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Sample records for crack parasite genome

  1. Rodent malaria parasites : genome organization & comparative genomics

    NARCIS (Netherlands)

    Kooij, Taco W.A.

    2006-01-01

    The aim of the studies described in this thesis was to investigate the genome organization of rodent malaria parasites (RMPs) and compare the organization and gene content of the genomes of RMPs and the human malaria parasite P. falciparum. The release of the complete genome sequence of P.

  2. Genome Evolution of Plant-Parasitic Nematodes.

    Science.gov (United States)

    Kikuchi, Taisei; Eves-van den Akker, Sebastian; Jones, John T

    2017-08-04

    Plant parasitism has evolved independently on at least four separate occasions in the phylum Nematoda. The application of next-generation sequencing (NGS) to plant-parasitic nematodes has allowed a wide range of genome- or transcriptome-level comparisons, and these have identified genome adaptations that enable parasitism of plants. Current genome data suggest that horizontal gene transfer, gene family expansions, evolution of new genes that mediate interactions with the host, and parasitism-specific gene regulation are important adaptations that allow nematodes to parasitize plants. Sequencing of a larger number of nematode genomes, including plant parasites that show different modes of parasitism or that have evolved in currently unsampled clades, and using free-living taxa as comparators would allow more detailed analysis and a better understanding of the organization of key genes within the genomes. This would facilitate a more complete understanding of the way in which parasitism has shaped the genomes of plant-parasitic nematodes.

  3. Functional genomics approaches in parasitic helminths.

    Science.gov (United States)

    Hagen, J; Lee, E F; Fairlie, W D; Kalinna, B H

    2012-01-01

    As research on parasitic helminths is moving into the post-genomic era, an enormous effort is directed towards deciphering gene function and to achieve gene annotation. The sequences that are available in public databases undoubtedly hold information that can be utilized for new interventions and control but the exploitation of these resources has until recently remained difficult. Only now, with the emergence of methods to genetically manipulate and transform parasitic worms will it be possible to gain a comprehensive understanding of the molecular mechanisms involved in nutrition, metabolism, developmental switches/maturation and interaction with the host immune system. This review focuses on functional genomics approaches in parasitic helminths that are currently used, to highlight potential applications of these technologies in the areas of cell biology, systems biology and immunobiology of parasitic helminths. © 2011 Blackwell Publishing Ltd.

  4. A Feast of Malaria Parasite Genomes.

    Science.gov (United States)

    Carlton, Jane M; Sullivan, Steven A

    2017-03-08

    The Plasmodium genus has evolved over time and across hosts, complexifying our understanding of malaria. In a recent Nature paper, Rutledge et al. (2017) describe the genome sequences of three major human malaria parasite species, providing insight into Plasmodium evolution and raising the question of how many species there are. Copyright © 2017 Elsevier Inc. All rights reserved.

  5. Parasite Genome Projects and the Trypanosoma cruzi Genome Initiative

    Directory of Open Access Journals (Sweden)

    Wim Degrave

    1997-11-01

    Full Text Available Since the start of the human genome project, a great number of genome projects on other "model" organism have been initiated, some of them already completed. Several initiatives have also been started on parasite genomes, mainly through support from WHO/TDR, involving North-South and South-South collaborations, and great hopes are vested in that these initiatives will lead to new tools for disease control and prevention, as well as to the establishment of genomic research technology in developing countries. The Trypanosoma cruzi genome project, using the clone CL-Brener as starting point, has made considerable progress through the concerted action of more than 20 laboratories, most of them in the South. A brief overview of the current state of the project is given

  6. Highly rearranged mitochondrial genome in Nycteria parasites (Haemosporidia) from bats.

    Science.gov (United States)

    Karadjian, Gregory; Hassanin, Alexandre; Saintpierre, Benjamin; Gembu Tungaluna, Guy-Crispin; Ariey, Frederic; Ayala, Francisco J; Landau, Irene; Duval, Linda

    2016-08-30

    Haemosporidia parasites have mostly and abundantly been described using mitochondrial genes, and in particular cytochrome b (cytb). Failure to amplify the mitochondrial cytb gene of Nycteria parasites isolated from Nycteridae bats has been recently reported. Bats are hosts to a diverse and profuse array of Haemosporidia parasites that remain largely unstudied. There is a need to obtain more molecular data from chiropteran parasites. Such data would help to better understand the evolutionary history of Haemosporidia, which notably include the Plasmodium parasites, malaria's agents. We use next-generation sequencing to obtain the complete mitochondrial genome of Nycteria parasites from African Nycteris grandis (Nycteridae) and Rhinolophus alcyone (Rhinolophidae) and Asian Megaderma spasma (Megadermatidae). We report four complete mitochondrial genomes, including two rearranged mitochondrial genomes within Haemosporidia. Our results open outlooks into potentially undiscovered Haemosporidian diversity.

  7. Sequencing and annotation of mitochondrial genomes from individual parasitic helminths.

    Science.gov (United States)

    Jex, Aaron R; Littlewood, D Timothy; Gasser, Robin B

    2015-01-01

    Mitochondrial (mt) genomics has significant implications in a range of fundamental areas of parasitology, including evolution, systematics, and population genetics as well as explorations of mt biochemistry, physiology, and function. Mt genomes also provide a rich source of markers to aid molecular epidemiological and ecological studies of key parasites. However, there is still a paucity of information on mt genomes for many metazoan organisms, particularly parasitic helminths, which has often related to challenges linked to sequencing from tiny amounts of material. The advent of next-generation sequencing (NGS) technologies has paved the way for low cost, high-throughput mt genomic research, but there have been obstacles, particularly in relation to post-sequencing assembly and analyses of large datasets. In this chapter, we describe protocols for the efficient amplification and sequencing of mt genomes from small portions of individual helminths, and highlight the utility of NGS platforms to expedite mt genomics. In addition, we recommend approaches for manual or semi-automated bioinformatic annotation and analyses to overcome the bioinformatic "bottleneck" to research in this area. Taken together, these approaches have demonstrated applicability to a range of parasites and provide prospects for using complete mt genomic sequence datasets for large-scale molecular systematic and epidemiological studies. In addition, these methods have broader utility and might be readily adapted to a range of other medium-sized molecular regions (i.e., 10-100 kb), including large genomic operons, and other organellar (e.g., plastid) and viral genomes.

  8. Helicosporidia: a genomic snapshot of an early transition to parasitism

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    Yukun Sun

    2014-12-01

    Full Text Available Helicosporidia are gut parasites of invertebrates. These achlorophyllous, non-photosynthetic green algae are the first reported to infect insects. Helicosporidia are members of the green algal class Trebouxiophyceae and are further related to the photosynthetic and non-photosynthetic genera Auxenochlorella and Prototheca, respectively, the latter of which can also turn to parasitism under opportunistic conditions. Molecular analyses suggest that Helicosporidia diverged from other photosynthetic trebouxiophytes less than 200 million years ago and that its adaptation to parasitism is therefore recent. In this minireview, we summarize the current knowledge of helicosporidian genomics. Unlike many well-known parasitic lineages, the Helicosporidium sp. organelle and nuclear genomes have lost surprisingly little in terms of coding content aside from photosynthesis-related genes. While the small size of its nuclear genome compared to other sequenced trebouxiophycean representatives suggests that Helicosporidium is going through a streamlining process, this scenario cannot be ascertained at this stage. Genome expansions and contractions have occurred independently multiple times in the green algae, and the small size of the Helicosporidium genome may reflect a lack of expansion from a lean ancestor state rather than a tendency towards reduction.

  9. Genomic minimalism in the early diverging intestinal parasite Giardia lamblia.

    Science.gov (United States)

    Morrison, Hilary G; McArthur, Andrew G; Gillin, Frances D; Aley, Stephen B; Adam, Rodney D; Olsen, Gary J; Best, Aaron A; Cande, W Zacheus; Chen, Feng; Cipriano, Michael J; Davids, Barbara J; Dawson, Scott C; Elmendorf, Heidi G; Hehl, Adrian B; Holder, Michael E; Huse, Susan M; Kim, Ulandt U; Lasek-Nesselquist, Erica; Manning, Gerard; Nigam, Anuranjini; Nixon, Julie E J; Palm, Daniel; Passamaneck, Nora E; Prabhu, Anjali; Reich, Claudia I; Reiner, David S; Samuelson, John; Svard, Staffan G; Sogin, Mitchell L

    2007-09-28

    The genome of the eukaryotic protist Giardia lamblia, an important human intestinal parasite, is compact in structure and content, contains few introns or mitochondrial relics, and has simplified machinery for DNA replication, transcription, RNA processing, and most metabolic pathways. Protein kinases comprise the single largest protein class and reflect Giardia's requirement for a complex signal transduction network for coordinating differentiation. Lateral gene transfer from bacterial and archaeal donors has shaped Giardia's genome, and previously unknown gene families, for example, cysteine-rich structural proteins, have been discovered. Unexpectedly, the genome shows little evidence of heterozygosity, supporting recent speculations that this organism is sexual. This genome sequence will not only be valuable for investigating the evolution of eukaryotes, but will also be applied to the search for new therapeutics for this parasite.

  10. Regulatory hotspots in the malaria parasite genome dictate transcriptional variation.

    Directory of Open Access Journals (Sweden)

    Joseph M Gonzales

    2008-09-01

    Full Text Available The determinants of transcriptional regulation in malaria parasites remain elusive. The presence of a well-characterized gene expression cascade shared by different Plasmodium falciparum strains could imply that transcriptional regulation and its natural variation do not contribute significantly to the evolution of parasite drug resistance. To clarify the role of transcriptional variation as a source of stain-specific diversity in the most deadly malaria species and to find genetic loci that dictate variations in gene expression, we examined genome-wide expression level polymorphisms (ELPs in a genetic cross between phenotypically distinct parasite clones. Significant variation in gene expression is observed through direct co-hybridizations of RNA from different P. falciparum clones. Nearly 18% of genes were regulated by a significant expression quantitative trait locus. The genetic determinants of most of these ELPs resided in hotspots that are physically distant from their targets. The most prominent regulatory locus, influencing 269 transcripts, coincided with a Chromosome 5 amplification event carrying the drug resistance gene, pfmdr1, and 13 other genes. Drug selection pressure in the Dd2 parental clone lineage led not only to a copy number change in the pfmdr1 gene but also to an increased copy number of putative neighboring regulatory factors that, in turn, broadly influence the transcriptional network. Previously unrecognized transcriptional variation, controlled by polymorphic regulatory genes and possibly master regulators within large copy number variants, contributes to sweeping phenotypic evolution in drug-resistant malaria parasites.

  11. Aerobic mitochondria of parasitic protists: Diverse genomes and complex functions.

    Science.gov (United States)

    Zíková, Alena; Hampl, Vladimír; Paris, Zdeněk; Týč, Jiří; Lukeš, Julius

    In this review the main features of the mitochondria of aerobic parasitic protists are discussed. While the best characterized organelles are by far those of kinetoplastid flagellates and Plasmodium, we also consider amoebae Naegleria and Acanthamoeba, a ciliate Ichthyophthirius and related lineages. The simplistic view of the mitochondrion as just a power house of the cell has already been abandoned in multicellular organisms and available data indicate that this also does not apply for protists. We discuss in more details the following mitochondrial features: genomes, post-transcriptional processing, translation, biogenesis of iron-sulfur complexes, heme metabolism and the electron transport chain. Substantial differences in all these core mitochondrial features between lineages are compatible with the view that aerobic protists harbor organelles that are more complex and flexible than previously appreciated. Copyright © 2016 Elsevier B.V. All rights reserved.

  12. Crack

    Science.gov (United States)

    ... spending time in a rehab facility or getting cognitive-behavioral therapy or other treatments. Right now, there are no medicines to treat a crack addiction. If you smoke crack, talking with a counselor ...

  13. Genome sequencing of chimpanzee malaria parasites reveals possible pathways of adaptation to human hosts

    KAUST Repository

    Otto, Thomas D.

    2014-09-09

    Plasmodium falciparum causes most human malaria deaths, having prehistorically evolved from parasites of African Great Apes. Here we explore the genomic basis of P. falciparum adaptation to human hosts by fully sequencing the genome of the closely related chimpanzee parasite species P. reichenowi, and obtaining partial sequence data from a more distantly related chimpanzee parasite (P. gaboni). The close relationship between P. reichenowi and P. falciparum is emphasized by almost complete conservation of genomic synteny, but against this strikingly conserved background we observe major differences at loci involved in erythrocyte invasion. The organization of most virulence-associated multigene families, including the hypervariable var genes, is broadly conserved, but P. falciparum has a smaller subset of rif and stevor genes whose products are expressed on the infected erythrocyte surface. Genome-wide analysis identifies other loci under recent positive selection, but a limited number of changes at the host–parasite interface may have mediated host switching.

  14. Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita

    NARCIS (Netherlands)

    Abad, P.; Gouzy, J.; Aury, J.M.; Tytgat, T.O.G.; Smant, G.

    2008-01-01

    Plant-parasitic nematodes are major agricultural pests worldwide and novel approaches to control them are sorely needed. We report the draft genome sequence of the root-knot nematode Meloidogyne incognita, a biotrophic parasite of many crops, including tomato, cotton and coffee. Most of the

  15. The genome of Eimeria falciformis--reduction and specialization in a single host apicomplexan parasite.

    Science.gov (United States)

    Heitlinger, Emanuel; Spork, Simone; Lucius, Richard; Dieterich, Christoph

    2014-08-20

    The phylum Apicomplexa comprises important unicellular human parasites such as Toxoplasma and Plasmodium. Eimeria is the largest and most diverse genus of apicomplexan parasites and some species of the genus are the causative agent of coccidiosis, a disease economically devastating in poultry. We report a complete genome sequence of the mouse parasite Eimeria falciformis. We assembled and annotated the genome sequence to study host-parasite interactions in this understudied genus in a model organism host. The genome of E. falciformis is 44 Mb in size and contains 5,879 predicted protein coding genes. Comparative analysis of E. falciformis with Toxoplasma gondii shows an emergence and diversification of gene families associated with motility and invasion mainly at the level of the Coccidia. Many rhoptry kinases, among them important virulence factors in T. gondii, are absent from the E. falciformis genome. Surface antigens are divergent between Eimeria species. Comparisons with T. gondii showed differences between genes involved in metabolism, N-glycan and GPI-anchor synthesis. E. falciformis possesses a reduced set of transmembrane transporters and we suggest an altered mode of iron uptake in the genus Eimeria. Reduced diversity of genes required for host-parasite interaction and transmembrane transport allow hypotheses on host adaptation and specialization of a single host parasite. The E. falciformis genome sequence sheds light on the evolution of the Coccidia and helps to identify determinants of host-parasite interaction critical for drug and vaccine development.

  16. Parasitism drives host genome evolution: Insights from the Pasteuria ramosa-Daphnia magna system.

    Science.gov (United States)

    Bourgeois, Yann; Roulin, Anne C; Müller, Kristina; Ebert, Dieter

    2017-04-01

    Because parasitism is thought to play a major role in shaping host genomes, it has been predicted that genomic regions associated with resistance to parasites should stand out in genome scans, revealing signals of selection above the genomic background. To test whether parasitism is indeed such a major factor in host evolution and to better understand host-parasite interaction at the molecular level, we studied genome-wide polymorphisms in 97 genotypes of the planktonic crustacean Daphnia magna originating from three localities across Europe. Daphnia magna is known to coevolve with the bacterial pathogen Pasteuria ramosa for which host genotypes (clonal lines) are either resistant or susceptible. Using association mapping, we identified two genomic regions involved in resistance to P. ramosa, one of which was already known from a previous QTL analysis. We then performed a naïve genome scan to test for signatures of positive selection and found that the two regions identified with the association mapping further stood out as outliers. Several other regions with evidence for selection were also found, but no link between these regions and phenotypic variation could be established. Our results are consistent with the hypothesis that parasitism is driving host genome evolution. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

  17. Genomic insights into the origin of parasitism in the emerging plant pathogen Bursaphelenchus xylophilus.

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    Taisei Kikuchi

    2011-09-01

    Full Text Available Bursaphelenchus xylophilus is the nematode responsible for a devastating epidemic of pine wilt disease in Asia and Europe, and represents a recent, independent origin of plant parasitism in nematodes, ecologically and taxonomically distinct from other nematodes for which genomic data is available. As well as being an important pathogen, the B. xylophilus genome thus provides a unique opportunity to study the evolution and mechanism of plant parasitism. Here, we present a high-quality draft genome sequence from an inbred line of B. xylophilus, and use this to investigate the biological basis of its complex ecology which combines fungal feeding, plant parasitic and insect-associated stages. We focus particularly on putative parasitism genes as well as those linked to other key biological processes and demonstrate that B. xylophilus is well endowed with RNA interference effectors, peptidergic neurotransmitters (including the first description of ins genes in a parasite stress response and developmental genes and has a contracted set of chemosensory receptors. B. xylophilus has the largest number of digestive proteases known for any nematode and displays expanded families of lysosome pathway genes, ABC transporters and cytochrome P450 pathway genes. This expansion in digestive and detoxification proteins may reflect the unusual diversity in foods it exploits and environments it encounters during its life cycle. In addition, B. xylophilus possesses a unique complement of plant cell wall modifying proteins acquired by horizontal gene transfer, underscoring the impact of this process on the evolution of plant parasitism by nematodes. Together with the lack of proteins homologous to effectors from other plant parasitic nematodes, this confirms the distinctive molecular basis of plant parasitism in the Bursaphelenchus lineage. The genome sequence of B. xylophilus adds to the diversity of genomic data for nematodes, and will be an important resource in

  18. Long- and short-term selective forces on malaria parasite genomes

    DEFF Research Database (Denmark)

    Nygaard, Sanne; Braunstein, Alexander; Malsen, Gareth

    2010-01-01

    Plasmodium parasites, the causal agents of malaria, result in more than 1 million deaths annually. Plasmodium are unicellular eukaryotes with small ~23 Mb genomes encoding ~5200 protein-coding genes. The protein-coding genes comprise about half of these genomes. Although evolutionary processes ha...

  19. Draft genome sequence of the intestinal parasite Blastocystis subtype 4-isolate WR1

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    Ivan Wawrzyniak

    2015-06-01

    Full Text Available The intestinal protistan parasite Blastocystis is characterized by an extensive genetic variability with 17 subtypes (ST1–ST17 described to date. Only the whole genome of a human ST7 isolate was previously sequenced. Here we report the draft genome sequence of Blastocystis ST4-WR1 isolated from a laboratory rodent at Singapore.

  20. A comprehensive evaluation of rodent malaria parasite genomes and gene expression

    KAUST Repository

    Otto, Thomas D

    2014-10-30

    Background: Rodent malaria parasites (RMP) are used extensively as models of human malaria. Draft RMP genomes have been published for Plasmodium yoelii, P. berghei ANKA (PbA) and P. chabaudi AS (PcAS). Although availability of these genomes made a significant impact on recent malaria research, these genomes were highly fragmented and were annotated with little manual curation. The fragmented nature of the genomes has hampered genome wide analysis of Plasmodium gene regulation and function. Results: We have greatly improved the genome assemblies of PbA and PcAS, newly sequenced the virulent parasite P. yoelii YM genome, sequenced additional RMP isolates/lines and have characterized genotypic diversity within RMP species. We have produced RNA-seq data and utilized it to improve gene-model prediction and to provide quantitative, genome-wide, data on gene expression. Comparison of the RMP genomes with the genome of the human malaria parasite P. falciparum and RNA-seq mapping permitted gene annotation at base-pair resolution. Full-length chromosomal annotation permitted a comprehensive classification of all subtelomeric multigene families including the `Plasmodium interspersed repeat genes\\' (pir). Phylogenetic classification of the pir family, combined with pir expression patterns, indicates functional diversification within this family. Conclusions: Complete RMP genomes, RNA-seq and genotypic diversity data are excellent and important resources for gene-function and post-genomic analyses and to better interrogate Plasmodium biology. Genotypic diversity between P. chabaudi isolates makes this species an excellent parasite to study genotype-phenotype relationships. The improved classification of multigene families will enhance studies on the role of (variant) exported proteins in virulence and immune evasion/modulation.

  1. The genome of the simian and human malaria parasite Plasmodium knowlesi

    DEFF Research Database (Denmark)

    Pain, A; Böhme, U; Berry, A E

    2008-01-01

    Plasmodium knowlesi is an intracellular malaria parasite whose natural vertebrate host is Macaca fascicularis (the 'kra' monkey); however, it is now increasingly recognized as a significant cause of human malaria, particularly in southeast Asia. Plasmodium knowlesi was the first malaria parasite...... species in which antigenic variation was demonstrated, and it has a close phylogenetic relationship to Plasmodium vivax, the second most important species of human malaria parasite (reviewed in ref. 4). Despite their relatedness, there are important phenotypic differences between them, such as host blood...... cell preference, absence of a dormant liver stage or 'hypnozoite' in P. knowlesi, and length of the asexual cycle (reviewed in ref. 4). Here we present an analysis of the P. knowlesi (H strain, Pk1(A+) clone) nuclear genome sequence. This is the first monkey malaria parasite genome to be described...

  2. Genomics and peptidomics of neuropeptides and protein hormones present in the parasitic wasp Nasonia vitripennis

    DEFF Research Database (Denmark)

    Hauser, Frank; Neupert, Susanne; Williamson, Michael

    2010-01-01

    Neuropeptides and protein hormones constitute a very important group of signaling molecules, regulating central physiological processes such as reproduction, development, and behavior. Using a bioinformatics approach, we screened the recently sequenced genome of the parasitic wasp, Nasonia vitrip...... melanogaster, Aedes aegypti (both Diptera), Bombyx mori (Lepidoptera), Tribolium castaneum (Coleoptera), Apis mellifera (Hymenoptera), and Acyrthosiphon pisum (Hemiptera). This lower number of neuropeptide genes might be related to Nasonia's parasitic life....

  3. Comparative Genomics and Systems Biology of Malaria Parasites Plasmodium

    Science.gov (United States)

    Cai, Hong; Zhou, Zhan; Gu, Jianying; Wang, Yufeng

    2013-01-01

    Malaria is a serious infectious disease that causes over one million deaths yearly. It is caused by a group of protozoan parasites in the genus Plasmodium. No effective vaccine is currently available and the elevated levels of resistance to drugs in use underscore the pressing need for novel antimalarial targets. In this review, we survey omics centered developments in Plasmodium biology, which have set the stage for a quantum leap in our understanding of the fundamental processes of the parasite life cycle and mechanisms of drug resistance and immune evasion. PMID:24298232

  4. The genome of the obligate intracellular parasite Trachipleistophora hominis: new insights into microsporidian genome dynamics and reductive evolution.

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    Eva Heinz

    Full Text Available The dynamics of reductive genome evolution for eukaryotes living inside other eukaryotic cells are poorly understood compared to well-studied model systems involving obligate intracellular bacteria. Here we present 8.5 Mb of sequence from the genome of the microsporidian Trachipleistophora hominis, isolated from an HIV/AIDS patient, which is an outgroup to the smaller compacted-genome species that primarily inform ideas of evolutionary mode for these enormously successful obligate intracellular parasites. Our data provide detailed information on the gene content, genome architecture and intergenic regions of a larger microsporidian genome, while comparative analyses allowed us to infer genomic features and metabolism of the common ancestor of the species investigated. Gene length reduction and massive loss of metabolic capacity in the common ancestor was accompanied by the evolution of novel microsporidian-specific protein families, whose conservation among microsporidians, against a background of reductive evolution, suggests they may have important functions in their parasitic lifestyle. The ancestor had already lost many metabolic pathways but retained glycolysis and the pentose phosphate pathway to provide cytosolic ATP and reduced coenzymes, and it had a minimal mitochondrion (mitosome making Fe-S clusters but not ATP. It possessed bacterial-like nucleotide transport proteins as a key innovation for stealing host-generated ATP, the machinery for RNAi, key elements of the early secretory pathway, canonical eukaryotic as well as microsporidian-specific regulatory elements, a diversity of repetitive and transposable elements, and relatively low average gene density. Microsporidian genome evolution thus appears to have proceeded in at least two major steps: an ancestral remodelling of the proteome upon transition to intracellular parasitism that involved reduction but also selective expansion, followed by a secondary compaction of genome

  5. Insight into tradeoff between wood decay and parasitism from the genome of a fungal forest pathogen

    Science.gov (United States)

    Ake Olson; Andrea Aerts; Fred Asiegbu; Lassaad Belbahri; Ourdia Bouzid; Anders Broberg; Bjorn Canback; Pedro M. Coutinho; Dan Cullen; Kerstin Dalman; Giuliana Deflorio; Linda T.A. van Diepen; Christophe Dunand; Sebastien Duplessis; Mikael Durling; Paolo Gonthier; Jane Grimwood; Carl Gunnar Fossdal; David Hansson; Bernard Henrissat; Ari Hietala; Kajsa Himmelsrand; Dirk Hoffmeister; Nils Hogberg; Timothy Y. James; Magnus Karlsson; Annegret Kohler; Ursula Kues; Yong-Hwan Lee; Yao-Cheng Lin; Marten Lind; Erika Lindquist; Vincent Lombard; Susan Lucas; Karl Lunden; Emmanuelle Morin; Claude Murat; Jongsun Park; Tommaso Raffaello; Pierre Rouze; Asaf Salamov; Jeremy Schmutz; Halvor Solheim; Jerry Stahlberg; Heriberto Velez; Ronald P. deVries; Ad Wiebenga; Steve Woodward; Igor Yakovlev; Matteo Garbelotto; Francis Martin; Igor V. Grigoriev; Jan. Stenlid

    2012-01-01

    • Parasitism and saprotrophic wood decay are two fungal strategies fundamental for succession and nutrient cycling in forest ecosystems. An opportunity to assess the trade-off between these strategies is provided by the forest pathogen and wood decayer Heterobasidion annosum sensu lato. • We report the annotated genome sequence and transcript...

  6. Parasites

    Centers for Disease Control (CDC) Podcasts

    2010-05-06

    In this podcast, a listener wants to know what to do if he thinks he has a parasite or parasitic disease.  Created: 5/6/2010 by National Center for Emerging and Zoonotic Infectious Diseases (NCEZID).   Date Released: 5/6/2010.

  7. The Complete Mitochondrial Genome of the Foodborne Parasitic Pathogen Cyclospora cayetanensis.

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    Hediye Nese Cinar

    Full Text Available Cyclospora cayetanensis is a human-specific coccidian parasite responsible for several food and water-related outbreaks around the world, including the most recent ones involving over 900 persons in 2013 and 2014 outbreaks in the USA. Multicopy organellar DNA such as mitochondrion genomes have been particularly informative for detection and genetic traceback analysis in other parasites. We sequenced the C. cayetanensis genomic DNA obtained from stool samples from patients infected with Cyclospora in Nepal using the Illumina MiSeq platform. By bioinformatically filtering out the metagenomic reads of non-coccidian origin sequences and concentrating the reads by targeted alignment, we were able to obtain contigs containing Eimeria-like mitochondrial, apicoplastic and some chromosomal genomic fragments. A mitochondrial genomic sequence was assembled and confirmed by cloning and sequencing targeted PCR products amplified from Cyclospora DNA using primers based on our draft assembly sequence. The results show that the C. cayetanensis mitochondrion genome is 6274 bp in length, with 33% GC content, and likely exists in concatemeric arrays as in Eimeria mitochondrial genomes. Phylogenetic analysis of the C. cayetanensis mitochondrial genome places this organism in a tight cluster with Eimeria species. The mitochondrial genome of C. cayetanensis contains three protein coding genes, cytochrome (cytb, cytochrome C oxidase subunit 1 (cox1, and cytochrome C oxidase subunit 3 (cox3, in addition to 14 large subunit (LSU and nine small subunit (SSU fragmented rRNA genes.

  8. Genomic Characterization for Parasitic Weeds of the Genus Striga by Sample Sequence Analysis

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    Matt C. Estep

    2012-03-01

    Full Text Available Generation of ∼2200 Sanger sequence reads or ∼10,000 454 reads for seven Lour. DNA samples (five species allowed identification of the highly repetitive DNA content in these genomes. The 14 most abundant repeats in these species were identified and partially assembled. Annotation indicated that they represent nine long terminal repeat (LTR retrotransposon families, three tandem satellite repeats, one long interspersed element (LINE retroelement, and one DNA transposon. All of these repeats are most closely related to repetitive elements in other closely related plants and are not products of horizontal transfer from their host species. These repeats were differentially abundant in each species, with the LTR retrotransposons and satellite repeats most responsible for variation in genome size. Each species had some repetitive elements that were more abundant and some less abundant than the other species examined, indicating that no single element or any unilateral growth or decrease trend in genome behavior was responsible for variation in genome size and composition. Genome sizes were determined by flow sorting, and the values of 615 Mb [ (L. Kuntze], 1330 Mb [ (Willd. Vatke], 1425 Mb [ (Delile Benth.] and 2460 Mb ( Benth. suggest a ploidy series, a prediction supported by repetitive DNA sequence analysis. Phylogenetic analysis using six chloroplast loci indicated the ancestral relationships of the five most agriculturally important species, with the unexpected result that the one parasite of dicotyledonous plants ( was found to be more closely related to some of the grass parasites than many of the grass parasites are to each other.

  9. A survey of innovation through duplication in the reduced genomes of twelve parasites.

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    Jeremy D DeBarry

    Full Text Available We characterize the prevalence, distribution, divergence, and putative functions of detectable two-copy paralogs and segmental duplications in the Apicomplexa, a phylum of parasitic protists. Apicomplexans are mostly obligate intracellular parasites responsible for human and animal diseases (e.g. malaria and toxoplasmosis. Gene loss is a major force in the phylum. Genomes are small and protein-encoding gene repertoires are reduced. Despite this genomic streamlining, duplications and gene family amplifications are present. The potential for innovation introduced by duplications is of particular interest. We compared genomes of twelve apicomplexans across four lineages and used orthology and genome cartography to map distributions of duplications against genome architectures. Segmental duplications appear limited to five species. Where present, they correspond to regions enriched for multi-copy and species-specific genes, pointing toward roles in adaptation and innovation. We found a phylum-wide association of duplications with dynamic chromosome regions and syntenic breakpoints. Trends in the distribution of duplicated genes indicate that recent, species-specific duplicates are often tandem while most others have been dispersed by genome rearrangements. These trends show a relationship between genome architecture and gene duplication. Functional analysis reveals: proteases, which are vital to a parasitic lifecycle, to be prominent in putative recent duplications; a pair of paralogous genes in Toxoplasma gondii previously shown to produce the rate-limiting step in dopamine synthesis in mammalian cells, a possible link to the modification of host behavior; and phylum-wide differences in expression and subcellular localization, indicative of modes of divergence. We have uncovered trends in multiple modes of duplicate divergence including sequence, intron content, expression, subcellular localization, and functions of putative recent duplicates that

  10. The Ditylenchus destructor genome provides new insights into the evolution of plant parasitic nematodes.

    Science.gov (United States)

    Zheng, Jinshui; Peng, Donghai; Chen, Ling; Liu, Hualin; Chen, Feng; Xu, Mengci; Ju, Shouyong; Ruan, Lifang; Sun, Ming

    2016-07-27

    Plant-parasitic nematodes were found in 4 of the 12 clades of phylum Nematoda. These nematodes in different clades may have originated independently from their free-living fungivorous ancestors. However, the exact evolutionary process of these parasites is unclear. Here, we sequenced the genome sequence of a migratory plant nematode, Ditylenchus destructor We performed comparative genomics among the free-living nematode, Caenorhabditis elegans and all the plant nematodes with genome sequences available. We found that, compared with C. elegans, the core developmental control processes underwent heavy reduction, though most signal transduction pathways were conserved. We also found D. destructor contained more homologies of the key genes in the above processes than the other plant nematodes. We suggest that Ditylenchus spp. may be an intermediate evolutionary history stage from free-living nematodes that feed on fungi to obligate plant-parasitic nematodes. Based on the facts that D. destructor can feed on fungi and has a relatively short life cycle, and that it has similar features to both C. elegans and sedentary plant-parasitic nematodes from clade 12, we propose it as a new model to study the biology, biocontrol of plant nematodes and the interaction between nematodes and plants. © 2016 The Author(s).

  11. Aerobic mitochondria of parasitic protists: diverse genomes and complex functions

    Czech Academy of Sciences Publication Activity Database

    Zíková, Alena; Hampl, V.; Paris, Zdeněk; Týč, Jiří; Lukeš, Julius

    2016-01-01

    Roč. 209, 1-2 (2016), s. 46-57 ISSN 0166-6851 R&D Projects: GA ČR GA15-21974S; GA MŠk LL1205 Institutional support: RVO:60077344 Keywords : protists * mitochondrion * genomes * repliation * RNA editing * ribosomes * electron transport chain * iron-sulfur cluster * heme Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.536, year: 2016

  12. Improved genomic resources and new bioinformatic workflow for the carcinogenic parasite Clonorchis sinensis: Biotechnological implications.

    Science.gov (United States)

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

    Clonorchis sinensis (family Opisthorchiidae) is an important foodborne parasite that has a major socioeconomic impact on ~35 million people predominantly in China, Vietnam, Korea and the Russian Far East. In humans, infection with C. sinensis causes clonorchiasis, a complex hepatobiliary disease that can induce cholangiocarcinoma (CCA), a malignant cancer of the bile ducts. Central to understanding the epidemiology of this disease is knowledge of genetic variation within and among populations of this parasite. Although most published molecular studies seem to suggest that C. sinensis represents a single species, evidence of karyotypic variation within C. sinensis and cryptic species within a related opisthorchiid fluke (Opisthorchis viverrini) emphasise the importance of studying and comparing the genes and genomes of geographically distinct isolates of C. sinensis. Recently, we sequenced, assembled and characterised a draft nuclear genome of a C. sinensis isolate from Korea and compared it with a published draft genome of a Chinese isolate of this species using a bioinformatic workflow established for comparing draft genome assemblies and their gene annotations. We identified that 50.6% and 51.3% of the Korean and Chinese C. sinensis genomic scaffolds were syntenic, respectively. Within aligned syntenic blocks, the genomes had a high level of nucleotide identity (99.1%) and encoded 15 variable proteins likely to be involved in diverse biological processes. Here, we review current technical challenges of using draft genome assemblies to undertake comparative genomic analyses to quantify genetic variation between isolates of the same species. Using a workflow that overcomes these challenges, we report on a high-quality draft genome for C. sinensis from Korea and comparative genomic analyses, as a basis for future investigations of the genetic structures of C. sinensis populations, and discuss the biotechnological implications of these explorations. Copyright © 2018

  13. Draft genome of neurotropic nematode parasite Angiostrongylus cantonensis, causative agent of human eosinophilic meningitis.

    Science.gov (United States)

    Yong, Hoi-Sen; Eamsobhana, Praphathip; Lim, Phaik-Eem; Razali, Rozaimi; Aziz, Farhanah Abdul; Rosli, Nurul Shielawati Mohamed; Poole-Johnson, Johan; Anwar, Arif

    2015-08-01

    Angiostrongylus cantonensis is a bursate nematode parasite that causes eosinophilic meningitis (or meningoencephalitis) in humans in many parts of the world. The genomic data from A. cantonensis will form a useful resource for comparative genomic and chemogenomic studies to aid the development of diagnostics and therapeutics. We have sequenced, assembled and annotated the genome of A. cantonensis. The genome size is estimated to be ∼260 Mb, with 17,280 genomic scaffolds, 91X coverage, 81.45% for complete and 93.95% for partial score based on CEGMA analysis of genome completeness. The number of predicted genes of ≥300 bp was 17,482. A total of 7737 predicted protein-coding genes of ≥50 amino acids were identified in the assembled genome. Among the proteins of known function, kinases are the most abundant followed by transferases. The draft genome contains 34 excretory-secretory proteins (ES), a minimum of 44 Nematode Astacin (NAS) metalloproteases, 12 Homeobox (HOX) genes, and 30 neurotransmitters. The assembled genome size (260 Mb) is larger than those of Pristionchus pacificus, Caenorhabditis elegans, Necator americanus, Caenorhabditis briggsae, Trichinella spiralis, Brugia malayi and Loa loa, but smaller than Haemonchus contortus and Ascaris suum. The repeat content (25%) is similar to H. contortus. The GC content (41.17%) is lower compared to P. pacificus (42.7%) and H. contortus (43.1%) but higher compared to C. briggsae (37.69%), A. suum (37.9%) and N. americanus (40.2%) while the scaffold N50 is 42,191. This draft genome will facilitate the understanding of many unresolved issues on the parasite and the disorder it causes. Copyright © 2015 Elsevier B.V. All rights reserved.

  14. Spatial variation in the parasite communities and genomic structure of urban rats in New York City.

    Science.gov (United States)

    Angley, L P; Combs, M; Firth, C; Frye, M J; Lipkin, I; Richardson, J L; Munshi-South, J

    2018-02-01

    Brown rats (Rattus norvegicus) are a globally distributed pest. Urban habitats can support large infestations of rats, posing a potential risk to public health from the parasites and pathogens they carry. Despite the potential influence of rodent-borne zoonotic diseases on human health, it is unclear how urban habitats affect the structure and transmission dynamics of ectoparasite and microbial communities (all referred to as "parasites" hereafter) among rat colonies. In this study, we use ecological data on parasites and genomic sequencing of their rat hosts to examine associations between spatial proximity, genetic relatedness and the parasite communities associated with 133 rats at five sites in sections of New York City with persistent rat infestations. We build on previous work showing that rats in New York carry a wide variety of parasites and report that these communities differ significantly among sites, even across small geographical distances. Ectoparasite community similarity was positively associated with geographical proximity; however, there was no general association between distance and microbial communities of rats. Sites with greater overall parasite diversity also had rats with greater infection levels and parasite species richness. Parasite community similarity among sites was not linked to genetic relatedness of rats, suggesting that these communities are not associated with genetic similarity among host individuals or host dispersal among sites. Discriminant analysis identified site-specific associations of several parasite species, suggesting that the presence of some species within parasite communities may allow researchers to determine the sites of origin for newly sampled rats. The results of our study help clarify the roles that colony structure and geographical proximity play in determining the ecology of R. norvegicus as a significant urban reservoir of zoonotic diseases. Our study also highlights the spatial variation present in urban

  15. Long- and short-term selective forces on malaria parasite genomes

    KAUST Repository

    Nygaard, Sanne

    2010-09-09

    Plasmodium parasites, the causal agents of malaria, result in more than 1 million deaths annually. Plasmodium are unicellular eukaryotes with small ~23 Mb genomes encoding ~5200 protein-coding genes. The protein-coding genes comprise about half of these genomes. Although evolutionary processes have a significant impact on malaria control, the selective pressures within Plasmodium genomes are poorly understood, particularly in the non-protein-coding portion of the genome. We use evolutionary methods to describe selective processes in both the coding and non-coding regions of these genomes. Based on genome alignments of seven Plasmodium species, we show that protein-coding, intergenic and intronic regions are all subject to purifying selection and we identify 670 conserved non-genic elements. We then use genome-wide polymorphism data from P. falciparum to describe short-term selective processes in this species and identify some candidate genes for balancing (diversifying) selection. Our analyses suggest that there are many functional elements in the non-genic regions of these genomes and that adaptive evolution has occurred more frequently in the protein-coding regions of the genome. © 2010 Nygaard et al.

  16. The Echinococcus canadensis (G7) genome: a key knowledge of parasitic platyhelminth human diseases.

    Science.gov (United States)

    Maldonado, Lucas L; Assis, Juliana; Araújo, Flávio M Gomes; Salim, Anna C M; Macchiaroli, Natalia; Cucher, Marcela; Camicia, Federico; Fox, Adolfo; Rosenzvit, Mara; Oliveira, Guilherme; Kamenetzky, Laura

    2017-02-27

    The parasite Echinococcus canadensis (G7) (phylum Platyhelminthes, class Cestoda) is one of the causative agents of echinococcosis. Echinococcosis is a worldwide chronic zoonosis affecting humans as well as domestic and wild mammals, which has been reported as a prioritized neglected disease by the World Health Organisation. No genomic data, comparative genomic analyses or efficient therapeutic and diagnostic tools are available for this severe disease. The information presented in this study will help to understand the peculiar biological characters and to design species-specific control tools. We sequenced, assembled and annotated the 115-Mb genome of E. canadensis (G7). Comparative genomic analyses using whole genome data of three Echinococcus species not only confirmed the status of E. canadensis (G7) as a separate species but also demonstrated a high nucleotide sequences divergence in relation to E. granulosus (G1). The E. canadensis (G7) genome contains 11,449 genes with a core set of 881 orthologs shared among five cestode species. Comparative genomics revealed that there are more single nucleotide polymorphisms (SNPs) between E. canadensis (G7) and E. granulosus (G1) than between E. canadensis (G7) and E. multilocularis. This result was unexpected since E. canadensis (G7) and E. granulosus (G1) were considered to belong to the species complex E. granulosus sensu lato. We described SNPs in known drug targets and metabolism genes in the E. canadensis (G7) genome. Regarding gene regulation, we analysed three particular features: CpG island distribution along the three Echinococcus genomes, DNA methylation system and small RNA pathway. The results suggest the occurrence of yet unknown gene regulation mechanisms in Echinococcus. This is the first work that addresses Echinococcus comparative genomics. The resources presented here will promote the study of mechanisms of parasite development as well as new tools for drug discovery. The availability of a high

  17. Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites

    KAUST Repository

    Woo, Yong

    2015-07-15

    The eukaryotic phylum Apicomplexa encompasses thousands of obligate intracellular parasites of humans and animals with immense socio-economic and health impacts. We sequenced nuclear genomes of Chromera velia and Vitrella brassicaformis, free-living non-parasitic photosynthetic algae closely related to apicomplexans. Proteins from key metabolic pathways and from the endomembrane trafficking systems associated with a free-living lifestyle have been progressively and non-randomly lost during adaptation to parasitism. The free-living ancestor contained a broad repertoire of genes many of which were repurposed for parasitic processes, such as extracellular proteins, components of a motility apparatus, and DNA- and RNA-binding protein families. Based on transcriptome analyses across 36 environmental conditions, Chromera orthologs of apicomplexan invasion-related motility genes were co-regulated with genes encoding the flagellar apparatus, supporting the functional contribution of flagella to the evolution of invasion machinery. This study provides insights into how obligate parasites with diverse life strategies arose from a once free-living phototrophic marine alga. © Woo et al.

  18. Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites

    KAUST Repository

    Woo, Yong; Ansari, Hifzur Rahman; Otto, Thomas D.; Linger, Christen M K; Olisko, Martin K.; Michá lek, Jan; Saxena, Alka; Shanmugam, Dhanasekaran; Tayyrov, Annageldi; Veluchamy, Alaguraj; Ali, Shahjahan; Bernal, Axel; Del Campo, Javier; Cihlá ř, Jaromí r; Flegontov, Pavel; Gornik, Sebastian G.; Hajdušková , Eva; Horá k, Aleš; Janouškovec, Jan; Katris, Nicholas J.; Mast, Fred D.; Miranda-Saavedra, Diego; Mourier, Tobias; Naeem, Raeece; Nair, Mridul; Panigrahi, Aswini Kumar; Rawlings, Neil D.; Padron Regalado, Eriko; Ramaprasad, Abhinay; Samad, Nadira; Tomčala, Aleš; Wilkes, Jon; Neafsey, Daniel E.; Doerig, Christian; Bowler, Chris; Keeling, Patrick J.; Roos, David S.; Dacks, Joel B.; Templeton, Thomas J.; Waller, Ross F.; Lukeš, Julius; Oborní k, Miroslav; Pain, Arnab

    2015-01-01

    The eukaryotic phylum Apicomplexa encompasses thousands of obligate intracellular parasites of humans and animals with immense socio-economic and health impacts. We sequenced nuclear genomes of Chromera velia and Vitrella brassicaformis, free-living non-parasitic photosynthetic algae closely related to apicomplexans. Proteins from key metabolic pathways and from the endomembrane trafficking systems associated with a free-living lifestyle have been progressively and non-randomly lost during adaptation to parasitism. The free-living ancestor contained a broad repertoire of genes many of which were repurposed for parasitic processes, such as extracellular proteins, components of a motility apparatus, and DNA- and RNA-binding protein families. Based on transcriptome analyses across 36 environmental conditions, Chromera orthologs of apicomplexan invasion-related motility genes were co-regulated with genes encoding the flagellar apparatus, supporting the functional contribution of flagella to the evolution of invasion machinery. This study provides insights into how obligate parasites with diverse life strategies arose from a once free-living phototrophic marine alga. © Woo et al.

  19. Hybridization and polyploidy enable genomic plasticity without sex in the most devastating plant-parasitic nematodes.

    Directory of Open Access Journals (Sweden)

    Romain Blanc-Mathieu

    2017-06-01

    Full Text Available Root-knot nematodes (genus Meloidogyne exhibit a diversity of reproductive modes ranging from obligatory sexual to fully asexual reproduction. Intriguingly, the most widespread and devastating species to global agriculture are those that reproduce asexually, without meiosis. To disentangle this surprising parasitic success despite the absence of sex and genetic exchanges, we have sequenced and assembled the genomes of three obligatory ameiotic and asexual Meloidogyne. We have compared them to those of relatives able to perform meiosis and sexual reproduction. We show that the genomes of ameiotic asexual Meloidogyne are large, polyploid and made of duplicated regions with a high within-species average nucleotide divergence of ~8%. Phylogenomic analysis of the genes present in these duplicated regions suggests that they originated from multiple hybridization events and are thus homoeologs. We found that up to 22% of homoeologous gene pairs were under positive selection and these genes covered a wide spectrum of predicted functional categories. To biologically assess functional divergence, we compared expression patterns of homoeologous gene pairs across developmental life stages using an RNAseq approach in the most economically important asexually-reproducing nematode. We showed that >60% of homoeologous gene pairs display diverged expression patterns. These results suggest a substantial functional impact of the genome structure. Contrasting with high within-species nuclear genome divergence, mitochondrial genome divergence between the three ameiotic asexuals was very low, signifying that these putative hybrids share a recent common maternal ancestor. Transposable elements (TE cover a ~1.7 times higher proportion of the genomes of the ameiotic asexual Meloidogyne compared to the sexual relative and might also participate in their plasticity. The intriguing parasitic success of asexually-reproducing Meloidogyne species could be partly explained by

  20. Rapid evolution of the mitochondrial genome in Chalcidoid wasps (Hymenoptera: Chalcidoidea driven by parasitic lifestyles.

    Directory of Open Access Journals (Sweden)

    Jin-Hua Xiao

    Full Text Available Among the Chalcidoids, hymenopteran parasitic wasps that have diversified lifestyles, a partial mitochondrial genome has been reported only from Nasonia. This genome had many unusual features, especially a dramatic reorganization and a high rate of evolution. Comparisons based on more mitochondrial genomic data from the same superfamily were required to reveal weather these unusual features are peculiar to Nasonia or not. In the present study, we sequenced the nearly complete mitochondrial genomes from the species Philotrypesis. pilosa and Philotrypesis sp., both of which were associated with Ficus hispida. The acquired data included all of the protein-coding genes, rRNAs, and most of the tRNAs, and in P. pilosa the control region. High levels of nucleotide divergence separated the two species. A comparison of all available hymenopteran mitochondrial genomes (including a submitted partial genome from Ceratosolen solmsi revealed that the Chalcidoids had dramatic mitochondrial gene rearrangments, involved not only the tRNAs, but also several protein-coding genes. The AT-rich control region was translocated and inverted in Philotrypesis. The mitochondrial genomes also exhibited rapid rates of evolution involving elevated nonsynonymous mutations.

  1. Drug target prediction and prioritization: using orthology to predict essentiality in parasite genomes

    Directory of Open Access Journals (Sweden)

    Hall Ross S

    2010-04-01

    Full Text Available Abstract Background New drug targets are urgently needed for parasites of socio-economic importance. Genes that are essential for parasite survival are highly desirable targets, but information on these genes is lacking, as gene knockouts or knockdowns are difficult to perform in many species of parasites. We examined the applicability of large-scale essentiality information from four model eukaryotes, Caenorhabditis elegans, Drosophila melanogaster, Mus musculus and Saccharomyces cerevisiae, to discover essential genes in each of their genomes. Parasite genes that lack orthologues in their host are desirable as selective targets, so we also examined prediction of essential genes within this subset. Results Cross-species analyses showed that the evolutionary conservation of genes and the presence of essential orthologues are each strong predictors of essentiality in eukaryotes. Absence of paralogues was also found to be a general predictor of increased relative essentiality. By combining several orthology and essentiality criteria one can select gene sets with up to a five-fold enrichment in essential genes compared with a random selection. We show how quantitative application of such criteria can be used to predict a ranked list of potential drug targets from Ancylostoma caninum and Haemonchus contortus - two blood-feeding strongylid nematodes, for which there are presently limited sequence data but no functional genomic tools. Conclusions The present study demonstrates the utility of using orthology information from multiple, diverse eukaryotes to predict essential genes. The data also emphasize the challenge of identifying essential genes among those in a parasite that are absent from its host.

  2. Population genomic structure and adaptation in the zoonotic malaria parasite Plasmodium knowlesi

    KAUST Repository

    Assefa, Samuel

    2015-10-06

    Malaria cases caused by the zoonotic parasite Plasmodium knowlesi are being increasingly reported throughout Southeast Asia and in travelers returning from the region. To test for evidence of signatures of selection or unusual population structure in this parasite, we surveyed genome sequence diversity in 48 clinical isolates recently sampled from Malaysian Borneo and in five lines maintained in laboratory rhesus macaques after isolation in the 1960s from Peninsular Malaysia and the Philippines. Overall genomewide nucleotide diversity (π = 6.03 × 10) was much higher than has been seen in worldwide samples of either of the major endemic malaria parasite species Plasmodium falciparum and Plasmodium vivax. A remarkable substructure is revealed within P. knowlesi, consisting of two major sympatric clusters of the clinical isolates and a third cluster comprising the laboratory isolates. There was deep differentiation between the two clusters of clinical isolates [mean genomewide fixation index (F) = 0.21, with 9,293 SNPs having fixed differences of F = 1.0]. This differentiation showed marked heterogeneity across the genome, with mean F values of different chromosomes ranging from 0.08 to 0.34 and with further significant variation across regions within several chromosomes. Analysis of the largest cluster (cluster 1, 38 isolates) indicated long-term population growth, with negatively skewed allele frequency distributions (genomewide average Tajima\\'s D = -1.35). Against this background there was evidence of balancing selection on particular genes, including the circumsporozoite protein (csp) gene, which had the top Tajima\\'s D value (1.57), and scans of haplotype homozygosity implicate several genomic regions as being under recent positive selection.

