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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.

  2. 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.

  3. Preliminary Study on Distribution and Abundance of Chaetognaths (Arrow Worms) in the Gulf of Mexico.

    NASA Astrophysics Data System (ADS)

    Gilmartin, J.; Yang, Q.; Liu, H.

    2016-02-01

    The distribution of zooplankton presumably reflect ocean conditions. Chaetognaths (arrow worms) consist of an important zooplankton component and are recognized as a significant trophic link between smaller marine zooplankton, such as copepods, and larger predators, including many commercially important fish species. Arrow worms are raptorial predators which feed mainly on zooplankton and larval fish, which may affect recruitment dynamics of fish. Despite their trophic significance, there is limited information on the distribution and abundance of arrow worms in terms of environmental conditions in the Gulf of Mexico (GoM). In this study, we processed zooplankton samples that were collected using 200 µm vertical plankton nets at inshore and offshore stations in the GoM during spring and summer of 2015. Concurrently, we collected vertical profiles of temperature, salinity and density using a CTD in the spring, and surface temperature, salinity and dissolved oxygen in the summer. Our preliminary results indicate that Sagitta friderici and Sagitta tenius are abundant species in offshore stations. Furthermore, we explore the relationship between arrow worm species abundance and distribution with relation to physical variables in the region. This research will improve our understanding on the abundance and distribution of arrow worms in terms of ocean conditions in the GoM.

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

    PubMed Central

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

    2013-01-01

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

  5. 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. 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. Copyright © 2014 Elsevier Inc. All rights reserved.

  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. 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.

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

    PubMed

    Duvert, M; Salat, C

    1980-01-01

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

  12. 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.

  13. 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. Copyright © 2016 Elsevier Ltd. All rights reserved.

  14. Time's Arrows Today

    NASA Astrophysics Data System (ADS)

    Savitt, Steven F.

    1997-06-01

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

  15. Programmed Worms.

    ERIC Educational Resources Information Center

    Piele, Donald T.

    1982-01-01

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

  16. 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)

  17. 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

  18. Intrauterine Arrow Injury.

    PubMed

    Goswami, Jayanta Kumar; Lahiri, Kaushik

    2017-01-01

    Injury of a pregnant lady risks both mother and fetus. Various modes of injuries are possible. But arrow injury is not usually heard of in today's world. We have reported a male child delivered with a cut injury on the face. It was caused by a penetrating arrow hitting his mother in her lower abdomen at term. The injury of the baby was repaired successfully.

  19. Intrauterine Arrow Injury

    PubMed Central

    Goswami, Jayanta Kumar; Lahiri, Kaushik

    2017-01-01

    Injury of a pregnant lady risks both mother and fetus. Various modes of injuries are possible. But arrow injury is not usually heard of in today's world. We have reported a male child delivered with a cut injury on the face. It was caused by a penetrating arrow hitting his mother in her lower abdomen at term. The injury of the baby was repaired successfully. PMID:28082780

  20. Bow and arrow dynamics

    NASA Astrophysics Data System (ADS)

    Marlow, W. C.

    1981-04-01

    Past analyses of bow and arrow dynamics have assumed the string to be inextensible. This results in predictions of efficiencies that are significantly higher than measured values (efficiencies over 90% are predicted versus 70% to 85% for measurements, circa 1960). The present analysis allows for an elastic string. It is found that arrow exit then takes place when the string and bow limbs still have substantial kinetic energy, and therefore this energy is unavailable for kinetic energy of the arrow. Moreover, the potential energy remaining in the string and bow limb system can also reduce the amount of energy available for the arrow. For the Hickman model of a long bow used in this study, the elastic string prediction of efficiency is 78%, whereas the inelastic prediction is 92%. The analysis utilizes a Lagrangian distributed mass formulation to develop the governing equations of motion and to generate an equivalent point mass model. The equations of motion were numerically integrated to obtain efficiency, arrow velocity, virtual masses, string tension, string extension, arrow exit time, string and limb potential energies, system momentum, and the dynamic force required to hold the bow handle stationary. Estimates of the effect of air resistance were made and found to be less than 2% of the total system energy. The vibratory dynamics of the string and bow limbs subsequent to arrow exit was analyzed. The results of the elastic string considerations are in reasonable agreement with experimental data and negate the usual explanation for the long-standing discrepancy between theory and experiment as due to air resistance and hysteresis losses in the string and bow limbs.

  1. Penetrating craniofacial arrow injury.

    PubMed

    Jain, Dk; Aggarwal, Gaurav; Lubana, Ps; Moses, Sonia

    2010-01-01

    Arrow injuries are an extinct form of injury in most parts of the developed world, but are still seen, albeit infrequently in developing countries. Reports of penetrating injuries of the craniofacial region secondary to projectiles are few and far between. The morbidity-free outcome of surgical removal, in case of penetrating arrow injuries, despite the delay in presentation and, moreover, in the emergency surgical practice, are the salient points to be remembered whilst managing such cases, for 'what the mind knows is what the eyes see and what the eyes see is what can be practiced'. We report the case of a patient who was attacked by a projectile fired from a crossbow. Immediate surgery under general anesthesia was required to remove the arrow, with utmost care to avoid any neurovascular compromise to the facial nerve, as well as minimize postoperative complications such as otitis media and subsequent meningitis.

  2. [Homicide by bow and arrow].

    PubMed

    Germerott, Tanja; Jänisch, Stefanie; Tröger, Hans Dieter; Günther, Detlef

    2010-01-01

    Since the invention of firearms, arrow wounds represent a rarity in the daily routine of forensic pathologists. In the present paper, we describe a homicide by a broadhead arrow shot from a compound bow in a domestic environment. Based on this homicide, we discuss the characteristics of the lesion caused by broadhead arrows and field-tip arrows. We look critically at the free saleability of this equipment mostly used for sport shooting in Germany.

  3. 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.

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

    PubMed Central

    Thollesson, Mikael; Norenburg, Jon L

    2003-01-01

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

  5. 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…

  6. Arrow trauma to cervical spine.

    PubMed

    Geissinger, Gregory; Magid, Gail A; McMahon, Robert C

    2009-07-01

    A 50-year-old man was the victim of an accidental arrow shooting while hunting. The arrow entered his posterolateral neck and came to rest in the space between the C1/C2 vertebrae in his cervical spine. He was able to maintain his own cervical immobilization. His hunting partners drove him to meet emergency medical technicians, who stabilized the arrow shaft, transferred him to a backboard and gurney, and continued manual cervical immobilization en route to a local hospital. Cervical spine X-ray results compelled an air ambulance transfer to a trauma center where he underwent surgical intervention to remove the arrow. Following approximately 12 months of physical and occupational therapy, he returned to work full-time. Adherence to training and utilization of proven techniques involving pre-hospital transfers and positioning of cervically injured patients proved imperative to the patient's ultimate recovery.

  7. Arrow-arrow correlations for the six-vertex model.

    PubMed

    Falco, P

    2013-09-01

    The six-vertex model on a square lattice is "exactly solvable" because an exact formula for the free energy can be obtained by the Bethe ansatz. However, exact formulas for the correlations of local bulk observables, such as the orientation of the arrow at a given edge, are, in general, not available. In this Rapid Communication, we consider the isotropic "zero-field" six-vertex model at small Δ. We derive the long-distance asymptotic formula of arrow-arrow correlations, which display power law decays with one anomalous exponent. Our method is based on an interacting fermion representation of the six-vertex model and does not use any information obtained from the exact solution.

  8. Worm-stars and half-worms

    PubMed Central

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

    2014-01-01

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

  9. 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.

  10. 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.

  11. 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…

  12. 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…

  13. 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.

  14. A subquantum arrow of time

    NASA Astrophysics Data System (ADS)

    Nieuwenhuizen, Theo M.

    2014-04-01

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

  15. 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.

  16. Bow-arrow interaction in archery.

    PubMed

    Kooi, B W

    1998-11-01

    A mathematical model of the flight of the arrow during its discharge from a bow was proposed by Pekalski (1990). His description of the model was incomplete. In this paper, I give a full description of the model. Furthermore, I propose some improvements that make his model more consistent with reality. One achievement is the modelling of contact of the arrow and grip; the pressure button is modelled as a unilateral elastic support. The acceleration force acting upon the arrow during the launch is predicted by an advanced mathematical model of bow dynamics. There is a satisfactory conformity of the simulation and experimental results. The new model predicts that the arrow leaves the pressure button before it leaves the string, as reported previously. The ability to model arrow dynamics can be used to improve the adjustment of the bow-arrow system for optimal performance.

  17. Interactions between worms and malaria: good worms or bad worms?

    PubMed

    Nacher, Mathieu

    2011-09-12

    In the past decade there have been an increasing number of studies on co-infections between worms and malaria. However, this increased interest has yielded results that have been at times conflicting and made it difficult to clearly grasp the outcome of this interaction. Despite the heterogeneity of study designs, reviewing the growing body of research may be synthesized into some broad trends: Ascaris emerges mostly as protective from malaria and its severe manifestations, whereas hookworm seems to increase malaria incidence. As efforts are made to de-worm populations in malaria endemic areas, there is still no clear picture of the impact these programmes have in terms of quantitative and qualitative changes in malaria.

  18. Time's arrow: A numerical experiment

    NASA Astrophysics Data System (ADS)

    Fowles, G. Richard

    1994-04-01

    The dependence of time's arrow on initial conditions is illustrated by a numerical example in which plane waves produced by an initial pressure pulse are followed as they are multiply reflected at internal interfaces of a layered medium. Wave interactions at interfaces are shown to be analogous to the retarded and advanced waves of point sources. The model is linear and the calculation is exact and demonstrably time reversible; nevertheless the results show most of the features expected of a macroscopically irreversible system, including the approach to the Maxwell-Boltzmann distribution, ergodicity, and concomitant entropy increase.

  19. A life without worms

    PubMed Central

    Nkurunungi, Gyaviira; Andia Biraro, Irene; Mpairwe, Harriet; Elliott, Alison M.

    2017-01-01

    Abstract Worms have co-evolved with humans over millions of years. To survive, they manipulate host systems by modulating immune responses so that they cause (in the majority of hosts) relatively subtle harm. Anthelminthic treatment has been promoted as a measure for averting worm specific pathology and to mitigate subtle morbidities which may include effects on anaemia, growth, cognitive function and economic activity. With our changing environment marked by rapid population growth, urbanisation, better hygiene practices and anthelminthic treatment, there has been a decline in worm infections and other infectious diseases and a rise in non-communicable diseases such as allergy, diabetes and cardiovascular disease. This review reflects upon our age-old interaction with worms, and the broader ramifications of life without worms for vaccine responses and susceptibility to other infections, and for allergy-related and metabolic disease. We touch upon the controversy around the benefits of mass drug administration for the more-subtle morbidities that have been associated with worm infections and then focus our attention on broader, additional aspects of life without worms, which may be either beneficial or detrimental. PMID:28340138

  20. Arrows in Comprehending and Producing Mechanical Diagrams

    ERIC Educational Resources Information Center

    Heiser, Julie; Tversky, Barbara

    2006-01-01

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

  1. 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)

  2. 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)

  3. 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…

  4. 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…

  5. Dracunculiasis (guinea worm disease)

    PubMed Central

    Greenaway, Chris

    2004-01-01

    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. PMID:14970098

  6. 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.

  7. Worm Infections in Children.

    PubMed

    Weatherhead, Jill E; Hotez, Peter J

    2015-08-01

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

  8. Environmental and Molecular Science Laboratory Arrow

    SciTech Connect

    2016-06-24

    Arrows is a software package that combines NWChem, SQL and NOSQL databases, email, and social networks (e.g. Twitter, Tumblr) that simplifies molecular and materials modeling and makes these modeling capabilities accessible to all scientists and engineers. EMSL Arrows is very simple to use. The user just emails chemical reactions to arrows@emsl.pnnl.gov and then an email is sent back with thermodynamic, reaction pathway (kinetic), spectroscopy, and other results. EMSL Arrows parses the email and then searches the database for the compounds in the reactions. If a compound isn't there, an NWChem calculation is setup and submitted to calculate it. Once the calculation is finished the results are entered into the database and then results are emailed back.

  9. 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

  10. Illustrating cerebral function: the iconography of arrows.

    PubMed

    Schott, G D

    2000-12-29

    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.

  11. Penetrated arrow shot injury in anterior neck.

    PubMed

    Aremu, Shuaib K; Dike, Benjamin

    2011-03-01

    Although gunshot injuries are the most common penetrating anterior neck injuries in the developed world, this finding is not the case in the developing world, where knives, spears, arrows, and machetes are the preferred weapons, particularly in tribal societies. To present the case report of a patient with arrow shot injury to the anterior neck. A 48 year old cattle rearer in a village in northern part of Nigeria presented with 3 hr history of an arrow shot in anterior part of the neck which he sustained the while trying to prevent some armed robbers from stealing his cow. There was scanty bleeding from the site with the arrow in-situ sealing the wound. The entrance point of the arrow, about 1 cm in diameter, was just at the anterior border of the right sternocleidomastoid muscle; about 4 cm above the medial end of the right clavicle. There was a small skin bruise with slight swelling and tenderness around the opening but no active bleeding and no crepitus. Penetrating neck trauma from arrow shot may lead to potentially life-threatening injuries. A prompt diagnosis, a systematic treatment protocol, and an experienced trauma team are necessary to prevent a potential catastroph.

  12. Mathematical origin of time arrow

    NASA Astrophysics Data System (ADS)

    Shimansky, Yury

    2005-03-01

    Laws describing the main types of physical interactions are symmetrical with respect to the direction of time flow. At the same time, many virtually irreversible processes are observed. This ``time arrow'' paradox usually is associated with the law of entropy increase. The fact that physical systems obey this law regardless of their physical nature suggests that it may be based on a certain, yet unknown, mathematical principle. Here it is demonstrated that, if, on a time micro scale, the intensity of fluctuations of a certain parameter depends on the parameter's value, it would appear to an external observer on a time macro scale that the parameter tends to be modified in the direction of fluctuation intensity decrease. It is shown that the law of entropy increase is a consequence of this principle, if it is applied to entropy as a state variable of a thermodynamic system. The fundamental nature of this principle suggests that it must operate on virtually every level of physical reality. The principle is of great potential value for understanding mechanisms of self-organization, learning, adaptation, and evolution.

  13. 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…

  14. "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.

  15. "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.

  16. 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…

  17. A Can of Sea Worms

    ERIC Educational Resources Information Center

    Zinn, Donald J.

    1977-01-01

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

  18. 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)

  19. A transcriptomic analysis of the phylum Nematoda.

    PubMed

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

    2004-12-01

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

  20. On the recovery of horsehair worms, Gordius sp. (Nematomorpha: Gordiida) from pork in Shillong, India.

    PubMed

    Yadav, Arun K; Schmidt-Rhaesa, Andreas; Laha, R; Sen, A

    2017-03-01

    The members of the phylum Nematomorpha, called as horsehair or gordian worms, are the parasites of arthropods and emerge from their host for reproduction and early development in water. There are about 360 species of nematomorphs described till date. Although, horsehair worms are parasites of arthropod species, sporadic cases of their occurrence have also been reported from several other hosts, including man. This paper describes a case history of the occurrence of two nematomorph worms in the meat of a pig in Shillong, India. The worms were reported to have emerged in live condition from pork bought by a consumer from local market in Shillong. One of the recovered specimens was studied by scanning electron microscopy for species determination and identified as Gordius sp., mainly on the basis of flat polygonal areoles and fine bristles on the cuticle.

  1. 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

  2. WormBase

    PubMed Central

    Howe, Kevin; Davis, Paul; Paulini, Michael; Tuli, Mary Ann; Williams, Gary; Yook, Karen; Durbin, Richard; Kersey, Paul; Sternberg, Paul W.

    2012-01-01

    WormBase (www.wormbase.org) has been serving the scientific community for over 11 years as the central repository for genomic and genetic information for the soil nematode Caenorhabditis elegans. The resource has evolved from its beginnings as a database housing the genomic sequence and genetic and physical maps of a single species, and now represents the breadth and diversity of nematode research, currently serving genome sequence and annotation for around 20 nematodes. In this article, we focus on WormBase’s role of genome sequence annotation, describing how we annotate and integrate data from a growing collection of nematode species and strains. We also review our approaches to sequence curation, and discuss the impact on annotation quality of large functional genomics projects such as modENCODE. PMID:24058818

  3. 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.

  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. Electromyography of arrow release in archery.

    PubMed

    Hennessy, M P; Parker, A W

    1990-01-01

    An electronic arrow movement detector was used to accurately locate the muscle activity associated with release of the arrow during shooting in archery. Digital computer analysis of the electromyograms from thirty shots for two archers facilitated an examination of the relationship between the measured activity of the muscles and their function during release. Changes present in the direct and integrated electromyograms of muscles acting at the wrist and elbow joints of the bow arm and the shoulder of the draw arm tended to anticipate the moment of arrow release. These changes would produce muscular force to reduce unwanted movement at this critical phase of the shot in the bow arm and initiate release of the bow string by the fingers. This study provides a detailed quantitative analysis of the muscular action of the technique and identifies possibilities for prevention of injury by improving the understanding of muscle action in shooting.

  7. Entanglement and the thermodynamic arrow of time

    NASA Astrophysics Data System (ADS)

    Jennings, David; Rudolph, Terry

    2010-06-01

    We discuss quantum entanglement in the context of the thermodynamic arrow of time. We review the role of correlations in entropy-decreasing events and prove that the occurrence of a transformation between two thermodynamic states constitutes a new type of entanglement witness, one not defined as a separating plane in state space between separable and entangled states, but as a physical process dependent on the local initial properties of the states. Extending work by Partovi, we consider a general entangled multipartite system that allows large reversals of the thermodynamic arrow of time. We describe a hierarchy of arrows that arises from the different correlations allowed in a quantum state and examine these features in the context of Maxwell’s Demon. We examine in detail the case of three qubits, and also propose some simple experimental demonstrations possible with small numbers of qubits.

  8. Genome microsatellite diversity within the Apicomplexa phylum.

    PubMed

    Isaza, Juan Pablo; Alzate, Juan Fernando

    2016-12-01

    The Apicomplexa phylum groups include unicellular and obligate intracellular protozoan parasites with an apical complex used for attachment and invasion to host cells. In this study, we analyze single sequence repeats (SSRs) in the whole genome of 20 apicomplexan organisms that represent four different lineages within the phylum. Only perfect SSRs with at least 12 nucleotides and composed of 2-6 mers were included. To better understand the association of SSR types with the genomic regions, the SSRs were classified accordingly with the genomic location into exon, intron and intergenic categories. Our results showed heterogeneous SSRs density within the studied genomes. However, the most frequent SSRs types were di- and tri-nucleotide repeats. The former was associated with intergenic regions, while the latter was associated with exon regions.

  9. 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.

  10. Decision Making in the Arrow of Time

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  11. 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.

  12. Loiasis: African eye worm.

    PubMed

    Padgett, Jeannie J; Jacobsen, Kathryn H

    2008-10-01

    The filarial parasite Loa loa is transmitted by Chrysops fly bites. Loiasis is endemic in rainforest areas of West and Central Africa, and sporadic cases have also been diagnosed in travellers and migrants. Whilst many infected persons are asymptomatic, microfilariae may be detected in the blood or adult worms may be seen under the skin or the sclera of the eye. Mass treatment programmes for onchocerciasis have raised concern about the risk of severe adverse effects when ivermectin is distributed in areas co-endemic for onchocerciasis and loiasis.

  13. 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.

  14. 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.

  15. WormKill to WormBoss--can we sell sustainable sheep worm control?

    PubMed

    Woodgate, R G; Love, S

    2012-05-04

    Despite the economic importance of nematodes for sheep enterprises, it is often difficult to convince producers to adopt best practice in worm control. In this paper we discuss key issues in effecting change by communicating worm control messages. The adoption of new strategies is affected by many factors including the relative advantage, complexity, compatibility and the ability to trial the proposed change. The visibility of the problem to be solved and proposed positive outcome are also important. Extension campaigns from the last 30 years, including "WormKill" and "CRACK", are used as examples, and future opportunities and tools, including the internet, for promoting best practice in sheep worm management are discussed.

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

    PubMed

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

    2007-03-07

    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.

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

    PubMed

    Hossfeld, B

    1996-12-01

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

  18. 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.

  19. 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.

  20. Suicide using a compound bow and arrow.

    PubMed

    Cina, S J; Radentz, S S; Smialek, J E

    1998-03-01

    Accidental, suicidal, and homicidal injuries have been caused by arrows fired from crossbows. To our knowledge, a case of suicide using a full-size compound bow to fire a projectile has not been reported in the English literature. Described is a case of a 17-year-old man who shot himself in the chest with a broadhead hunting arrow fired from a compound bow. Examination of the footwear suggests that the decedent drew the bowstring with his left foot while holding the bow in his hands. The mechanism of injury is discussed. When dealing with a longbow-related fatality, examination of the weaponry used and reenactment of the fatal methodology are critical in determining whether self-inflicted injury is a probability.

  1. Magnetic charges, inertia, and arrow of time

    NASA Astrophysics Data System (ADS)

    Magnon, Anne M. R.

    1990-02-01

    The prerelativistic concept of inertial mass (as opposed to gravitational mass) is reconsidered in view of a possible relationship between inertia and magnetic (mass) monopoles. Assuming that such “fictitious” (topological) charges could have developed in the chaotic early cosmology, a physical principle is suggested, based on dissipation of topological charges and decoupling of interactions, which could have governed the onset of inertia and of the arrow of time, and controlled the critical balance between mass density and expansion rate in the FRW universe. In view of the recent accomplishments in the detection of Dirac monopoles, a generalization of the Eötvos experiment is proposed which could shed light on the grand unification regime. A comment is given on the issue of relating the psychological and the cosmological arrows of time.

  2. Worms by number.

    PubMed

    Glasby, C J; Glasby, S P; Pleijel, F

    2008-09-22

    This paper investigates alternation patterns in length, shape and orientation of dorsal cirri (fleshy segmental appendages) of phyllodocidans, a large group of polychaete worms (Annelida). We document the alternation patterns in several families of Phyllodocida (Syllidae, Hesionidae, Sigalionidae, Polynoidae, Aphroditidae and Acoetidae) and identify the simple mathematical rule bases that describe the progression of these sequences. Two fundamentally different binary alternation patterns were found on the first four segments: 1011 for nereidiform families and 1010 for aphroditiform families. The alternation pattern in all aphroditiform families matches a simple one-dimensional cellular automaton and that for Syllidae (nereidiform) matches the Fibonacci string sequence. Hesionidae (nereidiform) showed the greatest variation in alternation patterns, but all corresponded to various known substitution rules. Comparison of binary patterns of the first 22 segments using a distance measure supports the current ideas on phylogeny within Phyllodocida. These results suggest that gene(s) involved in post-larval segmental growth employ a switching sequence that corresponds to simple mathematical substitution rules.

  3. Molecular determinants archetypical to the phylum Nematoda

    PubMed Central

    2009-01-01

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

  4. Molecular determinants archetypical to the phylum Nematoda.

    PubMed

    Yin, Yong; Martin, John; Abubucker, Sahar; Wang, Zhengyuan; Wyrwicz, Lucjan; Rychlewski, Leszek; McCarter, James P; Wilson, Richard K; Mitreva, Makedonka

    2009-03-18

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

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

    USDA-ARS?s Scientific Manuscript database

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

  6. Penetrating injury of ascending aorta with arrow in situ.

    PubMed

    Lakhotia, Siddharth; Prakash, Shashi; Singh, Dinesh Kumar; Kumar, Ashok; Panigrahi, Debasish

    2012-04-01

    Penetrating injuries of the aorta are rare and highly lethal; very few patients are able to reach the hospital alive. We report a case of penetrating injury into the ascending aorta with the arrow still in situ, shot by a bow in a tribal region of India. The wound of entry into the aorta was sealed by the arrow itself. The patient came to us walking and supporting the arrow with his left hand. He was operated on, and the arrow was successfully removed from the aorta. Copyright © 2012 The Society of Thoracic Surgeons. Published by Elsevier Inc. All rights reserved.

  7. Quantum voting and violation of Arrow's impossibility theorem

    NASA Astrophysics Data System (ADS)

    Bao, Ning; Yunger Halpern, Nicole

    2017-06-01

    We propose a quantum voting system in the spirit of quantum games such as the quantum prisoner's dilemma. Our scheme enables a constitution to violate a quantum analog of Arrow's impossibility theorem. Arrow's theorem is a claim proved deductively in economics: Every (classical) constitution endowed with three innocuous-seeming properties is a dictatorship. We construct quantum analogs of constitutions, of the properties, and of Arrow's theorem. A quantum version of majority rule, we show, violates this quantum Arrow conjecture. Our voting system allows for tactical-voting strategies reliant on entanglement, interference, and superpositions. This contribution to quantum game theory helps elucidate how quantum phenomena can be harnessed for strategic advantage.

  8. An arrow penetrating at base of the skull successfully removed.

    PubMed

    Misra, Saibal; Anwar, Tarique; Basak, Bijan; Ghosh, Debasish

    2010-03-01

    A 30-year-old male presented with accidental injury with an arrow which referred to us from a peripheral village hospital. It was found that the arrow was penetrating through the nasal bones. An xray skull lateral view showed the tip of the arrow penetrating into the posterior wall of the sphenoid sinus. As the patient had no clinical evidence of neurological or vascular injury, he was immediately operated upon and the arrow was removed. Patient was discharged in good condition and a 3-month follow-up was normal.

  9. On the time arrows, and randomness in cosmological signals

    NASA Astrophysics Data System (ADS)

    Gurzadyan, V. G.; Sargsyan, S.; Yegorian, G.

    2013-09-01

    Arrows of time - thermodynamical, cosmological, electromagnetic, quantum mechanical, psychological - are basic properties of Nature. For a quantum system-bath closed system the de-correlated initial conditions and no-memory (Markovian) dynamics are outlined as necessary conditions for the appearance of the thermodynamical arrow. The emergence of the arrow for the system evolving according to non-unitary dynamics due to the presence of the bath, then, is a result of limited observability, and we conjecture the arrow in the observable Universe as determined by the dark sector acting as a bath. The voids in the large scale matter distribution induce hyperbolicity of the null geodesics, with possible observational consequences.

