Science.gov

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. 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.

  4. 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.

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

    PubMed Central

    Sundberg, Per; Strand, Malin

    2016-01-01

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

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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)

  13. 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

  14. 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

  15. 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.

  16. [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.

  17. 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

  18. 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…

  19. 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…

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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)

  5. 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.

  6. 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…

  7. 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.

  8. 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

  9. 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.

  10. 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.

  11. 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

  12. 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)

  13. "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.

  14. 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…

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. Metagenomics of the Methane Ice Worm, Hesiocaeca methanicola

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

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

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. The internet worm

    NASA Technical Reports Server (NTRS)

    Denning, Peter J.

    1989-01-01

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

  12. 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.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. 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.

  3. 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…

  4. 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,…

  5. 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.

  6. 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.

  7. 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.

  8. Relation between the psychological and thermodynamic arrows of time

    NASA Astrophysics Data System (ADS)

    Mlodinow, Leonard; Brun, Todd A.

    2014-05-01

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

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

    EPA Pesticide Factsheets

    This page contains the final 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.

  10. 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.

  11. 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.

  12. 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].

  13. 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)

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. 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.

  2. 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).

  3. 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... bow or arrow described in subparagraph (1) or (2) of this paragraph; and (4) Any quiver suitable...

  4. 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.

  5. 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]…

  6. 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…

  7. 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

  8. 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.

  9. 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

  10. 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.

  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. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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

  7. 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.

  8. 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

  9. 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).

  10. 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 ...

  11. 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.

  12. 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.

  13. 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.

  14. 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

  15. 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

  16. 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.

  17. [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.

  18. 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.

  19. 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.

  20. 75 FR 26889 - Airworthiness Directives; Arrow Falcon Exporters, Inc. (previously Utah State University) et al...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-13

    ... to read as follows: Arrow Falcon Exporters, Inc. (previously Utah State University); Firefly Aviation... International Aviation, Inc.); International Helicopters, Inc.; Precision Helicopters, LLC; Robinson Air...

  1. 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.

  2. 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

  3. 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

  4. 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.

  5. 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.

  6. 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

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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

  12. 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.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  14. 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

  15. 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

  16. 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.

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. 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.…

  2. 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,…

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. 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

  9. Pan-phylum Comparison of Nematode Metabolic Potential.

    PubMed

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

    2015-05-01

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

  10. 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

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. 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

  2. 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.

  3. 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

  4. 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}.

  5. 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

  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. 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

  8. 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.

  9. 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…

  10. 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.

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

    PubMed

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

    2016-09-01

    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.

  12. 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

  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. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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].

  19. 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.

  20. 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.

  1. 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.

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

    PubMed

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

    2012-12-01

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

  3. 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.

  4. 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.

  5. 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.

  6. 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

  7. 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.

  8. 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".

  9. 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.

  10. 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

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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

  17. 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

  18. 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.

  19. 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}.

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

    SciTech Connect

    David Atwood; Marc Sher

    1997-07-01

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

  1. 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

  2. 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.

  3. 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.

  4. 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.

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

    PubMed

    Lin, Wei; Li, Jinhua; Pan, Yongxin

    2012-02-01

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

  6. 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.

  7. 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

  8. 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

  9. 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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  11. 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.

  12. 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.

  13. 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

  14. 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.

  15. 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

  16. 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.

  17. 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

  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. 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).

  20. 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.

  1. 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…

  2. 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.

  3. 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…

  4. 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…

  5. 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.

  6. 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…

  7. 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…

  8. 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…

  9. 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…

  10. 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

  11. 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

  12. 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

  13. 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.

  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. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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.

  1. 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

  2. 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

  3. 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.

  4. 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

  5. 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.

  6. 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

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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

  19. 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.

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

    PubMed Central

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

    2014-01-01

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

  1. 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.

  2. 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.

  3. 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}

  4. 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}

  5. 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.

  6. 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.

  7. 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.

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

    SciTech Connect

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

    1985-02-01

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

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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

  18. 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.

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

    PubMed

    Schliemann, S

    2014-10-01

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

  20. 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}

  1. 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.

  2. 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.

  3. 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.

  4. 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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2014-01-01

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

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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

  15. 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.

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

    SciTech Connect

    J. L. Goity; Longzhe Zhang

    1997-02-01

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

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. 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.

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. 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

  11. 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

  12. 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.

  13. 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.

  14. 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

  15. [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.

  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

    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.

  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. 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

  19. 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.

  20. 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

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

    SciTech Connect

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

    1995-05-10

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

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

    NASA Technical Reports Server (NTRS)

    Manro, M. E.

    1976-01-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1975-01-01

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

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

    NASA Technical Reports Server (NTRS)

    Rao, D. M.

    1981-01-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1975-01-01

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

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

    NASA Technical Reports Server (NTRS)

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

    2003-01-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1975-01-01

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

  8. Fcc r arrow bct phase transition in Th at extreme compressions: Theory

    SciTech Connect

    Eriksson, O. ); Soederlind, P. ); Wills, J.M. )

    1992-06-01

    The experimentally observed fcc{r arrow}bct crystallographic phase transition in Th, at {similar to}1 Mbar, is reproduced by means of full-potential, linear-muffin-tin-orbitals calculations. Both the calculated volume and pressure for which the transition occurs, agrees with the experimental data. The calculated pressure dependence of the {ital c}/{ital a} ratio of the bct structure is also in good agreement wtih experimental data. Calculations for La predict the fcc phase to be stable over the bct phase up to {similar to}7 Mbar.

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

    NASA Technical Reports Server (NTRS)

    Manro, M. E.

    1982-01-01

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

  10. [Upsilon](1[ital S])[r arrow][gamma]+noninteracting particles

    SciTech Connect

    Balest, R.; Cho, K.; Ford, T.; Johnson, D.R.; Lingel, K.; Lohner, M.; Rankin, P.; Smith, J.G.; Alexander, J.P.; Bebek, C.; Berkelman, K.; Bloom, K.; Browder, T.E.; Cassel, D.G.; Cho, H.A.; Coffman, D.M.; Crowcroft, D.S.; Drell, P.S.; Dumas, D.; Ehrlich, R.; Gaidarev, P.; Galik, R.S.; Garcia-Sciveres, M.; Geiser, B.; Gittelman, B.; Gray, S.W.; Hartill, D.L.; Heltsley, B.K.; Henderson, S.; Jones, C.D.; Jones, S.L.; Kandaswamy, J.; Katayama, N.; Kim, P.C.; Kreinick, D.L.; Ludwig, G.S.; Masui, J.; Mevissen, J.; Mistry, N.B.; Ng, C.R.; Nordberg, E.; Patterson, J.R.; Peterson, D.; Riley, D.; Salman, S.; Sapper, M.; Wuerthwein, F.; Urish, M.M.; Avery, P.; Freyberger, A.; Rodriguez, J.; Yang, S.; Yelton, J.; Cinabro, D.; Liu, T.; Saulnier, M.; Wilson, R.; Yamamoto, H.; Bergfeld, T.; Eisenstein, B.I.; Gollin, G.; Ong, B.; Palmer, M.; Selen, M.; Thaler, J.J.; Edwards, K.W.; Ogg, M.; Bellerive, A.; Britton, D.I.; Hyatt, E.R.F.; MacFarlane, D.B.; Patel, P.M.; Spaan, B.; Sadoff, A.J.; Ammar, R.; Ba

    1995-03-01

    We consider the decay of [Upsilon](1[ital S]) particles produced at CESR into a photon which is observed by the CLEO detector plus particles which are not seen. These could be real particles which fall outside of our acceptance, or particles which are noninteracting. We report the results of our search fo the process [Upsilon](1[ital S])[r arrow][gamma]+ unseen'' for photon energies [gt]1 GeV, obtaining limits for the case where unseen'' is either a single particle or a particle-antiparticle pair. Our upper limits represent the highest sensitivity measurements for such decays to date.

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

    PubMed

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

    2003-03-22

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

  12. Theoretical evaluation of high-speed aerodynamics for arrow-wing configurations

    NASA Technical Reports Server (NTRS)

    Dollyhigh, S. M.

    1979-01-01

    The use of the theoretical methods to calculate the high-speed aerodynamic characteristics of arrow-wing supersonic cruise configurations was studied. Included are correlations of theoretical predictions with wind-tunnel data at Mach numbers from 0.8 to 2.7, examples of the use of theoretical methods to extrapolate the wind-tunnel data to full-scale flight condition, and presentation of a typical supersonic data package for an advanced supersonic transport application. A brief description of the methods and their application is given.

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

    NASA Technical Reports Server (NTRS)

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

    1976-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    1987-04-01

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

  15. 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

  16. Radiative corrections to the decays K{sub L}{sup 0} {r_arrow} e{sup +}e{sup {minus}} and K{sub L}{sup 0} {r_arrow} {mu}{sup +} {mu}{sup {minus}}

    SciTech Connect

    Dicus, D.A.; Repko, W.W.

    1998-12-31

    The authors calculate the rates and lepton ({ell}) invariant mass distributions for decays of the form 0{sup {minus}+} {r_arrow} {ell}{sup +}{ell}{sup {minus}}{gamma}, which are important radiative corrections to the purely leptonic decays 0{sup {minus}+} {r_arrow} {ell}{sup +}{ell}{sup {minus}}. The approach uses the loop diagrams which arise by including the two photon intermediate state and they retain the imaginary parts of the loops--a radiative extension of the unitarity bound for the process. These results are compared with those obtained using a model in which the meson couples directly to the leptons.

  17. Results on {nu}{sub {mu}}{r_arrow}{nu}{sub e} oscillations from pion decay in flight neutrinos

    SciTech Connect

    Church, E.D.; McIlhany, K.; Stancu, I.; Strossman, W.; VanDalen, G.J.; Vernon, W.; Caldwell, D.O.; Yellin, S.; Smith, D.; Waltz, J.; Cohen, I.; Burman, R.L.; Donahue, J.B.; Federspiel, F.J.; Garvey, G.T.; Louis, W.C.; Mills, G.B.; Sandberg, V.; Tayloe, R.; White, D.H.; Gunasingha, R.M.; Imlay, R.; Kim, H.J.; Metcalf, W.; Wadia, N.; Johnston, K.; Reeder, R.A.; Fazely, A.; Athanassopoulos, C.; Auerbach, L.B.; Majkic, R.; Works, D.; Xiao, Y.

    1998-10-01

    A search for {nu}{sub {mu}}{r_arrow}{nu}{sub e} oscillations has been conducted at the Los Alamos Meson Physics Facility using {nu}{sub {mu}} from {pi}{sup +} decay in flight. An excess in the number of beam-related events from the {nu}{sub e}C{r_arrow}e{sup {minus}}X inclusive reaction is observed. The excess is too large to be explained by normal {nu}{sub e} contamination in the beam at a confidence level greater than 99{percent}. If interpreted as an oscillation signal, the observed oscillation probability of (2.6{plus_minus}1.0{plus_minus}0.5){times}10{sup {minus}3} is consistent with the previously reported {bar {nu}}{sub {mu}}{r_arrow}{bar {nu}}{sub e} oscillation evidence from LSND. {copyright} {ital 1998} {ital The American Physical Society}

  18. Measurement of the B0 Lifetime with Partial Reconstruction of overline B o right arrow D *+rho-

    NASA Astrophysics Data System (ADS)

    Soffer, A.

    2002-03-01

    A sample of about 5500 overline B0 right arrow D (sup asterisk +) rho - and 700 overline B0 right arrow D(sup asterisk +) alpha -1 events is identified, using the technique of partial reconstruction, among 22.7 million B overline B pairs collected by the BABAR experiment at the PEP-II storage ring. With these events, the B 0 lifetime is measured to be 1.616 plus or minus 0.064 plus or minus 0.075 ps. As the first time-dependent analysis conducted with partial reconstruction of overline B 0 right arrow D (sup asterisk +) rho -, this measurement serves as validation for the procedures required to measure sin(2beta + gamma) with this technique.

  19. Contributions to the Dart versus Arrow Debate: New Data from Holocene Projectile Points from Southeastern and Southern Brazil.

    PubMed

    Okumura, Mercedes; Araujo, Astolfo G M

    2015-01-01

    Lithic bifacial points are very common in the southern and southeastern regions of the Brazilian territory. Dated from Early to Late Holocene, these artifacts have not been studied in terms of their propulsion system. Given the characteristics of the bow and arrow compared to the atlatl and dart, there are important differences in the size and weight of arrowheads and dart points. Applying the techniques proposed by Shott (1997), Bradbury (1997), Fenenga (1953), Hughes (1998), and Hildebrandt and King (2012) to specimens recovered from eight sites dating from the early to the late Holocene, this work aims to present preliminary results to better understand the potential presence of darts and arrows in southeastern and southern Brazil. There was a variation in the results according to the application of different techniques. At least one set of points, dated from the Early Holocene, presented quite a high proportion of specimens classified as arrows, indicating the presence of points that could be used as arrowheads.

  20. 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

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

    SciTech Connect

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

    1994-03-01

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

  2. 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.

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

    SciTech Connect

    Heiles, C.

    1984-08-01

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

  4. 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 %.

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

    PubMed

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

    2012-12-01

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

  6. 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.

  7. 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%.

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

    PubMed

    Suzuki, T; Takagi, T; Ohta, S

    1990-02-15

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

  9. Global distribution patterns and pangenomic diversity of the candidate phylum "Latescibacteria" (WS3).

    PubMed

    Farag, Ibrahim F; Youssef, Noha H; Elshahed, Mostafa S

    2017-03-17

    We investigated the global distribution patterns and pangenomic diversity of the candidate phylum "Latescibacteria" (WS3) in 16S rRNA gene as well as metagenomic datasets. We document distinct distribution patterns for various "Latescibacteria" orders in 16S rRNA gene datasets, with prevalence of orders sediment_1 in terrestrial, PBSIII_9 in groundwater and temperate freshwater, and GN03 in pelagic marine, saline-hypersaline, and wastewater habitats. Using a fragment recruitment approach, we identified 68.9 Mb of "Latescibacteria"-affiliated contigs in publicly available metagenomic datasets comprising 73,079 proteins. Metabolic reconstruction suggests a prevalent saprophytic lifestyle in all "Latescibacteria" orders, with marked capacities for the degradation of proteins, lipids, and polysaccharides predominant in plant, bacterial, fungal/crustacean, and eukaryotic algal cell walls. As well, extensive transport and central metabolic pathways for the metabolism of imported monomers were identified. Interestingly, genes and domains suggestive of the production of a cellulosome, e.g. protein-coding genes harboring dockerin I domains attached to a glycosyl hydrolase, and scaffoldin-encoding genes harboring cohesin I and CBM37 domains, were identified in orders PBSIII_9, GN03, and MSB-4E2 fragments recovered from four anoxic aquatic habitats; hence extending the cellulosomal production capabilities in Bacteria beyond the Gram-positive Firmicutes. In addition to fermentative pathways, a complete electron transport chain with terminal cytochrome C oxidases Caa3 (for operation under high oxygen tension), and Cbb3 (for operation under low oxygen tension) were identified in PBSIII_9, and GN03 fragments recovered from oxygenated, and partially/seasonally oxygenated aquatic habitats. Our metagenomic recruitment effort hence represents a comprehensive pangenomic view of this yet-uncultured phylum, and provides broader and complimentary insights to those gained from genome

  10. New ideas to improve searches for {mu}{sup +} {r_arrow} e{sup +}{gamma}

    SciTech Connect

    Cooper, M.D.

    1997-11-01

    Searching for decays that change total lepton family number is an excellent method to explore potential physics beyond the Standard Model because those processes are predicted to be zero except when new physics is present. Essentially all extensions of the Standard Model that introduce new, heavy particles predict the existence of these rare decays, though the most probable channel is highly model dependent. Recently, the prejudice has grown within the physics community that supersymmetry is an extension that is likely to be related to nature. Barbieri, Hall, and Strumia show that rare decays are signatures for grand unified supersymmetry and calculate the rates for {mu}{sup +} {r_arrow} e{sup +}{gamma} and related processes for a wide range of parameters of these models. They conclude that {mu}{sup +} {r_arrow} e{sup +}{gamma} has the largest rate by more than two orders of magnitude, and it ranges between the current experimental limit and 10{sup {minus}14}. Hence, there is continuing interest in the community for an experiment that could have a sensitivity near 10{sup {minus}14}. Lessons are drawn from the experience of the MEGA experiment in searching for {mu}{sup +} to e{sup +}{gamma}. In light of that experience, some ideas are evaluated regarding new searches that might take place in the ERA of a source of low-energy muons associated with a muon collider.

  11. 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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed Central

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

    1992-01-01

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

  14. Korean indigenous bacterial species with valid names belonging to the phylum Actinobacteria.

    PubMed

    Bae, Kyung Sook; Kim, Mi Sun; Lee, Ji Hee; Kang, Joo Won; Kim, Dae In; Lee, Ji Hee; Seong, Chi Nam

    2016-12-01

    To understand the isolation and classification state of actinobacterial species with valid names for Korean indigenous isolates, isolation source, regional origin, and taxonomic affiliation of the isolates were studied. At the time of this writing, the phylum Actinobacteria consisted of only one class, Actinobacteria, including five subclasses, 10 orders, 56 families, and 330 genera. Moreover, new taxa of this phylum continue to be discovered. Korean actinobacterial species with a valid name has been reported from 1995 as Tsukamurella inchonensis isolated from a clinical specimen. In 1997, Streptomyces seoulensis was validated with the isolate from the natural Korean environment. Until Feb. 2016, 256 actinobacterial species with valid names originated from Korean territory were listed on LPSN. The species were affiliated with three subclasses (Acidimicrobidae, Actinobacteridae, and Rubrobacteridae), four orders (Acidimicrobiales, Actinomycetales, Bifidobacteriales, and Solirubrobacterales), 12 suborders, 36 families, and 93 genera. Most of the species belonged to the subclass Actinobacteridae, and almost of the members of this subclass were affiliated with the order Actinomycetales. A number of novel isolates belonged to the families Nocardioidaceae, Microbacteriaceae, Intrasporangiaceae, and Streptomycetaceae as well as the genera Nocardioides, Streptomyces, and Microbacterium. Twenty-six novel genera and one novel family, Motilibacteraceae, were created first with Korean indigenous isolates. Most of the Korean indigenous actionobacterial species were isolated from natural environments such as soil, seawater, tidal flat sediment, and fresh-water. A considerable number of species were isolated from artificial resources such as fermented foods, wastewater, compost, biofilm, and water-cooling systems or clinical specimens. Korean indigenous actinobacterial species were isolated from whole territory of Korea, and especially a large number of species were from Jeju

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

    PubMed

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

    2012-02-01

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

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

    PubMed

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

    2014-07-01

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

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

    SciTech Connect

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

    1988-11-20

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

  18. Language of Mechanisms: Exam Analysis Reveals Students' Strengths, Strategies, and Errors When Using the Electron-Pushing Formalism (Curved Arrows) in New Reactions

    ERIC Educational Resources Information Center

    Flynn, Alison B.; Featherstone, Ryan B.