  3. Comparative genome analysis reveals a conserved family of actin-like proteins in apicomplexan parasites

    Directory of Open Access Journals (Sweden)

    Sibley L David

    2005-12-01

    Full Text Available Abstract Background The phylum Apicomplexa is an early-branching eukaryotic lineage that contains a number of important human and animal pathogens. Their complex life cycles and unique cytoskeletal features distinguish them from other model eukaryotes. Apicomplexans rely on actin-based motility for cell invasion, yet the regulation of this system remains largely unknown. Consequently, we focused our efforts on identifying actin-related proteins in the recently completed genomes of Toxoplasma gondii, Plasmodium spp., Cryptosporidium spp., and Theileria spp. Results Comparative genomic and phylogenetic studies of apicomplexan genomes reveals that most contain only a single conventional actin and yet they each have 8–10 additional actin-related proteins. Among these are a highly conserved Arp1 protein (likely part of a conserved dynactin complex, and Arp4 and Arp6 homologues (subunits of the chromatin-remodeling machinery. In contrast, apicomplexans lack canonical Arp2 or Arp3 proteins, suggesting they lost the Arp2/3 actin polymerization complex on their evolutionary path towards intracellular parasitism. Seven of these actin-like proteins (ALPs are novel to apicomplexans. They show no phylogenetic associations to the known Arp groups and likely serve functions specific to this important group of intracellular parasites. Conclusion The large diversity of actin-like proteins in apicomplexans suggests that the actin protein family has diverged to fulfill various roles in the unique biology of intracellular parasites. Conserved Arps likely participate in vesicular transport and gene expression, while apicomplexan-specific ALPs may control unique biological traits such as actin-based gliding motility.

  4. Population genomic scan for candidate signatures of balancing selection to guide antigen characterization in malaria parasites.

    Science.gov (United States)

    Amambua-Ngwa, Alfred; Tetteh, Kevin K A; Manske, Magnus; Gomez-Escobar, Natalia; Stewart, Lindsay B; Deerhake, M Elizabeth; Cheeseman, Ian H; Newbold, Christopher I; Holder, Anthony A; Knuepfer, Ellen; Janha, Omar; Jallow, Muminatou; Campino, Susana; Macinnis, Bronwyn; Kwiatkowski, Dominic P; Conway, David J

    2012-01-01

    Acquired immunity in vertebrates maintains polymorphisms in endemic pathogens, leading to identifiable signatures of balancing selection. To comprehensively survey for genes under such selection in the human malaria parasite Plasmodium falciparum, we generated paired-end short-read sequences of parasites in clinical isolates from an endemic Gambian population, which were mapped to the 3D7 strain reference genome to yield high-quality genome-wide coding sequence data for 65 isolates. A minority of genes did not map reliably, including the hypervariable var, rifin, and stevor families, but 5,056 genes (90.9% of all in the genome) had >70% sequence coverage with minimum read depth of 5 for at least 50 isolates, of which 2,853 genes contained 3 or more single nucleotide polymorphisms (SNPs) for analysis of polymorphic site frequency spectra. Against an overall background of negatively skewed frequencies, as expected from historical population expansion combined with purifying selection, the outlying minority of genes with signatures indicating exceptionally intermediate frequencies were identified. Comparing genes with different stage-specificity, such signatures were most common in those with peak expression at the merozoite stage that invades erythrocytes. Members of clag, PfMC-2TM, surfin, and msp3-like gene families were highly represented, the strongest signature being in the msp3-like gene PF10_0355. Analysis of msp3-like transcripts in 45 clinical and 11 laboratory adapted isolates grown to merozoite-containing schizont stages revealed surprisingly low expression of PF10_0355. In diverse clonal parasite lines the protein product was expressed in a minority of mature schizonts (<1% in most lines and ∼10% in clone HB3), and eight sub-clones of HB3 cultured separately had an intermediate spectrum of positive frequencies (0.9 to 7.5%), indicating phase variable expression of this polymorphic antigen. This and other identified targets of balancing selection are now

  5. Population genomic scan for candidate signatures of balancing selection to guide antigen characterization in malaria parasites.

    Directory of Open Access Journals (Sweden)

    Alfred Amambua-Ngwa

    Full Text Available Acquired immunity in vertebrates maintains polymorphisms in endemic pathogens, leading to identifiable signatures of balancing selection. To comprehensively survey for genes under such selection in the human malaria parasite Plasmodium falciparum, we generated paired-end short-read sequences of parasites in clinical isolates from an endemic Gambian population, which were mapped to the 3D7 strain reference genome to yield high-quality genome-wide coding sequence data for 65 isolates. A minority of genes did not map reliably, including the hypervariable var, rifin, and stevor families, but 5,056 genes (90.9% of all in the genome had >70% sequence coverage with minimum read depth of 5 for at least 50 isolates, of which 2,853 genes contained 3 or more single nucleotide polymorphisms (SNPs for analysis of polymorphic site frequency spectra. Against an overall background of negatively skewed frequencies, as expected from historical population expansion combined with purifying selection, the outlying minority of genes with signatures indicating exceptionally intermediate frequencies were identified. Comparing genes with different stage-specificity, such signatures were most common in those with peak expression at the merozoite stage that invades erythrocytes. Members of clag, PfMC-2TM, surfin, and msp3-like gene families were highly represented, the strongest signature being in the msp3-like gene PF10_0355. Analysis of msp3-like transcripts in 45 clinical and 11 laboratory adapted isolates grown to merozoite-containing schizont stages revealed surprisingly low expression of PF10_0355. In diverse clonal parasite lines the protein product was expressed in a minority of mature schizonts (<1% in most lines and ∼10% in clone HB3, and eight sub-clones of HB3 cultured separately had an intermediate spectrum of positive frequencies (0.9 to 7.5%, indicating phase variable expression of this polymorphic antigen. This and other identified targets of balancing

  6. Population genomic structure and adaptation in the zoonotic malaria parasite Plasmodium knowlesi

    KAUST Repository

    Assefa, Samuel; Lim, Caeul; Preston, Mark D.; Duffy, Craig W.; Nair, Mridul; Adroub, Sabir; Kadir, Khamisah A.; Goldberg, Jonathan M.; Neafsey, Daniel E.; Divis, Paul; Clark, Taane G.; Duraisingh, Manoj T.; Conway, David J.; Pain, Arnab; Singh, Balbir

    2015-01-01

    Malaria cases caused by the zoonotic parasite Plasmodium knowlesi are being increasingly reported throughout Southeast Asia and in travelers returning from the region. To test for evidence of signatures of selection or unusual population structure in this parasite, we surveyed genome sequence diversity in 48 clinical isolates recently sampled from Malaysian Borneo and in five lines maintained in laboratory rhesus macaques after isolation in the 1960s from Peninsular Malaysia and the Philippines. Overall genomewide nucleotide diversity (π = 6.03 × 10) was much higher than has been seen in worldwide samples of either of the major endemic malaria parasite species Plasmodium falciparum and Plasmodium vivax. A remarkable substructure is revealed within P. knowlesi, consisting of two major sympatric clusters of the clinical isolates and a third cluster comprising the laboratory isolates. There was deep differentiation between the two clusters of clinical isolates [mean genomewide fixation index (F) = 0.21, with 9,293 SNPs having fixed differences of F = 1.0]. This differentiation showed marked heterogeneity across the genome, with mean F values of different chromosomes ranging from 0.08 to 0.34 and with further significant variation across regions within several chromosomes. Analysis of the largest cluster (cluster 1, 38 isolates) indicated long-term population growth, with negatively skewed allele frequency distributions (genomewide average Tajima's D = -1.35). Against this background there was evidence of balancing selection on particular genes, including the circumsporozoite protein (csp) gene, which had the top Tajima's D value (1.57), and scans of haplotype homozygosity implicate several genomic regions as being under recent positive selection.

  7. Evidence-based annotation of the malaria parasite's genome using comparative expression profiling.

    Directory of Open Access Journals (Sweden)

    Yingyao Zhou

    2008-02-01

    Full Text Available A fundamental problem in systems biology and whole genome sequence analysis is how to infer functions for the many uncharacterized proteins that are identified, whether they are conserved across organisms of different phyla or are phylum-specific. This problem is especially acute in pathogens, such as malaria parasites, where genetic and biochemical investigations are likely to be more difficult. Here we perform comparative expression analysis on Plasmodium parasite life cycle data derived from P. falciparum blood, sporozoite, zygote and ookinete stages, and P. yoelii mosquito oocyst and salivary gland sporozoites, blood and liver stages and show that type II fatty acid biosynthesis genes are upregulated in liver and insect stages relative to asexual blood stages. We also show that some universally uncharacterized genes with orthologs in Plasmodium species, Saccharomyces cerevisiae and humans show coordinated transcription patterns in large collections of human and yeast expression data and that the function of the uncharacterized genes can sometimes be predicted based on the expression patterns across these diverse organisms. We also use a comprehensive and unbiased literature mining method to predict which uncharacterized parasite-specific genes are likely to have roles in processes such as gliding motility, host-cell interactions, sporozoite stage, or rhoptry function. These analyses, together with protein-protein interaction data, provide probabilistic models that predict the function of 926 uncharacterized malaria genes and also suggest that malaria parasites may provide a simple model system for the study of some human processes. These data also provide a foundation for further studies of transcriptional regulation in malaria parasites.

  8. Plastid genome structure and loss of photosynthetic ability in the parasitic genus Cuscuta.

    Science.gov (United States)

    Revill, Meredith J W; Stanley, Susan; Hibberd, Julian M

    2005-09-01

    The genus Cuscuta (dodder) is composed of parasitic plants, some species of which appear to be losing the ability to photosynthesize. A molecular phylogeny was constructed using 15 species of Cuscuta in order to assess whether changes in photosynthetic ability and alterations in structure of the plastid genome relate to phylogenetic position within the genus. The molecular phylogeny provides evidence for four major clades within Cuscuta. Although DNA blot analysis showed that Cuscuta species have smaller plastid genomes than tobacco, and that plastome size varied significantly even within one Cuscuta clade, dot blot analysis indicated that the dodders possess homologous sequence to 101 genes from the tobacco plastome. Evidence is provided for significant rates of DNA transfer from plastid to nucleus in Cuscuta. Size and structure of Cuscuta plastid genomes, as well as photosynthetic ability, appear to vary independently of position within the phylogeny, thus supporting the hypothesis that within Cuscuta photosynthetic ability and organization of the plastid genome are changing in an unco-ordinated manner.

  9. Complete DNA sequences of the plastid genomes of two parasitic flowering plant species, Cuscuta reflexa and Cuscuta gronovii.

    Science.gov (United States)

    Funk, Helena T; Berg, Sabine; Krupinska, Karin; Maier, Uwe G; Krause, Kirsten

    2007-08-22

    The holoparasitic plant genus Cuscuta comprises species with photosynthetic capacity and functional chloroplasts as well as achlorophyllous and intermediate forms with restricted photosynthetic activity and degenerated chloroplasts. Previous data indicated significant differences with respect to the plastid genome coding capacity in different Cuscuta species that could correlate with their photosynthetic activity. In order to shed light on the molecular changes accompanying the parasitic lifestyle, we sequenced the plastid chromosomes of the two species Cuscuta reflexa and Cuscuta gronovii. Both species are capable of performing photosynthesis, albeit with varying efficiencies. Together with the plastid genome of Epifagus virginiana, an achlorophyllous parasitic plant whose plastid genome has been sequenced, these species represent a series of progression towards total dependency on the host plant, ranging from reduced levels of photosynthesis in C. reflexa to a restricted photosynthetic activity and degenerated chloroplasts in C. gronovii to an achlorophyllous state in E. virginiana. The newly sequenced plastid genomes of C. reflexa and C. gronovii reveal that the chromosome structures are generally very similar to that of non-parasitic plants, although a number of species-specific insertions, deletions (indels) and sequence inversions were identified. However, we observed a gradual adaptation of the plastid genome to the different degrees of parasitism. The changes are particularly evident in C. gronovii and include (a) the parallel losses of genes for the subunits of the plastid-encoded RNA polymerase and the corresponding promoters from the plastid genome, (b) the first documented loss of the gene for a putative splicing factor, MatK, from the plastid genome and (c) a significant reduction of RNA editing. Overall, the comparative genomic analysis of plastid DNA from parasitic plants indicates a bias towards a simplification of the plastid gene expression

  10. Complete DNA sequences of the plastid genomes of two parasitic flowering plant species, Cuscuta reflexa and Cuscuta gronovii

    Directory of Open Access Journals (Sweden)

    Maier Uwe G

    2007-08-01

    Full Text Available Abstract Background The holoparasitic plant genus Cuscuta comprises species with photosynthetic capacity and functional chloroplasts as well as achlorophyllous and intermediate forms with restricted photosynthetic activity and degenerated chloroplasts. Previous data indicated significant differences with respect to the plastid genome coding capacity in different Cuscuta species that could correlate with their photosynthetic activity. In order to shed light on the molecular changes accompanying the parasitic lifestyle, we sequenced the plastid chromosomes of the two species Cuscuta reflexa and Cuscuta gronovii. Both species are capable of performing photosynthesis, albeit with varying efficiencies. Together with the plastid genome of Epifagus virginiana, an achlorophyllous parasitic plant whose plastid genome has been sequenced, these species represent a series of progression towards total dependency on the host plant, ranging from reduced levels of photosynthesis in C. reflexa to a restricted photosynthetic activity and degenerated chloroplasts in C. gronovii to an achlorophyllous state in E. virginiana. Results The newly sequenced plastid genomes of C. reflexa and C. gronovii reveal that the chromosome structures are generally very similar to that of non-parasitic plants, although a number of species-specific insertions, deletions (indels and sequence inversions were identified. However, we observed a gradual adaptation of the plastid genome to the different degrees of parasitism. The changes are particularly evident in C. gronovii and include (a the parallel losses of genes for the subunits of the plastid-encoded RNA polymerase and the corresponding promoters from the plastid genome, (b the first documented loss of the gene for a putative splicing factor, MatK, from the plastid genome and (c a significant reduction of RNA editing. Conclusion Overall, the comparative genomic analysis of plastid DNA from parasitic plants indicates a bias towards

  11. Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus Cuscuta.

    Science.gov (United States)

    McNeal, Joel R; Kuehl, Jennifer V; Boore, Jeffrey L; de Pamphilis, Claude W

    2007-10-24

    Plastid genome content and protein sequence are highly conserved across land plants and their closest algal relatives. Parasitic plants, which obtain some or all of their nutrition through an attachment to a host plant, are often a striking exception. Heterotrophy can lead to relaxed constraint on some plastid genes or even total gene loss. We sequenced plastid genomes of two species in the parasitic genus Cuscuta along with a non-parasitic relative, Ipomoea purpurea, to investigate changes in the plastid genome that may result from transition to the parasitic lifestyle. Aside from loss of all ndh genes, Cuscuta exaltata retains photosynthetic and photorespiratory genes that evolve under strong selective constraint. Cuscuta obtusiflora has incurred substantially more change to its plastid genome, including loss of all genes for the plastid-encoded RNA polymerase. Despite extensive change in gene content and greatly increased rate of overall nucleotide substitution, C. obtusiflora also retains all photosynthetic and photorespiratory genes with only one minor exception. Although Epifagus virginiana, the only other parasitic plant with its plastid genome sequenced to date, has lost a largely overlapping set of transfer-RNA and ribosomal genes as Cuscuta, it has lost all genes related to photosynthesis and maintains a set of genes which are among the most divergent in Cuscuta. Analyses demonstrate photosynthetic genes are under the highest constraint of any genes within the plastid genomes of Cuscuta, indicating a function involving RuBisCo and electron transport through photosystems is still the primary reason for retention of the plastid genome in these species.

  12. Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus Cuscuta

    Directory of Open Access Journals (Sweden)

    Kuehl Jennifer V

    2007-10-01

    Full Text Available Abstract Background Plastid genome content and protein sequence are highly conserved across land plants and their closest algal relatives. Parasitic plants, which obtain some or all of their nutrition through an attachment to a host plant, are often a striking exception. Heterotrophy can lead to relaxed constraint on some plastid genes or even total gene loss. We sequenced plastid genomes of two species in the parasitic genus Cuscuta along with a non-parasitic relative, Ipomoea purpurea, to investigate changes in the plastid genome that may result from transition to the parasitic lifestyle. Results Aside from loss of all ndh genes, Cuscuta exaltata retains photosynthetic and photorespiratory genes that evolve under strong selective constraint. Cuscuta obtusiflora has incurred substantially more change to its plastid genome, including loss of all genes for the plastid-encoded RNA polymerase. Despite extensive change in gene content and greatly increased rate of overall nucleotide substitution, C. obtusiflora also retains all photosynthetic and photorespiratory genes with only one minor exception. Conclusion Although Epifagus virginiana, the only other parasitic plant with its plastid genome sequenced to date, has lost a largely overlapping set of transfer-RNA and ribosomal genes as Cuscuta, it has lost all genes related to photosynthesis and maintains a set of genes which are among the most divergent in Cuscuta. Analyses demonstrate photosynthetic genes are under the highest constraint of any genes within the plastid genomes of Cuscuta, indicating a function involving RuBisCo and electron transport through photosystems is still the primary reason for retention of the plastid genome in these species.

  13. A draft genome of the honey bee trypanosomatid parasite Crithidia mellificae.

    Directory of Open Access Journals (Sweden)

    Charles Runckel

    Full Text Available Since 2006, honey bee colonies in North America and Europe have experienced increased annual mortality. These losses correlate with increased pathogen incidence and abundance, though no single etiologic agent has been identified. Crithidia mellificae is a unicellular eukaryotic honey bee parasite that has been associated with colony losses in the USA and Belgium. C. mellificae is a member of the family Trypanosomatidae, which primarily includes other insect-infecting species (e.g., the bumble bee pathogen Crithidia bombi, as well as species that infect both invertebrate and vertebrate hosts including human pathogens (e.g.,Trypanosoma cruzi, T. brucei, and Leishmania spp.. To better characterize C. mellificae, we sequenced the genome and transcriptome of strain SF, which was isolated and cultured in 2010. The 32 megabase draft genome, presented herein, shares a high degree of conservation with the related species Leishmania major. We estimate that C. mellificae encodes over 8,300 genes, the majority of which are orthologs of genes encoded by L. major and other Leishmania or Trypanosoma species. Genes unique to C. mellificae, including those of possible bacterial origin, were annotated based on function and include genes putatively involved in carbohydrate metabolism. This draft genome will facilitate additional investigations of the impact of C. mellificae infection on honey bee health and provide insight into the evolution of this unique family.

  14. Surface antigens and potential virulence factors from parasites detected by comparative genomics of perfect amino acid repeats

    Directory of Open Access Journals (Sweden)

    Adler Joël

    2007-12-01

    Full Text Available Abstract Background Many parasitic organisms, eukaryotes as well as bacteria, possess surface antigens with amino acid repeats. Making up the interface between host and pathogen such repetitive proteins may be virulence factors involved in immune evasion or cytoadherence. They find immunological applications in serodiagnostics and vaccine development. Here we use proteins which contain perfect repeats as a basis for comparative genomics between parasitic and free-living organisms. Results We have developed Reptile http://reptile.unibe.ch, a program for proteome-wide probabilistic description of perfect repeats in proteins. Parasite proteomes exhibited a large variance regarding the proportion of repeat-containing proteins. Interestingly, there was a good correlation between the percentage of highly repetitive proteins and mean protein length in parasite proteomes, but not at all in the proteomes of free-living eukaryotes. Reptile combined with programs for the prediction of transmembrane domains and GPI-anchoring resulted in an effective tool for in silico identification of potential surface antigens and virulence factors from parasites. Conclusion Systemic surveys for perfect amino acid repeats allowed basic comparisons between free-living and parasitic organisms that were directly applicable to predict proteins of serological and parasitological importance. An on-line tool is available at http://genomics.unibe.ch/dora.

  15. The genomic features of parasitism, Polyembryony and immune evasion in the endoparasitic wasp Macrocentrus cingulum.

    Science.gov (United States)

    Yin, Chuanlin; Li, Meizhen; Hu, Jian; Lang, Kun; Chen, Qiming; Liu, Jinding; Guo, Dianhao; He, Kang; Dong, Yipei; Luo, Jiapeng; Song, Zhenkun; Walters, James R; Zhang, Wenqing; Li, Fei; Chen, Xuexin

    2018-05-30

    Parasitoid wasps are well-known natural enemies of major agricultural pests and arthropod borne diseases. The parasitoid wasp Macrocentrus cingulum (Hymenoptera: Braconidae) has been widely used to control the notorious insect pests Ostrinia furnacalis (Asian Corn Borer) and O. nubilalis (European corn borer). One striking phenomenon exhibited by M. cingulum is polyembryony, the formation of multiple genetically identical offspring from a single zygote. Moreover, M. cingulum employs a passive parasitic strategy by preventing the host's immune system from recognizing the embryo as a foreign body. Thus, the embryos evade the host's immune system and are not encapsulated by host hemocytes. Unfortunately, the mechanism of both polyembryony and immune evasion remains largely unknown. We report the genome of the parasitoid wasp M. cingulum. Comparative genomics analysis of M. cingulum and other 11 insects were conducted, finding some gene families with apparent expansion or contraction which might be linked to the parasitic behaviors or polyembryony of M. cingulum. Moreover, we present the evidence that the microRNA miR-14b regulates the polyembryonic development of M. cingulum by targeting the c-Myc Promoter-binding Protein 1 (MBP-1), histone-lysine N-methyltransferase 2E (KMT2E) and segmentation protein Runt. In addition, Hemomucin, an O-glycosylated transmembrane protein, protects the endoparasitoid wasp larvae from being encapsulated by host hemocytes. Motif and domain analysis showed that only the hemomucin in two endoparasitoids, M. cingulum and Venturia canescens, possessing the ability of passive immune evasion has intact mucin domain and similar O-glycosylation patterns, indicating that the hemomucin is a key factor modulating the immune evasion. The microRNA miR-14b participates in the regulation of polyembryonic development, and the O-glycosylation of the mucin domain in the hemomucin confers the passive immune evasion in this wasp. These key findings provide

  16. Systematics and plastid genome evolution of the cryptically photosynthetic parasitic plant genus Cuscuta (Convolvulaceae

    Directory of Open Access Journals (Sweden)

    Kuehl Jennifer V

    2007-12-01

    Full Text Available Abstract Background The genus Cuscuta L. (Convolvulaceae, commonly known as dodders, are epiphytic vines that invade the stems of their host with haustorial feeding structures at the points of contact. Although they lack expanded leaves, some species are noticeably chlorophyllous, especially as seedlings and in maturing fruits. Some species are reported as crop pests of worldwide distribution, whereas others are extremely rare and have local distributions and apparent niche specificity. A strong phylogenetic framework for this large genus is essential to understand the interesting ecological, morphological and molecular phenomena that occur within these parasites in an evolutionary context. Results Here we present a well-supported phylogeny of Cuscuta using sequences of the nuclear ribosomal internal transcribed spacer and plastid rps2, rbcL and matK from representatives across most of the taxonomic diversity of the genus. We use the phylogeny to interpret morphological and plastid genome evolution within the genus. At least three currently recognized taxonomic sections are not monophyletic and subgenus Cuscuta is unequivocally paraphyletic. Plastid genes are extremely variable with regards to evolutionary constraint, with rbcL exhibiting even higher levels of purifying selection in Cuscuta than photosynthetic relatives. Nuclear genome size is highly variable within Cuscuta, particularly within subgenus Grammica, and in some cases may indicate the existence of cryptic species in this large clade of morphologically similar species. Conclusion Some morphological characters traditionally used to define major taxonomic splits within Cuscuta are homoplastic and are of limited use in defining true evolutionary groups. Chloroplast genome evolution seems to have evolved in a punctuated fashion, with episodes of loss involving suites of genes or tRNAs followed by stabilization of gene content in major clades. Nearly all species of Cuscuta retain some

  17. Systematics and plastid genome evolution of the cryptically photosynthetic parasitic plant genus Cuscuta (Convolvulaceae).

    Science.gov (United States)

    McNeal, Joel R; Arumugunathan, Kathiravetpilla; Kuehl, Jennifer V; Boore, Jeffrey L; Depamphilis, Claude W

    2007-12-13

    The genus Cuscuta L. (Convolvulaceae), commonly known as dodders, are epiphytic vines that invade the stems of their host with haustorial feeding structures at the points of contact. Although they lack expanded leaves, some species are noticeably chlorophyllous, especially as seedlings and in maturing fruits. Some species are reported as crop pests of worldwide distribution, whereas others are extremely rare and have local distributions and apparent niche specificity. A strong phylogenetic framework for this large genus is essential to understand the interesting ecological, morphological and molecular phenomena that occur within these parasites in an evolutionary context. Here we present a well-supported phylogeny of Cuscuta using sequences of the nuclear ribosomal internal transcribed spacer and plastid rps2, rbcL and matK from representatives across most of the taxonomic diversity of the genus. We use the phylogeny to interpret morphological and plastid genome evolution within the genus. At least three currently recognized taxonomic sections are not monophyletic and subgenus Cuscuta is unequivocally paraphyletic. Plastid genes are extremely variable with regards to evolutionary constraint, with rbcL exhibiting even higher levels of purifying selection in Cuscuta than photosynthetic relatives. Nuclear genome size is highly variable within Cuscuta, particularly within subgenus Grammica, and in some cases may indicate the existence of cryptic species in this large clade of morphologically similar species. Some morphological characters traditionally used to define major taxonomic splits within Cuscuta are homoplastic and are of limited use in defining true evolutionary groups. Chloroplast genome evolution seems to have evolved in a punctuated fashion, with episodes of loss involving suites of genes or tRNAs followed by stabilization of gene content in major clades. Nearly all species of Cuscuta retain some photosynthetic ability, most likely for nutrient

  18. The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence.

    Science.gov (United States)

    Eves-van den Akker, Sebastian; Laetsch, Dominik R; Thorpe, Peter; Lilley, Catherine J; Danchin, Etienne G J; Da Rocha, Martine; Rancurel, Corinne; Holroyd, Nancy E; Cotton, James A; Szitenberg, Amir; Grenier, Eric; Montarry, Josselin; Mimee, Benjamin; Duceppe, Marc-Olivier; Boyes, Ian; Marvin, Jessica M C; Jones, Laura M; Yusup, Hazijah B; Lafond-Lapalme, Joël; Esquibet, Magali; Sabeh, Michael; Rott, Michael; Overmars, Hein; Finkers-Tomczak, Anna; Smant, Geert; Koutsovoulos, Georgios; Blok, Vivian; Mantelin, Sophie; Cock, Peter J A; Phillips, Wendy; Henrissat, Bernard; Urwin, Peter E; Blaxter, Mark; Jones, John T

    2016-06-10

    The yellow potato cyst nematode, Globodera rostochiensis, is a devastating plant pathogen of global economic importance. This biotrophic parasite secretes effectors from pharyngeal glands, some of which were acquired by horizontal gene transfer, to manipulate host processes and promote parasitism. G. rostochiensis is classified into pathotypes with different plant resistance-breaking phenotypes. We generate a high quality genome assembly for G. rostochiensis pathotype Ro1, identify putative effectors and horizontal gene transfer events, map gene expression through the life cycle focusing on key parasitic transitions and sequence the genomes of eight populations including four additional pathotypes to identify variation. Horizontal gene transfer contributes 3.5 % of the predicted genes, of which approximately 8.5 % are deployed as effectors. Over one-third of all effector genes are clustered in 21 putative 'effector islands' in the genome. We identify a dorsal gland promoter element motif (termed DOG Box) present upstream in representatives from 26 out of 28 dorsal gland effector families, and predict a putative effector superset associated with this motif. We validate gland cell expression in two novel genes by in situ hybridisation and catalogue dorsal gland promoter element-containing effectors from available cyst nematode genomes. Comparison of effector diversity between pathotypes highlights correlation with plant resistance-breaking. These G. rostochiensis genome resources will facilitate major advances in understanding nematode plant-parasitism. Dorsal gland promoter element-containing effectors are at the front line of the evolutionary arms race between plant and parasite and the ability to predict gland cell expression a priori promises rapid advances in understanding their roles and mechanisms of action.

  19. In-depth comparative analysis of malaria parasite genomes reveals protein-coding genes linked to human disease in Plasmodium falciparum genome.

    Science.gov (United States)

    Liu, Xuewu; Wang, Yuanyuan; Liang, Jiao; Wang, Luojun; Qin, Na; Zhao, Ya; Zhao, Gang

    2018-05-02

    Plasmodium falciparum is the most virulent malaria parasite capable of parasitizing human erythrocytes. The identification of genes related to this capability can enhance our understanding of the molecular mechanisms underlying human malaria and lead to the development of new therapeutic strategies for malaria control. With the availability of several malaria parasite genome sequences, performing computational analysis is now a practical strategy to identify genes contributing to this disease. Here, we developed and used a virtual genome method to assign 33,314 genes from three human malaria parasites, namely, P. falciparum, P. knowlesi and P. vivax, and three rodent malaria parasites, namely, P. berghei, P. chabaudi and P. yoelii, to 4605 clusters. Each cluster consisted of genes whose protein sequences were significantly similar and was considered as a virtual gene. Comparing the enriched values of all clusters in human malaria parasites with those in rodent malaria parasites revealed 115 P. falciparum genes putatively responsible for parasitizing human erythrocytes. These genes are mainly located in the chromosome internal regions and participate in many biological processes, including membrane protein trafficking and thiamine biosynthesis. Meanwhile, 289 P. berghei genes were included in the rodent parasite-enriched clusters. Most are located in subtelomeric regions and encode erythrocyte surface proteins. Comparing cluster values in P. falciparum with those in P. vivax and P. knowlesi revealed 493 candidate genes linked to virulence. Some of them encode proteins present on the erythrocyte surface and participate in cytoadhesion, virulence factor trafficking, or erythrocyte invasion, but many genes with unknown function were also identified. Cerebral malaria is characterized by accumulation of infected erythrocytes at trophozoite stage in brain microvascular. To discover cerebral malaria-related genes, fast Fourier transformation (FFT) was introduced to extract

  20. Genome sequencing of chimpanzee malaria parasites reveals possible pathways of adaptation to human hosts

    KAUST Repository

    Otto, Thomas D.; Rayner, Julian C.; Bö hme, Ulrike; Pain, Arnab; Spottiswoode, Natasha; Sanders, Mandy; Quail, Michael; Ollomo, Benjamin; Renaud, Franç ois; Thomas, Alan W.; Prugnolle, Franck; Conway, David J.; Newbold, Chris; Berriman, Matthew

    2014-01-01

    related chimpanzee parasite species P. reichenowi, and obtaining partial sequence data from a more distantly related chimpanzee parasite (P. gaboni). The close relationship between P. reichenowi and P. falciparum is emphasized by almost complete

  1. A highly rearranged mitochondrial genome in Nycteria parasites (Haemosporidia) from bats

    OpenAIRE

    Karadjian , Gregory; Hassanin , Alexandre; Saintpierre , Benjamin; Gembu Tungaluna , Guy-Crispin; Ariey , Frederic; Ayala , Francisco J.; Landau , Irene; Duval , Linda

    2016-01-01

    International audience; Haemosporidia parasites have mostly and abundantly been described using mitochondrial genes, and in particular cytochrome b (cytb). Failure to amplify the mitochondrial cytb gene of Nycteria parasites isolated from Nycteridae bats has been recently reported. Bats are hosts to a diverse and profuse array of Haemosporidia parasites that remain largely unstudied. There is a need to obtain more molecular data from chiropteran parasites. Such data would help to better under...

  2. The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode

    KAUST Repository

    Cotton, James A; Lilley, Catherine J; Jones, Laura M; Kikuchi, Taisei; Reid, Adam J; Thorpe, Peter; Tsai, Isheng J; Beasley, Helen; Blok, Vivian; Cock, Peter J A; den Akker, Sebastian Eves-van; Holroyd, Nancy; Hunt, Martin; Mantelin, Sophie; Naghra, Hardeep; Pain, Arnab; Palomares-Rius, Juan E; Zarowiecki, Magdalena; Berriman, Matthew; Jones, John T; Urwin, Peter E

    2014-01-01

    -knot nematodes are the two most important plant parasitic nematode groups and together represent a global threat to food security. Results: We present the complete genome sequence of G. pallida, together with transcriptomic data from most of the nematode life

  3. The role of parasite-driven selection in shaping landscape genomic structure in red grouse (Lagopus lagopus scotica).

    Science.gov (United States)

    Wenzel, Marius A; Douglas, Alex; James, Marianne C; Redpath, Steve M; Piertney, Stuart B

    2016-01-01

    Landscape genomics promises to provide novel insights into how neutral and adaptive processes shape genome-wide variation within and among populations. However, there has been little emphasis on examining whether individual-based phenotype-genotype relationships derived from approaches such as genome-wide association (GWAS) manifest themselves as a population-level signature of selection in a landscape context. The two may prove irreconcilable as individual-level patterns become diluted by high levels of gene flow and complex phenotypic or environmental heterogeneity. We illustrate this issue with a case study that examines the role of the highly prevalent gastrointestinal nematode Trichostrongylus tenuis in shaping genomic signatures of selection in red grouse (Lagopus lagopus scotica). Individual-level GWAS involving 384 SNPs has previously identified five SNPs that explain variation in T. tenuis burden. Here, we examine whether these same SNPs display population-level relationships between T. tenuis burden and genetic structure across a small-scale landscape of 21 sites with heterogeneous parasite pressure. Moreover, we identify adaptive SNPs showing signatures of directional selection using F(ST) outlier analysis and relate population- and individual-level patterns of multilocus neutral and adaptive genetic structure to T. tenuis burden. The five candidate SNPs for parasite-driven selection were neither associated with T. tenuis burden on a population level, nor under directional selection. Similarly, there was no evidence of parasite-driven selection in SNPs identified as candidates for directional selection. We discuss these results in the context of red grouse ecology and highlight the broader consequences for the utility of landscape genomics approaches for identifying signatures of selection. © 2015 John Wiley & Sons Ltd.

  4. Genome content analysis yields new insights into the relationship between the human malaria parasite Plasmodium falciparum and its anopheline vectors.

    Science.gov (United States)

    Oppenheim, Sara J; Rosenfeld, Jeffrey A; DeSalle, Rob

    2017-02-27

    The persistent and growing gap between the availability of sequenced genomes and the ability to assign functions to sequenced genes led us to explore ways to maximize the information content of automated annotation for studies of anopheline mosquitos. Specifically, we use genome content analysis of a large number of previously sequenced anopheline mosquitos to follow the loss and gain of protein families over the evolutionary history of this group. The importance of this endeavor lies in the potential for comparative genomic studies between Anopheles and closely related non-vector species to reveal ancestral genome content dynamics involved in vector competence. In addition, comparisons within Anopheles could identify genome content changes responsible for variation in the vectorial capacity of this family of important parasite vectors. The competence and capacity of P. falciparum vectors do not appear to be phylogenetically constrained within the Anophelinae. Instead, using ancestral reconstruction methods, we suggest that a previously unexamined component of vector biology, anopheline nucleotide metabolism, may contribute to the unique status of anophelines as P. falciparum vectors. While the fitness effects of nucleotide co-option by P. falciparum parasites on their anopheline hosts are not yet known, our results suggest that anopheline genome content may be responding to selection pressure from P. falciparum. Whether this response is defensive, in an attempt to redress improper nucleotide balance resulting from P. falciparum infection, or perhaps symbiotic, resulting from an as-yet-unknown mutualism between anophelines and P. falciparum, is an open question that deserves further study. Clearly, there is a wealth of functional information to be gained from detailed manual genome annotation, yet the rapid increase in the number of available sequences means that most researchers will not have the time or resources to manually annotate all the sequence data they

  5. Comparative genomics of the Apicomplexan parasites Toxoplasma gondii and Neospora caninum 

    DEFF Research Database (Denmark)

    Reid, Adam James; Vermont, Sarah J.; Cotton, James A.

    2012-01-01

    Coccidian parasites have a major impact on human and animal health world-wide and are among the most successful and widespread parasitic protozoa. They include Neospora caninum which is a leading cause of abortion in cattle and one of its nearest relatives, Toxoplasma gondii. Despite its close...... almost exclusively on molecules which control the interaction of the parasite with the host cell. We show that some secreted invasion-related proteins and surface genes which are known to control virulence and host cell interactions in Toxoplasma are dramatically altered in their expression...... and functionality in Neospora and propose that evolution of these genes may underpin the ecological niches inhabited by coccidian parasites....

  6. Long- and short-term selective forces on malaria parasite genomes

    KAUST Repository

    Nygaard, Sanne; Braunstein, Alexander; Malsen, Gareth; Van Dongen, Stijn; Gardner, Paul P.; Krogh, Anders; Otto, Thomas D.; Pain, Arnab; Berriman, Matthew; McAuliffe, Jon; Dermitzakis, Emmanouil T.; Jeffares, Daniel C.

    2010-01-01

    of these genomes. Although evolutionary processes have a significant impact on malaria control, the selective pressures within Plasmodium genomes are poorly understood, particularly in the non-protein-coding portion of the genome. We use evolutionary methods

  7. Novel type of linear mitochondrial genomes with dual flip-flop inversion system in apicomplexan parasites, Babesia microti and Babesia rodhaini

    Directory of Open Access Journals (Sweden)

    Hikosaka Kenji

    2012-11-01

    Full Text Available Abstract Background Mitochondrial (mt genomes vary considerably in size, structure and gene content. The mt genomes of the phylum Apicomplexa, which includes important human pathogens such as the malaria parasite Plasmodium, also show marked diversity of structure. Plasmodium has a concatenated linear mt genome of the smallest size (6-kb; Babesia and Theileria have a linear monomeric mt genome (6.5-kb to 8.2-kb with terminal inverted repeats; Eimeria, which is distantly related to Plasmodium and Babesia/Theileria, possesses a mt genome (6.2-kb with a concatemeric form similar to that of Plasmodium; Cryptosporidium, the earliest branching lineage within the phylum Apicomplexa, has no mt genome. We are interested in the evolutionary origin of linear mt genomes of Babesia/Theileria, and have investigated mt genome structures in members of archaeopiroplasmid, a lineage branched off earlier from Babesia/Theileria. Results The complete mt genomes of archaeopiroplasmid parasites, Babesia microti and Babesia rodhaini, were sequenced. The mt genomes of B. microti (11.1-kb and B. rodhaini (6.9-kb possess two pairs of unique inverted repeats, IR-A and IR-B. Flip-flop inversions between two IR-As and between two IR-Bs appear to generate four distinct genome structures that are present at an equi-molar ratio. An individual parasite contained multiple mt genome structures, with 20 copies and 2 – 3 copies per haploid nuclear genome in B. microti and B. rodhaini, respectively. Conclusion We found a novel linear monomeric mt genome structure of B. microti and B. rhodhaini equipped with dual flip-flop inversion system, by which four distinct genome structures are readily generated. To our knowledge, this study is the first to report the presence of two pairs of distinct IR sequences within a monomeric linear mt genome. The present finding provides insight into further understanding of evolution of mt genome structure.

  8. Assembled Plastid and Mitochondrial Genomes, as well as Nuclear Genes, Place the Parasite Family Cynomoriaceae in the Saxifragales.

    Science.gov (United States)

    Bellot, Sidonie; Cusimano, Natalie; Luo, Shixiao; Sun, Guiling; Zarre, Shahin; Gröger, Andreas; Temsch, Eva; Renner, Susanne S

    2016-08-03

    Cynomoriaceae, one of the last unplaced families of flowering plants, comprise one or two species or subspecies of root parasites that occur from the Mediterranean to the Gobi Desert. Using Illumina sequencing, we assembled the mitochondrial and plastid genomes as well as some nuclear genes of a Cynomorium specimen from Italy. Selected genes were also obtained by Sanger sequencing from individuals collected in China and Iran, resulting in matrices of 33 mitochondrial, 6 nuclear, and 14 plastid genes and rDNAs enlarged to include a representative angiosperm taxon sampling based on data available in GenBank. We also compiled a new geographic map to discern possible discontinuities in the parasites' occurrence. Cynomorium has large genomes of 13.70-13.61 (Italy) to 13.95-13.76 pg (China). Its mitochondrial genome consists of up to 49 circular subgenomes and has an overall gene content similar to that of photosynthetic angiosperms, while its plastome retains only 27 of the normally 116 genes. Nuclear, plastid and mitochondrial phylogenies place Cynomoriaceae in Saxifragales, and we found evidence for several horizontal gene transfers from different hosts, as well as intracellular gene transfers. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  9. The Paramecium germline genome provides a niche for intragenic parasitic DNA: evolutionary dynamics of internal eliminated sequences.

    Science.gov (United States)

    Arnaiz, Olivier; Mathy, Nathalie; Baudry, Céline; Malinsky, Sophie; Aury, Jean-Marc; Denby Wilkes, Cyril; Garnier, Olivier; Labadie, Karine; Lauderdale, Benjamin E; Le Mouël, Anne; Marmignon, Antoine; Nowacki, Mariusz; Poulain, Julie; Prajer, Malgorzata; Wincker, Patrick; Meyer, Eric; Duharcourt, Sandra; Duret, Laurent; Bétermier, Mireille; Sperling, Linda

    2012-01-01

    Insertions of parasitic DNA within coding sequences are usually deleterious and are generally counter-selected during evolution. Thanks to nuclear dimorphism, ciliates provide unique models to study the fate of such insertions. Their germline genome undergoes extensive rearrangements during development of a new somatic macronucleus from the germline micronucleus following sexual events. In Paramecium, these rearrangements include precise excision of unique-copy Internal Eliminated Sequences (IES) from the somatic DNA, requiring the activity of a domesticated piggyBac transposase, PiggyMac. We have sequenced Paramecium tetraurelia germline DNA, establishing a genome-wide catalogue of -45,000 IESs, in order to gain insight into their evolutionary origin and excision mechanism. We obtained direct evidence that PiggyMac is required for excision of all IESs. Homology with known P. tetraurelia Tc1/mariner transposons, described here, indicates that at least a fraction of IESs derive from these elements. Most IES insertions occurred before a recent whole-genome duplication that preceded diversification of the P. aurelia species complex, but IES invasion of the Paramecium genome appears to be an ongoing process. Once inserted, IESs decay rapidly by accumulation of deletions and point substitutions. Over 90% of the IESs are shorter than 150 bp and present a remarkable size distribution with a -10 bp periodicity, corresponding to the helical repeat of double-stranded DNA and suggesting DNA loop formation during assembly of a transpososome-like excision complex. IESs are equally frequent within and between coding sequences; however, excision is not 100% efficient and there is selective pressure against IES insertions, in particular within highly expressed genes. We discuss the possibility that ancient domestication of a piggyBac transposase favored subsequent propagation of transposons throughout the germline by allowing insertions in coding sequences, a fraction of the

  10. The Paramecium germline genome provides a niche for intragenic parasitic DNA: evolutionary dynamics of internal eliminated sequences.

    Directory of Open Access Journals (Sweden)

    Olivier Arnaiz

    Full Text Available Insertions of parasitic DNA within coding sequences are usually deleterious and are generally counter-selected during evolution. Thanks to nuclear dimorphism, ciliates provide unique models to study the fate of such insertions. Their germline genome undergoes extensive rearrangements during development of a new somatic macronucleus from the germline micronucleus following sexual events. In Paramecium, these rearrangements include precise excision of unique-copy Internal Eliminated Sequences (IES from the somatic DNA, requiring the activity of a domesticated piggyBac transposase, PiggyMac. We have sequenced Paramecium tetraurelia germline DNA, establishing a genome-wide catalogue of -45,000 IESs, in order to gain insight into their evolutionary origin and excision mechanism. We obtained direct evidence that PiggyMac is required for excision of all IESs. Homology with known P. tetraurelia Tc1/mariner transposons, described here, indicates that at least a fraction of IESs derive from these elements. Most IES insertions occurred before a recent whole-genome duplication that preceded diversification of the P. aurelia species complex, but IES invasion of the Paramecium genome appears to be an ongoing process. Once inserted, IESs decay rapidly by accumulation of deletions and point substitutions. Over 90% of the IESs are shorter than 150 bp and present a remarkable size distribution with a -10 bp periodicity, corresponding to the helical repeat of double-stranded DNA and suggesting DNA loop formation during assembly of a transpososome-like excision complex. IESs are equally frequent within and between coding sequences; however, excision is not 100% efficient and there is selective pressure against IES insertions, in particular within highly expressed genes. We discuss the possibility that ancient domestication of a piggyBac transposase favored subsequent propagation of transposons throughout the germline by allowing insertions in coding sequences, a

  11. Complete avian malaria parasite genomes reveal features associated with lineage-specific evolution in birds and mammals

    Science.gov (United States)

    Böhme, Ulrike; Otto, Thomas D.; Cotton, James A.; Steinbiss, Sascha; Sanders, Mandy; Oyola, Samuel O.; Nicot, Antoine; Gandon, Sylvain; Patra, Kailash P.; Herd, Colin; Bushell, Ellen; Modrzynska, Katarzyna K.; Billker, Oliver; Vinetz, Joseph M.; Rivero, Ana; Newbold, Chris I.; Berriman, Matthew

    2018-01-01

    Avian malaria parasites are prevalent around the world and infect a wide diversity of bird species. Here, we report the sequencing and analysis of high-quality draft genome sequences for two avian malaria species, Plasmodium relictum and Plasmodium gallinaceum. We identify 50 genes that are specific to avian malaria, located in an otherwise conserved core of the genome that shares gene synteny with all other sequenced malaria genomes. Phylogenetic analysis suggests that the avian malaria species form an outgroup to the mammalian Plasmodium species, and using amino acid divergence between species, we estimate the avian- and mammalian-infective lineages diverged in the order of 10 million years ago. Consistent with their phylogenetic position, we identify orthologs of genes that had previously appeared to be restricted to the clades of parasites containing Plasmodium falciparum and Plasmodium vivax, the species with the greatest impact on human health. From these orthologs, we explore differential diversifying selection across the genus and show that the avian lineage is remarkable in the extent to which invasion-related genes are evolving. The subtelomeres of the P. relictum and P. gallinaceum genomes contain several novel gene families, including an expanded surf multigene family. We also identify an expansion of reticulocyte binding protein homologs in P. relictum, and within these proteins, we detect distinct regions that are specific to nonhuman primate, humans, rodent, and avian hosts. For the first time in the Plasmodium lineage, we find evidence of transposable elements, including several hundred fragments of LTR-retrotransposons in both species and an apparently complete LTR-retrotransposon in the genome of P. gallinaceum. PMID:29500236

  12. Genome-wide diversity and differentiation in New World populations of the human malaria parasite Plasmodium vivax.

    Directory of Open Access Journals (Sweden)

    Thais C de Oliveira

    2017-07-01

    Full Text Available The Americas were the last continent colonized by humans carrying malaria parasites. Plasmodium falciparum from the New World shows very little genetic diversity and greater linkage disequilibrium, compared with its African counterparts, and is clearly subdivided into local, highly divergent populations. However, limited available data have revealed extensive genetic diversity in American populations of another major human malaria parasite, P. vivax.We used an improved sample preparation strategy and next-generation sequencing to characterize 9 high-quality P. vivax genome sequences from northwestern Brazil. These new data were compared with publicly available sequences from recently sampled clinical P. vivax isolates from Brazil (BRA, total n = 11 sequences, Peru (PER, n = 23, Colombia (COL, n = 31, and Mexico (MEX, n = 19.We found that New World populations of P. vivax are as diverse (nucleotide diversity π between 5.2 × 10-4 and 6.2 × 10-4 as P. vivax populations from Southeast Asia, where malaria transmission is substantially more intense. They display several non-synonymous nucleotide substitutions (some of them previously undescribed in genes known or suspected to be involved in antimalarial drug resistance, such as dhfr, dhps, mdr1, mrp1, and mrp-2, but not in the chloroquine resistance transporter ortholog (crt-o gene. Moreover, P. vivax in the Americas is much less geographically substructured than local P. falciparum populations, with relatively little between-population genome-wide differentiation (pairwise FST values ranging between 0.025 and 0.092. Finally, P. vivax populations show a rapid decline in linkage disequilibrium with increasing distance between pairs of polymorphic sites, consistent with very frequent outcrossing. We hypothesize that the high diversity of present-day P. vivax lineages in the Americas originated from successive migratory waves and subsequent admixture between parasite lineages from geographically

  13. Genome-wide diversity and differentiation in New World populations of the human malaria parasite Plasmodium vivax.

    Science.gov (United States)

    de Oliveira, Thais C; Rodrigues, Priscila T; Menezes, Maria José; Gonçalves-Lopes, Raquel M; Bastos, Melissa S; Lima, Nathália F; Barbosa, Susana; Gerber, Alexandra L; Loss de Morais, Guilherme; Berná, Luisa; Phelan, Jody; Robello, Carlos; de Vasconcelos, Ana Tereza R; Alves, João Marcelo P; Ferreira, Marcelo U

    2017-07-01

    The Americas were the last continent colonized by humans carrying malaria parasites. Plasmodium falciparum from the New World shows very little genetic diversity and greater linkage disequilibrium, compared with its African counterparts, and is clearly subdivided into local, highly divergent populations. However, limited available data have revealed extensive genetic diversity in American populations of another major human malaria parasite, P. vivax. We used an improved sample preparation strategy and next-generation sequencing to characterize 9 high-quality P. vivax genome sequences from northwestern Brazil. These new data were compared with publicly available sequences from recently sampled clinical P. vivax isolates from Brazil (BRA, total n = 11 sequences), Peru (PER, n = 23), Colombia (COL, n = 31), and Mexico (MEX, n = 19). We found that New World populations of P. vivax are as diverse (nucleotide diversity π between 5.2 × 10-4 and 6.2 × 10-4) as P. vivax populations from Southeast Asia, where malaria transmission is substantially more intense. They display several non-synonymous nucleotide substitutions (some of them previously undescribed) in genes known or suspected to be involved in antimalarial drug resistance, such as dhfr, dhps, mdr1, mrp1, and mrp-2, but not in the chloroquine resistance transporter ortholog (crt-o) gene. Moreover, P. vivax in the Americas is much less geographically substructured than local P. falciparum populations, with relatively little between-population genome-wide differentiation (pairwise FST values ranging between 0.025 and 0.092). Finally, P. vivax populations show a rapid decline in linkage disequilibrium with increasing distance between pairs of polymorphic sites, consistent with very frequent outcrossing. We hypothesize that the high diversity of present-day P. vivax lineages in the Americas originated from successive migratory waves and subsequent admixture between parasite lineages from geographically diverse sites

  14. Genome-wide diversity and differentiation in New World populations of the human malaria parasite Plasmodium vivax

    Science.gov (United States)

    de Oliveira, Thais C.; Rodrigues, Priscila T.; Menezes, Maria José; Gonçalves-Lopes, Raquel M.; Bastos, Melissa S.; Lima, Nathália F.; Barbosa, Susana; Gerber, Alexandra L.; Loss de Morais, Guilherme; Berná, Luisa; Phelan, Jody; Robello, Carlos; de Vasconcelos, Ana Tereza R.