  10. Dental worm disease.

    PubMed

    Sabbatani, Sergio; Fiorino, Sirio

    2016-12-01

    During human evolution, the period in which groups of humans stopped harvesting fruits and seeds growing wild and introduced the cultivation of cereals as well as the domestication of animals represents a very important event. This circumstance had a considerable impact on human pathocenosis, increasing the risk of infectious diseases of animal origin. The aim of this review was to summarise the archaeological and palaeo-pathological evidence in the literature concerning this topic. Starting from early prehistory (about 1.5 million years ago) up to the historical period, several authors have described the changes in human habits and the consequent changes in food supply, leading to the transition from a protein- to a carbohydrate-rich diet across a broad interval of time. This led to additional problems for human health. The increased accumulation of carbohydrate debris in the odonto-stomatological apparatus, without the appropriate use of hygiene in the oral cavity, increased the risk of infectious disease involving the mouth. Therefore, since the Neolithic period there has been a higher risk of tooth caries, abscesses, deep infection of the teeth roots, reaching also the mandibular and maxillary bone. Several hypotheses have been proposed by the distinct civilizations, which have alternated in the different ages, to explain the cause of these human health problems, including the idea that a "dental worm" could be involved in this process, such as in the Sumerian period. We describe and discuss further modifications of this theory, developed in Egypt, Assyria, Babylon, China, Greece, in Etruscan cities and in Rome in ancient times as well as in the Middle Ages, and the evolution of scientific thought on this topic in the past 300 years. In addition, the results of some palaeo-pathological studies, which were performed on human remains, such as the maxillary bone and teeth, mainly in different geographical areas in Italy, are examined and reported.

  11. 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.

  12. Complete mitochondrial genome sequence of Urechis caupo, a representative of the phylum Echiura

    PubMed Central

    Boore, Jeffrey L

    2004-01-01

    Background Mitochondria contain small genomes that are physically separate from those of nuclei. Their comparison serves as a model system for understanding the processes of genome evolution. Although hundreds of these genome sequences have been reported, the taxonomic sampling is highly biased toward vertebrates and arthropods, with many whole phyla remaining unstudied. This is the first description of a complete mitochondrial genome sequence of a representative of the phylum Echiura, that of the fat innkeeper worm, Urechis caupo. Results This mtDNA is 15,113 nts in length and 62% A+T. It contains the 37 genes that are typical for animal mtDNAs in an arrangement somewhat similar to that of annelid worms. All genes are encoded by the same DNA strand which is rich in A and C relative to the opposite strand. Codons ending with the dinucleotide GG are more frequent than would be expected from apparent mutational biases. The largest non-coding region is only 282 nts long, is 71% A+T, and has potential for secondary structures. Conclusions Urechis caupo mtDNA shares many features with those of the few studied annelids, including the common usage of ATG start codons, unusual among animal mtDNAs, as well as gene arrangements, tRNA structures, and codon usage biases. PMID:15369601

  13. 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.

  14. AlN antiresonant layer ARROW waveguides

    NASA Astrophysics Data System (ADS)

    Pelegrini, M. V.; Carvalho, D. O.; Alayo, M. I.; Pereyra, I.

    2010-02-01

    Aluminum Nitride (AlN) is a wide band gap III-V semiconductor material often used for optical applications due to its transparency and high refractive index. We have produced and characterized AlN thin films by reactive r.f. magnetron sputtering in different Ar-N2 atmospheres in order to verify the best gaseous concentration to be utilized as anti-resonant layer in ARROW waveguides. The corresponding films were characterized by Fourier transform infrared spectroscopy (FTIR), Rutherford backscattering spectroscopy (RBS), Ellipsometry and visible optical absorption. The AlN properties did not varied significantly between the films deposited with 20 and 70 sccm of N2, most of the variations occurred for films deposited with 18 sccm of N2 or below. The film deposited with 20 sccm was selected to be used as the first ARROW layer in the fabricated waveguides. Two routines were used to design the waveguides parameters, the transfer matrix method (TMM) and the semi-vectorial non-uniform finite difference method (NU-FDM). Attenuation as low as 3.5dB/cm was obtained for a 7 μm wide waveguide.

  15. Probability of Intrinsic Time-Arrow from Information Loss

    NASA Astrophysics Data System (ADS)

    Diósi, Lajos

    Time-arrow s=±, intrinsic to a concrete physical system, is associated with the direction of information loss I displayed by the random evolution of the given system. When the information loss tends to zero the intrinsic time-arrow becomes uncertain. We propose the heuristic relationship for the probability of the intrinsic time-arrow. The main parts of the present work are trying to confirm this heuristic equation. The probability of intrinsic time arrow is defined by Bayesian inference from the observed random process. From irreversible thermodynamic systems, the proposed heuristic probabilities follow via the Gallavotti-Cohen relations between time-reversed random processes. In order to explore the underlying microscopic mechanism, a trivial microscopic process is analyzed and an obvious discrepancy is identified. It can be resolved by quantum theory. The corresponding trivial quantum process will exactly confirm the proposed heuristic time-arrow probability.

  16. 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

  17. 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.

  18. SKNy worms and long life.

    PubMed

    Jasper, Heinrich

    2008-03-21

    Interactions between insulin signaling and stress-response pathways can markedly impact life span. In this issue, Tullet et al. (2008) demonstrate that the worm homolog of Nrf2, called SKN-1, a transcription factor that switches on expression of antioxidant genes, is an important component of such signaling interactions.

  19. 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.

  20. 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.

  1. Work-place homicide by bow and arrow.

    PubMed

    Eriksson, A; Georén, B; Oström, M

    2000-07-01

    Arrow wounds represent an unusual class of wounds rarely seen by most forensic pathologists. In this paper we present a case of homicide by bow and arrow and the characteristics of such injuries. The essential characteristics of the lesions obtained from conically-tapered field points and from hunting broadhead tips are described and discussed in relation to injuries caused by firearm bullets. In the present case, three arrows struck the victim, and the order in which the injuries were sustained are analyzed. We also discuss the possibilities of localizing the shooter relative to the victim by analysis of the trajectories.

  2. Worm-like artifacts in exfoliative cytology.

    PubMed

    Martínez-Girón, Rafael; González-López, José Rafael; Esteban, José-Guillermo; García-Miralles, María Teresa; Alvarez-de-los-Heros, Carlos; Ribas-Barceló, Andrés

    2006-09-01

    The presence of worms in cytological smears is occasionally reported, although various other structures exist that may be confused with such parasites. We present eight worm-like artifacts observed in routine Papanicolaou smears. Recognition of these structures is important to avoid overvaluation or confusion with true worms. (c) 2006 Wiley-Liss, Inc.

  3. 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)

  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. 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…

  6. 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,…

  7. 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…

  8. Synthetic Minor NSR Permit: Arrow Pipeline, LLC - Station #7

    EPA Pesticide Factsheets

    This page contains the administratively revised synthetic minor permit to construct for the Arrow Pipeline, LLC, Station #7, located within the exterior boundaries of the Fort Berthold Indian Reservation in Dunn County, North Dakota.

  9. Clinical reliability of the "furcation arrow" as a diagnostic marker.

    PubMed

    Deas, David E; Moritz, Alan J; Mealey, Brian L; McDonnell, Howard T; Powell, Charles A

    2006-08-01

    The radiographic entity known as the "furcation arrow" has long been used in practice even though little is known about its usefulness as a clinical indicator. The definitive study of the furcation arrow suggests that its presence on a radiograph reliably predicts furcation invasion, but this has not been confirmed in an in vivo investigation. The purpose of this study was to evaluate the furcation arrow in a clinical setting, testing the assertion that the furcation arrow image is an accurate predictor of furcation invasion. Specifically, we sought to determine the following. First, what is the prevalence of furcation arrow images in the radiographs of maxillary molars with periodontitis? Second, what is the interexaminer agreement on what constitutes a furcation arrow? Third, how does the presence or absence of a furcation arrow correlate with the true clinical status of the furcation? Fourth, what is the sensitivity and specificity of the furcation arrow as a diagnostic indicator? Eighty-nine patients requiring surgical treatment of periodontitis in the maxillary molar regions were included in this study. Before surgery, one of five calibrated examiners viewed periapical and bitewing radiographs of the surgical site and recorded the presence or absence of a furcation arrow at each proximal furcation. Before administering anesthesia, the same examiner recorded a Hamp index value of each proximal furcation, with a second Hamp index taken after flap reflection and debridement. After surgery, each of the four remaining examiners independently reviewed the radiographs for furcation arrows. Descriptive statistical analysis was performed to correlate the appearance of the furcation arrow image to the actual degree of furcation invasion as determined by the intrasurgical Hamp index. A total of 164 maxillary molars were examined, providing 328 interproximal furcations; 111 (33.8%) furcations were determined at surgical debridement to have a furcation invasion of Hamp

  10. 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.

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

    SciTech Connect

    HEARD, F.J.

    2000-02-10

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

  12. Relation between the psychological and thermodynamic arrows of time

    NASA Astrophysics Data System (ADS)

    Mlodinow, Leonard; Brun, Todd A.

    2014-05-01

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

  13. The arrow of time and the expansion of the universe

    NASA Astrophysics Data System (ADS)

    Qadir, Asghar

    1987-04-01

    It is pointed out that a model used to test any suggestion regarding the arrow of time in a cosmological contect, must have sufficient complexity. The clain of Zeh that the arrow of time defined by a universal wavefunction does not permit a reversal of cosmic expansion to be observed, is refuted on these grounds. On leave from the Department of Mathematics, Quaid-i-Azam University, Islamabad, Pakistan.

  14. 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.

  15. Arrow wounds: major stimulus in the history of surgery.

    PubMed

    Karger, B; Sudhues, H; Brinkmann, B

    2001-12-01

    To illustrate how the high incidence of arrow wounds provided a major stimulus for the development of surgery until a century ago, we conducted a literature search. Our research shows that archaic peoples developed considerable surgical skill for extraction of arrows, including thoracotomy and trephination. A classical Hindu veda describes a variety of extraction methods, and Homer's Iliad introduces the term iatros, which means "he who extracts arrows." Hippocrates of Kos and Galen, representatives of the humoral doctrine, both shunned surgical intervention and considered purulence a drainage of materia peccans (spoiled humors). Cornelius Celsus was the first to systematically differentiate removal of arrows per extractionem and per expulsionem. Celsus recommended the spoon of Diocles, an ancient surgical instrument specially designed for extraction of arrows. Paulus of Aegina favored rapid extraction, aggressive therapy, and ligature on both sides of a vessel before extraction efforts. Paulus was the first to describe a special instrument for the removal of detached arrowheads per expulsionem (propulsorium). In medieval Europe, the standard of surgery declined drastically. The classical procedure under the dominant influence of the humoral concept was to await pus before extraction and to burn the wound with boiling oil and a branding iron. Arab authors had conserved the knowledge of Celsus and Paulus, and in Europe a renewal was achieved by Ambroise Paré, who has been called the creator of modern surgery. The incidence of arrow wounds increased once more in the American West. Joseph H. Bill, a famous U.S. Army Surgeon preoccupied with arrow wounds, favored rapid extraction and aggressive therapy, and he taught recruits not to apply traction on the shaft. The principles established by Celsus, Paulus, Paré, and Bill not only mark important landmarks in the evolution of surgery but can also serve as the basis for modern treatment of arrow wounds, which still

  16. 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].

  17. India eradicates guinea worm disease.

    PubMed

    Sharma, R

    2000-03-11

    The WHO officially certifies India and other countries of the South East Asian regions as free of guinea worm disease. The eradication was made possible through the efforts of the Indian government to launch a national guinea worm eradication program in 1983-84, and a sustained campaign at the grass-roots level by agencies such as the UN International Children's Fund and the WHO in collaboration with the government. The recognition was based on the report gathered by three members of the 4th International Commission for Certification of Dracunculiasis Eradication, who visited India in November 1999 and conducted an investigation in 62 villages in 5 states where the disease had been endemic. Also, the national eradication program had been evaluated 7 times and showed remarkable achievement.

  18. Research on flight stability of non rotating fin arrow shaft

    NASA Astrophysics Data System (ADS)

    Guo, Yachao; He, Guanglin; Zhang, Jiashuo

    2017-09-01

    To research the influence of the variable density fin arrow shaft warhead on flight stability, three different structures of non rotating fin arrow shaft warhead of the individual small caliber cluster arrow projectile is put forward and designed. The aerodynamic characteristics, static stability reserve and the change of the attack angle in the fin arrow shaft warhead are calculated and analyzed through using the static stability reserve theory and the rigid body trajectory equations. The results show that the static stability reserve of the variable density steel-aluminum composite fin arrow shaft warhead is about 21% ~ 27%, which is obviously higher than 13% ~ 17% of the single density steel material. When the initial velocity is 280 m/s and range is 100 m, the attack angle of the fin arrow shaft warhead of variable density and single density are reduced from ± 5 degree to within ± 1 degree.It is indicated that dynamic stability is guaranteed; however, dynamic stability of the former is better than that of the latter according to the decay rate of the attack angle.

  19. 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.

  20. Better security levels for broken arrows

    NASA Astrophysics Data System (ADS)

    Xie, Fuchun; Furon, Teddy; Fontaine, Caroline

    2010-01-01

    This paper deals with the security of the robust zero-bit watermarking technique "Broken Arrows" (BA),1 which was invented and tested for the international challenge BOWS-2.2 The results of the first episode of the challenge showed that BA is very robust and we proposed last year an enhancement called "Averaging Wavelet Coefficients" (AWC),3 which further strengthens the robustness against the worst attack disclosed during this BOWS-2's first episode.4 However, in the second and third episodes of the challenge, during which the pirates could observe plenty of pictures watermarked with the same secret key, security flaws have been revealed and discussed.5 Here we propose counterattacks to these security flaws, investigating BA and its variant AWC. We propose two counterattack directions: to use the embedding technique AWC instead of BA, and to regulate the system parameters to lighten the watermarking embedding footprint. We also discuss these directions in the context of traitor tracing.6 Experimental results show that following these recommendations is sufficient to counter these attacks.

  1. Electrodynamic arrow of time and cosmology

    NASA Astrophysics Data System (ADS)

    Radecke, Hans-Dieter

    Simplified mathematical models were used for the examination of the relationship between the arrows of time of electrodynamics and cosmology. The model of a 1-D harmonic oscillator, coupled to a scalar field, was first used. The combined system of coupled differential equations could be exactly resolved and allowed an examination of the field solution type, with regard to retard and advance in the framework of the cosmological geometry of the standard model, by which a closed universe was taken as a basis. It was shown that the oscillation radiation was clearly retarded at the big bang, and clearly advanced at the final explosion. In order to interpolate between these asymptotical boundary values, it was necessary to consider the radiation absorption of the cosmical medium. The general behavior of the considered system solutions showed that only the retarded radiation prevailed at big bang. Because of the cosmical absorption, its amplitude was completely attenuated to zero, before the universe heat death was installed. The advanced field amplitude is to be preceived after the universe contraction beginning and swings to a maximal value which is reached at the final explosion.

  2. 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.

  3. 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.

  4. 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. Copyright © 2013 Elsevier B.V. All rights reserved.

  5. Description of 'Synergistetes' phyl. nov. and emended description of the phylum 'Deferribacteres' and of the family Syntrophomonadaceae, phylum 'Firmicutes'.

    PubMed

    Jumas-Bilak, Estelle; Roudière, Laurent; Marchandin, Hélène

    2009-05-01

    The number of bacterial phyla has greatly increased in the past decade. Among them, a candidate division named 'Synergistes' was proposed in a phylogenetic study on the global diversity of bacteria. We previously described the genus Jonquetella and suggested that it belonged to this not yet well-delineated candidate phylum. 16S rRNA gene based-phylogeny studies were conducted using four reconstruction methods and 599 sequences forming five datasets were used in an alternative treeing approach. These analyses indicated that the genera Aminiphilus, Aminobacterium, Aminomonas, Anaerobaculum, Dethiosulfovibrio, Jonquetella, Synergistes, Thermanaerovibrio and Thermovirga should be grouped in the same high-level taxon. This taxon was shown to be a phylum-rank lineage in the domain Bacteria and, because of the prior use of the name Synergistes for a genus, the name 'Synergistetes' is proposed for this candidate phylum. We also propose an emended delineation of the phylum 'Deferribacteres', which is now only represented by the family Deferribacteriaceae. The emended family Syntrophomonadaceae is limited to the genera Pelospora, Syntrophomonas, Syntrophothermus and Thermosyntropha.

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

    PubMed Central

    Bejan, Adrian

    2014-01-01

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

  7. 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.

  8. Gaze and arrow distractors influence saccade trajectories similarly.

    PubMed

    Hermens, Frouke; Walker, Robin

    2010-11-01

    Perceiving someone's averted eye-gaze is thought to result in an automatic shift of attention and in the preparation of an oculomotor response in the direction of perceived gaze. Although gaze cues have been regarded as being special in this respect, recent studies have found evidence for automatic attention shifts with nonsocial stimuli, such as arrow cues. Here, we directly compared the effects of social and nonsocial cues on eye movement preparation by examining the modulation of saccade trajectories made in the presence of eye-gaze, arrows, or peripheral distractors. At a short stimulus onset asynchrony (SOA) between the distractor and the target, saccades deviated towards the direction of centrally presented arrow distractors, but away from the peripheral distractors. No significant trajectory deviations were found for gaze distractors. At the longer SOA, saccades deviated away from the direction of the distractor for all three distractor types, but deviations were smaller for the centrally presented gaze and arrow distractors. These effects were independent of whether line-drawings or photos of faces were used and could not be explained by differences in the spatial properties of the peripheral distractor. The results suggest that all three types of distractors (gaze, arrow, peripheral) can induce the automatic programming of an eye movement. Moreover, the findings suggest that gaze and arrow distractors affect oculomotor preparation similarly, whereas peripheral distractors, which are classically regarded as eliciting an automatic shift of attention and an oculomotor response, induce a stronger and faster acting influence on response preparation and the corresponding inhibition of that response.

  9. Silicon-based dual ARROW power splitters with remote coupling.

    PubMed

    Hsu, Hsin-Feng; Hsu, Ming-Shun; Lu, Ming-Feng; Huang, Yang-Tung

    2015-03-10

    In this research, Si-based power splitters based on dual antiresonant reflecting optical waveguides (ARROW) with remote coupling by a separation distance of 30 μm were designed and realized. Characterization of the power splitters with different lengths of the coupling region was performed. Measurement characteristics of fabricated devices with the propagation losses lower than 1.90 dB/cm and the imbalances lower than 0.60 dB show that our dual ARROW power splitters can be efficiently realized.

  10. 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…

  11. 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…

  12. Intraocular live male filarial Loa loa worm.

    PubMed

    Eballe, André Omgbwa; Epée, Emillienne; Koki, Godefroy; Owono, Didier; Mvogo, Côme Ebana; Bella, Assumpta Lucienne

    2008-12-01

    We report a case of Loa loa filariasis in an 8-month-old child who presented with a 3-month history of irritated acute red eye and insomnia. Examination revealed a living and active adult Loa loa worm in the anterior chamber of the left eye. The worm was extracted under general anesthetic.

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

    NASA Astrophysics Data System (ADS)

    Savitt, S. F.

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

  14. The Effect of Arrow Mass and Shape on Penetration into a Target

    NASA Astrophysics Data System (ADS)

    Shyam, S.; Gurram, A.; Madireddy, S.

    2016-12-01

    We conducted an archery experiment in order to quantify how aerodynamic design impacted the depth of arrow impact. Research shows that the smaller the surface area of an object, the more easily it travels through the air and the deeper it penetrates a target (Benson 2014). Momentum also affects how far and fast the arrow will go and therefore, how deep it will penetrate into the target. Therefore, a combination of an arrow with greater momentum and better aerodynamics will help the arrow fly faster and penetrate the target deeper. Mass, velocity, momentum, acceleration, force, and drag are the factors that acted on our experiment and produced its results. We hypothesized that the arrow with a thin shaft and pointed arrowhead would penetrate deepest, as opposed to both arrows with no arrowheads or arrows with thick shafts and blunt arrowheads. We tested our hypothesis by having a well-trained archer shoot different types of arrows into a target. We used arrows with shaft lengths of 7 cm and 5.3 cm, coupled with either pointed, blunt, or no arrowhead. We measured the time to target and arrow penetration (in cm) to see which style reached the target the fastest and penetrated the deepest. The results demonstrated that arrows with thin shafts and pointed arrowheads penetrated our target the deepest, followed by arrows with thick shafts and blunt arrowheads. Arrows with thin shafts and blunt arrowheads came after, and arrows with thick shafts and pointed arrowheads came last in depth of penetration. The arrows with no arrowheads either barely penetrated the target, or bounced back. We were able to conclude that the thinner the shaft and the more pointed the arrowhead, the better the arrow cuts the air. This is because, according to the principles of aerodynamics, it creates less drag since the surface area is smaller. However, mass also plays an important role in force through momentum, which also significantly affected our results.

  15. Worms and Humans: A Happy Divorce?

    PubMed Central

    Akuffo, Hannah; Britton, Sven; Schön, Thomas

    2017-01-01

    Chronic asymptomatic worm infection, often in combination with tuberculosis (TB), is common in low-income countries. Indeed, a life without worm infestation, as is now the case in most high-income countries, is a recent condition for humankind. Worms and Mycobacterium tuberculosis give rise to different immune response patterns (Th2 vs. Th1 driven), and we have studied whether chronic worm infection affects the susceptibility to and control of TB in the low income country of Ethiopia. Our results, as well of those in the general literature, are inconclusive, although we have some rather strong data in support of adult deworming in relation to vaccination with bacillus Calmette-Guérin (BCG) against TB. In addition, we discuss briefly the putative relationship between chronic worm infestation and autoimmunity/allergy.

  16. Worms and Humans: A Happy Divorce?

    PubMed

    Akuffo, Hannah; Britton, Sven; Schön, Thomas

    2015-01-01

    Chronic asymptomatic worm infection, often in combination with tuberculosis (TB), is common in low-income countries. Indeed, a life without worm infestation, as is now the case in most high-income countries, is a recent condition for humankind. Worms and Mycobacterium tuberculosis give rise to different immune response patterns (Th2 vs. Th1 driven), and we have studied whether chronic worm infection affects the susceptibility to and control of TB in the low income country of Ethiopia. Our results, as well of those in the general literature, are inconclusive, although we have some rather strong data in support of adult deworming in relation to vaccination with bacillus Calmette-Guérin (BCG) against TB. In addition, we discuss briefly the putative relationship between chronic worm infestation and autoimmunity/allergy.

  17. Global eradication of Guinea worm.

    PubMed

    Periès, H; Cairncross, S

    1997-11-01

    Little more than a decade ago, it was estimated that over three million cases of dracunculiasis occurred worldwide. Since then, the numbers have fallen dramatically, thanks to the water supply initiatives of the 1980s and, more recently, the national guinea worm eradication programmes implemented in a score of endemic countries. Hervé Periès and Sandy Cairncross discuss how eradication will require the containment of cases in the remaining endemic areas, together with the simultaneous strengthening of surveillance to permit the certification of eradication. This aim requires existing strategies to be adapted to maintain their efficacy and also to improve their sustainability and cost-effectiveness. Sudan with its civil war, and more than a hundred thousand reported cases, remains a major obstacle to rapid achievement of the goal.

  18. 26 CFR 48.4161(b)-1 - Imposition and rates of tax; bows and arrows.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 26 Internal Revenue 16 2011-04-01 2011-04-01 false Imposition and rates of tax; bows and arrows... § 48.4161(b)-1 Imposition and rates of tax; bows and arrows. (a) Imposition of tax. Section 4161(b...) Any bow that has a draw weight of 10 pounds or more; (2) Any arrow that measures 18 inches overall or...

  19. 26 CFR 48.4161(b)-1 - Imposition and rates of tax; bows and arrows.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 26 Internal Revenue 16 2013-04-01 2013-04-01 false Imposition and rates of tax; bows and arrows... § 48.4161(b)-1 Imposition and rates of tax; bows and arrows. (a) Imposition of tax. Section 4161(b...) Any bow that has a draw weight of 10 pounds or more; (2) Any arrow that measures 18 inches overall or...

  20. 26 CFR 48.4161(b)-1 - Imposition and rates of tax; bows and arrows.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 26 Internal Revenue 16 2012-04-01 2012-04-01 false Imposition and rates of tax; bows and arrows... § 48.4161(b)-1 Imposition and rates of tax; bows and arrows. (a) Imposition of tax. Section 4161(b...) Any bow that has a draw weight of 10 pounds or more; (2) Any arrow that measures 18 inches overall or...

  1. 26 CFR 48.4161(b)-1 - Imposition and rates of tax; bows and arrows.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 26 Internal Revenue 16 2010-04-01 2010-04-01 true Imposition and rates of tax; bows and arrows. 48... Imposition and rates of tax; bows and arrows. (a) Imposition of tax. Section 4161(b) imposes a tax on the... a draw weight of 10 pounds or more; (2) Any arrow that measures 18 inches overall or more in length...

  2. Cystic hematoma formation following use of a biodegradable arrow for meniscal repair.

    PubMed

    Hechtman, K S; Uribe, J W

    1999-03-01

    This is a case report of a cystic hematoma formation following the use of a biodegradable arrow for repair of a medial meniscus tear. A literature search found no previous report of this complication. Open hematoma debridement and arrow removal were effective in the treatment of this complication following all-inside meniscal repair with a biodegradable arrow.

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. Phylogenetic analyses of phylum Actinobacteria based on whole genome sequences.

