from these two families are also very similar in their metabolic and physiological properties and they consist of aerobic or microaerophilic bacteria, which generally obtain energy by oxidation of hydrogen or reduced sulfur compounds by molecular oxygen. Based upon their strong association in phylogenetic trees, unique shared presence of large numbers of CSIs in different proteins, and similarities in their metabolic and

  2. Electro-worming: The behaviors of Caenorhabditis (C.) elegans in DC and AC electric fields

    NASA Astrophysics Data System (ADS)

    Chuang, Han-Sheng; Raizen, David M.; Dabbish, Nooreen; Bau, Haim H.

    2011-09-01

    The video showcases how C. elegans worms respond to DC and AC electrical stimulations. Gabel et al (2007) demonstrated that in the presence of DC and low frequency AC fields, worms of stage L2 and larger propel themselves towards the cathode. Rezai et al (2010) have demonstrated that this phenomenon, dubbed electrotaxis, can be used to control the motion of worms. In the video, we reproduce Rezai's experimental results. Furthermore, we show, for the first time, that worms can be trapped with high frequency, nonuniform electric fields. We studied the effect of the electric field on the nematode as a function of field intensity and frequency and identified a range of electric field intensities and frequencies that trap worms without apparent adverse effect on their viability. Worms tethered by dielectrophoresis (DEP) avoid blue light, indicating that at least some of the nervous system functions remain unimpaired in the presence of the electric field. DEP is useful to dynamically confine nematodes for observations, sort them according to size, and separate dead worms from live ones.

  3. The provision of potable water in eradication of Guinea worm infection in Ezza North, Southeastern, Nigeria.

    PubMed

    Ede, Alison Okorie; Nwaokoro, Joakin Chidozie; Iwuala, C C; Amadi, A N; Akpelu, Ugochinyere Alvana

    2014-10-01

    Guinea worm is a parasite found in unprotected drinking water sources, causes considerable morbidity and loss of agricultural production among rural people. The study was to determine the current status of Guinea worm infection in Ezza North and to evaluate the impact of control measures on guinea worm infection. A total of 200 individuals in Ezza North Southeastern, Nigeria were examined for guinea worm infection. A standardized questionnaire was used to determine the effect of potable water on guinea worm eradication/control, the source of drinking water, information on the knowledge, attitude, symptom management practices, availability of health facilities and boreholes installation status. The instrument for data collection was well constructed, validated and reliable tested questionnaire by an expert. Data obtained was analyzed using Epi-Info model 3.4 versions. Results of a study indicated majority of the respondents 195 (97.5 %) have access to safe drinking water supply which indicated no case of Guinea worm infection. The active use of potable water supply was found among the age group of 20-30 years 71 (35.5 %) and higher in male (57.5 %) than females (42.5 %). The drastic reduction of Guinea worm infection to zero (0) level in Ezza North were due to multiple factors as health education, availability of functional boreholes, presence of health centers for immediate treatment if any case discovered.

  4. Guinea worm disease--a chance for successful eradication in the Volta Region, Ghana.

    PubMed

    Diamenu, S K; Nyaku, A A

    1998-08-01

    A guinea worm eradication program in two farming communities in the Akatsi District in the Volta region of Ghana was initially threatened by failure to apply simple preventive practices. Persistent monitoring and education on the use of locally supplied, inexpensive materials for water filtration has turned the program around. In March 1996, the Volta rural water supply and sanitation (VRWSS) project commissioned a guinea worm prevalence and knowledge, attitude and practice (KAP) study to collect baseline prevalence data. This study revealed some of the factors that contributed to the persistent high prevalence of guinea worm in the two communities. The community's only source of potable drinking water was irrigation dams which also served as the source of guinea worm infection. The Last quarterly report stated that guinea worm cases had been reduced from 62 to 5 in the two communities. Lessons learnt from Avega and Avevi will be extended to other guinea worm endemic communities that have registered with the project in the region. The prospect of total eradication of guinea worm in the region now exists.

  5. 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.

  6. 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.

  7. The correlation between Clostridium-difficile infection and human gut concentrations of Bacteroidetes phylum and clostridial species.

    PubMed

    Goldberg, E; Amir, I; Zafran, M; Gophna, U; Samra, Z; Pitlik, S; Bishara, J

    2014-03-01

    We aimed to assess differences in bacterial intensities of Bacteroidetes phylum and different clostridial species in the human intestines with respect to C. difficile infection. Patients with a stool assay for C. difficile toxin were identified via the microbiology laboratory in our institute. Bacterial populations were quantified from stool samples of four groups of patients: Group I-patients with C. difficile associated diarrhea (CDAD); Group II-asymptomatic C. difficile carriers; Group III-patients with non-C. difficile diarrhea; Group IV-patients with no diarrhea and negative stool samples for the C. difficile toxin (control group). Stool was examined for three genes-C. difficile toxin A gene, 16S rRNA gene from Clostridium thermocellum representing other clostridial species, and 16S rRNA gene from Bacteroides fragilis representing the Bacteroidetes phylum. Fifty-nine patients underwent analysis of the stool (CDAD group 14, carriers group 14, non-C. difficile diarrhea group 16, control group 15). C. difficile concentration was highest in the CDAD group, followed by the carriers group. Higher concentrations of both clostridial species and Bacteriodetes were observed in the control and non-C. difficile diarrhea groups compared to the CDAD and carriers groups. We demonstrated an inverse association between infection with C. difficile and the abundance of Bacteroidetes phylum and other clostridial species in human intestines. Studies with larger samples and broader diagnostic procedures are needed in order to better explore and understand this association.

  8. 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

  9. 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.

  10. 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.

  11. 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.