    2017-01-01

    Background The Americas were the last continent colonized by humans carrying malaria parasites. Plasmodium falciparum from the New World shows very little genetic diversity and greater linkage disequilibrium, compared with its African counterparts, and is clearly subdivided into local, highly divergent populations. However, limited available data have revealed extensive genetic diversity in American populations of another major human malaria parasite, P. vivax. Methods We used an improved sample preparation strategy and next-generation sequencing to characterize 9 high-quality P. vivax genome sequences from northwestern Brazil. These new data were compared with publicly available sequences from recently sampled clinical P. vivax isolates from Brazil (BRA, total n = 11 sequences), Peru (PER, n = 23), Colombia (COL, n = 31), and Mexico (MEX, n = 19). Principal findings/Conclusions We found that New World populations of P. vivax are as diverse (nucleotide diversity π between 5.2 × 10−4 and 6.2 × 10−4) as P. vivax populations from Southeast Asia, where malaria transmission is substantially more intense. They display several non-synonymous nucleotide substitutions (some of them previously undescribed) in genes known or suspected to be involved in antimalarial drug resistance, such as dhfr, dhps, mdr1, mrp1, and mrp-2, but not in the chloroquine resistance transporter ortholog (crt-o) gene. Moreover, P. vivax in the Americas is much less geographically substructured than local P. falciparum populations, with relatively little between-population genome-wide differentiation (pairwise FST values ranging between 0.025 and 0.092). Finally, P. vivax populations show a rapid decline in linkage disequilibrium with increasing distance between pairs of polymorphic sites, consistent with very frequent outcrossing. We hypothesize that the high diversity of present-day P. vivax lineages in the Americas originated from successive migratory waves and subsequent admixture between

  15. Large differences in the genome organization of different plant Trypanosomatid parasites (Phytomonas spp.) reveal wide evolutionary divergences between taxa.

    Science.gov (United States)

    Marín, C; Dollet, M; Pagès, M; Bastien, P

    2009-03-01

    All currently known plant trypanosomes have been grouped in the genus Phytomonas spp., although they can differ greatly in terms of both their biological properties and effects upon the host. Those parasitizing the phloem sap are specifically associated with lethal syndromes in Latin America, such as, phloem necrosis of coffee, 'Hartrot' of coconut and 'Marchitez sorpresiva' of oil palm, that inflict considerable economic losses in endemic countries. The genomic organization of one group of Phytomonas (D) considered as representative of the genus has been published previously. The present work presents the genomic structure of two representative isolates from the pathogenic phloem-restricted group (H) of Phytomonas, analyzed by pulsed field gel electrophoresis followed by hybridization with chromosome-specific DNA markers. It came as a surprise to observe an extremely different genomic organization in this group as compared with that of group D. Most notably, the chromosome number is 7 in this group (with a genome size of 10 Mb) versus 21 in the group D (totalling 25 Mb). These data unravel an unsuspected genomic diversity within plant trypanosomatids, that may justify a further debate about their division into different genera.

  16. A comprehensive evaluation of rodent malaria parasite genomes and gene expression

    KAUST Repository

    Otto, Thomas D; Bö hme, Ulrike; Jackson, Andrew P; Hunt, Martin; Franke-Fayard, Blandine; Hoeijmakers, Wieteke A M; Religa, Agnieszka A; Robertson, Lauren; Sanders, Mandy; Ogun, Solabomi A; Cunningham, Deirdre; Erhart, Annette; Billker, Oliver; Khan, Shahid M; Stunnenberg, Hendrik G; Langhorne, Jean; Holder, Anthony A; Waters, Andrew P; Newbold, Chris I; Pain, Arnab; Berriman, Matthew; Janse, Chris J

    2014-01-01

    Plasmodium biology. Genotypic diversity between P. chabaudi isolates makes this species an excellent parasite to study genotype-phenotype relationships. The improved classification of multigene families will enhance studies on the role of (variant) exported

  17. Role of transposon-derived small RNAs in the interplay between genomes and parasitic DNA in rice.

    Directory of Open Access Journals (Sweden)

    Misuzu Nosaka

    2012-09-01

    Full Text Available RNA silencing is a defense system against "genomic parasites" such as transposable elements (TE, which are potentially harmful to host genomes. In plants, transcripts from TEs induce production of double-stranded RNAs (dsRNAs and are processed into small RNAs (small interfering RNAs, siRNAs that suppress TEs by RNA-directed DNA methylation. Thus, the majority of TEs are epigenetically silenced. On the other hand, most of the eukaryotic genome is composed of TEs and their remnants, suggesting that TEs have evolved countermeasures against host-mediated silencing. Under some circumstances, TEs can become active and increase in copy number. Knowledge is accumulating on the mechanisms of TE silencing by the host; however, the mechanisms by which TEs counteract silencing are poorly understood. Here, we show that a class of TEs in rice produces a microRNA (miRNA to suppress host silencing. Members of the microRNA820 (miR820 gene family are located within CACTA DNA transposons in rice and target a de novo DNA methyltransferase gene, OsDRM2, one of the components of epigenetic silencing. We confirmed that miR820 negatively regulates the expression of OsDRM2. In addition, we found that expression levels of various TEs are increased quite sensitively in response to decreased OsDRM2 expression and DNA methylation at TE loci. Furthermore, we found that the nucleotide sequence of miR820 and its recognition site within the target gene in some Oryza species have co-evolved to maintain their base-pairing ability. The co-evolution of these sequences provides evidence for the functionality of this regulation. Our results demonstrate how parasitic elements in the genome escape the host's defense machinery. Furthermore, our analysis of the regulation of OsDRM2 by miR820 sheds light on the action of transposon-derived small RNAs, not only as a defense mechanism for host genomes but also as a regulator of interactions between hosts and their parasitic elements.

  18. Genomic characterization and phylogenetic position of two new species in Rhabdoviridae infecting the parasitic copepod, salmon louse (Lepeophtheirus salmonis).

    Science.gov (United States)

    Økland, Arnfinn Lodden; Nylund, Are; Øvergård, Aina-Cathrine; Blindheim, Steffen; Watanabe, Kuninori; Grotmol, Sindre; Arnesen, Carl-Erik; Plarre, Heidrun

    2014-01-01

    Several new viruses have emerged during farming of salmonids in the North Atlantic causing large losses to the industry. Still the blood feeding copepod parasite, Lepeophtheirus salmonis, remains the major challenge for the industry. Histological examinations of this parasite have revealed the presence of several virus-like particles including some with morphologies similar to rhabdoviruses. This study is the first description of the genome and target tissues of two new species of rhabdoviruses associated with pathology in the salmon louse. Salmon lice were collected at different Atlantic salmon (Salmo salar) farming sites on the west coast of Norway and prepared for histology, transmission electron microscopy and Illumina sequencing of the complete RNA extracted from these lice. The nearly complete genomes, around 11,600 nucleotides encoding the five typical rhabdovirus genes N, P, M, G and L, of two new species were obtained. The genome sequences, the putative protein sequences, and predicted transcription strategies for the two viruses are presented. Phylogenetic analyses of the putative N and L proteins indicated closest similarity to the Sigmavirus/Dimarhabdoviruses cluster, however, the genomes of both new viruses are significantly diverged with no close affinity to any of the existing rhabdovirus genera. In situ hybridization, targeting the N protein genes, showed that the viruses were present in the same glandular tissues as the observed rhabdovirus-like particles. Both viruses were present in all developmental stages of the salmon louse, and associated with necrosis of glandular tissues in adult lice. As the two viruses were present in eggs and free-living planktonic stages of the salmon louse vertical, transmission of the viruses are suggested. The tissues of the lice host, Atlantic salmon, with the exception of skin at the attachment site for the salmon louse chalimi stages, were negative for these two viruses.

  19. Genomic Characterization and Phylogenetic Position of Two New Species in Rhabdoviridae Infecting the Parasitic Copepod, Salmon Louse (Lepeophtheirus salmonis)

    Science.gov (United States)

    Økland, Arnfinn Lodden; Nylund, Are; Øvergård, Aina-Cathrine; Blindheim, Steffen; Watanabe, Kuninori; Grotmol, Sindre; Arnesen, Carl-Erik; Plarre, Heidrun

    2014-01-01

    Several new viruses have emerged during farming of salmonids in the North Atlantic causing large losses to the industry. Still the blood feeding copepod parasite, Lepeophtheirus salmonis, remains the major challenge for the industry. Histological examinations of this parasite have revealed the presence of several virus-like particles including some with morphologies similar to rhabdoviruses. This study is the first description of the genome and target tissues of two new species of rhabdoviruses associated with pathology in the salmon louse. Salmon lice were collected at different Atlantic salmon (Salmo salar) farming sites on the west coast of Norway and prepared for histology, transmission electron microscopy and Illumina sequencing of the complete RNA extracted from these lice. The nearly complete genomes, around 11 600 nucleotides encoding the five typical rhabdovirus genes N, P, M, G and L, of two new species were obtained. The genome sequences, the putative protein sequences, and predicted transcription strategies for the two viruses are presented. Phylogenetic analyses of the putative N and L proteins indicated closest similarity to the Sigmavirus/Dimarhabdoviruses cluster, however, the genomes of both new viruses are significantly diverged with no close affinity to any of the existing rhabdovirus genera. In situ hybridization, targeting the N protein genes, showed that the viruses were present in the same glandular tissues as the observed rhabdovirus-like particles. Both viruses were present in all developmental stages of the salmon louse, and associated with necrosis of glandular tissues in adult lice. As the two viruses were present in eggs and free-living planktonic stages of the salmon louse vertical, transmission of the viruses are suggested. The tissues of the lice host, Atlantic salmon, with the exception of skin at the attachment site for the salmon louse chalimi stages, were negative for these two viruses. PMID:25402203

  20. Genomic characterization and phylogenetic position of two new species in Rhabdoviridae infecting the parasitic copepod, salmon louse (Lepeophtheirus salmonis.

    Directory of Open Access Journals (Sweden)

    Arnfinn Lodden Økland

    Full Text Available Several new viruses have emerged during farming of salmonids in the North Atlantic causing large losses to the industry. Still the blood feeding copepod parasite, Lepeophtheirus salmonis, remains the major challenge for the industry. Histological examinations of this parasite have revealed the presence of several virus-like particles including some with morphologies similar to rhabdoviruses. This study is the first description of the genome and target tissues of two new species of rhabdoviruses associated with pathology in the salmon louse. Salmon lice were collected at different Atlantic salmon (Salmo salar farming sites on the west coast of Norway and prepared for histology, transmission electron microscopy and Illumina sequencing of the complete RNA extracted from these lice. The nearly complete genomes, around 11,600 nucleotides encoding the five typical rhabdovirus genes N, P, M, G and L, of two new species were obtained. The genome sequences, the putative protein sequences, and predicted transcription strategies for the two viruses are presented. Phylogenetic analyses of the putative N and L proteins indicated closest similarity to the Sigmavirus/Dimarhabdoviruses cluster, however, the genomes of both new viruses are significantly diverged with no close affinity to any of the existing rhabdovirus genera. In situ hybridization, targeting the N protein genes, showed that the viruses were present in the same glandular tissues as the observed rhabdovirus-like particles. Both viruses were present in all developmental stages of the salmon louse, and associated with necrosis of glandular tissues in adult lice. As the two viruses were present in eggs and free-living planktonic stages of the salmon louse vertical, transmission of the viruses are suggested. The tissues of the lice host, Atlantic salmon, with the exception of skin at the attachment site for the salmon louse chalimi stages, were negative for these two viruses.

  1. Asexual populations of the human malaria parasite, Plasmodium falciparum, use a two-step genomic strategy to acquire accurate, beneficial DNA amplifications.

    Directory of Open Access Journals (Sweden)

    Jennifer L Guler

    Full Text Available Malaria drug resistance contributes to up to a million annual deaths. Judicious deployment of new antimalarials and vaccines could benefit from an understanding of early molecular events that promote the evolution of parasites. Continuous in vitro challenge of Plasmodium falciparum parasites with a novel dihydroorotate dehydrogenase (DHODH inhibitor reproducibly selected for resistant parasites. Genome-wide analysis of independently-derived resistant clones revealed a two-step strategy to evolutionary success. Some haploid blood-stage parasites first survive antimalarial pressure through fortuitous DNA duplications that always included the DHODH gene. Independently-selected parasites had different sized amplification units but they were always flanked by distant A/T tracks. Higher level amplification and resistance was attained using a second, more efficient and more accurate, mechanism for head-to-tail expansion of the founder unit. This second homology-based process could faithfully tune DNA copy numbers in either direction, always retaining the unique DNA amplification sequence from the original A/T-mediated duplication for that parasite line. Pseudo-polyploidy at relevant genomic loci sets the stage for gaining additional mutations at the locus of interest. Overall, we reveal a population-based genomic strategy for mutagenesis that operates in human stages of P. falciparum to efficiently yield resistance-causing genetic changes at the correct locus in a successful parasite. Importantly, these founding events arise with precision; no other new amplifications are seen in the resistant haploid blood stage parasite. This minimizes the need for meiotic genetic cleansing that can only occur in sexual stage development of the parasite in mosquitoes.

  2. Evidence for suppression of immunity as a driver for genomic introgressions and host range expansion in races of Albugo candida, a generalist parasite

    DEFF Research Database (Denmark)

    McMullan, Mark; Gardiner, Anastasia; Bailey, Kate

    2015-01-01

    How generalist parasites with wide host ranges can evolve is a central question in parasite evolution. Albugo candida is an obligate biotrophic parasite that consists of many physiological races that each specialize on distinct Brassicaceae host species. By analyzing genome sequence assemblies...... by normally non-infecting races. This facilitates introgression and the exchange of effector repertoires, and may enable the evolution of novel races that can undergo clonal population expansion on new hosts. We discuss recent studies on hybridization in other eukaryotes such as yeast, Heliconius butterflies...

  3. Comparative genomics of the apicomplexan parasites Toxoplasma gondii and neospora caninum: Coccidia differing in host range and transmission strategy

    KAUST Repository

    Reid, Adam James

    2012-03-22

    Toxoplasma gondii is a zoonotic protozoan parasite which infects nearly one third of the human population and is found in an extraordinary range of vertebrate hosts. Its epidemiology depends heavily on horizontal transmission, especially between rodents and its definitive host, the cat. Neospora caninum is a recently discovered close relative of Toxoplasma, whose definitive host is the dog. Both species are tissue-dwelling Coccidia and members of the phylum Apicomplexa; they share many common features, but Neospora neither infects humans nor shares the same wide host range as Toxoplasma, rather it shows a striking preference for highly efficient vertical transmission in cattle. These species therefore provide a remarkable opportunity to investigate mechanisms of host restriction, transmission strategies, virulence and zoonotic potential. We sequenced the genome of N. caninum and transcriptomes of the invasive stage of both species, undertaking an extensive comparative genomics and transcriptomics analysis. We estimate that these organisms diverged from their common ancestor around 28 million years ago and find that both genomes and gene expression are remarkably conserved. However, in N. caninum we identified an unexpected expansion of surface antigen gene families and the divergence of secreted virulence factors, including rhoptry kinases. Specifically we show that the rhoptry kinase ROP18 is pseudogenised in N. caninum and that, as a possible consequence, Neospora is unable to phosphorylate host immunity-related GTPases, as Toxoplasma does. This defense strategy is thought to be key to virulence in Toxoplasma. We conclude that the ecological niches occupied by these species are influenced by a relatively small number of gene products which operate at the host-parasite interface and that the dominance of vertical transmission in N. caninum may be associated with the evolution of reduced virulence in this species.

  4. Draft genome sequence of the intestinal parasite Blastocystis subtype 4-isolate WR1

    NARCIS (Netherlands)

    Wawrzyniak, Ivan; Courtine, Damien; Osman, Marwan; Hubans-Pierlot, Christine; Cian, Amandine; Nourrisson, Céline; Chabe, Magali; Poirier, Philippe; Bart, Aldert; Polonais, Valérie; Delgado-Viscogliosi, Pilar; El Alaoui, Hicham; Belkorchia, Abdel; van Gool, Tom; Tan, Kevin S. W.; Ferreira, Stéphanie; Viscogliosi, Eric; Delbac, Frédéric

    2015-01-01

    (ST1-ST17) described to date. Only the whole genome of a human ST7 isolate was previously sequenced. Here we report the draft genome sequence of Blastocystis ST4-WR1 isolated from a laboratory rodent at Singapore. (C) 2015 The Authors. Published by Elsevier Inc

  5. Comparative genome-wide analysis and evolutionary history of haemoglobin-processing and haem detoxification enzymes in malarial parasites.

    Science.gov (United States)

    Ponsuwanna, Patrath; Kochakarn, Theerarat; Bunditvorapoom, Duangkamon; Kümpornsin, Krittikorn; Otto, Thomas D; Ridenour, Chase; Chotivanich, Kesinee; Wilairat, Prapon; White, Nicholas J; Miotto, Olivo; Chookajorn, Thanat

    2016-01-29

    Malaria parasites have evolved a series of intricate mechanisms to survive and propagate within host red blood cells. Intra-erythrocytic parasitism requires these organisms to digest haemoglobin and detoxify iron-bound haem. These tasks are executed by haemoglobin-specific proteases and haem biocrystallization factors that are components of a large multi-subunit complex. Since haemoglobin processing machineries are functionally and genetically linked to the modes of action and resistance mechanisms of several anti-malarial drugs, an understanding of their evolutionary history is important for drug development and drug resistance prevention. Maximum likelihood trees of genetic repertoires encoding haemoglobin processing machineries within Plasmodium species, and with the representatives of Apicomplexan species with various host tropisms, were created. Genetic variants were mapped onto existing three-dimensional structures. Genome-wide single nucleotide polymorphism data were used to analyse the selective pressure and the effect of these mutations at the structural level. Recent expansions in the falcipain and plasmepsin repertoires are unique to human malaria parasites especially in the Plasmodium falciparum and P. reichenowi lineage. Expansion of haemoglobin-specific plasmepsins occurred after the separation event of Plasmodium species, but the other members of the plasmepsin family were evolutionarily conserved with one copy for each sub-group in every Apicomplexan species. Haemoglobin-specific falcipains are separated from invasion-related falcipain, and their expansions within one specific locus arose independently in both P. falciparum and P. vivax lineages. Gene conversion between P. falciparum falcipain 2A and 2B was observed in artemisinin-resistant strains. Comparison between the numbers of non-synonymous and synonymous mutations suggests a strong selective pressure at falcipain and plasmepsin genes. The locations of amino acid changes from non

  6. Tsetse Fly Genome Breakthrough: The FAO and IAEA Crack the Code

    International Nuclear Information System (INIS)

    Dixit, Aabha

    2014-01-01

    With the breakthrough in sequencing the genome of the tsetse fly species Glossina morsitans in April 2014, another milestone has been achieved in helping to solve a problem that has had horrendous ramifications for Africa. Finding a solution to the havoc created by tsetse flies to livestock has been a major challenge for the combined scientific efforts of the IAEA and the Food and Agriculture Organization of the United Nations (FAO), as well as for the World Health Organization (WHO), which has focused on combating human sleeping sickness. Joint research over the past decades to block the spread of severe infection from tsetse flies resulted in the introduction by the FAO and IAEA of the environmentally friendly sterile insect technique (SIT), a biologically-based method for the management of key insect pests of agricultural, medical and veterinary importance. A form of insect birth control, the SIT involves releasing mass-bred male flies that have been sterilized by low doses of radiation into infested areas, where they mate with wild females. These do not produce offspring and, as a result, the technique can suppress and, if applied systematically on an area-wide basis, eventually eradicate populations of wild flies. The newly acquired knowledge of the tsetse fly genome provides a wealth of information for the improvement of the entire SIT package and can help unravel interactions between tsetse flies, symbionts and trypanosomes. The decoding of the genome was detailed in a press release issued by the IAEA on 24 April 2014 entitled Tsetse Fly Genome Breakthrough Brings Hope for African Farmers. Tsetse flies were successfully eradicated in 1997 from the Tanzanian island of Zanzibar using the SIT. Ethiopia and Senegal are making significant progress in infested areas with the same method. The FAO and IAEA are helping 14 countries control tsetse populations through applying area-wide integrated pest management approaches

  7. Genome and transcriptome studies of the protozoan parasites Trypanosoma cruzi and Giardia intestinalis

    OpenAIRE

    Franzén, Oscar

    2012-01-01

    Trypanosoma cruzi and Giardia intestinalis are two human pathogens and protozoan parasites responsible for the diseases Chagas disease and giardiasis, respectively. Both diseases cause su ering and illness in several million individuals. The former disease occurs primarily in South America and Central America, and the latter disease occurs worldwide. Current therapeutics are toxic and lack e cacy, and potential vaccines are far from the market. Increased knowledge about the bio...

  8. Quantitative Seq-LGS: Genome-Wide Identification of Genetic Drivers of Multiple Phenotypes in Malaria Parasites

    KAUST Repository

    Abkallo, Hussein M.

    2016-10-01

    Identifying the genetic determinants of phenotypes that impact on disease severity is of fundamental importance for the design of new interventions against malaria. Traditionally, such discovery has relied on labor-intensive approaches that require significant investments of time and resources. By combining Linkage Group Selection (LGS), quantitative whole genome population sequencing and a novel mathematical modeling approach (qSeq-LGS), we simultaneously identified multiple genes underlying two distinct phenotypes, identifying novel alleles for growth rate and strain specific immunity (SSI), while removing the need for traditionally required steps such as cloning, individual progeny phenotyping and marker generation. The detection of novel variants, verified by experimental phenotyping methods, demonstrates the remarkable potential of this approach for the identification of genes controlling selectable phenotypes in malaria and other apicomplexan parasites for which experimental genetic crosses are amenable.

  9. Insight into trade-off between wood decay and parasitism from the genome of a fungal forest pathogen

    Energy Technology Data Exchange (ETDEWEB)

    Olson, Ake; Aerts, Andrea; Asiegbu, Fred; Belbahri, Lassaad; Bouzid, Ourdia; Broberg, Anders; Canback, Bjorn; Coutinho, Pedro M.; Cullen, Dan; Dalman, Kerstin; Deflorio, Giuliana; van Diepen, Linda T. A.; Dunand, Christophe; Duplessis, Sebastien; Durling, Mikael; Gonthier, Paolo; Grimwood, Jane; Fossdal, Carl Gunnar; Hansson, David; Henrissat, Bernard; Hietala, Ari; Himmelstrand, Kajsa; Hoffmeister, Dirk; Hogberg, Nils; James, Timothy Y.; Karlsson, Magnus; Kohler, Annegret; Lucas, Susan; Lunden, Karl; Morin, Emmanuelle; Murat, Claude; Park, Jongsun; Raffaello, Tommaso; Rouze, Pierre; Salamov, Asaf; Schmutz, Jeremy; Solheim, Halvor; Stahlberg, Jerry; Velez, Heriberto; de Vries, Ronald P.; Wiebenga, Ad; Woodward, Steve; Yakovlev, Igor; Garbelotto, Matteo; Martin, Francis; Grigoriev, Igor V.; Stenlid, Jan

    2012-01-01

    Parasitism and saprotrophic wood decay are two fungal strategies fundamental for succession and nutrient cycling in forest ecosystems. An opportunity to assess the trade-off between these strategies is provided by the forest pathogen and wood decayer Heterobasidion annosum sensu lato. We report the annotated genome sequence and transcript profiling, as well as the quantitative trait loci mapping, of one member of the species complex: H. irregulare. Quantitative trait loci critical for pathogenicity, and rich in transposable elements, orphan and secreted genes, were identified. A wide range of cellulose-degrading enzymes are expressed during wood decay. By contrast, pathogenic interaction between H. irregulare and pine engages fewer carbohydrate-active enzymes, but involves an increase in pectinolytic enzymes, transcription modules for oxidative stress and secondary metabolite production. Our results show a trade-off in terms of constrained carbohydrate decomposition and membrane transport capacity during interaction with living hosts. Our findings establish that saprotrophic wood decay and necrotrophic parasitism involve two distinct, yet overlapping, processes.

  10. The genomic organization of four b-1,4-endoglucanase genes in plant-parasitic cyst nematodes and its evolutionary implications.

    NARCIS (Netherlands)

    Yan, Y.; Smant, G.; Stokkermans, J.P.W.G.; Qin Ling,; Baum, T.J.; Schots, A.; Davis, E.L.

    1998-01-01

    The genomic organization of genes encoding -1,4-endoglucanases (cellulases) from the plant-parasitic cyst nematodes Heterodera glycines and Globodera rostochiensis (HG-eng1, Hg-eng2, GR-eng1, and GR-eng2) was investigated. HG-eng1 and GR-eng1 both contained eight introns and structural domains of

  11. PEST sequences in the malaria parasite Plasmodium falciparum: a genomic study

    Directory of Open Access Journals (Sweden)

    Bell Angus

    2003-06-01

    Full Text Available Abstract Background Inhibitors of the protease calpain are known to have selectively toxic effects on Plasmodium falciparum. The enzyme has a natural inhibitor calpastatin and in eukaryotes is responsible for turnover of proteins containing short sequences enriched in certain amino acids (PEST sequences. The genome of P. falciparum was searched for this protease, its natural inhibitor and putative substrates. Methods The publicly available P. falciparum genome was found to have too many errors to permit reliable analysis. An earlier annotation of chromosome 2 was instead examined. PEST scores were determined for all annotated proteins. The published genome was searched for calpain and calpastatin homologs. Results Typical PEST sequences were found in 13% of the proteins on chromosome 2, including a surprising number of cell-surface proteins. The annotated calpain gene has a non-biological "intron" that appears to have been created to avoid an unrecognized frameshift. Only the catalytic domain has significant similarity with the vertebrate calpains. No calpastatin homologs were found in the published annotation. Conclusion A calpain gene is present in the genome and many putative substrates of this enzyme have been found. Calpastatin homologs may be found once the re-annotation is completed. Given the selective toxicity of calpain inhibitors, this enzyme may be worth exploring further as a potential drug target.

  12. The Organellar Genomes of Chromera and Vitrella, the Phototrophic Relatives of Apicomplexan Parasites

    Czech Academy of Sciences Publication Activity Database

    Oborník, Miroslav; Lukeš, Julius

    2015-01-01

    Roč. 69, October 2015 (2015), s. 129-144 ISSN 0066-4227 R&D Projects: GA ČR GBP501/12/G055 EU Projects: European Commission(XE) 316304 Institutional support: RVO:60077344 Keywords : organellar genomes * mitochondrion * plastid * Apicomplexa * Alveolata * Chromera Subject RIV: EE - Microbiology, Virology Impact factor: 10.536, year: 2015

  13. The Organellar Genomes of Chromera and Vitrella, the Phototrophic Relatives of Apicomplexan Parasites

    Czech Academy of Sciences Publication Activity Database

    Oborník, Miroslav; Lukeš, J.

    2015-01-01

    Roč. 69, č. 2015 (2015), s. 129-144 ISSN 0066-4227 R&D Projects: GA ČR GBP501/12/G055; GA MŠk ED2.1.00/03.0110 Institutional support: RVO:61388971 Keywords : organellar genomes * mitochondrion * plastid Subject RIV: EE - Microbiology, Virology Impact factor: 10.536, year: 2015

  14. Comparative genomics of a plant-parasitic nematode endosymbiont suggest a role in nutritional symbiosis

    Science.gov (United States)

    Bacterial mutualists can increase the biochemical capacity of animals. Highly co-evolved nutritional mutualists do this by synthesizing nutrients missing from the host's diet. Genomics tools have recently advanced the study of these partnerships. Here we examined the endosymbiont Xiphinematobacter (...

  15. Genome profiling of sterol synthesis shows convergent evolution in parasites and guides chemotherapeutic attack.

    Science.gov (United States)

    Fügi, Matthias A; Gunasekera, Kapila; Ochsenreiter, Torsten; Guan, Xueli; Wenk, Markus R; Mäser, Pascal

    2014-05-01

    Sterols are an essential class of lipids in eukaryotes, where they serve as structural components of membranes and play important roles as signaling molecules. Sterols are also of high pharmacological significance: cholesterol-lowering drugs are blockbusters in human health, and inhibitors of ergosterol biosynthesis are widely used as antifungals. Inhibitors of ergosterol synthesis are also being developed for Chagas's disease, caused by Trypanosoma cruzi. Here we develop an in silico pipeline to globally evaluate sterol metabolism and perform comparative genomics. We generate a library of hidden Markov model-based profiles for 42 sterol biosynthetic enzymes, which allows expressing the genomic makeup of a given species as a numerical vector. Hierarchical clustering of these vectors functionally groups eukaryote proteomes and reveals convergent evolution, in particular metabolic reduction in obligate endoparasites. We experimentally explore sterol metabolism by testing a set of sterol biosynthesis inhibitors against trypanosomatids, Plasmodium falciparum, Giardia, and mammalian cells, and by quantifying the expression levels of sterol biosynthetic genes during the different life stages of T. cruzi and Trypanosoma brucei. The phenotypic data correlate with genomic makeup for simvastatin, which showed activity against trypanosomatids. Other findings, such as the activity of terbinafine against Giardia, are not in agreement with the genotypic profile.

  16. Rapid, Selection-Free, High-Efficiency Genome Editing in Protozoan Parasites Using CRISPR-Cas9 Ribonucleoproteins

    Directory of Open Access Journals (Sweden)

    Lia Carolina Soares Medeiros

    2017-11-01

    Full Text Available Trypanosomatids (order Kinetoplastida, including the human pathogens Trypanosoma cruzi (agent of Chagas disease, Trypanosoma brucei, (African sleeping sickness, and Leishmania (leishmaniasis, affect millions of people and animals globally. T. cruzi is considered one of the least studied and most poorly understood tropical disease-causing parasites, in part because of the relative lack of facile genetic engineering tools. This situation has improved recently through the application of clustered regularly interspaced short palindromic repeats–CRISPR-associated protein 9 (CRISPR-Cas9 technology, but a number of limitations remain, including the toxicity of continuous Cas9 expression and the long drug marker selection times. In this study, we show that the delivery of ribonucleoprotein (RNP complexes composed of recombinant Cas9 from Staphylococcus aureus (SaCas9, but not from the more routinely used Streptococcus pyogenes Cas9 (SpCas9, and in vitro-transcribed single guide RNAs (sgRNAs results in rapid gene edits in T. cruzi and other kinetoplastids at frequencies approaching 100%. The highly efficient genome editing via SaCas9/sgRNA RNPs was obtained for both reporter and endogenous genes and observed in multiple parasite life cycle stages in various strains of T. cruzi, as well as in T. brucei and Leishmania major. RNP complex delivery was also used to successfully tag proteins at endogenous loci and to assess the biological functions of essential genes. Thus, the use of SaCas9 RNP complexes for gene editing in kinetoplastids provides a simple, rapid, and cloning- and selection-free method to assess gene function in these important human pathogens.

  17. Ultra Large Gene Families: A Matter of Adaptation or Genomic Parasites?

    Directory of Open Access Journals (Sweden)

    Philipp H. Schiffer

    2016-08-01

    Full Text Available Gene duplication is an important mechanism of molecular evolution. It offers a fast track to modification, diversification, redundancy or rescue of gene function. However, duplication may also be neutral or (slightly deleterious, and often ends in pseudo-geneisation. Here, we investigate the phylogenetic distribution of ultra large gene families on long and short evolutionary time scales. In particular, we focus on a family of NACHT-domain and leucine-rich-repeat-containing (NLR-genes, which we previously found in large numbers to occupy one chromosome arm of the zebrafish genome. We were interested to see whether such a tight clustering is characteristic for ultra large gene families. Our data reconfirm that most gene family inflations are lineage-specific, but we can only identify very few gene clusters. Based on our observations we hypothesise that, beyond a certain size threshold, ultra large gene families continue to proliferate in a mechanism we term “run-away evolution”. This process might ultimately lead to the failure of genomic integrity and drive species to extinction.

  18. A three-genome phylogeny of malaria parasites (Plasmodium and closely related genera): evolution of life-history traits and host switches.

    Science.gov (United States)

    Martinsen, Ellen S; Perkins, Susan L; Schall, Jos J

    2008-04-01

    Phylogenetic analysis of genomic data allows insights into the evolutionary history of pathogens, especially the events leading to host switching and diversification, as well as alterations of the life cycle (life-history traits). Hundreds, perhaps thousands, of malaria parasite species exploit squamate reptiles, birds, and mammals as vertebrate hosts as well as many genera of dipteran vectors, but the evolutionary and ecological events that led to this diversification and success remain unresolved. For a century, systematic parasitologists classified malaria parasites into genera based on morphology, life cycle, and vertebrate and insect host taxa. Molecular systematic studies based on single genes challenged the phylogenetic significance of these characters, but several significant nodes were not well supported. We recovered the first well resolved large phylogeny of Plasmodium and related haemosporidian parasites using sequence data for four genes from the parasites' three genomes by combining all data, correcting for variable rates of substitution by gene and site, and using both Bayesian and maximum parsimony analyses. Major clades are associated with vector shifts into different dipteran families, with other characters used in traditional parasitological studies, such as morphology and life-history traits, having variable phylogenetic significance. The common parasites of birds now placed into the genus Haemoproteus are found in two divergent clades, and the genus Plasmodium is paraphyletic with respect to Hepatocystis, a group of species with very different life history and morphology. The Plasmodium of mammal hosts form a well supported clade (including Plasmodium falciparum, the most important human malaria parasite), and this clade is associated with specialization to Anopheles mosquito vectors. The Plasmodium of birds and squamate reptiles all fall within a single clade, with evidence for repeated switching between birds and squamate hosts.

  19. The Eukaryotic Pathogen Databases: a functional genomic resource integrating data from human and veterinary parasites.

    Science.gov (United States)

    Harb, Omar S; Roos, David S

    2015-01-01

    Over the past 20 years, advances in high-throughput biological techniques and the availability of computational resources including fast Internet access have resulted in an explosion of large genome-scale data sets "big data." While such data are readily available for download and personal use and analysis from a variety of repositories, often such analysis requires access to seldom-available computational skills. As a result a number of databases have emerged to provide scientists with online tools enabling the interrogation of data without the need for sophisticated computational skills beyond basic knowledge of Internet browser utility. This chapter focuses on the Eukaryotic Pathogen Databases (EuPathDB: http://eupathdb.org) Bioinformatic Resource Center (BRC) and illustrates some of the available tools and methods.

  20. The evolutionary dynamics of variant antigen genes in Babesia reveal a history of genomic innovation underlying host-parasite interaction

    KAUST Repository

    Jackson, Andrew P.

    2014-05-05

    Babesia spp. are tick-borne, intraerythrocytic hemoparasites that use antigenic variation to resist host immunity, through sequential modification of the parasite-derived variant erythrocyte surface antigen (VESA) expressed on the infected red blood cell surface. We identified the genomic processes driving antigenic diversity in genes encoding VESA (ves1) through comparative analysis within and between three Babesia species, (B. bigemina, B. divergens and B. bovis). Ves1 structure diverges rapidly after speciation, notably through the evolution of shortened forms (ves2) from 5? ends of canonical ves1 genes. Phylogenetic analyses show that ves1 genes are transposed between loci routinely, whereas ves2 genes are not. Similarly, analysis of sequence mosaicism shows that recombination drives variation in ves1 sequences, but less so for ves2, indicating the adoption of different mechanisms for variation of the two families. Proteomic analysis of the B. bigemina PR isolate shows that two dominant VESA1 proteins are expressed in the population, whereas numerous VESA2 proteins are co-expressed, consistent with differential transcriptional regulation of each family. Hence, VESA2 proteins are abundant and previously unrecognized elements of Babesia biology, with evolutionary dynamics consistently different to those of VESA1, suggesting that their functions are distinct. 2014 The Author(s) 2014.

  1. The evolutionary dynamics of variant antigen genes in Babesia reveal a history of genomic innovation underlying host-parasite interaction

    KAUST Repository

    Jackson, Andrew P.; Otto, Thomas D.; Darby, Alistair; Ramaprasad, Abhinay; Xia, Dong; Echaide, Ignacio Eduardo; Farber, Marisa; Gahlot, Sunayna; Gamble, John; Gupta, Dinesh; Gupta, Yask; Jackson, Louise; Malandrin, Laurence; Malas, Tareq B.; Moussa, Ehab; Nair, Mridul; Reid, Adam J.; Sanders, Mandy; Sharma, Jyotsna; Tracey, Alan; Quail, Mike A.; Weir, William; Wastling, Jonathan M.; Hall, Neil; Willadsen, Peter; Lingelbach, Klaus; Shiels, Brian; Tait, Andy; Berriman, Matt; Allred, David R.; Pain, Arnab

    2014-01-01

    Babesia spp. are tick-borne, intraerythrocytic hemoparasites that use antigenic variation to resist host immunity, through sequential modification of the parasite-derived variant erythrocyte surface antigen (VESA) expressed on the infected red blood cell surface. We identified the genomic processes driving antigenic diversity in genes encoding VESA (ves1) through comparative analysis within and between three Babesia species, (B. bigemina, B. divergens and B. bovis). Ves1 structure diverges rapidly after speciation, notably through the evolution of shortened forms (ves2) from 5? ends of canonical ves1 genes. Phylogenetic analyses show that ves1 genes are transposed between loci routinely, whereas ves2 genes are not. Similarly, analysis of sequence mosaicism shows that recombination drives variation in ves1 sequences, but less so for ves2, indicating the adoption of different mechanisms for variation of the two families. Proteomic analysis of the B. bigemina PR isolate shows that two dominant VESA1 proteins are expressed in the population, whereas numerous VESA2 proteins are co-expressed, consistent with differential transcriptional regulation of each family. Hence, VESA2 proteins are abundant and previously unrecognized elements of Babesia biology, with evolutionary dynamics consistently different to those of VESA1, suggesting that their functions are distinct. 2014 The Author(s) 2014.

  2. The evolutionary dynamics of variant antigen genes in Babesia reveal a history of genomic innovation underlying host–parasite interaction

    Science.gov (United States)

    Jackson, Andrew P.; Otto, Thomas D.; Darby, Alistair; Ramaprasad, Abhinay; Xia, Dong; Echaide, Ignacio Eduardo; Farber, Marisa; Gahlot, Sunayna; Gamble, John; Gupta, Dinesh; Gupta, Yask; Jackson, Louise; Malandrin, Laurence; Malas, Tareq B.; Moussa, Ehab; Nair, Mridul; Reid, Adam J.; Sanders, Mandy; Sharma, Jyotsna; Tracey, Alan; Quail, Mike A.; Weir, William; Wastling, Jonathan M.; Hall, Neil; Willadsen, Peter; Lingelbach, Klaus; Shiels, Brian; Tait, Andy; Berriman, Matt; Allred, David R.; Pain, Arnab

    2014-01-01

    Babesia spp. are tick-borne, intraerythrocytic hemoparasites that use antigenic variation to resist host immunity, through sequential modification of the parasite-derived variant erythrocyte surface antigen (VESA) expressed on the infected red blood cell surface. We identified the genomic processes driving antigenic diversity in genes encoding VESA (ves1) through comparative analysis within and between three Babesia species, (B. bigemina, B. divergens and B. bovis). Ves1 structure diverges rapidly after speciation, notably through the evolution of shortened forms (ves2) from 5′ ends of canonical ves1 genes. Phylogenetic analyses show that ves1 genes are transposed between loci routinely, whereas ves2 genes are not. Similarly, analysis of sequence mosaicism shows that recombination drives variation in ves1 sequences, but less so for ves2, indicating the adoption of different mechanisms for variation of the two families. Proteomic analysis of the B. bigemina PR isolate shows that two dominant VESA1 proteins are expressed in the population, whereas numerous VESA2 proteins are co-expressed, consistent with differential transcriptional regulation of each family. Hence, VESA2 proteins are abundant and previously unrecognized elements of Babesia biology, with evolutionary dynamics consistently different to those of VESA1, suggesting that their functions are distinct. PMID:24799432

  3. The evolutionary dynamics of variant antigen genes in Babesia reveal a history of genomic innovation underlying host-parasite interaction.

    Science.gov (United States)

    Jackson, Andrew P; Otto, Thomas D; Darby, Alistair; Ramaprasad, Abhinay; Xia, Dong; Echaide, Ignacio Eduardo; Farber, Marisa; Gahlot, Sunayna; Gamble, John; Gupta, Dinesh; Gupta, Yask; Jackson, Louise; Malandrin, Laurence; Malas, Tareq B; Moussa, Ehab; Nair, Mridul; Reid, Adam J; Sanders, Mandy; Sharma, Jyotsna; Tracey, Alan; Quail, Mike A; Weir, William; Wastling, Jonathan M; Hall, Neil; Willadsen, Peter; Lingelbach, Klaus; Shiels, Brian; Tait, Andy; Berriman, Matt; Allred, David R; Pain, Arnab

    2014-06-01

    Babesia spp. are tick-borne, intraerythrocytic hemoparasites that use antigenic variation to resist host immunity, through sequential modification of the parasite-derived variant erythrocyte surface antigen (VESA) expressed on the infected red blood cell surface. We identified the genomic processes driving antigenic diversity in genes encoding VESA (ves1) through comparative analysis within and between three Babesia species, (B. bigemina, B. divergens and B. bovis). Ves1 structure diverges rapidly after speciation, notably through the evolution of shortened forms (ves2) from 5' ends of canonical ves1 genes. Phylogenetic analyses show that ves1 genes are transposed between loci routinely, whereas ves2 genes are not. Similarly, analysis of sequence mosaicism shows that recombination drives variation in ves1 sequences, but less so for ves2, indicating the adoption of different mechanisms for variation of the two families. Proteomic analysis of the B. bigemina PR isolate shows that two dominant VESA1 proteins are expressed in the population, whereas numerous VESA2 proteins are co-expressed, consistent with differential transcriptional regulation of each family. Hence, VESA2 proteins are abundant and previously unrecognized elements of Babesia biology, with evolutionary dynamics consistently different to those of VESA1, suggesting that their functions are distinct. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  4. The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode.

    Science.gov (United States)

    Cotton, James A; Lilley, Catherine J; Jones, Laura M; Kikuchi, Taisei; Reid, Adam J; Thorpe, Peter; Tsai, Isheng J; Beasley, Helen; Blok, Vivian; Cock, Peter J A; Eves-van den Akker, Sebastian; Holroyd, Nancy; Hunt, Martin; Mantelin, Sophie; Naghra, Hardeep; Pain, Arnab; Palomares-Rius, Juan E; Zarowiecki, Magdalena; Berriman, Matthew; Jones, John T; Urwin, Peter E

    2014-03-03

    Globodera pallida is a devastating pathogen of potato crops, making it one of the most economically important plant parasitic nematodes. It is also an important model for the biology of cyst nematodes. Cyst nematodes and root-knot nematodes are the two most important plant parasitic nematode groups and together represent a global threat to food security. We present the complete genome sequence of G. pallida, together with transcriptomic data from most of the nematode life cycle, particularly focusing on the life cycle stages involved in root invasion and establishment of the biotrophic feeding site. Despite the relatively close phylogenetic relationship with root-knot nematodes, we describe a very different gene family content between the two groups and in particular extensive differences in the repertoire of effectors, including an enormous expansion of the SPRY domain protein family in G. pallida, which includes the SPRYSEC family of effectors. This highlights the distinct biology of cyst nematodes compared to the root-knot nematodes that were, until now, the only sedentary plant parasitic nematodes for which genome information was available. We also present in-depth descriptions of the repertoires of other genes likely to be important in understanding the unique biology of cyst nematodes and of potential drug targets and other targets for their control. The data and analyses we present will be central in exploiting post-genomic approaches in the development of much-needed novel strategies for the control of G. pallida and related pathogens.

  5. Experimental evolution, genetic analysis and genome re-sequencing reveal the mutation conferring artemisinin resistance in an isogenic lineage of malaria parasites

    KAUST Repository

    Hunt, Paul

    2010-09-16

    Background: Classical and quantitative linkage analyses of genetic crosses have traditionally been used to map genes of interest, such as those conferring chloroquine or quinine resistance in malaria parasites. Next-generation sequencing technologies now present the possibility of determining genome-wide genetic variation at single base-pair resolution. Here, we combine in vivo experimental evolution, a rapid genetic strategy and whole genome re-sequencing to identify the precise genetic basis of artemisinin resistance in a lineage of the rodent malaria parasite, Plasmodium chabaudi. Such genetic markers will further the investigation of resistance and its control in natural infections of the human malaria, P. falciparum.Results: A lineage of isogenic in vivo drug-selected mutant P. chabaudi parasites was investigated. By measuring the artemisinin responses of these clones, the appearance of an in vivo artemisinin resistance phenotype within the lineage was defined. The underlying genetic locus was mapped to a region of chromosome 2 by Linkage Group Selection in two different genetic crosses. Whole-genome deep coverage short-read re-sequencing (IlluminaSolexa) defined the point mutations, insertions, deletions and copy-number variations arising in the lineage. Eight point mutations arise within the mutant lineage, only one of which appears on chromosome 2. This missense mutation arises contemporaneously with artemisinin resistance and maps to a gene encoding a de-ubiquitinating enzyme.Conclusions: This integrated approach facilitates the rapid identification of mutations conferring selectable phenotypes, without prior knowledge of biological and molecular mechanisms. For malaria, this model can identify candidate genes before resistant parasites are commonly observed in natural human malaria populations. 2010 Hunt et al; licensee BioMed Central Ltd.

  6. The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode

    KAUST Repository

    Cotton, James A

    2014-03-03

    Background: Globodera pallida is a devastating pathogen of potato crops, making it one of the most economically important plant parasitic nematodes. It is also an important model for the biology of cyst nematodes. Cyst nematodes and root-knot nematodes are the two most important plant parasitic nematode groups and together represent a global threat to food security. Results: We present the complete genome sequence of G. pallida, together with transcriptomic data from most of the nematode life cycle, particularly focusing on the life cycle stages involved in root invasion and establishment of the biotrophic feeding site. Despite the relatively close phylogenetic relationship with root-knot nematodes, we describe a very different gene family content between the two groups and in particular extensive differences in the repertoire of effectors, including an enormous expansion of the SPRY domain protein family in G. pallida, which includes the SPRYSEC family of effectors. This highlights the distinct biology of cyst nematodes compared to the root-knot nematodes that were, until now, the only sedentary plant parasitic nematodes for which genome information was available. We also present in-depth descriptions of the repertoires of other genes likely to be important in understanding the unique biology of cyst nematodes and of potential drug targets and other targets for their control. Conclusions: The data and analyses we present will be central in exploiting post-genomic approaches in the development of much-needed novel strategies for the control of G. pallida and related pathogens. 2014 Cotton et al.; licensee BioMed Central Ltd.

  7. Comparative genome analysis of three eukaryotic parasites with differing abilities to transform leukocytes reveals key mediators of theileria-induced leukocyte transformation

    KAUST Repository

    Hayashida, Kyoko

    2012-09-04

    We sequenced the genome of Theileria orientalis, a tick-borne apicomplexan protozoan parasite of cattle. The focus of this study was a comparative genome analysis of T. orientalis relative to other highly pathogenic Theileria species, T. parva and T. annulata. T. parva and T. annulata induce transformation of infected cells of lymphocyte or macrophage/monocyte lineages; in contrast, T. orientalis does not induce uncontrolled proliferation of infected leukocytes and multiplies predominantly within infected erythrocytes. While synteny across homologous chromosomes of the three Theileria species was found to be well conserved overall, subtelomeric structures were found to differ substantially, as T. orientalis lacks the large tandemly arrayed subtelomere-encoded variable secreted protein-encoding gene family. Moreover, expansion of particular gene families by gene duplication was found in the genomes of the two transforming Theileria species, most notably, the TashAT/TpHN and Tar/Tpr gene families. Gene families that are present only in T. parva and T. annulata and not in T. orientalis, Babesia bovis, or Plasmo-dium were also identified. Identification of differences between the genome sequences of Theileria species with different abilities to transform and immortalize bovine leukocytes will provide insight into proteins and mechanisms that have evolved to induce and regulate this process. The T. orientalis genome database is available at http://totdb.czc.hokudai.ac.jp/. 2012 Hayashida et al. T.

  8. Corrosion cracking

    International Nuclear Information System (INIS)

    Goel, V.S.