    PubMed

    Verma, Mansi; Lal, Devi; Kaur, Jaspreet; Saxena, Anjali; Kaur, Jasvinder; Anand, Shailly; Lal, Rup

    2013-09-01

    Actinobacteria constitute one of the largest and ancient taxonomic phylum within the domain bacteria and are well known for their secondary metabolites. Considerable variation in the metabolic properties, genome size and GC content of the members of this phylum has been observed. Therefore, the placement of new or existing species based on 16S rRNA gene sometimes becomes problematic due to the low congruence level. In the present study, phylogeny of ninety actinobacterial genomes was reconstructed using single gene and whole genome based data. Where alignment-free phylogenetic method was found to be more robust, the concatenation of 94 proteins improved the resolution which all single gene based phylogenies failed to resolve. The comprehensive analysis of 94 conserved proteins resulted in a total of 42,447 informative sites, which is so far the largest meta-alignment obtained for this phylum. But the ultimate resolved phylogeny was obtained by generating a consensus tree by combining the information from single gene and genome based phylogenies. The present investigation clearly revealed that the consensus approach is a useful tool for phylogenetic inference and the taxonomic affiliations must be based on this approach. The consensus approach suggested that there is a need for taxonomic amendments of the orders Frankiales and Micrococcales.

  8. Mobile genetic elements in the bacterial phylum Acidobacteria.

    PubMed

    Challacombe, Jean; Kuske, Cheryl

    2012-07-01

    Analysis of the genome of Candidatus Solibacter usitatus Ellin6076, a member of the phylum Acidobacteria, revealed a large number of genes associated with mobile genetic elements. These genes encoded transposases, insertion sequence elements and phage integrases. When the amino acid sequences of the mobile element-associated genes were compared, many of them had high (90-100%) amino acid sequence identities, suggesting that these genes may have recently duplicated and dispersed throughout the genome. Although phage integrase encoding genes were prevalent in the Can. S. usitatus Ellin6076 genome, no intact prophage regions were found. This suggests that the Can. S. usitatus Ellin6076 large genome arose by horizontal gene transfer via ancient bacteriophage and/or plasmid-mediated transduction, followed by widespread small-scale gene duplications, resulting in an increased number of paralogs encoding traits that could provide selective metabolic, defensive and regulatory advantages in the soil environment. Here we examine the mobile element repertoire of Can. S. usitatus Ellin6076 in comparison to other genomes from the Acidobacteria phylum, reviewing published studies and contributing some new analyses. We also discuss the presence and potential roles of mobile elements in members of this phylum that inhabit a variety of environments.

  9. Multivacuum initial conditions and the arrow of time

    NASA Astrophysics Data System (ADS)

    Bousso, Raphael; Zukowski, Claire

    2013-05-01

    Depending on the type and arrangement of metastable vacua in the theory, initial conditions in a de Sitter vacuum with arbitrarily large entropy can be compatible with the observed arrow of time, if the causal patch or related measures are used to regulate divergences. An important condition, however, is that the initial vacuum cannot produce observers from rare fluctuations (Boltzmann brains). Here we consider more general initial conditions where multiple vacua have nonzero initial probability. We examine whether the prediction of an arrow of time is destroyed by a small initial admixture of vacua that can produce Boltzmann brains. We identify general criteria and apply them to two nontrivial examples of such initial probability distributions. The Hartle-Hawking state is superexponentially dominated by the vacuum with smallest positive cosmological constant, so one might expect that other initial vacua can be neglected; but in fact, their inclusion drastically narrows the range of theory parameters for which an arrow of time is predicted. The dominant eigenvector of the global rate equation of eternal inflation is dominated by the longest-lived metastable vacuum. If an arrow of time emerges in the single-initial-vacuum approximation, then we find that this conclusion survives the admixture of other initial vacua. By global-local measure duality, this result amounts to a successful consistency test of certain global cutoffs, including light-cone time and scale-factor time.

  10. 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.

  11. 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…

  12. 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]…

  13. 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]…

  14. 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…

  15. 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

  16. 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.

  17. 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.

  18. An introduction to worm lab: from culturing worms to mutagenesis.

    PubMed

    Chaudhuri, Jyotiska; Parihar, Manish; Pires-daSilva, Andre

    2011-01-11

    This protocol describes procedures to maintain nematodes in the laboratory and how to mutagenize them using two alternative methods: ethyl methane sulfonate (EMS) and 4, 5', 8-trimethylpsoralen combined with ultraviolet light (TMP/UV). Nematodes are powerful biological systems for genetics studies because of their simple body plan and mating system, which is composed of self-fertilizing hermaphrodites and males that can generate hundreds of progeny per animal. Nematodes are maintained in agar plates containing a lawn of bacteria and can be easily transferred from one plate to another using a pick. EMS is an alkylating agent commonly used to induce point mutations and small deletions, while TMP/UV mainly induces deletions. Depending on the species of nematode being used, concentrations of EMS and TMP will have to be optimized. To isolate recessive mutations of the nematode Pristionchus pacificus, animals of the F2 generation were visually screened for phenotypes. To illustrate these methods, we mutagenized worms and looked for Uncoordinated (Unc), Dumpy (Dpy) and Transformer (Tra) mutants.

  19. Cupid's Arrow: An Innovative Nanosat to Sample Venus' Upper Atmosphere

    NASA Technical Reports Server (NTRS)

    Bienstock, Bernie; Darrach, Murray; Madzunkov, Stojan; Sotin, Christophe

    2016-01-01

    In NASA's Discovery 2014 AO, the opportunity to propose a Technology Demonstration Opportunity (TDO) to enhance the primary mission was specified. For the Venus Emissivity, Radio Science, InSAR, Topography, and Spectroscopy (VERITAS) mission, we elected to include the Cupid's Arrow nanosat TDO to sample and measure the abundances of noble gases and their isotopic ratios in Venus's upper atmosphere below the homopause. This paper will provide a basic overview of the VERITAS mission, with a focus on the Cupid's Arrow concept including a description of the mission, spacecraft design, and JPL's quadrupole ion trap mass spectrometer (QITMS) instrument specifications and design. In previous planetary entry probe mission designs, particularly at Venus, engineers w ere focused on entry and descent. A landed probe was also proposed for the New Frontiers SAGE mission. For Cupid's Arrow, the nanosat is designed to skim through the upper atmosphere, just below the homopause, in order to sample the atmosphere, perform the analysis, and then exit the atmosphere to transmit its data to the orbiting VERITAS spacecraft. Cupid's Arrow is a compelling addition to the VERITAS geology mission. A key missing link in our understanding of Venus' evolution is the noble gas abundances and their isotopic ratios. Not since Pioneer Venus have these measurements been made in the Venus atmosphere and never in the upper atmosphere, just below the homopause, to the degree of accuracy that will be accomplished by VERITAS' Cupid's Arrow nanosat.Such measurements were ranked as the number 1 investigation of the number 1 objective of the goal "Atmospheric Formation, Evolution, and Climate History ".

  20. Measurement of the. pi. sup + r arrow e sup +. nu. branching ratio

    SciTech Connect

    Britton, D.I.; Ahmad, S.; Bryman, D.A.; Burnham, R.A.; Clifford, E.T.H.; Kitching, P.; Kuno, Y.; Macdonald, J.A.; Numao, T.; Olin, A.; Poutissou, J. ); Dixit, M.S. )

    1992-05-18

    A new measurement of the {pi}{sup +}{r arrow}{ital e}{sup +}{nu} branching ratio gives {ital R}{sub {pi}{ital e}{nu}}={Gamma}({pi}{r arrow}{ital e}{nu}+{pi}{r arrow}{ital e}{nu}{gamma})/{Gamma} ({pi}{r arrow}{mu}{nu}+{pi}{r arrow}{mu}{nu}{gamma}) =(1.2265{plus minus}0.0034(stat){plus minus}0.0044(sys)){times}10{sup {minus}4}. This result is in agreement with standard model calculations and confirms the hypothesis of electron-muon universality at the 0.2% level.

  1. 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.

  2. 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.

  3. WDDD: Worm Developmental Dynamics Database

    PubMed Central

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

    2013-01-01

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

  4. Where are we on worms?

    PubMed Central

    Elliott, David E.; Weinstock, Joel V

    2013-01-01

    Purpose of Review There is something about living in an industrialized country that dramatically increases the risk of acquiring inflammatory bowel disease. Loss of routine exposure to parasitic worms (helminths), due to modern highly hygienic life styles, likely contributes to this risk. This article reviews current understanding on how helminths influence intestinal inflammation and mucosal immune responses. Recent findings IBD emerges in populations as regions develop socioeconomically and loose exposure to previously ubiquitous helminthic infections. Helminthic infections provided strong selective pressure for the dissemination of gene variants, many of which predispose to development of IBD. In animal models of IBD, helminth colonization suppresses intestinal inflammation through multiple mechanisms including induction of innate and adaptive regulatory circuits. Trials using helminths like hookworm (Necator americanus) or porcine whipworm (Trichuris suis) show that they are safe and may be effective therapies for the control of the aberrant intestinal inflammation seen in Crohn’s disease and ulcerative colitis. Summary Evidence is accumulating that highly hygienic living conditions create risk for developing immune-mediated disease such as IBD. To live in their host, helminths have developed the ability to activate cells of innate and adaptive immunity that suppress inflammation. Therapeutic trials using helminths are in progress. PMID:23079675

  5. Where are we on worms?

    PubMed

    Elliott, David E; Weinstock, Joel V

    2012-11-01

    There is something about living in an industrialized country that dramatically increases the risk of acquiring inflammatory bowel disease (IBD). Loss of routine exposure to parasitic worms (helminths), due to modern highly hygienic life styles, likely contributes to this risk. This article reviews current understanding on how helminths influence intestinal inflammation and mucosal immune responses. IBD emerges in populations as regions develop socioeconomically and lose exposure to previously ubiquitous helminthic infections. Helminthic infections provided strong selective pressure for the dissemination of gene variants, many of which predispose to development of IBD. In animal models of IBD, helminth colonization suppresses intestinal inflammation through multiple mechanisms including induction of innate and adaptive regulatory circuits. Trials using helminths like hookworm (Necator americanus) or porcine whipworm (Trichuris suis) show that they are safe and may be effective therapies for the control of the aberrant intestinal inflammation seen in Crohn's disease and ulcerative colitis. Evidence is accumulating that highly hygienic living conditions create risk for developing immune-mediated disease such as IBD. To live in their host, helminths have developed the ability to activate cells of innate and adaptive immunity that suppress inflammation. Therapeutic trials using helminths are in progress.

  6. WDDD: Worm Developmental Dynamics Database.

    PubMed

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

    2013-01-01

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

  7. 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.

  8. Do 'Early Birds' Get the Healthier Worm?

    MedlinePlus

    ... medlineplus.gov/news/fullstory_163902.html Do 'Early Birds' Get the Healthier Worm? Late-to-bed types ... 2017 FRIDAY, March 3, 2017 (HealthDay News) -- Early birds may have a leg up over night owls ...

  9. Assessment of worm gearing for helicopter transmissions

    NASA Technical Reports Server (NTRS)

    Chaiko, Lev

    1990-01-01

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

  10. 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.

  11. Optimal design for an end face engagement worm gear with multiple worm-wheel meshing

    NASA Astrophysics Data System (ADS)

    Deng, Xingqiao; Zhu, Weibing; Chen, Yonghong; Chen, Shouan; Wang, Jinge

    2017-01-01

    To solve the problem for lacking a special mechanical transmission that could provide multiple outputs with high transmission efficiency and good lubrication in the modern industrial, a novel worm gear, named end face engagement worm gear, with multiple worm-wheel meshing is proposed for the first time. The essential parameters for the worm gear are optimized to enhance lubrication and meshing properties. Moreover, analysis of variance(ANOVA) is applied to determine the optimum levels and to determine the influence of parameters. The ANOVA results show that the novel end face engagement worm gear with multiple worm wheels provides high lubrication(the lubrication angle is more than 89°) and meshing performance(the induce normal curvature is less than 0.0002 mm-1). The interaction between center distance and roller slant distance most strongly influences the lubrication angle(contributed 51.6%), followed by the parameters of center distance(contributed 25.0%), roller slant distance(contributed 16.4%), tooth angle of gear, gear ratio, and roller radius. In addition, roller radius most strongly influences the induced normal curvature(contributed 39.4%), followed by roller slant distance(contributed 15.2%), tooth angle of the gear(contributed 9.0%), center distance, and gear ratio. The proposed worm gear helps to enrich the no-backlash high precision worm drive and the optimal design method can provide a useful reference on performance improvement of other worm gear.

  12. 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

  13. Mesophilic Crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota.

    PubMed

    Brochier-Armanet, Céline; Boussau, Bastien; Gribaldo, Simonetta; Forterre, Patrick

    2008-03-01

    The archaeal domain is currently divided into two major phyla, the Euryarchaeota and Crenarchaeota. During the past few years, diverse groups of uncultivated mesophilic archaea have been discovered and affiliated with the Crenarchaeota. It was recently recognized that these archaea have a major role in geochemical cycles. Based on the first genome sequence of a crenarchaeote, Cenarchaeum symbiosum, we show that these mesophilic archaea are different from hyperthermophilic Crenarchaeota and branch deeper than was previously assumed. Our results indicate that C. symbiosum and its relatives are not Crenarchaeota, but should be considered as a third archaeal phylum, which we propose to name Thaumarchaeota (from the Greek 'thaumas', meaning wonder).

  14. [Research progress on mitochondrial genome structure in the phylum apicomplexa].

    PubMed

    Li, Xue-mei; Li, Xiao-bing; Huang, Wei

    2014-10-01

    Mitochondria are ubiquitous organelles in all eukaryotic cells which are essential for a series of cellular processes and signal transduction. The phylum Apicomplexa includes series of unicellular eukaryotes and some of them are clinically or economically important parasites. Recent studies have demonstrated that apicomplexan parasites' mitochondrial genomes exhibit remarkably diverse structures and they are ideal biological models to comprehend the evolution of mitochondrial genomes. This paper summarizes the mitochondrial genome structure of some representative apicomplexan, highlights their structure characteristics along with evolution process, and briefly describes their nuclear mitochondrial DNA and nuclear plastid DNA.

  15. Damped Arrow-Hurwicz algorithm for sphere packing

    NASA Astrophysics Data System (ADS)

    Degond, Pierre; Ferreira, Marina A.; Motsch, Sebastien

    2017-03-01

    We consider algorithms that, from an arbitrarily sampling of N spheres (possibly overlapping), find a close packed configuration without overlapping. These problems can be formulated as minimization problems with non-convex constraints. For such packing problems, we observe that the classical iterative Arrow-Hurwicz algorithm does not converge. We derive a novel algorithm from a multi-step variant of the Arrow-Hurwicz scheme with damping. We compare this algorithm with classical algorithms belonging to the class of linearly constrained Lagrangian methods and show that it performs better. We provide an analysis of the convergence of these algorithms in the simple case of two spheres in one spatial dimension. Finally, we investigate the behaviour of our algorithm when the number of spheres is large in two and three spatial dimensions.

  16. 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.

  17. Recent developments in the field of arrow and dart poisons.

    PubMed

    Philippe, Geneviève; Angenot, Luc

    2005-08-22

    Arrow and dart poisons, considered as conventional natural sources for future drug discovery, have already provided numerous biologically active molecules used as drugs in therapeutic applications or in pharmacological research. Plants containing alkaloids or cardiotonic glycosides have generally been the main ingredients responsible for the efficacy of these poisons, although some animals, such as frogs, have also been employed. This paper, without being exhaustive, reports the greater strides made during the past 15 years in the understanding of the chemical nature and biological properties of arrow and dart poison constituents. Examples both of promising biological properties shown by these molecules and of crucial discoveries achieved by their use as pharmacological tools are given. Further studies of these toxic principles are likely to enable scientists to find new valuable lead compounds, useful in many fields of research, like oncology, inflammation and infectious diseases.

  18. [ital b][r arrow][ital s][gamma] and [ital Z][r arrow][ital b[bar b

    SciTech Connect

    Park, G.T. Astroparticle Physics Group, Houston Advanced Research Center , The Woodlands, Texas 77381 )

    1994-07-01

    We perform a combined analysis of two stringent constraints on the two Higgs doublet model: one coming from the recently announced CLEO II bound on [ital B]([ital b][r arrow][ital s][gamma]) and the other from the recent CERN LEP data on the ratio [Gamma]([ital Z][r arrow][ital b[bar b

  19. 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.

  20. Emergence of randomness and arrow of time in quantum walks

    SciTech Connect

    Shikano, Yutaka; Chisaki, Kota; Konno, Norio; Segawa, Etsuo

    2010-06-15

    Quantum walks are powerful tools not only for constructing the quantum speedup algorithms but also for describing specific models in physical processes. Furthermore, the discrete time quantum walk has been experimentally realized in various setups. We apply the concept of the quantum walk to the problems in quantum foundations. We show that randomness and the arrow of time in the quantum walk gradually emerge by periodic projective measurements from the mathematically obtained limit distribution under the time-scale transformation.

  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.

  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. Observation of large oscillator strengths for both 1 r arrow 2 and 1 r arrow 3 intersubband transitions of step quantum wells

    SciTech Connect

    Mii, Y.J.; Wang, K.L.; Karunasiri, R.P.G.; Yuh, P.F. )

    1990-03-12

    Both 1{r arrow}2 and 1{r arrow}3 intersubband transitions have been observed in a step quantum well structure consisting of 60 A GaAs wells, 90 A Al{sub 0.18}Ga{sub 0.82}As steps, and 280 A Al{sub 0.44}Ga{sub 0.56}As barriers. The transition energy and oscillator strength are 112 meV and 0.23 for the 1{r arrow}2 transition and 150 meV and 0.15 for the 1{r arrow}3 transition, respectively. The asymmetric property of a step quantum well allows the normally forbidden 1{r arrow}3 transition to occur. The relaxation of the selection rule suggests a possibility of using optical pumping for infrared laser applications.

  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. 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.

  6. Chordate evolution and the three-phylum system.

    PubMed

    Satoh, Noriyuki; Rokhsar, Daniel; Nishikawa, Teruaki

    2014-11-07

    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.

  7. 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

  8. A molecular evolutionary framework for the phylum Nematoda.

    PubMed

    Blaxter, M L; De Ley, P; Garey, J R; Liu, L X; Scheldeman, P; Vierstraete, A; Vanfleteren, J R; Mackey, L Y; Dorris, M; Frisse, L M; Vida, J T; Thomas, W K

    1998-03-05

    Nematodes are important: parasitic nematodes threaten the health of plants, animals and humans on a global scale; interstitial nematodes pervade sediment and soil ecosystems in overwhelming numbers; and Caenorhabditis elegans is a favourite experimental model system. A lack of clearly homologous characters and the absence of an informative fossil record have prevented us from deriving a consistent evolutionary framework for the phylum. Here we present a phylogenetic analysis, using 53 small subunit ribosomal DNA sequences from a wide range of nematodes. With this analysis, we can compare animal-parasitic, plant-parasitic and free-living taxa using a common measurement. Our results indicate that convergent morphological evolution may be extensive and that present higher-level classification of the Nematoda will need revision. We identify five major clades within the phylum, all of which include parasitic species. We suggest that animal parasitism arose independently at least four times, and plant parasitism three times. We clarify the relationship of C. elegans to major parasitic groups; this will allow more effective exploitation of our genetic and biological knowledge of this model species.

  9. 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.

  10. 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

  11. Disulfide-Functionalized Diblock Copolymer Worm Gels.

    PubMed

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

    2015-08-10

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

  12. Follow the sign! Top-down contingent attentional capture of masked arrow cues.

    PubMed

    Reuss, Heiko; Pohl, Carsten; Kiesel, Andrea; Kunde, Wilfried

    2011-01-01

    Arrow cues and other overlearned spatial symbols automatically orient attention according to their spatial meaning. This renders them similar to exogenous cues that occur at stimulus location. Exogenous cues trigger shifts of attention even when they are presented subliminally. Here, we investigate to what extent the mechanisms underlying the orienting of attention by exogenous cues and by arrow cues are comparable by analyzing the effects of visible and masked arrow cues on attention. In Experiment 1, we presented arrow cues with overall 50% validity. Visible cues, but not masked cues, lead to shifts of attention. In Experiment 2, the arrow cues had an overall validity of 80%. Now both visible and masked arrows lead to shifts of attention. This is in line with findings that subliminal exogenous cues capture attention only in a top-down contingent manner, that is, when the cues fit the observer's intentions.

  13. Enhancing the heavy Higgs boson [r arrow][ital WW] signal at hadron-hadron colliders

    SciTech Connect

    Field, R.D.; Griffin, P.A. )

    1994-07-01

    The jet-jet profile methods that we developed to enhance the heavy Higgs boson [r arrow][ital ZZ] signal over its backgrounds at a proton-proton collider energy of 40 TeV are extended to the heavy Higgs boson [r arrow][ital WW] signal and backgrounds. The dominant background is now the pair production of top quarks via the subprocess [ital gg][r arrow][ital t[bar t

  14. Arrow shaft injury of the wrist and hand: case report, management, and surgical technique.

    PubMed

    Launikitis, Robert A; Viegas, Steven F

    2009-01-01

    A case of accidental, self-inflicted injury to the hand from a hollow carbon shaft arrow which broke in its midshaft while attempting to shoot the arrow from a compound bow is presented. Basic knowledge of low velocity gunshot wounds and arrow injuries was applied in the treatment of this injury along with a unique management technique. The outcome, including hand function was good without any functional loss.

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

    PubMed

    2011-01-01

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

  16. 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

  17. 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.

  18. Illumination for Worm Tracking and Behavioral Imaging

    PubMed Central

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

    2016-01-01

    Neurobiological research in genetically tractable organisms relies heavily on robust assays for behavioral phenotypes. The simple body plan of the nematode Caenorhabditis elegans makes it particularly amenable to the use of automated microscopy and image analysis to describe behavioral patterns quantitatively. This protocol provides an approach for obtaining uniform illumination during worm tracking. Good lighting can be more of an art than a science. Once the system is set up, it will be necessary to play with it, testing the results after each adjustment to ensure that the analysis software is able to clearly identify the worm and its boundaries. Although the protocol was developed for use in a single-worm tracker, it addresses factors important for the generation of reproducible, standardized images in all systems. PMID:22135668

  19. 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

  20. Visuospatial attention shifts by gaze and arrow cues: an ERP study.

    PubMed

    Hietanen, Jari K; Leppänen, Jukka M; Nummenmaa, Lauri; Astikainen, Piia

    2008-06-18

    Orienting of visual attention can be automatically triggered not only by illumination changes occurring in the visual periphery but also by centrally presented gaze and arrow cues. We investigated whether the automatic shifts of visuospatial attention triggered by centrally displayed gaze and arrow cues rely on the same neural systems. To this end we measured event-related potentials (ERPs) time-locked to the cue and target onsets while the participants (n=17) performed a spatial cuing task. In the task, the participants detected and responded to laterally presented targets preceded by centrally presented, non-predictive, gaze or arrow cues. Manual reaction times and target-triggered ERP data showed that both gaze and arrow cues automatically oriented attention and facilitated subsequent processing of target stimuli. However, the cue-triggered electrophysiological data indicated that the ERPs elicited by the gaze and arrow cues were different at lateral parietal and fronto-central electrode sites. Most notably, for the arrows, we found a typical early attention direction negativity (EDAN) effect occurring 220-260 ms after the cue onset. The ERPs were shifted in the negative direction when the arrows pointed to a direction which was contralateral to the recorded hemisphere as compared to arrows with ipsilateral direction. This effect was not observed for the gaze stimuli. These results provide further support for earlier behavioral and neuroimaging studies indicating that automatic orienting of attention by arrow cues and gaze cues are based on different neural mechanisms.

  1. Which way is which? Examining symbolic control of attention with compound arrow cues.

    PubMed

    Mills, Mark; Dodd, Michael D

    2016-10-01

    Spatial symbols can generate attentional biases toward peripheral locations compatible with the symbol's meaning. An important question concerns how one symbol is selected when competing symbols are present. Studies examining this issue for spatially distinct symbols have suggested that selection depends on the task goals. In the present study, we examined whether the influence of competing symbolic stimuli (arrows) at different levels of structure on attentional control also depends on the task goals. Participants made simple detection responses to a peripheral target preceded by a spatially uninformative compound arrow (global arrow composed of local arrows). In addition, participants were required to perform a secondary task in which they matched the orientation of the global arrow (global task) or the location of a uniquely colored local arrow (local task) to a test display presented immediately following a detection response. When the global and local arrows pointed at opposite locations, a local cueing effect emerged in the local task, and a global cueing effect in the global task, indicating that the task goals influenced the selection of the level of structure. However, when the local level was spatially neutral (global arrow, local rectangles), a cueing effect was observed independent of task, and when the global level was spatially neutral (global rectangle, local arrows), a cueing effect was observed in the local task only, suggesting that global processing was obligatory and local processing optional. These findings suggest that attentional effects triggered by the global level are more strongly reflexive than those triggered by the local level.

  2. 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.

  3. 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.

  4. Cabibbo-angle-favored, -suppressed, and -doubly-suppressed D r arrow PP and D r arrow VP decays in SU(3) symmetry with final-state interactions

    SciTech Connect

    Verma, R.C.; Kamal, A.N. . Theoretical Physics Institute University of Alberta, Edmonton, Alberta . Department of Physics)

    1991-02-01

    We have studied Cabibbo-angle-favored, -suppressed, and -doubly-suppressed {ital D}{r arrow}{ital PP} and {ital D}{r arrow}{ital VP} decays in a nonet-symmetry and a broken-nonet-symmetry scheme, with the inclusion of final-state-interaction phases. For {ital D}{r arrow}{ital VP} decays, the implications of sextet dominance are also investigated. In the discussion we have argued that the symmetry approach, as also the diagrammatic approach used by other authors, does not fare as well in describing {ital D}{r arrow}{ital VP} decays as the factorization approach, particularly in describing {ital B}({ital D}{sub {ital s}}{sup +}{r arrow}{omega}{pi}{sup +}), {ital B}({ital D}{sub {ital s}}{sup +}{r arrow}{phi}{pi}{sup +}), and {ital B}({ital D}{sub {ital s}}{sup +}{r arrow}{rho}{sup 0}{pi}{sup +}).