    2017-01-01

    This study investigated students' successes, strategies, and common errors in their answers to questions that involved the electron-pushing (curved arrow) formalism (EPF), part of organic chemistry's language. We analyzed students' answers to two question types on midterms and final exams: (1) draw the electron-pushing arrows of a reaction step,…

  19. WormBase 2016: expanding to enable helminth genomic research

    PubMed Central

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

    2016-01-01

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

  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.

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

    van Passel, Mark W J; Kant, Ravi; Palva, Airi; Lucas, Susan; Copeland, Alex; Lapidus, Alla; Glavina del Rio, Tijana; Dalin, Eileen; Tice, Hope; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Davenport, Karen Walston; Sims, David; Brettin, Thomas S; Detter, John C; Han, Shunsheng; Larimer, Frank W; Land, Miriam L; Hauser, Loren; Kyrpides, Nikolaos; Ovchinnikova, Galina; Richardson, P Paul; de Vos, Willem M; Smidt, Hauke; Zoetendal, Erwin G

    2011-05-01

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

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

    SciTech Connect

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

    2011-01-01

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

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

    PubMed

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

    2016-04-01

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

  5. Description of Fimbriimonas ginsengisoli gen. nov., sp. nov. within the Fimbriimonadia class nov., of the phylum Armatimonadetes.

    PubMed

    Im, Wan-Taek; Hu, Zi-Ye; Kim, Kyoung-Ho; Rhee, Sung-Keun; Meng, Han; Lee, Sung-Taik; Quan, Zhe-Xue

    2012-08-01

    Strain Gsoil 348(T) was isolated from a ginseng field soil sample by selecting micro-colonies from one-fifth strength modified R2A agar medium after a long incubation period. 16S rRNA gene sequence analysis indicated that the strain is related to members of the phylum Armatimonadetes (formerly called candidate phylum OP10). Strain Gsoil 348(T) is mesophilic, strictly aerobic, non-motile and rod-shaped. It only grows in low nutrient media. The major respiratory quinones are menaquinones MK-11 and MK-10, and the main fatty acids are iso-C(15:0), iso-C(17:0), C(16:0) and C(16:1) ω11c. The G+C content is 61.4 mol%. The 16S rRNA gene sequences in public databases belonging to the phylum Armatimonadetes were clustered here into 6 groups. Five of these groups constituted a coherent cluster distinct from the sequences of other phyla in phylogenetic trees that were constructed using multiple-outgroup sequences from 49 different phyla. On the basis of polyphasic taxonomic analyses, it is proposed that strain Gsoil 348(T) (= KACC 14959(T) = JCM 17079(T)) should be placed in Fimbriimonas ginsengisoli gen. nov., sp. nov., as the cultured representative of the Fimbriimonadia class. nov., corresponding with Group 4 of the phylum Armatimonadetes.

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

    PubMed Central

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

    2016-01-01

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

  7. Bioaccumulation and food-chain analysis for evaluating ecological risks in terrestrial and wetland habitats: Availability-transfer factors (ATFs) in soil {r_arrow} soil macroinvertebrate {r_arrow} amphibian food chains

    SciTech Connect

    Linder, G.; Bollman, M.; Callahan, C.; Gillette, C.; Nebeker, A.; Wilborn, D.

    1998-12-31

    As part of the ecological risk assessment process for terrestrial and wetland habitats, the evaluation of bioaccumulative chemicals of concern (BCCs) is frequently pursued through food-chain analysis with a subsequent comparison of daily doses to benchmark toxicity reference values, when available. Food-chain analysis has frequently been applied to the analysis of exposure to BCCs identified as chemicals of potential ecological concern (COPECs) in the ecological risk assessment process. Here, designed studies focused on wetland food-chains such as hydric soil {r_arrow} soil macroinvertebrate {r_arrow} amphibian and terrestrial food-chains such as soil {r_arrow} plant {r_arrow} small mammal illustrate an approach for the derivation and validation of trophic transfer factors for metals considered as COPECs such as cadmium, chromium, copper, lead, and zinc. The results clearly indicate that the transfer of chemicals between trophic levels is critical in the bioaccumulation process in wetland and terrestrial food-chains and is influenced by numerous interacting abiotic and biotic factors, including physicochemical properties of soil, and the role, if any, that the metal has in the receptor as a required trace element.

  8. Biological Survey Along the St. Lawrence River for the St. Lawrence Seaway. Additional Locks and other Navigation Improvements Study.

    DTIC Science & Technology

    1979-01-01

    only one month (Table 6). Nine phylums were represented - Porifera, Coelenterata, Platyhelminthes , Nematoda, Nematomorpha, Firyozoa, Annel-ida...Hydroids) - colonies Phylum Platyhelminthes Class Turbellaria (Flatworms) Phylum Nematoda (Roundworms) Phylum Nematomorpha (Horsehair worms) Phylum

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-04-01

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

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

    PubMed

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

    2016-04-01

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

  12. Recognition of Damaged Arrow-Road Markings by Visible Light Camera Sensor Based on Convolutional Neural Network

    PubMed Central

    Vokhidov, Husan; Hong, Hyung Gil; Kang, Jin Kyu; Hoang, Toan Minh; Park, Kang Ryoung

    2016-01-01

    Automobile driver information as displayed on marked road signs indicates the state of the road, traffic conditions, proximity to schools, etc. These signs are important to insure the safety of the driver and pedestrians. They are also important input to the automated advanced driver assistance system (ADAS), installed in many automobiles. Over time, the arrow-road markings may be eroded or otherwise damaged by automobile contact, making it difficult for the driver to correctly identify the marking. Failure to properly identify an arrow-road marker creates a dangerous situation that may result in traffic accidents or pedestrian injury. Very little research exists that studies the problem of automated identification of damaged arrow-road marking painted on the road. In this study, we propose a method that uses a convolutional neural network (CNN) to recognize six types of arrow-road markings, possibly damaged, by visible light camera sensor. Experimental results with six databases of Road marking dataset, KITTI dataset, Málaga dataset 2009, Málaga urban dataset, Naver street view dataset, and Road/Lane detection evaluation 2013 dataset, show that our method outperforms conventional methods. PMID:27999301

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

    ERIC Educational Resources Information Center

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

    2011-01-01

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

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

    ERIC Educational Resources Information Center

    Falvo, David A.; Suits, Jerry P.

    2009-01-01

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

  15. Observation of [ital D][sup 0][r arrow][ital K][sup +][pi][sup [minus

    SciTech Connect

    Cinabro, D.; Henderson, S.; Liu, T.; Saulnier, M.; Wilson, R.; Yamamoto, H.; Bergfeld, T.; Eisenstein, B.I.; Gollin, G.; Ong, B.; Palmer, M.; Selen, M.; Thaler, J.J.; Sadoff, A.J.; Ammar, R.; Ball, S.; Baringer, P.; Bean, A.; Besson, D.; Coppage, D.; Copty, N.; Davis, R.; Hancock, N.; Kelly, M.; Kwak, N.; Lam, H.; Kubota, Y.; Lattery, M.; Nelson, J.K.; Patton, S.; Perticone, D.; Poling, R.; Savinov, V.; Schrenk, S.; Wang, R.; Alam, M.S.; Kim, I.J.; Nemati, B.; O'Neill, J.J.; Severini, H.; Sun, C.R.; Zoeller, M.M.; Crawford, G.; Daubenmier, C.M.; Fulton, R.; Fujino, D.; Gan, K.K.; Honscheid, K.; Kagan, H.; Kass, R.; Lee, J.; Malchow, R.; Morrow, F.; Skovpen, Y.; Sung, M.; White, C.; Butler, F.; Fu, X.; Kalbfleisch, G.; Ross, W.R.; Skubic, P.; Snow, J.; Wang, P.L.; Wood, M.; Brown, D.N.; Fast, J.; McIlwain, R.L.; Miao, T.; Miller, D.H.; Modesitt, M.; Payne, D.; Shibata, E.I.; Shipsey, I.P.J.; Wang, P.N.; Battle, M.; Ernst, J.; Kwon, Y.; Roberts, S.; Thorndike, E.H.; Wang, C.H.; Dominick,

    1994-03-07

    Using the CLEO II data sample, with an integrated luminosity of 1.8 fb[sup [minus]1] at and near the [Upsilon](4[ital S]) resonance, we have observed a signal for [ital D][sup 0][r arrow][ital K][sup +][pi][sup [minus

  16. Literature as Tool for Sustainable Development: A Comparative Literary Analysis of Achebe's "Arrow of God" and Tahir's "The Last Imam"

    ERIC Educational Resources Information Center

    Sani, Abubakar Mohammed

    2014-01-01

    This paper aims at a theoretical comparative textual analysis of two novels; Chinua Achebe's "Arrow of God" (1964) and Ibrahim Tahir's "The Last Imam" (1984). The focus is on their similarities generally and roles played by the heroes in their different societies as political and religious leaders of the different societies and…

  17. New result on K{sup +} {r_arrow} {pi}{sup +} {nu}{bar {nu}} from BNL E787

    SciTech Connect

    REDLINGER,G.

    1999-06-21

    E787 at BNL has reported evidence for the rare decay K{sup +} {r_arrow} {pi}{sup +}{nu}{bar {nu}}, based on the observation of one candidate event. In this paper, we present the result of analyzing a new dataset of comparable sensitivity to the published result.

  18. Comparison of gunshot wounds and field-tipped arrow wounds using morphological criteria and chemical spot tests.

    PubMed

    Randall, B; Newby, P

    1989-05-01

    Arrow wounds represent an unusual class of wounds rarely seen by most death investigators. Although the edged, broadhead-tipped arrow produces a wound usually characteristic of archery/crossbow weapons, the plain, field-tipped arrow wound can be confused with gunshot injuries in those cases in which powder residue or firearm projectiles or fragments or both are not recovered. We present a case of a deer carcass with a wound of uncertain firearm or archery origin which initiated a comparison of firearm wounds and archery wounds on fresh road-killed deer. We found the following features to be valuable in the differentiation of gunshot wounds and field-tipped archery wounds: First, the majority of the gunshot wounds (but none of the arrow wounds) had identifiable, macroscopic, wipe-off material and chemically identifiable wipe-off residue by spot test. Second, the archery wound defects had very inconspicuous abrasion rings as compared to the often prominent abrasion rings of gunshot wounds. Third, the actual central defect in the archery wounds was more likely to be oblong or slit-like compared to the gunshot wound defects, which were more likely to be round.

  19. Effect of a simulated engine jet blowing above an arrow wing at Mach 2.0

    NASA Technical Reports Server (NTRS)

    Shrout, B. L.; Hayes, C.

    1977-01-01

    The effects of a gas jet simulating a turbojet engine exhaust blowing above a cambered and twisted arrow wing were investigated. Tests were conducted in the Langley 4-foot supersonic pressure tunnel at a Mach number of 2.0. Nozzle pressure ratios from 1 to 64 were tested with both helium and air used as jet gases. The tests were conducted at angles of attack from -2 deg to 8 deg at a Reynolds number of 9,840,000 per meter. Only the forces and moments on the wing were measured. Results of the investigation indicated that the jet blowing over the wing caused reductions in maximum lift-drag ratio of about 4 percent for helium and 6 percent for air at their respective design nozzle pressure ratios, relative to jet-off data. Moderate changes in the longitudinal, vertical, or angular positions of the jet relative to the wing had little effect on the wing aerodynamic characteristics.

  20. Scavenging interactions between the arrow tooth eel Synaphobranchus kaupii and the Portuguese dogfish Centroscymnus coelolepis.

    PubMed

    Jamieson, A J; Fujii, T; Bagley, P M; Priede, I G

    2011-07-01

    A scavenging interaction between the arrow tooth eel Synaphobranchus kaupii and the Portuguese dogfish Centroscymnus coelolepis, both ubiquitous components of fish assemblages at bathyal depths, was observed. Using a baited camera between 1297 and 2453 m in the eastern Atlantic Ocean continental slope, it was shown that despite consistently rapid arrival times of S. kaupii (<5 min), their feeding bouts (indicated by acute peak in numbers) did not take place until shortly after C. coelolepis arrived and removed the exterior surface of the bait (skipjack tuna Katsuwonus pelamis carcass). Change in the numbers of S. kaupii was hence dependent on the arrival of a more powerful scavenger throughout the study site, and at the deeper stations where the population of C. coelolepis declined, S. kaupii was observed to be present but waited for >2 h before feeding, thus contradicting conventional scavenging assumptions in the presence of a food fall.

  1. Scan path entropy and arrow plots: capturing scanning behavior of multiple observers

    PubMed Central

    Hooge, Ignace; Camps, Guido

    2013-01-01

    Designers of visual communication material want their material to attract and retain attention. In marketing research, heat maps, dwell time, and time to AOI first hit are often used as evaluation parameters. Here we present two additional measures (1) “scan path entropy” to quantify gaze guidance and (2) the “arrow plot” to visualize the average scan path. Both are based on string representations of scan paths. The latter also incorporates transition matrices and time required for 50% of the observers to first hit AOIs (T50). The new measures were tested in an eye tracking study (48 observers, 39 advertisements). Scan path entropy is a sensible measure for gaze guidance and the new visualization method reveals aspects of the average scan path and gives a better indication in what order global scanning takes place. PMID:24399993

  2. Asymmetric transport of light in arrow-shape photonic crystal waveguides

    NASA Astrophysics Data System (ADS)

    Rahal, H.; AbdelMalek, F.

    2017-03-01

    In this paper, we report a design of an asymmetric light propagation based on the Photonic Crystal (PC) structure. The proposed PC is constructed of an arrow-shaped structure integrating different rows of air holes which offer more than 65% transmission in one direction and less than 1% in the opposite direction. The proposed PC is based on the use of two parallel PC waveguides with different air holes in a single platform. The design, optimization and performance of the PC waveguide devices are carried out by employing in-house accurate 2D Finite Difference Time Domain (2D FDTD) computational techniques. Our preliminary numerical simulation results show that complete asymmetric transmission can be achieved in the proposed single structure which would play a significant contribution on realization of high-volume nanoscale photonic integrated circuitry.

  3. Evaluation of structural design concepts for an arrow-wing supersonic cruise aircraft

    NASA Technical Reports Server (NTRS)

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

    1977-01-01

    An analytical study was performed to determine the best structural approach for design of primary wing and fuselage structure of a Mach 2.7 arrow wing supersonic cruise aircraft. Concepts were evaluated considering near term start of design. Emphasis was placed on the complex interactions between thermal stress, static aeroelasticity, flutter, fatigue and fail safe design, static and dynamic loads, and the effects of variations in structural arrangements, concepts and materials on these interactions. Results indicate that a hybrid wing structure incorporating low profile convex beaded and honeycomb sandwich surface panels of titanium alloy 6Al-4V were the most efficient. The substructure includes titanium alloy spar caps reinforced with boron polyimide composites. The fuselage shell consists of hat stiffened skin and frame construction of titanium alloy 6Al-4V. A summary of the study effort is presented, and a discussion of the overall logic, design philosophy and interaction between the analytical methods for supersonic cruise aircraft design are included.

  4. Titanium and advanced composite structures for a supersonic cruise arrow wing configuration

    NASA Technical Reports Server (NTRS)

    Turner, M. J.; Hoy, J. M.

    1976-01-01

    Structural design studies were made, based on current technology and on an estimate of technology to be available in the mid 1980's, to assess the relative merits of structural concepts and materials for an advanced arrow wing configuration cruising at Mach 2.7. Preliminary studies were made to insure compliance of the configuration with general design criteria, integrate the propulsion system with the airframe, and define an efficient structural arrangement. Material and concept selection, detailed structural analysis, structural design and airplane mass analysis were completed based on current technology. Based on estimated future technology, structural sizing for strength and a preliminary assessment of the flutter of a strength designed composite structure were completed. An advanced computerized structural design system was used, in conjunction with a relatively complex finite element model, for detailed analysis and sizing of structural members.

  5. Study of advanced composite structural design concepts for an arrow wing supersonic cruise configuration

    NASA Technical Reports Server (NTRS)

    Turner, M. J.; Grande, D. L.

    1978-01-01

    Based on estimated graphite and boron fiber properties, allowable stresses and strains were established for advanced composite materials. Stiffened panel and conventional sandwich panel concepts were designed and analyzed, using graphite/polyimide and boron/polyimide materials. The conventional sandwich panel was elected as the structural concept for the modified wing structure. Upper and lower surface panels of the arrow wing structure were then redesigned, using high strength graphite/polyimide sandwich panels, retaining the titanium spars and ribs from the prior study. The ATLAS integrated analysis and design system was used for stress analysis and automated resizing of surface panels. Flutter analysis of the hybrid structure showed a significant decrease in flutter speed relative to the titanium wing design. The flutter speed was increased to that of the titanium design by selective increase in laminate thickness and by using graphite fibers with properties intermediate between high strength and high modulus values.

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

    PubMed

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

    2015-12-01

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

  7. Grunting for worms: seismic vibrations cause Diplocardia earthworms to emerge from the soil

    PubMed Central

    Mitra, O.; Callaham, M.A.; Smith, M.L.; Yack, J.E.