  12. Nitrification expanded: discovery, physiology and genomics of a nitrite-oxidizing bacterium from the phylum Chloroflexi

    PubMed Central

    Sorokin, Dimitry Y; Lücker, Sebastian; Vejmelkova, Dana; Kostrikina, Nadezhda A; Kleerebezem, Robbert; Rijpstra, W Irene C; Damsté, Jaap S Sinninghe; Le Paslier, Denis; Muyzer, Gerard; Wagner, Michael; van Loosdrecht, Mark C M; Daims, Holger

    2012-01-01

    Nitrite-oxidizing bacteria (NOB) catalyze the second step of nitrification, a major process of the biogeochemical nitrogen cycle, but the recognized diversity of this guild is surprisingly low and only two bacterial phyla contain known NOB. Here, we report on the discovery of a chemolithoautotrophic nitrite oxidizer that belongs to the widespread phylum Chloroflexi not previously known to contain any nitrifying organism. This organism, named Nitrolancetus hollandicus, was isolated from a nitrifying reactor. Its tolerance to a broad temperature range (25–63 °C) and low affinity for nitrite (Ks=1 mℳ), a complex layered cell envelope that stains Gram positive, and uncommon membrane lipids composed of 1,2-diols distinguish N. hollandicus from all other known nitrite oxidizers. N. hollandicus grows on nitrite and CO2, and is able to use formate as a source of energy and carbon. Genome sequencing and analysis of N. hollandicus revealed the presence of all genes required for CO2 fixation by the Calvin cycle and a nitrite oxidoreductase (NXR) similar to the NXR forms of the proteobacterial nitrite oxidizers, Nitrobacter and Nitrococcus. Comparative genomic analysis of the nxr loci unexpectedly indicated functionally important lateral gene transfer events between Nitrolancetus and other NOB carrying a cytoplasmic NXR, suggesting that horizontal transfer of the NXR module was a major driver for the spread of the capability to gain energy from nitrite oxidation during bacterial evolution. The surprising discovery of N. hollandicus significantly extends the known diversity of nitrifying organisms and likely will have implications for future research on nitrification in natural and engineered ecosystems. PMID:22763649

  13. Genome sequencing of a single cell of the widely distributed marine subsurface Dehalococcoidia, phylum Chloroflexi

    PubMed Central

    Wasmund, Kenneth; Schreiber, Lars; Lloyd, Karen G; Petersen, Dorthe G; Schramm, Andreas; Stepanauskas, Ramunas; Jørgensen, Bo Barker; Adrian, Lorenz

    2014-01-01

    Bacteria of the class Dehalococcoidia (DEH), phylum Chloroflexi, are widely distributed in the marine subsurface, yet metabolic properties of the many uncultivated lineages are completely unknown. This study therefore analysed genomic content from a single DEH cell designated ‘DEH-J10' obtained from the sediments of Aarhus Bay, Denmark. Real-time PCR showed the DEH-J10 phylotype was abundant in upper sediments but was absent below 160 cm below sea floor. A 1.44 Mbp assembly was obtained and was estimated to represent up to 60.8% of the full genome. The predicted genome is much larger than genomes of cultivated DEH and appears to confer metabolic versatility. Numerous genes encoding enzymes of core and auxiliary beta-oxidation pathways were identified, suggesting that this organism is capable of oxidising various fatty acids and/or structurally related substrates. Additional substrate versatility was indicated by genes, which may enable the bacterium to oxidise aromatic compounds. Genes encoding enzymes of the reductive acetyl-CoA pathway were identified, which may also enable the fixation of CO2 or oxidation of organics completely to CO2. Genes encoding a putative dimethylsulphoxide reductase were the only evidence for a respiratory terminal reductase. No evidence for reductive dehalogenase genes was found. Genetic evidence also suggests that the organism could synthesise ATP by converting acetyl-CoA to acetate by substrate-level phosphorylation. Other encoded enzymes putatively conferring marine adaptations such as salt tolerance and organo-sulphate sulfohydrolysis were identified. Together, these analyses provide the first insights into the potential metabolic traits that may enable members of the DEH to occupy an ecological niche in marine sediments. PMID:23966099

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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.

  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.

  20. Inter-phylum HGT has shaped the metabolism of many mesophilic and anaerobic bacteria

    PubMed Central

    Caro-Quintero, Alejandro; Konstantinidis, Konstantinos T

    2015-01-01

    Genome sequencing has revealed that horizontal gene transfer (HGT) is a major evolutionary process in bacteria. Although it is generally assumed that closely related organisms engage in genetic exchange more frequently than distantly related ones, the frequency of HGT among distantly related organisms and the effect of ecological relatedness on the frequency has not been rigorously assessed. Here, we devised a novel bioinformatic pipeline, which minimized the effect of over-representation of specific taxa in the available databases and other limitations of homology-based approaches by analyzing genomes in standardized triplets, to quantify gene exchange between bacterial genomes representing different phyla. Our analysis revealed the existence of networks of genetic exchange between organisms with overlapping ecological niches, with mesophilic anaerobic organisms showing the highest frequency of exchange and engaging in HGT twice as frequently as their aerobic counterparts. Examination of individual cases suggested that inter-phylum HGT is more pronounced than previously thought, affecting up to ∼16% of the total genes and ∼35% of the metabolic genes in some genomes (conservative estimation). In contrast, ribosomal and other universal protein-coding genes were subjected to HGT at least 150 times less frequently than genes encoding the most promiscuous metabolic functions (for example, various dehydrogenases and ABC transport systems), suggesting that the species tree based on the former genes may be reliable. These results indicated that the metabolic diversity of microbial communities within most habitats has been largely assembled from preexisting genetic diversity through HGT and that HGT accounts for the functional redundancy among phyla. PMID:25314320