  5. 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

  6. Filarial Worms Reduce Plasmodium Infectivity in Mosquitoes

    PubMed Central

    Aliota, Matthew T.; Chen, Cheng-Chen; Dagoro, Henry; Fuchs, Jeremy F.; Christensen, Bruce M.

    2011-01-01

    Background Co-occurrence of malaria and filarial worm parasites has been reported, but little is known about the interaction between filarial worm and malaria parasites with the same Anopheles vector. Herein, we present data evaluating the interaction between Wuchereria bancrofti and Anopheles punctulatus in Papua New Guinea (PNG). Our field studies in PNG demonstrated that An. punctulatus utilizes the melanization immune response as a natural mechanism of filarial worm resistance against invading W. bancrofti microfilariae. We then conducted laboratory studies utilizing the mosquitoes Armigeres subalbatus and Aedes aegypti and the parasites Brugia malayi, Brugia pahangi, Dirofilaria immitis, and Plasmodium gallinaceum to evaluate the hypothesis that immune activation and/or development by filarial worms negatively impact Plasmodium development in co-infected mosquitoes. Ar. subalbatus used in this study are natural vectors of P. gallinaceum and B. pahangi and they are naturally refractory to B. malayi (melanization-based refractoriness). Methodology/Principal Findings Mosquitoes were dissected and Plasmodium development was analyzed six days after blood feeding on either P. gallinaceum alone or after taking a bloodmeal containing both P. gallinaceum and B. malayi or a bloodmeal containing both P. gallinaceum and B. pahangi. There was a significant reduction in the prevalence and mean intensity of Plasmodium infections in two species of mosquito that had dual infections as compared to those mosquitoes that were infected with Plasmodium alone, and was independent of whether the mosquito had a melanization immune response to the filarial worm or not. However, there was no reduction in Plasmodium development when filarial worms were present in the bloodmeal (D. immitis) but midgut penetration was absent, suggesting that factors associated with penetration of the midgut by filarial worms likely are responsible for the observed reduction in malaria parasite infections

  7. 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.

  8. 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.

  9. Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota.

    PubMed

    Vanwonterghem, Inka; Evans, Paul N; Parks, Donovan H; Jensen, Paul D; Woodcroft, Ben J; Hugenholtz, Philip; Tyson, Gene W

    2016-10-03

    Methanogenesis is the primary biogenic source of methane in the atmosphere and a key contributor to climate change. The long-standing dogma that methanogenesis originated within the Euryarchaeota was recently challenged by the discovery of putative methane-metabolizing genes in members of the Bathyarchaeota, suggesting that methanogenesis may be more phylogenetically widespread than currently appreciated. Here, we present the discovery of divergent methyl-coenzyme M reductase genes in population genomes recovered from anoxic environments with high methane flux that belong to a new archaeal phylum, the Verstraetearchaeota. These archaea encode the genes required for methylotrophic methanogenesis, and may conserve energy using a mechanism similar to that proposed for the obligate H2-dependent methylotrophic Methanomassiliicoccales and recently described Candidatus 'Methanofastidiosa'. Our findings indicate that we are only beginning to understand methanogen diversity and support an ancient origin for methane metabolism in the Archaea, which is changing our understanding of the global carbon cycle.

  10. Microbiome and metabolic disease: revisiting the bacterial phylum Bacteroidetes.

    PubMed

    Johnson, Elizabeth L; Heaver, Stacey L; Walters, William A; Ley, Ruth E

    2017-01-01

    Bacterial species composition in the gut has emerged as an important factor in obesity and its related metabolic diseases such as type 2 diabetes. Out of thousands of bacterial species-level phylotypes inhabiting the human gut, the majority belong to two dominant phyla, the Bacteroidetes and Firmicutes. Members of the Bacteroidetes in particular have been associated with human metabolic diseases. However, their associations with disease are not always consistent between studies. Delving deeper into the diversity within the Bacteroidetes reveals a vast diversity in genomes and capacities, which partly explain how not all members respond equally to similar environmental conditions in their hosts. Here, we discuss the Bacteroidetes phylum, associations of its members with metabolic phenotypes, and efforts to characterize functionally their interactions with their hosts. Harnessing the Bacteroidetes to promote metabolic health will require a nuanced understanding of how specific strains interact with their microbial neighbors and their hosts under various conditions.

  11. 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.

  12. 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

  13. 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.

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

    USDA-ARS?s Scientific Manuscript database

    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 ...

  15. Time arrow is influenced by the dark energy

    NASA Astrophysics Data System (ADS)

    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.

  16. 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.

  17. SCAR arrow-wing active flutter suppression system

    NASA Technical Reports Server (NTRS)

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

    1977-01-01

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

  18. 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

  19. Guinea worm disease--the final chapter?

    PubMed

    Muller, Ralph

    2005-11-01

    The global campaign for the eradication of dracunculiasis has succeeded in reducing the incidence of guinea worm disease by >99% in the past 20 years. This has been accomplished by the provision of safe drinking water supplies, filtration of drinking water, chemical control of intermediate hosts, case containment and, crucially, local health-education initiatives.

  20. 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

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

    PubMed

    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

    2013-06-25

    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.

  2. 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.

  3. 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.

  4. Intestinal worms: strategies to control disease.

    PubMed

    Hall, A; Chan, M S

    1994-11-01

    Of the 512 million inhabitants of sub-Saharan Africa, an estimated 200-250 million are infected with the following intestinal nematodes: Ascaris lumbricoides, Trichuris trichiura, and hookworm. Disease in not more common or evident in this population, however, because most species of worms do not multiply in their hosts and because these worms have a life-span of 1-3 years so worm burdens are acquired gradually over a period of years. Also, disease caused by worms is usually related to worm burden (which has indistinct characteristics) as well as to age and health of the host. Thus, onset of disease can be slow and the diseases tend to be chronic rather than acute. Infestation can be diagnosed easily by microscopic examination of stool which will reveal the prevalence of infection but not the prevalence of disease (heavy infection). Prevalence is affected by age group, and 70% of all worms are present in only 20% of a given community (who are, therefore, the most likely to be diseased from the worms and most likely to transmit disease). With the goal of most control programs being the control of disease rather than of infection, the first task is to identify and treat the heavily-infected people. Since individual identification can be costly, one strategy is to treat everyone or to treat those groups who are most heavily infected. For example, adults in Africa are the most appropriate targets for hookworm treatment, and a large proportion of all disease due to A. lumbricoides and T. trichiura can be eliminated through mass treatment of school children. Removing sources of infection will also remove sources of transmission. It will still be necessary to identify localities where prevalence is above 50% and, thus, call for treatment. Albendazole and mebendazole are effective drugs to treat all species. Levamisole is effective against S. lumbricoides and hookworm, and pyrantel pamoate is effective against A. lumbricoides. The school delivery system for treatment is

  5. 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.

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

    NASA Astrophysics Data System (ADS)

    Erdmann, Wolfram; Speer, Thomas

    1997-04-01

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

  7. 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.…

  8. 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,…

  9. V sup 0 r arrow P sup 0 P sup 0. gamma. decay rates

    SciTech Connect

    Fajfer, S. ); Oakes, R.J. )

    1990-10-01

    The radiative decay processes of the type {ital V}{sup 0}{r arrow}{ital P}{sup 0}{ital P}{sup 0}{gamma} are described by the gauged Wess-Zumino terms in a low-energy effective Lagrangian, there being no bremsstrahlung contributions. Using such an effective Lagrangian, describing pseudoscalar and vector mesons, we have calculated the branching ratios for the decays {omega}{r arrow}{pi}{sup 0}{pi}{sup 0}{gamma}, {omega}{r arrow}{pi}{sup 0}{eta}{gamma}, {rho}{r arrow}{pi}{sup 0}{pi}{sup 0}{gamma}, {rho}{r arrow}{pi}{sup 0}{eta}{gamma}, {phi}{r arrow}{pi}{sup 0}{pi}{sup 0}{gamma}, {phi}{r arrow}{pi}{sup 0}{eta}{gamma}, and {phi}{r arrow}{ital K}{sup 0}{ital {bar K}}{sup 0}{gamma}. Since scalar mesons have been neglected, these rates provide estimates of the expected backgrounds in searches for {ital J}{sup {pi}}=0{sup +} resonances, particularly the possible four-quark states in {phi} decays.

  10. 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,…

  11. 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.…

  12. 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.

  13. 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

  14. 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.

  15. Bloodstain pattern analysis in a case of suicide with a compound bow and arrow.

    PubMed

    Wilson, Christopher I; Altschul, Samuel; Mead, Anthony; Flannagan, Lisa M

    2004-03-01

    The incidence of human fatalities due to arrow injuries in the medical literature is rare. We report an incident involving a 46-year-old man who was found in his secured apartment with a fatal arrow wound of his chest and abdomen. The initial scene investigation suggested that the victim impaled himself with an arrow attached to a razor-sharp, 4-bladed broad-head hunting tip before collapsing on the floor. However, analysis of the bloodstain patterns suggested that the victim used the compound bow to propel the arrow. When investigating deaths due to bows and arrows, thorough scene investigation along with bloodstain pattern analysis is essential in determining the mechanism of injury and manner of death.

  16. New Limit for the Lepton-Family-Number Nonconserving Decay [mu][sup +][r arrow]e[sup +] [gamma

    SciTech Connect

    Wright, S.C. ); Cooper, P.S. ); Chen, Y.K.; Dzemidzic, M.; Empl, A.; Hungerford, E.V. III; Lan, K.A.; Mayes, B.W. II; von Witsch, W.H. ); Knott, J.E.; Stantz, K.M.; Szymanski, J.J. ); Brooks, M.L.; Cooper, M.D.; Hogan, G.E.; Kroupa, M.A.; Mischke, R.E.; Stanislaus, T.D.; Szymanski, J.J. ); Hughes, E.B.; Jui, C.C. ); Gagliardi, C.A.; Tribble, R.E.; Tu, X.L.; Van Ausdeln, L.A. ); Koetke, D.D.; Manweiler, R.; Stanislaus, T.D. ); Ziock, K.O. (University

    1999-08-01

    An experiment has been performed to search for the muon- and electron-number nonconserving decay [mu][sup +][r arrow]e[sup +][gamma] . The upper limit for the branching ratio is found to be [Gamma]([mu][sup +][r arrow]e[sup +][gamma] ) /[Gamma]([mu][sup +][r arrow]e[sup +][nu] [bar [nu

  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. 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.

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

    PubMed Central

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

    2006-01-01

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

  20. Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida.

    PubMed

    Bourlat, Sarah J; Juliusdottir, Thorhildur; Lowe, Christopher J; Freeman, Robert; Aronowicz, Jochanan; Kirschner, Mark; Lander, Eric S; Thorndyke, Michael; Nakano, Hiroaki; Kohn, Andrea B; Heyland, Andreas; Moroz, Leonid L; Copley, Richard R; Telford, Maximilian J

    2006-11-02

    Deuterostomes comprise vertebrates, the related invertebrate chordates (tunicates and cephalochordates) and three other invertebrate taxa: hemichordates, echinoderms and Xenoturbella. The relationships between invertebrate and vertebrate deuterostomes are clearly important for understanding our own distant origins. Recent phylogenetic studies of chordate classes and a sea urchin have indicated that urochordates might be the closest invertebrate sister group of vertebrates, rather than cephalochordates, as traditionally believed. More remarkable is the suggestion that cephalochordates are closer to echinoderms than to vertebrates and urochordates, meaning that chordates are paraphyletic. To study the relationships among all deuterostome groups, we have assembled an alignment of more than 35,000 homologous amino acids, including new data from a hemichordate, starfish and Xenoturbella. We have also sequenced the mitochondrial genome of Xenoturbella. We support the clades Olfactores (urochordates and vertebrates) and Ambulacraria (hemichordates and echinoderms). Analyses using our new data, however, do not support a cephalochordate and echinoderm grouping and we conclude that chordates are monophyletic. Finally, nuclear and mitochondrial data place Xenoturbella as the sister group of the two ambulacrarian phyla. As such, Xenoturbella is shown to be an independent phylum, Xenoturbellida, bringing the number of living deuterostome phyla to four.

  1. An unusual primary sigma factor in the Bacteroidetes phylum.

    PubMed

    Vingadassalom, Didier; Kolb, Annie; Mayer, Claudine; Rybkine, Tania; Collatz, Ekkehard; Podglajen, Isabelle

    2005-05-01

    The presence of housekeeping gene promoters with a unique consensus sequence in Bacteroides fragilis, previously described by Bayley et al. (2000, FEMS Microbiol Lett 193: 149-154), suggested the existence of a particular primary sigma factor. The single rpoD-like gene observed in the B. fragilis genome, and similarly in those of other members of the Bacteroidetes phylum, was found to be essential. It encodes a protein, sigma(ABfr), of only 32.7 kDa that is produced with equal abundance during all phases of growth and was concluded to be the primary sigma factor. sigma(ABfr) and its orthologues in the Bacteroidetes are unusual primary sigma factors in that they lack region 1.1, have a unique signature made up of 29 strictly identical amino acids and are the only RpoD factors that cluster with the RpoS factors. Although binding to the Escherichia coli core RNA polymerase, sigma(ABfr) does not support transcription initiation from any promoter when it is part of the heterologous holoenzyme, while in the reconstituted homologous holoenzyme it does so only from typical B. fragilis, including rrs, promoters but not from the lacUV5 or RNA I promoters.

  2. Discovery of multiple neuropeptide families in the phylum Platyhelminthes

    PubMed Central

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

    2009-01-01

    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

  3. 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

  4. WormBase: Annotating many nematode genomes.

    PubMed

    Howe, Kevin; Davis, Paul; Paulini, Michael; Tuli, Mary Ann; Williams, Gary; Yook, Karen; Durbin, Richard; Kersey, Paul; Sternberg, Paul W

    2012-01-01

    WormBase (www.wormbase.org) has been serving the scientific community for over 11 years as the central repository for genomic and genetic information for the soil nematode Caenorhabditis elegans. The resource has evolved from its beginnings as a database housing the genomic sequence and genetic and physical maps of a single species, and now represents the breadth and diversity of nematode research, currently serving genome sequence and annotation for around 20 nematodes. In this article, we focus on WormBase's role of genome sequence annotation, describing how we annotate and integrate data from a growing collection of nematode species and strains. We also review our approaches to sequence curation, and discuss the impact on annotation quality of large functional genomics projects such as modENCODE.

  5. Asexual reproduction in a sipunculan worm.

    PubMed

    Rice, M E

    1970-03-20

    The sipunculan worm Aspidosiphon brocki reproduces asexually by transverse fision into two unequal parts, the smaller part comprising the posterior fifth of the animal. Prior to fission each part regenerates the structures essential to the formation of a new individual. The smaller posterior part (daughter) regenerates an anterior body, including introvert, anterior gut, retractor muscles, and nephridia, whereas the larger anterior part (parent) regenerates only the posterior body wall.

  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. 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.

  8. 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.

  9. Janus sequences of quantum measurements and the arrow of time

    NASA Astrophysics Data System (ADS)

    Jordan, Andrew N.; Chantasri, Areeya; Murch, Kater; Dressel, Justin; Korotkov, Alexander N.

    2017-05-01

    We examine the time reversal symmetry of quantum measurement sequences by introducing a forward and backward Janus sequence of measurements. If the forward sequence of measurements creates a sequence of quantum states in time, starting from an initial state and ending in a final state, then the backward sequence begins with the time-reversed final state, exactly retraces the intermediate states, and ends with the time-reversed initial state. We prove that such a sequence can always be constructed, showing that unless the measurements are ideal projections, it is impossible to tell if a given sequence of measurements is progressing forward or backward in time. A statistical arrow of time emerges only because typically the forward sequence is more probable than the backward sequence.

  10. Theoretical evaluation of high speed aerodynamics for arrow wing configurations

    NASA Technical Reports Server (NTRS)

    Dollyhigh, S. M.

    1978-01-01

    A limited study in the use of theoretical methods to calculate the high speed aerodynamics of arrow wing supersonic cruise configurations was conducted. The study consisted of correlations with existing wind tunnel data at Mach numbers from 0.8 to 2.7, using theoretical methods to extrapolate the wind tunnel data to full scale flight conditions, and presentation of a typical supersonic data package for an advanced supersonic transport application prepared using the theoretical methods. A brief description of the methods and their application was given. In general, all three methods had excellent correlation with wind tunnel data at supersonic speeds for drag and lift characteristics and fair to poor agreement with pitching moment characteristics. The VORLAX program had excellent correlation with wind tunnel data at subsonic speeds for lift and pitching moment characteristics and fair agreement in drag characteristics.

  11. Guinea worm: from Robert Leiper to eradication.

    PubMed

    Tayeh, Ahmed; Cairncross, Sandy; Cox, Francis E G

    2017-06-27

    Guinea worm disease, dracunculiasis or dracontiasis, is an ancient disease with records going back over 4500 years, but until the beginning of the 20th century, little was known about its life cycle, particularly how humans became infected. In 1905, Robert Thomas Leiper was sent by the British colonial authorities to West Africa to investigate the spread of Guinea worm disease and to recommend measures to prevent it. While carrying out his investigations, he made important contributions to the aetiology, epidemiology and public health aspects of Guinea worm disease and provided definitive answers to many outstanding questions. First, he tested the validity of previous theories; second, he confirmed the role of water fleas, which he identified as Cyclops, as the intermediate hosts in the life cycle; third, he investigated the development of the parasite in its intermediate host; and fourth, he recommended measures to prevent the disease. [The crustacean Order Cyclopoida in the Family Cyclopidae contains 25 genera, including Cyclops which itself contains over 400 species and may not even be a valid taxon. It is not known how many of these species (or indeed species belonging to related genera) can act as intermediate hosts of Dracunculus medinensis nor do we know which species Fedchenko, Leiper and other workers used in their experiments. It is, therefore, best to use the terms copepod, or copopoid crustacean rather than Cyclops in scientific texts. In this paper, these crustaceans are referred to as copepods except when referring to an original text.] Leiper described the remarkable changes that took place when an infected copepod was placed in a dilute solution of hydrochloric acid; the copepod was immediately killed, but the Dracunculus larvae survived and were released into the surrounding water. From this, he concluded that if a person swallowed an infected copepod, their gastric juice would produce similar results. He next infected monkeys by feeding them

  12. Neuropeptide-like protein diversity in phylum Nematoda.

    PubMed

    McVeigh, Paul; Alexander-Bowman, Susan; Veal, Emma; Mousley, Angela; Marks, Nikki J; Maule, Aaron G

    2008-11-01

    This study reports the identification of nematode neuropeptide-like protein (nlp) sequelogs from the GenBank expressed sequence tag (EST) database, using BLAST (Basic Local Alignment Search Tool) search methodology. Search strings derived from peptides encoded by the 45 known Caenorhabditis elegans nlp genes were used to identify more than 1000 ESTs encoding a total of 26 multi-species nlp sequelogs. The remaining 18 nlps (nlp-4, -16, -24 through -36, -39, -41 and -45) were identified only in C. elegans, while the sole EST representative of nlp-23 was from Caenorhabditis remanei. Several ESTs encoding putative antibacterial peptides similar to those encoded by the C. elegans genes nlp-24-33 were observed in several parasite species. A novel gene (nlp-46) was identified, encoding a single, amidated dodecapeptide (NIA[I/T]GR[G/A]DG[F/L]RPG) in eight species. Secretory signal peptides were identified in at least one species representing each nlp sequelog, confirming that all 46 nematode nlp genes encode secretory peptides. A random sub-set of C. elegans NLPs was tested physiologically in Ascaris suum ovijector and body wall muscle bioassays. None of the peptides tested were able to modulate ovijector activity, while only three displayed measurable myoactivity on somatic body wall muscle. AFAAGWNRamide (from nlp-23) and AVNPFLDSIamide (nlp-3) both produced a relaxation of body wall muscle, while AIPFNGGMYamide (nlp-10) induced a transient contraction. Numerical analyses of nlp-encoding ESTs demonstrate that nlp-3, -13, -14, -15 and -18 are amongst the most highly represented transcripts in the dataset. Using available bioinformatics resources, this study delineates the nlp complement of phylum Nematoda, providing a rich source of neuropeptide ligands for deorphanisation of nematode neuropeptide receptors.

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

    PubMed Central

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

    2016-01-01

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

  14. 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.

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

    PubMed Central

    2009-01-01

    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. PMID:19604374

  16. 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

  17. Controlling attention to gaze and arrows in attention deficit hyperactivity disorder.

    PubMed

    Marotta, Andrea; Pasini, Augusto; Menotti, Erica; Pasquini, Alessia; Pitzianti, Maria Bernarda; Casagrande, Maria

    2017-05-01

    The aim of this research was to assess implicit processing of social and non-social distracting cues in children with ADHD. Young people with ADHD and matched controls were asked to classify target words (LEFT/RIGHT) which were accompanied by a distracter eye-gaze or arrow. Typically developing participants showed evidence of interference effects from both eye-gaze and arrow distracters. In contrast, the ADHD group showed evidence of interference effects from arrow but failed to show interference from eye-gaze. This absence of interference effects from eye-gaze observed in the participants with ADHD may reflect an attentional impairment in attending to socially relevant information.

  18. 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.

  19. Aquatic worms eating waste sludge in a continuous system.

    PubMed

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

    2009-10-01

    Aquatic worms are a biological approach to decrease the amount of biological waste sludge produced at waste water treatment plants. A new reactor concept was recently introduced in which the aquatic oligochaete Lumbriculus variegatus is immobilised in a carrier material. The current paper describes the experiments that were performed to test whether this concept could also be applied in continuous operation, for which worm growth is an important condition. This was tested for two mesh sizes of the carrier material. With an increase in mesh size from 300 to 350 microm, worm biomass growth was possible in the reactor at a rate of 0.013 d(-1) and with a yield of 0.13 g dw/g VSS digested by the worms. Mass balances over the worm reactors showed the importance of correcting for natural sludge breakdown, as the contribution of the worms to total VSS reduction was 41-71%.

  20. Experiences in the development of the Mighty Worm

    NASA Astrophysics Data System (ADS)

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

    1993-02-01

    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.

  1. Search for the decay. pi. sup 0 r arrow. gamma. + X

    SciTech Connect

    Atiya, M.S.; Chiang, I.; Frank, J.S.; Haggerty, J.S.; Ito, M.M.; Kycia, T.F.; Li, K.K.; Littenberg, L.S.; Stevens, A.J.; Sambamurti, A.; Strand, R.C. ); Louis, W.C. ); Akerib, D.S.; Marlow, D.R.; Meyers, P.D.; Selen, M.A.; Shoemaker, F.C.; Smith, A.J.S. ); Blackmore, E.W.; Bryman, D.A.; Felawka, L.; Kitching, P.; Konaka, A.; Kuno, Y.; Macdonald, J.A.; Numao, T.; Padley, P.; Poutissou, J.; Poutissou, R.; Roy, J.; Turcot, A.S. )

    1992-08-03

    A search for the decay {pi}{sup 0}{r arrow}{gamma}{ital X}, where {ital X} is any long-lived weakly interacting neutral vector particle with mass smaller than the neutral pion pass, was performed using neutral pions tagged by {ital K}{sup +}{r arrow}{pi}{sup +}{pi}{sup 0}. A 90%-C.L. upper limit for the branching ratio of the two-body decay {ital B}({pi}{sup 0}{r arrow}{gamma}{ital X}){lt}5{times}10{sup {minus}4} is set. Limits are also set for three-body decays {pi}{sup 0}{r arrow}{gamma}{ital XX}{prime}.

  2. 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

  3. 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…

  4. 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…

  5. 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.

  6. 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.

  7. [A Case of Transoral Penetrating Head Injury from a Crossbow-Fired Arrow].

    PubMed

    Nakamura, Naoto; Fujita, Yuichi; Nakamizo, Satoshi; Sakagami, Yoshio; Okazaki, Ken; Kida, Kouta

    2017-09-01

    Penetrating head injuries are extremely rare in Japan. The authors describe a case involving a penetrating head injury from an arrow fired from a crossbow. A 52-year-old man who had shot himself transorally in a suicide attempt was admitted to the authors' hospital. On admission, he was conscious and exhibited no neurological deficits. The end of the arrow was visible inside his oral cavity. Computed tomography revealed the arrow had penetrated the right cerebellum and occipital lobe, resulting in a very small hematoma. Digital subtraction angiography revealed no significant vascular injuries. After considering these findings and the nature of the object, the authors decided to remove the arrow from the cranium by pulling it from the patient's oral cavity. To remove the arrow, surgery was performed with several devices, including intraoperative X-ray, endoscopy, and intraoperative angiography. The authors were able to completely remove the arrow, and the patient experienced no new deficits, except mild ataxia and mild dysphasia, and no signs of cerebral infection or cerebrospinal fluid leakage after the surgery. Although most cases of penetrating head injuries require craniotomies, the authors were able to safely remove the foreign object in this case without performing a craniotomy. Because guidelines for the treatment of penetrating head injuries have not been established, the treatment of each case must be modified according to the nature of the foreign object and the findings of preoperative imaging techniques.

  8. Epidemiological studies on guinea-worm infection.

    PubMed

    Reddy, C R; Narasaiah, I L; Parvathi, G

    1969-04-01

    Dracontiasis is one of the most easily preventable of the tropical parasitic diseases, yet in India the infection is still present in large numbers of people and causes extreme degrees of morbidity and incapacitation.The 10 000 inhabitants of 4 villages in South India were interviewed and the prevalence of guinea-worm infection was found to vary from 11% to 54%; the prevalence increased with the proportion of the population using step-wells. Questioning revealed that infections with more than one worm at a time had occurred in 707 out of 1759 infected persons, that reinfections were common and that many people had suffered for long periods.A survey of the water supplies in a district of South India with a population of about 1.87 million showed that more than 0.5 million people were at risk of contracting the disease. The necessity for protected water supplies and for the conversion of step-wells into draw-wells is urgent.

  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. 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

  11. 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.

  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 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

  15. 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

    2016-09-01

    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.

  16. 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. © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. Uganda's successful Guinea Worm Eradication Program.