    2008-01-01

    Harvesting earthworms by a practice called ‘worm grunting’ is a widespread and profitable business in the southeastern USA. Although a variety of techniques are used, most involve rhythmically scraping a wooden stake driven into the ground, with a flat metal object. A common assumption is that vibrations cause the worms to surface, but this phenomenon has not been studied experimentally. We demonstrate that Diplocardia earthworms emerge from the soil within minutes following the onset of grunting. Broadband low frequency (below 500 Hz) pulsed vibrations were present in the soil throughout the area where worms were harvested, and the number of worms emerging decreased as the seismic signal decayed over distance. The findings are discussed in relation to two hypotheses: that worms are escaping vibrations caused by digging foragers and that worms are surfacing in response to vibrations caused by falling rain. PMID:18854292

  8. STUDIES ON THE METABOLISM OF THE FILARIAL WORM, LITOMOSOIDES CARINII

    PubMed Central

    Bueding, Ernest

    1949-01-01

    The filarial worm, Litomosoides carinii, has a high rate of aerobic and anaerobic glucose metabolism. Aerobically 30 to 45 per cent of the glucose utilized was converted to lactic acid, 25 to 35 per cent to acetic acid, and 10 to 20 per cent to a polysaccharide. Anaerobically over 80 per cent of the total carbohydrate removed by the filariae was metabolized to lactic acid, the remainder was accounted for by the production of acetic acid. The high rates of aerobic and anaerobic lactic acid production and of aerobic polysaccharide synthesis, as well as the absence of a postanaerobic increase of the oxygen uptake, differentiate the filarial worm, L. carinii, from the known metabolic characteristics of all other helminths and of most other invertebrates. The rate of aerobic lactate and pyruvate utilization by the filariae appears to be much slower than that of glucose. Anaerobically, dismutation of two moles of pyruvate to one mole of lactate, one mole of acetate, and one mole of CO2, occurred. Aerobically, acetate production from pyruvate exceeded that of lactate. A significant proportion of the pyruvate metabolized aerobically by the filariae was not oxidized to acetate. In the presence of fluoroacetate, aerobic incubation of the filariae in a glucose-containing medium produced a marked decrease in the respiration of the organisms, an accumulation of pyruvate, a decreased formation of acetate, and an increase in aerobic glycolysis. Low concentrations of fluoroacetate (1 x 10–3 M) inhibited the oxidative metabolism of pyruvate which did not result in the conversion of pyruvate to acetate; higher concentrations of this inhibitor produced also a decreased oxidation of pyruvate to acetate. No evidence has been obtained that fluoroacetate inhibits the respiration of the filariae because of a competitive inhibition of acetate oxidation. Respiration and glycolysis of filariae were markedly decreased by low concentrations of p-chloromercuric benzoate. This inhibition could

  9. Genomic Analysis of Caldithrix abyssi, the Thermophilic Anaerobic Bacterium of the Novel Bacterial Phylum Calditrichaeota

    PubMed Central

    Kublanov, Ilya V.; Sigalova, Olga M.; Gavrilov, Sergey N.; Lebedinsky, Alexander V.; Rinke, Christian; Kovaleva, Olga; Chernyh, Nikolai A.; Ivanova, Natalia; Daum, Chris; Reddy, T.B.K.; Klenk, Hans-Peter; Spring, Stefan; Göker, Markus; Reva, Oleg N.; Miroshnichenko, Margarita L.; Kyrpides, Nikos C.; Woyke, Tanja; Gelfand, Mikhail S.; Bonch-Osmolovskaya, Elizaveta A.

    2017-01-01

    The genome of Caldithrix abyssi, the first cultivated representative of a phylum-level bacterial lineage, was sequenced within the framework of Genomic Encyclopedia of Bacteria and Archaea (GEBA) project. The genomic analysis revealed mechanisms allowing this anaerobic bacterium to ferment peptides or to implement nitrate reduction with acetate or molecular hydrogen as electron donors. The genome encoded five different [NiFe]- and [FeFe]-hydrogenases, one of which, group 1 [NiFe]-hydrogenase, is presumably involved in lithoheterotrophic growth, three other produce H2 during fermentation, and one is apparently bidirectional. The ability to reduce nitrate is determined by a nitrate reductase of the Nap family, while nitrite reduction to ammonia is presumably catalyzed by an octaheme cytochrome c nitrite reductase εHao. The genome contained genes of respiratory polysulfide/thiosulfate reductase, however, elemental sulfur and thiosulfate were not used as the electron acceptors for anaerobic respiration with acetate or H2, probably due to the lack of the gene of the maturation protein. Nevertheless, elemental sulfur and thiosulfate stimulated growth on fermentable substrates (peptides), being reduced to sulfide, most probably through the action of the cytoplasmic sulfide dehydrogenase and/or NAD(P)-dependent [NiFe]-hydrogenase (sulfhydrogenase) encoded by the genome. Surprisingly, the genome of this anaerobic microorganism encoded all genes for cytochrome c oxidase, however, its maturation machinery seems to be non-operational due to genomic rearrangements of supplementary genes. Despite the fact that sugars were not among the substrates reported when C. abyssi was first described, our genomic analysis revealed multiple genes of glycoside hydrolases, and some of them were predicted to be secreted. This finding aided in bringing out four carbohydrates that supported the growth of C. abyssi: starch, cellobiose, glucomannan and xyloglucan. The genomic analysis

  10. Genomic Analysis of Caldithrix abyssi, the Thermophilic Anaerobic Bacterium of the Novel Bacterial Phylum Calditrichaeota.

    PubMed

    Kublanov, Ilya V; Sigalova, Olga M; Gavrilov, Sergey N; Lebedinsky, Alexander V; Rinke, Christian; Kovaleva, Olga; Chernyh, Nikolai A; Ivanova, Natalia; Daum, Chris; Reddy, T B K; Klenk, Hans-Peter; Spring, Stefan; Göker, Markus; Reva, Oleg N; Miroshnichenko, Margarita L; Kyrpides, Nikos C; Woyke, Tanja; Gelfand, Mikhail S; Bonch-Osmolovskaya, Elizaveta A

    2017-01-01

    The genome of Caldithrix abyssi, the first cultivated representative of a phylum-level bacterial lineage, was sequenced within the framework of Genomic Encyclopedia of Bacteria and Archaea (GEBA) project. The genomic analysis revealed mechanisms allowing this anaerobic bacterium to ferment peptides or to implement nitrate reduction with acetate or molecular hydrogen as electron donors. The genome encoded five different [NiFe]- and [FeFe]-hydrogenases, one of which, group 1 [NiFe]-hydrogenase, is presumably involved in lithoheterotrophic growth, three other produce H2 during fermentation, and one is apparently bidirectional. The ability to reduce nitrate is determined by a nitrate reductase of the Nap family, while nitrite reduction to ammonia is presumably catalyzed by an octaheme cytochrome c nitrite reductase εHao. The genome contained genes of respiratory polysulfide/thiosulfate reductase, however, elemental sulfur and thiosulfate were not used as the electron acceptors for anaerobic respiration with acetate or H2, probably due to the lack of the gene of the maturation protein. Nevertheless, elemental sulfur and thiosulfate stimulated growth on fermentable substrates (peptides), being reduced to sulfide, most probably through the action of the cytoplasmic sulfide dehydrogenase and/or NAD(P)-dependent [NiFe]-hydrogenase (sulfhydrogenase) encoded by the genome. Surprisingly, the genome of this anaerobic microorganism encoded all genes for cytochrome c oxidase, however, its maturation machinery seems to be non-operational due to genomic rearrangements of supplementary genes. Despite the fact that sugars were not among the substrates reported when C. abyssi was first described, our genomic analysis revealed multiple genes of glycoside hydrolases, and some of them were predicted to be secreted. This finding aided in bringing out four carbohydrates that supported the growth of C. abyssi: starch, cellobiose, glucomannan and xyloglucan. The genomic analysis

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

    PubMed

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

    2015-12-24

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

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

    PubMed Central

    Loewer, Barry

    2012-01-01

    In this paper, I will argue that there is an important connection between two questions concerning how certain features of the macro world emerge from the laws and processes of fundamental microphysics and suggest an approach to answering these questions. The approach involves a kind of emergence but quite different from ‘top-down’ emergence discussed at the conference, for which an earlier version of this paper was written. The two questions are (i) How do ‘the arrows of time’ emerge from microphysics? (ii) How do macroscopic special science laws and causation emerge from microphysics? Answering these questions is especially urgent for those, who like myself, think that a certain version of physicalism, which I call ‘micro-physical completeness’ (MC), is true. According to MC, there are fundamental dynamical laws that completely govern (deterministically or probabilistically), the evolution of all micro-physical events and there are no additional ontologically independent dynamical or causal special science laws. In other words, there is no ontologically independent ‘top-down’ causation. Of course, MC does not imply that physicists now or ever will know or propose the complete laws of physics. Or even if the complete laws were known we would know how special science properties and laws reduce to laws and properties of fundamental physics. Rather, MC is a contingent metaphysical claim about the laws of our world. After a discussion of the two questions, I will argue the key to showing how it is possible for the arrows of time and the special science laws to emerge from microphysics and a certain account of how thermodynamics is related to fundamental dynamical laws. PMID:23386956

  13. Lift-Drag Ratios for an Arrow Wing With Bodies at Mach Number 3

    NASA Technical Reports Server (NTRS)

    Jorgensen, Leland H.

    1959-01-01

    Force and moment characteristics, including lift-drag ratios, have been measured for bodies of circular and elliptic cross section alone and combined with a warped arrow wing. The test Mach number was 2.94, and the Reynolds number was 3.5 x 10(exp 6) (based on wing mean aerodynamic chord). The experimental results show that for equal volume the use of an elliptical body can result in a noticeably higher maximum lift-drag ratio than that obtained through use of a circular body. Methods for estimating the aerodynamic characteristics have been assessed by comparing computed with experimental results. Because of good agreement of the predictions with experiment, maximum lift-drag ratios have been computed for the arrow wing in combination with bodies of various sizes. These calculations have shown that, for an efficient wing-body combination, little loss in maximum lift-drag ratio results from considerable extension of afterbody length. For example, for a wing-body configuration having a maximum lift-drag ratio of about 7.1, a loss in maximum lift-drag ratio of less than 0.2 results from a 40-percent increase in body volume by extension of afterbody length. It also appears that with body length fixed, maximum lift-drag ratio decreases almost linearly with increase in body diameter. For a wing- body combination employing a body of circular cross section, a decrease in maximum lift-drag ratio from about 9.1 for zero body diameter to about 4.6 for a body diameter of 13.5 percent of the body length was computed.

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

    PubMed

    Loewer, Barry

    2012-02-06

    In this paper, I will argue that there is an important connection between two questions concerning how certain features of the macro world emerge from the laws and processes of fundamental microphysics and suggest an approach to answering these questions. The approach involves a kind of emergence but quite different from 'top-down' emergence discussed at the conference, for which an earlier version of this paper was written. The two questions are (i) How do 'the arrows of time' emerge from microphysics? (ii) How do macroscopic special science laws and causation emerge from microphysics? Answering these questions is especially urgent for those, who like myself, think that a certain version of physicalism, which I call 'micro-physical completeness' (MC), is true. According to MC, there are fundamental dynamical laws that completely govern (deterministically or probabilistically), the evolution of all micro-physical events and there are no additional ontologically independent dynamical or causal special science laws. In other words, there is no ontologically independent 'top-down' causation. Of course, MC does not imply that physicists now or ever will know or propose the complete laws of physics. Or even if the complete laws were known we would know how special science properties and laws reduce to laws and properties of fundamental physics. Rather, MC is a contingent metaphysical claim about the laws of our world. After a discussion of the two questions, I will argue the key to showing how it is possible for the arrows of time and the special science laws to emerge from microphysics and a certain account of how thermodynamics is related to fundamental dynamical laws.

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

    NASA Technical Reports Server (NTRS)

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

    1993-01-01

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

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

    PubMed

    Awofeso, Niyi

    2013-08-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

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

    PubMed Central

    2012-01-01

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

  19. Photonic crystal fiber in the polychaete worm Pherusa sp.

    PubMed

    Trzeciak, Tomasz M; Vukusic, Peter

    2009-12-01

    Setae of the polychaete worm Pherusa exhibit remarkably strong photonic effects, which arise from their two-dimensional-periodic internal structure of hexagonally packed cylindrical channels. The hexagonal order is limited to monocrystalline domains of different orientation, which results in an overall polycrystalline effect. A detailed experimental and theoretical investigation of this structure reveals that the internal photonic structure is carefully tuned with respect to its lattice constant in order to provide an optical response coinciding with the visible wavelength rage. A further optimization is observed for the packing fraction of cylindrical channels in order to maximize the width of photonic band gaps, and hence the reflectance of incident visible light.

  20. Pet roundworms and hookworms: a continuing need for global worming.

    PubMed

    Traversa, Donato

    2012-05-10

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

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

    PubMed

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

    2014-02-25

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

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

    USGS Publications Warehouse

    Mech, L.D.

    2008-01-01

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

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

    PubMed

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

    1993-01-01

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

  4. Calorithrix insularis gen. nov., sp. nov., a novel representative of the phylum Calditrichaeota.

    PubMed

    Kompantseva, Elena I; Kublanov, Ilya V; Perevalova, Anna A; Chernyh, Nikolay A; Toshchakov, Stepan V; Litti, Yuriy V; Antipov, Alexey N; Bonch-Osmolovskaya, Elizaveta A; Miroshnichenko, Margarita L

    2016-12-16

    A moderately thermophilic, anaerobic bacterium designated as strain KRT was isolated from a shallow water submarine hydrothermal vent (Kunashir Island, Southern Kurils, Russia). Cells of the strain KRT were thin (0.2-0.3 µm), flexible, motile, Gram-negative rods of variable length. Optimal growth conditions: pH 6.6, 55°C, 1-3% (w/v) NaCl. Strain KRT was able to ferment a wide range of proteinaceous substrates, pyruvate, mono-, di- and polysaccharides. The best growth occurred with proteinaceous compounds. Nitrate significantly stimulated the growth on proteinaceous substrates decreasing H2 formation, ammonium being the main product of nitrate reduction. Strain KRT did not need the presence of reducing agent in the medium and tolerated the presence of oxygen in the gas phase up to 3% (v/v). In the presence of nitrate aerotolerance of isolate KRT was enhanced up to 6-8% O2 (v/v). Strain KRT was able to grow chemolithoheterotrophicaly oxidizing H2 and reducing nitrate to ammonium. Yeast extract (0.05 g l-1) was required for growth. The G + C content of the genomic DNA of strain KRT was 47.3 mol°/o. 16S rRNA gene sequence analysis placed isolate KRT in the phylum Calditrichaeota where it represented a novel genus and species for which the name Calorithrix insularis gen. nov., sp. nov. was proposed with the type strain KRT (= DSM 101605T = VKM B-3022T).

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

    PubMed

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

    2015-01-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-01-01

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

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

    PubMed

    Gibson, Amanda Kyle; Fuentes, Jesualdo Arturo

    2015-02-01

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

  9. A phylogenetic test of the Red Queen Hypothesis: Outcrossing and parasitism in the Nematode phylum

    PubMed Central

    Gibson, Amanda Kyle; Fuentes, Jesualdo Arturo

    2017-01-01

    Sexual outcrossing is costly relative to selfing and asexuality, yet it is ubiquitous in nature, a paradox that has long puzzled evolutionary biologists. The Red Queen Hypothesis argues that outcrossing is maintained by antagonistic interactions between host and parasites. Most tests of this hypothesis focus on the maintenance of outcrossing in hosts. The Red Queen makes an additional prediction that parasitic taxa are more likely to be outcrossing than their free-living relatives. We test this prediction in the diverse Nematode phylum using phylogenetic comparative methods to evaluate trait correlations. In support of the Red Queen, we demonstrate a significant correlation between parasitism and outcrossing in this clade. We find that this correlation is driven by animal parasites, for which outcrossing is significantly enriched relative to both free-living and plant parasitic taxa. Finally, we test hypotheses for the evolutionary history underlying the correlation of outcrossing and animal parasitism. Our results demonstrate that selfing and asexuality are significantly less likely to arise on parasitic lineages than on free-living ones. The findings of this study are consistent with the Red Queen Hypothesis. Moreover, they suggest that the maintenance of genetic variation is an important factor in the persistence of parasitic lineages. PMID:25403727

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

    PubMed

    Kostrouchova, Marta; Kostrouch, Zdenek

    2015-02-01

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

  11. Development of a multilocus-based approach for sponge (phylum Porifera) identification: refinement and limitations

    PubMed Central

    Yang, Qi; Franco, Christopher M. M.; Sorokin, Shirley J.; Zhang, Wei

    2017-01-01

    For sponges (phylum Porifera), there is no reliable molecular protocol available for species identification. To address this gap, we developed a multilocus-based Sponge Identification Protocol (SIP) validated by a sample of 37 sponge species belonging to 10 orders from South Australia. The universal barcode COI mtDNA, 28S rRNA gene (D3–D5), and the nuclear ITS1-5.8S-ITS2 region were evaluated for their suitability and capacity for sponge identification. The highest Bit Score was applied to infer the identity. The reliability of SIP was validated by phylogenetic analysis. The 28S rRNA gene and COI mtDNA performed better than the ITS region in classifying sponges at various taxonomic levels. A major limitation is that the databases are not well populated and possess low diversity, making it difficult to conduct the molecular identification protocol. The identification is also impacted by the accuracy of the morphological classification of the sponges whose sequences have been submitted to the database. Re-examination of the morphological identification further demonstrated and improved the reliability of sponge identification by SIP. Integrated with morphological identification, the multilocus-based SIP offers an improved protocol for more reliable and effective sponge identification, by coupling the accuracy of different DNA markers. PMID:28150727

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

    PubMed

    Ogino, Kazutoyo; Tsuneki, Kazuhiko; Furuya, Hidetaka

    2007-06-01

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

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

    PubMed

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

    2014-12-01

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

  14. Development of a multilocus-based approach for sponge (phylum Porifera) identification: refinement and limitations.

    PubMed

    Yang, Qi; Franco, Christopher M M; Sorokin, Shirley J; Zhang, Wei

    2017-02-02

    For sponges (phylum Porifera), there is no reliable molecular protocol available for species identification. To address this gap, we developed a multilocus-based Sponge Identification Protocol (SIP) validated by a sample of 37 sponge species belonging to 10 orders from South Australia. The universal barcode COI mtDNA, 28S rRNA gene (D3-D5), and the nuclear ITS1-5.8S-ITS2 region were evaluated for their suitability and capacity for sponge identification. The highest Bit Score was applied to infer the identity. The reliability of SIP was validated by phylogenetic analysis. The 28S rRNA gene and COI mtDNA performed better than the ITS region in classifying sponges at various taxonomic levels. A major limitation is that the databases are not well populated and possess low diversity, making it difficult to conduct the molecular identification protocol. The identification is also impacted by the accuracy of the morphological classification of the sponges whose sequences have been submitted to the database. Re-examination of the morphological identification further demonstrated and improved the reliability of sponge identification by SIP. Integrated with morphological identification, the multilocus-based SIP offers an improved protocol for more reliable and effective sponge identification, by coupling the accuracy of different DNA markers.