    1985-01-01

    This book presents the papers given at a conference on alloy corrosion cracking. Topics considered at the conference included the effect of niobium addition on intergranular stress corrosion cracking, corrosion-fatigue cracking in fossil-fueled-boilers, fracture toughness, fracture modes, hydrogen-induced thresholds, electrochemical and hydrogen permeation studies, the effect of seawater on fatigue crack propagation of wells for offshore structures, the corrosion fatigue of carbon steels in seawater, and stress corrosion cracking and the mechanical strength of alloy 600

  9. Inconsistencies of genome annotations in apicomplexan parasites revealed by 5'-end-one-pass and full-length sequences of oligo-capped cDNAs

    Directory of Open Access Journals (Sweden)

    Sugano Sumio

    2009-07-01

    Full Text Available Abstract Background Apicomplexan parasites are causative agents of various diseases including malaria and have been targets of extensive genomic sequencing. We generated 5'-EST collections for six apicomplexa parasites using our full-length oligo-capping cDNA library method. To improve upon the current genome annotations, as well as to validate the importance for physical cDNA clone resources, we generated a large-scale collection of full-length cDNAs for several apicomplexa parasites. Results In this study, we used a total of 61,056 5'-end-single-pass cDNA sequences from Plasmodium falciparum, P. vivax, P. yoelii, P. berghei, Cryptosporidium parvum, and Toxoplasma gondii. We compared these partially sequenced cDNA sequences with the currently annotated gene models and observed significant inconsistencies between the two datasets. In particular, we found that on average 14% of the exons in the current gene models were not supported by any cDNA evidence, and that 16% of the current gene models may contain at least one mis-annotation and should be re-evaluated. We also identified a large number of transcripts that had been previously unidentified. For 732 cDNAs in T. gondii, the entire sequences were determined in order to evaluate the annotated gene models at the complete full-length transcript level. We found that 41% of the T. gondii gene models contained at least one inconsistency. We also identified and confirmed by RT-PCR 140 previously unidentified transcripts found in the intergenic regions of the current gene annotations. We show that the majority of these discrepancies are due to questionable predictions of one or two extra exons in the upstream or downstream regions of the genes. Conclusion Our data indicates that the current gene models are likely to still be incomplete and have much room for improvement. Our unique full-length cDNA information is especially useful for further refinement of the annotations for the genomes of

  10. Early detection of fatigue cracks by means of nondestructive testing, NDT; Tidig detektering av utmattningssprickor genom ofoerstoerande provning, OFP

    Energy Technology Data Exchange (ETDEWEB)

    Broddegaard, Mattias [Siemens Industrial Turbines, Finspaang (Sweden)

    2004-12-01

    Components in gas turbines, steam turbines and boilers are subjected to both high and low cycle fatigue. The lifetime of components is established by calculations based on conservative assumptions and safety factors, which means that most components will have a real life far exceeding the calculated. Conventional nondestructive testing is aimed at detecting macroscopic defects, such as cracks, inclusions and other discontinuities in the material. By having the possibility of detecting damage at a microscopic level, the risk of fractures in components subjected to fatigue can be reduced and the interval between testing occasions can be extended. The project goal has been to establish knowledge about possibilities and limitations for early detection of low and high cycle fatigue damage, by a literature survey and by practical experiments on low cycle fatigue specimens in 12% Cr-steel, for the following nondestructive testing methods: MWM (Meandering Winding Magnetometer) eddy current testing; and Nonlinear ultrasonics, both classical (second harmonic) and non-classical (crack closure). The project started with a literature survey. This resulted in a proposal for specimen design and selection of testing techniques and project partners. Manufacturing of specimens in 12% Cr-steel, designation X22CrMoV12-1, and low cycle fatigue testing at 300 deg C testing temperature was carried out at Siemens Industrial Turbines in Finspaang. Specimens with 0, 25, 50, 75 and 100% consumed life, based on the number of cycles to presence of macroscopic cracks, were produced. MWM eddy current testing was carried out by Jentek Sensors Inc. in the USA. Measurements with nonlinear ultrasonics were carried out by Siemens Corporate Technology in Munich and at Blekinge Univ. The specimens were finally examined in SEM and light optical microscope in Finspaang. In the literature, results showing that early detection of fatigue damage by nondestructive testing is possible, can be found. By

  11. The complete genome sequence of CrRV-Ch01, a new member of the family Rhabdoviridae in the parasitic copepod Caligus rogercresseyi present on farmed Atlantic salmon (Salmo salar) in Chile.

    Science.gov (United States)

    Økland, Arnfinn Lodden; Skoge, Renate Hvidsten; Nylund, Are

    2018-06-01

    We have determined the complete genome sequence of a new rhabdovirus, tentatively named Caligus rogercresseyi rhabdovirus Ch01 (CrRV-Ch01), which was found in the parasite Caligus rogercresseyi, present on farmed Atlantic salmon (Salmo salar) in Chile. The genome encodes the five canonical rhabdovirus proteins in addition to an unknown protein, in the order N-P-M-U (unknown)-G-L. Phylogenetic analysis showed that the virus clusters with two rhabdoviruses (Lepeophtheirus salmonis rhabdovirus No9 and Lepeophtheirus salmonis rhabdovirus No127) obtained from another parasitic caligid, Lepeophtheirus salmonis, present on farmed Atlantic salmon on the west coast of Norway.

  12. Genome-wide functional analysis of plasmodium protein phosphatases reveals key regulators of parasite development and differentiation

    KAUST Repository

    Guttery, David S.

    2014-07-09

    Reversible protein phosphorylation regulated by kinases and phosphatases controls many cellular processes. Although essential functions for the malaria parasite kinome have been reported, the roles of most protein phosphatases (PPs) during Plasmodium development are unknown. We report a functional analysis of the Plasmodium berghei protein phosphatome, which exhibits high conservation with the P. falciparum phosphatome and comprises 30 predicted PPs with differential and distinct expression patterns during various stages of the life cycle. Gene disruption analysis of P. berghei PPs reveals that half of the genes are likely essential for asexual blood stage development, whereas six are required for sexual development/sporogony in mosquitoes. Phenotypic screening coupled with transcriptome sequencing unveiled morphological changes and altered gene expression in deletion mutants of two N-myristoylated PPs. These findings provide systematic functional analyses of PPs in Plasmodium, identify how phosphatases regulate parasite development and differentiation, and can inform the identification of drug targets for malaria. © 2014 The Authors.

  13. Genome-wide functional analysis of plasmodium protein phosphatases reveals key regulators of parasite development and differentiation

    KAUST Repository

    Guttery, David  S.; Poulin, Benoit; Ramaprasad, Abhinay; Wall, Richard  J.; Ferguson, David  J.P.; Brady, Declan; Patzewitz, Eva-Maria; Whipple, Sarah; Straschil, Ursula; Wright, Megan  H.; Mohamed, Alyaa  M.A.H.; Radhakrishnan, Anand; Arold, Stefan T.; Tate, Edward  W.; Holder, Anthony  A.; Wickstead, Bill; Pain, Arnab; Tewari, Rita

    2014-01-01

    Reversible protein phosphorylation regulated by kinases and phosphatases controls many cellular processes. Although essential functions for the malaria parasite kinome have been reported, the roles of most protein phosphatases (PPs) during Plasmodium development are unknown. We report a functional analysis of the Plasmodium berghei protein phosphatome, which exhibits high conservation with the P. falciparum phosphatome and comprises 30 predicted PPs with differential and distinct expression patterns during various stages of the life cycle. Gene disruption analysis of P. berghei PPs reveals that half of the genes are likely essential for asexual blood stage development, whereas six are required for sexual development/sporogony in mosquitoes. Phenotypic screening coupled with transcriptome sequencing unveiled morphological changes and altered gene expression in deletion mutants of two N-myristoylated PPs. These findings provide systematic functional analyses of PPs in Plasmodium, identify how phosphatases regulate parasite development and differentiation, and can inform the identification of drug targets for malaria. © 2014 The Authors.

  14. Comparative genomics of the apicomplexan parasites Toxoplasma gondii and neospora caninum: Coccidia differing in host range and transmission strategy

    KAUST Repository

    Reid, Adam James; Vermont, Sarah J.; Cotton, James A.; Harris, David; Hill-Cawthorne, Grant A.; Kö nen-Waisman, Stephanie; Latham, Sophia M.; Mourier, Tobias; Norton, Rebecca; Quail, Michael A.; Sanders, Mandy; Shanmugam, Dhanasekaran; Sohal, Amandeep; Wasmuth, James D.; Brunk, Brian; Grigg, Michael E.; Howard, Jonathan C.; Parkinson, John; Roos, David S.; Trees, Alexander J.; Berriman, Matthew; Pain, Arnab; Wastling, Jonathan M.

    2012-01-01

    and transcriptomics analysis. We estimate that these organisms diverged from their common ancestor around 28 million years ago and find that both genomes and gene expression are remarkably conserved. However, in N. caninum we identified an unexpected expansion

  15. The complete mitochondrial genomes of three parasitic nematodes of birds: a unique gene order and insights into nematode phylogeny

    Science.gov (United States)

    2013-01-01

    Background Analyses of mitochondrial (mt) genome sequences in recent years challenge the current working hypothesis of Nematoda phylogeny proposed from morphology, ecology and nuclear small subunit rRNA gene sequences, and raise the need to sequence additional mt genomes for a broad range of nematode lineages. Results We sequenced the complete mt genomes of three Ascaridia species (family Ascaridiidae) that infest chickens, pigeons and parrots, respectively. These three Ascaridia species have an identical arrangement of mt genes to each other but differ substantially from other nematodes. Phylogenetic analyses of the mt genome sequences of the Ascaridia species, together with 62 other nematode species, support the monophylies of seven high-level taxa of the phylum Nematoda: 1) the subclass Dorylaimia; 2) the orders Rhabditida, Trichinellida and Mermithida; 3) the suborder Rhabditina; and 4) the infraorders Spiruromorpha and Oxyuridomorpha. Analyses of mt genome sequences, however, reject the monophylies of the suborders Spirurina and Tylenchina, and the infraorders Rhabditomorpha, Panagrolaimomorpha and Tylenchomorpha. Monophyly of the infraorder Ascaridomorpha varies depending on the methods of phylogenetic analysis. The Ascaridomorpha was more closely related to the infraorders Rhabditomorpha and Diplogasteromorpha (suborder Rhabditina) than they were to the other two infraorders of the Spirurina: Oxyuridorpha and Spiruromorpha. The closer relationship among Ascaridomorpha, Rhabditomorpha and Diplogasteromorpha was also supported by a shared common pattern of mitochondrial gene arrangement. Conclusions Analyses of mitochondrial genome sequences and gene arrangement has provided novel insights into the phylogenetic relationships among several major lineages of nematodes. Many lineages of nematodes, however, are underrepresented or not represented in these analyses. Expanding taxon sampling is necessary for future phylogenetic studies of nematodes with mt genome

  16. Functional genomics studies of Rhipicephalus (Boophilus) annulatus ticks in response to infection with the cattle protozoan parasite, Babesia bigemina

    Czech Academy of Sciences Publication Activity Database

    Antunes, S.; Galindo, R. C.; Almazán, C.; Rudenko, Natalia; Golovchenko, Maryna; Grubhoffer, Libor; Shkap, V.; do Rosário, A.; de la Fuente, J.; Domingos, A.

    2012-01-01

    Roč. 42, č. 2 (2012), s. 187-195 ISSN 0020-7519 Institutional research plan: CEZ:AV0Z60220518 Keywords : Tick * Genomics * Babesia * Rhipicephalus * Boophilus * RNA interference * Vaccine Subject RIV: EC - Immunology Impact factor: 3.637, year: 2012 http://www.sciencedirect.com/science/article/pii/S0020751912000033

  17. Draft genome of the honey bee ectoparasitic mite, Tropilaelaps mercedesae, is shaped by the parasitic life history.

    Science.gov (United States)

    Dong, Xiaofeng; Armstrong, Stuart D; Xia, Dong; Makepeace, Benjamin L; Darby, Alistair C; Kadowaki, Tatsuhiko

    2017-03-01

    The number of managed honey bee colonies has considerably decreased in many developed countries in recent years and ectoparasitic mites are considered as major threats to honey bee colonies and health. However, their general biology remains poorly understood. We sequenced the genome of Tropilaelaps mercedesae, the prevalent ectoparasitic mite infesting honey bees in Asia, and predicted 15 190 protein-coding genes that were well supported by the mite transcriptomes and proteomic data. Although amino acid substitutions have been accelerated within the conserved core genes of two mites, T. mercedesae and Metaseiulus occidentalis, T. mercedesae has undergone the least gene family expansion and contraction between the seven arthropods we tested. The number of sensory system genes has been dramatically reduced, but T. mercedesae contains all gene sets required to detoxify xenobiotics. T. mercedesae is closely associated with a symbiotic bacterium (Rickettsiella grylli-like) and Deformed Wing Virus, the most prevalent honey bee virus. T. mercedesae has a very specialized life history and habitat as the ectoparasitic mite strictly depends on the honey bee inside a stable colony. Thus, comparison of the genome and transcriptome sequences with those of a tick and free-living mites has revealed the specific features of the genome shaped by interaction with the honey bee and colony environment. Genome and transcriptome sequences of T. mercedesae, as well as Varroa destructor (another globally prevalent ectoparasitic mite of honey bee), not only provide insights into the mite biology, but may also help to develop measures to control the most serious pests of the honey bee. © The Author 2017. Published by Oxford University Press.

  18. Draft genome of the honey bee ectoparasitic mite, Tropilaelaps mercedesae, is shaped by the parasitic life history

    OpenAIRE

    Dong, Xiaofeng; Armstrong, Stuart D.; Xia, Dong; Makepeace, Benjamin L.; Darby, Alistair C.; Kadowaki, Tatsuhiko

    2017-01-01

    Abstract The number of managed honey bee colonies has considerably decreased in many developed countries in recent years and ectoparasitic mites are considered as major threats to honey bee colonies and health. However, their general biology remains poorly understood. We sequenced the genome of Tropilaelaps mercedesae, the prevalent ectoparasitic mite infesting honey bees in Asia, and predicted 15?190 protein-coding genes that were well supported by the mite transcriptomes and proteomic data....

  19. Repetitive elements in parasitic protozoa

    Directory of Open Access Journals (Sweden)

    Clayton Christine

    2010-05-01

    Full Text Available Abstract A recent paper published in BMC Genomics suggests that retrotransposition may be active in the human gut parasite Entamoeba histolytica. This adds to our knowledge of the various types of repetitive elements in parasitic protists and the potential influence of such elements on pathogenicity. See research article http://www.biomedcentral.com/1471-2164/11/321

  20. Inevitability of Genetic Parasites

    Science.gov (United States)

    Iranzo, Jaime; Puigbò, Pere; Lobkovsky, Alexander E.; Wolf, Yuri I.

    2016-01-01

    Abstract Almost all cellular life forms are hosts to diverse genetic parasites with various levels of autonomy including plasmids, transposons and viruses. Theoretical modeling of the evolution of primordial replicators indicates that parasites (cheaters) necessarily evolve in such systems and can be kept at bay primarily via compartmentalization. Given the (near) ubiquity, abundance and diversity of genetic parasites, the question becomes pertinent: are such parasites intrinsic to life? At least in prokaryotes, the persistence of parasites is linked to the rate of horizontal gene transfer (HGT). We mathematically derive the threshold value of the minimal transfer rate required for selfish element persistence, depending on the element duplication and loss rates as well as the cost to the host. Estimation of the characteristic gene duplication, loss and transfer rates for transposons, plasmids and virus-related elements in multiple groups of diverse bacteria and archaea indicates that most of these rates are compatible with the long term persistence of parasites. Notably, a small but non-zero rate of HGT is also required for the persistence of non-parasitic genes. We hypothesize that cells cannot tune their horizontal transfer rates to be below the threshold required for parasite persistence without experiencing highly detrimental side-effects. As a lower boundary to the minimum DNA transfer rate that a cell can withstand, we consider the process of genome degradation and mutational meltdown of populations through Muller’s ratchet. A numerical assessment of this hypothesis suggests that microbial populations cannot purge parasites while escaping Muller’s ratchet. Thus, genetic parasites appear to be virtually inevitable in cellular organisms. PMID:27503291

  1. Parasites: Water

    Science.gov (United States)

    ... Consultations, and General Public. Contact Us Parasites Home Water Language: English Español (Spanish) Recommend on Facebook Tweet Share Compartir Parasites can live in natural water sources. When outdoors, treat your water before drinking ...

  2. G-Quadruplex Identification in the Genome of Protozoan Parasites Points to Naphthalene Diimide Ligands as New Antiparasitic Agents.

    Science.gov (United States)

    Belmonte-Reche, Efres; Martínez-García, Marta; Guédin, Aurore; Zuffo, Michela; Arévalo-Ruiz, Matilde; Doria, Filippo; Campos-Salinas, Jenny; Maynadier, Marjorie; López-Rubio, José Juan; Freccero, Mauro; Mergny, Jean-Louis; Pérez-Victoria, José María; Morales, Juan Carlos

    2018-02-08

    G-quadruplexes (G4) are DNA secondary structures that take part in the regulation of gene expression. Putative G4 forming sequences (PQS) have been reported in mammals, yeast, bacteria, and viruses. Here, we present PQS searches on the genomes of T. brucei, L. major, and P. falciparum. We found telomeric sequences and new PQS motifs. Biophysical experiments showed that EBR1, a 29 nucleotide long highly repeated PQS in T. brucei, forms a stable G4 structure. G4 ligands based on carbohydrate conjugated naphthalene diimides (carb-NDIs) that bind G4's including hTel could bind EBR1 with selectivity versus dsDNA. These ligands showed important antiparasitic activity. IC 50 values were in the nanomolar range against T. brucei with high selectivity against MRC-5 human cells. Confocal microscopy confirmed these ligands localize in the nucleus and kinetoplast of T. brucei suggesting they can reach their potential G4 targets. Cytotoxicity and zebrafish toxicity studies revealed sugar conjugation reduces intrinsic toxicity of NDIs.

  3. Social Parasites

    Science.gov (United States)

    Lopez, Miguel A.; Nguyen, HoangKim T.; Oberholzer, Michael; Hill, Kent L.

    2011-01-01

    Summary of recent advances Protozoan parasites cause tremendous human suffering worldwide, but strategies for therapeutic intervention are limited. Recent studies illustrate that the paradigm of microbes as social organisms can be brought to bear on questions about parasite biology, transmission and pathogenesis. This review discusses recent work demonstrating adaptation of social behaviors by parasitic protozoa that cause African sleeping sickness and malaria. The recognition of social behavior and cell-cell communication as a ubiquitous property of bacteria has transformed our view of microbiology, but protozoan parasites have not generally been considered in this context. Works discussed illustrate the potential for concepts of sociomicrobiology to provide insight into parasite biology and should stimulate new approaches for thinking about parasites and parasite-host interactions. PMID:22020108

  4. Genomes

    National Research Council Canada - National Science Library

    Brown, T. A. (Terence A.)

    2002-01-01

    ... of genome expression and replication processes, and transcriptomics and proteomics. This text is richly illustrated with clear, easy-to-follow, full color diagrams, which are downloadable from the book's website...

  5. Fish parasites

    DEFF Research Database (Denmark)

    This book contains 22 chapters on some of the most important parasitic diseases in wild and farmed fish. International experts give updated reviews and provide solutions to the problems......This book contains 22 chapters on some of the most important parasitic diseases in wild and farmed fish. International experts give updated reviews and provide solutions to the problems...

  6. Parasitic diseases

    International Nuclear Information System (INIS)

    Rozenshtraukh, L.S.

    1983-01-01

    Foundations of roentgenological semiotics of parasitic diseases of lungs, w hich are of the greatest practical value, are presented. Roentgenological pictu res of the following parasitic diseases: hydatid and alveolar echinococcosis, pa ragonimiasis, toxoplasmosis, ascariasis, amebiasis, bilharziasis (Schistosomias is) of lungs, are considered

  7. Password cracking

    OpenAIRE

    Χριστοφάκης, Μιχαήλ Κ.

    2014-01-01

    Information security is the next big thing in computers society because of the rapidly growing security incidents and the outcomes of those. Hacking and cracking existed even from the start of the eighties decade when there was the first step of the interconnection through the internet between humans. From then and ever after there was a big explosion of such incidents mostly because of the worldwide web which was introduced in the early nineties. Following the huge steps forward of computers...

  8. Cracking hydrocarbons

    Energy Technology Data Exchange (ETDEWEB)

    Forwood, G F; Lane, M; Taplay, J G

    1921-10-07

    In cracking and hydrogenating hydrocarbon oils by passing their vapors together with steam over heated carbon derived from shale, wood, peat or other vegetable or animal matter, the gases from the condenser are freed from sulfuretted hydrogen, and preferably also from carbon dioxide, and passed together with oil vapors and steam through the retort. Carbon dioxide may be removed by passage through slaked lime, and sulfuretted hydrogen by means of hydrated oxide of iron. Vapors from high-boiling oils and those from low-boiling oils are passed alternately through the retort, so that carbon deposited from the high-boiling oils is used up during treatment of low-boiling oils.

  9. Energy parasites trigger oncogene mutation

    Czech Academy of Sciences Publication Activity Database

    Pokorný, Jiří; Pokorný, Jan; Jandová, Anna; Kobilková, J.; Vrba, J.; Vrba, J. jr.

    2016-01-01

    Roč. 92, č. 10 (2016), s. 577-582 ISSN 0955-3002 R&D Projects: GA ČR GA16-12757S Institutional support: RVO:68378271 ; RVO:67985882 Keywords : cancer initiation * cell-mediated immunity * coherent electromagnetic states * genome somatic mutation * LDH virus * parasitic energy consumption Subject RIV: BO - Biophysics Impact factor: 1.992, year: 2016

  10. Zoology: Invertebrates that Parasitize Invertebrates.

    Science.gov (United States)

    Giribet, Gonzalo

    2016-07-11

    The genome of an orthonectid, a group of highly modified parasitic invertebrates, is drastically reduced and compact, yet it shows the bilaterian gene toolkit. Phylogenetic analyses place the enigmatic orthonectids within Spiralia, although their exact placement remains uncertain. Copyright © 2016 Elsevier Ltd. All rights reserved.

  11. Parasitic Apologies

    Science.gov (United States)

    Galatolo, Renata; Ursi, Biagio; Bongelli, Ramona

    2016-01-01

    The action of apologizing can be accomplished as the main business of the interaction or incidentally while participants are doing something else. We refer to these apologies as "parasitic apologies," because they are produced "en passant" (Schegloff, 2007), and focus our analysis on this type of apology occurring at the…

  12. RNA trafficking in parasitic plant systems

    Science.gov (United States)

    LeBlanc, Megan; Kim, Gunjune; Westwood, James H.

    2012-01-01

    RNA trafficking in plants contributes to local and long-distance coordination of plant development and response to the environment. However, investigations of mobile RNA identity and function are hindered by the inherent difficulty of tracing a given molecule of RNA from its cell of origin to its destination. Several methods have been used to address this problem, but all are limited to some extent by constraints associated with accurately sampling phloem sap or detecting trafficked RNA. Certain parasitic plant species form symplastic connections to their hosts and thereby provide an additional system for studying RNA trafficking. The haustorial connections of Cuscuta and Phelipanche species are similar to graft junctions in that they are able to transmit mRNAs, viral RNAs, siRNAs, and proteins from the host plants to the parasite. In contrast to other graft systems, these parasites form connections with host species that span a wide phylogenetic range, such that a high degree of nucleotide sequence divergence may exist between host and parasites and allow confident identification of most host RNAs in the parasite system. The ability to identify host RNAs in parasites, and vice versa, will facilitate genomics approaches to understanding RNA trafficking. This review discusses the nature of host–parasite connections and the potential significance of host RNAs for the parasite. Additional research on host–parasite interactions is needed to interpret results of RNA trafficking studies, but parasitic plants may provide a fascinating new perspective on RNA trafficking. PMID:22936942

  13. RNA trafficking in parasitic plant systems

    Directory of Open Access Journals (Sweden)

    Megan L LeBlanc

    2012-08-01

    Full Text Available RNA trafficking in plants contributes to local and long-distance coordination of plant development and response to the environment. However, investigations of mobile RNA identity and function are hindered by the inherent difficulty of tracing a given molecule of RNA from its cell of origin to its destination. Several methods have been used to address this problem, but all are limited to some extent by constraints associated with accurately sampling phloem sap or detecting trafficked RNA. Certain parasitic plant species form symplastic connections to their hosts and thereby provide an additional system for studying RNA trafficking. The haustorial connections of Cuscuta and Phelipanche species are similar to graft junctions in that they are able to transmit mRNAs, viral RNAs, siRNAs and proteins from the host plants to the parasite. In contrast to other graft systems, these parasites form connections with host species that span a wide phylogenetic range, such that a high degree of nucleotide sequence divergence may exist between host and parasites and allow confident identification of most host RNAs in the parasite system. The ability to identify host RNAs in parasites, and vice versa, will facilitate genomics approaches to understanding RNA trafficking. This review discusses the nature of host parasite connections and the potential significance of host RNAs for the parasite. Additional research on host-parasite interactions is needed to interpret results of RNA trafficking studies, but parasitic plants may provide a fascinating new perspective on RNA trafficking.

  14. Modified Dugdale cracks and Fictitious cracks

    DEFF Research Database (Denmark)

    Nielsen, Lauge Fuglsang

    1998-01-01

    A number of theories are presented in the literature on crack mechanics by which the strength of damaged materials can be predicted. Among these are theories based on the well-known Dugdale model of a crack prevented from spreading by self-created constant cohesive flow stressed acting in local...... areas, so-called fictitious cracks, in front of the crack.The Modified Dugdale theory presented in this paper is also based on the concept of Dugdale cracks. Any cohesive stress distribution, however, can be considered in front of the crack. Formally the strength of a material weakened by a modified...... Dugdale crack is the same as if it has been weakened by the well-known Griffith crack, namely sigma_CR = (EG_CR/phi)^1/2 where E and 1 are Young's modulus and crack half-length respectively, and G_CR is the so-called critical energy release rate. The physical significance of G_CR, however, is different...

  15. Experimental evolution, genetic analysis and genome re-sequencing reveal the mutation conferring artemisinin resistance in an isogenic lineage of malaria parasites

    KAUST Repository

    Hunt, Paul; Martinelli, Axel; Modrzynska, Katarzyna; Borges, Sofia; Creasey, Alison; Rodrigues, Louise; Beraldi, Dario; Loewe, Laurence; Fawcett, Richard; Kumar, Sujai; Thomson, Marian; Trivedi, Urmi; Otto, Thomas D; Pain, Arnab; Blaxter, Mark; Cravo, Pedro

    2010-01-01

    was mapped to a region of chromosome 2 by Linkage Group Selection in two different genetic crosses. Whole-genome deep coverage short-read re-sequencing (IlluminaSolexa) defined the point mutations, insertions, deletions and copy-number variations arising

  16. Genome sequencing of the lizard parasite Leishmania tarentolae reveals loss of genes associated to the intracellular stage of human pathogenic species

    Science.gov (United States)

    Raymond, Frédéric; Boisvert, Sébastien; Roy, Gaétan; Ritt, Jean-François; Légaré, Danielle; Isnard, Amandine; Stanke, Mario; Olivier, Martin; Tremblay, Michel J.; Papadopoulou, Barbara; Ouellette, Marc; Corbeil, Jacques

    2012-01-01

    The Leishmania tarentolae Parrot-TarII strain genome sequence was resolved to an average 16-fold mean coverage by next-generation DNA sequencing technologies. This is the first non-pathogenic to humans kinetoplastid protozoan genome to be described thus providing an opportunity for comparison with the completed genomes of pathogenic Leishmania species. A high synteny was observed between all sequenced Leishmania species. A limited number of chromosomal regions diverged between L. tarentolae and L. infantum, while remaining syntenic to L. major. Globally, >90% of the L. tarentolae gene content was shared with the other Leishmania species. We identified 95 predicted coding sequences unique to L. tarentolae and 250 genes that were absent from L. tarentolae. Interestingly, many of the latter genes were expressed in the intracellular amastigote stage of pathogenic species. In addition, genes coding for products involved in antioxidant defence or participating in vesicular-mediated protein transport were underrepresented in L. tarentolae. In contrast to other Leishmania genomes, two gene families were expanded in L. tarentolae, namely the zinc metallo-peptidase surface glycoprotein GP63 and the promastigote surface antigen PSA31C. Overall, L. tarentolae's gene content appears better adapted to the promastigote insect stage rather than the amastigote mammalian stage. PMID:21998295

  17. Host-Parasite Interactions and Purifying Selection in a Microsporidian Parasite of Honey Bees.

    Directory of Open Access Journals (Sweden)

    Qiang Huang

    Full Text Available To clarify the mechanisms of Nosema ceranae parasitism, we deep-sequenced both honey bee host and parasite mRNAs throughout a complete 6-day infection cycle. By time-series analysis, 1122 parasite genes were significantly differently expressed during the reproduction cycle, clustering into 4 expression patterns. We found reactive mitochondrial oxygen species modulator 1 of the host to be significantly down regulated during the entire infection period. Our data support the hypothesis that apoptosis of honey bee cells was suppressed during infection. We further analyzed genome-wide genetic diversity of this parasite by comparing samples collected from the same site in 2007 and 2013. The number of SNP positions per gene and the proportion of non-synonymous substitutions per gene were significantly reduced over this time period, suggesting purifying selection on the parasite genome and supporting the hypothesis that a subset of N. ceranae strains might be dominating infection.

  18. Host-Parasite Interactions and Purifying Selection in a Microsporidian Parasite of Honey Bees.

    Science.gov (United States)

    Huang, Qiang; Chen, Yan Ping; Wang, Rui Wu; Cheng, Shang; Evans, Jay D

    2016-01-01

    To clarify the mechanisms of Nosema ceranae parasitism, we deep-sequenced both honey bee host and parasite mRNAs throughout a complete 6-day infection cycle. By time-series analysis, 1122 parasite genes were significantly differently expressed during the reproduction cycle, clustering into 4 expression patterns. We found reactive mitochondrial oxygen species modulator 1 of the host to be significantly down regulated during the entire infection period. Our data support the hypothesis that apoptosis of honey bee cells was suppressed during infection. We further analyzed genome-wide genetic diversity of this parasite by comparing samples collected from the same site in 2007 and 2013. The number of SNP positions per gene and the proportion of non-synonymous substitutions per gene were significantly reduced over this time period, suggesting purifying selection on the parasite genome and supporting the hypothesis that a subset of N. ceranae strains might be dominating infection.

  19. Cocaine (Coke, Crack) Facts

    Science.gov (United States)

    ... That People Abuse » Cocaine (Coke, Crack) Facts Cocaine (Coke, Crack) Facts Listen Cocaine is a white ... 69 KB) "My life was built around getting cocaine and getting high." ©istock.com/ Marjot Stacey is ...

  20. Parasitic diseases of lungs

    International Nuclear Information System (INIS)

    Rozenshtraukh, L.C.; Rybakova, N.I.; Vinner, M.G.

    1987-01-01

    Roentgenologic semiotics of the main parasitic diseases of lungs is described: echinococcosis, paragonimiasis, cysticercosis, toxoplasmosis, ascariasis, amebiosis and some rarely met parasitic diseases

  1. Functions of myosin motors tailored for parasitism

    DEFF Research Database (Denmark)

    Mueller, Christina; Graindorge, Arnault; Soldati-Favre, Dominique

    2017-01-01

    Myosin motors are one of the largest protein families in eukaryotes that exhibit divergent cellular functions. Their roles in protozoans, a diverse group of anciently diverged, single celled organisms with many prominent members known to be parasitic and to cause diseases in human and livestock......, are largely unknown. In the recent years many different approaches, among them whole genome sequencing, phylogenetic analyses and functional studies have increased our understanding on the distribution, protein architecture and function of unconventional myosin motors in protozoan parasites. In Apicomplexa......, myosins turn out to be highly specialized and to exhibit unique functions tailored to accommodate the lifestyle of these parasites....

  2. The origin of malarial parasites in orangutans.

    Directory of Open Access Journals (Sweden)

    M Andreína Pacheco

    Full Text Available BACKGROUND: Recent findings of Plasmodium in African apes have changed our perspectives on the evolution of malarial parasites in hominids. However, phylogenetic analyses of primate malarias are still missing information from Southeast Asian apes. In this study, we report molecular data for a malaria parasite lineage found in orangutans. METHODOLOGY/PRINCIPAL FINDINGS: We screened twenty-four blood samples from Pongo pygmaeus (Kalimantan, Indonesia for Plasmodium parasites by PCR. For all the malaria positive orangutan samples, parasite mitochondrial genomes (mtDNA and two antigens: merozoite surface protein 1 42 kDa (MSP-1(42 and circumsporozoite protein gene (CSP were amplified, cloned, and sequenced. Fifteen orangutans tested positive and yielded 5 distinct mitochondrial haplotypes not previously found. The haplotypes detected exhibited low genetic divergence among them, indicating that they belong to one species. We report phylogenetic analyses using mitochondrial genomes, MSP-1(42 and CSP. We found that the orangutan malaria parasite lineage was part of a monophyletic group that includes all the known non-human primate malaria parasites found in Southeast Asia; specifically, it shares a recent common ancestor with P. inui (a macaque parasite and P. hylobati (a gibbon parasite suggesting that this lineage originated as a result of a host switch. The genetic diversity of MSP-1(42 in orangutans seems to be under negative selection. This result is similar to previous findings in non-human primate malarias closely related to P. vivax. As has been previously observed in the other Plasmodium species found in non-human primates, the CSP shows high polymorphism in the number of repeats. However, it has clearly distinctive motifs from those previously found in other malarial parasites. CONCLUSION: The evidence available from Asian apes indicates that these parasites originated independently from those found in Africa, likely as the result of host

  3. Considering RNAi experimental design in parasitic helminths.

    Science.gov (United States)

    Dalzell, Johnathan J; Warnock, Neil D; McVeigh, Paul; Marks, Nikki J; Mousley, Angela; Atkinson, Louise; Maule, Aaron G

    2012-04-01

    Almost a decade has passed since the first report of RNA interference (RNAi) in a parasitic helminth. Whilst much progress has been made with RNAi informing gene function studies in disparate nematode and flatworm parasites, substantial and seemingly prohibitive difficulties have been encountered in some species, hindering progress. An appraisal of current practices, trends and ideals of RNAi experimental design in parasitic helminths is both timely and necessary for a number of reasons: firstly, the increasing availability of parasitic helminth genome/transcriptome resources means there is a growing need for gene function tools such as RNAi; secondly, fundamental differences and unique challenges exist for parasite species which do not apply to model organisms; thirdly, the inherent variation in experimental design, and reported difficulties with reproducibility undermine confidence. Ideally, RNAi studies of gene function should adopt standardised experimental design to aid reproducibility, interpretation and comparative analyses. Although the huge variations in parasite biology and experimental endpoints make RNAi experimental design standardization difficult or impractical, we must strive to validate RNAi experimentation in helminth parasites. To aid this process we identify multiple approaches to RNAi experimental validation and highlight those which we deem to be critical for gene function studies in helminth parasites.

  4. Investigation of Helicopter Longeron Cracks

    Science.gov (United States)

    Newman, John A.; Baughman, James; Wallace, Terryl A.

    2009-01-01

    Four cracked longerons, containing a total of eight cracks, were provided for study. Cracked regions were cut from the longerons. Load was applied to open the cracks, enabling crack surface examination. Examination revealed that crack propagation was driven by fatigue loading in all eight cases. Fatigue crack initiation appears to have occurred on the top edge of the longerons near geometric changes that affect component bending stiffness. Additionally, metallurgical analysis has revealed a local depletion in alloying elements in the crack initiation regions that may be a contributing factor. Fatigue crack propagation appeared to be initially driven by opening-mode loading, but at a crack length of approximately 0.5 inches (12.7 mm), there is evidence of mixed-mode crack loading. For the longest cracks studied, shear-mode displacements destroyed crack-surface features of interest over significant portions of the crack surfaces.

  5. Crack detecting method

    International Nuclear Information System (INIS)

    Narita, Michiko; Aida, Shigekazu

    1998-01-01

    A penetration liquid or a slow drying penetration liquid prepared by mixing a penetration liquid and a slow drying liquid is filled to the inside of an artificial crack formed to a member to be detected such as of boiler power generation facilities and nuclear power facilities. A developing liquid is applied to the periphery of the artificial crack on the surface of a member to be detected. As the slow-drying liquid, an oil having a viscosity of 56 is preferably used. Loads are applied repeatedly to the member to be detected, and when a crack is caused to the artificial crack, the permeation liquid penetrates into the crack. The penetration liquid penetrated into the crack is developed by the developing liquid previously coated to the periphery of the artificial crack of the surface of the member to be detected. When a crack is caused, since the crack is developed clearly even if it is a small opening, the crack can be recognized visually reliably. (I.N.)

  6. Curvilinear crack layer propagation

    Science.gov (United States)

    Chudnovsky, Alexander; Chaoui, Kamel; Moet, Abdelsamie

    1987-01-01

    An account is given of an experiment designed to allow observation of the effect of damage orientation on the direction of crack growth in the case of crack layer propagation, using polystyrene as the model material. The direction of crack advance under a given loading condition is noted to be determined by a competition between the tendency of the crack to maintain its current direction and the tendency to follow the orientation of the crazes at its tip. The orientation of the crazes is, on the other hand, determined by the stress field due to the interaction of the crack, the crazes, and the hole. The changes in craze rotation relative to the crack define the active zone rotation.

  7. Big bang in the evolution of extant malaria parasites.

    Science.gov (United States)

    Hayakawa, Toshiyuki; Culleton, Richard; Otani, Hiroto; Horii, Toshihiro; Tanabe, Kazuyuki

    2008-10-01

    Malaria parasites (genus Plasmodium) infect all classes of terrestrial vertebrates and display host specificity in their infections. It is therefore assumed that malaria parasites coevolved intimately with their hosts. Here, we propose a novel scenario of malaria parasite-host coevolution. A phylogenetic tree constructed using the malaria parasite mitochondrial genome reveals that the extant primate, rodent, bird, and reptile parasite lineages rapidly diverged from a common ancestor during an evolutionary short time period. This rapid diversification occurred long after the establishment of the primate, rodent, bird, and reptile host lineages, which implies that host-switch events contributed to the rapid diversification of extant malaria parasite lineages. Interestingly, the rapid diversification coincides with the radiation of the mammalian genera, suggesting that adaptive radiation to new mammalian hosts triggered the rapid diversification of extant malaria parasite lineages.

  8. Chemotherapeutic targets in parasites: contemporary strategies

    National Research Council Canada - National Science Library

    Mansour, Tag E; Mansour, Joan MacKinnon

    2002-01-01

    ... identify effective antiparasitic agents. An introduction to the early development of parasite chemotherapy is followed by an overview of biophysical techniques and genomic and proteomic analyses. Several chapters are devoted to specific types of chemotherapeutic agents and their targets in malaria, trypanosomes, leishmania, and amitochondrial...

  9. Energy parasites trigger oncogene mutation.

    Science.gov (United States)

    Pokorný, Jiří; Pokorný, Jan; Jandová, Anna; Kobilková, Jitka; Vrba, Jan; Vrba, Jan

    2016-10-01

    Cancer initialization can be explained as a result of parasitic virus energy consumption leading to randomized genome chemical bonding. Analysis of experimental data on cell-mediated immunity (CMI) containing about 12,000 cases of healthy humans, cancer patients and patients with precancerous cervical lesions disclosed that the specific cancer and the non-specific lactate dehydrogenase-elevating (LDH) virus antigen elicit similar responses. The specific antigen is effective only in cancer type of its origin but the non-specific antigen in all examined cancers. CMI results of CIN patients display both healthy and cancer state. The ribonucleic acid (RNA) of the LDH virus parasitizing on energy reduces the ratio of coherent/random oscillations. Decreased effect of coherent cellular electromagnetic field on bonding electrons in biological macromolecules leads to elevating probability of random genome reactions. Overlapping of wave functions in biological macromolecules depends on energy of the cellular electromagnetic field which supplies energy to bonding electrons for selective chemical bonds. CMI responses of cancer and LDH virus antigens in all examined healthy, precancerous and cancer cases point to energy mechanism in cancer initiation. Dependence of the rate of biochemical reactions on biological electromagnetic field explains yet unknown mechanism of genome mutation.

  10. The genome and genetics of a high oxidative stress tolerant Serratia sp. LCN16 isolated from the plant parasitic nematode Bursaphelenchus xylophilus.

    Science.gov (United States)

    Vicente, Claudia S L; Nascimento, Francisco X; Ikuyo, Yoriko; Cock, Peter J A; Mota, Manuel; Hasegawa, Koichi

    2016-04-23

    Pine wilt disease (PWD) is a worldwide threat to pine forests, and is caused by the pine wood nematode (PWN) Bursaphelenchus xylophilus. Bacteria are known to be associated with PWN and may have an important role in PWD. Serratia sp. LCN16 is a PWN-associated bacterium, highly resistant to oxidative stress in vitro, and which beneficially contributes to the PWN survival under these conditions. Oxidative stress is generated as a part of the basal defense mechanism used by plants to combat pathogenic invasion. Here, we studied the biology of Serratia sp. LCN16 through genome analyses, and further investigated, using reverse genetics, the role of two genes directly involved in the neutralization of H2O2, namely the H2O2 transcriptional factor oxyR; and the H2O2-targeting enzyme, catalase katA. Serratia sp. LCN16 is phylogenetically most closely related to the phytosphere group of Serratia, which includes S. proteamaculans, S. grimessi and S. liquefaciens. Likewise, Serratia sp. LCN16 shares many features with endophytes (plant-associated bacteria), such as genes coding for plant polymer degrading enzymes, iron uptake/transport, siderophore and phytohormone synthesis, aromatic compound degradation and detoxification enzymes. OxyR and KatA are directly involved in the high tolerance to H2O2 of Serratia sp. LCN16. Under oxidative stress, Serratia sp. LCN16 expresses katA independently of OxyR in contrast with katG which is under positive regulation of OxyR. Serratia sp. LCN16 mutants for oxyR (oxyR::int(614)) and katA (katA::int(808)) were sensitive to H2O2 in relation with wild-type, and both failed to protect the PWN from H2O2-stress exposure. Moreover, both mutants showed different phenotypes in terms of biofilm production and swimming/swarming behaviors. This study provides new insights into the biology of PWN-associated bacteria Serratia sp. LCN16 and its extreme resistance to oxidative stress conditions, encouraging further research on the potential role of this

  11. Crack layer theory

    Science.gov (United States)

    Chudnovsky, A.

    1987-01-01

    A damage parameter is introduced in addition to conventional parameters of continuum mechanics and consider a crack surrounded by an array of microdefects within the continuum mechanics framework. A system consisting of the main crack and surrounding damage is called crack layer (CL). Crack layer propagation is an irreversible process. The general framework of the thermodynamics of irreversible processes are employed to identify the driving forces (causes) and to derive the constitutive equation of CL propagation, that is, the relationship between the rates of the crack growth and damage dissemination from one side and the conjugated thermodynamic forces from another. The proposed law of CL propagation is in good agreement with the experimental data on fatigue CL propagation in various materials. The theory also elaborates material toughness characterization.

  12. Atomistics of crack propagation

    International Nuclear Information System (INIS)

    Sieradzki, K.; Dienes, G.J.; Paskin, A.; Massoumzadeh, B.

    1988-01-01

    The molecular dynamic technique is used to investigate static and dynamic aspects of crack extension. The material chosen for this study was the 2D triangular solid with atoms interacting via the Johnson potential. The 2D Johnson solid was chosen for this study since a sharp crack in this material remains stable against dislocation emission up to the critical Griffith load. This behavior allows for a meaningful comparison between the simulation results and continuum energy theorems for crack extension by appropriately defining an effective modulus which accounts for sample size effects and the non-linear elastic behavior of the Johnson solid. Simulation results are presented for the stress fields of moving cracks and these dynamic results are discussed in terms of the dynamic crack propagation theories, of Mott, Eshelby, and Freund

  13. Genomics approaches in the understanding of Entamoeba ...

    African Journals Online (AJOL)

    Entamoeba histolytica is the intestinal protozoan parasite responsible for amebic colitis and liver abscesses, which cause mortality in many developing countries. The sequencing of the parasite genome provides new insights into the cellular workings and genome evolution of this major human pathogen. Here, we reviewed ...

  14. Women and Parasitic Diseases

    Science.gov (United States)

    ... Consultations, and General Public. Contact Us Parasites Home Women Recommend on Facebook Tweet Share Compartir Infection with ... of parasites can lead to unique consequences for women. Some examples are given below. Infection with Toxoplasma ...

  15. Immunity to parasitic infection

    National Research Council Canada - National Science Library

    Lamb, Tracey J

    2012-01-01

    ... may be manipulated to develop therapeutic interventions against parasitic infection. For easy reference, the most commonly studied parasites are examined in individual chapters written by investigators at the forefront of their field...

  16. Immunity to parasitic infection

    National Research Council Canada - National Science Library

    Lamb, Tracey J

    2012-01-01

    .... Often endemic in developing countries many parasitic diseases are neglected in terms of research funding and much remains to be understood about parasites and the interactions they have with the immune system...

  17. Pets and Parasites

    Science.gov (United States)

    ... good news is that this rarely happens. Most pet-to-people diseases can be avoided by following a few ... your doctor Can a parasite cause death in people and pets? Can human disease from a parasite be treated ...

  18. Parasites as prey

    NARCIS (Netherlands)

    Goedknegt, M.A.; Welsh, J.E.; Thieltges, D.W.

    2012-01-01

    Parasites are usually considered to use their hosts as a resource for energy. However, there is increasing awareness that parasites can also become a resource themselves and serve as prey for other organisms. Here we describe various types of predation in which parasites act as prey for other

  19. Neglected Parasitic Infections: Toxocariasis

    Centers for Disease Control (CDC) Podcasts

    This podcast is an overview of the Clinician Outreach and Communication Activity (COCA) Call: Neglected Parasitic Infections in the United States. Neglected Parasitic Infections are a group of diseases that afflict vulnerable populations and are often not well studied or diagnosed. A subject matter expert from CDC's Division of Parasitic Diseases and Malaria describes the epidemiology, diagnosis, and treatment of toxocariasis.

  20. Cracked gas generator

    Energy Technology Data Exchange (ETDEWEB)

    Abthoff, J; Schuster, H D; Gabler, R

    1976-11-17

    A small cracked-gas generator in a vehicle driven, in particular, by an air combustion engine has been proposed for the economic production of the gases necessary for low toxicity combustion from diesel fuel. This proceeds via catalytic crack-gasification and exploitation of residual heat from exhaust gases. This patent application foresees the insertion of one of the catalysts supporting the cracked-gas reaction in a container through which the reacting mixture for cracked-gas production flows in longitudinal direction. Further, air ducts are embedded in the catalyst through which exhaust gases and fresh air flow in counter direction to the cracked gas flow in the catalyst. The air vents are connected through heat conduction to the catalyst. A cracked gas constituting H/sub 2//CO/CO/sub 2//CH/sub 4/ and H/sub 2/O can be produced from the air-fuel mixture using appropriate catalysts. By the addition of 5 to 25% of cracked gas to the volume of air drawn in by the combustion engine, a more favourable combustion can be achieved compared to that obtained under normal combustion conditions.

  1. Paradigms for parasite conservation.

    Science.gov (United States)

    Dougherty, Eric R; Carlson, Colin J; Bueno, Veronica M; Burgio, Kevin R; Cizauskas, Carrie A; Clements, Christopher F; Seidel, Dana P; Harris, Nyeema C

    2016-08-01

    Parasitic species, which depend directly on host species for their survival, represent a major regulatory force in ecosystems and a significant component of Earth's biodiversity. Yet the negative impacts of parasites observed at the host level have motivated a conservation paradigm of eradication, moving us farther from attainment of taxonomically unbiased conservation goals. Despite a growing body of literature highlighting the importance of parasite-inclusive conservation, most parasite species remain understudied, underfunded, and underappreciated. We argue the protection of parasitic biodiversity requires a paradigm shift in the perception and valuation of their role as consumer species, similar to that of apex predators in the mid-20th century. Beyond recognizing parasites as vital trophic regulators, existing tools available to conservation practitioners should explicitly account for the unique threats facing dependent species. We built upon concepts from epidemiology and economics (e.g., host-density threshold and cost-benefit analysis) to devise novel metrics of margin of error and minimum investment for parasite conservation. We define margin of error as the risk of accidental host extinction from misestimating equilibrium population sizes and predicted oscillations, while minimum investment represents the cost associated with conserving the additional hosts required to maintain viable parasite populations. This framework will aid in the identification of readily conserved parasites that present minimal health risks. To establish parasite conservation, we propose an extension of population viability analysis for host-parasite assemblages to assess extinction risk. In the direst cases, ex situ breeding programs for parasites should be evaluated to maximize success without undermining host protection. Though parasitic species pose a considerable conservation challenge, adaptations to conservation tools will help protect parasite biodiversity in the face of

  2. Inspecting cracks in foam insulation

    Science.gov (United States)

    Cambell, L. W.; Jung, G. K.

    1979-01-01

    Dye solution indicates extent of cracking by penetrating crack and showing original crack depth clearly. Solution comprised of methylene blue in denatured ethyl alcohol penetrates cracks completely and evaporates quickly and is suitable technique for usage in environmental or structural tests.

  3. Modelling of Corrosion Cracks

    DEFF Research Database (Denmark)

    Thoft-Christensen, Palle

    Modelling of corrosion cracking of reinforced concrete structures is complicated as a great number of uncertain factors are involved. To get a reliable modelling a physical and mechanical understanding of the process behind corrosion in needed.......Modelling of corrosion cracking of reinforced concrete structures is complicated as a great number of uncertain factors are involved. To get a reliable modelling a physical and mechanical understanding of the process behind corrosion in needed....

  4. Cracking the Gender Codes

    DEFF Research Database (Denmark)

    Rennison, Betina Wolfgang

    2016-01-01

    extensive work to raise the proportion of women. This has helped slightly, but women remain underrepresented at the corporate top. Why is this so? What can be done to solve it? This article presents five different types of answers relating to five discursive codes: nature, talent, business, exclusion...... in leadership management, we must become more aware and take advantage of this complexity. We must crack the codes in order to crack the curve....

  5. SSRI Facilitated Crack Dancing

    Directory of Open Access Journals (Sweden)

    Ravi Doobay

    2017-01-01

    Full Text Available Choreoathetoid movement secondary to cocaine use is a well-documented phenomenon better known as “crack dancing.” It consists of uncontrolled writhing movements secondary to excess dopamine from cocaine use. We present a 32-year-old male who had been using cocaine for many years and was recently started on paroxetine, a selective serotonin reuptake inhibitor (SSRI for worsening depression four weeks before presentation. He had been doing cocaine every 2 weeks for the last three years and had never “crack danced” before this episode. The authors have conducted a thorough literature review and cited studies that suggest “crack dancing” is associated with excess dopamine. There has never been a documented case report of an SSRI being linked with “crack dancing.” The authors propose that the excess dopaminergic effect of the SSRI lowered the dopamine threshold for “crack dancing.” There is a communication with the Raphe Nucleus and the Substantia Nigra, which explains how the SSRI increases dopamine levels. This is the first documented case of an SSRI facilitating the “crack dance.”

  6. Natural zeolite bitumen cracking

    Energy Technology Data Exchange (ETDEWEB)

    Kuznicki, S.M.; McCaffrey, W.C.; Bian, J.; Wangen, E.; Koenig, A. [Alberta Univ., Edmonton, AB (Canada). Dept. of Chemical and Materials Engineering

    2006-07-01

    A study was conducted to demonstrate how low cost heavy oil upgrading in the field could reduce the need for diluents while lowering the cost for pipelining. Low cost field upgrading could also contribute to lowering contaminant levels. The performance of visbreaking processes could be improved by using disposable cracking agents. In turn, the economics of field upgrading of in-situ derived bitumen would be improved. However, in order to be viable, such agents would have to be far less expensive than current commercial cracking catalysts. A platy natural zeolite was selected for modification and testing due to its unique chemical and morphological properties. A catalyst-bearing oil sand was then heat-treated for 1 hour at 400 degrees C in a sealed microreactor. Under these mild cracking conditions, the catalyst-bearing oil sand produced extractable products of much lower viscosity. The products also contained considerably more gas oil and middle distillates than raw oil sand processed under the same conditions as thermal cracking alone. According to model cracking studies using hexadecane, these modified mineral zeolites may be more active cracking agents than undiluted premium commercial FCC catalyst. These materials hold promise for partial upgrading schemes to reduce solvent requirements in the field. tabs., figs.