    PubMed

    Rwakimari, John B; Hopkins, Donald R; Ruiz-Tiben, Ernesto

    2006-07-01

    Having begun its national Guinea Worm Eradication Program (UGWEP) in 1991 (1991 population, 16.6 million) with the third-highest number of cases reported by any endemic country, and ranked as the second-highest endemic country in the world in 1993, by 2004, Uganda celebrated its first full calendar year with no indigenous cases of the disease. Systematic interventions began in 1992 and were gradually intensified until the final indigenous case occurred in July 2003. The favorable concentration of most cases in relatively few northern districts of the country was partly offset by chronic insecurity in much of the endemic area and by repeated importations of cases from neighboring Sudan. Strong support and dedicated leadership by government officials and external partners were keys to this program's dramatic success. This program cost approximately US dollar 5.6 million.

  2. Early Cambrian sipunculan worms from southwest China.

    PubMed Central

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

    2004-01-01

    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

  3. 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.

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

    PubMed

    Laugrand, Frédéric; Oosten, Jarich

    2010-01-01

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

  5. 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.

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

    PubMed

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

    2013-05-01

    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.

  7. Interactions between worm infections and malaria.

    PubMed

    Nacher, Mathieu

    2004-04-01

    Helminths are the most prevalent parasitic infections and malaria is the deadliest parasitic disease. Helminths have been reported to be protective against the severe forms of malaria but they were also possibly linked to increased malaria-incidence and gametocyte carriage. Connecting the dots between observations suggests that statistical regularities throughout the evolution of worms and malaria parasites in the same hosts, may have led to the emergence of non-zero interactions as observed in iterated prisoners dilemma games. Thus by protecting the host, helminths protect themselves and their reproductive potential, but also favor the dissemination and reproduction of Plasmodium falciparum. The proximate causes of this evolutionarily stable strategy might be mediated by IgE and the CD23/NO pathway, the protective role of IL10 in helminth-infected patients, and possibly the hematological consequences of worms. The chronic activation of the CD23/NO pathway might be instrumental in downregulating the expression of cytoadherence receptors thus reducing sequestration of parasitized red blood cells in the deep organs. Mild anemia in helminth-infected patients might favor gametocytogenesis and send attractive cues to the vector. This framework leads to numerous testable hypotheses and could explain certain singularities regarding the double edged role of IgE and NO. Among these hypotheses, there are 2 practical ones: the impact of helminths on malaria vaccine candidates, and the theoretical risk of increasing the severity of malaria after anthelmintics. The capacity for increased IgE responses could thus have been vital in our ancestor's wormy and malarious past. Allergies may be what remains of it in the modern world.

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

    SciTech Connect

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

    1996-12-31

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

  9. Arrows of time and the beginning of the universe

    NASA Astrophysics Data System (ADS)

    Vilenkin, Alexander

    2013-08-01

    I examine two cosmological scenarios in which the thermodynamic arrow of time points in opposite directions in the asymptotic past and future. The first scenario, suggested by Aguirre and Gratton, assumes that the two asymptotic regions are separated by a de Sitter-like bounce, with low-entropy boundary conditions imposed at the bounce. Such boundary conditions naturally arise from quantum cosmology with Hartle-Hawking wave function of the universe. The bounce hypersurface breaks de Sitter invariance and represents the beginning of the universe in this model. The second scenario, proposed by Carroll and Chen, assumes some generic initial conditions on an infinite spacelike Cauchy surface. They argue that the resulting spacetime will be nonsingular, apart from black holes that could be formed as the initial data is evolved, and will exhibit eternal inflation in both time directions. Here I show, assuming the null convergence condition, that the Cauchy surface in a nonsingular (apart from black holes) universe with two asymptotically inflating regions must necessarily be compact. I also argue that the size of the universe at the bounce between the two asymptotic regions cannot much exceed the de Sitter horizon. The spacetime structure is then very similar to that in the Aguirre-Gratton scenario and does require special boundary conditions at the bounce. If cosmological singularities are allowed, then an infinite Cauchy surface with “random” initial data will generally produce inflating regions in both time directions. These regions, however, will be surrounded by singularities and will have singularities in their past or future.

  10. 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].

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

    PubMed

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

    1992-09-15

    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.

  13. 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

  14. Identification of distinctive molecular traits that are characteristic of the phylum "Deinococcus-Thermus" and distinguish its main constituent groups.

    PubMed

    Ho, Jonathan; Adeolu, Mobolaji; Khadka, Bijendra; Gupta, Radhey S

    2016-10-01

    The phylum "Deinococcus-Thermus" contains two heavily researched groups of extremophilic bacteria: the highly radioresistant order Deinococcales and the thermophilic order Thermales. Very few characteristics are known that are uniquely shared by members of the phylum "Deinococcus-Thermus". Comprehensive phylogenetic and comparative analyses of >65 "Deinococcus-Thermus" genomes reported here have identified numerous molecular signatures in the forms of conserved signature insertions/deletions (CSIs) and conserved signature proteins (CSPs), which provide distinguishing characteristics of the phylum "Deinococcus-Thermus" and its main groups. We have identified 58 unique CSIs and 155 unique CSPs that delineate different phylogenetic groups within the phylum. Of these identified traits, 24 CSIs and 29 CSPs are characteristic of the phylum "Deinococcus-Thermus" and they provide novel and reliable means to circumscribe/describe this phylum. An additional 3 CSIs and 3 CSPs are characteristic of the order Deinococcales, and 6 CSIs and 51 CSPs are characteristic of the order Thermales. The remaining 25 CSIs and 72 CSPs identified in this study are distinctive traits of genus level groups within the phylum "Deinococcus-Thermus". The molecular characteristics identified in this work provide novel and independent support for the common ancestry of the members of the phylum "Deinococcus-Thermus" and provide a new means to distinguish the main constituent clades of the phylum. Additionally, the CSIs and CSPs identified in this work may play a role in the unique extremophilic adaptations of the members of this phylum and further functional analyses of these characteristics could provide novel biochemical insights into the unique adaptations found within the phylum "Deinococcus-Thermus".

  15. Fixation of osteochondral fragments in the human knee using Meniscus Arrows.

    PubMed

    Wouters, Diederick B; Burgerhof, Johannes G M; de Hosson, Jeff T M; Bos, Rudolf R M

    2011-02-01

    The aim of this study is to compare the hold in bone of Meniscus Arrows and Smart Nails, followed by the report of the results of the clinical application of Meniscus Arrows as fixation devices. First, pull-out tests were performed to analyse the holdfast of both nails in bone. Statistical analysis showed no significant difference; therefore, the thinner Meniscus Arrow was chosen as fixation device in the patient series of two patients with a symptomatic Osteochondritis dissecans fragment and three patients with an osteochondral fracture of a femur condyle. The cartilage margins were glued with Tissuecoll. All fragments consolidated. Second look arthroscopy in three patients showed fixed fragments with stable, congruent cartilage edges. At an average follow-up period of 5 years no pain, effusion, locking, restricted range of motion or signs of osteoarthritis were reported. Based on the results of the pull-out tests and available clinical studies, Meniscus Arrows and Smart Nails are both likely to perform adequately as fixation devices in the treatment of Osteochondritis dissecans and osteochondral fractures in the knee. They both provide the advantage of one stage surgery. However, based on their smaller diameter, the Meniscus Arrows should be preferred for this indication.

  16. Measurement of the Amplitude Ratio between the Decays B^0 arrow J/ψ \\overlineK^*0 (\\overlineK^*0arrow K^-π^+) and B^0 arrow J/ψ K^*0 (K^*0arrow K^+π^-)

    NASA Astrophysics Data System (ADS)

    Baak, Max

    2003-04-01

    We report a study of the time-dependent rate of decay for the process B^0arrow J/ψ K^*0 (K^*0arrow K^+π^-) in 82 fb-1 of e^+e^- annihilation data collected by the BaBar detector at center-of-mass energies near the Υ(4S) resonance. We search for a deviation in the B decay-time distributions from usual B^0\\overlineB^0 oscillations. Such a deviation would be an indication for a wrong-flavor amplitude B^0arrow J/ψ \\overlineK^*0 and a sign for new physics. A non-zero wrong-flavor amplitude could lead to a done by measuring the coefficients of the s(Δ m_dt) distributions for the J/ψ \\overlineK^*0. The result a limit on the potential difference between the measured values of sin(2β) using B^0/\\overlineB^0 arrow J/ψ KS and B^0/\\overlineB^0 arrow J/ψ KL decays.

  17. De-worming school children and hygiene intervention.

    PubMed

    Luong, T V

    2003-06-01

    Helminths or worm infestations refer to worms that live as parasites in the human body and are a fundamental cause of disease associated with health and nutrition problems beyond gastrointestinal tract disturbances. Globally, over 3.5 billion people are infected with intestinal worms, of which 1.47 billion are with roundworm, 1.3 billion people with hookworm and 1.05 billion with whipworm. School children aged 5 - 15 years suffer the highest infection rate and worm burden that attributes to poor sanitation and hygiene. About 400 million school-age children are infected with roundworm, whipworm and hookworm worldwide, a large proportion of whom are found in the East Asia region (Cambodia, China, Lao PDR, Thailand and Vietnam). These parasites consume nutrients from children they infect, thus retarding their physical development. They destroy tissues and organs, cause abdominal pain, diarrhoea, intestinal obstruction, anaemia, ulcers and other health problems. All of these consequences of infection can slow cognitive development and thus impair learning. De-worming school children by anthelmintic drug treatment is a curative approach for expelling the heavy worm load. However, drug therapy alone is only a short-term measure of reducing worm infection and re-infection is frequent. Control measures through improved sanitation, hygiene and de-worming are needed to prevent infection and re-infection. UNICEF has supported many governments in this (and other) regions to assist in the provision of water supply and sanitary facilities and intensive hygiene education in many schools through the Water, Environment and Sanitation (WES) programme. The UNICEF supported school sanitation and hygiene education (SSHE) programme, and other programmes, could effectively enhance behaviour change in children to break the routes of worm transmission and other waterborne diseases.

  18. 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.

  19. Preparation of Samples for Single-Worm Tracking

    PubMed Central

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

    2016-01-01

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

  20. Phylogenetic delineation of the novel phylum Armatimonadetes (former candidate division OP10) and definition of two novel candidate divisions.

    PubMed

    Lee, K C Y; Herbold, C W; Dunfield, P F; Morgan, X C; McDonald, I R; Stott, M B

    2013-04-01

    Small-subunit (SSU) rRNA gene sequences associated with the phylum Armatimonadetes were analyzed using multiple phylogenetic methods, clarifying both the phylum boundary and the affiliation of previously ambiguous groupings. Here we define the Armatimonadetes as 10 class-level groups and reclassify two previously associated groups as candidate divisions WS1 and FBP.

  1. Phylogenetic Delineation of the Novel Phylum Armatimonadetes (Former Candidate Division OP10) and Definition of Two Novel Candidate Divisions

    PubMed Central

    Herbold, C. W.; Dunfield, P. F.; Morgan, X. C.; McDonald, I. R.; Stott, M. B.

    2013-01-01

    Small-subunit (SSU) rRNA gene sequences associated with the phylum Armatimonadetes were analyzed using multiple phylogenetic methods, clarifying both the phylum boundary and the affiliation of previously ambiguous groupings. Here we define the Armatimonadetes as 10 class-level groups and reclassify two previously associated groups as candidate divisions WS1 and FBP. PMID:23377935

  2. Complete Genome Sequence of Acidaminococcus intestini RYC-MR95, a Gram-Negative Bacterium from the Phylum Firmicutes

    PubMed Central

    D'Auria, Giuseppe; Galán, Juan-Carlos; Rodríguez-Alcayna, Manuel; Moya, Andrés; Baquero, Fernando; Latorre, Amparo

    2011-01-01

    Acidaminococcus intestini belongs to the family Acidaminococcaceae, order Selenomonadales, class Negativicutes, phylum Firmicutes. Negativicutes show the double-membrane system of Gram-negative bacteria, although their chromosomal backbone is closely related to that of Gram-positive bacteria of the phylum Firmicutes. The complete genome of a clinical A. intestini strain is here presented. PMID:22123762

  3. 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

    2015-06-11

    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.

  4. A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data

    USDA-ARS?s Scientific Manuscript database

    Zygomycete fungi were classified as a single phylum, Zygomycota, based on sexual reproduction by zygospores, frequent asexual reproduction by sporangia, absence of multicellular sporocarps, and production of coenocytic hyphae, all with some exceptions. Molecular phylogenies based on one or a few gen...

  5. 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.

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

    PubMed Central

    Li, Jinhua; Pan, Yongxin

    2012-01-01

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

  7. Complete Genome of Ignavibacterium album, a Metabolically Versatile, Flagellated, Facultative Anaerobe from the Phylum Chlorobi.

    PubMed

    Liu, Zhenfeng; Frigaard, Niels-Ulrik; Vogl, Kajetan; Iino, Takao; Ohkuma, Moriya; Overmann, Jörg; Bryant, Donald A

    2012-01-01

    Prior to the recent discovery of Ignavibacterium album (I. album), anaerobic photoautotrophic green sulfur bacteria (GSB) were the only members of the bacterial phylum Chlorobi that had been grown axenically. In contrast to GSB, sequence analysis of the 3.7-Mbp genome of I. album shows that this recently described member of the phylum Chlorobi is a chemoheterotroph with a versatile metabolism. I. album lacks genes for photosynthesis and sulfur oxidation but has a full set of genes for flagella and chemotaxis. The occurrence of genes for multiple electron transfer complexes suggests that I. album is capable of organoheterotrophy under both oxic and anoxic conditions. The occurrence of genes encoding enzymes for CO(2) fixation as well as other enzymes of the reductive TCA cycle suggests that mixotrophy may be possible under certain growth conditions. However, known biosynthetic pathways for several amino acids are incomplete; this suggests that I. album is dependent upon on exogenous sources of these metabolites or employs novel biosynthetic pathways. Comparisons of I. album and other members of the phylum Chlorobi suggest that the physiology of the ancestors of this phylum might have been quite different from that of modern GSB.

  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

    2014-02-04

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

    PubMed

    Lin, Wei; Li, Jinhua; Pan, Yongxin

    2012-02-01

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

  11. Draft Genome Sequence of Microbacterium sp. Strain UCD-TDU (Phylum Actinobacteria)

    PubMed Central

    Bendiks, Zachary A.; Lang, Jenna M.; Darling, Aaron E.; Coil, David A.

    2013-01-01

    Here, we present the draft genome sequence of Microbacterium sp. strain UCD-TDU, a member of the phylum Actinobacteria. The assembly contains 3,746,321 bp (in 8 scaffolds). This strain was isolated from a residential toilet as part of an undergraduate student research project to sequence reference genomes of microbes from the built environment. PMID:23516225

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

    PubMed Central

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

    2013-01-01

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

  13. Type I Cutaneous Meningioma (Rudimentary Meningocele) With Intradural Attachment to the Phylum Terminale.

    PubMed

    Mazloom, Sean E; Holliday, Alex C; Coman, Garrett C; Chavan, Rahul N; Kolodney, Michael S; Grider, Douglas J

    2016-12-01

    Cutaneous meningiomas (CM) are a small subset of meningiomas, further classified into three subtypes. The authors present a 15-year-old male with a symptomatic congenital type I CM and describe the histopathological and immunohistochemical findings. To the authors' knowledge, this is the first report of an extraspinal lumbar type I CM with intradural attachment to the phylum terminale.

  14. Insights into the distribution and abundance of the ubiquitous Candidatus Saccharibacteria phylum following tag pyrosequencing

    PubMed Central

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

    2014-01-01

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

  15. 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.

  16. 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

  17. Demonstration of a liquid core optical ring resonator sensor coupled with an ARROW waveguide array

    NASA Astrophysics Data System (ADS)

    White, Ian M.; Oveys, Hesam; Fan, Xudong; Smith, Terry L.; Zhang, Junying

    2007-02-01

    The liquid core optical ring resonator (LCORR) sensor is a newly developed capillary-based ring resonator that integrates microfluidics with photonic sensing technology. The circular cross-section of the capillary forms a ring resonator that supports whispering gallery modes (WGM). The WGM evanescent field is exposed to the capillary core and detects the aqueous samples conducted by the capillary using a label-free protocol. The high-Q of the WGM allows for repetitive light-analyte interaction, resulting in excellent sensitivity. Recently a detection limit of the LCORR on the order of 10 -6 refractive index units was reported. In this work, we have further integrated the LCORR with an anti-resonant reflective optical waveguide (ARROW) array for multiplexed sensor development. The ARROW, with an array of 8 waveguides separated by 250 microns each, consists of a core and a lower reflective double-layer with alternating high and low refractive index, and thus has a significant evanescent field above the waveguide. The WGM is excited at each LCORR/ARROW junction simultaneously when the LCORR is brought into contact with the ARROW array. We experimentally investigated the optimal waveguide geometry for WGM excitation using a range of waveguide heights from 2 to 5 microns. Furthermore, the LCORR/ARROW system is utilized for a biomolecule sensing demonstration. The LCORR/ARROW system is not only essential for assembling a robust, practical, and densely multiplexed sensor array, but also enables on-capillary flow analysis that has broad applications in capillary electrophoresis, chromatography, and lab-on-a-chip development.

  18. 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.

  19. 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

  20. 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…

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

    NASA Technical Reports Server (NTRS)

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

    1988-01-01

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

  2. MEGA: A search for the decay {mu}{r_arrow}{ital e}{gamma}

    SciTech Connect

    Szymanski, J.J.; Amann, J.F.; Baker, K.; Barlow, D.; Black, K.; Bolton, R.D.; Brooks, M.; Carius, S.; Chen, Y.; Cooper, M.D.; Cooper, P.S.; Crocker, J.; Dzemidzic, M.; Fisk, R.J.; Flick, J.; Foreman, W.; Gagliardi, C.A.; Haim, D.; Hallin, A.; Harrison, R.; Hart, G.; Hoffman, C.M.; Hogan, G.E.; Hughes, E.B.; Hungerford, E.V. III; Johnston, K.; Jui, C.; Kim, G.J.; Knott, J.E.

    1995-07-10

    The MEGA experiment is designed to search for the rare decay {mu}{r_arrow}{ital e}{gamma} with a branching ratio sensitivity of {similar_to}5{times}10{sup {minus}13}. Production data have been taken during 1992 and 1993, and the detector is working as expected. Following a complete analysis, the present data set should represent an improvement of 12--15 in sensitivity over the previous limit of {mu}{r_arrow}{ital e}{gamma}. {copyright} {ital 1995} {ital American} {ital Institute} {ital of} {ital Physics}.

  3. Search for Supernarrow Dibaryons Production in pd [right arrow] p + pX1 and pd [right arrow] p + dX2 Reactions

    NASA Astrophysics Data System (ADS)

    Fil'kov, L. V.; Kashevarov, V. L.; Konobeevski, E. S.; Mordovskoy, M. V.; Potashev, S. I.; Simonov, V. A.; Skorkin, V. M.

    2002-06-01

    We study a production of supernarrow dibaryons, the decay of which into two nucleons is forbidden by the Pauli exclusion principle, in the reactions pd [right arrow] p+pX1 and pd [right arrow] p + dX2 at Linear Accelerator of INR (Moscow). Dibaryons with masses 1904plus-or-minus2, 1926plus-or-minus2 and 1942plus-or-minus2 MeV have been observed in missing mass MpX1 spectra. In missing mass MX1 spectra, the peaks at MX1 = 966plus-or-minus2, 986plus-or-minus2, and 1003plus-or-minus2 MeV have been found. The analysis of the data obtained leads to the conclusion that the observed dibaryons are supernarrow dibaryons. The possible interpretation of "exotic baryon states" with small masses is discussed.

  4. 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.

  5. Branching fractions of B{sup plus} {r_arrow} {Psi}(2S)K{sup plus} and B{sup O} {r_arrow} {Psi}(2S)K{sup {asterisk}0} decays at CDF

    SciTech Connect

    Warburton, A.

    1996-07-01

    This paper describes the observation of the decays B{sup {plus}} {r_arrow} {psi}(2S)K{sup {plus}} and B{sup 0} {r_arrow} {psi}(2S)K{sup {asterisk}}(892){sup 0} in 1.8 TeV p{ovr p} collisions and presents measurements of the branching fractions Br(B{sup {plus}} {r_arrow} {psi}(2S)K{sup {plus}}) and Br(B{sup 0} {r_arrow} {psi}(2S)K{sup {asterisk}}(892){sup 0}) relative to Br(B{sup {plus}} {r_arrow} J/{psi}K{sup {plus}}) and Br(B{sup 0} {r_arrow} J/{psi}K{sup {asterisk}}(892){sup 0}), respectively. The {psi}(2S) mesons are reconstructed in both the {psi}(2S) {r_arrow} {mu}{sup {plus}}{mu}{sup {minus}} and {psi}(2S) {r_arrow} J/{psi}{pi}{sup {plus}}{pi}{sup {minus}} channels. The world average branching fractions for the J/{psi} channels are used to extract the absolute branching fractions Br(B{sup {plus}} {r_arrow} {psi}(2S)K{sup {plus}}) = (6.8{plus_minus}1.0(stat.){plus_minus}1.4(syst.)){times}10{sup {minus}4} and Br(B{sup 0} {r_arrow} {psi}(2S)K{sup {asterisk}}(892){sup 0}) = (9.0{plus_minus}2.1(stat.){plus_minus}2. 0(syst.)){times}10{sup {minus}4}. 9 refs., 13 figs., 8 tabs.

  6. 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.

  7. 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

  8. 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…

  9. 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

  10. 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

  11. 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

  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. 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…

  15. WormBase: a comprehensive resource for nematode research.

    PubMed

    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.

  16. 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

  17. 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

  18. Uncertainties from long range effects in [ital B][r arrow][ital K][sup *][gamma

    SciTech Connect

    Golowich, E. ); Pakvasa, S. )

    1995-02-01

    We reconsider the long-range'' component of the radiative transition [ital B][r arrow][ital K][sup *][gamma]. A careful analysis of the vector dominance amplitude [ital B][r arrow][ital V][sub 1][ital V][sub 2][r arrow][ital V][sub 1][gamma] is carried out, with emphasis on the role of gauge invariance. The procedure for incorporating phenomenological [ital B][r arrow][ital V][sub 1][ital V][sub 2] data is identified, and polarization data, only recently available, is employed to estimate the magnitude of the vector dominance effect. We summarize uncertainties in the [ital B][r arrow][ital K][sup *][gamma] radiative transition produced by long-range effects and provide suggestions for further experimental work.

  19. Armatimonas rosea gen. nov., sp. nov., of a novel bacterial phylum, Armatimonadetes phyl. nov., formally called the candidate phylum OP10.

    PubMed

    Tamaki, Hideyuki; Tanaka, Yasuhiro; Matsuzawa, Hiroaki; Muramatsu, Mizuho; Meng, Xian-Ying; Hanada, Satoshi; Mori, Kazuhiro; Kamagata, Yoichi

    2011-06-01

    A novel aerobic, chemoheterotrophic bacterium, strain YO-36(T), isolated from the rhizoplane of an aquatic plant (a reed, Phragmites australis) inhabiting a freshwater lake in Japan, was morphologically, physiologically and phylogenetically characterized. Strain YO-36(T) was Gram-negative and ovoid to rod-shaped, and formed pinkish hard colonies on agar plates. Strain YO-36(T) grew at 20-40 °C with optimum growth at 30-35 °C, whilst no growth was observed at 15 °C or 45 °C. The pH range for growth was 5.5-8.5 with an optimum at pH 6.5. Strain YO-36(T) utilized a limited range of substrates, such as sucrose, gentiobiose, pectin, gellan gum and xanthan gum. The strain contained C(16 : 0), C(16 : 1), C(14 : 0) and C(15 : 0) as the major cellular fatty acids and menaquinone-12 as the respiratory quinone. The G+C content of the genomic DNA was 62.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YO-36(T) belonged to the candidate phylum OP10 comprised solely of environmental 16S rRNA gene clone sequences except for two strains, P488 and T49 isolated from geothermal soil in New Zealand; strain YO-36(T) showed less than 80 % sequence similarity to strains P488 and T47. Based on the phylogetic and phenotypic findings, a new genus and species, Armatimonas rosea gen. nov., sp. nov., is proposed for the isolate (type strain YO-36(T)  = NBRC 105658(T)  = DSM 23562(T)). In addition, a new bacterial phylum named Armatimonadetes phyl. nov. is proposed for the candidate phylum OP10 represented by A. rosea gen. nov., sp. nov. and Armatimonadaceae fam. nov., Armatimonadales ord. nov., and Armatimonadia classis nov.

  20. A phylogenomic and molecular signature based approach for characterization of the phylum Spirochaetes and its major clades: proposal for a taxonomic revision of the phylum.

    PubMed

    Gupta, Radhey S; Mahmood, Sharmeen; Adeolu, Mobolaji

    2013-01-01

    The Spirochaetes species cause many important diseases including syphilis and Lyme disease. Except for their containing a distinctive endoflagella, no other molecular or biochemical characteristics are presently known that are specific for either all Spirochaetes or its different families. We report detailed comparative and phylogenomic analyses of protein sequences from Spirochaetes genomes to understand their evolutionary relationships and to identify molecular signatures for this group. These studies have identified 38 conserved signature indels (CSIs) that are specific for either all members of the phylum Spirochaetes or its different main clades. Of these CSIs, a 3 aa insert in the FlgC protein is uniquely shared by all sequenced Spirochaetes providing a molecular marker for this phylum. Seven, six, and five CSIs in different proteins are specific for members of the families Spirochaetaceae, Brachyspiraceae, and Leptospiraceae, respectively. Of the 19 other identified CSIs, 3 are uniquely shared by members of the genera Sphaerochaeta, Spirochaeta, and Treponema, whereas 16 others are specific for the genus Borrelia. A monophyletic grouping of the genera Sphaerochaeta, Spirochaeta, and Treponema distinct from the genus Borrelia is also strongly supported by phylogenetic trees based upon concatenated sequences of 22 conserved proteins. The molecular markers described here provide novel and more definitive means for identification and demarcation of different main groups of Spirochaetes. To accommodate the extensive genetic diversity of the Spirochaetes as revealed by different CSIs and phylogenetic analyses, it is proposed that the four families of this phylum should be elevated to the order level taxonomic ranks (viz. Spirochaetales, Brevinematales ord. nov., Brachyspiriales ord. nov., and Leptospiriales ord. nov.). It is further proposed that the genera Borrelia and Cristispira be transferred to a new family Borreliaceae fam. nov. within the order

  1. Discrete Modeling of the Worm Spread with Random Scanning

    NASA Astrophysics Data System (ADS)

    Uchida, Masato

    In this paper, we derive a set of discrete time difference equations that models the spreading process of computer worms such as Code-Red and Slammer, which uses a common strategy called “random scanning” to spread through the Internet. We show that the derived set of discrete time difference equations has an exact relationship with the Kermack and McKendrick susceptible-infectious-removed (SIR) model, which is known as a standard continuous time model for worm spreading.