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

    PubMed

    Stürmer, Sidney Luiz

    2012-05-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed Central

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

    2015-01-01

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

  19. 'Candidatus Thermochlorobacter aerophilum:' an aerobic chlorophotoheterotrophic member of the phylum Chlorobi defined by metagenomics and metatranscriptomics.

    PubMed

    Liu, Zhenfeng; Klatt, Christian G; Ludwig, Marcus; Rusch, Douglas B; Jensen, Sheila I; Kühl, Michael; Ward, David M; Bryant, Donald A

    2012-10-01

    An uncultured member of the phylum Chlorobi, provisionally named 'Candidatus Thermochlorobacter aerophilum', occurs in the microbial mats of alkaline siliceous hot springs at the Yellowstone National Park. 'Ca. T. aerophilum' was investigated through metagenomic and metatranscriptomic approaches. 'Ca. T. aerophilum' is a member of a novel, family-level lineage of Chlorobi, a chlorophototroph that synthesizes type-1 reaction centers and chlorosomes similar to cultivated relatives among the green sulfur bacteria, but is otherwise very different physiologically. 'Ca. T. aerophilum' is proposed to be an aerobic photoheterotroph that cannot oxidize sulfur compounds, cannot fix N(2), and does not fix CO(2) autotrophically. Metagenomic analyses suggest that 'Ca. T. aerophilum' depends on other mat organisms for fixed carbon and nitrogen, several amino acids, and other important nutrients. The failure to detect bchU suggests that 'Ca. T. aerophilum' synthesizes bacteriochlorophyll (BChl) d, and thus it occupies a different ecological niche than other chlorosome-containing chlorophototrophs in the mat. Transcription profiling throughout a diel cycle revealed distinctive gene expression patterns. Although 'Ca. T. aerophilum' probably photoassimilates organic carbon sources and synthesizes most of its cell materials during the day, it mainly transcribes genes for BChl synthesis during late afternoon and early morning, and it synthesizes and assembles its photosynthetic apparatus during the night.

  20. Bio-inspired microfluidics: The case of the velvet worm

    NASA Astrophysics Data System (ADS)

    Concha, Andres; Mellado, Paula; Morera-Brenes, Bernal; Sampaio-Costa, Cristiano; Mahadevan, L.; Monge-Najera, Julian

    The rapid squirt of a proteinaceous slime jet endow velvet worms (Onychophora) with a unique mechanism for defense from predators and for capturing prey by entangling them in a disordered web that immobilizes their target. However, to date neither qualitative nor quantitative descriptions have been provided for this unique adaptation. We have investigated the mechanism that allows velvet worms the fast oscillatory motion of their oral papillae and the exiting liquid jet that oscillates with frequencies f ~ 30 - 60 Hz. Using anatomical images and high speed videography, we show that even without fast muscular action of the papilla, a strong contraction of the slime reservoir and the geometry of the reservoir-papilla system suffices to accelerate the slime to speeds up to v ~ 5 m /s in about Δt ~ 60 ms. A theoretical analysis and a physical simulacrum allow us to infer that this fast oscillatory motion is the result of an elastohydrodynamic instability driven by the interplay between the elasticity of oral papillae and the fast unsteady flow during squirting. We propose several applications that can be implemented using this instability, ranging from high-throughput droplet production, printing, and micro-nanofiber production among others. A.C was partially supported by Fondecyt Grant 11130075.

  1. Lessons from bloodless worms: heme homeostasis in C. elegans.

    PubMed

    Sinclair, Jason; Hamza, Iqbal

    2015-06-01

    Heme is an essential cofactor for proteins involved in diverse biological processes such as oxygen transport, electron transport, and microRNA processing. Free heme is hydrophobic and cytotoxic, implying that specific trafficking pathways must exist for the delivery of heme to target hemoproteins which reside in various subcellular locales. Although heme biosynthesis and catabolism have been well characterized, the pathways for trafficking heme within and between cells remain poorly understood. Caenorhabditis elegans serves as a unique animal model for uncovering these pathways because, unlike vertebrates, the worm lacks enzymes to synthesize heme and therefore is crucially dependent on dietary heme for sustenance. Using C. elegans as a genetic animal model, several novel heme trafficking molecules have been identified. Importantly, these proteins have corresponding homologs in vertebrates underscoring the power of using C. elegans, a bloodless worm, in elucidating pathways in heme homeostasis and hematology in humans. Since iron deficiency and anemia are often exacerbated by parasites such as helminths and protozoa which also rely on host heme for survival, C. elegans will be an ideal model to identify anti-parasitic drugs that target heme transport pathways unique to the parasite.

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

    PubMed

    Liu, Li-Na; Wang, Cheng-Ye

    2014-11-18

    The yellow meal worm (Tenebrio molitor L.) is an important resource insect typically used as animal feed additive. It is also widely used for biological research. The first complete mitochondrial genome of T. molitor was determined for the first time by long PCR and conserved primer walking approaches. The results showed that the entire mitogenome of T. molitor was 15 785 bp long, with 72.35% A+T content [deposited in GenBank with accession number KF418153]. The gene order and orientation were the same as the most common type suggested as ancestral for insects. Two protein-coding genes used atypical start codons (CTA in ND2 and AAT in COX1), and the remaining 11 protein-coding genes started with a typical insect initiation codon ATN. All tRNAs showed standard clover-leaf structure, except for tRNA(Ser) (AGN), which lacked a dihydrouridine (DHU) arm. The newly added T. molitor mitogenome could provide information for future studies on yellow meal worm.

  3. Meandering worms: mechanics of undulatory burrowing in muds

    PubMed Central

    Dorgan, Kelly M.; Law, Chris J.; Rouse, Greg W.

    2013-01-01

    Recent work has shown that muddy sediments are elastic solids through which animals extend burrows by fracture, whereas non-cohesive granular sands fluidize around some burrowers. These different mechanical responses are reflected in the morphologies and behaviours of their respective inhabitants. However, Armandia brevis, a mud-burrowing opheliid polychaete, lacks an expansible anterior consistent with fracturing mud, and instead uses undulatory movements similar to those of sandfish lizards that fluidize desert sands. Here, we show that A. brevis neither fractures nor fluidizes sediments, but instead uses a third mechanism, plastically rearranging sediment grains to create a burrow. The curvature of the undulating body fits meander geometry used to describe rivers, and changes in curvature driven by muscle contraction are similar for swimming and burrowing worms, indicating that the same gait is used in both sediments and water. Large calculated friction forces for undulatory burrowers suggest that sediment mechanics affect undulatory and peristaltic burrowers differently; undulatory burrowing may be more effective for small worms that live in sediments not compacted or cohesive enough to extend burrows by fracture. PMID:23446526

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

    PubMed

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

    2015-01-01

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

  5. Haemonchus contortus infection in sheep: parasite fecundity correlates with worm size and host lymphocyte counts.

    PubMed

    Rowe, Anthony; McMaster, Kate; Emery, David; Sangster, Nicholas

    2008-05-31

    Two experiments were conducted to elucidate the timing and nature of the sheep immune response to Haemonchus contortus (Barber's pole worm). The first experiment examined the establishment of H. contortus populations and the immune response by comparing a bolus infection of third-stage larvae in naïve sheep with a group previously primed by a trickle infection. The second experiment used staggered doses of ivermectin-resistant larvae to compare the development of adult worms during different durations of trickle infection with ivermectin-sensitive larvae. Infections successfully generated pathological signs of haemonchosis such as anaemia. Image analysis software was used to measure the area and perimeter of worms collected at post-mortem, and the number of eggs present in individual adult females (fecundity) was significantly correlated with worm size. A significant inverse correlation was found between blood lymphocyte counts and worm fecundity. The absence of correlation between worm fecundity and other leukocyte and erythrocyte counts highlighted the specificity of the lymphocyte response. This is the first report of a link between haematology profiles and worm fecundity in haemonchosis. The correlation observed between adult worm size and egg content leads to the hypothesis that egg production in H. contortus is limited by immune regulation of worm size and presumably growth. Mean worm size and fecundity declined as sheep received more prolonged trickle infections before necropsy, confirming previous reports that immune responses to adult worms are enhanced by ongoing larval challenge. Immunohistochemical results showed trends consistent with a Th2 (humoral) immune response which has been implicated in reducing nematode burdens in several species.

  6. A full scale worm reactor for efficient sludge reduction by predation in a wastewater treatment plant.

    PubMed

    Tamis, J; van Schouwenburg, G; Kleerebezem, R; van Loosdrecht, M C M

    2011-11-15

    Sludge predation can be an effective solution to reduce sludge production at a wastewater treatment plant. Oligochaete worms are the natural consumers of biomass in benthic layers in ecosystems. In this study the results of secondary sludge degradation by the aquatic Oligochaete worm Aulophorus furcatus in a 125 m(3) reactor and further sludge conversion in an anaerobic tank are presented. The system was operated over a period of 4 years at WWTP Wolvega, the Netherlands and was fed with secondary sludge from a low loaded activated sludge process. It was possible to maintain a stable and active population of the aquatic worm species A. furcatus during the full period. Under optimal conditions a sludge conversion of 150-200 kg TSS/d or 1.2-1.6 kg TSS/m(3)/d was established in the worm reactor. The worms grew as a biofilm on carrier material in the reactor. The surface specific conversion rate reached 140-180 g TSS/m(2)d and the worm biomass specific conversion rate was 0.5-1 g TSS sludge/g dry weight worms per day. The sludge reduction under optimal conditions in the worm reactor was 30-40%. The degradation by worms was an order of magnitude larger than the endogenous conversion rate of the secondary sludge. Effluent sludge from the worm reactor was stored in an anaerobic tank where methanogenic processes became apparent. It appeared that besides reducing the sludge amount, the worms' activity increased anaerobic digestibility, allowing for future optimisation of the total system by maximising sludge reduction and methane formation. In the whole system it was possible to reduce the amount of sludge by at least 65% on TSS basis. This is a much better total conversion than reported for anaerobic biodegradability of secondary sludge of 20-30% efficiency in terms of TSS reduction.

  7. Design and analysis of SEIQR worm propagation model in mobile internet

    NASA Astrophysics Data System (ADS)

    Xiao, Xi; Fu, Peng; Dou, Changsheng; Li, Qing; Hu, Guangwu; Xia, Shutao

    2017-02-01

    The mobile Internet has considerably facilitated daily life in recent years. However, it has become the breeding ground for lots of new worms, including the Bluetooth-based worm, the SMS/MMS-based worm and the Wi-Fi-based worm. At present, Wi-Fi is widely used for mobile devices to connect to the Internet. But it exposes these devices to the dangerous environment. Most current worm propagation models aim to solve the problems of computer worms. They cannot be used directly in the mobile environment, particularly in the Wi-Fi scenario, because of the differences between computers and mobile devices. In this paper, we propose a worm propagation model in the Wi-Fi environment, called SEIQR (Susceptible-Exposed-Infectious- Quarantined-Recovered). In the model, infected nodes can be quarantined by the Wi-Fi base station, and a new state named the Quarantined state (Q) is established to represent these infected nodes. Based on this model, we present an effective method to inhibit the spread of the Wi-Fi-based worms. Furthermore, related stabilities of the worm-free and endemic equilibriums are studied based on the basic reproduction number R0. The worm-free equilibrium is locally and globally asymptotically stable if R0 < 1, whereas the endemic equilibrium is locally asymptotically stable if R0 < 1. Finally, we evaluate the performance of our model by comprehensive experiments with different infection rates and quarantine rates. The results indicate that our mechanism can combat the worms propagated via Wi-Fi.

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

    PubMed

    Gupta, Radhey S; Lali, Ricky

    2013-09-01

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

  9. Complete genome sequence and cell structure of Limnochorda pilosa, a Gram-negative spore former within the phylum Firmicutes.

    PubMed

    Watanabe, Miho; Kojima, Hisaya; Fukui, Manabu

    2016-01-06

    Limnochorda pilosa is a pleomorphic facultative anaerobe and the sole species in the class Limnochordia, which has tentatively been placed in the phylum Firmicutes. In the present study, the complete genome sequence of L. pilosa HC45T was obtained and analyzed. The genome size was 3.82 Mbp and the G+C content was 69.73%. Phylogenetic analyses based on the 30S-50S ribosomal proteins and 23S rRNA gene consistently indicated that L. pilosa is phylogenetically isolated from the other members of the phylum Firmicutes. Ultrastructural observation revealed that L. pilosa possesses a Gram-negative-type cell wall and the capacity to form endospores. Accordingly, the L. pilosa genome has characteristics that are specific to Gram-negative bacteria and contains many genes that are involved in sporulation. On the other hand, several sporulation genes were absent in L. pilosa genome although they have been regarded as essential for endospore-forming system of the phylum Firmicutes. The gyrB gene of L. pilosa possesses an intein sequence. The genome has a high percentage of GTG start codons and lacks several conserved genes related to cell division.

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

    PubMed

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

    2014-03-01

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

  11. Genome analysis of Elusimicrobium minutum, the first cultivated representative of the Elusimicrobia phylum (formerly Termite Group 1)

    SciTech Connect

    Herlemann, D. P. R.; Geissinger, O.; Ikeda-Ohtsubo, W.; Kunin, V.; Sun, H.; Lapidus, A.; Hugenholtz, P.; Brune, A.

    2009-02-01

    The candidate phylum Termite group 1 (TG1), is regularly 1 encountered in termite hindguts but is present also in many other habitats. Here we report the complete genome sequence (1.64 Mbp) of Elusimicrobium minutum strain Pei191{sup T}, the first cultured representative of the TG1 phylum. We reconstructed the metabolism of this strictly anaerobic bacterium isolated from a beetle larva gut and discuss the findings in light of physiological data. E. minutum has all genes required for uptake and fermentation of sugars via the Embden-Meyerhof pathway, including several hydrogenases, and an unusual peptide degradation pathway comprising transamination reactions and leading to the formation of alanine, which is excreted in substantial amounts. The presence of genes encoding lipopolysaccharide biosynthesis and the presence of a pathway for peptidoglycan formation are consistent with ultrastructural evidence of a Gram-negative cell envelope. Even though electron micrographs showed no cell appendages, the genome encodes many genes putatively involved in pilus assembly. We assigned some to a type II secretion system, but the function of 60 pilE-like genes remains unknown. Numerous genes with hypothetical functions, e.g., polyketide synthesis, non-ribosomal peptide synthesis, antibiotic transport, and oxygen stress protection, indicate the presence of hitherto undiscovered physiological traits. Comparative analysis of 22 concatenated single-copy marker genes corroborated the status of Elusimicrobia (formerly TG1) as a separate phylum in the bacterial domain, which was so far based only on 16S rRNA sequence analysis.

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

    PubMed

    Sanghvi, P K

    1989-05-01

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

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

    PubMed Central

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

    2016-01-01

    Thermosulfurimonas dismutans S95T, isolated from a deep-sea hydrothermal vent is the first bacterium of the phylum Thermodesulfobacteria reported to grow by the disproportionation of elemental sulfur, sulfite, or thiosulfate with carbon dioxide as the sole carbon source. In contrast to its phylogenetically close relatives, which are dissimilatory sulfate-reducers, T. dismutans is unable to grow by sulfate respiration. The features of this organism and its 2,1 Mb draft genome sequence are described in this report. Genome analysis revealed that the T. dismutans genome contains the set of genes for dissimilatory sulfate reduction including ATP sulfurylase, the AprA and B subunits of adenosine-5′-phosphosulfate reductase, and dissimilatory sulfite reductase. The oxidation of elemental sulfur to sulfite could be enabled by APS reductase-associated electron transfer complex QmoABC and heterodisulfide reductase. The genome also contains several membrane-linked molybdopterin oxidoreductases that are thought to be involved in sulfur metabolism as subunits of thiosulfate, polysulfide, or tetrathionate reductases. Nitrate could be used as an electron acceptor and reduced to ammonium, as indicated by the presence of periplasmic nitrate and nitrite reductases. Autotrophic carbon fixation is enabled by the Wood–Ljungdahl pathway, and the complete set of genes that is required for nitrogen fixation is also present in T. dismutans. Overall, our results provide genomic insights into energy and carbon metabolism of chemolithoautotrophic sulfur-disproportionating bacterium that could be important primary producer in microbial communities of deep-sea hydrothermal vents. PMID:27379079

  14. The zooflagellates Stephanopogon and Percolomonas are a clade (class Percolatea: Phylum Percolozoa).

    PubMed

    Cavalier-Smith, Thomas; Nikolaev, Sergey

    2008-01-01

    The enigmatic marine protozoan Stephanopogon was first classified with ciliate protozoa because its pellicle also has rows of cilia. As ciliates have nuclear dimorphism with separate germline and somatic nuclei, Stephanopogon with several identical nuclei was regarded as a model for a hypothetical homokaryotic ancestor of ciliates. When electron microscopy revealed radical differences from ciliates this idea was abandoned, but its evolutionary position remains controversial, affinities with three other phyla being suggested. We sequenced 18S rDNA from Stephanopogon aff. minuta and actin genes from it and Stephanopogon apogon to clarify their evolutionary position. Phylogenetic analyses of 18S rRNA nest S. aff. minuta and Stephanopogon minuta securely within the protozoan phylum Percolozoa with zooflagellates of the genus Percolomonas, their closest relatives, comprising the clade Percolatea. This supports a previous grouping of Stephanopogon (order Pseudociliatida) with Percolomonas (order Percolomonadida) as a purely zooflagellate class Percolatea within Percolozoa, in contrast to the fundamentally amoeboid Heterolobosea, which are probably ancestral to Percolatea. Stephanopogon actins evolve exceptionally fast: actin trees place them as a long branch within bikont eukaryotes without revealing their sisters. We establish Percolomonadidae fam. n. for Percolomonas, excluding Pharyngomonas kirbyi g., sp. n. and Pharyngomonas (=Tetramastix=Percolomonas) salina comb. n., which unlike Percolomonas have two anterior and two posterior cilia and a pocket-like pharynx, like "Macropharyngomonas", now grouped with Pharyngomonas as a new purely zooflagellate class Pharyngomonadea, within a new subphylum Pharyngomonada; this contrasts them with the revised ancestrally amoeboflagellate subphylum Tetramitia. We discuss evolution of the percolozoan cytoskeleton and different body forms.