  7. Ultrasonic sizing of fatigue cracks

    International Nuclear Information System (INIS)

    Burns, D.J.

    1983-12-01

    Surface and buried fatigue cracks in steel plates have been sized using immersion probes as transmitters-receivers, angled to produce shear waves in the steel. Sizes have been estimated by identifying the ultrasonic waves diffracted from the crack tip and by measuring the time taken for a signal to travel to and from the crack tip. The effects of compression normal to a fatigue crack and of crack front curvature are discussed. Another diffraction technique, developed by UKAEA, Harwell, is reviewed

  8. A consistent partly cracked XFEM element for cohesive crack growth

    DEFF Research Database (Denmark)

    Asferg, Jesper L.; Poulsen, Peter Noe; Nielsen, Leif Otto

    2007-01-01

    Present extended finite element method (XFEM) elements for cohesive crack growth may often not be able to model equal stresses on both sides of the discontinuity when acting as a crack-tip element. The authors have developed a new partly cracked XFEM element for cohesive crack growth with extra...... enrichments to the cracked elements. The extra enrichments are element side local and were developed by superposition of the standard nodal shape functions for the element and standard nodal shape functions for a sub-triangle of the cracked element. With the extra enrichments, the crack-tip element becomes...... capable of modelling variations in the discontinuous displacement field on both sides of the crack and hence also capable of modelling the case where equal stresses are present on each side of the crack. The enrichment was implemented for the 3-node constant strain triangle (CST) and a standard algorithm...

  9. A crack growth evaluation method for interacting multiple cracks

    International Nuclear Information System (INIS)

    Kamaya, Masayuki

    2003-01-01

    When stress corrosion cracking or corrosion fatigue occurs, multiple cracks are frequently initiated in the same area. According to section XI of the ASME Boiler and Pressure Vessel Code, multiple cracks are considered as a single combined crack in crack growth analysis, if the specified conditions are satisfied. In crack growth processes, however, no prescription for the interference between multiple cracks is given in this code. The JSME Post-Construction Code, issued in May 2000, prescribes the conditions of crack coalescence in the crack growth process. This study aimed to extend this prescription to more general cases. A simulation model was applied, to simulate the crack growth process, taking into account the interference between two cracks. This model made it possible to analyze multiple crack growth behaviors for many cases (e.g. different relative position and length) that could not be studied by experiment only. Based on these analyses, a new crack growth analysis method was suggested for taking into account the interference between multiple cracks. (author)

  10. Foodborne parasites from wildlife

    DEFF Research Database (Denmark)

    Kapel, Christian Moliin Outzen; Fredensborg, Brian Lund

    2015-01-01

    The majority of wild foods consumed by humans are sourced from intensively managed or semi-farmed populations. Management practices inevitably affect wildlife density and habitat characteristics, which are key elements in the transmission of parasites. We consider the risk of transmission...... of foodborne parasites to humans from wildlife maintained under natural or semi-natural conditions. A deeper understanding will be useful in counteracting foodborne parasites arising from the growing industry of novel and exotic foods....

  11. Parasites, Plants, and People.

    Science.gov (United States)

    Johnson, Marion; Moore, Tony

    2016-06-01

    Anthelminthic resistance is acknowledged worldwide and is a major problem in Aotearoa New Zealand, thus alternative parasite management strategies are imperative. One Health is an initiative linking animal, human, and environmental health. Parasites, plants, and people illustrate the possibilities of providing diverse diets for stock thereby lowering parasite burdens, improving the cultural wellbeing of a local community, and protecting the environment. Copyright © 2016 Elsevier Ltd. All rights reserved.

  12. Intestinal parasites and tuberculosis

    Directory of Open Access Journals (Sweden)

    Anuar Alonso Cedeño-Burbano

    2017-10-01

    Conclusions: The available evidence was insufficient to affirm that intestinal parasites predispose to developing tuberculous. The studies carried out so far have found statistically insignificant results.

  13. Neglected Parasitic Infections: Toxocariasis

    Centers for Disease Control (CDC) Podcasts

    2012-01-05

    This podcast is an overview of the Clinician Outreach and Communication Activity (COCA) Call: Neglected Parasitic Infections in the United States. Neglected Parasitic Infections are a group of diseases that afflict vulnerable populations and are often not well studied or diagnosed. A subject matter expert from CDC's Division of Parasitic Diseases and Malaria describes the epidemiology, diagnosis, and treatment of toxocariasis.  Created: 1/5/2012 by Center for Global Health, Division of Parasitic Diseases and Malaria (DPDM); Emergency Risk Communication Branch (ERCB)/Joint Information Center (JIC), Office of Public Health Preparedness and Response (OPHPR).   Date Released: 1/9/2012.

  14. Nonlinear crack mechanics

    International Nuclear Information System (INIS)

    Khoroshun, L.P.

    1995-01-01

    The characteristic features of the deformation and failure of actual materials in the vicinity of a crack tip are due to their physical nonlinearity in the stress-concentration zone, which is a result of plasticity, microfailure, or a nonlinear dependence of the interatomic forces on the distance. Therefore, adequate models of the failure mechanics must be nonlinear, in principle, although linear failure mechanics is applicable if the zone of nonlinear deformation is small in comparison with the crack length. Models of crack mechanics are based on analytical solutions of the problem of the stress-strain state in the vicinity of the crack. On account of the complexity of the problem, nonlinear models are bason on approximate schematic solutions. In the Leonov-Panasyuk-Dugdale nonlinear model, one of the best known, the actual two-dimensional plastic zone (the nonlinearity zone) is replaced by a narrow one-dimensional zone, which is then modeled by extending the crack with a specified normal load equal to the yield point. The condition of finite stress is applied here, and hence the length of the plastic zone is determined. As a result of this approximation, the displacement in the plastic zone at the abscissa is nonzero

  15. Statistical crack mechanics

    International Nuclear Information System (INIS)

    Dienes, J.K.

    1993-01-01

    Although it is possible to simulate the ground blast from a single explosive shot with a simple computer algorithm and appropriate constants, the most commonly used modelling methods do not account for major changes in geology or shot energy because mechanical features such as tectonic stresses, fault structure, microcracking, brittle-ductile transition, and water content are not represented in significant detail. An alternative approach for modelling called Statistical Crack Mechanics is presented in this paper. This method, developed in the seventies as a part of the oil shale program, accounts for crack opening, shear, growth, and coalescence. Numerous photographs and micrographs show that shocked materials tend to involve arrays of planar cracks. The approach described here provides a way to account for microstructure and give a representation of the physical behavior of a material at the microscopic level that can account for phenomena such as permeability, fragmentation, shear banding, and hot-spot formation in explosives

  16. Cracking the Cipher Challenge

    CERN Document Server

    CERN. Geneva. Audiovisual Unit; Singh, Simon

    2002-01-01

    In the back of 'The Code Book', a history of cryptography, Simon Singh included a series of 10 encoded messages, each from a different period of history. The first person to crack all 10 messages would win a prize of £10,000. Now that the prize has been won, Simon can reveal the story behind the Cipher Challenge. Along the way he will show how mathematics can be used to crack codes, the role it played in World War Two and how it helps to guarantee security in the Information Age.

  17. PARASITES OF FISH

    Science.gov (United States)

    The intent of this chapter is to describe the parasites of importance to fishes maintained and used in laboratory settings. In contrast to the frist edition, the focus will be only on those parasites that pose a serious threat to or are common in fishes held in these confined en...

  18. Parasites from the Past

    DEFF Research Database (Denmark)

    Søe, Martin Jensen; Fredensborg, Brian Lund; Nejsum, Peter

    will investigate how the diversity of food-borne parasitic infections has changed with cultural and dietary habits, hunting practice and intensity of animal husbandry. This is done by isolating and typing ancient DNA remains from parasite eggs found in archeological samples from across Denmark....

  19. Microstructural modelling of creep crack growth from a blunted crack

    NARCIS (Netherlands)

    Onck, P.R.; Giessen, E. van der

    1998-01-01

    The effect of crack tip blunting on the initial stages of creep crack growth is investigated by means of a planar microstructural model in which grains are represented discretely. The actual linking-up process of discrete microcracks with the macroscopic crack is simulated, with full account of the

  20. The neurotropic parasite Toxoplasma gondii increases dopamine metabolism.

    Directory of Open Access Journals (Sweden)

    Emese Prandovszky

    Full Text Available The highly prevalent parasite Toxoplasma gondii manipulates its host's behavior. In infected rodents, the behavioral changes increase the likelihood that the parasite will be transmitted back to its definitive cat host, an essential step in completion of the parasite's life cycle. The mechanism(s responsible for behavioral changes in the host is unknown but two lines of published evidence suggest that the parasite alters neurotransmitter signal transduction: the disruption of the parasite-induced behavioral changes with medications used to treat psychiatric disease (specifically dopamine antagonists and identification of a tyrosine hydroxylase encoded in the parasite genome. In this study, infection of mammalian dopaminergic cells with T. gondii enhanced the levels of K+-induced release of dopamine several-fold, with a direct correlation between the number of infected cells and the quantity of dopamine released. Immunostaining brain sections of infected mice with dopamine antibody showed intense staining of encysted parasites. Based on these analyses, T. gondii orchestrates a significant increase in dopamine metabolism in neural cells. Tyrosine hydroxylase, the rate-limiting enzyme for dopamine synthesis, was also found in intracellular tissue cysts in brain tissue with antibodies specific for the parasite-encoded tyrosine hydroxylase. These observations provide a mechanism for parasite-induced behavioral changes. The observed effects on dopamine metabolism could also be relevant in interpreting reports of psychobehavioral changes in toxoplasmosis-infected humans.

  1. Linear Cracking in Bridge Decks

    Science.gov (United States)

    2018-03-01

    Concrete cracking in bridge decks remains an important issue relative to deck durability. Cracks can allow increased penetration of chlorides, which can result in premature corrosion of the reinforcing steel and subsequent spalling of the concrete de...

  2. Crack detection '86

    International Nuclear Information System (INIS)

    1986-01-01

    The participants of the conference heard 36 papers of which 13 were incorporated in INIS. The incorporated papers deal with the quality control of the equipment of nuclear power plants, with technical specifications and possibilities of diverse crack detection devices, as well as with personnel training for nondestructive materials testing. (E.S.)

  3. Sexual reproduction and genetic exchange in parasitic protists.

    Science.gov (United States)

    Weedall, Gareth D; Hall, Neil

    2015-02-01

    A key part of the life cycle of an organism is reproduction. For a number of important protist parasites that cause human and animal disease, their sexuality has been a topic of debate for many years. Traditionally, protists were considered to be primitive relatives of the 'higher' eukaryotes, which may have diverged prior to the evolution of sex and to reproduce by binary fission. More recent views of eukaryotic evolution suggest that sex, and meiosis, evolved early, possibly in the common ancestor of all eukaryotes. However, detecting sex in these parasites is not straightforward. Recent advances, particularly in genome sequencing technology, have allowed new insights into parasite reproduction. Here, we review the evidence on reproduction in parasitic protists. We discuss protist reproduction in the light of parasitic life cycles and routes of transmission among hosts.

  4. Host-parasite interactions and ecology of the malaria parasite-a bioinformatics approach.

    Science.gov (United States)

    Izak, Dariusz; Klim, Joanna; Kaczanowski, Szymon

    2018-04-25

    Malaria remains one of the highest mortality infectious diseases. Malaria is caused by parasites from the genus Plasmodium. Most deaths are caused by infections involving Plasmodium falciparum, which has a complex life cycle. Malaria parasites are extremely well adapted for interactions with their host and their host's immune system and are able to suppress the human immune system, erase immunological memory and rapidly alter exposed antigens. Owing to this rapid evolution, parasites develop drug resistance and express novel forms of antigenic proteins that are not recognized by the host immune system. There is an emerging need for novel interventions, including novel drugs and vaccines. Designing novel therapies requires knowledge about host-parasite interactions, which is still limited. However, significant progress has recently been achieved in this field through the application of bioinformatics analysis of parasite genome sequences. In this review, we describe the main achievements in 'malarial' bioinformatics and provide examples of successful applications of protein sequence analysis. These examples include the prediction of protein functions based on homology and the prediction of protein surface localization via domain and motif analysis. Additionally, we describe PlasmoDB, a database that stores accumulated experimental data. This tool allows data mining of the stored information and will play an important role in the development of malaria science. Finally, we illustrate the application of bioinformatics in the development of population genetics research on malaria parasites, an approach referred to as reverse ecology.

  5. Crack closure, a literature study

    Science.gov (United States)

    Holmgren, M.

    1993-08-01

    In this report crack closure is treated. The state of the art is reviewed. Different empirical formulas for determining the crack closure are compared with each other, and their benefits are discussed. Experimental techniques for determining the crack closure stress are discussed, and some results from fatigue tests are also reported. Experimental data from the literature are reported.

  6. [What makes a parasite "transforming"? Insights into cancer from the agents of an exotic pathology, Theileria spp].

    Science.gov (United States)

    Cheeseman, K M; Weitzman, J B

    2017-02-01

    Theileria are obligate eukaryotic intracellular parasites of cattle. The diseases they cause, Tropical theileriosis and East Coast Fever, cause huge economic loss in East African, Mediterranean and central and South-East Asian countries. These apicomplexan parasites are the only intracellular eukaryotic parasites known to transform their host cell and represent a unique model to study host-parasite interactions and mechanisms of cancer onset.Here, we review how Theileria parasites induce transformation of their leukocyte host cell and discuss similarities with tumorigenesis. We describe how genomic innovation, epigenetic changes and hijacking of signal transductions enable a eukaryotic parasite to transform its host cell.

  7. Children and Parasitic Diseases

    Science.gov (United States)

    ... because they disproportionately affect impoverished people. More on: Neglected Tropical Diseases Prevention One of the most important ways to help prevent these parasitic diseases is to teach children the importance of washing hands correctly with soap ...

  8. Parasites and the skin

    African Journals Online (AJOL)

    2009-06-11

    Jun 11, 2009 ... those conditions that are encountered in daily practice and to remind you of those ... care conditions. Parasitic infections can be solely confined to the skin, as seen ..... endemic areas or may become chronic and disseminate.

  9. Parasitic Diseases: Glossary

    Science.gov (United States)

    ... of the leg. Endemic: A disease that is native to a particular geographic region. Epidemiology: The study ... parasites/glossary.html) T Telediagnosis: The transmission of digital images captured from a clinical specimen and sent ...

  10. Choked flow through cracks

    International Nuclear Information System (INIS)

    Feburie, V.; Giot, M.; Granger, S.; Seynhaeve, J.M.

    1992-06-01

    The leaks through steam-generator cracks are the subject of a research carried out in cooperation between EDF and UCL. A software called ECREVISSE to predict the mass flow rate has been developed and has been successfully validated. The purpose of the paper is to present the mathematical model used in ECREVISSE as well as some comparison between the results and the presently available data. The model takes into account the persistence of some metastable liquid in the crack and the special flow pattern which appears in such particular geometry. Although the model involves the use of several correlations (friction, heat transfer), no adjustment of parameters against the data has been needed, neither in the single-phase part of the flow, or in the two-phase part. (authors). 8 figs., 1 tab., 20 refs

  11. Delayed hydride cracking: alternative pre-cracking method

    International Nuclear Information System (INIS)

    Mieza, Juan I.; Ponzoni, Lucio M.E.; Vigna, Gustavo L.; Domizzi, Gladys

    2009-01-01

    The internal components of nuclear reactors built-in Zr alloys are prone to a failure mechanism known as Delayed Hydride Cracking (DHC). This situation has triggered numerous scientific studies in order to measure the crack propagation velocity and the threshold stress intensity factor associated to DHC. Tests are carried out on fatigued pre-crack samples to ensure similar test conditions and comparable results. Due to difficulties in implementing the fatigue pre-crack method it would be desirable to replace it with a pre-crack produced by the same process of DHC, for which is necessary to demonstrate equivalence of this two methods. In this work tests on samples extracted from two Zr-2.5 Nb tubes were conducted. Some of the samples were heat treated to obtain a range in their metallurgical properties as well as different DHC velocities. A comparison between velocities measured in test samples pre-cracked by fatigue and RDIH is done, demonstrating that the pre-cracking method does not affect the measured velocity value. In addition, the incubation (t inc ), which is the time between the application of the load and the first signal of crack propagation, in samples pre-cracked by RDIH, was measured. It was found that these times are sufficiently short, even in the worst cases (lower speed) and similar to the ones of fatigued pre-cracked samples. (author)

  12. Fatigue Crack Topography.

    Science.gov (United States)

    1984-01-01

    alloys (2). [--I Fig. 6. Fatigue fracture in Nitrile- butadien rubber ( NBR ). Fig. 7. The characteristic features of fatigue fracture in press moulded...in plastics and even in rubber . It follows therefore, that fatigue fractures must also occur in the mineral layers of our earth or in the rock on...effective until the weakest point yields and forms a crack. To get a feeling for this process, you can imagine that the stressed article is made of rubber

  13. Distributed password cracking

    OpenAIRE

    Crumpacker, John R.

    2009-01-01

    Approved for public release, distribution unlimited Password cracking requires significant processing power, which in today's world is located at a workstation or home in the form of a desktop computer. Berkeley Open Infrastructure for Network Computing (BOINC) is the conduit to this significant source of processing power and John the Ripper is the key. BOINC is a distributed data processing system that incorporates client-server relationships to generically process data. The BOINC structu...

  14. Utopia Cracks and Polygons

    Science.gov (United States)

    2003-01-01

    MGS MOC Release No. MOC2-339, 23 April 2003This Mars Global Surveyor (MGS) Mars Orbiter Camera (MOC) image shows a pattern of polygonal cracks and aligned, elliptical pits in western Utopia Planitia. The picture covers an area about 3 km (about 1.9 mi) wide near 44.9oN, 274.7oW. Sunlight illuminates the scene from the left.

  15. Imaging of parasitic diseases

    International Nuclear Information System (INIS)

    Haddad, Maurice C.

    2008-01-01

    This book provides an overview of the imaging findings of parasitic diseases using modern imaging equipment. The chapters consist of short descriptions of causative pathogens, epidemiology, modes of transmission, pathology, clinical manifestations, laboratory tests, and imaging findings, with illustrative examples of parasitic diseases that can affect various systems of the human body. Tables summarizing key diagnostic features and clinical data pertinent to diagnosis are also included. This book is intended for radiologists worldwide. (orig.)

  16. Imaging of parasitic diseases

    Energy Technology Data Exchange (ETDEWEB)

    Haddad, Maurice C. [American Univ. of Beirut Medical Center (Lebanon). Dept. of Diagnostic Radiology; Abd El Bagi, Mohamed E. [Riyadh Military Hospital (Saudi Arabia). Radiology and Imaging Dept. 920W; Tamraz, Jean C. (eds.) [CHU Hotel-Dieu de France, Beirut (Lebanon)

    2008-07-01

    This book provides an overview of the imaging findings of parasitic diseases using modern imaging equipment. The chapters consist of short descriptions of causative pathogens, epidemiology, modes of transmission, pathology, clinical manifestations, laboratory tests, and imaging findings, with illustrative examples of parasitic diseases that can affect various systems of the human body. Tables summarizing key diagnostic features and clinical data pertinent to diagnosis are also included. This book is intended for radiologists worldwide. (orig.)

  17. Pathoecology of Chiribaya parasitism

    Directory of Open Access Journals (Sweden)

    Martinson Elizabeth

    2003-01-01

    Full Text Available The excavations of Chiribaya culture sites in the Osmore drainage of southern Peru focused on the recovery of information about prehistoric disease, including parasitism. The archaeologists excavated human, dog, guinea pig, and llama mummies. These mummies were analyzed for internal and external parasites. The results of the analysis and reconstruction of prehistoric life from the excavations allows us to interpret the pathoecology of the Chiribaya culture.

  18. Cracking hydrocarbons. [British patent

    Energy Technology Data Exchange (ETDEWEB)

    Heyl, G E

    1926-05-06

    The vapors from a still in which oils, coal tar, pitch, creosote, and c. or solid carbonaccous material such as coal or shale are cracked by being heated to 600/sup 0/ to 1000/sup 0/C. are passed through a fractionating column to remove high-boiling constituents which are passed into a second cracking still. The vapors from this still are treated to separate high-boiling fractions which are passed into a third still. The sills preferably contain removable troughs or liners, which are freed from carbon deposits either after removal from the still or by a scraping disc which is rotated in and moved along the trough. Oil to be cracked is forced by a pump through a preheater to a still. Vapours pass through a carbon separator and dephlegmator to a condenser. The reflux from the dephlegmator is forced by a pump to a still, the vapors from which pass through a carbon separator and a dephlegmator, the reflux from which is passed into a third still fitted with a separate carbon separator, dephlegmator and final condenser.

  19. Musa sebagai Model Genom

    Directory of Open Access Journals (Sweden)

    RITA MEGIA

    2005-12-01

    Full Text Available During the meeting in Arlington, USA in 2001, the scientists grouped in PROMUSA agreed with the launching of the Global Musa Genomics Consortium. The Consortium aims to apply genomics technologies to the improvement of this important crop. These genome projects put banana as the third model species after Arabidopsis and rice that will be analyzed and sequenced. Comparing to Arabidopsis and rice, banana genome provides a unique and powerful insight into structural and in functional genomics that could not be found in those two species. This paper discussed these subjects-including the importance of banana as the fourth main food in the world, the evolution and biodiversity of this genetic resource and its parasite.

  20. Prevalence of Parasitic Contamination

    Science.gov (United States)

    Ismail, Yazan

    2016-01-01

    One of the main ways in transmitting parasites to humans is through consuming contaminated raw vegetables. The aim of this study was to evaluate the prevalence of parasitological contamination (helminthes eggs, Giardia and Entamoeba histolytica cysts) of salad vegetables sold at supermarkets and street vendors in Amman and Baqa’a – Jordan. A total of 133 samples of salad vegetables were collected and examined for the prevalence of parasites. It was found that 29% of the samples were contaminated with different parasites. Of the 30 lettuce, 33 tomato, 42 parsley and 28 cucumber samples examined the prevalence of Ascaris spp. eggs was 43%, 15%, 21% and 4%; Toxocara spp. eggs was 30%, 0%, 0% and 4%; Giardia spp. cysts was 23%, 6%, 0% and 0%; Taenia/Echinococcus eggs was 20%, 0%, 5% and 0%; Fasciola hepatica eggs was 13%, 3%, 2% and 0%; and E. histolytica cysts was 10%, 6%, 0% and 0%, respectively. There was no significant difference in the prevalence of parasite in salad vegetables either between supermarkets and street vendors, or between Amman and Baqa’a, Ascaris spp. was found to be the highest prevalent parasite in salad vegetables from supermarkets and street vendors and from Amman and Baqa’a. Our results pointed out that, the parasitic contamination of salad vegetables found in our study might be caused by irrigating crops with faecal contaminated water. We concluded that salad vegetables sold in Amman and Baqa’a may cause a health risk to consumers.

  1. Parasites in marine food webs

    Science.gov (United States)

    Lafferty, Kevin D.

    2013-01-01

    Most species interactions probably involve parasites. This review considers the extent to which marine ecologists should consider parasites to fully understand marine communities. Parasites are influential parts of food webs in estuaries, temperate reefs, and coral reefs, but their ecological importance is seldom recognized. Though difficult to observe, parasites can have substantial biomass, and they can be just as common as free-living consumers after controlling for body mass and trophic level. Parasites have direct impacts on the energetics of their hosts and some affect host behaviors, with ecosystem-level consequences. Although they cause disease, parasites are sensitive components of ecosystems. In particular, they suffer secondary extinctions due to biodiversity loss. Some parasites can also return to a system after habitat restoration. For these reasons, parasites can make good indicators of ecosystem integrity. Fishing can indirectly increase or decrease parasite populations and the effects of climate change on parasites are likely to be equally as complex.

  2. Investigation of Cracks Found in Helicopter Longerons

    Science.gov (United States)

    Newman, John A.; Baughman, James M.; Wallace, Terryl A.

    2009-01-01

    Four cracked longerons, containing a total of eight cracks, were provided for study. Cracked regions were cut from the longerons. Load was applied to open the cracks, enabling crack surface examination. Examination revealed that crack propagation was driven by fatigue loading in all eight cases. Fatigue crack initiation appears to have occurred on the top edge of the longerons near geometric changes that affect component bending stiffness. Additionally, metallurigical analysis has revealed a local depletion in alloying elements in the crack initiation regions that may be a contributing factor. Fatigue crack propagation appeared to be initially driven by opening-mode loading, but at a crack length of approximately 0.5 inches (12.7 mm), there is evidence of mixed-mode crack loading. For the longest cracks studied, shear-mode displacements destroyed crack-surface features of interest over significant portions of the crack surfaces.

  3. Modified Dugdale crack models - some easy crack relations

    DEFF Research Database (Denmark)

    Nielsen, Lauge Fuglsang

    1997-01-01

    the same strength as a plain Dugdale model. The critical energy release rates Gamma_CR, however, become different. Expressions (with easy computer algorithms) are presented in the paper which relate critical energy release rates and crack geometry to arbitrary cohesive stress distributions.For future...... lifetime analysis of viscoelastic materials strain energy release rates, crack geometries, and cohesive stress distributions are considered as related to sub-critical loads sigma stress-deformation tests......The Dugdale crack model is widely used in materials science to predict strength of defective (cracked) materials. A stable Dugdale crack in an elasto-plastic material is prevented from spreading by uniformly distributed cohesive stresses acting in narrow areas at the crack tips. These stresses...

  4. Drug target identification in protozoan parasites.

    Science.gov (United States)

    Müller, Joachim; Hemphill, Andrew

    2016-08-01

    Despite the fact that diseases caused by protozoan parasites represent serious challenges for public health, animal production and welfare, only a limited panel of drugs has been marketed for clinical applications. Herein, the authors investigate two strategies, namely whole organism screening and target-based drug design. The present pharmacopoeia has resulted from whole organism screening, and the mode of action and targets of selected drugs are discussed. However, the more recent extensive genome sequencing efforts and the development of dry and wet lab genomics and proteomics that allow high-throughput screening of interactions between micromolecules and recombinant proteins has resulted in target-based drug design as the predominant focus in anti-parasitic drug development. Selected examples of target-based drug design studies are presented, and calcium-dependent protein kinases, important drug targets in apicomplexan parasites, are discussed in more detail. Despite the enormous efforts in target-based drug development, this approach has not yet generated market-ready antiprotozoal drugs. However, whole-organism screening approaches, comprising of both in vitro and in vivo investigations, should not be disregarded. The repurposing of already approved and marketed drugs could be a suitable strategy to avoid fastidious approval procedures, especially in the case of neglected or veterinary parasitoses.

  5. Global gene expression analysis of the zoonotic parasite Trichinella spiralis revealed novel genes in host parasite interaction.

    Directory of Open Access Journals (Sweden)

    Xiaolei Liu

    Full Text Available BACKGROUND: Trichinellosis is a typical food-borne zoonotic disease which is epidemic worldwide and the nematode Trichinella spiralis is the main pathogen. The life cycle of T. spiralis contains three developmental stages, i.e. adult worms, new borne larva (new borne L1 larva and muscular larva (infective L1 larva. Stage-specific gene expression in the parasites has been investigated with various immunological and cDNA cloning approaches, whereas the genome-wide transcriptome and expression features of the parasite have been largely unknown. The availability of the genome sequence information of T. spiralis has made it possible to deeply dissect parasite biology in association with global gene expression and pathogenesis. METHODOLOGY AND PRINCIPAL FINDINGS: In this study, we analyzed the global gene expression patterns in the three developmental stages of T. spiralis using digital gene expression (DGE analysis. Almost 15 million sequence tags were generated with the Illumina RNA-seq technology, producing expression data for more than 9,000 genes, covering 65% of the genome. The transcriptome analysis revealed thousands of differentially expressed genes within the genome, and importantly, a panel of genes encoding functional proteins associated with parasite invasion and immuno-modulation were identified. More than 45% of the genes were found to be transcribed from both strands, indicating the importance of RNA-mediated gene regulation in the development of the parasite. Further, based on gene ontological analysis, over 3000 genes were functionally categorized and biological pathways in the three life cycle stage were elucidated. CONCLUSIONS AND SIGNIFICANCE: The global transcriptome of T. spiralis in three developmental stages has been profiled, and most gene activity in the genome was found to be developmentally regulated. Many metabolic and biological pathways have been revealed. The findings of the differential expression of several protein

  6. Crack retardation by load reduction during fatigue crack propagation

    International Nuclear Information System (INIS)

    Kim, Hyun Soo; Nam, Ki Woo; Ahn, Seok Hwan; Do, Jae Yoon

    2003-01-01

    Fracture life and crack retardation behavior were examined experimentally using CT specimens of aluminum alloy 5083. Crack retardation life and fracture life were a wide difference between 0.8 and 0.6 in proportion to ratio of load reduction. The wheeler model retardation parameter was used successfully to predict crack growth behavior. By using a crack propagation rule, prediction of fracture life can be evaluated quantitatively. A statistical approach based on Weibull distribution was applied to the test data to evaluate the dispersion in the retardation life and fracture life by the change of load reduction

  7. Ductile crack growth simulation from near crack tip dissipated energy

    International Nuclear Information System (INIS)

    Marie, S.; Chapuliot, S.

    2000-01-01

    A method to calculate ductile tearing in both small scale fracture mechanics specimens and cracked components is presented. This method is based on an estimation of the dissipated energy calculated near the crack tip. Firstly, the method is presented. It is shown that a characteristic parameter G fr can be obtained, relevant to the dissipated energy in the fracture process. The application of the method to the calculation of side grooved crack tip (CT) specimens of different sizes is examined. The value of G fr is identified by comparing the calculated and experimental load line displacement versus crack extension curve for the smallest CT specimen. With this identified value, it is possible to calculate the global behaviour of the largest specimen. The method is then applied to the calculation of a pipe containing a through-wall thickness crack subjected to a bending moment. This pipe is made of the same material as the CT specimens. It is shown that it is possible to simulate the global behaviour of the structure including the prediction of up to 90-mm crack extension. Local terms such as the equivalent stress or the crack tip opening angle are found to be constant during the crack extension process. This supports the view that G fr controls the fields in the vicinity near the crack tip. (orig.)

  8. A Cas9 transgenic Plasmodium yoelii parasite for efficient gene editing.

    Science.gov (United States)

    Qian, Pengge; Wang, Xu; Yang, Zhenke; Li, Zhenkui; Gao, Han; Su, Xin-Zhuan; Cui, Huiting; Yuan, Jing

    2018-06-01

    The RNA-guided endonuclease Cas9 has applied as an efficient gene-editing method in malaria parasite Plasmodium. However, the size (4.2 kb) of the commonly used Cas9 from Streptococcus pyogenes (SpCas9) limits its utility for genome editing in the parasites only introduced with cas9 plasmid. To establish the endogenous and constitutive expression of Cas9 protein in the rodent malaria parasite P. yoelii, we replaced the coding region of an endogenous gene sera1 with the intact SpCas9 coding sequence using the CRISPR/Cas9-mediated genome editing method, generating the cas9-knockin parasite (PyCas9ki) of the rodent malaria parasite P. yoelii. The resulted PyCas9ki parasite displays normal progression during the whole life cycle and possesses the Cas9 protein expression in asexual blood stage. By introducing the plasmid (pYCs) containing only sgRNA and homologous template elements, we successfully achieved both deletion and tagging modifications for different endogenous genes in the genome of PyCas9ki parasite. This cas9-knockin PyCas9ki parasite provides a new platform facilitating gene functions study in the rodent malaria parasite P. yoelii. Copyright © 2018 Elsevier B.V. All rights reserved.

  9. Sequence mining and transcript profiling to explore cyst nematode parasitism

    Directory of Open Access Journals (Sweden)

    Recknor Justin

    2009-01-01

    Full Text Available Abstract Background Cyst nematodes are devastating plant parasites that become sedentary within plant roots and induce the transformation of normal plant cells into elaborate feeding cells with the help of secreted effectors, the parasitism proteins. These proteins are the translation products of parasitism genes and are secreted molecular tools that allow cyst nematodes to infect plants. Results We present here the expression patterns of all previously described parasitism genes of the soybean cyst nematode, Heterodera glycines, in all major life stages except the adult male. These insights were gained by analyzing our gene expression dataset from experiments using the Affymetrix Soybean Genome Array GeneChip, which contains probeset sequences for 6,860 genes derived from preparasitic and parasitic H. glycines life stages. Targeting the identification of additional H. glycines parasitism-associated genes, we isolated 633 genes encoding secretory proteins using algorithms to predict secretory signal peptides. Furthermore, because some of the known H. glycines parasitism proteins have strongest similarity to proteins of plants and microbes, we searched for predicted protein sequences that showed their highest similarities to plant or microbial proteins and identified 156 H. glycines genes, some of which also contained a signal peptide. Analyses of the expression profiles of these genes allowed the formulation of hypotheses about potential roles in parasitism. This is the first study combining sequence analyses of a substantial EST dataset with microarray expression data of all major life stages (except adult males for the identification and characterization of putative parasitism-associated proteins in any parasitic nematode. Conclusion We have established an expression atlas for all known H. glycines parasitism genes. Furthermore, in an effort to identify additional H. glycines genes with putative functions in parasitism, we have reduced the

  10. Transport proteins of parasitic protists and their role in nutrient salvage.

    Science.gov (United States)

    Dean, Paul; Major, Peter; Nakjang, Sirintra; Hirt, Robert P; Embley, T Martin

    2014-01-01

    The loss of key biosynthetic pathways is a common feature of important parasitic protists, making them heavily dependent on scavenging nutrients from their hosts. This is often mediated by specialized transporter proteins that ensure the nutritional requirements of the parasite are met. Over the past decade, the completion of several parasite genome projects has facilitated the identification of parasite transporter proteins. This has been complemented by functional characterization of individual transporters along with investigations into their importance for parasite survival. In this review, we summarize the current knowledge on transporters from parasitic protists and highlight commonalities and differences in the transporter repertoires of different parasitic species, with particular focus on characterized transporters that act at the host-pathogen interface.

  11. Cracking of anisotropic cylindrical polytropes

    Energy Technology Data Exchange (ETDEWEB)

    Mardan, S.A. [University of the Management and Technology, Department of Mathematics, Lahore (Pakistan); Azam, M. [University of Education, Division of Science and Technology, Lahore (Pakistan)

    2017-06-15

    We study the appearance of cracking in charged anisotropic cylindrical polytropes with generalized polytropic equation. We investigate the existence of cracking in two different kinds of polytropes existing in the literature through two different assumptions: (a) local density perturbation with conformally flat condition, and (b) perturbing polytropic index, charge and anisotropy parameters. We conclude that cracking appears in both kinds of polytropes for a specific range of density and model parameters. (orig.)

  12. Cryptography cracking codes

    CERN Document Server

    2014-01-01

    While cracking a code might seem like something few of us would encounter in our daily lives, it is actually far more prevalent than we may realize. Anyone who has had personal information taken because of a hacked email account can understand the need for cryptography and the importance of encryption-essentially the need to code information to keep it safe. This detailed volume examines the logic and science behind various ciphers, their real world uses, how codes can be broken, and the use of technology in this oft-overlooked field.

  13. Stress corrosion cracking

    International Nuclear Information System (INIS)

    Dietzel, W.; Turnbull, A.

    2007-01-01

    Comprehensive Structural Integrity is a reference work which covers all activities involved in the assurance of structural integrity. It provides engineers and scientists with an unparalleled depth of knowledge in the disciplines involved. The new online Volume 11 is dedicated to the mechanical characteristics of materials. This paper contains the chapter 11.03 and is structured as follows: General aspects of SCC testing; Non-precracked specimens; Precracked specimens - the fracture mechanics approach to SCC; Crack growth measurement; Limitations of the LEFM approach to SCC; The use of SCC data; Guide to selection of mechanical scc test method

  14. Anthelmintic metabolism in parasitic helminths: proteomic insights.

    Science.gov (United States)

    Brophy, Peter M; MacKintosh, Neil; Morphew, Russell M

    2012-08-01

    Anthelmintics are the cornerstone of parasitic helminth control. Surprisingly, understanding of the biochemical pathways used by parasitic helminths to detoxify anthelmintics is fragmented, despite the increasing global threat of anthelmintic resistance within the ruminant and equine industries. Reductionist biochemistry has likely over-estimated the enzymatic role of glutathione transferases in anthelmintic metabolism and neglected the potential role of the cytochrome P-450 superfamily (CYPs). Proteomic technologies offers the opportunity to support genomics, reverse genetics and pharmacokinetics, and provide an integrated insight into both the cellular mechanisms underpinning response to anthelmintics and also the identification of biomarker panels for monitoring the development of anthelmintic resistance. To date, there have been limited attempts to include proteomics in anthelmintic metabolism studies. Optimisations of membrane, post-translational modification and interaction proteomic technologies in helminths are needed to especially study Phase I CYPs and Phase III ABC transporter pumps for anthelmintics and their metabolites.

  15. Grand-scale theft: kleptoplasty in parasitic plants?

    Science.gov (United States)

    Krause, Kirsten

    2015-04-01

    The angiosperm Rafflesia lives as an obligate holoparasite in intimate contact with its hosts, vines in the genus Tetrastigma. The hosts are forced to supply the parasite with all the necessary nutrients. Novel data tentatively suggest that the thievery may happen on a larger scale and include entire organellar genomes. Copyright © 2015 Elsevier Ltd. All rights reserved.

  16. Malaria Parasite Metabolic Pathways (MPMP) Upgraded with Targeted Chemical Compounds

    KAUST Repository

    Ginsburg, Hagai

    2015-10-31

    Malaria Parasite Metabolic Pathways (MPMP) is the website for the functional genomics of intraerythrocytic Plasmodium falciparum. All the published information about targeted chemical compounds has now been added. Users can find the drug target and publication details linked to a drug database for further information about the medicinal properties of each compound.

  17. Malaria Parasite Metabolic Pathways (MPMP) Upgraded with Targeted Chemical Compounds

    KAUST Repository

    Ginsburg, Hagai; Abdel-Haleem, Alyaa M.

    2015-01-01

    Malaria Parasite Metabolic Pathways (MPMP) is the website for the functional genomics of intraerythrocytic Plasmodium falciparum. All the published information about targeted chemical compounds has now been added. Users can find the drug target and publication details linked to a drug database for further information about the medicinal properties of each compound.

  18. Malaria Parasite Metabolic Pathways (MPMP) Upgraded with Targeted Chemical Compounds.

    Science.gov (United States)

    Ginsburg, Hagai; Abdel-Haleem, Alyaa M

    2016-01-01

    Malaria Parasite Metabolic Pathways (MPMP) is the website for the functional genomics of intraerythrocytic Plasmodium falciparum. All the published information about targeted chemical compounds has now been added. Users can find the drug target and publication details linked to a drug database for further information about the medicinal properties of each compound. Copyright © 2015 Elsevier Ltd. All rights reserved.

  19. Characterizing Ancylostoma caninum transcriptome and exploring nematode parasitic adaptation

    Directory of Open Access Journals (Sweden)

    Hawdon John

    2010-05-01

    Full Text Available Abstract Background Hookworm infection is one of the most important neglected diseases in developing countries, with approximately 1 billion people infected worldwide. To better understand hookworm biology and nematode parasitism, the present study generated a near complete transcriptome of the canine hookworm Ancylostoma caninum to a very high coverage using high throughput technology, and compared it to those of the free-living nematode Caenorhabditis elegans and the parasite Brugia malayi. Results The generated transcripts from four developmental stages, infective L3, serum stimulated L3, adult male and adult female, covered 93% of the A. caninum transcriptome. The broad diversity among nematode transcriptomes was confirmed, and an impact of parasitic adaptation on transcriptome diversity was inferred. Intra-population analysis showed that A. caninum has higher coding sequence diversity than humans. Examining the developmental expression profiles of A. caninum revealed major transitions in gene expression from larval stages to adult. Adult males expressed the highest number of selectively expressed genes, but adult female expressed the highest number of selective parasitism-related genes. Genes related to parasitism adaptation and A. caninum specific genes exhibited more expression selectivity while those conserved in nematodes tend to be consistently expressed. Parasitism related genes were expressed more selectively in adult male and female worms. The comprehensive analysis of digital expression profiles along with transcriptome comparisons enabled identification of a set of parasitism genes encoding secretory proteins in animal parasitic nematode. Conclusions This study validated the usage of deep sequencing for gene expression profiling. Parasitic adaptation of the canine hookworm is related to its diversity and developmental dynamics. This comprehensive comparative genomic and expression study substantially improves our understanding of

  20. Internal parasites of reptiles.

    Science.gov (United States)

    Raś-Noryńska, Małgorzata; Sokół, Rajmund

    2015-01-01

    Nowadays a growing number of exotic reptiles are kept as pets. The aim of this study was to determine the species of parasites found in reptile patients of veterinary practices in Poland. Fecal samples obtained from 76 lizards, 15 turtles and 10 snakes were examined by flotation method and direct smear stained with Lugol's iodine. In 63 samples (62.4%) the presence of parasite eggs and oocysts was revealed. Oocysts of Isospora spp. (from 33% to 100% of the samples, depending on the reptilian species) and Oxyurids eggs (10% to 75%) were predominant. In addition, isolated Eimeria spp. oocysts and Giardia intestinalis cysts were found, as well as Strongylus spp. and Hymenolepis spp. eggs. Pet reptiles are often infected with parasites, some of which are potentially dangerous to humans. A routine parasitological examination should be done in such animals.

  1. Malaria parasites: the great escape

    Directory of Open Access Journals (Sweden)

    Laurent Rénia

    2016-11-01

    Full Text Available Parasites of the genus Plasmodium have a complex life cycle. They alternate between their final mosquito host and their intermediate hosts. The parasite can be either extra- or intracellular, depending on the stage of development. By modifying their shape, motility, and metabolic requirements, the parasite adapts to the different environments in their different hosts. The parasite has evolved to escape the multiple immune mechanisms in the host that try to block parasite development at the different stages of their development. In this article, we describe the mechanisms reported thus far that allow the Plasmodium parasite to evade innate and adaptive immune responses.

  2. Catalytic cracking of lignites

    Energy Technology Data Exchange (ETDEWEB)

    Seitz, M.; Nowak, S.; Naegler, T.; Zimmermann, J. [Hochschule Merseburg (Germany); Welscher, J.; Schwieger, W. [Erlangen-Nuernberg Univ. (Germany); Hahn, T. [Halle-Wittenberg Univ., Halle (Germany)

    2013-11-01

    A most important factor for the chemical industry is the availability of cheap raw materials. As the oil price of crude oil is rising alternative feedstocks like coal are coming into focus. This work, the catalytic cracking of lignite is part of the alliance ibi (innovative Braunkohlenintegration) to use lignite as a raw material to produce chemicals. With this new one step process without an input of external hydrogen, mostly propylene, butenes and aromatics and char are formed. The product yield depends on manifold process parameters. The use of acid catalysts (zeolites like MFI) shows the highest amount of the desired products. Hydrogen rich lignites with a molar H/C ratio of > 1 are to be favoured. Due to primary cracking and secondary reactions the ratio between catalyst and lignite, temperature and residence time are the most important parameter to control the product distribution. Experiments at 500 C in a discontinuous rotary kiln reactor show yields up to 32 wt-% of hydrocarbons per lignite (maf - moisture and ash free) and 43 wt-% char, which can be gasified. Particularly, the yields of propylene and butenes as main products can be enhanced four times to about 8 wt-% by the use of catalysts while the tar yield decreases. In order to develop this innovative process catalyst systems fixed on beads were developed for an easy separation and regeneration of the used catalyst from the formed char. (orig.)

  3. Crack closure and growth behavior of short fatigue cracks under random loading (part I : details of crack closure behavior)

    International Nuclear Information System (INIS)

    Lee, Shin Young; Song, Ji Ho

    2000-01-01

    Crack closure and growth behavior of physically short fatigue cracks under random loading are investigated by performing narrow-and wide-band random loading tests for various stress ratios. Artificially prepared two-dimensional, short through-thickness cracks are used. The closure behavior of short cracks under random loading is discussed, comparing with that of short cracks under constant-amplitude loading and also that of long cracks under random loading. Irrespective of random loading spectrum or block length, the crack opening load of short cracks is much lower under random loading than under constant-amplitude loading corresponding to the largest load cycle in a random load history, contrary to the behavior of long cracks that the crack opening load under random loading is nearly the same as or slightly higher than constant-amplitude results. This result indicates that the largest load cycle in a random load history has an effect to enhance crack opening of short cracks

  4. Crack Tip Parameters for Growing Cracks in Linear Viscoelastic Materials

    DEFF Research Database (Denmark)

    Brincker, Rune

    In this paper the problem of describing the asymptotic fields around a slowly growing crack in a linearly viscoelastic material is considered. It is shown that for plane mixed mode problems the asymptotic fields must be described by 6 parameters: 2 stress intensity factors and 4 deformation...... intensity factors. In the special case of a constant Poisson ratio only 2 deformation intensity factors are needed. Closed form solutions are given both for a slowly growing crack and for a crack that is suddenly arrested at a point at the crack extension path. Two examples are studied; a stress boundary...... value problem, and a displacement boundary value problem. The results show that the stress intensity factors and the displacement intensity factors do not depend explicitly upon the velocity of the crack tip....

  5. An Unusual Prohibitin Regulates Malaria Parasite Mitochondrial Membrane Potential

    Directory of Open Access Journals (Sweden)

    Joachim Michael Matz

    2018-04-01

    Full Text Available Summary: Proteins of the stomatin/prohibitin/flotillin/HfIK/C (SPFH family are membrane-anchored and perform diverse cellular functions in different organelles. Here, we investigate the SPFH proteins of the murine malaria model parasite Plasmodium berghei, the conserved prohibitin 1, prohibitin 2, and stomatin-like protein and an unusual prohibitin-like protein (PHBL. The SPFH proteins localize to the parasite mitochondrion. While the conserved family members could not be deleted from the Plasmodium genome, PHBL was successfully ablated, resulting in impaired parasite fitness and attenuated virulence in the mammalian host. Strikingly, PHBL-deficient parasites fail to colonize the Anopheles vector because of complete arrest during ookinete development in vivo. We show that this arrest correlates with depolarization of the mitochondrial membrane potential (ΔΨmt. Our results underline the importance of SPFH proteins in the regulation of core mitochondrial functions and suggest that fine-tuning of ΔΨmt in malarial parasites is critical for colonization of the definitive host. : Matz et al. present an experimental genetics study of an unusual prohibitin-like protein in the malaria parasite and find that it regulates mitochondrial membrane polarity. Ablation of this protein causes almost complete mitochondrial depolarization in the mosquito vector, which, in turn, leads to a block in malaria parasite transmission. Keywords: Plasmodium berghei, malaria, SPFH, prohibitin, stomatin-like protein, mitochondrion, membrane potential, ookinete, transmission

  6. Past Intestinal Parasites.

    Science.gov (United States)

    Le Bailly, Matthieu; Araújo, Adauto

    2016-08-01

    This chapter aims to provide some key points for researchers interested in the study of ancient gastrointestinal parasites. These few pages are dedicated to my colleague and friend, Prof. Adauto Araújo (1951-2015), who participated in the writing of this chapter. His huge efforts in paleoparasitology contributed to the development and promotion of the discipline during more than 30 years.

  7. Enteric parasites and AIDS

    Directory of Open Access Journals (Sweden)

    Sérgio Cimerman

    1999-11-01

    Full Text Available OBJECTIVE: To report on the importance of intestinal parasites in patients with AIDS, showing relevant data in the medical literature, with special emphasis on epidemiology, diagnosis and treatment of enteroparasitosis, especially cryptosporidiasis, isosporiasis, microsporidiasis and strongyloidiasis. DESIGN: Narrative review.

  8. Cracking in Drying Colloidal Films

    Science.gov (United States)

    Singh, Karnail B.; Tirumkudulu, Mahesh S.

    2007-05-01

    It has long been known that thick films of colloidal dispersions such as wet clays, paints, and coatings crack under drying. Although capillary stresses generated during drying have been recently identified as the cause for cracking, the existence of a maximum crack-free film thickness that depends on particle size, rigidity, and packing has not been understood. Here, we identify two distinct regimes for crack-free films based on the magnitude of compressive strain at the maximum attainable capillary pressure and show remarkable agreement of measurements with our theory. We anticipate our results to not only form the basis for design of coating formulations for the paints, coatings, and ceramics industry but also assist in the production of crack-free photonic band gap crystals.

  9. Crack tip stress and strain

    International Nuclear Information System (INIS)

    Francois, D.

    1975-01-01

    The study of potential energy variations in a loaded elastic solid containing a crack leads to determination of the crack driving force G. Generalization of this concept to cases other than linear elasticity leads to definition of the integral J. In a linear solid, the crack tip stress field is characterized by a single parameter: the stress-intensity factor K. When the crack tip plastic zone size is confined to the elastic singularity J=G, it is possible to establish relationship between these parameters and plastic strain (and in particular the crack tip opening displacement delta). The stress increases because of the triaxiality effect. This overload rises with increasing strain hardening. When the plastic zone size expands, using certain hypotheses, delta can be calculated. The plastic strain intensity is exclusively dependent on parameter J [fr

  10. Prediction of Crack Growth Aqueous Environments.

    Science.gov (United States)

    1983-06-01

    ORGANIZATION NAME AND ADDRESS 10. PROGRAM ELEMENT. PROJECT. TASK AREA & WORK UNIT NUMBERS SRI International 333 Ravenswood Avenue Menlo Park, CA 94025 II...34no crack" has at least a vestigial rupture, associated with cyclic loading of the oxide film at the crack tip. The curve labeled "crack" was obtained...be an effect of crack opening. For the data set labeled "crack", the vestigial crack, although short, is very tight and the impedance is large. Under

  11. Tensile cracks in creeping solids

    International Nuclear Information System (INIS)

    Riedel, H.; Rice, J.R.