  2. 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.

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

    PubMed Central

    Grant, Katherine A. J.; Gorman, Alice R.; Vizard, Victoria; Plackett, Harriet; Gamble, Margaret L.

    2016-01-01

    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

  4. Bacterial Microbiota Associated with the Glacier Ice Worm Is Dominated by Both Worm-Specific and Glacier-Derived Facultative Lineages.

    PubMed

    Murakami, Takumi; Segawa, Takahiro; Dial, Roman; Takeuchi, Nozomu; Kohshima, Shiro; Hongoh, Yuichi

    2017-03-31

    The community structure of bacteria associated with the glacier ice worm Mesenchytraeus solifugus was analyzed by amplicon sequencing of 16S rRNA genes and their transcripts. Ice worms were collected from two distinct glaciers in Alaska, Harding Icefield and Byron Glacier, and glacier surfaces were also sampled for comparison. Marked differences were observed in bacterial community structures between the ice worm and glacier surface samples. Several bacterial phylotypes were detected almost exclusively in the ice worms, and these bacteria were phylogenetically affiliated with either animal-associated lineages or, interestingly, clades mostly consisting of glacier-indigenous species. The former included bacteria that belong to Mollicutes, Chlamydiae, Rickettsiales, and Lachnospiraceae, while the latter included Arcicella and Herminiimonas phylotypes. Among these bacteria enriched in ice worm samples, Mollicutes, Arcicella, and Herminiimonas phylotypes were abundantly and consistently detected in the ice worm samples; these phylotypes constituted the core microbiota associated with the ice worm. A fluorescence in situ hybridization analysis showed that Arcicella cells specifically colonized the epidermis of the ice worms. Other bacterial phylotypes detected in the ice worm samples were also abundantly recovered from the respective habitat glaciers; these bacteria may be food for ice worms to digest or temporary residents. Nevertheless, some were overrepresented in the ice worm RNA samples; they may also function as facultative gut bacteria. Our results indicate that the community structure of bacteria associated with ice worms is distinct from that in the associated glacier and includes worm-specific and facultative, glacier-indigenous lineages.

  5. Bacterial Microbiota Associated with the Glacier Ice Worm Is Dominated by Both Worm-Specific and Glacier-Derived Facultative Lineages

    PubMed Central

    Murakami, Takumi; Segawa, Takahiro; Dial, Roman; Takeuchi, Nozomu; Kohshima, Shiro; Hongoh, Yuichi

    2017-01-01

    The community structure of bacteria associated with the glacier ice worm Mesenchytraeus solifugus was analyzed by amplicon sequencing of 16S rRNA genes and their transcripts. Ice worms were collected from two distinct glaciers in Alaska, Harding Icefield and Byron Glacier, and glacier surfaces were also sampled for comparison. Marked differences were observed in bacterial community structures between the ice worm and glacier surface samples. Several bacterial phylotypes were detected almost exclusively in the ice worms, and these bacteria were phylogenetically affiliated with either animal-associated lineages or, interestingly, clades mostly consisting of glacier-indigenous species. The former included bacteria that belong to Mollicutes, Chlamydiae, Rickettsiales, and Lachnospiraceae, while the latter included Arcicella and Herminiimonas phylotypes. Among these bacteria enriched in ice worm samples, Mollicutes, Arcicella, and Herminiimonas phylotypes were abundantly and consistently detected in the ice worm samples; these phylotypes constituted the core microbiota associated with the ice worm. A fluorescence in situ hybridization analysis showed that Arcicella cells specifically colonized the epidermis of the ice worms. Other bacterial phylotypes detected in the ice worm samples were also abundantly recovered from the respective habitat glaciers; these bacteria may be food for ice worms to digest or temporary residents. Nevertheless, some were overrepresented in the ice worm RNA samples; they may also function as facultative gut bacteria. Our results indicate that the community structure of bacteria associated with ice worms is distinct from that in the associated glacier and includes worm-specific and facultative, glacier-indigenous lineages. PMID:28302989

  6. 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.

  7. 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

  8. Phylogeny and molecular signatures for the phylum Thermotogae and its subgroups.

    PubMed

    Gupta, Radhey S; Bhandari, Vaibhav

    2011-06-01

    Thermotogae species are currently identified mainly on the basis of their unique toga and distinct branching in the rRNA and other phylogenetic trees. No biochemical or molecular markers are known that clearly distinguish the species from this phylum from all other bacteria. The taxonomic/evolutionary relationships within this phylum, which consists of a single family, are also unclear. We report detailed phylogenetic analyses on Thermotogae species based on concatenated sequences for many ribosomal as well as other conserved proteins that identify a number of distinct clades within this phylum. Additionally, comprehensive analyses of protein sequences from Thermotogae genomes have identified >60 Conserved Signature Indels (CSI) that are specific for the Thermotogae phylum or its different subgroups. Eighteen CSIs in important proteins such as PolI, RecA, TrpRS and ribosomal proteins L4, L7/L12, S8, S9, etc. are uniquely present in various Thermotogae species and provide molecular markers for the phylum. Many CSIs were specific for a number of Thermotogae subgroups. Twelve of these CSIs were specific for a clade consisting of various Thermotoga species except Tt. lettingae, which was separated from other Thermotoga species by a long branch in phylogenetic trees; Fourteen CSIs were specific for a clade consisting of the Fervidobacterium and Thermosipho genera and eight additional CSIs were specific for the genus Thermosipho. In addition, the existence of a clade consisting of the deep branching species Petrotoga mobilis, Kosmotoga olearia and Thermotogales bacterium mesG1 was supported by seven CSIs. The deep branching of this clade was also supported by a number of CSIs that were present in various Thermotogae species, but absent in this clade and all other bacteria. Most of these clades were strongly supported by phylogenetic analyses based on two datasets of protein sequences and they identify potential higher taxonomic grouping (viz. families) within this phylum

  9. Observation of D sub s sup + r arrow K sup 0 K sup + and D sub s sup + r arrow K sup 0 K sup + and an upper limit on D sub s sup + r arrow K sup 0. pi. sup +

    SciTech Connect

    Adler, J.; Bai, Z.; Becker, J.J.; Blaylock, G.T.; Bolton, T.; Brient, J.; Brown, J.S.; Bunnell, K.O.; Burchell, M.; Burnett, T.H.; and others; Mark III Collaboration

    1989-09-18

    We report the first observation of the decay {ital D}{sub {ital s}}{sup +}{r arrow}{bar K}{sup 0}{ital K}{sup +} and a new measurement of the decay {ital D}{sub {ital s}}{sup +}{r arrow}{ital {bar K}} *(892){sup 0}{ital K}{sup +}. The data were collected at {radical}{ital s}=4.14 GeV with the Mark III detector at the SLAC {ital e}{sup +}{ital e}{sup {minus}} storage ring at SPEAR. We obtain the relative branching fractions {ital B}({ital D}{sup +}{sub {ital s}}{r arrow}{ital {bar K}}{sup 0}{ital K}{sup +}/ {ital B}{ital D}{sub {ital s}}{sup +}{r arrow}{phi}{pi}{sup +})=0.92{plus minus}0.32{plus minus}0.20 and {ital B}({ital D}{sub {ital s}}{sup +}{r arrow}{ital {bar K}}{sup *0}{ital K}{sup +})/ {ital B}({ital D}{sub {ital s}}{sup +}{r arrow}{phi}{pi}{sup +})=0.84{plus minus}0.30{plus minus}0.22, using our new determination of {sigma}{ital B}({ital D}{sub {ital s}}{sup +}{r arrow}{phi}{pi}{sup +}). A search for the Cabibbo-suppressed decay {ital D}{ital s}{sup +}{r arrow}{ital K}{sup 0}{pi}{sup +} yields a limit {ital B}({ital D}{sub {ital s}}{sup +}{r arrow}{ital K}{sup 0}{pi}{sup +})/{ital B}({ital D}{sub {ital s}}{sup +}{r arrow}{phi}{pi}{sup +}){lt}0.21 at the 90% confidence level.

  10. Pycellerator: an arrow-based reaction-like modelling language for biological simulations.

    PubMed

    Shapiro, Bruce E; Mjolsness, Eric

    2016-02-15

    We introduce Pycellerator, a Python library for reading Cellerator arrow notation from standard text files, conversion to differential equations, generating stand-alone Python solvers, and optionally running and plotting the solutions. All of the original Cellerator arrows, which represent reactions ranging from mass action, Michales-Menten-Henri (MMH) and Gene-Regulation (GRN) to Monod-Wyman-Changeaux (MWC), user defined reactions and enzymatic expansions (KMech), were previously represented with the Mathematica extended character set. These are now typed as reaction-like commands in ASCII text files that are read by Pycellerator, which includes a Python command line interface (CLI), a Python application programming interface (API) and an iPython notebook interface. Cellerator reaction arrows are now input in text files. The arrows are parsed by Pycellerator and translated into differential equations in Python, and Python code is automatically generated to solve the system. Time courses are produced by executing the auto-generated Python code. Users have full freedom to modify the solver and utilize the complete set of standard Python tools. The new libraries are completely independent of the old Cellerator software and do not require Mathematica. All software is available (GPL) from the github repository at https://github.com/biomathman/pycellerator/releases. Details, including installation instructions and a glossary of acronyms and terms, are given in the Supplementary information. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  11. 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. Copyright © 2013 Wiley Periodicals, Inc.

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

    ERIC Educational Resources Information Center

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

    2012-01-01

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

  13. 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…

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

    PubMed

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

    2016-05-01

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

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

    ERIC Educational Resources Information Center

    Ferguson, Robert; Bodner, George M.

    2008-01-01

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

  16. Activation of frontoparietal attention networks by non-predictive gaze and arrow cues.

    PubMed

    Joseph, Robert M; Fricker, Zachary; Keehn, Brandon

    2015-02-01

    Gaze and arrow cues automatically orient visual attention, even when they have no predictive value, but the neural circuitry by which they direct attention is not clear. Recent evidence has indicated that the ventral frontoparietal attention network is primarily engaged by breaches of a viewer's cue-related expectations. Accordingly, we hypothesized that to the extent that non-predictive gaze and arrow cues automatically engender expectations with regard to cue location, they should activate the ventral attention network when they cue attention invalidly. Using event-related fMRI, we found that invalid gaze but not arrow cues activated the ventral attention network, specifically in the area of the right temporal parietal junction (TPJ), as well as nodes along the dorsal attention network associated with a redirection of attention to the correct target location. In additional whole-brain analyses, facilitation of behavioral response time by valid gaze cues was linearly associated with the degree of activation in the right TPJ. We conclude from our findings that gaze direction elicits potent expectations in humans with regard to an actor's intention that engage attention networks if not differently from, at least more robustly than, arrow cues. © The Author (2014). Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

  17. 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…

  18. 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…

  19. Activation of frontoparietal attention networks by non-predictive gaze and arrow cues

    PubMed Central

    Fricker, Zachary; Keehn, Brandon

    2015-01-01

    Gaze and arrow cues automatically orient visual attention, even when they have no predictive value, but the neural circuitry by which they direct attention is not clear. Recent evidence has indicated that the ventral frontoparietal attention network is primarily engaged by breaches of a viewer’s cue-related expectations. Accordingly, we hypothesized that to the extent that non-predictive gaze and arrow cues automatically engender expectations with regard to cue location, they should activate the ventral attention network when they cue attention invalidly. Using event-related fMRI, we found that invalid gaze but not arrow cues activated the ventral attention network, specifically in the area of the right temporal parietal junction (TPJ), as well as nodes along the dorsal attention network associated with a redirection of attention to the correct target location. In additional whole-brain analyses, facilitation of behavioral response time by valid gaze cues was linearly associated with the degree of activation in the right TPJ. We conclude from our findings that gaze direction elicits potent expectations in humans with regard to an actor’s intention that engage attention networks if not differently from, at least more robustly than, arrow cues. PMID:24748545

  20. 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…

  1. 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).

  2. 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…

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

    PubMed

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

    2012-08-20

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

  4. Disconnection of the rubber tip of arrow-trerotola percutaneous thrombolytic device.

    PubMed

    Kim, Han Myun; Kim, Hyo-Cheol; Woo, Sungmin; Son, Kyu Ri; Jae, Hwan Jun

    2014-01-01

    A rubber tip disconnection of Arrow-Trerotola percutaneous thrombolytic device (PTD) may occur occasionally. We experienced 5 cases of a rubber tip disconnection among 453 mechanical thrombectomy sessions with the use of PTD. We present a report about these five cases and suggest possible causes for the occurrences.

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

    ERIC Educational Resources Information Center

    Ferguson, Robert; Bodner, George M.

    2008-01-01

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

  6. 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…

  7. 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…

  8. 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…

  9. Upper limit on the branching ratio for the decay. pi. sup 0 r arrow. nu. nu

    SciTech Connect

    Atiya, M.S.; Chiang, I.; Frank, J.S.; Haggerty, J.S.; Ito, M.M.; Kycia, T.F.; Li, K.K.; Littenberg, L.S.; Stevens, A.; Strand, R.C. ); Louis, W.C. ); Akerib, D.S.; Marlow, D.R.; Meyers, P.D.; Selen, M.A.; Shoemaker, F.C.; Smith, A.J.S. ); Azuelos, G.; Blackmore, E.W.; Bryman, D.A.; Felawka, L.; Kitching, P.; Kuno, Y.; Macdonald, J.A.; Numao, T.; Padley, P.; Poutissou, J.; Poutissou, R.; Roy, J. V6T 2A3)

    1991-04-29

    An experimental upper limit on the branching ratio for the decay {pi}{sup 0}{r arrow}{nu}{bar {nu}} is set at 8.3{times}10{sup {minus}7} (90% C.L.). This decay is forbidden if neutrinos are purely left handed. The limit also applies to any decays of the {pi}{sup 0} to weakly interacting neutrals.

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

    PubMed

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

    2014-11-01

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

  11. Axin and the Axin/Arrow-binding protein DCAP mediate glucose-glycogen metabolism.

    PubMed

    Yamazaki, Hiroto; Yanagawa, Shin ichi

    2003-05-02

    Axin was found as a negative regulator of the canonical Wnt pathway. Human LRP5 was originally found as a candidate gene of insulin dependent diabetes mellitus (IDDM), but its Drosophila homolog, Arrow, works as a co-receptor of the canonical Wnt signal. In our previous paper, we found a new Drosophila Axin (Daxin)-binding SH3 protein, DCAP, a homolog of mammalian CAV family protein. Among the subtypes, DCAPL3 shows significant homology with CAP, an essential component of glucose transport in insulin signal. Further binding assay revealed that DCAP binds to not only Axin but also Arrow, and Axin binds to not only GSK3beta but also Arrow. However, overexpression and RNAi experiments of DCAP do not affect the canonical Wnt pathway. As DCAP is expressed predominantly in insulin-target organs, and as RNAi of DCAP disrupts the pattern of endogenous glycogen accumulation in late stage embryos, we suggest that DCAP is also involved in glucose transport. Moreover, early stage embryos lacking maternal Axin show significant delay of initial glycogen decomposition, and RNAi of Axin in S2 cells revealed quite increase of endogenous glycogen level as well as GSK3beta. These results suggest that Axin and DCAP mediate glucose-glycogen metabolism in embryo. In addition, the interaction among Axin, Arrow, and DCAP implies a possible cross-talk between Wnt signal and insulin signal.

  12. 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…

  13. 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…

  14. 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…

  15. 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…

  16. Early Twentieth Century Arrow, Javelin, and Dart Games of the Western Native American.

    ERIC Educational Resources Information Center

    Pesavento, Wilma J.

    The general purpose of this study was to determine whether the traditional native American ball games continued to be positive culture traits of the American Indian in the early twentieth century. The investigation was centered about (1) determining the current arrow, javelin, and dart games of western native Americans, (2) determining the…

  17. The cued recognition task: dissociating the abrupt onset effect from the social and arrow cueing effect.

    PubMed

    Xu, Buyun; Tanaka, James W

    2015-01-01

    In a standard center cueing paradigm, participants are asked to identify a target object presented either to the left or the right of a center cue (e.g., eye gaze, head-turn, arrow, etc.). When the center cue is non-predictive (e.g., the arrow points to the correct location of the target only 50 % of the time), the target can still be identified faster at the validly cued location than at the invalidly cued location. However, the abrupt onset of an object can elicit reflexive attention orientation. It is important to investigate whether this abrupt onset effect interferes with the cueing effect elicited by center cues because this interference effect, if it exists, should be controlled for in order to improve the test validity of the center cueing task. In an attentional cueing paradigm, we examined how the abrupt appearance of an exogenous target object mitigates the influence of center cues involving either a head turn (Experiment 1) or an arrow (Experiment 2). In Experiment 1, a non-predictive head-turn cue was followed by a target object (circle or square) presented in the left or right visual field. In the non-distractor condition, the target object was presented by itself. In this case, it is assumed that the sudden appearance of the target provides an orienting cue to the observer. To equalize the cueing effect of the target object, we presented a competing distractor object (triangle) in the opposite visual field to the target object. The participant's task was to categorize the target object as either a circle or square while ignoring the non-target triangle object in the opposite visual field. In Experiment 2, the arrow version of the cued recognition task was used, in which a single-headed arrow pointed to the object. The results from both experiments showed that both the non-predictive head-turn and arrow cues produced a reliable cueing effect in the distractor and non-distractor conditions. However, the magnitude of the cueing effect was greater in

  18. 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. Copyright © 2015, American Association for the Advancement of Science.

  19. 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.

  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.

    PubMed

    Gherna, R; Woese, C R

    1992-12-01

    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. 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.

  3. 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

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

    PubMed

    Geyer, Kathrin K; Chalmers, Iain W; Mackintosh, Neil; Hirst, Julie E; Geoghegan, Rory; Badets, Mathieu; Brophy, Peter M; Brehm, Klaus; Hoffmann, Karl F

    2013-07-09

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

  5. Phylogenetic framework and molecular signatures for the main clades of the phylum Actinobacteria.

    PubMed

    Gao, Beile; Gupta, Radhey S

    2012-03-01

    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.

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

    PubMed Central

    2013-01-01

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

  7. Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing.

    PubMed

    Shih, Patrick M; Wu, Dongying; Latifi, Amel; Axen, Seth D; Fewer, David P; Talla, Emmanuel; Calteau, Alexandra; Cai, Fei; Tandeau de Marsac, Nicole; Rippka, Rosmarie; Herdman, Michael; Sivonen, Kaarina; Coursin, Therese; Laurent, Thierry; Goodwin, Lynne; Nolan, Matt; Davenport, Karen W; Han, Cliff S; Rubin, Edward M; Eisen, Jonathan A; Woyke, Tanja; Gugger, Muriel; Kerfeld, Cheryl A

    2013-01-15

    The cyanobacterial phylum encompasses oxygenic photosynthetic prokaryotes of a great breadth of morphologies and ecologies; they play key roles in global carbon and nitrogen cycles. The chloroplasts of all photosynthetic eukaryotes can trace their ancestry to cyanobacteria. Cyanobacteria also attract considerable interest as platforms for "green" biotechnology and biofuels. To explore the molecular basis of their different phenotypes and biochemical capabilities, we sequenced the genomes of 54 phylogenetically and phenotypically diverse cyanobacterial strains. Comparison of cyanobacterial genomes reveals the molecular basis for many aspects of cyanobacterial ecophysiological diversity, as well as the convergence of complex morphologies without the acquisition of novel proteins. This phylum-wide study highlights the benefits of diversity-driven genome sequencing, identifying more than 21,000 cyanobacterial proteins with no detectable similarity to known proteins, and foregrounds the diversity of light-harvesting proteins and gene clusters for secondary metabolite biosynthesis. Additionally, our results provide insight into the distribution of genes of cyanobacterial origin in eukaryotic nuclear genomes. Moreover, this study doubles both the amount and the phylogenetic diversity of cyanobacterial genome sequence data. Given the exponentially growing number of sequenced genomes, this diversity-driven study demonstrates the perspective gained by comparing disparate yet related genomes in a phylum-wide context and the insights that are gained from it.

  8. 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

  9. A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data.

    PubMed

    Spatafora, Joseph W; Chang, Ying; Benny, Gerald L; Lazarus, Katy; Smith, Matthew E; Berbee, Mary L; Bonito, Gregory; Corradi, Nicolas; Grigoriev, Igor; Gryganskyi, Andrii; James, Timothy Y; O'Donnell, Kerry; Roberson, Robert W; Taylor, Thomas N; Uehling, Jessie; Vilgalys, Rytas; White, Merlin M; Stajich, Jason E

    2016-09-01

    Zygomycete fungi were classified as a single phylum, Zygomycota, based on sexual reproduction by zygospores, frequent asexual reproduction by sporangia, absence of multicellular sporocarps, and production of coenocytic hyphae, all with some exceptions. Molecular phylogenies based on one or a few genes did not support the monophyly of the phylum, however, and the phylum was subsequently abandoned. Here we present phylogenetic analyses of a genome-scale data set for 46 taxa, including 25 zygomycetes and 192 proteins, and we demonstrate that zygomycetes comprise two major clades that form a paraphyletic grade. A formal phylogenetic classification is proposed herein and includes two phyla, six subphyla, four classes and 16 orders. On the basis of these results, the phyla Mucoromycota and Zoopagomycota are circumscribed. Zoopagomycota comprises Entomophtoromycotina, Kickxellomycotina and Zoopagomycotina; it constitutes the earliest diverging lineage of zygomycetes and contains species that are primarily parasites and pathogens of small animals (e.g. amoeba, insects, etc.) and other fungi, i.e. mycoparasites. Mucoromycota comprises Glomeromycotina, Mortierellomycotina, and Mucoromycotina and is sister to Dikarya. It is the more derived clade of zygomycetes and mainly consists of mycorrhizal fungi, root endophytes, and decomposers of plant material. Evolution of trophic modes, morphology, and analysis of genome-scale data are discussed. © 2016 by The Mycological Society of America.

  10. Gliding motility and Por secretion system genes are widespread among members of the phylum bacteroidetes.

    PubMed

    McBride, Mark J; Zhu, Yongtao

    2013-01-01

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

  11. 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.

  12. 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.

  13. Phylum-wide general protein O-glycosylation system of the Bacteroidetes.

    PubMed

    Coyne, Michael J; Fletcher, C Mark; Chatzidaki-Livanis, Maria; Posch, Gerald; Schaffer, Christina; Comstock, Laurie E

    2013-05-01

    The human gut symbiont Bacteroides fragilis has a general protein O-glycosylation system in which numerous extracytoplasmic proteins are glycosylated at a three amino acid motif. In B. fragilis, protein glycosylation is a fundamental and essential property as mutants with protein glycosylation defects have impaired growth and are unable to competitively colonize the mammalian intestine. In this study, we analysed the phenotype of B. fragilis mutants with defective protein glycosylation and found that the glycan added to proteins is comprised of a core glycan and an outer glycan. The genetic region encoding proteins for the synthesis of the outer glycan is conserved within a Bacteroides species but divergent between species. Unlike the outer glycan, an antiserum raised to the core glycan reacted with all Bacteroidetes species tested, from all four classes of the phylum. We found that diverse Bacteroidetes species synthesize numerous glycoproteins and glycosylate proteins at the same three amino acid motif. The wide-spread conservation of this protein glycosylation system within the phylum suggests that this system of post-translational protein modification evolved early, before the divergence of the four classes of Bacteroidetes, and has been maintained due to its physiological importance to the diverse species of this phylum.

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

    PubMed Central

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

    2015-01-01

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

  15. Sludge reduction using aquatic worms under different aeration regimes.

    PubMed

    Cai, Lu; Gao, Ding; Wang, Kan; Liu, Hong-Tao; Wan, Xiao-Ming

    2017-03-01

    Adding aquatic worms to a wastewater treatment system can reduce sludge production through predation. The aeration level is crucial for success. To evaluate aeration impacts on sludge reduction and determine an optimal aeration regime, this study investigated the processes of in-situ sludge reduction, using aquatic worms exposed to different aeration levels. The experiment also compared treatment results between a conventional reactor and an aquatic worm reactor (WR). Results indicated that the recommended concentration of dissolved oxygen (DO) was 2.5 mg L(-1). The removal rate of chemical oxygen demand remained steady at 80% when the DO concentration was higher than 2.5 mg L(-1), while the removal rate of ammonia nitrogen continued to moderately increase. Increasing the DO concentration to 5 mg L(-1) did not improve sludge reduction, and consumed more power. With a DO concentration of 2.5 mg L(-1) and a power of 0.19 kWh t(-1) water, the absolute sludge reduction and relative sludge reduction rates in the WR were 60.0% and 45.7%, respectively, and the daily aquatic worm growth rate was 0.150 d(-1) during the 17-d test. Therefore, at the recommended aeration regime, aquatic worms reduced the sludge without increasing the power consumption or deteriorating the effluent.