  15. Analysis of the Na+/Ca2+ exchanger gene family within the phylum Nematoda.

    PubMed

    He, Chao; O'Halloran, Damien M

    2014-01-01

    Na+/Ca2+ exchangers are low affinity, high capacity transporters that rapidly transport calcium at the plasma membrane, mitochondrion, endoplasmic (and sarcoplasmic) reticulum, and the nucleus. Na+/Ca2+ exchangers are widely expressed in diverse cell types where they contribute homeostatic balance to calcium levels. In animals, Na+/Ca2+ exchangers are divided into three groups based upon stoichiometry: Na+/Ca2+ exchangers (NCX), Na+/Ca2+/K+ exchangers (NCKX), and Ca2+/Cation exchangers (CCX). In mammals there are three NCX genes, five NCKX genes and one CCX (NCLX) gene. The genome of the nematode Caenorhabditis elegans contains ten Na+/Ca2+ exchanger genes: three NCX; five CCX; and two NCKX genes. Here we set out to characterize structural and taxonomic specializations within the family of Na+/Ca2+ exchangers across the phylum Nematoda. In this analysis we identify Na+/Ca2+ exchanger genes from twelve species of nematodes and reconstruct their phylogenetic and evolutionary relationships. The most notable feature of the resulting phylogenies was the heterogeneous evolution observed within exchanger subtypes. Specifically, in the case of the CCX exchangers we did not detect members of this class in three Clade III nematodes. Within the Caenorhabditis and Pristionchus lineages we identify between three and five CCX representatives, whereas in other Clade V and also Clade IV nematode taxa we only observed a single CCX gene in each species, and in the Clade III nematode taxa that we sampled we identify NCX and NCKX encoding genes but no evidence of CCX representatives using our mining approach. We also provided re-annotation for predicted CCX gene structures from Heterorhabditis bacteriophora and Caenorhabditis japonica by RT-PCR and sequencing. Together, these findings reveal a complex picture of Na+/Ca2+ transporters in nematodes that suggest an incongruent evolutionary history of proteins that provide central control of calcium dynamics.

  16. Analysis of the Na+/Ca2+ Exchanger Gene Family within the Phylum Nematoda

    PubMed Central

    He, Chao; O'Halloran, Damien M.

    2014-01-01

    Na+/Ca2+ exchangers are low affinity, high capacity transporters that rapidly transport calcium at the plasma membrane, mitochondrion, endoplasmic (and sarcoplasmic) reticulum, and the nucleus. Na+/Ca2+ exchangers are widely expressed in diverse cell types where they contribute homeostatic balance to calcium levels. In animals, Na+/Ca2+ exchangers are divided into three groups based upon stoichiometry: Na+/Ca2+ exchangers (NCX), Na+/Ca2+/K+ exchangers (NCKX), and Ca2+/Cation exchangers (CCX). In mammals there are three NCX genes, five NCKX genes and one CCX (NCLX) gene. The genome of the nematode Caenorhabditis elegans contains ten Na+/Ca2+ exchanger genes: three NCX; five CCX; and two NCKX genes. Here we set out to characterize structural and taxonomic specializations within the family of Na+/Ca2+ exchangers across the phylum Nematoda. In this analysis we identify Na+/Ca2+ exchanger genes from twelve species of nematodes and reconstruct their phylogenetic and evolutionary relationships. The most notable feature of the resulting phylogenies was the heterogeneous evolution observed within exchanger subtypes. Specifically, in the case of the CCX exchangers we did not detect members of this class in three Clade III nematodes. Within the Caenorhabditis and Pristionchus lineages we identify between three and five CCX representatives, whereas in other Clade V and also Clade IV nematode taxa we only observed a single CCX gene in each species, and in the Clade III nematode taxa that we sampled we identify NCX and NCKX encoding genes but no evidence of CCX representatives using our mining approach. We also provided re-annotation for predicted CCX gene structures from Heterorhabditis bacteriophora and Caenorhabditis japonica by RT-PCR and sequencing. Together, these findings reveal a complex picture of Na+/Ca2+ transporters in nematodes that suggest an incongruent evolutionary history of proteins that provide central control of calcium dynamics. PMID:25397810

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

    PubMed Central

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

    2012-01-01

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

  18. Phylogenetic placement of the enigmatic parasite, Polypodium hydriforme, within the Phylum Cnidaria

    PubMed Central

    2008-01-01

    Background Polypodium hydriforme is a parasite with an unusual life cycle and peculiar morphology, both of which have made its systematic position uncertain. Polypodium has traditionally been considered a cnidarian because it possesses nematocysts, the stinging structures characteristic of this phylum. However, recent molecular phylogenetic studies using 18S rDNA sequence data have challenged this interpretation, and have shown that Polypodium is a close relative to myxozoans and together they share a closer affinity to bilaterians than cnidarians. Due to the variable rates of 18S rDNA sequences, these results have been suggested to be an artifact of long-branch attraction (LBA). A recent study, using multiple protein coding markers, shows that the myxozoan Buddenbrockia, is nested within cnidarians. Polypodium was not included in this study. To further investigate the phylogenetic placement of Polypodium, we have performed phylogenetic analyses of metazoans with 18S and partial 28S rDNA sequences in a large dataset that includes Polypodium and a comprehensive sampling of cnidarian taxa. Results Analyses of a combined dataset of 18S and partial 28S sequences, and partial 28S alone, support the placement of Polypodium within Cnidaria. Removal of the long-branched myxozoans from the 18S dataset also results in Polypodium being nested within Cnidaria. These results suggest that previous reports showing that Polypodium and Myxozoa form a sister group to Bilateria were an artifact of long-branch attraction. Conclusion By including 28S rDNA sequences and a comprehensive sampling of cnidarian taxa, we demonstrate that previously conflicting hypotheses concerning the phylogenetic placement of Polypodium can be reconciled. Specifically, the data presented provide evidence that Polypodium is indeed a cnidarian and is either the sister taxon to Hydrozoa, or part of the hydrozoan clade, Leptothecata. The former hypothesis is consistent with the traditional view that Polypodium

  19. On the Extent and Origins of Genic Novelty in the Phylum Nematoda

    PubMed Central

    Wasmuth, James; Schmid, Ralf; Hedley, Ann; Blaxter, Mark

    2008-01-01

    Background The phylum Nematoda is biologically diverse, including parasites of plants and animals as well as free-living taxa. Underpinning this diversity will be commensurate diversity in expressed genes, including gene sets associated specifically with evolution of parasitism. Methods and Findings Here we have analyzed the extensive expressed sequence tag data (available for 37 nematode species, most of which are parasites) and define over 120,000 distinct putative genes from which we have derived robust protein translations. Combined with the complete proteomes of Caenorhabditis elegans and Caenorhabditis briggsae, these proteins have been grouped into 65,000 protein families that in turn contain 40,000 distinct protein domains. We have mapped the occurrence of domains and families across the Nematoda and compared the nematode data to that available for other phyla. Gene loss is common, and in particular we identify nearly 5,000 genes that may have been lost from the lineage leading to the model nematode C. elegans. We find a preponderance of novelty, including 56,000 nematode-restricted protein families and 26,000 nematode-restricted domains. Mapping of the latest time-of-origin of these new families and domains across the nematode phylogeny revealed ongoing evolution of novelty. A number of genes from parasitic species had signatures of horizontal transfer from their host organisms, and parasitic species had a greater proportion of novel, secreted proteins than did free-living ones. Conclusions These classes of genes may underpin parasitic phenotypes, and thus may be targets for development of effective control measures. PMID:18596977

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

    PubMed

    Caro-Quintero, Alejandro; Konstantinidis, Konstantinos T

    2015-03-17

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

  1. In Silico Analysis of the Metabolic Potential and Niche Specialization of Candidate Phylum "Latescibacteria" (WS3)

    PubMed Central

    Youssef, Noha H.; Farag, Ibrahim F.; Rinke, Christian; Hallam, Steven J.; Woyke, Tanja; Elshahed, Mostafa S.

    2015-01-01

    The “Latescibacteria” (formerly WS3), member of the Fibrobacteres–Chlorobi–Bacteroidetes (FCB) superphylum, represents a ubiquitous candidate phylum found in terrestrial, aquatic, and marine ecosystems. Recently, single-cell amplified genomes (SAGs) representing the “Latescibacteria” were obtained from the anoxic monimolimnion layers of Sakinaw Lake (British Columbia, Canada), and anoxic sediments of a coastal lagoon (Etoliko lagoon, Western Greece). Here, we present a detailed in-silico analysis of the four SAGs to gain some insights on their metabolic potential and apparent ecological roles. Metabolic reconstruction suggests an anaerobic fermentative mode of metabolism, as well as the capability to degrade multiple polysaccharides and glycoproteins that represent integral components of green (Charophyta and Chlorophyta) and brown (Phaeophycaea) algae cell walls (pectin, alginate, ulvan, fucan, hydroxyproline-rich glycoproteins), storage molecules (starch and trehalose), and extracellular polymeric substances (EPSs). The analyzed SAGs also encode dedicated transporters for the uptake of produced sugars and amino acids/oligopeptides, as well as an extensive machinery for the catabolism of all transported sugars, including the production of a bacterial microcompartment (BMC) to sequester propionaldehyde, a toxic intermediate produced during fucose and rhamnose metabolism. Finally, genes for the formation of gas vesicles, flagella, type IV pili, and oxidative stress response were found, features that could aid in cellular association with algal detritus. Collectively, these results indicate that the analyzed “Latescibacteria” mediate the turnover of multiple complex organic polymers of algal origin that reach deeper anoxic/microoxic habitats in lakes and lagoons. The implications of such process on our understanding of niche specialization in microbial communities mediating organic carbon turnover in stratified water bodies are discussed. PMID

  2. In Silico Analysis of the Metabolic Potential and Niche Specialization of Candidate Phylum "Latescibacteria" (WS3).

    PubMed

    Youssef, Noha H; Farag, Ibrahim F; Rinke, Christian; Hallam, Steven J; Woyke, Tanja; Elshahed, Mostafa S

    2015-01-01

    The "Latescibacteria" (formerly WS3), member of the Fibrobacteres-Chlorobi-Bacteroidetes (FCB) superphylum, represents a ubiquitous candidate phylum found in terrestrial, aquatic, and marine ecosystems. Recently, single-cell amplified genomes (SAGs) representing the "Latescibacteria" were obtained from the anoxic monimolimnion layers of Sakinaw Lake (British Columbia, Canada), and anoxic sediments of a coastal lagoon (Etoliko lagoon, Western Greece). Here, we present a detailed in-silico analysis of the four SAGs to gain some insights on their metabolic potential and apparent ecological roles. Metabolic reconstruction suggests an anaerobic fermentative mode of metabolism, as well as the capability to degrade multiple polysaccharides and glycoproteins that represent integral components of green (Charophyta and Chlorophyta) and brown (Phaeophycaea) algae cell walls (pectin, alginate, ulvan, fucan, hydroxyproline-rich glycoproteins), storage molecules (starch and trehalose), and extracellular polymeric substances (EPSs). The analyzed SAGs also encode dedicated transporters for the uptake of produced sugars and amino acids/oligopeptides, as well as an extensive machinery for the catabolism of all transported sugars, including the production of a bacterial microcompartment (BMC) to sequester propionaldehyde, a toxic intermediate produced during fucose and rhamnose metabolism. Finally, genes for the formation of gas vesicles, flagella, type IV pili, and oxidative stress response were found, features that could aid in cellular association with algal detritus. Collectively, these results indicate that the analyzed "Latescibacteria" mediate the turnover of multiple complex organic polymers of algal origin that reach deeper anoxic/microoxic habitats in lakes and lagoons. The implications of such process on our understanding of niche specialization in microbial communities mediating organic carbon turnover in stratified water bodies are discussed.

  3. Observation of the Decay {ital K}{sup +} {r_arrow} {pi}{sup +}{mu}{sup +}{mu}{sup {minus}}

    SciTech Connect

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

    1997-12-01

    We have observed the rare decay K{sup +} {r_arrow} {pi}{sup +}{mu}{sup +}{mu}{sup {minus}} and measured the branching ratio {Gamma}(K{sup +} {r_arrow} {pi}{sup +}{mu}{sup +}{mu}{sup {minus}}) /{Gamma}(K{sup +} {r_arrow} all)=[5.0{plus_minus}0.4(stat){plus_minus} 0.7(syst){plus_minus}0.6(th)]{times}10{sup {minus}8}. We compare this result with predictions from chiral perturbation theory and estimates based on the decay K{sup +} {r_arrow} {pi}{sup +}e{sup +}e{sup {minus}}. {copyright} {ital 1997} {ital The American Physical Society}

  4. Worms in the College Classroom: More than Just a Composting Demonstration

    ERIC Educational Resources Information Center

    Kelley, Rebecca L.

    2010-01-01

    Although worm bins have been used by K-12 and nonformal educators for decades, there is little evidence of their use in postsecondary education. The ease of use, maintenance, affordability, portability, and diversity of scientific concepts that can be demonstrated with a worm bin make it a valuable tool in college science classrooms. The purpose…

  5. Defending against Internet worms using a phase space method from chaos theory

    NASA Astrophysics Data System (ADS)

    Hu, Jing; Gao, Jianbo; Rao, Nageswara S.

    2007-04-01

    Enterprise networks are facing ever-increasing security threats from Distributed Denial of Service (DDoS) attacks, worms, viruses, intrusions, Trojans, port scans, and network misuses, and thus effective monitoring approaches to quickly detect these activities are greatly needed. In this paper, we employ chaos theory and propose an interesting phase space method to detect Internet worms. An Internet worm is a self-propagating program that automatically replicates itself to vulnerable systems and spreads across the Internet. Most deployed worm-detection systems are signature-based. They look for specific byte sequences (called attack signatures) that are known to appear in the attack traffic. Conventionally, the signatures are manually identified by human experts through careful analysis of the byte sequence from captured attack traffic. We propose to embed the traffic sequence to a high-dimensional phase space using chaos theory. We have observed that the signature sequence of a specific worm will occupy specific regions in the phase space, which may be appropriately called the invariant subspace of the worm. The invariant subspace of the worm separates itself widely from the subspace of the normal traffic. This separation allows us to construct three simple metrics, each of which completely separates 100 normal traffic streams from 200 worm traffic streams, without training in the conventional sense. Therefore, the method is at least as accurate as any existing methods. More importantly, our method is much faster than existing methods, such as based on expectation maximization and hidden Markov models.

  6. Guinea Worm (Dracunculus medinensis) Infection in a Wild-Caught Frog, Chad

    PubMed Central

    Cleveland, Christopher A.; Zirimwabagabo, Hubert; Yabsley, Michael J.; Ouakou, Philippe Tchindebet; Ruiz-Tiben, Ernesto

    2016-01-01

    A third-stage (infective) larva of Dracunculus medinensis, the causative agent of Guinea worm disease, was recovered from a wild-caught Phrynobatrachus francisci frog in Chad. Although green frogs (Lithobates clamitans) have been experimentally infected with D. medinensis worms, our findings prove that frogs can serve as natural paratenic hosts. PMID:27560598

  7. Guinea Worm (Dracunculus medinensis) Infection in a Wild-Caught Frog, Chad.

    PubMed

    Eberhard, Mark L; Cleveland, Christopher A; Zirimwabagabo, Hubert; Yabsley, Michael J; Ouakou, Philippe Tchindebet; Ruiz-Tiben, Ernesto

    2016-11-01

    A third-stage (infective) larva of Dracunculus medinensis, the causative agent of Guinea worm disease, was recovered from a wild-caught Phrynobatrachus francisci frog in Chad. Although green frogs (Lithobates clamitans) have been experimentally infected with D. medinensis worms, our findings prove that frogs can serve as natural paratenic hosts.

  8. Measurement of the Neutral B Meson Lifetime using Partially Reconstructed Bo right arrow D (sup asterisk -) pi + Decays

    NASA Astrophysics Data System (ADS)

    Zito, M.

    2002-03-01

    The neutral B meson lifetime has been measured with the data collected by the BABAR detector at the PEP-II storage ring during the year 2000 for a total integrated luminosity of 20.3 fb to the minus 1 power. The B0 right arrow D(sup asterisk -)pi+ decays have been selected with a partial reconstruction method in which only the fast pion from the B0 decay and the slow pion from D(sup asterisk -) right arrow overline Do pi- are reconstructed. The B0 lifetime has been measured to be 1.510 + or - 0.040 + or - 0.038 ps with a sample of 6971 + or - 241 reconstructed signal events.