    1979-02-01

    The loading parameter determining the stress and strain fields near a crack tip, and thereby the growth of the crack, under creep conditions is discussed. Relevant loading parameters considered are the stress intensity factor K/sub I/, the path-independent integral C*, and the net section stress sigma/sub net/. The material behavior is modelled as elastic-nonlinear viscous where the nonlinear term describes power law creep. At the time t = 0 load is applied to the cracked specimen, and in the first instant the stress distribution is elastic. Subsequently, creep deformation relaxes the initial stress concentration at the crack tip, and creep strains develop rapidly near the crack tip. These processes may be analytically described by self-similar solutions for short times t. Small scale yielding may be defined. In creep problems, this means that elastic strains dominate almost everywhere except in a small creep zone which grows around the crack tip. If crack growth ensues while the creep zone is still small compared with the crack length and the specimen size, the stress intensity factor governs crack growth behavior. If the calculated creep zone becomes larger than the specimen size, the stresses become finally time-independent and the elastic strain rates can be neglected. In this case, the stress field is the same as in the fully-plastic limit of power law hardening plasticity. The loading parameter which determines the near tip fields uniquely is then the path-independent integral C*.K/sub I/ and C* characterize opposite limiting cases. The case applied in a given situation is decided by comparing the creep zone size with the specimen size and the crack length. Besides several methods of estimating the creep zone size, a convenient expression for a characteristic time is derived, which characterizes the transition from small scale yielding to extensive creep of the whole specimen

  12. Microbial minimalism: genome reduction in bacterial pathogens.

    Science.gov (United States)

    Moran, Nancy A

    2002-03-08

    When bacterial lineages make the transition from free-living or facultatively parasitic life cycles to permanent associations with hosts, they undergo a major loss of genes and DNA. Complete genome sequences are providing an understanding of how extreme genome reduction affects evolutionary directions and metabolic capabilities of obligate pathogens and symbionts.

  13. Buckling Analysis of Edge Cracked Sandwich Plate

    Directory of Open Access Journals (Sweden)

    Rasha Mohammed Hussein

    2016-07-01

    Full Text Available This work presents mainly the buckling load of sandwich plates with or without crack for different cases. The buckling loads are analyzed experimentally and numerically by using ANSYS 15. The experimental investigation was to fabricate the cracked sandwich plate from stainless steel and PVC to find mechanical properties of stainless steel and PVC such as young modulus. The buckling load for different aspect ratio, crack length, cracked location and plate without crack found. The experimental results were compared with that found from ANSYS program. Present of crack is decreased the buckling load and that depends on crack size, crack location and aspect ratio.

  14. Analysis of short and long crack behavior and single overload effect by crack opening stress

    International Nuclear Information System (INIS)

    Song, Sam Hong; Lee, Kyeong Ro

    1999-01-01

    The study analyzed the behaviors of short and long crack as well as the effect of single tensile overload on the crack behaviors by using fatigue crack opening behavior. Crack opening stress is measured by an elastic compliance method which may precisely and continuously provide many data using strain gages during experiment. The unusual growth behaviors of short crack and crack after the single tensile overload applied, was explained by the variations of crack opening stress. In addition, fatigue crack growth rate was expressed as a linear form for short crack as for long crack by using effective stress intensity factor range as fracture mechanical parameter, which is based on crack closure concept. And investigation is performed with respect to the relation between plastic zone size formed at the crack tip and crack retardation, crack length and the number of cycles promoted or retarded, and the overload effect on the fatigue life

  15. Role of parasites in cancer.

    Science.gov (United States)

    Mandong, B M; Ngbea, J A; Raymond, Vhriterhire

    2013-01-01

    In areas of parasitic endemicity, the occurrence of cancer that is not frequent may be linked with parasitic infection. Epidemiological correlates between some parasitic infections and cancer is strong, suggesting a strong aetiological association. The common parasites associated with human cancers are schistosomiasis, malaria, liver flukes (Clonorchis sinenses, Opistorchis viverrini). To review the pathology, literature and methods of diagnosis. Literature review from peer reviewed Journals cited in PubMed and local journals. Parasites may serve as promoters of cancer in endemic areas of infection.

  16. In silico ionomics segregates parasitic from free-living eukaryotes.

    Science.gov (United States)

    Greganova, Eva; Steinmann, Michael; Mäser, Pascal; Fankhauser, Niklaus

    2013-01-01

    Ion transporters are fundamental to life. Due to their ancient origin and conservation in sequence, ion transporters are also particularly well suited for comparative genomics of distantly related species. Here, we perform genome-wide ion transporter profiling as a basis for comparative genomics of eukaryotes. From a given predicted proteome, we identify all bona fide ion channels, ion porters, and ion pumps. Concentrating on unicellular eukaryotes (n = 37), we demonstrate that clustering of species according to their repertoire of ion transporters segregates obligate endoparasites (n = 23) on the one hand, from free-living species and facultative parasites (n = 14) on the other hand. This surprising finding indicates strong convergent evolution of the parasites regarding the acquisition and homeostasis of inorganic ions. Random forest classification identifies transporters of ammonia, plus transporters of iron and other transition metals, as the most informative for distinguishing the obligate parasites. Thus, in silico ionomics further underscores the importance of iron in infection biology and suggests access to host sources of nitrogen and transition metals to be selective forces in the evolution of parasitism. This finding is in agreement with the phenomenon of iron withholding as a primordial antimicrobial strategy of infected mammals.

  17. Protein moonlighting in parasitic protists.

    Science.gov (United States)

    Ginger, Michael L

    2014-12-01

    Reductive evolution during the adaptation to obligate parasitism and expansions of gene families encoding virulence factors are characteristics evident to greater or lesser degrees in all parasitic protists studied to date. Large evolutionary distances separate many parasitic protists from the yeast and animal models upon which classic views of eukaryotic biochemistry are often based. Thus a combination of evolutionary divergence, niche adaptation and reductive evolution means the biochemistry of parasitic protists is often very different from their hosts and to other eukaryotes generally, making parasites intriguing subjects for those interested in the phenomenon of moonlighting proteins. In common with other organisms, the contribution of protein moonlighting to parasite biology is only just emerging, and it is not without controversy. Here, an overview of recently identified moonlighting proteins in parasitic protists is provided, together with discussion of some of the controversies.

  18. Probabilistic Analysis of Crack Width

    Directory of Open Access Journals (Sweden)

    J. Marková

    2000-01-01

    Full Text Available Probabilistic analysis of crack width of a reinforced concrete element is based on the formulas accepted in Eurocode 2 and European Model Code 90. Obtained values of reliability index b seem to be satisfactory for the reinforced concrete slab that fulfils requirements for the crack width specified in Eurocode 2. However, the reliability of the slab seems to be insufficient when the European Model Code 90 is considered; reliability index is less than recommended value 1.5 for serviceability limit states indicated in Eurocode 1. Analysis of sensitivity factors of basic variables enables to find out variables significantly affecting the total crack width.

  19. Multispecimen fatigue crack propagation testing

    International Nuclear Information System (INIS)

    Ermi, A.M.; Bauer, R.E.; Chin, B.A.; Straalsund, J.L.

    1981-01-01

    Chains of miniature center-cracked-tension specimens were tested on a conventional testing machine and on a prototypic in-reactor fatigue machine as part of the fusion reactor materials alloy development program. Annealed and 20 percent cold-worked 316 stainless steel specimens were cycled under various conditions of temperature, frequency, stress ratio and chain length. Crack growth rates determined from multispecimen visual measurements and from an electrical potential technique were consistent with those obtained by conventional test methods. Results demonstrate that multispecimen chain testing is a valid method of obtaining fatigue crack propagation information for alloy development. 8 refs

  20. Monitoring crack growth using thermography

    International Nuclear Information System (INIS)

    Djedjiga, Ait Aouita; Abdeldjalil, Ouahabi

    2008-01-01

    The purpose of this work is to present a novel strategy for real-time monitoring crack growth of materials. The process is based on the use of thermal data extracted along the horizontal axis of symmetry of single edge notch tension (SENT) specimens, during fatigue tests. These data are exploited using an implemented program to detect in situ the growth of fatigue crack, with the critical size and propagation speed of the crack. This technique has the advantage to be applicable to a wide range of materials regardless of their electrical conductivity and their surface texture. (authors)

  1. Password Cracking Using Sony Playstations

    Science.gov (United States)

    Kleinhans, Hugo; Butts, Jonathan; Shenoi, Sujeet

    Law enforcement agencies frequently encounter encrypted digital evidence for which the cryptographic keys are unknown or unavailable. Password cracking - whether it employs brute force or sophisticated cryptanalytic techniques - requires massive computational resources. This paper evaluates the benefits of using the Sony PlayStation 3 (PS3) to crack passwords. The PS3 offers massive computational power at relatively low cost. Moreover, multiple PS3 systems can be introduced easily to expand parallel processing when additional power is needed. This paper also describes a distributed framework designed to enable law enforcement agents to crack encrypted archives and applications in an efficient and cost-effective manner.

  2. Peroxisomes in parasitic protists.

    Science.gov (United States)

    Gabaldón, Toni; Ginger, Michael L; Michels, Paul A M

    Representatives of all major lineages of eukaryotes contain peroxisomes with similar morphology and mode of biogenesis, indicating a monophyletic origin of the organelles within the common ancestor of all eukaryotes. Peroxisomes originated from the endoplasmic reticulum, but despite a common origin and shared morphological features, peroxisomes from different organisms show a remarkable diversity of enzyme content and the metabolic processes present can vary dependent on nutritional or developmental conditions. A common characteristic and probable evolutionary driver for the origin of the organelle is an involvement in lipid metabolism, notably H 2 O 2 -dependent fatty-acid oxidation. Subsequent evolution of the organelle in different lineages involved multiple acquisitions of metabolic processes-often involving retargeting enzymes from other cell compartments-and losses. Information about peroxisomes in protists is still scarce, but available evidence, including new bioinformatics data reported here, indicate striking diversity amongst free-living and parasitic protists from different phylogenetic supergroups. Peroxisomes in only some protists show major involvement in H 2 O 2 -dependent metabolism, as in peroxisomes of mammalian, plant and fungal cells. Compartmentalization of glycolytic and gluconeogenic enzymes inside peroxisomes is characteristic of kinetoplastids and diplonemids, where the organelles are hence called glycosomes, whereas several other excavate parasites (Giardia, Trichomonas) have lost peroxisomes. Amongst alveolates and amoebozoans patterns of peroxisome loss are more complicated. Often, a link is apparent between the niches occupied by the parasitic protists, nutrient availability, and the absence of the organelles or their presence with a specific enzymatic content. In trypanosomatids, essentiality of peroxisomes may be considered for use in anti-parasite drug discovery. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. Subsurface metals fatigue cracking without and with crack tip

    Directory of Open Access Journals (Sweden)

    Andrey Shanyavskiy

    2013-07-01

    Full Text Available Very-High-Cycle-Fatigue regime for metals was considered and mechanisms of the subsurface crack origination were introduced. In many metals first step of crack origination takes place with specific area formation because of material pressing and rotation that directed to transition in any volume to material ultra-high-plasticity with nano-structure appearing. Then by the border of the nano-structure takes place volume rotation and fracture surface creates with spherical particles which usually named Fine-Granular-Area. In another case there takes place First-Smooth-Facet occurring in area of origin due to whirls appearing by the one of the slip systems under discussed the same stress-state conditions. Around Fine-Granular-Area or First-Smooth-Facet there plastic zone appeared and, then, subsurface cracking develops by the same manner as for through cracks. In was discussed quantum-mechanical nature of fatigue crack growth in accordance with Yang’s modulus quantization for low level of deformations. New simply equation was considered for describing subsurface cracking in metals out of Fine-Granular-Area or Fist-Smooth-Facet.

  4. Unusual thiol-based redox metabolism of parasitic flukes.

    Science.gov (United States)

    Tripathi, Timir; Suttiprapa, Sutas; Sripa, Banchob

    2017-08-01

    Parasitic flukes are exposed to free radicals and, to a greater extent, reactive oxygen species (ROS) during their life cycle. Despite being relentlessly exposed to ROS released by activated immune cells, these parasites can survive for many years in the host. Cellular thiol-based redox metabolism plays a crucial role in parasite survival within their hosts. Evidence shows that oxidative stress and redox homeostasis maintenance are important clinical and pathobiochemical as well as effective therapeutic principles in various diseases. The characterization of redox and antioxidant enzymes is likely to yield good target candidates for novel drugs and vaccines. The absence of active catalase in fluke parasites offers great potential for the development of chemotherapeutic agents that act by perturbing the redox equilibrium of the cell. One of the redox-sensitive enzymes, thioredoxin glutathione reductase (TGR), has been accepted as a drug target against blood fluke infections, and related clinical trials are in progress. TGR is the sole enzyme responsible for Trx and GSH reduction in parasitic flukes. The availability of helminth genomes has accelerated the research on redox metabolism of flukes; however, significant achievements have yet to be attained. The present review summarizes current knowledge on the redox and antioxidant system of the parasitic flukes. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  5. Normocyte-binding protein required for human erythrocyte invasion by the zoonotic malaria parasitePlasmodium knowlesi

    KAUST Repository

    Moon, Robert W.; Sharaf, Hazem; Hastings, Claire H.; Ho, Yung Shwen; Nair, Mridul; Rchiad, ‍ Zineb; Knuepfer, Ellen; Ramaprasad, Abhinay; Mohring, Franziska; Amir, Amirah; Yusuf, Noor A.; Hall, Joanna; Almond, Neil; Lau, Yee Ling; Pain, Arnab; Blackman, Michael J.; Holder, Anthony A.

    2016-01-01

    The dominant cause of malaria in Malaysia is now Plasmodium knowlesi, a zoonotic parasite of cynomolgus macaque monkeys found throughout South East Asia. Comparative genomic analysis of parasites adapted to in vitro growth in either cynomolgus or human RBCs identified a genomic deletion that includes the gene encoding normocyte-binding protein Xa (NBPXa) in parasites growing in cynomolgus RBCs but not in human RBCs. Experimental deletion of the NBPXa gene in parasites adapted to growth in human RBCs (which retain the ability to grow in cynomolgus RBCs) restricted them to cynomolgus RBCs, demonstrating that this gene is selectively required for parasite multiplication and growth in human RBCs. NBPXa-null parasites could bind to human RBCs, but invasion of these cells was severely impaired. Therefore, NBPXa is identified as a key mediator of P. knowlesi human infection and may be a target for vaccine development against this emerging pathogen.

  6. Normocyte-binding protein required for human erythrocyte invasion by the zoonotic malaria parasitePlasmodium knowlesi

    KAUST Repository

    Moon, Robert W.

    2016-06-15

    The dominant cause of malaria in Malaysia is now Plasmodium knowlesi, a zoonotic parasite of cynomolgus macaque monkeys found throughout South East Asia. Comparative genomic analysis of parasites adapted to in vitro growth in either cynomolgus or human RBCs identified a genomic deletion that includes the gene encoding normocyte-binding protein Xa (NBPXa) in parasites growing in cynomolgus RBCs but not in human RBCs. Experimental deletion of the NBPXa gene in parasites adapted to growth in human RBCs (which retain the ability to grow in cynomolgus RBCs) restricted them to cynomolgus RBCs, demonstrating that this gene is selectively required for parasite multiplication and growth in human RBCs. NBPXa-null parasites could bind to human RBCs, but invasion of these cells was severely impaired. Therefore, NBPXa is identified as a key mediator of P. knowlesi human infection and may be a target for vaccine development against this emerging pathogen.

  7. Cracks in Utopia

    Science.gov (United States)

    1999-01-01

    Many of the craters found on the northern plains of Mars have been partly filled or buried by some material (possibly sediment). The Mars Global Surveyor (MGS) Mars Orbiter Camera (MOC) image presented here (MOC2-136b, above left) shows a high-resolution view of a tiny portion of the floor of one of these northern plains craters. The crater, located in Utopia Planitia at 44oN, 258oW, is shown on the right (MOC2-136a)with a small white box to indicate the location of the MOC image. The MOC image reveals that the material covering the floor of this crater is cracked and pitted. The origin and source of material that has been deposited in this crater is unknown.The MOC image was acquired in June 1999 and covers an area only 1.1 kilometers (0.7 miles) wide at a resolution of 1.8 meters (6 feet) per pixel. The context picture is a mosaic of Viking 2 orbiter images 010B53 and 010B55, taken in 1976. Both images are illuminated from the left. Malin Space Science Systems and the California Institute of Technology built the MOC using spare hardware from the Mars Observer mission. MSSS operates the camera from its facilities in San Diego, CA. The Jet Propulsion Laboratory's Mars Surveyor Operations Project operates the Mars Global Surveyor spacecraft with its industrial partner, Lockheed Martin Astronautics, from facilities in Pasadena, CA and Denver, CO.

  8. Super oil cracking update

    International Nuclear Information System (INIS)

    Mulraney, D.

    1997-01-01

    The conversion of residual fuel oil to usable middle distillates was discussed. The residue conversion processing paths are usually based on separation, carbon rejection, or hydrogen addition principles. Super Oil Cracking (SOC) uses a slurry catalyst system in a new, tubular reactor to achieve high levels of hydrothermal conversion. SOC can upgrade a variety of heavy, high metals residue feedstocks with high yields of middle distillates. The SOC products can also be further treated into feedstocks for FCC or hydrocracking. The SOC process can be incorporated easily into a refinery to obtain incremental residue conversion directly. It can also be integrated with other residue processes, acting as a demetallization and decarbonization step which results in enhanced overall conversion. The relative rate of coke formation and its handling are distinguishing characteristics between residue upgrading technologies. The SOC process operates at higher temperatures that other residue hydrocracking processes resulting in higher rates of thermal decomposition, thus preventing coke formation. SOC process can operate as a stand-alone upgrader or can be integrated with other bottoms processing steps to extend the refiner's range of options for increasing bottoms conversion.3 tabs., 14 figs

  9. Metallurgy of stress corrosion cracking

    International Nuclear Information System (INIS)

    Donovan, J.A.

    1973-01-01

    The susceptibility of metals and alloys to stress corrosion is discussed in terms of the relationship between structural characteristics (crystal structure, grains, and second phases) and defects (vacancies, dislocations, and cracks) that exist in metals and alloys. (U.S.)

  10. Peridynamic model for fatigue cracking.

    Energy Technology Data Exchange (ETDEWEB)

    Silling, Stewart Andrew; Abe Askari (Boeing)

    2014-10-01

    The peridynamic theory is an extension of traditional solid mechanics in which the field equations can be applied on discontinuities, such as growing cracks. This paper proposes a bond damage model within peridynamics to treat the nucleation and growth of cracks due to cyclic loading. Bond damage occurs according to the evolution of a variable called the "remaining life" of each bond that changes over time according to the cyclic strain in the bond. It is shown that the model reproduces the main features of S-N data for typical materials and also reproduces the Paris law for fatigue crack growth. Extensions of the model account for the effects of loading spectrum, fatigue limit, and variable load ratio. A three-dimensional example illustrates the nucleation and growth of a helical fatigue crack in the torsion of an aluminum alloy rod.

  11. Shapes formed by interacting cracks

    Science.gov (United States)

    Daniels, Karen

    2012-02-01

    Brittle failure through multiple cracks occurs in a wide variety of contexts, from microscopic failures in dental enamel and cleaved silicon to geological faults and planetary ice crusts. In each of these situations, with complicated stress geometries and different microscopic mechanisms, pairwise interactions between approaching cracks nonetheless produce characteristically curved fracture paths. We investigate the origins of this widely observed ``en passant'' crack pattern by fracturing a rectangular slab which is notched on each long side and subjected to quasi-static uniaxial strain from the short side. The two cracks propagate along approximately straight paths until they pass each other, after which they curve and release a lens-shaped fragment. We find that, for materials with diverse mechanical properties, each curve has an approximately square-root shape, and that the length of each fragment is twice its width. We are able to explain the origins of this universal shape with a simple geometrical model.

  12. The crack growth mechanism in asphaltic mixes

    NARCIS (Netherlands)

    Jacobs, M.M.J.; Hopman, P.C.; Molenaar, A.A.A.

    1995-01-01

    The crack growth mechanism in asphalt concrete (Ac) mixes is studied. In cyclic tests on several asphaltic mixes crack growth is measured, both with crack foils and with cOD-gauges. It is found that crack growth in asphaltic mixes is described by three processes which are parallel in time: cohesive

  13. Dynamic Crack Branching - A Photoelastic Evaluation,

    Science.gov (United States)

    1982-05-01

    0.41 mPai and a 0.18 MPa, and predicted a theoretical kinking angle of 84°whichagreed well with experimentally measured angle. After crack kinking...Consistent crack branching’at KIb = 2.04 MPaI -i- and r = 1.3 mm verified this crack branching criterion. The crack branching angle predicted by--.’ DD

  14. 21 CFR 137.190 - Cracked wheat.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 2 2010-04-01 2010-04-01 false Cracked wheat. 137.190 Section 137.190 Food and... Related Products § 137.190 Cracked wheat. Cracked wheat is the food prepared by so cracking or cutting into angular fragments cleaned wheat other than durum wheat and red durum wheat that, when tested by...

  15. Crack propagation in dynamic thermoelasticity

    International Nuclear Information System (INIS)

    Bui, H.D.

    1980-01-01

    We study the singular thermoelastic fields near the crack tip, in the linear strain assumption. The equations are coupled and non linear. The asymptotic expansions of the displacement and the temperature are given for the first and the second order. It is shown that the temperature is singular when the crack propagates. However, this field does not change the dominant singularity of the mechanical field which is the same as that obtained in the theory of isothermal elasticity [fr

  16. Evaluation of crack interaction effect for in-plane surface cracks using elastic finite element analyses

    International Nuclear Information System (INIS)

    Huh, Nam Su; Choi, Suhn; Park, Keun Bae; Kim, Jong Min; Choi, Jae Boong; Kim, Young Jin

    2008-01-01

    The crack-tip stress fields and fracture mechanics assessment parameters, such as the elastic stress intensity factor and the elastic-plastic J-integral, for a surface crack can be significantly affected by adjacent cracks. Such a crack interaction effect due to multiple cracks can magnify the fracture mechanics assessment parameters. There are many factors to be considered, for instance the relative distance between adjacent cracks, crack shape and loading condition, to quantify a crack interaction effect on the fracture mechanics assessment parameters. Thus, the current guidance on a crack interaction effect (crack combination rule), including ASME Sec. XI, BS7910, British Energy R6 and API RP579, provide different rules for combining multiple surface cracks into a single surface crack. The present paper investigates a crack interaction effect by evaluating the elastic stress intensity factor of adjacent surface cracks in a plate along the crack front through detailed 3-dimensional elastic finite element analyses. The effects of the geometric parameters, the relative distance between cracks and the crack shape, on the stress intensity factor are systematically investigated. As for the loading condition, only axial tension is considered. Based on the elastic finite element results, the acceptability of the crack combination rules provided in the existing guidance was investigated, and the relevant recommendations on a crack interaction for in-plane surface cracks in a plate were discussed

  17. Parasitism finds many solutions to the same problems in red algae (Florideophyceae, Rhodophyta).

    Science.gov (United States)

    Freese, Jillian M; Lane, Christopher E

    2017-06-01

    Parasitic red algae evolve from a common ancestor with their hosts, parasitizing cousins using familiar cellular mechanisms. They have independently evolved over one hundred times within the exclusively multicellular red algal class Florideophyceae. Reduced morphology, a lack of pigmentation, and direct cell-cell connections with their hosts are markers of red algal parasitism. With so many potential evolutionary pathways, red algal parasite diversity offers a unique test case to understand the earliest stages of this lifestyle transition. Molecular and morphological investigations led to the categorization of these parasites based on their relationship to their host. "Adelphoparasites" are phylogenetically close to their hosts, often infecting a sister species, whereas "alloparasites" are more distantly related to their hosts. The differentiation of these parasites, based on their phylogenetic relationship to their host, has resulted in a simplified classification of these parasites that may not reflect the many evolutionary pathways they take to arrive at a similar endpoint. Accordingly, many parasites fall into a gray area between adelphoparasite and alloparasite definitions, challenging the established features we use to classify them. Molecular phylogenetic research has been essential in identifying gaps in knowledge, but microscopy needs to be reincorporated in order to address red algal parasite developmental variation to establish a new paradigm. The joint utilization of molecular and microscopic methods will be critical in identifying the genomic and physiological traits of both nascent and well-established parasites. Copyright © 2017 Elsevier B.V. All rights reserved.

  18. Parasitic worms: how many really?

    Science.gov (United States)

    Strona, Giovanni; Fattorini, Simone

    2014-04-01

    Accumulation curves are useful tools to estimate species diversity. Here we argue that they can also be used in the study of global parasite species richness. Although this basic idea is not completely new, our approach differs from the previous ones as it treats each host species as an independent sample. We show that randomly resampling host-parasite records from the existing databases makes it possible to empirically model the relationship between the number of investigated host species, and the corresponding number of parasite species retrieved from those hosts. This method was tested on 21 inclusive lists of parasitic worms occurring on vertebrate hosts. All of the obtained models conform well to a power law curve. These curves were then used to estimate global parasite species richness. Results obtained with the new method suggest that current predictions are likely to severely overestimate parasite diversity. Copyright © 2014 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.

  19. Compressive failure with interacting cracks

    International Nuclear Information System (INIS)

    Yang Guoping; Liu Xila

    1993-01-01

    The failure processes in concrete and other brittle materials are just the results of the propagation, coalescence and interaction of many preexisting microcracks or voids. To understand the real behaviour of the brittle materials, it is necessary to bridge the gap from the relatively matured one crack behaviour to the stochastically distributed imperfections, that is, to concern the crack propagation and interaction of microscopic mechanism with macroscopic parameters of brittle materials. Brittle failure in compression has been studied theoretically by Horii and Nemat-Nasser (1986), in which a closed solution was obtained for a preexisting flaw or some special regular flaws. Zaitsev and Wittmann (1981) published a paper on crack propagation in compression, which is so-called numerical concrete, but they did not take account of the interaction among the microcracks. As for the modelling of the influence of crack interaction on fracture parameters, many studies have also been reported. Up till now, some researcher are working on crack interaction considering the ratios of SIFs with and without consideration of the interaction influences, there exist amplifying or shielding effects of crack interaction which are depending on the relative positions of these microcracks. The present paper attempts to simulate the whole failure process of brittle specimen in compression, which includes the complicated coupling effects between the interaction and propagation of randomly distributed or other typical microcrack configurations step by step. The lengths, orientations and positions of microcracks are all taken as random variables. The crack interaction among many preexisting random microcracks is evaluated with the help of a simple interaction matrix (Yang and Liu, 1991). For the subcritically stable propagation of microcracks in mixed mode fracture, fairly known maximum hoop stress criterion is adopted to compute branching lengths and directions at each tip of the crack

  20. One Health: parasites and beyond…

    OpenAIRE

    Blake, DP; Betson, ME

    2016-01-01

    The field of parasitism is broad, encompassing relationships between organisms where one benefits at the expense of another. Traditionally the discipline focuses on eukaryotes, with the study of bacteria and viruses complementary but distinct. Nonetheless, parasites vary in size and complexity from single celled protozoa, to enormous plants like those in the genus Rafflesia. Lifecycles range from obligate intracellular to extensive exoparasitism. Examples of parasites include high profile med...

  1. Transformation of the rodent malaria parasite Plasmodium chabaudi.

    Science.gov (United States)

    Spence, Philip J; Cunningham, Deirdre; Jarra, William; Lawton, Jennifer; Langhorne, Jean; Thompson, Joanne

    2011-04-01

    The rodent malaria parasite Plasmodium chabaudi chabaudi shares many features with human malaria species, including P. falciparum, and is the in vivo model of choice for many aspects of malaria research in the mammalian host, from sequestration of parasitized erythrocytes, to antigenic variation and host immunity and immunopathology. This protocol describes an optimized method for the transformation of mature blood-stage P.c. chabaudi and a description of a vector that targets efficient, single crossover integration into the P.c. chabaudi genome. Transformed lines are reproducibly generated and selected within 14-20 d, and show stable long-term protein expression even in the absence of drug selection. This protocol, therefore, provides the scientific community with a robust and reproducible method to generate transformed P.c. chabaudi parasites expressing fluorescent, bioluminescent and model antigens that can be used in vivo to dissect many of the fundamental principles of malaria infection.

  2. Parasite communities: patterns and processes

    National Research Council Canada - National Science Library

    Esch, Gerald W; Bush, Albert O; Aho, John M

    1990-01-01

    .... Taking examples from many hosts including molluscs, marine and freshwater fish, amphibians, reptiles, birds and mammals, this book shows how parasitic communities are influenced by a multitude...

  3. Targeting protein-protein interactions for parasite control.

    Directory of Open Access Journals (Sweden)

    Christina M Taylor

    2011-04-01

    Full Text Available Finding new drug targets for pathogenic infections would be of great utility for humanity, as there is a large need to develop new drugs to fight infections due to the developing resistance and side effects of current treatments. Current drug targets for pathogen infections involve only a single protein. However, proteins rarely act in isolation, and the majority of biological processes occur via interactions with other proteins, so protein-protein interactions (PPIs offer a realm of unexplored potential drug targets and are thought to be the next-generation of drug targets. Parasitic worms were chosen for this study because they have deleterious effects on human health, livestock, and plants, costing society billions of dollars annually and many sequenced genomes are available. In this study, we present a computational approach that utilizes whole genomes of 6 parasitic and 1 free-living worm species and 2 hosts. The species were placed in orthologous groups, then binned in species-specific orthologous groups. Proteins that are essential and conserved among species that span a phyla are of greatest value, as they provide foundations for developing broad-control strategies. Two PPI databases were used to find PPIs within the species specific bins. PPIs with unique helminth proteins and helminth proteins with unique features relative to the host, such as indels, were prioritized as drug targets. The PPIs were scored based on RNAi phenotype and homology to the PDB (Protein DataBank. EST data for the various life stages, GO annotation, and druggability were also taken into consideration. Several PPIs emerged from this study as potential drug targets. A few interactions were supported by co-localization of expression in M. incognita (plant parasite and B. malayi (H. sapiens parasite, which have extremely different modes of parasitism. As more genomes of pathogens are sequenced and PPI databases expanded, this methodology will become increasingly

  4. Improvement of elastic-plastic fatigue crack growth evaluation method. 2. Crack opening behavior

    Energy Technology Data Exchange (ETDEWEB)

    Takahashi, Yukio [Central Research Inst. of Electric Power Industry, Tokyo (Japan)

    2001-05-01

    Evaluation of crack growth behavior under cyclic loading is often required in the structural integrity assessment of cracked components. Closing and re-opening of the crack give large influence on crack growth rate through the change of fracture mechanics parameters. Based on the finite element analysis for a center-cracked plate, dependency of crack opening ratio on applied stress range and mean stress was examined. Simple formulae for representing the results were derived for plane stress and plane strain conditions. (author)

  5. Parasitism and calfhood diseases.

    Science.gov (United States)

    Herlich, H; Douvres, F W

    1977-02-01

    That animals can and do acquire an effective immunity against helminth parasites has been demonstrated extensively experimentally, and the fact that domestic animals such as cattle, sheep, and horses become adults while maintaining good health in spite of constant exposure to reinfection long has suggested that immunity must be important to such survival. Although our attempts to date to vaccinate calves against helminth parasites have either failed or been unsatisfactory because of the pathosis induced by the experimental vaccines, the results are not surprising or discouraging. In contrast to the long history of immunization research on bacterial and viral diseases, only within a relatively short time have serious efforts been directed at exploiting hostal immunity for prevention and control of helminthic diseases. Unlike the comparatively simple structures of viruses and bacteria, helminths are complex multicellular animals with vast arrays of antigens and complicated physiological and immunological interactions with their hosts. Much more fundamental information on helminth-bovine interactions, on helminth antigens, and on cattle antibody systems must be developed before progress on control of cattle helminths by vaccination can be meaningful.

  6. Cracking in Flexural Reinforced Concrete Members

    DEFF Research Database (Denmark)

    Rasmussen, Annette Beedholm; Fisker, Jakob; Hagsten, Lars German

    2017-01-01

    The system of cracks developing in reinforced concrete is in many aspects essential when modelling structures in both serviceability- and ultimate limit state. This paper discusses the behavior concerning crack development in flexural members observed from tests and associates it with two different...... existing models. From the investigations an approach is proposed on how to predict the crack pattern in flexural members involving two different crack systems; primary flexural cracks and local secondary cracks. The results of the approach is in overall good agreement with the observed tests and captures...... the pronounced size effect associated with flexural cracking in which the crack spacing and crack widths are approximately proportional to the depth of the member....

  7. Dynamic ductile fracture of a central crack

    Science.gov (United States)

    Tsai, Y. M.

    1976-01-01

    A central crack, symmetrically growing at a constant speed in a two dimensional ductile material subject to uniform tension at infinity, is investigated using the integral transform methods. The crack is assumed to be the Dugdale crack, and the finite stress condition at the crack tip is satisfied during the propagation of the crack. Exact expressions of solution are obtained for the finite stress condition at the crack tip, the crack shape, the crack opening displacement, and the energy release rate. All those expressions are written as the product of explicit dimensional quantities and a nondimensional dynamic correction function. The expressions reduce to the associated static results when the crack speed tends to zero, and the nondimensional dynamic correction functions were calculated for various values of the parameter involved.

  8. Fatigue cracking in road pavement

    Science.gov (United States)

    Mackiewicz, P.

    2018-05-01

    The article presents the problem of modelling fatigue phenomena occurring in the road pavement. The example of two selected pavements shows the changes occurring under the influence of the load in different places of the pavement layers. Attention is paid to various values of longitudinal and transverse strains generated at the moment of passing the wheel on the pavement. It was found that the key element in the crack propagation analysis is the method of transferring the load to the pavement by the tire and the strain distribution in the pavement. During the passage of the wheel in the lower layers of the pavement, a complex stress state arises. Then vertical, horizontal and tangent stresses with various values appear. The numerical analyses carried out with the use of finite element methods allowed to assess the strain and stress changes occurring in the process of cracking road pavement. It has been shown that low-thickness pavements are susceptible to fatigue cracks arising "bottom to top", while pavements thicker are susceptible to "top to bottom" cracks. The analysis of the type of stress allowed to determine the cracking mechanism.

  9. Steel weldability. Underbead cold cracking

    International Nuclear Information System (INIS)

    Marquet, F.; Defourny, J.; Bragard, A.

    1977-01-01

    The problem of underbead cold cracking has been studied by the implant technique. This approach allows to take into account in a quantitative manner the different factors acting on the cold cracking phenomenon: structure under the weld bead, level of restraint, hydrogen content in the molten metal. The influence of the metallurgical factors depending from the chemical composition of the steel has been examined. It appeared that carbon equivalent is an important factor to explain cold cracking sensitivity but that it is not sufficient to characterize the steel. The results have shown that vanadium may have a deleterious effect on the resistance to cold cracking when the hydrogen content is high and that small silicon additions are beneficient. The influence of the diffusible hydrogen content has been checked and the important action of pre- and postheating has been shown. These treatments allow the hydrogen to escape from the weld before the metal has been damaged. Some inclusions (sulphides) may also decrease the influence of hydrogen. A method based on the implant tests has been proposed which allows to choose and to control safe welding conditions regarding cold cracking

  10. Role of hydrogen in stress corrosion cracking

    International Nuclear Information System (INIS)

    Mehta, M.L.

    1981-01-01

    Electrochemical basis for differentiation between hydrogen embrittlement and active path corrosion or anodic dissolution crack growth mechanisms is examined. The consequences of recently demonstrated acidification in crack tip region irrespective of electrochemical conditions at the bulk surface of the sample are that the hydrogen can evolve within the crack and may be involved in the cracking process. There are basically three aspects of hydrogen involvement in stress corrosion cracking. In dissolution models crack propagation is assumed to be caused by anodic dissolution on the crack tip sustained by cathodic reduction of hydrogen from electrolyte within the crack. In hydrogen induced structural transformation models it is postulated that hydrogen is absorbed locally at the crack tip producing structural changes which facilitate crack propagation. In hydrogen embrittlement models hydrogen is absorbed by stressed metal from proton reduction from the electrolyte within the crack and there is interaction between lattice and hydrogen resulting in embrittlement of material at crack tip facilitating crack propagation. In the present paper, the role of hydrogen in stress corrosion crack growth in high strength steels, austenitic stainless steels, titanium alloys and high strength aluminium alloys is discussed. (author)

  11. A crack opening stress equation for fatigue crack growth

    Science.gov (United States)

    Newman, J. C., Jr.

    1984-01-01

    A general crack opening stress equation is presented which may be used to correlate crack growth rate data for various materials and thicknesses, under constant amplitude loading, once the proper constraint factor has been determined. The constraint factor, alpha, is a constraint on tensile yielding; the material yields when the stress is equal to the product of alpha and sigma. Delta-K (LEFM) is plotted against rate for 2024-T3 aluminum alloy specimens 2.3 mm thick at various stress ratios. Delta-K sub eff was plotted against rate for the same data with alpha = 1.8; the rates correlate well within a factor of two.

  12. Seismic behaviour of un-cracked and cracked thin pipes

    International Nuclear Information System (INIS)

    Blay, N.; Brunet, G.; Gantenbein, F.; Aguilar, J.

    1995-01-01

    In order to evaluate the seismic behaviour of un-cracked and cracked thin pipes, subjected to high acceleration levels, seismic tests and calculations have been performed on straight thin pipes made of 316L stainless steel, loaded in pure bending by a permanent static and dynamic loading. The seismic tests were carried out on the AZALEE shaking table of the CEA laboratory TAMARIS. The influence of the elasto-plastic model with isotropic or kinematic hardening are studied. 5 refs., 7 figs., 2 tabs

  13. Unique physiology of host-parasite interactions in microsporidia infections.

    Science.gov (United States)

    Williams, Bryony A P

    2009-11-01

    Microsporidia are intracellular parasites of all major animal lineages and have a described diversity of over 1200 species and an actual diversity that is estimated to be much higher. They are important pathogens of mammals, and are now one of the most common infections among immunocompromised humans. Although related to fungi, microsporidia are atypical in genomic biology, cell structure and infection mechanism. Host cell infection involves the rapid expulsion of a polar tube from a dormant spore to pierce the host cell membrane and allow the direct transfer of the spore contents into the host cell cytoplasm. This intimate relationship between parasite and host is unique. It allows the microsporidia to be highly exploitative of the host cell environment and cause such diverse effects as the induction of hypertrophied cells to harbour prolific spore development, host sex ratio distortion and host cell organelle and microtubule reorganization. Genome sequencing has revealed that microsporidia have achieved this high level of parasite sophistication with radically reduced proteomes and with many typical eukaryotic pathways pared-down to what appear to be minimal functional units. These traits make microsporidia intriguing model systems for understanding the extremes of reductive parasite evolution and host cell manipulation.

  14. Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes

    DEFF Research Database (Denmark)

    Alsmark, Cecilia; Foster, Peter G; Sicheritz-Pontén, Thomas

    2013-01-01

    BACKGROUND: The influence of lateral gene transfer on gene origins and biology in eukaryotes is poorly understood compared with those of prokaryotes. A number of independent investigations focusing on specific genes, individual genomes, or specific functional categories from various eukaryotes have...... approach to systematically investigate lateral gene transfer affecting the proteomes of thirteen, mainly parasitic, microbial eukaryotes, representing four of the six eukaryotic super-groups. All of the genomes investigated have been significantly affected by prokaryote-to-eukaryote lateral gene transfers...... indicated that lateral gene transfer does indeed affect eukaryotic genomes. However, the lack of common methodology and criteria in these studies makes it difficult to assess the general importance and influence of lateral gene transfer on eukaryotic genome evolution. RESULTS: We used a phylogenomic...

  15. Origins of amino acid transporter loci in trypanosomatid parasites

    Directory of Open Access Journals (Sweden)

    Jackson Andrew P

    2007-02-01

    Full Text Available Abstract Background Large amino acid transporter gene families were identified from the genome sequences of three parasitic protists, Trypanosoma brucei, Trypanosoma cruzi and Leishmania major. These genes encode molecular sensors of the external host environment for trypanosomatid cells and are crucial to modulation of gene expression as the parasite passes through different life stages. This study provides a comprehensive phylogenetic account of the origins of these genes, redefining each locus according to a positional criterion, through the integration of phyletic identity with comparative gene order information. Results Each locus was individually specified by its surrounding gene order and associated with homologs showing the same position ('homoeologs' in other species, where available. Bayesian and maximum likelihood phylogenies were in general agreement on systematic relationships and confirmed several 'orthology sets' of genes retained since divergence from the common ancestor. Reconciliation analysis quantified the scale of duplication and gene loss, as well as identifying further apparent orthology sets, which lacked conservation of genomic position. These instances suggested substantial genomic restructuring or transposition. Other analyses identified clear instances of evolutionary rate changes post-duplication, the effects of concerted evolution within tandem gene arrays and gene conversion events between syntenic loci. Conclusion Despite their importance to cell function and parasite development, the repertoires of AAT loci in trypanosomatid parasites are relatively fluid in both complement and gene dosage. Some loci are ubiquitous and, after an ancient origin through transposition, originated through descent from the ancestral trypanosomatid. However, reconciliation analysis demonstrated that unilateral expansions of gene number through tandem gene duplication, transposition of gene duplicates to otherwise well conserved genomic

  16. Mechanics of quasi-static crack growth

    Energy Technology Data Exchange (ETDEWEB)

    Rice, J R

    1978-10-01

    Results on the mechanics of quasi-static crack growth are reviewed. These include recent studies on the geometry and stability of crack paths in elastic-brittle solids, and on the thermodynamics of Griffith cracking, including environmental effects. The relation of crack growth criteria to non-elastic rheological models is considered and paradoxes with energy balance approaches, based on singular crack models, are discussed for visco-elastic, diffuso-elastic, and elastic-plastic materials. Also, recent approaches to prediction of stable crack growth in ductile, elastic-plastic solids are discussed.

  17. Cracking on anisotropic neutron stars

    Science.gov (United States)

    Setiawan, A. M.; Sulaksono, A.

    2017-07-01

    We study the effect of cracking of a local anisotropic neutron star (NS) due to small density fluctuations. It is assumed that the neutron star core consists of leptons, nucleons and hyperons. The relativistic mean field model is used to describe the core of equation of state (EOS). For the crust, we use the EOS introduced by Miyatsu et al. [1]. Furthermore, two models are used to describe pressure anisotropic in neutron star matter. One is proposed by Doneva-Yazadjiev (DY) [2] and the other is proposed by Herrera-Barreto (HB) [3]. The anisotropic parameter of DY and HB models are adjusted in order the predicted maximum mass compatible to the mass of PSR J1614-2230 [4] and PSR J0348+0432 [5]. We have found that cracking can potentially present in the region close to the neutron star surface. The instability due cracking is quite sensitive to the NS mass and anisotropic parameter used.

  18. Blastocystis, an unrecognized parasite: an overview of pathogenesis and diagnosis.

    Science.gov (United States)

    Wawrzyniak, Ivan; Poirier, Philippe; Viscogliosi, Eric; Dionigia, Meloni; Texier, Catherine; Delbac, Frédéric; Alaoui, Hicham El

    2013-10-01

    Blastocystis sp. is among the few enteric parasites with a prevalence that often exceeds 5% in the general population of industrialized countries and can reach 30-60% in developing countries. This parasite is frequently found in people who are immunocompromised (patients with human immunodeficiency virus/acquired immunodeficiency syndrome or cancer) and a higher risk of Blastocystis sp. infection has been found in people with close animal contact. Such prevalence in the human population and the zoonotic potential naturally raise questions about the impact of these parasites on public health and has increased interest in this area. Recent in vitro and in vivo studies have shed new light on the pathogenic power of this parasite, suggesting that Blastocystis sp. infection is associated with a variety of gastrointestinal disorders, may play a significant role in irritable bowel syndrome, and may be linked with cutaneous lesions (urticaria). Despite recent significant advances in the knowledge of the extensive genetic diversity of this species, the identification of extracellular proteases as virulence factors and the publication of one isolate genome, many aspects of the biology of Blastocystis sp. remain poorly investigated. In this review, we investigate several biological aspects of Blastocystis sp. (diversity and epidemiology, diagnosis tools and pathophysiology). These data pave the way for the following challenges concerning Blastocystis sp. research: deciphering key biological mechanisms and pathways of this parasite and clarification of its clinical impact in humans.

  19. Dynamic experiments on cracked pipes

    International Nuclear Information System (INIS)

    Petit, M.; Brunet, G.; Buland, P.

    1991-01-01

    In order to apply the leak before break concept to piping systems, the behavior of cracked pipes under dynamic, and especially seismic loading must be studied. In a first phase, an experimental program on cracked stainless steel pipes under quasi-static monotonic loading has been conducted. In this paper, the dynamic tests on the same pipe geometry are described. These tests have been performed on a shaking table with a mono frequency input signal. The main parameter of the tests is the frequency of excitation versus the frequency of the system

  20. Cracking and corrosion recovery boiler

    Energy Technology Data Exchange (ETDEWEB)

    Suik, H. [Tallinn Technical University, Horizon Pulp and Paper, Tallinn (Estonia)

    1998-12-31

    The corrosion of heat surfaces and the cracking the drums are the main problems of the recovery boiler. These phenomena have been appeared during long-term operation of boiler `Mitsubishi - 315` erected at 1964. Depth of the crack is depending on the number of shutdowns and on operation time. Corrosion intensity of different heat surfaces is varying depend on the metal temperature and the conditions at place of positioning of tube. The lowest intensity of corrosion is on the bank tubes and the greatest is on the tubes of the second stage superheater and on the tubes at the openings of air ports. (orig.) 5 refs.

  1. Cracking and corrosion recovery boiler

    Energy Technology Data Exchange (ETDEWEB)

    Suik, H [Tallinn Technical University, Horizon Pulp and Paper, Tallinn (Estonia)

    1999-12-31

    The corrosion of heat surfaces and the cracking the drums are the main problems of the recovery boiler. These phenomena have been appeared during long-term operation of boiler `Mitsubishi - 315` erected at 1964. Depth of the crack is depending on the number of shutdowns and on operation time. Corrosion intensity of different heat surfaces is varying depend on the metal temperature and the conditions at place of positioning of tube. The lowest intensity of corrosion is on the bank tubes and the greatest is on the tubes of the second stage superheater and on the tubes at the openings of air ports. (orig.) 5 refs.

  2. The Leishmania nicotinamidase is essential for NAD(+) production and parasite proliferation

    OpenAIRE

    Gazanion, Elodie; Garcia, Deborah; Silvestre, R.; Gérard, C.; Guichou, J. F.; Labesse, G.; Seveno, Martial; Cordeiro-Da-Silva, A.; Ouaissi, A.; Sereno, Denis; Vergnes, Baptiste

    2011-01-01

    NAD(+) is a central cofactor that plays important roles in cellular metabolism and energy production in all living cells. Genomics-based reconstruction of NAD(+) metabolism revealed that Leishmania protozoan parasites are NAD(+) auxotrophs. Consequently, these parasites require assimilating NAD(+) precursors (nicotinamide, nicotinic acid, nicotinamide riboside) from their host environment to synthesize NAD(+) by a salvage pathway. Nicotinamidase is a key enzyme of this salvage pathway that ca...

  3. Integrated parasite management

    DEFF Research Database (Denmark)

    Clausen, Jesper Hedegaard; Madsen, Henry; Van, Phan Thi

    2015-01-01

    communities at risk through mass drug administration. However, we argue that treatment alone will not reduce the risk from eating infected fish and that sustainable effective control must adopt an integrated FZT control approach based on education, infrastructure improvements, and management practices...... that target critical control points in the aquaculture production cycle identified from a thorough understanding of FZT and host biology and epidemiology. We present recommendations for an integrated parasite management (IPM) program for aquaculture farms.......Fishborne zoonotic trematodes (FZT) are an emerging problem and there is now a consensus that, in addition to wild-caught fish, fish produced in aquaculture present a major food safety risk, especially in Southeast Asia where aquaculture is important economically. Current control programs target...

  4. The Reflective Cracking in Flexible Pavements

    Directory of Open Access Journals (Sweden)

    Pais Jorge

    2013-07-01

    Full Text Available Reflective cracking is a major concern for engineers facing the problem of road maintenance and rehabilitation. The problem appears due to the presence of cracks in the old pavement layers that propagate into the pavement overlay layer when traffic load passes over the cracks and due to the temperature variation. The stress concentration in the overlay just above the existing cracks is responsible for the appearance and crack propagation throughout the overlay. The analysis of the reflective cracking phenomenon is usually made by numerical modeling simulating the presence of cracks in the existing pavement and the stress concentration in the crack tip is assessed to predict either the cracking propagation rate or the expected fatigue life of the overlay. Numerical modeling to study reflective cracking is made by simulating one crack in the existing pavement and the loading is usually applied considering the shear mode of crack opening. Sometimes the simulation considers the mode I of crack opening, mainly when temperature effects are predominant.

  5. Recent advances in modelling creep crack growth

    International Nuclear Information System (INIS)

    Riedel, H.

    1988-08-01

    At the time of the previous International Conference on Fracture, the C* integral had long been recognized as a promising load parameter for correlating crack growth rates in creep-ductile materials. The measured crack growth rates as a function of C* and of the temperature could be understood on the basis of micromechanical models. The distinction between C*-controlled and K I -controlled creep crack growth had been clarified and first attempts had been made to describe creep crack growth in the transient regime between elastic behavior and steady-state creep. This paper describes the progress in describing transient crack growth including the effect of primary creep. The effect of crack-tip geometry changes by blunting and by crack growth on the crack-tip fields and on the validity of C* is analyzed by idealizing the growing-crack geometry by a sharp notch and using recent solutions for the notch-tip fields. A few new three-dimensional calculations of C* are cited and important theoretical points are emphasized regarding the three-dimensional fields at crack tips. Finally, creep crack growth is described by continuum-damage models for which similarity solutions can be obtained. Crack growth under small-scale creep conditions turns out to be difficult to understand. Slightly different models yield very different crack growth rates. (orig.) With 4 figs

  6. Ancient DNA from latrines in Northern Europe and the Middle East (500 BC–1700 AD) reveals past parasites and diet

    DEFF Research Database (Denmark)

    Søe, Martin Jensen; Nejsum, Peter; Seersholm, Frederik Valeur

    2018-01-01

    , vertebrate and plant DNA proved highly informative in the study of ancient health, human-animal interactions as well as animal and plant dietary components. Most prominent were finding of soil-borne parasites transmitted directly between humans, but also meat-borne parasites that require consumption of raw...... or undercooked fish and pork. The detection of parasites for which sheep, horse, dog, pig, and rodents serves as definitive hosts are clear markers of domestic and synanthropic animals living in closer proximity of the respective sites. Finally, the reconstruction of full mitochondrial parasite genomes from...