  16. Meningeal worm in a reintroduced elk population in Kentucky.

    PubMed

    Larkin, Jeffery L; Alexy, Karen J; Bolin, David C; Maehr, David S; Cox, John J; Wichrowski, Michael W; Seward, Nathan W

    2003-07-01

    Meningeal worm (Parelaphostrongylus tenuis) has been implicated in the failure of several elk (Cervus elaphus) restoration attempts in the eastern United States. However, limited post-release monitoring and a paucity of published literature prevents a clear understanding of this parasite's role in past failures. During winters of 1997-2001, the Kentucky Department of Fish and Wildlife Resources translocated 1,044 elk from western states to eastern Kentucky (USA) in an effort to restore a free-ranging population. We monitored 521 radio-collared elk over 4 yr to determine the impact meningeal worm had on population establishment. Thirty (23%) of 129 non-capture related mortalities were attributed to meningeal worm. Twenty-two (73%) of these meningeal worm-caused mortalities were animals < 3 yr old. If younger elk born in Kentucky suffer higher mortality rates than older translocated elk, the population growth observed during the initial years of restoration may be temporary. Additional research is necessary to determine the influence meningeal worm will have on elk population growth in Kentucky.

  17. Tracking movement behavior of multiple worms on food.

    PubMed

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

    2011-12-01

    Neurobiological research in genetically tractable organisms relies heavily on robust assays for behavioral phenotypes. The simple body plan of the nematode Caenorhabditis elegans makes it particularly amenable to the use of automated microscopy and image analysis to describe behavioral patterns quantitatively. Forward genetic screens and screens of drug libraries require high-throughput phenotyping, a task traditionally incompatible with manual scoring of quantitatively varying behaviors. High-throughput automated analysis of C. elegans movement behavior is now possible with several different tracking software packages. The Multiworm Tracker (MWT) described here is designed for high-throughput analysis: it can record dozens of worms simultaneously at 30 frames per second for hours or days at a time. This is accomplished by performing all image analysis in real time, saving only the worm centroid, bearing, and outline data to the disk. To simplify image processing, the system focuses only on worms that have moved, and detects and discards worms that are touching rather than trying to isolate them computationally. Because the software is entirely automated, protocols can run unattended once the worms have been placed and the software has been started. The MWT does not save images for later analysis, but behavior can be validated manually with a companion analysis tool that replays recorded body postures. This protocol describes a basic basal movement assay on food using the MWT; similar protocols apply to related assays and to similar multiple animal trackers. The protocol can be extended to a variety of assays ranging from tap response to chemotaxis.

  18. The Gut Microbiota of Healthy Chilean Subjects Reveals a High Abundance of the Phylum Verrucomicrobia

    PubMed Central

    Fujio-Vejar, Sayaka; Vasquez, Yessenia; Morales, Pamela; Magne, Fabien; Vera-Wolf, Patricia; Ugalde, Juan A.; Navarrete, Paola; Gotteland, Martin

    2017-01-01

    The gut microbiota is currently recognized as an important factor regulating the homeostasis of the gastrointestinal tract and influencing the energetic metabolism of the host as well as its immune and central nervous systems. Determining the gut microbiota composition of healthy subjects is therefore necessary to establish a baseline allowing the detection of microbiota alterations in pathologic conditions. Accordingly, the aim of this study was to characterize the gut microbiota of healthy Chilean subjects using 16S rRNA gene sequencing. Fecal samples were collected from 41 young, asymptomatic, normal weight volunteers (age: 25 ± 4 years; ♀:48.8%; BMI: 22.5 ± 1.6 kg/m2) with low levels of plasma (IL6 and hsCRP) and colonic (fecal calprotectin) inflammatory markers. The V3-V4 region of the 16S rRNA gene of bacterial DNA was amplified and sequenced using MiSeq Illumina system. 109,180 ± 13,148 sequences/sample were obtained, with an α-diversity of 3.86 ± 0.37. The dominant phyla were Firmicutes (43.6 ± 9.2%) and Bacteroidetes (41.6 ± 13.1%), followed by Verrucomicrobia (8.5 ± 10.4%), Proteobacteria (2.8 ± 4.8%), Actinobacteria (1.8 ± 3.9%) and Euryarchaeota (1.4 ± 2.7%). The core microbiota representing the genera present in all the subjects included Bacteroides, Prevotella, Parabacteroides (phylum Bacteroidetes), Phascolarctobacterium, Faecalibacterium, Ruminococcus, Lachnospira, Oscillospira, Blautia, Dorea, Roseburia, Coprococcus, Clostridium, Streptococcus (phylum Firmicutes), Akkermansia (phylum Verrucomicrobia), and Collinsella (phylum Actinobacteria). Butyrate-producing genera including Faecalibacterium, Roseburia, Coprococcus, and Oscillospira were detected. The family Methanobacteriaceae was reported in 83% of the subjects and Desulfovibrio, the most representative sulfate-reducing genus, in 76%. The microbiota of the Chilean individuals significantly differed from those of Papua New Guinea and the Matses ethnic group and was closer to that of

  19. The impact of various distance between axes of worm gear on torque value. Worm gear test stand

    NASA Astrophysics Data System (ADS)

    Sobek, M.; Baier, A.; Grabowski, Ł.

    2017-08-01

    Transferring both rotational and translational movements in systems used in the automotive industry is a very important and complex issue. In addition, the situation becomes much more difficult and complicated when the design of the transition system requires a high precision of operation as well as a well definite and long operating life. Such requirements are imposed on all components of today’s motor vehicles. However, particular attention is paid to the elements that directly or indirectly affect the safety of persons traveling in the vehicle. Such components are undoubtedly components included as parts of the steering system of the vehicle. Power steering systems have been present in motor vehicles for more than a century. They go through continuous metamorphosis and they are getting better and better. Current power steering systems are based on an electric motor and some kind of transmission. Depending on the position of the drive relative to the steering column, different configurations of the transmission are used. This article will cover issues related to tests of power steering gearing using a worm drive. The worm drive is a very specific example of a propulsion system that uses twisted axles. Normally, in this type of transition you can find two gear units with the axis mounted with a 90° angle between. The components of the worm drive are a worm and a worm gear, also called a worm wheel. In terms of the geometrical form, the worm resembles a helical spur gear. The shape of the worm is similar to the shape of a screw with a trapezoidal thread. A correct matching of these two components ensures proper operation of the entire transmission. Incorrect positioning of the components in relation to each other can significantly reduce the lifetime of the drive unit, and also lead to abnormal work, eg by raising the noise level. This article describes a test method of finding the appropriate distance between the axles of both worm drive units by testing the

  20. 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

  1. 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.

  2. Community participation in the eradication of guinea worm disease.

    PubMed

    Cairncross, S; Braide, E I; Bugri, S Z

    1996-04-01

    As Guinea worm eradication programmes have got under way in endemic countries over the last decade, there has been a shift towards more participatory methods. The approach to surveillance has changed from periodic cross-sectional surveys to monthly village-based reporting of cases by a volunteer village health worker. At the same time, the emphasis regarding control interventions has moved from the provision of safe water supplies to health education. The new approach has proved very effective. The village health volunteers who carry out both surveillance and health education seem to be motivated largely by the social status of their role; still more commitment will be required of them in the final stages of eradication. It is to be hoped that the networks of village health workers established for Guinea worm eradication will find a useful role in health promotion after the worms have gone.

  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. Logistics of Guinea Worm Disease Eradication in South Sudan

    PubMed Central

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

    2014-01-01

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

  5. 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.

  6. 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

  7. 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.

  8. A new neutron polarimeter and measurement of {sup n}{sub E} from the {sup 2}H(e [downward right arrow] e' n [downward right arrow]){sup 1}H reaction

    SciTech Connect

    Richard Madey; A. Lai; Tom Eden

    1994-09-01

    In a continuing effort to improve the quality of measurements for extracting the neutron electronic form factor (G{sup n}{sub E} from the {sup 2}H[downward right arrow]e'n[downward right arrow]) {sup 1}H reaction, one of us (RM) proposed a new configuration for a neutron polarimeter (NPOL) to measure G{sup n}{sub E}from the {sup 2}H (e[downward right arrow], e'n[downward right arrow]){sup 1}H reaction in Bates E89-04 and CEBAF E93-038. Substantially higher count rates with this new neutron polarimeter reduce the uncertainties in G{sup n}{sub E}. A description of the new NPOL is given here followed by an outline of the experiment with projections of uncertainties in G{sup n}{sub E}.

  9. 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.

  10. Cellular clot formation in a sipunculan worm: entrapment of foreign particles, cell death and identification of a PGRP-related protein.

    PubMed

    Blanco, Guillermo A; Malchiodi, Emilio L; De Marzi, Mauricio C

    2008-10-01

    Clotting in animals having open or closed circulatory system comprises humoral and cellular mechanisms. Sipunculans are a small phylum of non-segmented marine worms that do not have a true circulatory system. These worms can form a cellular clot without transforming cell-free coelomic fluid into an insoluble mass. The clot may also contribute to immune response by entrapping foreign particles. We evaluated the formation of a cellular clot ex vivo in the sipunculan Themiste petricola after activation through glass contact and sea water, the ability to entrap magnetic beads and non-pathogen cyanobacteria particles within the clot, and the presence of a peptidoglycan recognition protein S (PGRP-S) antigen in cells forming the clot. Our results showed that the clot was formed by homotypic aggregation of large granular leukocytes (LGLs), a subtype of cells found in the coelomic fluid. Aggregated LGLs served to entrap magnetic beads and non-pathogen cyanobacteria particles, and PGRP-S antigen was detected both in non-activated LGLs and in activated homotypic aggregates through immunofluorescence, Western blot and flow cytometry. Cellular clots were found to be positive to Annexin V-FITC labelling. Complete disintegration of cytoplasm with shedding of microparticles, nuclear isolation and degradation were also observed by light microscopy and flow cytometry. In conclusion, cellular clot formation in Themiste petricola may serve both haemostatic and immune functions entailing rapid activation changes in LGLs, entrapment of foreign particles within a homotypic aggregate, and further cell death.

  11. Shai-Hulud: The quest for worm sign

    NASA Astrophysics Data System (ADS)

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

    2005-03-01

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

  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. 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.

  14. 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}

  15. [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.

  16. Parallelized quantum Monte Carlo algorithm with nonlocal worm updates.

    PubMed

    Masaki-Kato, Akiko; Suzuki, Takafumi; Harada, Kenji; Todo, Synge; Kawashima, Naoki

    2014-04-11

    Based on the worm algorithm in the path-integral representation, we propose a general quantum Monte Carlo algorithm suitable for parallelizing on a distributed-memory computer by domain decomposition. Of particular importance is its application to large lattice systems of bosons and spins. A large number of worms are introduced and its population is controlled by a fictitious transverse field. For a benchmark, we study the size dependence of the Bose-condensation order parameter of the hard-core Bose-Hubbard model with L×L×βt=10240×10240×16, using 3200 computing cores, which shows good parallelization efficiency.

  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. The facile synthesis of single crystalline palladium arrow-headed tripods and their application in formic acid electro-oxidation.

    PubMed

    Su, Na; Chen, Xueying; Ren, Yuanhang; Yue, Bin; Wang, Han; Cai, Wenbin; He, Heyong

    2015-04-28

    Single crystalline palladium arrow-headed tripods prepared via a simple one-pot strategy exhibit high electro-activity in formic acid oxidation, which could be a promising anodic catalyst for direct formic acid fuel cells.

  19. Search for Proton Decay through p {r_arrow} {bar {nu}}K{sup +} in a Large Water Cherenkov Detector

    SciTech Connect

    Fukuda, Y.; Hayakawa, T.; Inoue, K.; Ishihara, K.; Ishino, H.; Itow, Y.; Kajita, T.; Kameda, J.; Kasuga, S.; Kobayashi, K.; Kobayashi, Y.; Koshio, Y.; Miura, M.; Nakahata, M.; Nakayama, S.; Obayashi, Y.; Okada, A.; Okumura, K.; Sakurai, N.; Shiozawa, M.; Suzuki, Y.; Takeuchi, H.; Takeuchi, Y.; Totsuka, Y.; Yamada, S.; Earl, M.; Habig, A.; Kearns, E.; Messier, M.D.; Scholberg, K.; Stone, J.L.; Sulak, L.R.; Walter, C.W.; Goldhaber, M.; Barszczak, T.; Casper, D.; Gajewski, W.; Kropp, W.R.; Mine, S.; Price, L.R.; Smy, M.; Sobel, H.W.; Vagins, M.R.; Haines, T.J.; Kielczewska, D.; Ganezer, K.S.; Keig, W.E.; Ellsworth, R.W.; Tasaka, S.; Kibayashi, A.; Learned, J.G.; Matsuno, S.; Stenger, V.J.; Takemori, D.; Ishii, T.; Kanzaki, J.; Kobayashi, T.; Nakamura, K.; Nishikawa, K.; Oyama, Y.; Sakai, A.; Sakuda, M.; Sasaki, O.; Echigo, S.; Kohama, M.; Suzuki, A.T.; Haines, T.J.; Blaufuss, E.; Kim, B.K.; Sanford, R.; and others

    1999-08-01

    We present results of a search for proton decays, p{r_arrow}{bar {nu}}K{sup +} , using data from a 33 kt{center_dot}yr exposure of the Super-Kamiokande detector. Two decay modes of the kaon, K{sup +}{r_arrow}{mu}{sup +}{nu}{sub {mu}} and K{sup +}{r_arrow}{pi}{sup +}{pi}{sup 0} , were studied. The data were consistent with the background expected from atmospheric neutrinos; therefore a lower limit on the partial lifetime of the proton {tau}/B(p{r_arrow}{bar {nu}} K{sup +}) was found to be 6.7{times}10{sup 32} years at 90{percent} confidence level. {copyright} {ital 1999} {ital The American Physical Society}

  20. Flap effectiveness on subsonic longitudinal aerodynamic characteristics of a modified arrow wing

    NASA Technical Reports Server (NTRS)

    Quinto, P. F.; Paulson, J. W., Jr.

    1983-01-01

    An investigation of the subsonic longitudinal aerodynamic characteristics of a modified arrow-wing model was conducted in the Langley 4- by 7-Meter Tunnel. This investigation addressed the effectiveness of the leading and trailing edge flap deflections of this model. The arrow wing was tested at a Mach number of 0.02 and at an angle-of-attack range from -4 deg to 24 deg. The results of the investigation showed that deflecting the leading edge and trailing edge in combination could promote an attached-flow condition at the wing leading edge. Also, the leading edge suction could be maximized over the complete lift-coefficient range by scheduling a combination of leading and trailing edge flap deflections.

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

    NASA Technical Reports Server (NTRS)

    Lamar, John E.; Obara, Clifford J.

    2007-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Atmanspacher, Harald; Filk, Thomas; Scheingraber, Herbert

    2006-10-01

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

  3. Space Station ATCS radiator rotation profiles in LVLH, TEA/LVLH, Arrow and Gravity Gradient mode

    NASA Astrophysics Data System (ADS)

    Kantara, James J.; Graf, Jonathan

    1992-07-01

    Results are presented of an analysis of the Active Thermal Control System Central Thermal Bus radiator rotation profiles for the Space Station Freedom in local vertical/local horizontal (LVLH) two torgue equilibrium attitudes (MB11 and MB17), Arrow and Gravity Gradient modes, while maintaining radiator angular velocity and acceleration under 45 deg/min and 0.01 deg/sq sec, respectively. The model used in the analysis, which is an enhancement to the model described in the LESC-28760 (1990) technical memo, is structured to orient the radiator to the minimum environment during the sunlit portion of the orbit and to maximum environment during the dark-side portion. The results of the investigated cased indicate that, in order to minimize the environmental incident fluxes on the radiator and maximize the radiator heat rejection capabilities, the radiator should be allowed to rotate between -167 deg (Gravity Gradient mode) and 207 deg (Arrow mode).

  4. 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.

  5. High Statistics Measurement of B arrow Λc X and Σc X

    NASA Astrophysics Data System (ADS)

    Wappler, Frank

    1997-04-01

    This analysis is based on about 5 fb-1 of data recorded by the CLEO II detector operating at CESR on the Υ(4S) resonance and at center-of-mass energies just below the threshold for the production of B\\overlineB mesons. The first observation of the inclusive decays B arrow Λ_c^+ X, Σ_c^0 X and Σ_c^++X has already been reported by ARGUS (1988) and CLEO (1992). We now present a high statistics measurement of these decay modes. Improved values for branching fractions and momentum spectra will be presented. Results of the search for the inclusive decay B arrow Σ_c^+ X, which has not yet been observed, will also be presented.

  6. 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.

  7. Iroquois Engine for the Avro Arrow in the Propulsion Systems Laboratory

    NASA Image and Video Library

    1957-08-21

    A researcher examines the Orenda Iroquois PS.13 turbojet in a Propulsion Systems Laboratory test chamber at the National Advisory Committee for Aeronautics (NACA) Lewis Flight Propulsion Laboratory. The Iroquois was being developed to power the CF-105 Arrow fighter designed by the Avro Canada Company. Avro began design work on the Arrow jet fighter in 1952. The company’s Orenda branch suggested building a titanium-based PS.13 Iroquois engine after development problems arose with the British engines that Avro had originally intended to use. The 10-stage, 20,000-pound-thrust Iroquois would prove to be more powerful than any contemporary US or British turbojet. It was also significantly lighter and more fuel efficient. An Iroquois was sent to Cleveland in April 1957 so that Lewis researchers could study the engine’s basic performance for the air force in the Propulsion Systems Laboratory. The tests were run over a wide range of speeds and altitudes with variations in exhaust-nozzle area. Initial studies determined the Iroquois’s windmilling and ignition characteristics at high altitude. After operating for 64 minutes, the engine was reignited at altitudes up to the 63,000-foot limit of the facility. Various modifications were attempted to reduce the occurrence of stall but did not totally eradicate the problem. The Arrow jet fighter made its initial flight in March 1958 powered by a substitute engine. In February 1959, however, both the engine and the aircraft programs were cancelled. The world’s superpowers had quickly transitioned from bombers to ballistic missiles which rendered the Avro Arrow prematurely obsolete.

  8. 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.

  9. 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.

  10. Membrane Targeting of Disheveled Can Bypass the Need for Arrow/LRP5.

    PubMed

    Kaur, Prameet; Lam, Vanessa Yuk Man; Mannava, Anirudh Gautam; Suresh, Jahnavi; Jenny, Andreas; Tolwinski, Nicholas S

    2017-07-31

    The highly conserved Wnt signaling pathway regulates cell proliferation and differentiation in vertebrates and invertebrates. Upon binding of a Wnt ligand to a receptor of the Fz family, Disheveled (Dsh/Dvl) transduces the signal during canonical and non-canonical Wnt signaling. The specific details of how this process occurs have proven difficult to study, especially as Dsh appears to function as a switch between different branches of Wnt signaling. Here we focus on the membrane-proximal events that occur once Dsh is recruited to the membrane. We show that membrane-tethering of the Dsh protein is sufficient to induce canonical Wnt signaling activation even in the absence of the Wnt co-receptor Arrow/LRP5/6. We map the protein domains required for pathway activation in membrane tethered constructs finding that both the DEP and PDZ domains are dispensable for canonical signaling only in membrane-tethered Dsh, but not in untethered/normal Dsh. These data lead to a signal activation model, where Arrow is required to localize Dsh to the membrane during canonical Wnt signaling placing Dsh downstream of Arrow.

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

    PubMed

    VanPool, Todd L; O'Brien, Michael J

    2013-01-01

    The evolution of sociopolitical complexity, including heightened relations of cooperation and competition among large nonkin groups, has long been a central focus of anthropological research. Anthropologists suggest any number of variables that affect the waxing and waning of complexity and define the precise trajectories that groups take, including population density, subsistence strategies, warfare, the distribution of resources, and trade relationships. Changes in weaponry, here the introduction of the bow and arrow, can have profound implications for population aggregation and density, subsistence and settlement strategies, and access to resources, trade, and warfare.Bingham and Souza provide a general conceptual model for the relationship between complexity and the bow and arrow, arguing that this compound weapon system, whereby smaller projectiles travel at higher speed and are capable of hitting targets more accurately and at greater distances than hand-thrown darts, fundamentally favors the formation of larger groups because it allows for cost-effective means of dealing with conflicts of interest through social coercion, thereby dramatically transforming kin-based social relations. Here we consider the impacts the introduction of the bow and arrow had on sociopolitical complexity in the North American Southwest. Copyright © 2013 Wiley Periodicals, Inc.

  12. 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.

  13. Distribution of Hydrogenases in Cyanobacteria: A Phylum-Wide Genomic Survey

    PubMed Central

    Puggioni, Vincenzo; Tempel, Sébastien; Latifi, Amel

    2016-01-01

    Microbial Molecular hydrogen (H2) cycling plays an important role in several ecological niches. Hydrogenases (H2ases), enzymes involved in H2 metabolism, are of great interest for investigating microbial communities, and producing BioH2. To obtain an overall picture of the genetic ability of Cyanobacteria to produce H2ases, we conducted a phylum wide analysis of the distribution of the genes encoding these enzymes in 130 cyanobacterial genomes. The concomitant presence of the H2ase and genes involved in the maturation process, and that of well-conserved catalytic sites in the enzymes were the three minimal criteria used to classify a strain as being able to produce a functional H2ase. The [NiFe] H2ases were found to be the only enzymes present in this phylum. Fifty-five strains were found to be potentially able produce the bidirectional Hox enzyme and 33 to produce the uptake (Hup) enzyme. H2 metabolism in Cyanobacteria has a broad ecological distribution, since only the genomes of strains collected from the open ocean do not possess hox genes. In addition, the presence of H2ase was found to increase in the late branching clades of the phylogenetic tree of the species. Surprisingly, five cyanobacterial genomes were found to possess homologs of oxygen tolerant H2ases belonging to groups 1, 3b, and 3d. Overall, these data show that H2ases are widely distributed, and are therefore probably of great functional importance in Cyanobacteria. The present finding that homologs to oxygen-tolerant H2ases are present in this phylum opens new perspectives for applying the process of photosynthesis in the field of H2 production. PMID:28083017

  14. Distribution of Hydrogenases in Cyanobacteria: A Phylum-Wide Genomic Survey.

    PubMed

    Puggioni, Vincenzo; Tempel, Sébastien; Latifi, Amel

    2016-01-01

    Microbial Molecular hydrogen (H2) cycling plays an important role in several ecological niches. Hydrogenases (H2ases), enzymes involved in H2 metabolism, are of great interest for investigating microbial communities, and producing BioH2. To obtain an overall picture of the genetic ability of Cyanobacteria to produce H2ases, we conducted a phylum wide analysis of the distribution of the genes encoding these enzymes in 130 cyanobacterial genomes. The concomitant presence of the H2ase and genes involved in the maturation process, and that of well-conserved catalytic sites in the enzymes were the three minimal criteria used to classify a strain as being able to produce a functional H2ase. The [NiFe] H2ases were found to be the only enzymes present in this phylum. Fifty-five strains were found to be potentially able produce the bidirectional Hox enzyme and 33 to produce the uptake (Hup) enzyme. H2 metabolism in Cyanobacteria has a broad ecological distribution, since only the genomes of strains collected from the open ocean do not possess hox genes. In addition, the presence of H2ase was found to increase in the late branching clades of the phylogenetic tree of the species. Surprisingly, five cyanobacterial genomes were found to possess homologs of oxygen tolerant H2ases belonging to groups 1, 3b, and 3d. Overall, these data show that H2ases are widely distributed, and are therefore probably of great functional importance in Cyanobacteria. The present finding that homologs to oxygen-tolerant H2ases are present in this phylum opens new perspectives for applying the process of photosynthesis in the field of H2 production.

  15. 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

    2015-02-06

    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. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

  16. The opportunistic transmission of wireless worms between mobile devices

    NASA Astrophysics Data System (ADS)

    Rhodes, C. J.; Nekovee, M.

    2008-12-01

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

  17. 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

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

    NASA Astrophysics Data System (ADS)

    Tuncay, Çağlar

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

  19. 3-D Worm Tracker for Freely Moving C. elegans

    PubMed Central

    Kwon, Namseop; Pyo, Jaeyeon; Lee, Seung-Jae; Je, Jung Ho

    2013-01-01

    The manner in which the nervous system regulates animal behaviors in natural environments is a fundamental issue in biology. To address this question, C. elegans has been widely used as a model animal for the analysis of various animal behaviors. Previous behavioral assays have been limited to two-dimensional (2-D) environments, confining the worm motion to a planar substrate that does not reflect three-dimensional (3-D) natural environments such as rotting fruits or soil. Here, we develop a 3-D worm tracker (3DWT) for freely moving C. elegans in 3-D environments, based on a stereoscopic configuration. The 3DWT provides us with a quantitative trajectory, including the position and movement direction of the worm in 3-D. The 3DWT is also capable of recording and visualizing postures of the moving worm in 3-D, which are more complex than those in 2-D. Our 3DWT affords new opportunities for understanding the nervous system function that regulates animal behaviors in natural 3-D environments. PMID:23437394

  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. 3-D worm tracker for freely moving C. elegans.

    PubMed

    Kwon, Namseop; Pyo, Jaeyeon; Lee, Seung-Jae; Je, Jung Ho

    2013-01-01

    The manner in which the nervous system regulates animal behaviors in natural environments is a fundamental issue in biology. To address this question, C. elegans has been widely used as a model animal for the analysis of various animal behaviors. Previous behavioral assays have been limited to two-dimensional (2-D) environments, confining the worm motion to a planar substrate that does not reflect three-dimensional (3-D) natural environments such as rotting fruits or soil. Here, we develop a 3-D worm tracker (3DWT) for freely moving C. elegans in 3-D environments, based on a stereoscopic configuration. The 3DWT provides us with a quantitative trajectory, including the position and movement direction of the worm in 3-D. The 3DWT is also capable of recording and visualizing postures of the moving worm in 3-D, which are more complex than those in 2-D. Our 3DWT affords new opportunities for understanding the nervous system function that regulates animal behaviors in natural 3-D environments.

  2. 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).

  3. 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

  4. 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.