  9. The Cranked Arrow Wing Aerodynamics Project (CAWAP) and its Extension to the International Community as CAWAPI: Objectives and Overview

    NASA Technical Reports Server (NTRS)

    Lamar, John E.; Obara, Clifford J.

    2009-01-01

    This paper provides a brief history of the F-16XL-1 aircraft, its role in the High Speed Research (HSR) program and how it was morphed into the Cranked Arrow Wing Aerodynamics Project (CAWAP). Various flight, wind-tunnel and Computational Fluid Dynamics (CFD) data sets were generated during the CAWAP. These unique and open flight datasets for surface pressures, boundary-layer profiles and skin-friction distributions, along with surface flow data, are described and sample data comparisons given. This is followed by a description of how the project became internationalized to be known as Cranked Arrow Wing Aerodynamics Project International (CAWAPI) and is concluded by an introduction to the results of a 5-year CFD predictive study of data.

  10. Beetle and plant arrow poisons of the Ju|'hoan and Hai||om San peoples of Namibia (Insecta, Coleoptera, Chrysomelidae; Plantae, Anacardiaceae, Apocynaceae, Burseraceae).

    PubMed

    Chaboo, Caroline S; Biesele, Megan; Hitchcock, Robert K; Weeks, Andrea

    2016-01-01

    The use of archery to hunt appears relatively late in human history. It is poorly understood but the application of poisons to arrows to increase lethality must have occurred shortly after developing bow hunting methods; these early multi-stage transitions represent cognitive shifts in human evolution. This paper is a synthesis of widely-scattered literature in anthropology, entomology, and chemistry, dealing with San ("Bushmen") arrow poisons. The term San (or Khoisan) covers many indigenous groups using so-called 'click languages' in southern Africa. Beetles are used for arrow poison by at least eight San groups and one non-San group. Fieldwork and interviews with Ju|'hoan and Hai||om hunters in Namibia revealed major differences in the nature and preparation of arrow poisons, bow and arrow construction, and poison antidote. Ju|'hoan hunters use leaf-beetle larvae of Diamphidia Gerstaecker and Polyclada Chevrolat (Chrysomelidae: Galerucinae: Alticini) collected from soil around the host plants Commiphora africana (A. Rich.) Engl. and Commiphora angolensis Engl. (Burseracaeae). In the Nyae Nyae area of Namibia, Ju|'hoan hunters use larvae of Diamphidia nigroornata Ståhl. Larvae and adults live above-ground on the plants and eat leaves, but the San collect the underground cocoons to extract the mature larvae. Larval hemolymph is mixed with saliva and applied to arrows. Hai||om hunters boil the milky plant sap of Adenium bohemianum Schinz (Apocynaceae) to reduce it to a thick paste that is applied to their arrows. The socio-cultural, historical, and ecological contexts of the various San groups may determine differences in the sources and preparation of poisons, bow and arrow technology, hunting behaviors, poison potency, and perhaps antidotes.

  11. Beetle and plant arrow poisons of the Ju|’hoan and Hai||om San peoples of Namibia (Insecta, Coleoptera, Chrysomelidae; Plantae, Anacardiaceae, Apocynaceae, Burseraceae)

    PubMed Central

    Chaboo, Caroline S.; Biesele, Megan; Hitchcock, Robert K.; Weeks, Andrea

    2016-01-01

    Abstract The use of archery to hunt appears relatively late in human history. It is poorly understood but the application of poisons to arrows to increase lethality must have occurred shortly after developing bow hunting methods; these early multi-stage transitions represent cognitive shifts in human evolution. This paper is a synthesis of widely-scattered literature in anthropology, entomology, and chemistry, dealing with San (“Bushmen”) arrow poisons. The term San (or Khoisan) covers many indigenous groups using so-called ‘click languages’ in southern Africa. Beetles are used for arrow poison by at least eight San groups and one non-San group. Fieldwork and interviews with Ju|’hoan and Hai||om hunters in Namibia revealed major differences in the nature and preparation of arrow poisons, bow and arrow construction, and poison antidote. Ju|’hoan hunters use leaf-beetle larvae of Diamphidia Gerstaecker and Polyclada Chevrolat (Chrysomelidae: Galerucinae: Alticini) collected from soil around the host plants Commiphora africana (A. Rich.) Engl. and Commiphora angolensis Engl. (Burseracaeae). In the Nyae Nyae area of Namibia, Ju|’hoan hunters use larvae of Diamphidia nigroornata Ståhl. Larvae and adults live above-ground on the plants and eat leaves, but the San collect the underground cocoons to extract the mature larvae. Larval hemolymph is mixed with saliva and applied to arrows. Hai||om hunters boil the milky plant sap of Adenium bohemianum Schinz (Apocynaceae) to reduce it to a thick paste that is applied to their arrows. The socio-cultural, historical, and ecological contexts of the various San groups may determine differences in the sources and preparation of poisons, bow and arrow technology, hunting behaviors, poison potency, and perhaps antidotes. PMID:27006594

  12. Ethnophysiology and herbal treatments of intestinal worms in Dominica, West Indies.

    PubMed

    Quinlan, Marsha B; Quinlan, Robert J; Nolan, Justin M

    2002-04-01

    In rural Dominican ethnophysiology worms reside in a human organ called the 'worm bag'. Unchecked, worms can cause illness by growing in size and number, spreading out of the worm bag and into other organs. In this study of 'bush medicine', we use a measure of cognitive salience in free-listing tasks, which reveals five plants commonly used to treat intestinal worms. These were Ambrosia hispida (Asteraceae), Aristolochia trilobata (Aristlochiaceae), Chenopodium ambrosioides (Chenopodiaceae), Portulaca oleracea (Portulacaceae), and Artemisia absinthium (Asteraceae). Bioactive compounds appear to be present in all of these plants. The cognitive salience of these plant remedies coupled with evidence of biochemical properties suggest that they provide efficacious treatments for controlling intestinal parasite loads.

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

    PubMed

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

    1998-12-01

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

  14. Terminal deletion of the long arm of chromosome 3 [46,XX,del(3)(q27{r_arrow}qter)

    SciTech Connect

    Chitayat, D.; Babul, R.; Silver, M.M.

    1996-01-02

    We report on a terminal deletion of the long arm of chromosome 3[46,XX,del(3)(q27{r_arrow}qter)] in a female newborn infant who died 45 hours after delivery and had multiple congenital abnormalities including bilateral anophthalmia, congenital heart disease, and abnormal genitalia. The findings are compared to those of four previously reported cases with terminal de (3q). 8 refs., 4 figs., 1 tab.

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

    PubMed

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

    2013-03-01

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

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

    PubMed

    Elliott, David E; Weinstock, Joel V

    2009-01-01

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

  17. Laboratory Experiments on the Control of Cyclops Transmitting Guinea Worm

    PubMed Central

    Muller, Ralph

    1970-01-01

    Infection with the guinea worm (Dracunculus medinensis) affects millions of people living in rural areas in certain parts of the world. Usually, the standard of living is low and elaborate control measures would not be feasible. In this study, various insecticidal and molluscicidal compounds were tested in the laboratory for their toxicity to the intermediate hosts, namely, various species of cyclops, which often live in sources of potable water, such as step-wells, cisterns and ponds. Cheapness, low toxicity to mammals and ease of application, in conjunction with effectiveness against cyclops, are primary requisites for any compound accepted for widespread use. Abate, an insecticide, has been shown to be particularly promising in these respects. The timing and mode of application of compounds toxic to cyclops in various endemic regions are discussed. PMID:4247122

  18. Giant kidney worms in a patient with renal cell carcinoma.

    PubMed

    Kuehn, Jemima; Lombardo, Lindsay; Janda, William M; Hollowell, Courtney M P

    2016-03-07

    Dioctophyma renale (D. renale), or giant kidney worms, are the largest nematodes that infect mammals. Approximately 20 cases of human infection have been reported. We present a case of a 71-year-old man with a recent history of unintentional weight loss and painless haematuria, passing elongated erythematous tissue via his urethra. CT revealed a left renal mass with pulmonary nodules and hepatic lesions. On microscopy, the erythematous tissue passed was identified as D. renale. On subsequent renal biopsy, pathology was consistent with renal cell carcinoma. This is the first reported case of concomitant D. renale infection and renal cell carcinoma, and the second reported case of D. renale infection of the left kidney alone.

  19. Graphical method for profiling hob mill that generate cycloid worms

    NASA Astrophysics Data System (ADS)

    Teodor, V.; Berbinschi, S.; Baroiu, N.; Oancea, N.

    2015-11-01

    The hob mill for generating ordered curls of cycloid surface with non involute profiles may be profiled based on the fundamental theorems of surface enveloping - Olivier - as surface reciprocally enveloping with point like contact. In this paper, is proposed a methodology based on a complementary theorem of the surface enveloping in a graphical expression developed in a graphical design environment - CATIA. The graphical method presented in this paper is developed in two stages: determining of the rack gear model based on the solid model of the surface to be generated, using an original algorithm, following this, based on 3D modelling is determined the solid model of the primary peripheral surface of the hob mill. An application for a cycloid worm is presented - a central screw of helical pumps. In order to prove the quality of method, the analytical and graphical solutions are comparatively presented.

  20. Structure-Property Relationships for Branched Worm-Like Micelles

    NASA Astrophysics Data System (ADS)

    Beaucage, Gregory; Rai, Durgesh

    2013-03-01

    Micellar solutions can display a wide range of phase structure as a function of counter ion content, surfactant concentration, and the presence of ternary components. Under some conditions, common to consumer products, extended cylindrical structures that display persistence and other chain features of polymers are produced. These worm-like micelles (WLMs) can form branched structures that dynamically change under shear and even in quiescent conditions. The rheology of these branched WLMs is strongly dependent on migration of the branch points, and the dynamics of branch formation and removal. Persistence and other polymer-based descriptions are also of importance. We have recently developed a scattering model for branched polyolefins and other topologically complex materials that can quantify the branching density, branch length, branch functionality and the hyperbranch (branch-on-branch) content of polymers. This work is being extended to study branching in WLMs in work coupled with Ron Larson at UMich to predict rheological properties.

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

    PubMed Central

    Krauchunas, Amber R.; Singson, Andrew

    2016-01-01

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

  2. Wombs, Worms and Wolves: Constructing Cancer in Early Modern England

    PubMed Central

    Skuse, Alanna

    2014-01-01

    This essay examines medical and popular attitudes to cancer in the early modern period, c.1580–1720. Cancer, it is argued, was understood as a cruel and usually incurable disease, diagnosable by a well-defined set of symptoms understood to correspond to its etymological root, karkinos (the crab). It was primarily understood as produced by an imbalance of the humours, with women being particularly vulnerable. However, such explanations proved inadequate to make sense of the condition's malignancy, and medical writers frequently constructed cancer as quasi-sentient, zoomorphising the disease as an eating worm or wolf. In turn, these constructions materially influenced medical practice, in which practitioners swung between anxiety over ‘aggravating’ the disease and an adversarial approach which fostered the use of radical and dangerous ‘cures’ including caustics and surgery. PMID:25352720

  3. Microplastic ingestion decreases energy reserves in marine worms.

    PubMed

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

    2013-12-02

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

  4. Hybrid Epidemics—A Case Study on Computer Worm Conficker

    PubMed Central

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

    2015-01-01

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

  5. Community perception and role in prevention of Guinea worm disease.

    PubMed

    Omar, M A; Sufi, Q M; Gamba-Osiga, A

    1993-01-01

    In Kitgum district of northern Uganda in 1992, natural group and focus group discussions and key informant interviews were conducted to examine the knowledge, attitudes, practices, and beliefs of the people concerning Guinea Worm disease (GW disease) and its transmission, prevention, and treatment. Most people could describe the cause and treatment of Coo (local name of GW disease). More than 58% thought dirty or bad water was the main cause of Coo. 63.2% believed that drinking contaminated water was the cause. 13.1% did not know the cause of GW disease. Few people clearly understood how GW is transmitted. People received treatment from the nearest health unit (42%), traditional healers (34%), self-medication (16%), and drug shops (8%). 55.3% of key informants believed that Coo cases had increased. The perceived reasons for the increase were drinking dirty water (42.8%), migration (38.1%), no medicine (9.5%), and increased population (4.8%). Suggestions for community action to halt transmission of GW included provision of safe water, educating each other, boiling water, and filtering water. The community perceived that the government and nongovernmental organizations could drill new boreholes, bring in medications, repair broken boreholes, protect water sources, and provide education to stop the spread of GW disease. Water sources were shallow wells, streams, rivers, valley dams, and boreholes. 77.3% of boreholes did not work. Most other water sources were inadequately protected from GW infestation. Some community members perceived boiling water as tedious and difficult. Most people thought that there was nothing or little they could do to prevent contamination of water sources. Few had heard health education messages about Guinea Worm disease. Many people wanted the use of plays, drama, and videos in villages to communicate GW prevention messages.

  6. Two Leucobacter strains exert complementary virulence on Caenorhabditis including death by worm-star formation.

    PubMed

    Hodgkin, Jonathan; Félix, Marie-Anne; Clark, Laura C; Stroud, Dave; Gravato-Nobre, Maria J

    2013-11-04

    The nematode Caenorhabditis elegans has been much studied as a host for microbial infection. Some pathogens can infect its intestine, while others attack via its external surface. Cultures of Caenorhabditis isolated from natural environments have yielded new nematode pathogens, such as microsporidia and viruses. We report here a novel mechanism for bacterial attack on worms, discovered during investigation of a diseased and coinfected natural isolate of Caenorhabditis from Cape Verde. Two related coryneform pathogens (genus Leucobacter) were obtained from this isolate, which had complementary effects on C. elegans and related nematodes. One pathogen, Verde1, was able to cause swimming worms to stick together irreversibly by their tails, leading to the rapid formation of aggregated "worm-stars." Adult worms trapped in these aggregates were immobilized and subsequently died, with concomitant growth of bacteria. Trapped larval worms were sometimes able to escape from worm-stars by undergoing autotomy, separating their bodies into two parts. The other pathogen, Verde2, killed worms after rectal invasion, in a more virulent version of a previously studied infection. Resistance to killing by Verde2, by means of alterations in host surface glycosylation, resulted in hypersensitivity to Verde1, revealing a trade-off in bacterial susceptibility. Conversely, a sublethal surface infection of worms with Verde1 conferred partial protection against Verde2. The formation of worm-stars by Verde1 occurred only when worms were swimming in liquid but provides a striking example of asymmetric warfare as well as a bacterial equivalent to the trapping strategies used by nematophagous fungi.

  7. Observation of the Decay {ital K}{sup +} {r_arrow} {pi}{sup +}{gamma}{gamma}

    SciTech Connect

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

    1997-11-01

    The first observation of the decay K{sup +}{r_arrow}{pi}{sup +}{gamma}{gamma} is reported. A total of 31 events was observed with an estimated background of 5.1{plus_minus}3.3 events in the {pi}{sup +} momentum range from 100 to 180 MeV/{ital c}. The corresponding partial branching ratio, B(K{sup +}{r_arrow}{pi}{sup +}{gamma}{gamma} ,100 MeV/c{lt}P{sub {pi}{sup +} }{lt}180 MeV/c) , is [6.0{plus_minus}1.5(stat){plus_minus}0.7 (syst)]{times}10{sup {minus}7} . No K{sup +}{r_arrow}{pi}{sup +}{gamma}{gamma} decay was observed in the {pi}{sup +} momentum region greater than 215 MeV/{ital c}. The observed {pi}{sup +} momentum spectrum is compared with the predictions of chiral perturbation theory. {copyright} {ital 1997} {ital The American Physical Society}

  8. Study of advanced composite structural design concepts for an arrow wing supersonic cruise configuration, task 3

    NASA Technical Reports Server (NTRS)

    1978-01-01

    A structural design study was conducted to assess the relative merits of structural concepts using advanced composite materials for an advanced supersonic aircraft cruising at Mach 2.7. The configuration and structural arrangement developed during Task I and II of the study, was used as the baseline configuration. Allowable stresses and strains were established for boron and advanced graphite fibers based on projected fiber properties available in the next decade. Structural concepts were designed and analyzed using graphite polyimide and boron polyimide, applied to stiffened panels and conventional sandwich panels. The conventional sandwich panels were selected as the structural concept to be used on the wing structure. The upper and lower surface panels of the Task I arrow wing were redesigned using high-strength graphite polyimide sandwich panels over the titanium spars and ribs. The ATLAS computer system was used as the basis for stress analysis and resizing the surface panels using the loads from the Task II study, without adjustment for change in aeroelastic deformation. The flutter analysis indicated a decrease in the flutter speed compared to the baseline titanium wing design. The flutter analysis indicated a decrease in the flutter speed compared to the baseline titanium wing design. The flutter speed was increased to that of the titanium wing, with a weight penalty less than that of the metallic airplane.

  9. Threshold responses of Blackside Dace (Chrosomus cumberlandensis) and Kentucky Arrow Darter (Etheostoma spilotum) to stream conductivity

    USGS Publications Warehouse

    Hitt, Nathaniel P.; Floyd, Michael; Compton, Michael; McDonald, Kenneth

    2016-01-01

    Chrosomus cumberlandensis (Blackside Dace [BSD]) and Etheostoma spilotum (Kentucky Arrow Darter [KAD]) are fish species of conservation concern due to their fragmented distributions, their low population sizes, and threats from anthropogenic stressors in the southeastern United States. We evaluated the relationship between fish abundance and stream conductivity, an index of environmental quality and potential physiological stressor. We modeled occurrence and abundance of KAD in the upper Kentucky River basin (208 samples) and BSD in the upper Cumberland River basin (294 samples) for sites sampled between 2003 and 2013. Segmented regression indicated a conductivity change-point for BSD abundance at 343 μS/cm (95% CI: 123–563 μS/cm) and for KAD abundance at 261 μS/cm (95% CI: 151–370 μS/cm). In both cases, abundances were negligible above estimated conductivity change-points. Post-hoc randomizations accounted for variance in estimated change points due to unequal sample sizes across the conductivity gradients. Boosted regression-tree analysis indicated stronger effects of conductivity than other natural and anthropogenic factors known to influence stream fishes. Boosted regression trees further indicated threshold responses of BSD and KAD occurrence to conductivity gradients in support of segmented regression results. We suggest that the observed conductivity relationship may indicate energetic limitations for insectivorous fishes due to changes in benthic macroinvertebrate community composition.