  7. How have fisheries affected parasite communities?

    Science.gov (United States)

    Wood, Chelsea L; Lafferty, Kevin D

    2015-01-01

    To understand how fisheries affect parasites, we conducted a meta-analysis of studies that contrasted parasite assemblages in fished and unfished areas. Parasite diversity was lower in hosts from fished areas. Larger hosts had a greater abundance of parasites, suggesting that fishing might reduce the abundance of parasites by selectively removing the largest, most heavily parasitized individuals. After controlling for size, the effect of fishing on parasite abundance varied according to whether the host was fished and the parasite's life cycle. Parasites of unfished hosts were more likely to increase in abundance in response to fishing than were parasites of fished hosts, possibly due to compensatory increases in the abundance of unfished hosts. While complex life cycle parasites tended to decline in abundance in response to fishing, directly transmitted parasites tended to increase. Among complex life cycle parasites, those with fished hosts tended to decline in abundance in response to fishing, while those with unfished hosts tended to increase. However, among directly transmitted parasites, responses did not differ between parasites with and without fished hosts. This work suggests that parasite assemblages are likely to change substantially in composition in increasingly fished ecosystems, and that parasite life history and fishing status of the host are important in predicting the response of individual parasite species or groups to fishing.

  8. On multiple crack detection in beam structures

    Energy Technology Data Exchange (ETDEWEB)

    Moradi, Shapour; Kargozarfard, Mohammad [Shahid Chamran University, Ahvaz (Iran, Islamic Republic of)

    2013-01-15

    This study presents an inverse procedure to identify multiple cracks in beams using an evolutionary algorithm. By considering the crack detection procedure as an optimization problem, an objective function can be constructed based on the change of the eigenfrequencies and some strain energy parameters. Each crack is modeled by a rotational spring. The changes in natural frequencies due to the presence of the cracks are related to a damage index vector. Then, the bees algorithm, a swarm-based evolutionary optimization technique, is used to optimize the objective function and find the damage index vector, whose positive components show the number and position of the cracks. A second objective function is also optimized to find the crack depths. Several experimental studies on cracked cantilever beams are conducted to ensure the integrity of the proposed method. The results show that the number of cracks as well as their sizes and locations can be predicted well through this method.

  9. Polydnaviruses of Parasitic Wasps: Domestication of Viruses To Act as Gene Delivery Vectors

    Directory of Open Access Journals (Sweden)

    Michael R. Strand

    2012-01-01

    Full Text Available Symbiosis is a common phenomenon in which associated organisms can cooperate in ways that increase their ability to survive, reproduce, or utilize hostile environments. Here, we discuss polydnavirus symbionts of parasitic wasps. These viruses are novel in two ways: (1 they have become non-autonomous domesticated entities that cannot replicate outside of wasps; and (2 they function as a delivery vector of genes that ensure successful parasitism of host insects that wasps parasitize. In this review we discuss how these novelties may have arisen, which genes are potentially involved, and what the consequences have been for genome evolution.

  10. Flow cytometry-assisted rapid isolation of recombinant Plasmodium berghei parasites exemplified by functional analysis of aquaglyceroporin

    Science.gov (United States)

    Kenthirapalan, Sanketha; Waters, Andrew P.; Matuschewski, Kai; Kooij, Taco W.A.

    2012-01-01

    The most critical bottleneck in the generation of recombinant Plasmodium berghei parasites is the mandatory in vivo cloning step following successful genetic manipulation. This study describes a new technique for rapid selection of recombinant P. berghei parasites. The method is based on flow cytometry to isolate isogenic parasite lines and represents a major advance for the field, in that it will speed the generation of recombinant parasites as well as cut down on animal use significantly. High expression of GFP during blood infection, a prerequisite for robust separation of transgenic lines by flow cytometry, was achieved. Isogenic recombinant parasite populations were isolated even in the presence of a 100-fold excess of wild-type (WT) parasites. Aquaglyceroporin (AQP) loss-of-function mutants and parasites expressing a tagged AQP were generated to validate this approach. aqp− parasites grow normally within the WT phenotypic range during blood infection of NMRI mice. Similarly, colonization of the insect vector and establishment of an infection after mosquito transmission were unaffected, indicating that AQP is dispensable for life cycle progression in vivo under physiological conditions, refuting its use as a suitable drug target. Tagged AQP localized to perinuclear structures and not the parasite plasma membrane. We suggest that flow-cytometric isolation of isogenic parasites overcomes the major roadblock towards a genome-scale repository of mutant and transgenic malaria parasite lines. PMID:23137753

  11. Comparison of crack arrest methodologies

    International Nuclear Information System (INIS)

    Anon.

    1979-01-01

    The ASTM Cooperative Test Program Data were used to compare the static (K/sub Ia/) and dynamic (K/sud ID/, K/sub IDm/) approaches to crack arrest. K/sub Ia/ is not dependent on K/sub Q/. This is consistent with the requirements of the static approach, but not the dynamic one which requires that K/sub Ia/ decrease with K/sub Q/ if K/sub ID/ (= K/sub IDm/) is a constant. K/sub ID/ increases systematically with K/sub Q/ at a rate that is consistent with calculations based on the use of a constant value for K/sub Ia/ which is equal to its measured mean value. Only in the limiting case of very short crack jumps (associated with very low average crack speeds) can K/sub ID/ be identified as a minimum value at which K/sub ID/ = K/sub IDm/. In this case K/sub IDm/ approx. K/sub Ia/ approx. K/sub Im/. The latter is the idealized minimum value of K that will support the continued propagation of a running crack

  12. The analysis of cracked structures

    International Nuclear Information System (INIS)

    Davidson, I.

    1974-01-01

    A brief review of the general problem of stable crack systems in many classes of structures, notably reinforced concrete structures, is made. Very simple methods of analysis are derived and some elaboration is described, as well as methods of optimising the calculations. Analytical methods are compared with experiments

  13. Cracks in functionally graded materials

    International Nuclear Information System (INIS)

    Bahr, H.-A.; Balke, H.; Fett, T.; Hofinger, I.; Kirchhoff, G.; Munz, D.; Neubrand, A.; Semenov, A.S.; Weiss, H.-J.; Yang, Y.Y.

    2003-01-01

    The weight function method is described to analyze the crack growth behavior in functionally graded materials and in particular materials with a rising crack growth resistance curve. Further, failure of graded thermal barrier coatings (TBCs) under cyclic surface heating by laser irradiation is modeled on the basis of fracture mechanics. The damage of both graded and non-graded TBCs is found to develop in several distinct stages: vertical cracking→delamination→blistering→spalling. This sequence can be understood as an effect of progressive shrinkage due to sintering and high-temperature creep during thermal cycling, which increases the energy-release rate for vertical cracks which subsequently turn into delamination cracks. The results of finite element modeling, taking into account the TBC damage mechanisms, are compatible with experimental data. An increase of interface fracture toughness due to grading and a decrease due to ageing have been measured in a four-point bending test modified by a stiffening layer. Correlation with the damage observed in cyclic heating is discussed. It is explained in which way grading is able to reduce the damage

  14. Severity parameters for steam cracking

    NARCIS (Netherlands)

    Golombok, M.; Bijl, J.L.M.; Kornegoor, M.

    2001-01-01

    There are several ways to measure severity in steam cracking which are all a function of residence time, temperature, and pressure. Many measures of severity are not practicable for experimental purposes. Our experimental study shows that methane make is the best measure of severity because it is an

  15. Steam hydrocarbon cracking and reforming

    NARCIS (Netherlands)

    Golombok, M.

    2004-01-01

    Many industrial chemical processes are taught as distinct contrasting reactions when in fact the unifying comparisons are greater than the contrasts. We examine steam hydrocarbon reforming and steam hydrocarbon cracking as an example of two processes that operate under different chemical reactivity

  16. Petrochemical promoters in catalytic cracking

    International Nuclear Information System (INIS)

    Gomez, Maria; Vargas, Clemencia; Lizcano, Javier

    2010-01-01

    This study is based on the current scheme followed by a refinery with available Catalytic Cracking capacity to process new feedstocks such as Straight Run Naphtha and Naphthas from FCC. These feedstocks are of petrochemical interest to produce Ethane, Ethylene, Propylene, i-Butane, Toluene and Xylene. To evaluate the potential of these new streams versus the Cracking-charged Residues, it was performed a detailed chemical analysis on the structural groups in carbons [C1-C12] at the reactor product obtained in pilot plant. A catalyst with and without Propylene Promoter Additive was used. This study analyzes the differences in the chemical composition of the feedstocks, relating them to the yield of each petrochemical product. Straight Run Naphthas with a high content of Naphthenes, and Paraffines n[C5-C12] and i[C7-C12] are selective to the production of i-Butane and Propane, while Naphthas from FCC with a high content of n[C5-C12]Olefins, i-Olefins, and Aromatics are more selective to Propylene, Toluene, and Xylene. Concerning Catalytic Cracking of Naphthas, the Additive has similar selectivity for all the petrochemical products, their yields increase by about one point with 4%wt of Additive, while in cracking of Residues, the Additive increases in three points Propylene yield, corresponding to a selectivity of 50% (?C3= / ?LPG).

  17. Fatigue crack growth in fiber reinforced plastics

    Science.gov (United States)

    Mandell, J. F.

    1979-01-01

    Fatigue crack growth in fiber composites occurs by such complex modes as to frustrate efforts at developing comprehensive theories and models. Under certain loading conditions and with certain types of reinforcement, simpler modes of fatigue crack growth are observed. These modes are more amenable to modeling efforts, and the fatigue crack growth rate can be predicted in some cases. Thus, a formula for prediction of ligamented mode fatigue crack growth rate is available.

  18. Dynamic photoelastic investigation of crack arrest

    International Nuclear Information System (INIS)

    Irwin, G.R.; Dally, J.W.; Kobayashi, T.; Fourney, W.L.

    1977-01-01

    Crack arrest and crack arrest toughness are of great interest, particularly for studies pertaining to safety of nuclear reactor pressure vessels. Investigations are needed in which the instantaneous values of stress intensity factor (K) can be observed during crack propagation and arrest. Such observations are possible if the test specimens are made from plates of a transparent photoelastic sensitive material. Values of K as a function of crack speed are shown for Homalite 100 and various epoxy blends. 9 figures

  19. Crack Propagation by Finite Element Method

    OpenAIRE

    H. Ricardo, Luiz Carlos

    2017-01-01

    Crack propagation simulation began with the development of the finite element method; the analyses were conducted to obtain a basic understanding of the crack growth. Today structural and materials engineers develop structures and materials properties using this technique. The aim of this paper is to verify the effect of different crack propagation rates in determination of crack opening and closing stress of an ASTM specimen under a standard suspension spectrum loading from FD&E SAE Keyh...

  20. Crack detection using image processing

    International Nuclear Information System (INIS)

    Moustafa, M.A.A

    2010-01-01

    This thesis contains five main subjects in eight chapters and two appendices. The first subject discus Wiener filter for filtering images. In the second subject, we examine using different methods, as Steepest Descent Algorithm (SDA) and the Wavelet Transformation, to detect and filling the cracks, and it's applications in different areas as Nano technology and Bio-technology. In third subject, we attempt to find 3-D images from 1-D or 2-D images using texture mapping with Open Gl under Visual C ++ language programming. The fourth subject consists of the process of using the image warping methods for finding the depth of 2-D images using affine transformation, bilinear transformation, projective mapping, Mosaic warping and similarity transformation. More details about this subject will be discussed below. The fifth subject, the Bezier curves and surface, will be discussed in details. The methods for creating Bezier curves and surface with unknown distribution, using only control points. At the end of our discussion we will obtain the solid form, using the so called NURBS (Non-Uniform Rational B-Spline); which depends on: the degree of freedom, control points, knots, and an evaluation rule; and is defined as a mathematical representation of 3-D geometry that can accurately describe any shape from a simple 2-D line, circle, arc, or curve to the most complex 3-D organic free-form surface or (solid) which depends on finding the Bezier curve and creating family of curves (surface), then filling in between to obtain the solid form. Another representation for this subject is concerned with building 3D geometric models from physical objects using image-based techniques. The advantage of image techniques is that they require no expensive equipment; we use NURBS, subdivision surface and mesh for finding the depth of any image with one still view or 2D image. The quality of filtering depends on the way the data is incorporated into the model. The data should be treated with

  1. BWR pipe crack remedies evaluation

    International Nuclear Information System (INIS)

    Shack, W.J.; Kassner, T.F.; Maiya, P.S.; Park, J.Y.; Ruther, W.; Kuzay, T.; Rybicki, E.F.; Stonesifer, R.B.

    1988-01-01

    Piping in light-water-reactor power systems has been affected by several types of environmental degradation. This paper presents results from studies of (1) stress corrosion crack growth in fracture mechanics specimens of modified Type 347 SS and Type 304/308L SS weld overlay material, (2) heat-to-heat variations in stress corrosion cracking (SCC) of Types 316NG and 347 SS, (3) SCC of sensitized Type 304 SS in water with cupric ion or organic acid impurities, (4) electrochemical potential (ECP) measurements under gamma irradiation, (5) SCC of ferritic steels, (6) strain-controlled fatigue of Type 316NG SS in air at ambient temperature, and (7) through-wall residual stress measurements and finite-element calculation of residual stresses in weldments treated by a mechanical stress improvement process (MSIP). Fracture-mechanics crack-growth-rate tests on Type 316NG SS have shown that transgranular cracking can occur even in high purity environments, whereas no crack growth was observed in Type 347 SS even in impurity environments. In tests on weld overlay specimens, no cracks penetrated into the overlay even in impurity environments. Instead, the cracks branched when they approached the overlay, and then grew parallel to interface. In SCC tests on sensitized Type 304 SS, cupric ions at concentrations greater than ∼1 ppm were found to be deleterious, whereas organic acids at this concentration were not detrimental. Tests on several ferritic steels indicate a strong correlation between the sulfur content of the steels and susceptibility to SCC. External gamma radiation fields produced a large positive shift in the ECP of Type 304 SS at low dissolved-oxygen concentrations (<5 ppb), whereas in the absence of an external gamma field there was no difference in the ECP values of irradiated and nonirradiated material. Fatigue data for Type 316NG SS are consistent with the ASME code mean curve at high strains, but fall below the curve at low strains. Calculations of the

  2. Correction to the crack extension direction in numerical modelling of mixed mode crack paths

    DEFF Research Database (Denmark)

    Lucht, Tore; Aliabadi, M.H.

    2007-01-01

    In order to avoid introduction of an error when a local crack-growth criterion is used in an incremental crack growth formulation, each straight crack extension would have to be infinitesimal or have its direction corrected. In this paper a new procedure to correct the crack extension direction...

  3. Fatigue crack growth from a cracked elastic particle into a ductile matrix

    NARCIS (Netherlands)

    Groh, S.; Olarnrithinun, S.; Curtin, W. A.; Needleman, A.; Deshpande, V. S.; Van der Giessen, E.

    2008-01-01

    The monotonic and cyclic crack growth rate of cracks is strongly influenced by the microstructure. Here, the growth of cracks emanating from pre-cracked micron-scale elastic particles and growing into single crystals is investigated, with a focus on the effects of (i) plastic confinement due to the

  4. Assessment of cracking in dissimilar metal welds

    International Nuclear Information System (INIS)

    Jenssen, Anders; Norrgaard, K.; Lagerstroem, J.; Embring, G.; Tice, D.R.

    2001-08-01

    During the refueling in 2000, indications were observed by non-destructive testing at four locations in the reactor pressure vessel (RPV) nozzle to safe end weld in Ringhals 4. All indications were confined to the outlet nozzle (hotleg) oriented at 25 deg, a nozzle with documented repair welding. Six boat samples were removed from the four locations, and the samples were subsequently subjected to a metallographic examination. The objectives were to establish the fracture morphology, and if possible the root cause for cracking. The examination revealed that cracks were present at all four boat sample locations and that they all were confined to the weld metal, alloy 182. Cracking extended in the axial direction of the safe-end. There was no evidence of any cracks extending into the RPV-steel, or the stainless steel safe-end. All cracking was interdendritic and significantly branched. Among others, these observations strongly suggested crack propagation mainly was caused by interdendritic stress corrosion cracking. In addition, crack type defects and isolated areas on the fracture surfaces suggested the presence of hot cracking, which would have been formed during fabrication. The reason for crack initiation could not be established based on the boat samples examined. However, increased stress levels due to repair welding, cold work from grinding, and defects produced during fabrication, e. g. hot cracks, may alone or in combination have contributed to crack initiation

  5. Solidification cracking in austenitic stainless steel welds

    Indian Academy of Sciences (India)

    M. Senthilkumar (Newgen Imaging) 1461 1996 Oct 15 13:05:22

    Hot cracking in stainless steel welds is caused by low-melting eutectics containing impurities such as S, ... Total crack length (TCL), used extensively in hot cracking assessment, exhibits greater variability due to ... behaviour appear to be complex and the mechanisms thereof are not completely under- stood. Development of ...

  6. Universal Shapes formed by Interacting Cracks

    Science.gov (United States)

    Fender, Melissa; Lechenault, Frederic; Daniels, Karen

    2011-03-01

    Brittle failure through multiple cracks occurs in a wide variety of contexts, from microscopic failures in dental enamel and cleaved silicon to geological faults and planetary ice crusts. In each of these situations, with complicated curvature and stress geometries, pairwise interactions between approaching cracks nonetheless produce characteristically curved fracture paths known in the geologic literature as en passant cracks. While the fragmentation of solids via many interacting cracks has seen wide investigation, less attention has been paid to the details of individual crack-crack interactions. We investigate the origins of this widely observed crack pattern using a rectangular elastic plate which is notched on each long side and then subjected to quasistatic uniaxial strain from the short side. The two cracks propagate along approximately straight paths until the pass each other, after which they curve and release a lenticular fragment. We find that, for materials with diverse mechanical properties, the shape of this fragment has an aspect ratio of 2:1, with the length scale set by the initial cracks offset s and the time scale set by the ratio of s to the pulling velocity. The cracks have a universal square root shape, which we understand by using a simple geometric model and the crack-crack interaction.

  7. Problems of procedure for studying crack resistance

    International Nuclear Information System (INIS)

    Babak, A.V.; Uskov, E.I.

    1984-01-01

    Procedures are developed for studying crack resistance in sintered hot-worked tungsten within 20-2200 deg C. Certain structural properties of the installation for studying high-temperature crack resistance of tungsten are considered. Technological peculiarities of eccentric tensile strength of tungsten specimens and methodical peculiarities of initjation and fixation of initial cracks in specimens of different tungsten alloys are studied

  8. Identification of Multiple Loci Associated with Social Parasitism in Honeybees.

    Science.gov (United States)

    Wallberg, Andreas; Pirk, Christian W; Allsopp, Mike H; Webster, Matthew T

    2016-06-01

    In colonies of the honeybee Apis mellifera, the queen is usually the only reproductive female, which produces new females (queens and workers) by laying fertilized eggs. However, in one subspecies of A. mellifera, known as the Cape bee (A. m. capensis), worker bees reproduce asexually by thelytoky, an abnormal form of meiosis where two daughter nucleii fuse to form single diploid eggs, which develop into females without being fertilized. The Cape bee also exhibits a suite of phenotypes that facilitate social parasitism whereby workers lay such eggs in foreign colonies so their offspring can exploit their resources. The genetic basis of this switch to social parasitism in the Cape bee is unknown. To address this, we compared genome variation in a sample of Cape bees with other African populations. We find genetic divergence between these populations to be very low on average but identify several regions of the genome with extreme differentiation. The regions are strongly enriched for signals of selection in Cape bees, indicating that increased levels of positive selection have produced the unique set of derived phenotypic traits in this subspecies. Genetic variation within these regions allows unambiguous genetic identification of Cape bees and likely underlies the genetic basis of social parasitism. The candidate loci include genes involved in ecdysteroid signaling and juvenile hormone and dopamine biosynthesis, which may regulate worker ovary activation and others whose products localize at the centrosome and are implicated in chromosomal segregation during meiosis. Functional analysis of these loci will yield insights into the processes of reproduction and chemical signaling in both parasitic and non-parasitic populations and advance understanding of the process of normal and atypical meiosis.

  9. Identification of Multiple Loci Associated with Social Parasitism in Honeybees.

    Directory of Open Access Journals (Sweden)

    Andreas Wallberg

    2016-06-01

    Full Text Available In colonies of the honeybee Apis mellifera, the queen is usually the only reproductive female, which produces new females (queens and workers by laying fertilized eggs. However, in one subspecies of A. mellifera, known as the Cape bee (A. m. capensis, worker bees reproduce asexually by thelytoky, an abnormal form of meiosis where two daughter nucleii fuse to form single diploid eggs, which develop into females without being fertilized. The Cape bee also exhibits a suite of phenotypes that facilitate social parasitism whereby workers lay such eggs in foreign colonies so their offspring can exploit their resources. The genetic basis of this switch to social parasitism in the Cape bee is unknown. To address this, we compared genome variation in a sample of Cape bees with other African populations. We find genetic divergence between these populations to be very low on average but identify several regions of the genome with extreme differentiation. The regions are strongly enriched for signals of selection in Cape bees, indicating that increased levels of positive selection have produced the unique set of derived phenotypic traits in this subspecies. Genetic variation within these regions allows unambiguous genetic identification of Cape bees and likely underlies the genetic basis of social parasitism. The candidate loci include genes involved in ecdysteroid signaling and juvenile hormone and dopamine biosynthesis, which may regulate worker ovary activation and others whose products localize at the centrosome and are implicated in chromosomal segregation during meiosis. Functional analysis of these loci will yield insights into the processes of reproduction and chemical signaling in both parasitic and non-parasitic populations and advance understanding of the process of normal and atypical meiosis.

  10. Delayed hydride cracking: theoretical model testing to predict cracking velocity

    International Nuclear Information System (INIS)

    Mieza, Juan I.; Vigna, Gustavo L.; Domizzi, Gladys

    2009-01-01

    Pressure tubes from Candu nuclear reactors as any other component manufactured with Zr alloys are prone to delayed hydride cracking. That is why it is important to be able to predict the cracking velocity during the component lifetime from parameters easy to be measured, such as: hydrogen concentration, mechanical and microstructural properties. Two of the theoretical models reported in literature to calculate the DHC velocity were chosen and combined, and using the appropriate variables allowed a comparison with experimental results of samples from Zr-2.5 Nb tubes with different mechanical and structural properties. In addition, velocities measured by other authors in irradiated materials could be reproduced using the model described above. (author)

  11. Comparison of thermal cracking and hydro-cracking yield distributions

    Energy Technology Data Exchange (ETDEWEB)

    Romero, S.; Sayles, S. [KBC Advanced Technologies Inc., Houston, TX (United States)

    2009-07-01

    Operators of bitumen upgraders are faced with the challenge of obtaining maximum performance from existing equipment whose performance is already pushed to the limits. The main constraint is the primary upgrader processes, notably coking and hydrocracking. Under the current economic conditions, funding for new equipment is difficult. However, changes can be made to optimize unit performance by better understanding the basic kinetics in thermal cracking and hydrocracking. This paper reviewed the yield distribution differences between thermal cracking and hydrocracking to provide insight into the basic components of operational changes. The objective was to compare yields, product quality distributions and the elemental balances. The opportunities to increase production and improve performance were then analyzed quantitatively within the existing unit equipment limits. tabs., figs.

  12. Parasites in pet reptiles

    Directory of Open Access Journals (Sweden)

    Mavri Urška

    2011-05-01

    Full Text Available Abstract Exotic reptiles originating from the wild can be carriers of many different pathogens and some of them can infect humans. Reptiles imported into Slovenia from 2000 to 2005, specimens of native species taken from the wild and captive bred species were investigated. A total of 949 reptiles (55 snakes, 331 lizards and 563 turtles, belonging to 68 different species, were examined for the presence of endoparasites and ectoparasites. Twelve different groups (Nematoda (5, Trematoda (1, Acanthocephala (1, Pentastomida (1 and Protozoa (4 of endoparasites were determined in 26 (47.3% of 55 examined snakes. In snakes two different species of ectoparasites were also found. Among the tested lizards eighteen different groups (Nematoda (8, Cestoda (1, Trematoda (1, Acanthocephala (1, Pentastomida (1 and Protozoa (6 of endoparasites in 252 (76.1% of 331 examined animals were found. One Trombiculid ectoparasite was determined. In 563 of examined turtles eight different groups (Nematoda (4, Cestoda (1, Trematoda (1 and Protozoa (2 of endoparasites were determined in 498 (88.5% animals. In examined turtles three different species of ectoparasites were seen. The established prevalence of various parasites in reptiles used as pet animals indicates the need for examination on specific pathogens prior to introduction to owners.

  13. Analysis of crack opening stresses for center- and edge-crack tension specimens

    Directory of Open Access Journals (Sweden)

    Tong Di-Hua

    2014-04-01

    Full Text Available Accurate determination of crack opening stress is of central importance to fatigue crack growth analysis and life prediction based on the crack-closure model. This paper studies the crack opening behavior for center- and edge-crack tension specimens. It is found that the crack opening stress is affected by the crack tip element. By taking the crack tip element into account, a modified crack opening stress equation is given for the center-crack tension specimen. Crack surface displacement equations for an edge crack in a semi-infinite plate under remote uniform tension and partially distributed pressure are derived by using the weight function method. Based on these displacements, a crack opening stress equation for an edge crack in a semi-infinite plate under uniform tension has been developed. The study shows that the crack opening stress is geometry-dependent, and the weight function method provides an effective and reliable tool to deal with such geometry dependence.

  14. Crack modeling of rotating blades with cracked hexahedral finite element method

    Science.gov (United States)

    Liu, Chao; Jiang, Dongxiang

    2014-06-01

    Dynamic analysis is the basis in investigating vibration features of cracked blades, where the features can be applied to monitor health state of blades, detect cracks in an early stage and prevent failures. This work presents a cracked hexahedral finite element method for dynamic analysis of cracked blades, with the purpose of addressing the contradiction between accuracy and efficiency in crack modeling of blades in rotor system. The cracked hexahedral element is first derived with strain energy release rate method, where correction of stress intensity factors of crack front and formulation of load distribution of crack surface are carried out to improve the modeling accuracy. To consider nonlinear characteristics of time-varying opening and closure effects caused by alternating loads, breathing function is proposed for the cracked hexahedral element. Second, finite element method with contact element is analyzed and used for comparison. Finally, validation of the cracked hexahedral element is carried out in terms of breathing effects of cracked blades and natural frequency in different crack depths. Good consistency is acquired between the results with developed cracked hexahedral element and contact element, while the computation time is significantly reduced in the previous one. Therefore, the developed cracked hexahedral element achieves good accuracy and high efficiency in crack modeling of rotating blades.

  15. Acquisition of Inertia by a Moving Crack

    Science.gov (United States)

    Goldman, Tamar; Livne, Ariel; Fineberg, Jay

    2010-03-01

    We experimentally investigate the dynamics of “simple” tensile cracks. Within an effectively infinite medium, a crack’s dynamics perfectly correspond to inertialess behavior predicted by linear elastic fracture mechanics. Once a crack interacts with waves that it generated at earlier times, this description breaks down. Cracks then acquire inertia and sluggishly accelerate. Crack inertia increases with crack speed v and diverges as v approaches its limiting value. We show that these dynamics are in excellent accord with an equation of motion derived in the limit of an infinite strip [M. Marder, Phys. Rev. Lett. 66, 2484 (1991)PRLTAO0031-900710.1103/PhysRevLett.66.2484].

  16. Factors controlling nitrate cracking of mild steel

    International Nuclear Information System (INIS)

    Donovan, J.A.

    1977-01-01

    Nitrite and hydroxide ions inhibit the growth of nitrate stress corrosion cracks in mild steel. Crack growth measurements showed that sufficient concentrations of nitrite and hydroxide ions can prevent crack growth; however, insufficient concentrations of these ions did not influence the Stage II growth rate or the threshold stress intensity, but extended the initiation time. Stage III growth was discontinuous. Oxide formed in the grain boundaries ahead of the crack tip and oxide dissolution (Stage II) and fracture (Stage III) are the proposed mechanisms of nitrate stress corrosion crack growth

  17. Crack Propagation by Finite Element Method

    Directory of Open Access Journals (Sweden)

    Luiz Carlos H. Ricardo

    2018-01-01

    Full Text Available Crack propagation simulation began with the development of the finite element method; the analyses were conducted to obtain a basic understanding of the crack growth. Today structural and materials engineers develop structures and materials properties using this technique. The aim of this paper is to verify the effect of different crack propagation rates in determination of crack opening and closing stress of an ASTM specimen under a standard suspension spectrum loading from FDandE SAE Keyhole Specimen Test Load Histories by finite element analysis. To understand the crack propagation processes under variable amplitude loading, retardation effects are observed

  18. Fauna Europaea: Helminths (Animal Parasitic)

    Czech Academy of Sciences Publication Activity Database

    Gibson, D. I.; Bray, R. A.; Hunt, D.; Georgiev, B. B.; Scholz, Tomáš; Harris, P.D.; Bakke, T.A.; Pomajska, T.; Niewiadomska, K.; Kostadinova, Aneta; Tkach, V.; Bain, O.; Durette-Desset, M.-C.; Gibbons, L.; Moravec, František; Petter, A.; Dimitrova, Z.M.; Buchmann, K.; Valtonen, E. T.; de Jong, Y.

    -, č. 2 (2014), e1060 ISSN 1314-2828 Institutional support: RVO:60077344 Keywords : Acanthocephala * Biodiversity * Biodiversity Informatics * Cestoda * Fauna Europaea * Helminth * Monogenea * Nematoda * Parasite * Taxonomic indexing * Taxonomy * Trematoda * Zoology Subject RIV: EB - Genetics ; Molecular Biology

  19. Evolutionary genomics and population structure of Entamoeba histolytica

    Directory of Open Access Journals (Sweden)

    Koushik Das

    2014-11-01

    Full Text Available Amoebiasis caused by the gastrointestinal parasite Entamoeba histolytica has diverse disease outcomes. Study of genome and evolution of this fascinating parasite will help us to understand the basis of its virulence and explain why, when and how it causes diseases. In this review, we have summarized current knowledge regarding evolutionary genomics of E. histolytica and discussed their association with parasite phenotypes and its differential pathogenic behavior. How genetic diversity reveals parasite population structure has also been discussed. Queries concerning their evolution and population structure which were required to be addressed have also been highlighted. This significantly large amount of genomic data will improve our knowledge about this pathogenic species of Entamoeba.

  20. Adaptations in the energy metabolism of parasites

    NARCIS (Netherlands)

    van Grinsven, K.W.A.|info:eu-repo/dai/nl/304833436

    2009-01-01

    For this thesis fundamental research was performed on the metabolic adaptations found in parasites. Studying the adaptations in parasite metabolisms leads to a better understanding of parasite bioenergetics and can also result in the identification of new anti-parasitic drug targets. We focussed on

  1. Pervasiveness of parasites in pollinators.

    Directory of Open Access Journals (Sweden)

    Sophie E F Evison

    Full Text Available Many pollinator populations are declining, with large economic and ecological implications. Parasites are known to be an important factor in the some of the population declines of honey bees and bumblebees, but little is known about the parasites afflicting most other pollinators, or the extent of interspecific transmission or vectoring of parasites. Here we carry out a preliminary screening of pollinators (honey bees, five species of bumblebee, three species of wasp, four species of hoverfly and three genera of other bees in the UK for parasites. We used molecular methods to screen for six honey bee viruses, Ascosphaera fungi, Microsporidia, and Wolbachia intracellular bacteria. We aimed simply to detect the presence of the parasites, encompassing vectoring as well as actual infections. Many pollinators of all types were positive for Ascosphaera fungi, while Microsporidia were rarer, being most frequently found in bumblebees. We also detected that most pollinators were positive for Wolbachia, most probably indicating infection with this intracellular symbiont, and raising the possibility that it may be an important factor in influencing host sex ratios or fitness in a diversity of pollinators. Importantly, we found that about a third of bumblebees (Bombus pascuorum and Bombus terrestris and a third of wasps (Vespula vulgaris, as well as all honey bees, were positive for deformed wing virus, but that this virus was not present in other pollinators. Deformed wing virus therefore does not appear to be a general parasite of pollinators, but does interact significantly with at least three species of bumblebee and wasp. Further work is needed to establish the identity of some of the parasites, their spatiotemporal variation, and whether they are infecting the various pollinator species or being vectored. However, these results provide a first insight into the diversity, and potential exchange, of parasites in pollinator communities.

  2. Environmentally assisted cracking of LWR materials

    International Nuclear Information System (INIS)

    Chopra, O.K.; Chung, H.M.; Kassner, T.F.; Shack, W.J.

    1995-12-01

    Research on environmentally assisted cracking (EAC) of light water reactor materials has focused on (a) fatigue initiation in pressure vessel and piping steels, (b) crack growth in cast duplex and austenitic stainless steels (SSs), (c) irradiation-assisted stress corrosion cracking (IASCC) of austenitic SSs, and (d) EAC in high- nickel alloys. The effect of strain rate during different portions of the loading cycle on fatigue life of carbon and low-alloy steels in 289 degree C water was determined. Crack growth studies on wrought and cast SSs have been completed. The effect of dissolved-oxygen concentration in high-purity water on IASCC of irradiated Type 304 SS was investigated and trace elements in the steel that increase susceptibility to intergranular cracking were identified. Preliminary results were obtained on crack growth rates of high-nickel alloys in water that contains a wide range of dissolved oxygen and hydrogen concentrations at 289 and 320 degree C. The program on Environmentally Assisted Cracking of Light Water Reactor Materials is currently focused on four tasks: fatigue initiation in pressure vessel and piping steels, fatigue and environmentally assisted crack growth in cast duplex and austenitic SS, irradiation-assisted stress corrosion cracking of austenitic SSs, and environmentally assisted crack growth in high-nickel alloys. Measurements of corrosion-fatigue crack growth rates (CGRs) of wrought and cast stainless steels has been essentially completed. Recent progress in these areas is outlined in the following sections

  3. Finite element simulation for creep crack growth

    International Nuclear Information System (INIS)

    Miyazaki, Noriyuki; Sasaki, Toru; Nakagaki, Michihiko; Brust, F.W.

    1992-01-01

    A finite element method was applied to a generation phase simulation of creep crack growth. Experimental data on creep crack growth in a 1Cr-1Mo-1/4V steel compact tension specimen were numerically simulated using a node-release technique and the variations of various fracture mechanics parameters such as CTOA, J, C * and T * during creep crack growth were calculated. The path-dependencies of the integral parameters J, C * and T * were also obtained to examine whether or not they could characterize the stress field near the tip of a crack propagating under creep condition. The following conclusions were obtained from the present analysis. (1) The J integral shows strong path-dependency during creep crack growth, so that it is does not characterize creep crack growth. (2) The C * integral shows path-dependency to some extent during creep crack growth even in the case of Norton type steady state creep law. Strictly speaking, we cannot use it as a fracture mechanics parameter characterizing creep crack growth. It is, however, useful from the practical viewpoint because it correlates well the rate of creep crack growth. (3) The T * integral shows good path-independency during creep crack growth. Therefore, it is a candidate for a fracture mechanics parameter characterizing creep crack growth. (author)

  4. Paleoparasitology: the origin of human parasites

    Directory of Open Access Journals (Sweden)

    Adauto Araujo

    2013-09-01

    Full Text Available Parasitism is composed by three subsystems: the parasite, the host, and the environment. There are no organisms that cannot be parasitized. The relationship between a parasite and its host species most of the time do not result in damage or disease to the host. However, in a parasitic disease the presence of a given parasite is always necessary, at least in a given moment of the infection. Some parasite species that infect humans were inherited from pre-hominids, and were shared with other phylogenetically close host species, but other parasite species were acquired from the environment as humans evolved. Human migration spread inherited parasites throughout the globe. To recover and trace the origin and evolution of infectious diseases, paleoparasitology was created. Paleoparasitology is the study of parasites in ancient material, which provided new information on the evolution, paleoepidemiology, ecology and phylogenetics of infectious diseases.

  5. Phenomics, Genomics and Genetics in Plasmodium vinckei

    KAUST Repository

    Ramaprasad, Abhinay

    2017-11-01

    Rodent malaria parasites (RMPs) serve as tractable models for experimental genetics, and as valuable tools to study malaria parasite biology and host-parasitevector interactions. Plasmodium vinckei, one of four RMPs adapted to laboratory mice, is the most geographically widespread species and displays considerable phenotypic and genotypic diversity amongst its subspecies and strains. The phenotypes and genotypes of P. vinckei isolates have been relatively less characterized compared to other RMPs, hampering its use as an experimental model for malaria. Here, we have studied the phenotypes and sequenced the genomes and transcriptomes of ten P. vinckei isolates including representatives of all five subspecies, all of which were collected from wild thicket rats (Thamnomys rutilans) in sub-Saharan Central Africa between the late 1940s and mid 1960s. We have generated a comprehensive resource for P. vinckei comprising of five high-quality reference genomes, growth profiles and genotypes of P. vinckei isolates, and expression profiles of genes across the intra-erythrocytic developmental stages of the parasite. We observe significant phenotypic and genotypic diversity among P. vinckei isolates, making them particularly suitable for classical genetics and genomics-driven studies on malaria parasite biology. As part of a proof of concept study, we have shown that experimental genetic crosses can be performed between P. vinckei parasites to potentially identify genotype-phenotype relationships. We have also shown that they are amenable to genetic manipulation in the laboratory.

  6. Nonlocal Effects of Crack Curving.

    Science.gov (United States)

    1982-07-01

    close vTcinity of the crack tip. Supported by the Office of Naval Research. 2 For brittle solids, a fracture criterion based on the maximum tensile...Reidel Pubi. Co. Dordrecht. Holland. pp. 271-318, 1978. [13] A.S. Jayatilaka, Fracture of Engineering Brittle Materials, Appl. Sci. Publishers, London...Crescent leach Road, Glen Cove * Long Island, New Tork 11542 Commanding Officer (2) U.s Amy Research Office PO, Sax 12211 Research Triangle Park. C 27709 8

  7. Hydrogen-induced cracking: 2

    International Nuclear Information System (INIS)

    Puls, M.P.

    1984-12-01

    There is a strong motivation for understanding the factors controlling zirconium hydride reorientation under stress because of the important role this plays in hydrogen-induced crack growth and/or crack initiation in zirconium and its alloys, particularly under thermal cycling conditions. Following an approach developed by Sauthoff, an analysis of the orienting effect of external stress on the nucleation, growth and coarsening of γ- and delta-zirconium hydride precipitates in zirconium and its alloys is presented. The analysis is based on a previous theoretical study of some of the factors affecting hydride solubility in stressed and unstressed solids. Expressions are derived for the effect of stress on nucleation, growth and coarsening. We conclude, on the basis of these that the preferential orientation of hydride precipitates under stress is most efficient during the nucleation stage. The reason for this is that the overall driving force for nucleation, for the chosen parameters and the usual experimental conditions, is fairly small. Therefore, the driving force for orientating under stress can be a substantial fraction of the overall driving force. The analysis shows that hydride growth is unlikely to play a role in preferential orientation, but coarsening could be important under carefully chosen experimental conditions, which may be relevant to the hydride-cracking process

  8. The Growth of Small Corrosion Fatigue Cracks in Alloy 7075

    Science.gov (United States)

    Piascik, Robert S.

    2015-01-01

    The corrosion fatigue crack growth characteristics of small (greater than 35 micrometers) surface and corner cracks in aluminum alloy 7075 is established. The early stage of crack growth is studied by performing in situ long focal length microscope (500×) crack length measurements in laboratory air and 1% sodium chloride (NaCl) environments. To quantify the "small crack effect" in the corrosive environment, the corrosion fatigue crack propagation behavior of small cracks is compared to long through-the-thickness cracks grown under identical experimental conditions. In salt water, long crack constant K(sub max) growth rates are similar to small crack da/dN.

  9. Quarter elliptical crack growth using three dimensional finite element method and crack closure technique

    Energy Technology Data Exchange (ETDEWEB)

    Gozin, Mohammad-Hosein; Aghaie-Khafri, Mehrdad [K. N. Toosi University of Technology, Tehran (Korea, Republic of)

    2014-06-15

    Shape evolution of a quarter-elliptical crack emanating from a hole is studied. Three dimensional elastic-plastic finite element analysis of the fatigue crack closure was considered and the stress intensity factor was calculated based on the duplicated elastic model at each crack tip node. The crack front node was advanced proportional to the imposed effective stress intensity factor. Remeshing was applied at each step of the crack growth and solution mapping algorithm was considered. Crack growth retardation at free surfaces was successfully observed. A MATLAB-ABAQUS interference code was developed for the first time to perform crack growth on the basis of crack closure. Simulation results indicated that crack shape is sensitive to the remeshing strategy. Predictions based on the proposed models were in good agreement with Carlson's experiments results.

  10. Crack propagation in teeth: a comparison of perimortem and postmortem behavior of dental materials and cracks.

    Science.gov (United States)

    Hughes, Cris E; White, Crystal A

    2009-03-01

    This study presents a new method for understanding postmortem heat-induced crack propagation patterns in teeth. The results demonstrate that patterns of postmortem heat-induced crack propagation differ from perimortem and antemortem trauma-induced crack propagation patterns. Dental material of the postmortem tooth undergoes dehydration leading to a shrinking and more brittle dentin material and a weaker dentin-enamel junction. Dentin intertubule tensile stresses are amplified by the presence of the pulp cavity, and initiates crack propagation from the internal dentin, through the dentin-enamel junction and lastly the enamel. In contrast, in vivo perimortem and antemortem trauma-induced crack propagation initiates cracking from the external surface of the enamel toward the dentin-enamel junction where the majority of the energy of the crack is dissipated, eliminating the crack's progress into the dentin. These unique patterns of crack propagation can be used to differentiate postmortem taphonomy-induced damage from antemortem and perimortem trauma in teeth.

  11. Vibration based algorithm for crack detection in cantilever beam containing two different types of cracks

    Science.gov (United States)

    Behzad, Mehdi; Ghadami, Amin; Maghsoodi, Ameneh; Michael Hale, Jack

    2013-11-01

    In this paper, a simple method for detection of multiple edge cracks in Euler-Bernoulli beams having two different types of cracks is presented based on energy equations. Each crack is modeled as a massless rotational spring using Linear Elastic Fracture Mechanics (LEFM) theory, and a relationship among natural frequencies, crack locations and stiffness of equivalent springs is demonstrated. In the procedure, for detection of m cracks in a beam, 3m equations and natural frequencies of healthy and cracked beam in two different directions are needed as input to the algorithm. The main accomplishment of the presented algorithm is the capability to detect the location, severity and type of each crack in a multi-cracked beam. Concise and simple calculations along with accuracy are other advantages of this method. A number of numerical examples for cantilever beams including one and two cracks are presented to validate the method.

  12. Origin of the human malaria parasite Plasmodium falciparum in gorillas.

    Science.gov (United States)

    Liu, Weimin; Li, Yingying; Learn, Gerald H; Rudicell, Rebecca S; Robertson, Joel D; Keele, Brandon F; Ndjango, Jean-Bosco N; Sanz, Crickette M; Morgan, David B; Locatelli, Sabrina; Gonder, Mary K; Kranzusch, Philip J; Walsh, Peter D; Delaporte, Eric; Mpoudi-Ngole, Eitel; Georgiev, Alexander V; Muller, Martin N; Shaw, George M; Peeters, Martine; Sharp, Paul M; Rayner, Julian C; Hahn, Beatrice H

    2010-09-23

    Plasmodium falciparum is the most prevalent and lethal of the malaria parasites infecting humans, yet the origin and evolutionary history of this important pathogen remain controversial. Here we develop a single-genome amplification strategy to identify and characterize Plasmodium spp. DNA sequences in faecal samples from wild-living apes. Among nearly 3,000 specimens collected from field sites throughout central Africa, we found Plasmodium infection in chimpanzees (Pan troglodytes) and western gorillas (Gorilla gorilla), but not in eastern gorillas (Gorilla beringei) or bonobos (Pan paniscus). Ape plasmodial infections were highly prevalent, widely distributed and almost always made up of mixed parasite species. Analysis of more than 1,100 mitochondrial, apicoplast and nuclear gene sequences from chimpanzees and gorillas revealed that 99% grouped within one of six host-specific lineages representing distinct Plasmodium species within the subgenus Laverania. One of these from western gorillas comprised parasites that were nearly identical to P. falciparum. In phylogenetic analyses of full-length mitochondrial sequences, human P. falciparum formed a monophyletic lineage within the gorilla parasite radiation. These findings indicate that P. falciparum is of gorilla origin and not of chimpanzee, bonobo or ancient human origin.

  13. Application of acoustic emission to hydride cracking

    International Nuclear Information System (INIS)

    Sagat, S.; Ambler, J.F.R.; Coleman, C.E.

    1986-07-01

    Acoustic emission has been used for over a decade to study delayed hydride cracking (DHC) in zirconium alloys. At first acoustic emission was used primarily to detect the onset of DHC. This was possible because DHC was accompanied by very little plastic deformation of the material and furthermore the amplitudes of the acoustic pulses produced during cracking of the brittle hydride phase were much larger than those from dislocation motion and twinning. Acoustic emission was also used for measuring crack growth when it was found that for a suitable amplitude threshold, the total number of acoustic emission counts was linearly related to the cracked area. Once the proportionality constant was established, the acoustic counts could be converted to the crack length. Now the proportionality between the count rate and the crack growth rate is used to provide feedback between the crack length and the applied load, using computer technology. In such a system, the stress at the crack tip can be maintained constant during the test by adjusting the applied load as the crack progresses, or it can be changed in a predetermined manner, for example, to measure the threshold stress for cracking

  14. Fatigue crack propagation behavior under creep conditions

    International Nuclear Information System (INIS)

    Ohji, Kiyotsugu; Kubo, Shiro

    1991-01-01

    The crack propagation behavior of the SUS 304 stainless steel under creep-fatigue conditions was reviewed. Cracks propagated either in purely time-dependent mode or in purely cycle-dependent mode, depending on loading conditions. The time-dependent crack propagation rate was correlated with modified J-integral J * and the cycle-dependent crack propagation rate was correlated with J-integral range ΔJ f . Threshold was observed in the cycle-dependent crack propagation, and below this threshold the time-dependent crack propagation appeared. The crack propagation rates were uniquely characterized by taking the effective values of J * and ΔJ f , when crack closure was observed. Change in crack propagation mode occurred reversibly and was predicted by the competitive damage model. The threshold disappeared and the cycle-dependent crack propagation continued in a subthreshold region under variable amplitude conditions, where the threshold was interposed between the maximum and minimum ΔJ f . (orig.)

  15. A de-novo-assembly-based Data Analysis Pipeline for Plant Obligate Parasite Metatranscriptomic Studies

    Directory of Open Access Journals (Sweden)

    Li Guo

    2016-07-01

    Full Text Available Current and emerging plant diseases caused by obligate parasitic microbes such as rusts, downy mildews, and powdery mildews threaten worldwide crop production and food safety. These obligate parasites are typically unculturable in the laboratory, posing technical challenges to characterize them at the genetic and genomic level. Here we have developed a data analysis pipeline integrating several bioinformatic software programs. This pipeline facilitates rapid gene discovery and expression analysis of a plant host and its obligate parasite simultaneously by next generation sequencing of mixed host and pathogen RNA (i.e. metatranscriptomics. We applied this pipeline to metatranscriptomic sequencing data of sweet basil (Ocimum basilicum and its obligate downy mildew parasite Peronospora belbahrii, both lacking a sequenced genome. Even with a single data point, we were able to identify both candidate host defense genes and pathogen virulence genes that are highly expressed during infection. This demonstrates the power of this pipeline for identifying genes important in host-pathogen interactions without prior genomic information for either the plant host or the obligate biotrophic pathogen. The simplicity of this pipeline makes it accessible to researchers with limited computational skills and applicable to metatranscriptomic data analysis in a wide range of plant-obligate-parasite systems.

  16. Effects of δ-hydride precipitation at a crack tip on crack propagation in delayed hydride cracking of Zircaloy-2

    Energy Technology Data Exchange (ETDEWEB)

    Kubo, T., E-mail: kubo@nfd.co.jp [Nippon Nuclear Fuel Development Co., Ltd., 2163 Narita-cho, Oarai-machi, Ibaraki 311-1313 (Japan); Kobayashi, Y. [M.O.X. Co., Ltd., 1828-520 Hirasu-cho, Mito, Ibaraki 311-0853 (Japan)

    2013-08-15

    Highlights: • Steady state crack velocity of delayed hydride cracking in Zircaloy-2 was analyzed. • A large stress peak is induced at an end of hydride by volume expansion of hydride. • Hydrogen diffuses to the stress peak, thereby accelerating steady hydride growth. • Crack velocity was estimated from the calculated hydrogen flux into the stress peak. • There was good agreement between calculation results and experimental data. -- Abstract: Delayed hydride cracking (DHC) of Zircaloy-2 is one possible mechanism for the failure of boiling water reactor fuel rods in ramp tests at high burnup. Analyses were made for hydrogen diffusion around a crack tip to estimate the crack velocity of DHC in zirconium alloys, placing importance on effects of precipitation of δ-hydride. The stress distribution around the crack tip is significantly altered by precipitation of hydride, which was strictly analyzed using a finite element computer code. Then, stress-driven hydrogen diffusion under the altered stress distribution was analyzed by a differential method. Overlapping of external stress and hydride precipitation at a crack tip induces two stress peaks; one at a crack tip and the other at the front end of the hydride precipitate. Since the latter is larger than the former, more hydrogen diffuses to the front end of the hydride precipitate, thereby accelerating hydride growth compared with that in the absence of the hydride. These results indicated that, after hydride was formed in front of the crack tip, it grew almost steadily accompanying the interaction of hydrogen diffusion, hydride growth and the stress alteration by hydride precipitation. Finally, crack velocity was estimated from the calculated hydrogen flux into the crack tip as a function of temperature, stress intensity factor and material strength. There was qualitatively good agreement between calculation results and experimental data.

  17. Root parasitic plant Orobanche aegyptiaca and shoot parasitic plant Cuscuta australis obtained Brassicaceae-specific strictosidine synthase-like genes by horizontal gene transfer.