  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. Tracking Movement Behavior of Multiple Worms on Food

    PubMed Central

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

    2016-01-01

    Neurobiological research in genetically tractable organisms relies heavily on robust assays for behavioral phenotypes. The simple body plan of the nematode Caenorhabditis elegans makes it particularly amenable to the use of automated microscopy and image analysis to describe behavioral patterns quantitatively. Forward genetic screens and screens of drug libraries require high-throughput phenotyping, a task traditionally incompatible with manual scoring of quantitatively varying behaviors. High-throughput automated analysis of C. elegans movement behavior is now possible with several different tracking software packages. The Multiworm Tracker (MWT) described here is designed for high-throughput analysis: it can record dozens of worms simultaneously at 30 frames per second for hours or days at a time. This is accomplished by performing all image analysis in real time, saving only the worm centroid, bearing, and outline data to the disk. To simplify image processing, the system focuses only on worms that have moved, and detects and discards worms that are touching rather than trying to isolate them computationally. Because the software is entirely automated, protocols can run unattended once the worms have been placed and the software has been started. The MWT does not save images for later analysis, but behavior can be validated manually with a companion analysis tool that replays recorded body postures. This protocol describes a basic basal movement assay on food using the MWT; similar protocols apply to related assays and to similar multiple animal trackers. The protocol can be extended to a variety of assays ranging from tap response to chemotaxis. PMID:22135669

  7. Single and multiple worm infections of Echinostoma caproni (Trematoda) in the golden hamster.

    PubMed

    Fried, B; Huffman, J E; Weiss, P M

    1990-03-01

    Six of 10 hamsters fed a single metacercarial cyst of Echinostoma caproni (single-worm infections) and 13 of 19 hamsters fed either 2 or 5 cysts (multiple-worm infections) were infected with adult echinostomes at necropsy 22 days post-infection. Considerable histopathological changes to the small intestine occurred in hamsters carrying single-worm infections. There were no differences in either mean length, width or wet weight of echinostomes in single- versus multiple-worm infections. The mean number of eggs/worm from single-worm infections (525) was significantly greater than that from multiple-worm infections (288). The average percentage of fully developed miracidia/worm from single worms (94%) was similar to that from worms in multiple infections (92-95%). Single worms of E. caproni were capable of self-fertilization and production of viable eggs. Miracidia derived from single worms were as capable of infecting laboratory-reared Biomphalaria glabrata and producing patent rediae as were those from multiple infections.

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

    SciTech Connect

    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 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. 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.

  9. 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.

  10. 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; ...

    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

  11. Phylogeny of anaerobic fungi (phylum Neocallimastigomycota), with contributions from yak in China.

    PubMed

    Wang, Xuewei; Liu, Xingzhong; Groenewald, Johannes Z

    2017-01-01

    The phylum Neocallimastigomycota contains eight genera (about 20 species) of strictly anaerobic fungi. The evolutionary relationships of these genera are uncertain due to insufficient sequence data to infer their phylogenies. Based on morphology and molecular phylogeny, thirteen isolates obtained from yak faeces and rumen digesta in China were assigned to Neocallimastix frontalis (nine isolates), Orpinomyces joyonii (two isolates) and Caecomyces sp. (two isolates), respectively. The phylogenetic relationships of the eight genera were evaluated using complete ITS and partial LSU sequences, compared to the ITS1 region which has been widely used in this phylum in the past. Five monophyletic lineages corresponding to six of the eight genera were statistically supported. Isolates of Caecomyces and Cyllamyces were present in a single lineage and could not be separated properly. Members of Neocallimastigomycota with uniflagellate zoospores represented by Piromyces were polyphyletic. The Piromyces-like genus Oontomyces was consistently closely related to the traditional Anaeromyces, and separated the latter genus into two clades. The phylogenetic position of the Piromyces-like genus Buwchfawromyces remained unresolved. Orpinomyces and Neocallimastix, sharing polyflagellate zoospores, were supported as sister genera in the LSU phylogeny. Apparently ITS, specifically ITS1 alone, is not a good marker to resolve the generic affinities of the studied fungi. The LSU sequences are easier to align and appear to work well to resolve generic relationships. This study provides a comparative phylogenetic revision of Neocallimastigomycota isolates known from culture and sequence data.

  12. 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. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

  13. 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

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

    DOE PAGES

    Calteau, Alexandra; Fewer, David P.; Latifi, Amel; ...

    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

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

    SciTech Connect

    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

    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 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-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.

  17. 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

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

    DOE PAGES

    Eloe-Fadrosh, Emiley A.; Paez-Espino, David; Jarett, Jessica; ...

    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

  19. 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.

  20. 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.

  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. Copyright 2010 Elsevier Inc. All rights reserved.

  2. 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

  3. 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

  4. [Use of genes of carbon metabolism enzymes as molecular markers of Chlorobi Phylum representatives].

    PubMed

    Turova, T P; Kovaleva, O L; Gorlenko, V M; Ivanovskiĭ, R N

    2014-01-01

    This work examined the feasibility of using certain genes of carbon metabolism enzymes as molecular markers adequate for studying phylogeny and ecology of green sulfur bacteria (GSB) of the Chlorobi phylum. Primers designed to amplify the genes of ATP citrate lyase (aclB) and citrate synthase (gltA) revealed the respective genes in the genomes of all of the newly studied GSB strains. The phylogenetic trees constructed based on nucleotide sequences of these genes and amino acid sequences of the conceptually translated proteins were on the whole congruent with the 16S rRNA gene tree, with the single exception of GltA of Chloroherpeton thalassium, which formed a separate branch beyond the cluster comprised by other representatives of the Chlorobi phylum. Thus, the aclB genes but not gltA genes proved to be suitable for the design of primers specific to all Chlorobi representatives. Therefore, it was the aclB gene that was further used asa molecular marker to detect GSB in enrichment cultures and environmental samples. AclB phylotypes of GSB were revealed in all of the samples studied, with the exception of environmental samples from soda lakes. The identification of the revealed phylotypes was in agreement with the identification based on the FMO protein gene (fmo), is a well-known Chlorobi-specific molecular marker.

  5. The Distribution of Lectins across the Phylum Nematoda: A Genome-Wide Search.

    PubMed

    Bauters, Lander; Naalden, Diana; Gheysen, Godelieve

    2017-01-04

    Nematodes are a very diverse phylum that has adapted to nearly every ecosystem. They have developed specialized lifestyles, dividing the phylum into free-living, animal, and plant parasitic species. Their sheer abundance in numbers and presence in nearly every ecosystem make them the most prevalent animals on earth. In this research nematode-specific profiles were designed to retrieve predicted lectin-like domains from the sequence data of nematode genomes and transcriptomes. Lectins are carbohydrate-binding proteins that play numerous roles inside and outside the cell depending on their sugar specificity and associated protein domains. The sugar-binding properties of the retrieved lectin-like proteins were predicted in silico. Although most research has focused on C-type lectin-like, galectin-like, and calreticulin-like proteins in nematodes, we show that the lectin-like repertoire in nematodes is far more diverse. We focused on C-type lectins, which are abundantly present in all investigated nematode species, but seem to be far more abundant in free-living species. Although C-type lectin-like proteins are omnipresent in nematodes, we have shown that only a small part possesses the residues that are thought to be essential for carbohydrate binding. Curiously, hevein, a typical plant lectin domain not reported in animals before, was found in some nematode species.

  6. Phylum-specific environmental DNA analysis reveals remarkably high global biodiversity of Cercozoa (Protozoa).

    PubMed

    Bass, David; Cavalier-Smith, Thomas

    2004-11-01

    This study presents the first 18S rRNA multi-library environmental PCR survey of a single protozoan phylum, Cercozoa Cavalier-Smith 1998, from a range of different habitats. Phylogenetic analysis reveals at least nine novel clades within the phylum, several possibly at the level of order or above. Further experiments are described to ascertain the true ecological and geographical distributions of some clades that might be inferred from the tree to be restricted in either or both ways. These results suggest that the diversity of cercozoan taxa may run into thousands of lineages, making it comparable in diversity to the largest better-characterized protozoan phyla, e.g. Ciliophora (ciliates and suctorians) and Foraminifera. New sequences of cultured Spongomonas, Metromonas and Metopion are also presented. In the light of these additions, and the increased taxon sampling from the environmental libraries, some revisions of cercozoan classification are made: the transfer of Spongomonadea from Reticulofilosa to Monadofilosa; the removal of Metopiida from Sarcomonadea; and the creation of the new order Metromonadida, currently containing the single genus Metromonas. Although Metromonas groups with weak to moderate support with Chlorarachnea, it is here placed in superclass Monadofilosa, to which it is morphologically more similar.

  7. 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.

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

    PubMed

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

    2006-01-01

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

  9. 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

  10. Methane oxidation by an extremely acidophilic bacterium of the phylum Verrucomicrobia.

    PubMed

    Dunfield, Peter F; Yuryev, Anton; Senin, Pavel; Smirnova, Angela V; Stott, Matthew B; Hou, Shaobin; Ly, Binh; Saw, Jimmy H; Zhou, Zhemin; Ren, Yan; Wang, Jianmei; Mountain, Bruce W; Crowe, Michelle A; Weatherby, Tina M; Bodelier, Paul L E; Liesack, Werner; Feng, Lu; Wang, Lei; Alam, Maqsudul

    2007-12-06

    Aerobic methanotrophic bacteria consume methane as it diffuses away from methanogenic zones of soil and sediment. They act as a biofilter to reduce methane emissions to the atmosphere, and they are therefore targets in strategies to combat global climate change. No cultured methanotroph grows optimally below pH 5, but some environments with active methane cycles are very acidic. Here we describe an extremely acidophilic methanotroph that grows optimally at pH 2.0-2.5. Unlike the known methanotrophs, it does not belong to the phylum Proteobacteria but rather to the Verrucomicrobia, a widespread and diverse bacterial phylum that primarily comprises uncultivated species with unknown genotypes. Analysis of its draft genome detected genes encoding particulate methane monooxygenase that were homologous to genes found in methanotrophic proteobacteria. However, known genetic modules for methanol and formaldehyde oxidation were incomplete or missing, suggesting that the bacterium uses some novel methylotrophic pathways. Phylogenetic analysis of its three pmoA genes (encoding a subunit of particulate methane monooxygenase) placed them into a distinct cluster from proteobacterial homologues. This indicates an ancient divergence of Verrucomicrobia and Proteobacteria methanotrophs rather than a recent horizontal gene transfer of methanotrophic ability. The findings show that methanotrophy in the Bacteria is more taxonomically, ecologically and genetically diverse than previously thought, and that previous studies have failed to assess the full diversity of methanotrophs in acidic environments.

  11. The Distribution of Lectins across the Phylum Nematoda: A Genome-Wide Search

    PubMed Central

    Bauters, Lander; Naalden, Diana; Gheysen, Godelieve

    2017-01-01

    Nematodes are a very diverse phylum that has adapted to nearly every ecosystem. They have developed specialized lifestyles, dividing the phylum into free-living, animal, and plant parasitic species. Their sheer abundance in numbers and presence in nearly every ecosystem make them the most prevalent animals on earth. In this research nematode-specific profiles were designed to retrieve predicted lectin-like domains from the sequence data of nematode genomes and transcriptomes. Lectins are carbohydrate-binding proteins that play numerous roles inside and outside the cell depending on their sugar specificity and associated protein domains. The sugar-binding properties of the retrieved lectin-like proteins were predicted in silico. Although most research has focused on C-type lectin-like, galectin-like, and calreticulin-like proteins in nematodes, we show that the lectin-like repertoire in nematodes is far more diverse. We focused on C-type lectins, which are abundantly present in all investigated nematode species, but seem to be far more abundant in free-living species. Although C-type lectin-like proteins are omnipresent in nematodes, we have shown that only a small part possesses the residues that are thought to be essential for carbohydrate binding. Curiously, hevein, a typical plant lectin domain not reported in animals before, was found in some nematode species. PMID:28054982

  12. 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.

  13. Anaerobic fungi (phylum Neocallimastigomycota): advances in understanding their taxonomy, life cycle, ecology, role and biotechnological potential.

    PubMed

    Gruninger, Robert J; Puniya, Anil K; Callaghan, Tony M; Edwards, Joan E; Youssef, Noha; Dagar, Sumit S; Fliegerova, Katerina; Griffith, Gareth W; Forster, Robert; Tsang, Adrian; McAllister, Tim; Elshahed, Mostafa S

    2014-10-01

    Anaerobic fungi (phylum Neocallimastigomycota) inhabit the gastrointestinal tract of mammalian herbivores, where they play an important role in the degradation of plant material. The Neocallimastigomycota represent the earliest diverging lineage of the zoosporic fungi; however, understanding of the relationships of the different taxa (both genera and species) within this phylum is in need of revision. Issues exist with the current approaches used for their identification and classification, and recent evidence suggests the presence of several novel taxa (potential candidate genera) that remain to be characterised. The life cycle and role of anaerobic fungi has been well characterised in the rumen, but not elsewhere in the ruminant alimentary tract. Greater understanding of the 'resistant' phase(s) of their life cycle is needed, as is study of their role and significance in other herbivores. Biotechnological application of anaerobic fungi, and their highly active cellulolytic and hemi-cellulolytic enzymes, has been a rapidly increasing area of research and development in the last decade. The move towards understanding of anaerobic fungi using -omics based (genomic, transcriptomic and proteomic) approaches is starting to yield valuable insights into the unique cellular processes, evolutionary history, metabolic capabilities and adaptations that exist within the Neocallimastigomycota.

  14. 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.

  15. 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

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

    SciTech Connect

    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 higherature 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.

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

    DOE PAGES

    Eloe-Fadrosh, Emiley A.; Paez-Espino, David; Jarett, Jessica; ...

    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 higherature pH-neutral geothermal springs. This lineage had remained hidden as a taxonomic 'blind spot' because of mismatches in the primers commonly used for ribosomal gene surveys. Genome reconstruction from metagenomic data combined with single-cell genomics results in several high-quality genomes representing four genera from the new phylum. Metabolic reconstruction indicates a heterotrophic lifestyle withmore » conspicuous nutritional deficiencies, suggesting the need for metabolic complementarity with other microbes. Co-occurrence patterns identifies a number of putative partners, including an uncultured Armatimonadetes lineage. The discovery of Kryptonia within previously studied geothermal springs underscores the importance of globally sampled metagenomic data in detection of microbial novelty, and highlights the extraordinary diversity of microbial life still awaiting discovery.« less

  18. 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. Copyright © 2011 Elsevier Inc. All rights reserved.

  19. Perceptions and actions of Dutch sheep farmers concerning worm infections.

    PubMed

    Ploeger, H W; Antonis, A F G; Verkaik, J C; Vellema, P; Bokma-Bakker, M H

    2016-10-15

    Gastrointestinal (GI) nematode infections are considered among one of the toughest challenges sheep farmers face worldwide. Control still is largely based on the use of anthelmintics, but anthelmintic resistance is becoming rampant. To facilitate implementation of alternative nematode control strategies and to reduce anthelmintic usage, the purpose of this study was twofold: (i) to gain insight in common practices, knowledge gaps and perceptions of farmers regarding nematode control, and (ii) to provide foci of attention for improving parasite control practices and transfer of knowledge within the sheep husbandry. An internet-based questionnaire was made available to all sheep farmers pertaining to the year 2013, resulting in 450 entered questionnaires for analysis. The two most important nematodes mentioned, were Haemonchus contortus and, to a lesser extent, Nematodirus battus. Of all respondents, 25.6% said they did not have any worm problems. Of these, almost a third did notice clinical signs that can be related to worm infections and about three quarters did use anthelmintics. Overall, clinical symptoms mentioned by farmers matched the worm species they identified as the cause of problems. Ewes and lambs were treated up to 6 times in 2013. On average, ewes were treated 1.53 and lambs 2.05 times. Farmers who treated their ewes more often, also treated their lambs more often (P<0.001). Both ewes and lambs were frequently treated based on fixed moments such as around lambing, at weaning and before mating, rather than based on faecal egg counts. Treatments based on faecal egg counts were practiced, but on a minority of the farms (32.7%). The majority of the farms (75.6%) did not leave 2-5% of the sheep within a flock untreated. About 74% of farmers keep newly purchased animals quarantined for at least 10days, but some (13.4%) leave quarantined animals untreated nor check faecal egg counts. Of farmers who do treat their quarantined animals, just 12.6% check the

  20. 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.

  1. QuantWorm: A Comprehensive Software Package for Caenorhabditis elegans Phenotypic Assays

    PubMed Central

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

    2014-01-01

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

  2. SCOPS and COWS--'worming it out of UK farmers'.

    PubMed

    Taylor, M A

    2012-05-04

    Infections with gastrointestinal roundworms are an important cause of production losses in sheep and cattle. Worm control is a vital part of health and production management in sheep flocks and cattle herds in the UK, and good control is highly dependent on effective anthelmintics. Unfortunately, a direct and unavoidable consequence of using anthelmintics to control worm populations is selection for individuals that are resistant to the chemicals used. If left unchecked, anthelmintic resistance (AR) could prove to be one of the biggest challenges to sheep and cattle production and animal welfare within the UK. As a consequence of increasing reports of AR in sheep, a working group, "SCOPS" (sustainable control of parasites in sheep) was formed in 2003 with representatives from the UK sheep industry to promote practical guidelines for sheep farmers and their advisors. This led to the production of guidelines for 'sustainable worm control strategies for sheep' intended for veterinarians and sheep advisors, plus ongoing promotional literature aimed at farmers. Whilst there is some evidence of emerging resistance in roundworms of cattle, it appears to still be at a very low level in the UK. However the potential presence of such AR in cattle worms has been seen as a timely warning, which if ignored, could lead to a not dissimilar AR situation to that seen in sheep, and in other cattle areas around the world. Reports of AR in UK cattle nematodes have generally been limited to a small number of anecdotal reports of treatment failure with some macrocyclic lactone (ML) products, especially those formulated as pour-on preparations, and invariably involving the dose-limiting species, Cooperia oncophora. As a consequence of these observations, guidelines have been produced similar to those for sheep, for sustainable worm control strategies for cattle "COWS" (control of worms sustainably), and were launched in May 2010. Uptake and effectiveness of SCOPS recommendations are

  3. 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.

  4. 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.

  5. 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

  6. Long-term disability due to guinea worm disease.

    PubMed

    Hours, M; Cairncross, S

    1994-01-01

    The village-based surveillance system for guinea worm disease (dracunculiasis), which has been established in all endemic villages in Ghana, was used to carry out a retrospective study of long-term disability due to the disease. A sample of 195 cases was interviewed and examined, 12-18 months after emergence of the worm. Currently continuing pain when walking or working, attributable by its location and date of onset to the episode of dracunculiasis, was reported by 55 persons (28.2%). Some difficulty in performing at least one of 6 everyday physical activities, attributable after careful interview to the episode, was reported by 66 respondents (34.0%), of whom 10 (5.1%) were unable to carry out one of the activities. In one case, the disease had caused impairment of movement of the joints of the right thumb. The prevalence of serious permanent physical impairment among the cases in the study was thus 0.5%.

  7. 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.

  8. 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 %.

  9. 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.

  10. 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.

  11. 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.

  12. Decay of velvet worms (Onychophora), and bias in the fossil record of lobopodians.

    PubMed

    Murdock, Duncan Je; Gabbott, Sarah E; Mayer, Georg; Purnell, Mark A

    2014-11-29

    Fossil lobopodians, including animals proposed to have close affinity to modern onychophorans, are crucial to understanding the evolution of the panarthropod body plan and the phylum-level relationships between the ecdysozoan groups. Unfortunately, the key features of their anatomy are un-mineralized and subject to biases introduced during death, decay and preservation, yet the extent to which these fossils have been affected by the processes of post-mortem decay is entirely untested. Recent experimental work on chordates has highlighted a profound bias caused by decay, resulting in the erroneous interpretation of badly decayed specimens as primitive members of a clade (stemward slippage). The degree to which this bias affects organisms other than chordates is unknown. Here we use experimental decay of velvet worms (Onychophora) to examine the importance of decay bias in fossil lobopodians. Although we find stemward slippage is not significant in the interpretation of non-mineralized lobopodian fossils, the affect of decay is far from unbiased. Quantitative analysis reveals significant changes in body proportions during decay, a spectrum of decay resistance across anatomical features, and correlated decay of topologically associated characters. These results have significant implications for the interpretation of fossil lobopodian remains, demonstrating that features such as body outline and relative proportions are unreliable for taxonomy or phylogenetic reconstruction, unless decay is taken into account. Similarly, the non-independent loss of characters, due to juxtaposition in the body, during decay has the potential to bias phylogenetic analyses of non-biomineralized fossils. Our results are difficult to reconcile with interpretations of highly decay-prone tissues and structures, such as neural tissue, and complex musculature, in recently described Cambrian lobopodians. More broadly, we hypothesize that stemward slippage is unlikely to be a significant factor

  13. Analysis of Routing Worm Infection Rates on an IPV4

    DTIC Science & Technology

    2007-03-01

    effort. The help of Major David M. Kaziska during the final weeks of my thesis writing was a Godsend and I owe him a large debt of gratitude. All...ANALYSIS OF ROUTING WORM INFECTION RATES ON AN IPV4 NETWORK THESIS James E. Gorsuch, First Lieutenant, USAF AFIT/GCS/ENG/07-04...DISTRIBUTION UNLIMITED The views expressed in this thesis are those of the author and do not reflect the official policy or

  14. Multi-worm tracking using superposition of merit functions

    NASA Astrophysics Data System (ADS)

    Rivera, Linda Ivonne; Potsaid, Benjamin; Wen, John Ting-Yung

    2008-11-01

    Traditional solutions for long term imaging of living small biological specimens and microorganisms lack efficiency due to computationally expensive algorithms, and field of view limitations in optical microscopes. This paper describes a new algorithm that allows for real time tracking of multiple 1mm nematodes called Caenorhabditis elegans with a novel optical microscope design called the Adaptive Scanning Optical Microscope (ASOM), developed at the Center for Automation Technologies and Systems (CATS). Based on the real time experimentation, an improved algorithm to track multiple worms in the presence of entanglements is generated. The stages of this development start with an enhanced digital motion controller for the ASOM high speed scanning mirror to suppress undesired vibrations that limit the system capacity to track multiple organisms. The second phase is the integration of the ASOM apparatus, the high speed motion control, and a base tracking algorithm, all which allows for rapid image acquisition to track multiple C. elegans in real time. The base algorithm was developed at CATS and has been proven to track a single C. elegans in real time. Results demonstrating the efficacy of the complete system are presented. Lastly, an enhanced tracking algorithm is described that shows improved accuracy and robustness in tracking worms even when they become entangled. Taking into account the unique ASOM design, individual segments of the worm are tracked throughout an image sequence, and a mosaic pattern covering the entire worm is subsequently created. The algorithm takes advantage of geometric and dynamic knowledge of the C. elegans such as size, and movement patterns. The enhanced algorithm is tested on previously recorded footage. Simulated tracking experiments also illustrate the effectiveness of the enhanced algorithm and are presented.

  15. Wingless/Wnt signal transduction requires distinct initiation and amplification steps that both depend on Arrow/LRP.

    PubMed

    Baig-Lewis, Shahana; Peterson-Nedry, Wynne; Wehrli, Marcel

    2007-06-01

    Members of the Wg/Wnt family provide key intercellular signals during embryonic development and in the maintenance of homeostatic processes, but critical aspects of their signal transduction pathways remain controversial. We have found that canonical Wg signaling in Drosophila involves distinct initiation and amplification steps, both of which require Arrow/LRP. Expressing a chimeric Frizzled2-Arrow protein in flies that lack endogenous Wg or Arrow showed that this construct functions as an activated Wg receptor but is deficient in signal amplification. In contrast, a chimeric Arrow protein containing the dimerization domain of Torso acted as a potent amplifier of Wg signaling but could not initiate Wg signaling on its own. The two chimeric proteins synergized, so that their co-expression largely reconstituted the signaling levels achieved by expressing Wg itself. The amplification function of Arrow/LRP appears to be particularly important for long-range signaling, and may reflect a general mechanism for potentiating signals in the shallow part of a morphogen gradient.

  16. Wingless/Wnt signal transduction requires distinct initiation and amplification steps that both depend on Arrow/LRP

    PubMed Central

    Baig-Lewis, Shahana; Peterson-Nedry, Wynne; Wehrli, Marcel

    2007-01-01

    Members of the Wg/Wnt family provide key intercellular signals during embryonic development and in the maintenance of homeostatic processes, but critical aspects of their signal transduction pathways remain controversial. We have found that canonical Wg signaling in Drosophila involves distinct initiation and amplification steps, both of which require Arrow/LRP. Expressing a chimeric Frizzled2-Arrow protein in flies that lack endogenous Wg or Arrow showed that this construct functions as an activated Wg receptor but is deficient in signal amplification. In contrast, a chimeric Arrow protein containing the dimerization domain of Torso acted as a potent amplifier of Wg signaling but could not initiate Wg signaling on its own. The two chimeric proteins synergized, so that their co-expression largely reconstituted the signaling levels achieved by expressing Wg itself. The amplification function of Arrow/LRP appears to be particularly important for long-range signaling, and may reflect a general mechanism for potentiating signals in the shallow part of a morphogen gradient. PMID:17433287

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

    PubMed

    Bhandari, Vaibhav; Gupta, Radhey S

    2012-11-01

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

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

    PubMed

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

    2012-01-01

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

  19. Worm algorithm for the CP N - 1 model

    NASA Astrophysics Data System (ADS)

    Rindlisbacher, Tobias; de Forcrand, Philippe

    2017-05-01

    The CP N - 1 model in 2D is an interesting toy model for 4D QCD as it possesses confinement, asymptotic freedom and a non-trivial vacuum structure. Due to the lower dimensionality and the absence of fermions, the computational cost for simulating 2D CP N - 1 on the lattice is much lower than that for simulating 4D QCD. However, to our knowledge, no efficient algorithm for simulating the lattice CP N - 1 model for N > 2 has been tested so far, which also works at finite density. To this end we propose a new type of worm algorithm which is appropriate to simulate the lattice CP N - 1 model in a dual, flux-variables based representation, in which the introduction of a chemical potential does not give rise to any complications. In addition to the usual worm moves where a defect is just moved from one lattice site to the next, our algorithm additionally allows for worm-type moves in the internal variable space of single links, which accelerates the Monte Carlo evolution. We use our algorithm to compare the two popular CP N - 1 lattice actions and exhibit marked differences in their approach to the continuum limit.

  20. 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.