  10. ARGX-87: Accident Response Group Exercise, 1987: A Broken Arrow mini exercise. [Training

    SciTech Connect

    Schuld, E.P.; Cruff, D.F.

    1987-07-01

    A Broken Arrow mini exercise dubbed ''Accident Response Group Exercise - 1987'' (ARGX-87) was conducted on June 1, 1987 at the Lawrence Livermore National Laboratory (LLNL) and Sandia National Laboratories, Livermore (SNLL). The exercise started at 0445 PDT with a call from the Department of Energy (DOE) - EOC in Washington, DC, to the Albuquerque Operations (AL - ) - EOC. AL, in turn, called the Laboratory off-hour emergency number (Fire Dispatcher), who called the Laboratory Emergency Duty Officer (LEDO). The LEDO then contacted the Accident Response Group (ARG) Senior Scientific Advisor. Calls were placed to assemble appropriate members of the ARG in the ALERT Center. No phone number for SNLL was available at the Albuquerque Operations EOC, so a controller injected a message to SNLL to get them involved in the exercise. The messages received at the Laboratory identified the Air Force line item weapon system involved in the accident and the accident location. As people arrived at the ALERT Center they began discussing the details of the accident. They also started working the deployment logistics and other issues. Travel arrangements for the HOT SPOT equipment and ARG personnel were made for immediate deployment to the accident site in North Dakota. The exercise was terminated at 0840 as planned. While certain procedural deficiencies were noted, the exercise was considered a valuable learning experience. The results and observations from this experience will be used to refine the operating procedures and the training program.

  11. Supersonic Aerodynamic Design Improvements of an Arrow-Wing HSCT Configuration Using Nonlinear Point Design Methods

    NASA Technical Reports Server (NTRS)

    Unger, Eric R.; Hager, James O.; Agrawal, Shreekant

    1999-01-01

    This paper is a discussion of the supersonic nonlinear point design optimization efforts at McDonnell Douglas Aerospace under the High-Speed Research (HSR) program. The baseline for these optimization efforts has been the M2.4-7A configuration which represents an arrow-wing technology for the High-Speed Civil Transport (HSCT). Optimization work on this configuration began in early 1994 and continued into 1996. Initial work focused on optimization of the wing camber and twist on a wing/body configuration and reductions of 3.5 drag counts (Euler) were realized. The next phase of the optimization effort included fuselage camber along with the wing and a drag reduction of 5.0 counts was achieved. Including the effects of the nacelles and diverters into the optimization problem became the next focus where a reduction of 6.6 counts (Euler W/B/N/D) was eventually realized. The final two phases of the effort included a large set of constraints designed to make the final optimized configuration more realistic and they were successful albeit with a loss of performance.

  12. The Potential Landscape of Genetic Circuits Imposes the Arrow of Time in Stem Cell Differentiation

    PubMed Central

    Wang, Jin; Xu, Li; Wang, Erkang; Huang, Sui

    2010-01-01

    Abstract Differentiation from a multipotent stem or progenitor state to a mature cell is an essentially irreversible process. The associated changes in gene expression patterns exhibit time-directionality. This “arrow of time” in the collective change of gene expression across multiple stable gene expression patterns (attractors) is not explained by the regulated activation, the suppression of individual genes which are bidirectional molecular processes, or by the standard dynamical models of the underlying gene circuit which only account for local stability of attractors. To capture the global dynamics of this nonequilibrium system and gain insight in the time-asymmetry of state transitions, we computed the quasipotential landscape of the stochastic dynamics of a canonical gene circuit that governs branching cell fate commitment. The potential landscape reveals the global dynamics and permits the calculation of potential barriers between cell phenotypes imposed by the circuit architecture. The generic asymmetry of barrier heights indicates that the transition from the uncommitted multipotent state to differentiated states is inherently unidirectional. The model agrees with observations and predicts the extreme conditions for reprogramming cells back to the undifferentiated state. PMID:20655830

  13. Influence of the radius of the leading edge of worm vanes on the critical cavitation allowance of a pump

    SciTech Connect

    Shcherbatenko, I.V.; Khankin, V.P.

    1982-11-01

    This paper theoretically and experimentally investigates the influence of the cylindrical (curved) leading edge of the worm vanes on the cavitation characteristics of the pump. Considers the disruptive flow around the worm wheel with a constant screw spacing (pitch) of an ideal liquid flow. The proposed equations, verified on pumps with worms of different types and sizes with a wide range of attack angles, can be used for the calculation of the sucking capacity of high-speed worm centrifugal pumps.

  14. Environmental Sensing in Actinobacteria: a Comprehensive Survey on the Signaling Capacity of This Phylum

    PubMed Central

    Huang, Xiaoluo; Pinto, Daniela; Fritz, Georg

    2015-01-01

    , classify, and describe numerous novel and conserved signaling devices. Hence, our work serves as an important resource for any researcher interested in signal transduction of this important bacterial phylum, which contains organisms of ecological, biotechnological, and medical relevance. PMID:25986905

  15. Co-evolution of RNA polymerase with RbpA in the phylum Actinobacteria

    PubMed Central

    Dey, Abhinav; Adithi, V.R.; Chatterji, Dipankar

    2012-01-01

    The role of RbpA in the backdrop of M. smegmatis showed that it rescues mycobacterial RNA polymerase from rifampicin-mediated inhibition (Dey et al., 2010; Dey et al., 2011). Paget and co-workers (Paget et al., 2001; Newell et al., 2006) have revealed that RbpA homologs occur exclusively in actinobacteria. Newell et al. (2006) showed that MtbRbpA, when complemented in a ∆rbpA mutant of S. coelicolor, showed a low recovery of MIC (from 0.75 to 2 μg/ml) as compared to complementation by native RbpA of S. coelicolor (MIC increases from 0.75 to 11 μg/ml). Our studies on MsRbpA show that it is a differential marker for M. smegmatis RNA polymerase as compared to E. coli RNA polymerase at IC50 levels of rifampicin. A recent sequence-based analysis by Lane and Darst (2010) has shown that RNA polymerases from Proteobacteria and Actinobacteria have had a divergent evolution. E. coli is a representative of Proteobacteria and M. smegmatis is an Actinobacterium. RbpA has an exclusive occurrence in Actinobacteria. Since protein–protein interactions might not be conserved across different species, therefore, the probable reason for the indifference of MsRbpA toward E. coli RNA polymerase could be the lineage-specific differences between actinobacterial and proteobacterial RNA polymerases. These observations led us to ask the question as to whether the evolution of RbpA in Actinobacteria followed the same route as that of RNA polymerase subunits from actinobacterial species. We show that the exclusivity of RbpA in Actinobacteria and the unique evolution of RNA polymerase in this phylum share a co-evolutionary link. We have addressed this issue by a blending of experimental and bioinformatics based approaches. They comprise of induction of bacterial cultures coupled to rifampicin-tolerance, transcription assays and statistical comparison of phylogenetic trees for different pairs of proteins in actinobacteria. PMID:27896048

  16. Real-time PCR detection of bacteria belonging to the Firmicutes Phylum.

    PubMed

    Haakensen, M; Dobson, C M; Deneer, H; Ziola, B

    2008-07-31

    Members of the bacterial Phylum Firmicutes occupy a wide range of habitats and can be either beneficial or detrimental in diverse settings, including food- and beverage-related industries. Firmicutes are responsible for the vast majority of beer-spoilage incidents and, as such, they have a substantial financial impact in the brewing industry. Rapid detection and identification of a bacterium as a Firmicutes is difficult due to widespread genetic transfer and genome reduction resulting in phenotypic diversity in these bacteria. Here we describe a real-time multiplex PCR to detect and differentiate Firmicutes associated with beer-spoilage from non-Firmicutes bacteria that may be present as benign environmental contaminants. A region of the 16S rRNA gene was identified and predicted to be highly conserved amongst, and essentially specific for, Firmicutes. A real-time PCR assay using a hydrolysis probe targeting this region of the 16S rRNA gene was experimentally shown to detect ten genera of Firmicutes known to be beer spoilers, but does not cross-react with eleven of twelve non-Firmicutes genera which can periodically appear in beer. Only one non-Firmicutes species, Zymomonas mobilis, weakly reacted with the Firmicutes probe. This rPCR assay has a standard curve that is linear over six orders of magnitude of DNA, with a quantitation limit of DNA from <10 bacteria. When used to detect bacteria present in beer, the assay was able to detect 50-100 colony forming units (CFU) of Firmicutes directly from 2.5 cm membranes used to filter 100 ml of contaminated beer. Through incorporation of a 4.7 cm filter and an overnight pre-enrichment incubation, the sensitivity was increased to 2.5-10 CFU per package of beer (341 ml). When multiplexed with a second hydrolysis probe targeting a universal region of the 16S rRNA gene, the assay reliably differentiates between Firmicutes and non-Firmicutes bacteria found in breweries.

  17. Biouptake of chlorinated hydrocarbons from laboratory-spiked and field sediments by oligochaete worms

    SciTech Connect

    Oliver, B.G.

    1987-08-01

    The uptake and depuration of 37 chemicals from spiked Lake Ontario sediments by oligochaete worms has been studied at 8 and 20/sup 0/C in laboratory aquaria. The worms were found to rapidly accumulate the chemicals and reach peak concentrations within 2 weeks. The concentration of chemical in the sediment pore water appeared to be the major factor controlling the bioconcentration of chemicals by worms. The worm bioconcentration factors increased with increasing octanol-water partition coefficient of the chemicals. The worm-mediated fluxes of the chemicals from the sediments have also been estimated. Depuration studies showed in the half-lives of the chemicals in the worms ranged from less than 5 days to several months. Field worms and associated sediments from Lake Ontario near the Niagara River were analyzed. The agreement between the field and laboratory results was good for the more persistent chemicals because of time differences for sorting the two samples types. 30 references, 3 figures, 5 tables.

  18. Curcumin Generates Oxidative Stress and Induces Apoptosis in Adult Schistosoma mansoni Worms

    PubMed Central

    de Paula Aguiar, Daniela; Brunetto Moreira Moscardini, Mayara; Rezende Morais, Enyara; Graciano de Paula, Renato; Ferreira, Pedro Manuel; Afonso, Ana; Belo, Silvana; Tomie Ouchida, Amanda; Curti, Carlos; Cunha, Wilson Roberto; Rodrigues, Vanderlei

    2016-01-01

    Inducing apoptosis is an interesting therapeutic approach to develop drugs that act against helminthic parasites. Researchers have investigated how curcumin (CUR), a biologically active compound extracted from rhizomes of Curcuma longa, affects Schistosoma mansoni and several cancer cell lines. This study evaluates how CUR influences the induction of apoptosis and oxidative stress in couples of adult S. mansoni worms. CUR decreased the viability of adult worms and killed them. The tegument of the parasite suffered morphological changes, the mitochondria underwent alterations, and chromatin condensed. Different apoptotic parameters were determined in an attempt to understand how CUR affected adult S. mansoni worms. CUR induced DNA damage and fragmentation and increased the expression of SmCASP3/7 transcripts and the activity of Caspase 3 in female and male worms. However, CUR did not intensify the activity of Caspase 8 in female or male worms. Evaluation of the superoxide anion and different antioxidant enzymes helped to explore the mechanism of parasite death further. The level of superoxide anion and the activity of Superoxide Dismutase (SOD) increased, whereas the activity of Glutathione-S-Transferase (GST), Glutathione reductase (GR), and Glutathione peroxidase (GPX) decreased, which culminated in the oxidation of proteins in adult female and male worms incubated with CUR. In conclusion, CUR generated oxidative stress followed by apoptotic-like-events in both adult female and male S. mansoni worms, ultimately killing them. PMID:27875592

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

    PubMed

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

    2014-10-01

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

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

    PubMed

    Diamenu, S K; Nyaku, A A

    1998-08-01

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

  1. Worm infestations and development of autoimmunity in children – The ABIS study

    PubMed Central

    Jones, Michael P.; Faresjö, Åshild

    2017-01-01

    Worm infestations influence the immune system and may therefore decrease the risk for autoimmune diseases. The aim of the study was to determine whether children who have developed autoimmune disease were less likely to have had worm infestations in childhood. The ABIS-study is a prospective population-based cohort study of children born in southeast Sweden 1997/99. 17.055 children participated. As of June 2014 116 individuals had developed Type 1 diabetes, 181 celiac disease, and 53 Juvenile Rheumatoid Arthritis. The parents answered questions on worm infestations when the children were 1, 5 and 8 years of age. The ABIS registry was connected to the National Registry of Drug Prescriptions, and national registries for diagnosis of the studied diseases. We found no differences in incidence of worm infestations at 1, 5 or 8 years of age between children who developed autoimmune disease(s) or healthy controls. At 8 years in total 20.0% of the general child population had experienced a worm infestation; children who developed Type 1 diabetes, 21,3%, celiac disease 19,5% and JRA 18,8%. There was no difference in prescriptions of drugs for treatment of worm infestations between those who had and who had not developed Type 1 diabetes, celiac disease, Juvenile Rheumatoid Arthritis. We found no associations indicating that worm infestations in childhood does not play a role in the development of autoimmune diseases in Sweden. PMID:28333965

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

    NASA Astrophysics Data System (ADS)

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

    2011-09-01

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

  3. Chemistry and the worm: Caenorhabditis elegans as a platform for integrating chemical and biological research.

    PubMed

    Hulme, S Elizabeth; Whitesides, George M

    2011-05-16

    This Review discusses the potential usefulness of the worm Caenorhabditis elegans as a model organism for chemists interested in studying living systems. C. elegans, a 1 mm long roundworm, is a popular model organism in almost all areas of modern biology. The worm has several features that make it attractive for biology: it is small (<1000 cells), transparent, and genetically tractable. Despite its simplicity, the worm exhibits complex phenotypes associated with multicellularity: the worm has differentiated cells and organs, it ages and has a well-defined lifespan, and it is capable of learning and remembering. This Review argues that the balance between simplicity and complexity in the worm will make it a useful tool in determining the relationship between molecular-scale phenomena and organism-level phenomena, such as aging, behavior, cognition, and disease. Following an introduction to worm biology, the Review provides examples of current research with C. elegans that is chemically relevant. It also describes tools-biological, chemical, and physical-that are available to researchers studying the worm.

  4. Viability of developmental stages of Schistosoma mansoni quantified with xCELLigence worm real-time motility assay (xWORM).

    PubMed

    Rinaldi, Gabriel; Loukas, Alex; Brindley, Paul J; Irelan, Jeff T; Smout, Michael J

    2015-12-01

    Infection with helminth parasites causes morbidity and mortality in billions of people and livestock worldwide. Where anthelmintic drugs are available, drug resistance is a major problem in livestock parasites, and a looming threat to public health. Monitoring the efficacy of these medicines and screening for new drugs has been hindered by the lack of objective, high-throughput approaches. Several cell monitoring technologies have been adapted for parasitic worms, including video-, fluorescence-, metabolism enzyme- and impedance-based tools that minimize the screening bottleneck. Using the xCELLigence impedance-based system we previously developed a motility-viability assay that is applicable for a range of helminth parasites. Here we have improved substantially the assay by using diverse frequency settings, and have named it the xCELLigence worm real-time motility assay (xWORM). By utilizing strictly standardized mean difference analysis we compared the xWORM output measured with 10, 25 and 50 kHz frequencies to quantify the motility of schistosome adults (human blood flukes) and hatching of schistosome eggs. Furthermore, we have described a novel application of xWORM to monitor movement of schistosome cercariae, the developmental stage that is infectious to humans. For all three stages, 25 kHz was either optimal or near-optimal for monitoring and quantifying schistosome motility. These improvements in methodology sensitivity should enhance the capacity to screen small compound libraries for new drugs both for schistosomes and other helminth pathogens at large.

  5. How algae influence sessile marine organisms: The tube worms case of study

    NASA Astrophysics Data System (ADS)

    Casoli, Edoardo; Bonifazi, Andrea; Ardizzone, Giandomenico; Gravina, Maria Flavia

    2016-09-01

    Tube worms and phytobenthic assemblages in three infralittoral and shallow circalittoral Mediterranean benthic communities developed between 5 and 35 m depth at Punta del Lazzaretto (Giglio Island, Central Thyrrenian sea) were investigated. Despite being three algae-dominated habitats, these displayed different covering both in terms of algal layers and algal morphologies, reflecting different structural organizations. Twenty-eight serpulid taxa have been reported, increasing both diversity and density values from most photophilic to most sciaphilous habitats. Multivariate analyses showed how algal thalli and tube worm assemblages were strongly correlated; substrata are influenced both physically and biologically, providing different conditions for tube worm settlement.

  6. Species richness and macronutrient content of wawo worms (Polychaeta, Annelida) from Ambonese waters, Maluku, Indonesia.

    PubMed

    Pamungkas, Joko

    2015-01-01

    The aims of this research were to: (1) investigate the species richness of wawo worms, and to (2) analyze macronutrient content of the worms. Wawo worms were sampled using a fishing net on March 18(th)-19(th), 2014, from Ambonese waters, Maluku. As many as 26 wawo species belonging to 5 families were identified. Palola sp. was identified as the most abundant species of wawo, followed by Lysidiceoele, Horst 1905, Eunice spp. and nereidids. Results of the proximate analysis reveal that female epitokes of Palola sp. contain 10.78 % ash, 10.71 % moisture, 11.67 % crude fat, 54.72 % crude protein and 12.12 % carbohydrate.

  7. Thermo-responsive Diblock Copolymer Worm Gels in Non-polar Solvents

    PubMed Central

    2014-01-01

    Benzyl methacrylate (BzMA) is polymerized using a poly(lauryl methacrylate) macromolecular chain transfer agent (PLMA macro-CTA) using reversible addition–fragmentation chain transfer (RAFT) polymerization at 70 °C in n-dodecane. This choice of solvent leads to an efficient dispersion polymerization, with polymerization-induced self-assembly (PISA) occurring via the growing PBzMA block to produce a range of PLMA–PBzMA diblock copolymer nano-objects, including spheres, worms, and vesicles. In the present study, particular attention is paid to the worm phase, which forms soft free-standing gels at 20 °C due to multiple inter-worm contacts. Such worm gels exhibit thermo-responsive behavior: heating above 50 °C causes degelation due to the onset of a worm-to-sphere transition. Degelation occurs because isotropic spheres interact with each other much less efficiently than the highly anisotropic worms. This worm-to-sphere thermal transition is essentially irreversible on heating a dilute solution (0.10% w/w) but is more or less reversible on heating a more concentrated dispersion (20% w/w). The relatively low volatility of n-dodecane facilitates variable-temperature rheological studies, which are consistent with eventual reconstitution of the worm phase on cooling to 20 °C. Variable-temperature 1H NMR studies conducted in d26-dodecane confirm partial solvation of the PBzMA block at elevated temperature: surface plasticization of the worm cores is invoked to account for the observed change in morphology, because this is sufficient to increase the copolymer curvature and hence induce a worm-to-sphere transition. Small-angle X-ray scattering and TEM are used to investigate the structural changes that occur during the worm-to-sphere-to-worm thermal cycle; experiments conducted at 1.0 and 5.0% w/w demonstrate the concentration-dependent (ir)reversibility of these morphological transitions. PMID:24678949

  8. Experimental Investigation of a Point Design Optimized Arrow Wing HSCT Configuration

    NASA Technical Reports Server (NTRS)

    Narducci, Robert P.; Sundaram, P.; Agrawal, Shreekant; Cheung, S.; Arslan, A. E.; Martin, G. L.

    1999-01-01

    The M2.4-7A Arrow Wing HSCT configuration was optimized for straight and level cruise at a Mach number of 2.4 and a lift coefficient of 0.10. A quasi-Newton optimization scheme maximized the lift-to-drag ratio (by minimizing drag-to-lift) using Euler solutions from FL067 to estimate the lift and drag forces. A 1.675% wind-tunnel model of the Opt5 HSCT configuration was built to validate the design methodology. Experimental data gathered at the NASA Langley Unitary Plan Wind Tunnel (UPWT) section #2 facility verified CFL3D Euler and Navier-Stokes predictions of the Opt5 performance at the design point. In turn, CFL3D confirmed the improvement in the lift-to-drag ratio obtained during the optimization, thus validating the design procedure. A data base at off-design conditions was obtained during three wind-tunnel tests. The entry into NASA Langley UPWT section #2 obtained data at a free stream Mach number, M(sub infinity), of 2.55 as well as the design Mach number, M(sub infinity)=2.4. Data from a Mach number range of 1.8 to 2.4 was taken at UPWT section #1. Transonic and low supersonic Mach numbers, M(sub infinity)=0.6 to 1.2, was gathered at the NASA Langley 16 ft. Transonic Wind Tunnel (TWT). In addition to good agreement between CFD and experimental data, highlights from the wind-tunnel tests include a trip dot study suggesting a linear relationship between trip dot drag and Mach number, an aeroelastic study that measured the outboard wing deflection and twist, and a flap scheduling study that identifies the possibility of only one leading-edge and trailing-edge flap setting for transonic cruise and another for low supersonic acceleration.

  9. Lack of effect of ivermectin on prepatent guinea-worm: a single-blind, placebo-controlled trial.

    PubMed

    Issaka-Tinorgah, A; Magnussen, P; Bloch, P; Yakubu, A

    1994-01-01

    The effect of ivermectin on prepatent guinea-worm was tested in a single-blind placebo-controlled trial; 400 adults were randomly allocated to a single dose of ivermectin (150 micrograms/kg) or placebo. Fifty-four of the 385 participants who were followed for 15 months developed a total of 69 emergent guinea-worms. There was no significant difference in the proportion of persons with emergent guinea-worms between the 2 treatment groups; 58% appeared in males. 80% of emergent guinea-worms were located below the knee. Migration of guinea-worms in the tissues was not affected. It is concluded that ivermectin has no effect on prepatent guinea-worms nor does it disturb their migration pattern. No adverse reaction to treatment was seen. It appears that ivermectin can be used safely as mass chemotherapy against onchocerciasis and lymphatic filariasis in areas where guinea-worm is also endemic.

  10. Worm control practices on sheep farms in the Slovak Republic.

    PubMed

    Cernanská, Dana; Várady, Marián; Cudeková, Patrícia; Corba, Július

    2008-07-04

    A questionnaire to obtain information on worm control practices and sheep management was performed on 49 sheep farms in 2003 and 2004. The majority of Slovak farms kept native breeds Tsigai (22 farms) and Improved Valachian (14 farms). Farms were divided according to their altitude to lowland, upland and lower highland farms. Sizes of pastures and stocking rates for lowland, upland and lower highland farms were 81.5, 269.2, and 316.7 ha and 6.3, 2.6, and 2.9 sheep/ha, respectively. One third of farmers (33.3%) used permanent pastures and two thirds of breeders (66.7%) rotated sheep between pastures. Mean drenching rate for lambs and yearlings/adults was 1.76 and 1.70, respectively. The most frequently used drugs during period from 1999 to 2004 were albendazole and ivermectin. On 13 farms benzimidazole drugs were applied in spring before turn out and macrocyclic lactones in autumn before turn in. Benzimidazoles and macrocyclic lactones were used almost exclusively on 7 and 9 farms, respectively. Visual appraisal was the most common practice to determine weight of animals (87.8% of farmers). Weights of the heaviest animals were used for determination of anthelmintic doses only on 16.7% of farms. Coprological examinations were performed on 47.9% of farms, usually in frequency once per year (75%).

  11. Evolutionarily Conserved, Multitasking TRP Channels: Lessons from Worms and Flies

    PubMed Central

    Venkatachalam, Kartik; Luo, Junjie; Montell, Craig

    2015-01-01

    The Transient Receptor Potential (TRP) channel family is comprised of a large group of cation-permeable channels, which display an extraordinary diversity of roles in sensory signaling. TRPs allow animals to detect chemicals, mechanical force, light, and changes in temperature. Consequently, these channels control a plethora of animal behaviors. Moreover, their functions are not limited to the classical senses, as they are cellular sensors, which are critical for ionic homeostasis and metabolism. Two genetically tractable invertebrate model organisms, Caenorhabditis elegans and Drosophila melanogaster, have led the way in revealing a wide array of sensory roles and behaviors that depend on TRP channels. Two overriding themes have emerged from these studies. First, TRPs are multitasking proteins, and second, many functions and modes of activation of these channels are evolutionarily conserved, including some that were formerly thought to be unique to invertebrates, such as phototransduction. Thus, worms and flies offer the potential to decipher roles for mammalian TRPs, which would otherwise not be suspected. PMID:24961975

  12. Multiphase adhesive coacervates inspired by the Sandcastle worm.

    PubMed

    Kaur, Sarbjit; Weerasekare, G Mahika; Stewart, Russell J

    2011-04-01

    Water-borne, underwater adhesives were created by complex coacervation of synthetic copolyelectrolytes that mimic the proteins of the natural underwater adhesive of the sandcastle worm. To increase bond strengths, we created a second polymer network within cross-linked coacervate network by entrapping polyethylene glycol diacrylate (PEG-dA) monomers in the coacervate phase. Simultaneous polymerization of PEG-dA and cross-linking of the coacervate network resulted in maximum shear bond strengths of ∼1.2 MPa. Approximately 40% of the entrapped PEG-dA polymerized based on attenuated total reflectance-Fourier transform infrared spectroscopy. The monomer-filled coacervate had complex flow behavior, thickening at low shear rates and then thinning suddenly with a 16-fold drop in viscosity at shear rates near 6 s(-1). The microscale structure of the complex coacervates resembled a three-dimensional porous network of interconnected tubules. The sharp shear thinning behavior is conceptualized as a structural reorganization between the interspersed phases of the complex coacervate. The bond strength and complex fluid behavior of the monomer-filled coacervates have important implications for medical applications of the adhesives.

  13. Monosaccharide transport into hemocytes of a sipunculan worm Themiste dyscrita

    SciTech Connect

    Ingermann, R.L.; Hall, R.E.; Bissonnette, J.M.; Terwilliger, R.C.

    1985-07-01

    The hemerythrin-containing blood cells, or hemocytes, of the sipunculan worm Themiste dyscrita were found to have a stereospecific and nonconcentrative monosaccharide transport system. The transport system transferred both D-glucose and 3-O-methyl-D-glucose (3-OMG), and transport into cells by this system was rapid, reaching 50% equilibrium in approximately 20 s at 10 degrees C with an initial concentration gradient of 0.1 mM; the contribution to total uptake by simple diffusion was very small. 3-OMG uptake showed saturation kinetics with a low half-saturation constant (Km less than or equal to 0.1 mM). The uptake of labeled 3-OMG by the hemocytes was strongly inhibited by unlabeled 3-OMG, 2-deoxy-D-glucose, alpha- and beta-D-glucose, D-galactose, and D-mannose. It was moderately inhibited by D-xylose, only slightly by alpha-methyl-D-glucoside and D-fructose, and uninhibited by sucrose, L-glucose, or D-sorbitol. Phloretin was more potent than phloridzin in blocking entry of 3-OMG. Cytochalasin B did not bind tightly to the T. dyscrita transporter and was not a potent inhibitor of transport; it half-maximally inhibited 3-OMG transport at 0.1 mM. Therefore, despite some differences the data suggest functional similarities in the mechanism of monosaccharide transport into blood cells of mammals and this invertebrate.

  14. Dracunculiasis (Guinea Worm Disease) and the Eradication Initiative

    PubMed Central

    Cairncross, Sandy; Muller, Ralph; Zagaria, Nevio

    2002-01-01

    Dracunculiasis, also known as guinea worm disease, is caused by the large female of the nematode Dracunculus medinensis, which emerges painfully and slowly from the skin, usually on the lower limbs. The disease can infect animals, and sustainable animal cycles occur in North America and Central Asia but do not act as reservoirs of human infection. The disease is endemic across the Sahel belt of Africa from Mauritania to Ethiopia, having been eliminated from Asia and some African countries. It has a significant socioeconomic impact because of the temporary disability that it causes. Dracunculiasis is exclusively caught from drinking water, usually from ponds. A campaign to eradicate the disease was launched in the 1980s and has made significant progress. The strategy of the campaign is discussed, including water supply, health education, case management, and vector control. Current issues including the integration of the campaign into primary health care and the mapping of cases by using geographic information systems are also considered. Finally, some lessons for other disease control and eradication programs are outlined. PMID:11932231

  15. Silk worm Bm1 SINE RNA increases following cellular insults.

    PubMed

    Kimura, R H; Choudary, P V; Schmid, C W

    1999-08-15

    The effect of cell stresses upon the expression of the Bm1 short interspersed element (SINE) family in cultured silk worm cells is examined. Primer extension analysis shows that Bm1 repeats are transcribed by RNA polymerase III (Pol III) into cytoplasmic RNAs. Five consecutive T residues, which would normally terminate Pol III transcription, occur within the Bm1 consensus and are included within cDNA sequences representing these transcripts. In analogy to mammalian SINEs, the level of the Bm1 transcripts increases in response to either heat shock, inhibiting protein synthesis by cycloheximide or viral infection. The lifetime of Bm1 RNA increases following cell insults so that post-transcriptional events partially account for stress induced increases in its abundance. In the case of heat shock, the increase in Bm1 RNA follows the transient increase in hsp70 mRNA indicating that this response is temporally regulated to occur later in heat shock recovery. These results support the proposal that SINE RNAs serve a role in the cell stress response that predates the divergence of insects and mammals implying that SINEs are essentially a class of cell stress genes.

  16. Methane ice worms: Hesiocaeca methanicola colonizing fossil fuel reserves.

    PubMed

    Fisher, C R; MacDonald, I R; Sassen, R; Young, C M; Macko, S A; Hourdez, S; Carney, R S; Joye, S; McMullin, E

    2000-04-01

    During a research cruise in July 1997 in the Gulf of Mexico we discovered a gas hydrate approximately 1 m thick and over 2 m in diameter which had recently breached the sea floor at a depth of 540 m. The hydrate surface visible from the submarine was considerably greater than that of any other reported hydrate. Two distinct color bands of hydrate were present in the same mound, and the entire exposed surface of the hydrate was infested (2500 individuals/m2) with 2 to 4 cm-long worms, since described as a new species, Hesiocaeca methanicola, in the polychaete family Hesionidae (Desbruyères and Toulmond 1998). H. methanicola tissue stable isotope values are consistent with a chemo-autotrophic food source. No evidence of chemo-autotrophic symbionts was detected, but geochemical data support the presence of abundant free living bacteria on the hydrate. The activities of the polychaetes, grazing on the hydrate bacteria and supplying oxygen to their habitats, appears to contribute to the dissolution of hydrates in surface sediments.

  17. Sex pheromone of the cranberry blossom worm, Epiglaea apiata.

    PubMed

    Zhang, Aijun; Polavarapu, Sridhar

    2003-09-01

    The cranberry blossom worm, Epiglaea apiata (Grote) (Lepidoptera: Noctuidae), is a major pest of cranberries in New Jersey. The female sex pheromone of this moth was identified as a blend of (Z)-9-hexadecenyl acetate (Z9-16:Ac), (Z)-9-tetradecenyl acetate (Z9-14:Ac), and tetradecyl acetate (14:Ac) by gas chromatographic-electroantennographic detection and gas chromatography-mass spectrometry. The ratio of the components in extracts of the female pheromone gland was determined to be 65:2:33 of the Z9-16:Ac, Z9-14:Ac, and 14:Ac, respectively. The double bond positions of the pheromone components were confirmed by dimethyl disulfide derivatization. In addition to the above three components, a mixture of C4-C10 aliphatic acids was present in both gland extracts and effluvia collections, and the acids elicited significant EAD responses from male moth antennae. However, addition of the C4-C10 aliphatic acids to the pheromone blend did not significantly increase trap captures. Three-hundred- and 1000-microg doses of a synthetic blend containing Z9-16:Ac, Z9-14:Ac, and 14:Ac (65:2:33), on a rubber septum were more attractive to males than lower doses.

  18. Bioaccumulation and biological effects of cigarette litter in marine worms

    PubMed Central

    Wright, Stephanie L.; Rowe, Darren; Reid, Malcolm J.; Thomas, Kevin V.; Galloway, Tamara S.

    2015-01-01

    Marine debris is a global environmental issue. Smoked cigarette filters are the predominant coastal litter item; 4.5 trillion are littered annually, presenting a source of bioplastic microfibres (cellulose acetate) and harmful toxicants to marine environments. Despite the human health risks associated with smoking, little is known of the hazards cigarette filters present to marine life. Here we studied the impacts of smoked cigarette filter toxicants and microfibres on the polychaete worm Hediste diversicolor (ragworm), a widespread inhabitant of coastal sediments. Ragworms exposed to smoked cigarette filter toxicants in seawater at concentrations 60 fold lower than those reported for urban run-off exhibited significantly longer burrowing times, >30% weight loss, and >2-fold increase in DNA damage compared to ragworms maintained in control conditions. In contrast, ragworms exposed to smoked cigarette filter microfibres in marine sediment showed no significant effects. Bioconcentration factors for nicotine were 500 fold higher from seawater than from sediment. Our results illustrate the vulnerability of organisms in the water column to smoking debris and associated toxicants, and highlight the risks posed by smoked cigarette filter debris to aquatic life. PMID:26369692

  19. Functional brain regeneration in the acoel worm Symsagittifera roscoffensis

    PubMed Central

    Sprecher, Simon G.; Bernardo-Garcia, F. Javier; van Giesen, Lena; Hartenstein, Volker; Reichert, Heinrich; Neves, Ricardo; Bailly, Xavier; Martinez, Pedro; Brauchle, Michael

    2015-01-01

    ABSTRACT The ability of some animals to regrow their head and brain after decapitation provides a striking example of the regenerative capacity within the animal kingdom. The acoel worm Symsagittifera roscoffensis can regrow its head, brain and sensory head organs within only a few weeks after decapitation. How rapidly and to what degree it also reacquires its functionality to control behavior however remains unknown. We provide here a neuroanatomical map of the brain neuropils of the adult S. roscoffensis and show that after decapitation a normal neuroanatomical organization of the brain is restored in the majority of animals. By testing different behaviors we further show that functionality of both sensory perception and the underlying brain architecture are restored within weeks after decapitation. Interestingly not all behaviors are restored at the same speed and to the same extent. While we find that phototaxis recovered rapidly, geotaxis is not restored within 7 weeks. Our findings show that regeneration of the head, sensory organs and brain result in the restoration of directed navigation behavior, suggesting a tight coordination in the regeneration of certain sensory organs with that of their underlying neural circuits. Thus, at least in S. roscoffensis, the regenerative capacity of different sensory modalities follows distinct paths. PMID:26581588

  20. Dracunculiasis (Guinea worm disease) and the eradication initiative.

    PubMed

    Cairncross, Sandy; Muller, Ralph; Zagaria, Nevio

    2002-04-01

    Dracunculiasis, also known as guinea worm disease, is caused by the large female of the nematode Dracunculus medinensis, which emerges painfully and slowly from the skin, usually on the lower limbs. The disease can infect animals, and sustainable animal cycles occur in North America and Central Asia but do not act as reservoirs of human infection. The disease is endemic across the Sahel belt of Africa from Mauritania to Ethiopia, having been eliminated from Asia and some African countries. It has a significant socioeconomic impact because of the temporary disability that it causes. Dracunculiasis is exclusively caught from drinking water, usually from ponds. A campaign to eradicate the disease was launched in the 1980s and has made significant progress. The strategy of the campaign is discussed, including water supply, health education, case management, and vector control. Current issues including the integration of the campaign into primary health care and the mapping of cases by using geographic information systems are also considered. Finally, some lessons for other disease control and eradication programs are outlined.