    Science.gov (United States)

    Zhang, Dale; Qi, Jinfeng; Yue, Jipei; Huang, Jinling; Sun, Ting; Li, Suoping; Wen, Jian-Fan; Hettenhausen, Christian; Wu, Jinsong; Wang, Lei; Zhuang, Huifu; Wu, Jianqiang; Sun, Guiling

    2014-01-13

    Besides gene duplication and de novo gene generation, horizontal gene transfer (HGT) is another important way of acquiring new genes. HGT may endow the recipients with novel phenotypic traits that are important for species evolution and adaption to new ecological niches. Parasitic systems expectedly allow the occurrence of HGT at relatively high frequencies due to their long-term physical contact. In plants, a number of HGT events have been reported between the organelles of parasites and the hosts, but HGT between host and parasite nuclear genomes has rarely been found. A thorough transcriptome screening revealed that a strictosidine synthase-like (SSL) gene in the root parasitic plant Orobanche aegyptiaca and the shoot parasitic plant Cuscuta australis showed much higher sequence similarities with those in Brassicaceae than with those in their close relatives, suggesting independent gene horizontal transfer events from Brassicaceae to these parasites. These findings were strongly supported by phylogenetic analysis and their identical unique amino acid residues and deletions. Intriguingly, the nucleus-located SSL genes in Brassicaceae belonged to a new member of SSL gene family, which were originated from gene duplication. The presence of introns indicated that the transfer occurred directly by DNA integration in both parasites. Furthermore, positive selection was detected in the foreign SSL gene in O. aegyptiaca but not in C. australis. The expression of the foreign SSL genes in these two parasitic plants was detected in multiple development stages and tissues, and the foreign SSL gene was induced after wounding treatment in C. australis stems. These data imply that the foreign genes may still retain certain functions in the recipient species. Our study strongly supports that parasitic plants can gain novel nuclear genes from distantly related host species by HGT and the foreign genes may execute certain functions in the new hosts.

  18. The ecology of fish parasites with particular reference to helminth parasites and their salmonid fish hosts in Welsh rivers: a review of some of the central questions.

    Science.gov (United States)

    Thomas, J D

    2002-01-01

    Ecological studies carried out in Welsh rivers on the feeding behaviour of salmonid fish, their helminth parasites and intermediate hosts in the early 1950s and in 1998 have been used as a basis to review the literature dealing with the following questions. First, how are the helminth populations dispersed in space-time? Second, to what extent are the distributional patterns and the life history strategies of the parasites influenced by physicochemical factors? Third, to what extent are populations of helmith parasites in salmonid fish influenced by host characteristics including the genome, sex, age, size, social position and Feeding behaviour? Fourth, are the populations of parasites regulated in a density-dependent manner? Fifth, do the parasites influence the survival and wellbeing of their salmonid hosts and the evolution of sex? Sixth, to what extent is the parasite community influenced by environmental changes including those of an anthropogenic nature and can the parasites be used as bioindicators of pollution? As with most parasites the helminth species found were highly overdispersed thus making it necessary to undertake a log10 (1 + x) conversion for statistical analyses. Statistical analyses confirm that the genome, age and sex of salmonid fish hosts, the station and seasonal change in radiation levels were significant factors in predicting the number of parasites. The evidence given supports the hypothesis that the feeding behaviour and habitat selection by the host fish, their position in the social hierarchy and the overdispersed nature of the transmission sites are the key factors in causing differences in the parasitic fauna related to host species, age, size and sex. Differences in the helminth parasite community related to station can be explained on the basis of differences in water types, sediments and chemistry. Although the evidence presented is in accord with the consensus view that temperature is correlated with seasonal changes in the

  19. Glyoxalase diversity in parasitic protists.

    Science.gov (United States)

    Deponte, Marcel

    2014-04-01

    Our current knowledge of the isomerase glyoxalase I and the thioesterase glyoxalase II is based on a variety of prokaryotic and eukaryotic (model) systems with an emphasis on human glyoxalases. During the last decade, important insights on glyoxalase catalysis and structure-function relationships have also been obtained from parasitic protists. These organisms, including kinetoplastid and apicomplexan parasites, are particularly interesting, both because of their relevance as pathogens and because of their phylogenetic diversity and host-parasite co-evolution which has led to specialized organellar and metabolic adaptations. Accordingly, the glyoxalase repertoire and properties vary significantly among parasitic protists of different major eukaryotic lineages (and even between closely related organisms). For example, several protists have an insular or non-canonical glyoxalase. Furthermore, the structures and the substrate specificities of glyoxalases display drastic variations. The aim of the present review is to highlight such differences as well as similarities between the glyoxalases of parasitic protists and to emphasize the power of comparative studies for gaining insights into fundamental principles and alternative glyoxalase functions.

  20. Crack turning in integrally stiffened aircraft structures

    Science.gov (United States)

    Pettit, Richard Glen

    Current emphasis in the aircraft industry toward reducing manufacturing cost has created a renewed interest in integrally stiffened structures. Crack turning has been identified as an approach to improve the damage tolerance and fail-safety of this class of structures. A desired behavior is for skin cracks to turn before reaching a stiffener, instead of growing straight through. A crack in a pressurized fuselage encounters high T-stress as it nears the stiffener---a condition favorable to crack turning. Also, the tear resistance of aluminum alloys typically varies with crack orientation, a form of anisotropy that can influence the crack path. The present work addresses these issues with a study of crack turning in two-dimensions, including the effects of both T-stress and fracture anisotropy. Both effects are shown to have relation to the process zone size, an interaction that is central to this study. Following an introduction to the problem, the T-stress effect is studied for a slightly curved semi-infinite crack with a cohesive process zone, yielding a closed form expression for the future crack path in an infinite medium. For a given initial crack tip curvature and tensile T-stress, the crack path instability is found to increase with process zone size. Fracture orthotropy is treated using a simple function to interpolate between the two principal fracture resistance values in two-dimensions. An extension to three-dimensions interpolates between the six principal values of fracture resistance. Also discussed is the transition between mode I and mode II fracture in metals. For isotropic materials, there is evidence that the crack seeks out a direction of either local symmetry (pure mode I) or local asymmetry (pure mode II) growth. For orthotropic materials the favored states are not pure modal, and have mode mixity that is a function of crack orientation. Drawing upon these principles, two crack turning prediction approaches are extended to include fracture

  1. On applicability of crack shape characterization rules for multiple in-plane surface cracks

    International Nuclear Information System (INIS)

    Kim, Jong Min; Choi, Suhn; Park, Keun Bae; Choi, Jae Boong; Huh, Nam Su

    2009-01-01

    The fracture mechanics assessment parameters, such as the elastic stress intensity factor and the elastic-plastic J-integral, for a surface crack can be significantly affected by adjacent cracks. Regarding such an interaction effect, the relative distance between adjacent cracks, crack aspect ratio and loading condition were known to be important factors for multiple cracks, which affects the fracture mechanics assessment parameters. Although several guidance (ASME Sec. XI, BS7910, British Energy R6 and API RP579) on a crack interaction effect (crack combination rule) have been proposed and used for assessing the interaction effect, each guidance provides different rules for combining multiple surface cracks into a single surface crack. Based on the systematic elastic and elastic-plastic finite element analyses, the present study investigated the acceptability of the crack combination rules provided in the existing guidance, and the relevant recommendations on a crack interaction for in-plane surface cracks in a plate were discussed. To quantify the interaction effect, the elastic stress intensity factor and elastic-plastic J-integral along the crack front were used. As for the loading condition, only axial tension was considered. As a result, BS7910 seems to provide the most relevant crack combination rule for in-plane dual surface cracks, whereas API RP579 provides the most conservative results. In particular, ASME Sec. XI still seems to have some room for a revision to shorten the critical distance between two adjacent cracks for a crack combination. The overall tendency of the elastic-plastic analyses results is identical to that of the elastic analyses results.

  2. The fatigue life and fatigue crack through thickness behavior of a surface cracked plate, 2

    International Nuclear Information System (INIS)

    Nam, Ki-Woo; Fujibayashi, Shinpei; Ando, Kotoji; Ogura, Nobukazu.

    1987-01-01

    Most structures have a region where stresses concentrate, and the probability of fatigue crack initiation may be higher than in other parts. Therefore, to improve the reliability of an LBB design, it is necessary to evaluate the growth and through thickness behavior of fatigue cracks in the stress concentration part. In this paper, a fatigue crack growth test at a stress concentration region has been made on 3 % NiCrMo and HT 80 steel. Stress concentration is caused by a fillet on the plate. The main results obtained are as follows : (1) Before cracking through the plate thickness, stress concentration has a remarkable effect on the fatigue crack growth behavior and it flatens the shape of a surface crack. The crack growth behavior can be explained quantatively by using the Newman-Raju equation and the stress resolving method proposed by ASME B and P Code SecXI. (2) The da/dN-ΔK relation obtained in a stress concentration specimen shows good agreement with that obtained in a surface cracked smooth specimen. (3) It is shown that stress concentration caused by a fillet has little effect on the crack growth rate after cracking through the plate thickness. (4) By using the K value based on eq. (1), (2), particular crack growth behavior and the change in crack shape after cracking through thickness can be explained quantatively. (author)

  3. Recent advances in molecular biology of parasitic viruses.

    Science.gov (United States)

    Banik, Gouri Rani; Stark, Damien; Rashid, Harunor; Ellis, John T

    2014-01-01

    The numerous protozoa that can inhabit the human gastro-intestinal tract are known, yet little is understood of the viruses which infect these protozoa. The discovery, morphologic details, purification methods of virus-like particles, genome and proteome of the parasitic viruses, Entamoeba histolytica, Giardia lamblia, Trichomonas vaginalis, and the Eimeria sp. are described in this review. The protozoan viruses share many common features: most of them are RNA or double-stranded RNA viruses, ranging between 5 and 8 kilobases, and are spherical or icosahedral in shape with an average diameter of 30-40 nm. These viruses may influence the function and pathogenicity of the protozoa which they infect, and may be important to investigate from a clinical perspective. The viruses may be used as specific genetic transfection vectors for the parasites and may represent a research tool. This review provides an overview on recent advances in the field of protozoan viruses.

  4. Crack formation and prevention in colloidal drops

    Science.gov (United States)

    Kim, Jin Young; Cho, Kun; Ryu, Seul-A.; Kim, So Youn; Weon, Byung Mook

    2015-08-01

    Crack formation is a frequent result of residual stress release from colloidal films made by the evaporation of colloidal droplets containing nanoparticles. Crack prevention is a significant task in industrial applications such as painting and inkjet printing with colloidal nanoparticles. Here, we illustrate how colloidal drops evaporate and how crack generation is dependent on the particle size and initial volume fraction, through direct visualization of the individual colloids with confocal laser microscopy. To prevent crack formation, we suggest use of a versatile method to control the colloid-polymer interactions by mixing a nonadsorbing polymer with the colloidal suspension, which is known to drive gelation of the particles with short-range attraction. Gelation-driven crack prevention is a feasible and simple method to obtain crack-free, uniform coatings through drying-mediated assembly of colloidal nanoparticles.

  5. Online Bridge Crack Monitoring with Smart Film

    Directory of Open Access Journals (Sweden)

    Benniu Zhang

    2013-01-01

    Full Text Available Smart film crack monitoring method, which can be used for detecting initiation, length, width, shape, location, and propagation of cracks on real bridges, is proposed. Firstly, the fabrication of the smart film is developed. Then the feasibility of the method is analyzed and verified by the mechanical sensing character of the smart film under the two conditions of normal strain and crack initiation. Meanwhile, the coupling interference between parallel enameled wires of the smart film is discussed, and then low-frequency detecting signal and the custom communication protocol are used to decrease interference. On this basis, crack monitoring system with smart film is designed, where the collected crack data is sent to the remote monitoring center and the cracks are simulated and recurred. Finally, the monitoring system is applied to six bridges, and the effects are discussed.

  6. Fluid structural response of axially cracked cylinders

    International Nuclear Information System (INIS)

    Garnich, M.R.; Simonen, F.A.

    1985-03-01

    The fluid structural (FS) response of a cylindrical pressure vessel to a suddenly occurring longitudinal through-wall crack is predicted. The effects of vessel internals and depressurization of the compressed water on dynamic crack opening displacements are investigated. A three dimensional (3D) structural finite element model is used as a basis for the development of a two dimensional (2D) FS model. A slice of the vessel taken at the crack midspan and normal to the cylinder axis is modeled. Crack opening displacements are compared between the 2D and 3D models, between the different assumptions about fluid depressurization, and between the static and dynamic solutions. The results show that effects of dynamic amplification associated with the sudden opening of the crack in the cylinder are largely offset by the local depressurization of the fluid adjacent to the crack

  7. Adaptive numerical modeling of dynamic crack propagation

    International Nuclear Information System (INIS)

    Adouani, H.; Tie, B.; Berdin, C.; Aubry, D.

    2006-01-01

    We propose an adaptive numerical strategy that aims at developing reliable and efficient numerical tools to model dynamic crack propagation and crack arrest. We use the cohesive zone theory as behavior of interface-type elements to model crack. Since the crack path is generally unknown beforehand, adaptive meshing is proposed to model the dynamic crack propagation. The dynamic study requires the development of specific solvers for time integration. As both geometry and finite element mesh of the studied structure evolve in time during transient analysis, the stability behavior of dynamic solver becomes a major concern. For this purpose, we use the space-time discontinuous Galerkin finite element method, well-known to provide a natural framework to manage meshes that evolve in time. As an important result, we prove that the space-time discontinuous Galerkin solver is unconditionally stable, when the dynamic crack propagation is modeled by the cohesive zone theory, which is highly non-linear. (authors)

  8. A probabilistic model of brittle crack formation

    Science.gov (United States)

    Chudnovsky, A.; Kunin, B.

    1987-01-01

    Probability of a brittle crack formation in an elastic solid with fluctuating strength is considered. A set Omega of all possible crack trajectories reflecting the fluctuation of the strength field is introduced. The probability P(X) that crack penetration depth exceeds X is expressed as a functional integral over Omega of a conditional probability of the same event taking place along a particular path. Various techniques are considered to evaluate the integral. Under rather nonrestrictive assumptions, the integral is reduced to solving a diffusion-type equation. A new characteristic of fracture process, 'crack diffusion coefficient', is introduced. An illustrative example is then considered where the integration is reduced to solving an ordinary differential equation. The effect of the crack diffusion coefficient and of the magnitude of strength fluctuations on probability density of crack penetration depth is presented. Practical implications of the proposed model are discussed.

  9. Noncontact fatigue crack evaluation using thermoelastic

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Ji Min; An, Yun Kyu; Sohn, Hoon [KAIST, Daejeon (Korea, Republic of)

    2012-12-15

    This paper proposes a noncontact thermography technique for fatigue crack evaluation under a cyclic tensile loading. The proposed technique identifies and localizes an invisible fatigue crack without scanning, thus making it possible to instantaneously evaluate an incipient fatigue crack. Based on a thermoelastic theory, a new fatigue crack evaluation algorithm is proposed for the fatigue crack tip localization. The performance of the proposed algorithm is experimentally validated. To achieve this, the cyclic tensile loading is applied to a dog bone shape aluminum specimen using a universal testing machine, and the corresponding thermal responses induced by thermoelastic effects are captured by an infrared camera. The test results confirm that the fatigue crack is well identified and localized by comparing with its microscopic images.

  10. Numerical Study of Corrosion Crack Opening

    DEFF Research Database (Denmark)

    Thoft-Christensen, Palle; Frandsen, Henrik Lund; Svensson, Staffan

    2008-01-01

    is proportional. More recently, the constant of proportionality, the so-called crack-corrosion index, has been studied further with respect to its dependence on the diameter of the reinforcement and the concrete cover. In the present paper the above-mentioned work is presented and extended with more realistic 3D......-models of the cracked concrete beam. The crack-corrosion index is evaluated for a variation of different parameters, i.e. bar diameter, concrete cover, crack length and type of corrosion product. This paper is an extended version of a paper by Thoft-Christensen et al. (2005) presented at the IFIP WG 7.5 Conference...... for the corrosion crack opening. Experiments and theoretical analysis by a numerical method, FEM, support that the relation between the reduction of the reinforcement bar diameter due to corrosion and the corresponding increase in crack width for a given time interval, measured on the surface of a concrete specimen...

  11. Taming Parasites by Tailoring Them

    Directory of Open Access Journals (Sweden)

    Bingjian Ren

    2017-07-01

    Full Text Available The next-generation gene editing based on CRISPR (clustered regularly interspaced short palindromic repeats has been successfully implemented in a wide range of organisms including some protozoan parasites. However, application of such a versatile game-changing technology in molecular parasitology remains fairly underexplored. Here, we briefly introduce state-of-the-art in human and mouse research and usher new directions to drive the parasitology research in the years to come. In precise, we outline contemporary ways to embolden existing apicomplexan and kinetoplastid parasite models by commissioning front-line gene-tailoring methods, and illustrate how we can break the enduring gridlock of gene manipulation in non-model parasitic protists to tackle intriguing questions that remain long unresolved otherwise. We show how a judicious solicitation of the CRISPR technology can eventually balance out the two facets of pathogen-host interplay.

  12. Energy analysis of crack-damage interaction

    Science.gov (United States)

    Chudnovsky, A.; Wu, Shaofu

    1989-01-01

    The energy release rates associated with a main crack propagating into a surrounding damage zone, and a damage zone translation relative to the main crack, as well as an energy of interaction between the two are analyzed. The displacement and stress fields for the crack-damage interaction problem are reconstructed employing a semi-empirical stress analysis and experimental evaluation of the average craze density in the crazed zone.

  13. Measuring Crack Length in Coarse Grain Ceramics

    Science.gov (United States)

    Salem, Jonathan A.; Ghosn, Louis J.

    2010-01-01

    Due to a coarse grain structure, crack lengths in precracked spinel specimens could not be measured optically, so the crack lengths and fracture toughness were estimated by strain gage measurements. An expression was developed via finite element analysis to correlate the measured strain with crack length in four-point flexure. The fracture toughness estimated by the strain gaged samples and another standardized method were in agreement.

  14. Outcome of Endodontically Treated Cracked Teeth

    Science.gov (United States)

    2016-06-01

    directed by: CAPT Te!Ty Webb, D.D.S., M.S. A " cracked tooth" is defined as a thin surface enamel and dentin disruption of unknown depth, and is often...OUTCOME OF ENDODONTICALL Y TREATED CRACKED TEETH by David Michael Dow II, D.D.S. Lieutenant Commander, Dental Corps United States Navy A thesis...copyrighted material in the thesis manuscript titled: "Outcome ofEndodontically Treated Cracked Teeth" is appropriately acknowledged and, beyond

  15. Utilization of Different Omic Approaches to Unravel Stress Response Mechanisms in the Parasite Entamoeba histolytica

    Directory of Open Access Journals (Sweden)

    Shruti Nagaraja

    2018-02-01

    Full Text Available During its life cycle, the unicellular parasite Entamoeba histolytica is challenged by a wide variety of environmental stresses, such as fluctuation in glucose concentration, changes in gut microbiota composition, and the release of oxidative and nitrosative species from neutrophils and macrophages. The best mode of survival for this parasite is to continuously adapt itself to the dynamic environment of the host. Our ability to study the stress-induced responses and adaptive mechanisms of this parasite has been transformed through the development of genomics, proteomics or metabolomics (omics sciences. These studies provide insights into different facets of the parasite's behavior in the host. However, there is a dire need for multi-omics data integration to better understand its pathogenic nature, ultimately paving the way to identify new chemotherapeutic targets against amebiasis. This review provides an integration of the most relevant omics information on the mechanisms that are used by E. histolytica to resist environmental stresses.

  16. Observing copepods through a genomic lens

    Science.gov (United States)

    2011-01-01

    Background Copepods outnumber every other multicellular animal group. They are critical components of the world's freshwater and marine ecosystems, sensitive indicators of local and global climate change, key ecosystem service providers, parasites and predators of economically important aquatic animals and potential vectors of waterborne disease. Copepods sustain the world fisheries that nourish and support human populations. Although genomic tools have transformed many areas of biological and biomedical research, their power to elucidate aspects of the biology, behavior and ecology of copepods has only recently begun to be exploited. Discussion The extraordinary biological and ecological diversity of the subclass Copepoda provides both unique advantages for addressing key problems in aquatic systems and formidable challenges for developing a focused genomics strategy. This article provides an overview of genomic studies of copepods and discusses strategies for using genomics tools to address key questions at levels extending from individuals to ecosystems. Genomics can, for instance, help to decipher patterns of genome evolution such as those that occur during transitions from free living to symbiotic and parasitic lifestyles and can assist in the identification of genetic mechanisms and accompanying physiological changes associated with adaptation to new or physiologically challenging environments. The adaptive significance of the diversity in genome size and unique mechanisms of genome reorganization during development could similarly be explored. Genome-wide and EST studies of parasitic copepods of salmon and large EST studies of selected free-living copepods have demonstrated the potential utility of modern genomics approaches for the study of copepods and have generated resources such as EST libraries, shotgun genome sequences, BAC libraries, genome maps and inbred lines that will be invaluable in assisting further efforts to provide genomics tools for

  17. Observing copepods through a genomic lens

    Directory of Open Access Journals (Sweden)

    Johnson Stewart C

    2011-09-01

    Full Text Available Abstract Background Copepods outnumber every other multicellular animal group. They are critical components of the world's freshwater and marine ecosystems, sensitive indicators of local and global climate change, key ecosystem service providers, parasites and predators of economically important aquatic animals and potential vectors of waterborne disease. Copepods sustain the world fisheries that nourish and support human populations. Although genomic tools have transformed many areas of biological and biomedical research, their power to elucidate aspects of the biology, behavior and ecology of copepods has only recently begun to be exploited. Discussion The extraordinary biological and ecological diversity of the subclass Copepoda provides both unique advantages for addressing key problems in aquatic systems and formidable challenges for developing a focused genomics strategy. This article provides an overview of genomic studies of copepods and discusses strategies for using genomics tools to address key questions at levels extending from individuals to ecosystems. Genomics can, for instance, help to decipher patterns of genome evolution such as those that occur during transitions from free living to symbiotic and parasitic lifestyles and can assist in the identification of genetic mechanisms and accompanying physiological changes associated with adaptation to new or physiologically challenging environments. The adaptive significance of the diversity in genome size and unique mechanisms of genome reorganization during development could similarly be explored. Genome-wide and EST studies of parasitic copepods of salmon and large EST studies of selected free-living copepods have demonstrated the potential utility of modern genomics approaches for the study of copepods and have generated resources such as EST libraries, shotgun genome sequences, BAC libraries, genome maps and inbred lines that will be invaluable in assisting further efforts to

  18. Parasites and immunotherapy: with or against?

    Science.gov (United States)

    Yousofi Darani, Hossein; Yousefi, Morteza; Safari, Marzieh; Jafari, Rasool

    2016-06-01

    Immunotherapy is a sort of therapy in which antibody or antigen administrates to the patient in order to treat or reduce the severity of complications of disease. This kind of treatment practiced in a wide variety of diseases including infectious diseases, autoimmune disorders, cancers and allergy. Successful and unsuccessful immunotherapeutic strategies have been practiced in variety of parasitic infections. On the other hand parasites or parasite antigens have also been considered for immunotherapy against other diseases such as cancer, asthma and multiple sclerosis. In this paper immunotherapy against common parasitic infections, and also immunotherapy of cancer, asthma and multiple sclerosis with parasites or parasite antigens have been reviewed.

  19. Catalytic cracking of hydrocarbon oils

    Energy Technology Data Exchange (ETDEWEB)

    1940-09-12

    A process is described for the vapor phase catalytic cracking of hydrocarbon oils boiling substantially in the gas oil range. The reaction takes place in the presence of a solid catalyst between 700 to 900/sup 0/F under pressure between atmospheric and 400 psi. A gas containing between 20 and 90 mol % of free hydrogen is used. The reaction is allowed to proceed until consumption of the free begins. The reaction is discontinued at that point and the catalyst is regenerated for further use.

  20. Modelling of environmentally assisted cracking

    International Nuclear Information System (INIS)

    Aaltonen, P.; Saario, T.; Ehrnsten, U.; Haenninen, H.; Itaeaho, M.; Piippo, J.

    1998-01-01

    During the use of nuclear reactors the properties of the structural materials change. Variations in the operation environment, such as changes in water chemistry, may enhance the development and growth of flaws. Neutron radiation causes embrittlement for in-core vessel materials. Radiation, together with water chemistry, increases the possibility of stress corrosion cracking in stainless steels and superalloys used in the reactor internal parts. Research on structural materials endeavours to study the ageing mechanisms of materials, and the possibilities and methods of preventing or forecasting the damage caused to structures by ageing. (orig.)

  1. T-stresses for internally cracked components

    International Nuclear Information System (INIS)

    Fett, T.

    1997-12-01

    The failure of cracked components is governed by the stresses in the vicinity of the crack tip. The singular stress contribution is characterised by the stress intensity factor K, the first regular stress term is represented by the so-called T-stress. T-stress solutions for components containing an internal crack were computed by application of the Bundary Collocation Method (BCM). The results are compiled in form of tables or approximative relations. In addition a Green's function of T-stresses is proposed for internal cracks which enables to compute T-stress terms for any given stress distribution in the uncracked body. (orig.) [de

  2. The detectability of cracks using sonic IR

    Science.gov (United States)

    Morbidini, Marco; Cawley, Peter

    2009-05-01

    This paper proposes a methodology to study the detectability of fatigue cracks in metals using sonic IR (also known as thermosonics). The method relies on the validation of simple finite-element thermal models of the cracks and specimens in which the thermal loads have been defined by means of a priori measurement of the additional damping introduced in the specimens by each crack. This estimate of crack damping is used in conjunction with a local measurement of the vibration strain during ultrasonic excitation to retrieve the power released at the crack; these functions are then input to the thermal model of the specimens to find the resulting temperature rises (sonic IR signals). The method was validated on mild steel beams with two-dimensional cracks obtained in the low-cycle fatigue regime as well as nickel-based superalloy beams with three-dimensional "thumbnail" cracks generated in the high-cycle fatigue regime. The equivalent 40kHz strain necessary to obtain a desired temperature rise was calculated for cracks in the nickel superalloy set, and the detectability of cracks as a function of length in the range of 1-5mm was discussed.

  3. Semi-empirical crack tip analysis

    Science.gov (United States)

    Chudnovsky, A.; Ben Ouezdon, M.

    1988-01-01

    Experimentally observed crack opening displacements are employed as the solution of the multiple crack interaction problem. Then the near and far fields are reconstructed analytically by means of the double layer potential technqiue. Evaluation of the effective stress intensity factor resulting from the interaction of the main crack and its surrounding crazes in addition to the remotely applied load is presented as an illustrative example. It is shown that crazing (as well as microcracking) may constitute an alternative mechanism to Dugdale-Berenblatt models responsible for the cancellation of the singularity at the crack tip.

  4. On governing equations for crack layer propagation

    Science.gov (United States)

    Chudnovsky, A.; Botsis, J.

    1988-01-01

    Results of analysis on damage distribution of a crack layer, in a model material, supported the self-similarity hypothesis of damage evolution which has been adopted by the crack layer theory. On the basis of measurements of discontinuity density and the double layer potential technique, a solution to the crack damage interaction problem has been developed. Evaluation of the stress intensity factor illustrated the methodology. Analysis of experimental results showed that Arrhenius type constitutive relationship described very well the expansion of the active zone of a crack layer.

  5. An analysis for crack layer stability

    Science.gov (United States)

    Sehanobish, K.; Botsis, J.; Moet, A.; Chudnovsky, A.

    1986-01-01

    The problem of uncontrolled crack propagation and crack arrest is considered with respect to crack layer (CL) translational stability. CL propagation is determined by the difference between the energy release rate and the amount of energy required for material transformation, and necessary and sufficient conditions for CL instability are derived. CL propagation in polystyrene is studied for two cases. For the case of remotely applied fixed load fatigue, the sufficient condition of instability is shown to be met before the necessary condition, and the necessary condition controls the stability. For the fixed displacement case, neither of the instability conditions are met, and CL propagation remains stable, resulting in crack arrest.

  6. On cracking of charged anisotropic polytropes

    Energy Technology Data Exchange (ETDEWEB)

    Azam, M. [Division of Science and Technology, University of Education, Township Campus, Lahore-54590 (Pakistan); Mardan, S.A., E-mail: azam.math@ue.edu.pk, E-mail: syedalimardanazmi@yahoo.com [Department of Mathematics, University of the Management and Technology, C-II, Johar Town, Lahore-54590 (Pakistan)

    2017-01-01

    Recently in [1], the role of electromagnetic field on the cracking of spherical polytropes has been investigated without perturbing charge parameter explicitly. In this study, we have examined the occurrence of cracking of anisotropic spherical polytropes through perturbing parameters like anisotropic pressure, energy density and charge. We consider two different types of polytropes in this study. We discuss the occurrence of cracking in two different ways ( i ) by perturbing polytropic constant, anisotropy and charge parameter ( ii ) by perturbing polytropic index, anisotropy and charge parameter for each case. We conclude that cracking appears for a wide range of parameters in both cases. Also, our results are reduced to [2] in the absence of charge.

  7. Cracking of open traffic rigid pavement

    Directory of Open Access Journals (Sweden)

    Niken Chatarina

    2017-01-01

    Full Text Available The research is done by observing the growth of real structure cracking in Natar, Lampung, Indonesia compared to C. Niken’s et al research and literature study. The rigid pavement was done with open traffic system. There are two main crack types on Natar rigid pavement: cracks cross the road, and cracks spreads on rigid pavement surface. The observation of cracks was analyzed by analyzing material, casting, curing, loading and shrinkage mechanism. The relationship between these analysis and shrinkage mechanism was studied in concrete micro structure. Open traffic make hydration process occur under vibration; therefore, fresh concrete was compressed and tensioned alternately since beginning. High temperature together with compression, cement dissociation, the growth of Ca2+ at very early age leads abnormal swelling. No prevention from outside water movement leads hydration process occur with limited water which caused spreads fine cracks. Limited water improves shrinkage and plastic phase becomes shorter; therefore, rigid pavement can’t accommodate the abnormal swelling and shrinking alternately and creates the spread of cracks. Discontinuing casting the concrete makes both mix under different condition, the first is shrink and the second is swell and creates weak line on the border; so, the cracks appear as cracks across the road.

  8. Lateral rigidity of cracked concrete structures

    International Nuclear Information System (INIS)

    Castellani, A.; Chesi, C.

    1979-01-01

    Numerical results are discussed on the lateral rigidity of reinforced concrete structures with a given crack distribution. They have been favourably checked with experimental results for cylindrical shells under the effect of a thermal gradient producing vertical cracking or vertical plus horizontal cracking. The main effects characterizing the concrete behaviour are: (1) The shear transfer across a crack; (2) The shear transfer degradation after cyclic loading; (3) The tension stiffening provided by the concrete between crack and crack, in the normal stress transfer; (4) The temperature effect on the elastic moduli of concrete, when cracks are of thermal origin. Only the 1st effect is discussed on an experimental basis. Two broad cathegories of reinforced concrete structures have been investigated in this respect: shear walls of buildings and cylindrical containment structures. The main conclusions so far reached are: (1) Vertical cracks are unlikely to decrease the lateral rigidity to less than 80% of the original one, and to less than 90% when they do not involve the entire thickness of the wall; (2) The appearence of horizontal cracks can reduce the lateral rigidity by some 30% or more; (3) A noticeable but not yet evaluated influence is shown by cyclic loading. (orig.)

  9. Investigations of Low Temperature Time Dependent Cracking

    Energy Technology Data Exchange (ETDEWEB)

    Van der Sluys, W A; Robitz, E S; Young, B A; Bloom, J

    2002-09-30

    The objective of this project was to investigate metallurgical and mechanical phenomena associated with time dependent cracking of cold bent carbon steel piping at temperatures between 327 C and 360 C. Boiler piping failures have demonstrated that understanding the fundamental metallurgical and mechanical parameters controlling these failures is insufficient to eliminate it from the field. The results of the project consisted of the development of a testing methodology to reproduce low temperature time dependent cracking in laboratory specimens. This methodology was used to evaluate the cracking resistance of candidate heats in order to identify the factors that enhance cracking sensitivity. The resultant data was integrated into current available life prediction tools.

  10. Extreme genomes

    OpenAIRE

    DeLong, Edward F

    2000-01-01

    The complete genome sequence of Thermoplasma acidophilum, an acid- and heat-loving archaeon, has recently been reported. Comparative genomic analysis of this 'extremophile' is providing new insights into the metabolic machinery, ecology and evolution of thermophilic archaea.

  11. The fish parasite Ichthyophthirius multifiliis

    DEFF Research Database (Denmark)

    Jørgensen, Louise von Gersdorff

    2017-01-01

    Ichthyophthirius multifiliis, the causative agent of white spot disease (ichthyophthiriasis) is a major burden for fish farmers and aquarists globally. The parasite infects the skin and the gills of freshwater fish, which may acquire a protective adaptive immune response against this disease...... and recognition of carcinogenic and environmentally damaging effects the most efficient compounds are prohibited. A continuous search for novel substances, which are highly effective against the parasites and harmless for the fish is ongoing. These compounds should be environmentally friendly and cost...

  12. Probabilistic fracture mechanics of nuclear structural components. Consideration of transition from embedded crack to surface crack

    International Nuclear Information System (INIS)

    Yagawa, Genki; Yoshimura, Shinobu; Kanto, Yasuhiro

    1998-01-01

    This paper describes a probabilistic fracture mechanics (PFM) analysis of aged nuclear reactor pressure vessel (RPV) material. New interpolation formulas are first derived for both embedded elliptical surface cracks and semi-elliptical surface cracks. To investigate effects of transition from embedded crack to surface crack in PFM analyses, one of PFM round-robin problems set by JSME-RC111 committee, i.e. 'aged RPV under normal and upset operating conditions' is solved, employing the interpolation formulas. (author)

  13. Statistical distribution of time to crack initiation and initial crack size using service data

    Science.gov (United States)

    Heller, R. A.; Yang, J. N.

    1977-01-01

    Crack growth inspection data gathered during the service life of the C-130 Hercules airplane were used in conjunction with a crack propagation rule to estimate the distribution of crack initiation times and of initial crack sizes. A Bayesian statistical approach was used to calculate the fraction of undetected initiation times as a function of the inspection time and the reliability of the inspection procedure used.

  14. Grass genomes

    OpenAIRE

    Bennetzen, Jeffrey L.; SanMiguel, Phillip; Chen, Mingsheng; Tikhonov, Alexander; Francki, Michael; Avramova, Zoya

    1998-01-01

    For the most part, studies of grass genome structure have been limited to the generation of whole-genome genetic maps or the fine structure and sequence analysis of single genes or gene clusters. We have investigated large contiguous segments of the genomes of maize, sorghum, and rice, primarily focusing on intergenic spaces. Our data indicate that much (>50%) of the maize genome is composed of interspersed repetitive DNAs, primarily nested retrotransposons that in...

  15. Morphological and Molecular Descriptors of the Developmental Cycle of Babesia divergens Parasites in Human Erythrocytes.

    Directory of Open Access Journals (Sweden)

    Ingrid Rossouw

    2015-05-01

    Full Text Available Human babesiosis, especially caused by the cattle derived Babesia divergens parasite, is on the increase, resulting in renewed attentiveness to this potentially life threatening emerging zoonotic disease. The molecular mechanisms underlying the pathophysiology and intra-erythrocytic development of these parasites are poorly understood. This impedes concerted efforts aimed at the discovery of novel anti-babesiacidal agents. By applying sensitive cell biological and molecular functional genomics tools, we describe the intra-erythrocytic development cycle of B. divergens parasites from immature, mono-nucleated ring forms to bi-nucleated paired piriforms and ultimately multi-nucleated tetrads that characterizes zoonotic Babesia spp. This is further correlated for the first time to nuclear content increases during intra-erythrocytic development progression, providing insight into the part of the life cycle that occurs during human infection. High-content temporal evaluation elucidated the contribution of the different stages to life cycle progression. Moreover, molecular descriptors indicate that B. divergens parasites employ physiological adaptation to in vitro cultivation. Additionally, differential expression is observed as the parasite equilibrates its developmental stages during its life cycle. Together, this information provides the first temporal evaluation of the functional transcriptome of B. divergens parasites, information that could be useful in identifying biological processes essential to parasite survival for future anti-babesiacidal discoveries.

  16. Advances in the application of genetic manipulation methods to apicomplexan parasites.

    Science.gov (United States)

    Suarez, C E; Bishop, R P; Alzan, H F; Poole, W A; Cooke, B M

    2017-10-01

    Apicomplexan parasites such as Babesia, Theileria, Eimeria, Cryptosporidium and Toxoplasma greatly impact animal health globally, and improved, cost-effective measures to control them are urgently required. These parasites have complex multi-stage life cycles including obligate intracellular stages. Major gaps in our understanding of the biology of these relatively poorly characterised parasites and the diseases they cause severely limit options for designing novel control methods. Here we review potentially important shared aspects of the biology of these parasites, such as cell invasion, host cell modification, and asexual and sexual reproduction, and explore the potential of the application of relatively well-established or newly emerging genetic manipulation methods, such as classical transfection or gene editing, respectively, for closing important gaps in our knowledge of the function of specific genes and proteins, and the biology of these parasites. In addition, genetic manipulation methods impact the development of novel methods of control of the diseases caused by these economically important parasites. Transient and stable transfection methods, in conjunction with whole and deep genome sequencing, were initially instrumental in improving our understanding of the molecular biology of apicomplexan parasites and paved the way for the application of the more recently developed gene editing methods. The increasingly efficient and more recently developed gene editing methods, in particular those based on the CRISPR/Cas9 system and previous conceptually similar techniques, are already contributing to additional gene function discovery using reverse genetics and related approaches. However, gene editing methods are only possible due to the increasing availability of in vitro culture, transfection, and genome sequencing and analysis techniques. We envisage that rapid progress in the development of novel gene editing techniques applied to apicomplexan parasites of

  17. Deciphering the ubiquitin-mediated pathway in apicomplexan parasites: a potential strategy to interfere with parasite virulence.

    Science.gov (United States)

    Ponts, Nadia; Yang, Jianfeng; Chung, Duk-Won Doug; Prudhomme, Jacques; Girke, Thomas; Horrocks, Paul; Le Roch, Karine G

    2008-06-11

    Reversible modification of proteins through the attachment of ubiquitin or ubiquitin-like modifiers is an essential post-translational regulatory mechanism in eukaryotes. The conjugation of ubiquitin or ubiquitin-like proteins has been demonstrated to play roles in growth, adaptation and homeostasis in all eukaryotes, with perturbation of ubiquitin-mediated systems associated with the pathogenesis of many human diseases, including cancer and neurodegenerative disorders. Here we describe the use of an HMM search of functional Pfam domains found in the key components of the ubiquitin-mediated pathway necessary to activate and reversibly modify target proteins in eight apicomplexan parasitic protozoa for which complete or late-stage genome projects exist. In parallel, the same search was conducted on five model organisms, single-celled and metazoans, to generate data to validate both the search parameters employed and aid paralog classification in Apicomplexa. For each of the 13 species investigated, a set of proteins predicted to be involved in the ubiquitylation pathway has been identified and demonstrates increasing component members of the ubiquitylation pathway correlating with organism and genome complexity. Sequence homology and domain architecture analyses facilitated prediction of apicomplexan-specific protein function, particularly those involved in regulating cell division during these parasite's complex life cycles. This study provides a comprehensive analysis of proteins predicted to be involved in the apicomplexan ubiquitin-mediated pathway. Given the importance of such pathway in a wide variety of cellular processes, our data is a key step in elucidating the biological networks that, in part, direct the pathogenicity of these parasites resulting in a massive impact on global health. Moreover, apicomplexan-specific adaptations of the ubiquitylation pathway may represent new therapeutic targets for much needed drugs against apicomplexan parasites.

  18. Cancer genomics

    DEFF Research Database (Denmark)

    Norrild, Bodil; Guldberg, Per; Ralfkiær, Elisabeth Methner

    2007-01-01

    Almost all cells in the human body contain a complete copy of the genome with an estimated number of 25,000 genes. The sequences of these genes make up about three percent of the genome and comprise the inherited set of genetic information. The genome also contains information that determines whe...

  19. Chloride Penetration through Cracks in High-Performance Concrete and Surface Treatment System for Crack Healing

    Directory of Open Access Journals (Sweden)

    In-Seok Yoon

    2012-01-01

    Full Text Available For enhancing the service life of concrete structures, it is very important to minimize crack at surface. Even if these cracks are very small, the problem is to which extend these cracks may jeopardize the durability of these decks. It was proposed that crack depth corresponding with critical crack width from the surface is a crucial factor in view of durability design of concrete structures. It was necessary to deal with chloride penetration through microcracks characterized with the mixing features of concrete. This study is devoted to examine the effect of high strength concrete and reinforcement of steel fiber on chloride penetration through cracks. High strength concrete is regarded as an excellent barrier to resist chloride penetration. However, durability performance of cracked high strength concrete was reduced seriously up to that of ordinary cracked concrete. Steel fiber reinforcement is effective to reduce chloride penetration through cracks because steel fiber reinforcement can lead to reduce crack depth significantly. Meanwhile, surface treatment systems are put on the surface of the concrete in order to seal the concrete. The key-issue is to which extend a sealing is able to ensure that chloride-induced corrosion can be prevented. As a result, penetrant cannot cure cracks, however, coating and combined treatment can prevent chloride from flowing in concrete with maximum crack width of 0.06 mm and 0.08 mm, respectively.

  20. Interfacial Crack Arrest in Sandwich Panels with Embedded Crack Stoppers Subjected to Fatigue Loading

    DEFF Research Database (Denmark)

    Martakos, G.; Andreasen, J. H.; Berggreen, Christian

    2017-01-01

    A novel crack arresting device has been implemented in sandwich panels and tested using a special rig to apply out-of-plane loading on the sandwich panel face-sheets. Fatigue crack propagation was induced in the face-core interface of the sandwich panels which met the crack arrester. The effect o...

  1. On fatigue crack growth in ductile materials by crack-tip blunting

    DEFF Research Database (Denmark)

    Tvergaard, Viggo

    2004-01-01

    One of the basic mechanisms for fatigue crack growth in ductile metals is that depending on crack-tip blunting under tensile loads and re-sharpening of the crack-tip during unloading. In a standard numerical analysis accounting for finite strains it is not possible to follow this process during...

  2. Crack-opening area calculations for circumferential through-wall pipe cracks

    Energy Technology Data Exchange (ETDEWEB)

    Kishida, K.; Zahoor, A.

    1988-08-01

    This report describes the estimation schemes for crack opening displacement (COD) of a circumferential through-wall crack, then compares the COD predictions with pipe experimental data. Accurate predictions for COD are required to reliably predict the leak rate through a crack in leak-before-break applications.

  3. Crack-opening area calculations for circumferential through-wall pipe cracks

    International Nuclear Information System (INIS)

    Kishida, K.; Zahoor, A.

    1988-08-01

    This report describes the estimation schemes for crack opening displacement (COD) of a circumferential through-wall crack, then compares the COD predictions with pipe experimental data. Accurate predictions for COD are required to reliably predict the leak rate through a crack in leak-before-break applications

  4. Single Cell Genomics and Transcriptomics for Unicellular Eukaryotes

    Energy Technology Data Exchange (ETDEWEB)

    Ciobanu, Doina; Clum, Alicia; Singh, Vasanth; Salamov, Asaf; Han, James; Copeland, Alex; Grigoriev, Igor; James, Timothy; Singer, Steven; Woyke, Tanja; Malmstrom, Rex; Cheng, Jan-Fang

    2014-03-14

    Despite their small size, unicellular eukaryotes have complex genomes with a high degree of plasticity that allow them to adapt quickly to environmental changes. Unicellular eukaryotes live with prokaryotes and higher eukaryotes, frequently in symbiotic or parasitic niches. To this day their contribution to the dynamics of the environmental communities remains to be understood. Unfortunately, the vast majority of eukaryotic microorganisms are either uncultured or unculturable, making genome sequencing impossible using traditional approaches. We have developed an approach to isolate unicellular eukaryotes of interest from environmental samples, and to sequence and analyze their genomes and transcriptomes. We have tested our methods with six species: an uncharacterized protist from cellulose-enriched compost identified as Platyophrya, a close relative of P. vorax; the fungus Metschnikowia bicuspidate, a parasite of water flea Daphnia; the mycoparasitic fungi Piptocephalis cylindrospora, a parasite of Cokeromyces and Mucor; Caulochytrium protosteloides, a parasite of Sordaria; Rozella allomycis, a parasite of the water mold Allomyces; and the microalgae Chlamydomonas reinhardtii. Here, we present the four components of our approach: pre-sequencing methods, sequence analysis for single cell genome assembly, sequence analysis of single cell transcriptomes, and genome annotation. This technology has the potential to uncover the complexity of single cell eukaryotes and their role in the environmental samples.

  5. Can Parasites Really Reveal Environmental Impact?

    Science.gov (United States)

    This review assesses the usefulness of parasites as bioindicators of environmental impact. Relevant studies published in the past decade were compiled; factorial meta-analysis demonstrated significant effects and interactions between parasite levels and the presence and concentra...

  6. Parasitic Nematode Interactions with Mammals and Plants

    NARCIS (Netherlands)

    Jasmer, D.P.; Goverse, A.; Smant, G.

    2003-01-01

    Parasitic nematodes that infect humans, animals, and plants cause serious diseases that are deleterious to human health and agricultural productivity. Chemical and biological control methods have reduced the impact of these parasites. However, surviving environmental stages lead to persistent

  7. Toward forward genetic screens in malaria-causing parasites using the piggyBac transposon

    Directory of Open Access Journals (Sweden)

    de Koning-Ward Tania F

    2011-03-01

    Full Text Available Abstract The ability to analyze gene function in malaria-causing Plasmodium parasites has received a boost with a recent paper in BMC Genomics that describes a genome-wide mutagenesis system in the rodent malaria species Plasmodium berghei using the transposon piggyBac. This advance holds promise for identifying and validating new targets for intervention against malaria. But further improvements are still needed for the full power of genome-wide molecular genetic screens to be utilized in this organism. See research article: http://www.biomedcentral.com/1471-2164/12/155

  8. Everyday and Exotic Foodborne Parasites

    Directory of Open Access Journals (Sweden)

    Marilyn B Lee

    2000-01-01

    Full Text Available Everyday foodborne parasites, which are endemic in Canada, include the protozoans Entamoeba histolytica, Giardia lamblia and Cryptosporidium parvum. However, these parasites are most frequently acquired through unfiltered drinking water, homosexual activity or close personal contact such as in daycare centres and occasionally via a food vehicle. It is likely that many foodborne outbreaks from these protozoa go undetected. Transmission of helminth infections, such as tapeworms, is rare in Canada because of effective sewage treatment. However, a common foodborne parasite of significance is Toxoplasma gondii. Although infection can be acquired from accidental ingestion of oocysts from cat feces, infection can also result from consumption of tissue cysts in undercooked meat, such as pork or lamb. Congenital transmission poses an immense financial burden, costing Canada an estimated $240 million annually. Also of concern is toxoplasmosis in AIDS patients, which may lead to toxoplasmosis encephalitis, the second most common AIDS-related opportunistic infection of the central nervous system. Exotic parasites (ie, those acquired from abroad or from imported food are of growing concern because more Canadians are travelling and the number of Canada?s trading partners is increasing. Since 1996, over 3000 cases of Cyclospora infection reported in the United States and Canada were epidemiologically associated with importation of Guatemalan raspberries. Unlike toxoplasmosis, where strategies for control largely rest with individual practices, control of cyclosporiasis rests with government policy, which should prohibit the importation of foods at high risk.

  9. Intestinal Parasites of the Grasscutter

    African Journals Online (AJOL)

    User

    excretions of carrier cane rats (Oboegbulem. & Okoronkwo, 1990). The possibility of transmission of parasites of the grasscutter to humans cannot be overlooked. This is more so as some people do not only cherish grasscutter meat but also use the content of the gut both for medicinal purposes and for food (pers. comm.).

  10. Fish immunity to scuticociliate parasites

    NARCIS (Netherlands)

    Piazzon de Haro, M.C.; Leiro, J.M.; Lamas, J.

    2013-01-01

    Some species of scuticociliates (Ciliophora) behave as facultative parasites and produce severe mortalities in cultured fish. Pathogenic scuticociliates can cause surface lesions and can also penetrate inside the body, where they feed on tissue and proliferate in the blood and most internal organs,

  11. One Health: parasites and beyond.

    Science.gov (United States)

    Blake, Damer P; Betson, Martha

    2017-01-01

    The field of parasitism is broad, encompassing relationships between organisms where one benefits at the expense of another. Traditionally the discipline focuses on eukaryotes, with the study of bacteria and viruses complementary but distinct. Nonetheless, parasites vary in size and complexity from single celled protozoa, to enormous plants like those in the genus Rafflesia. Lifecycles range from obligate intracellular to extensive exoparasitism. Examples of parasites include high-profile medical and zoonotic pathogens such as Plasmodium, veterinary pathogens of wild and captive animals and many of the agents which cause neglected tropical diseases, stretching to parasites which infect plants and other parasites (e.g. Kikuchi et al. 2011; Hotez et al. 2014; Blake et al. 2015; Hemingway, 2015; Meekums et al. 2015; Sandlund et al. 2015). The breadth of parasitology has been matched by the variety of ways in which parasites are studied, drawing upon biological, chemical, molecular, epidemiological and other expertise. Despite such breadth bridging between disciplines has commonly been problematic, regardless of extensive encouragement from government agencies, peer audiences and funding bodies promoting multidisciplinary research. Now, progress in understanding and collaboration can benefit from establishment of the One Health concept (Zinsstag et al. 2012; Stark et al. 2015). One Health draws upon biological, environmental, medical, veterinary and social science disciplines in order to improve human, animal and environmental health, although it remains tantalizingly difficult to engage many relevant parties. For infectious diseases traditional divides have been exacerbated as the importance of wildlife reservoirs, climate change, food production systems and socio-economic diversity have been recognized but often not addressed in a multidisciplinary manner. In response the 2015 Autumn Symposium organized by the British Society for Parasitology (BSP; https

  12. Development of crack shape: LBB methodology for cracked pipes

    Energy Technology Data Exchange (ETDEWEB)

    Moulin, D.; Chapuliot, S.; Drubay, B. [Commissariat a l Energie Atomique, Gif sur Yvette (France)

    1997-04-01

    For structures like vessels or pipes containing a fluid, the Leak-Before-Break (LBB) assessment requires to demonstrate that it is possible, during the lifetime of the component, to detect a rate of leakage due to a possible defect, the growth of which would result in a leak before-break of the component. This LBB assessment could be an important contribution to the overall structural integrity argument for many components. The aim of this paper is to review some practices used for LBB assessment and to describe how some new R & D results have been used to provide a simplified approach of fracture mechanics analysis and especially the evaluation of crack shape and size during the lifetime of the component.

  13. Nuclear hormone receptors in parasitic helminths

    OpenAIRE

    Wu, Wenjie; LoVerde, Philip T

    2010-01-01

    Nuclear receptors (NRs) belong to a large protein superfamily that are important transcriptional modulators in metazoans. Parasitic helminths include parasitic worms from the Lophotrochozoa (Platyhelminths) and Ecdysozoa (Nematoda). NRs in parasitic helminths diverged into two different evolutionary lineages. NRs in parasitic Platyhelminths have orthologues in Deuterostomes, in arthropods or both with a feature of extensive gene loss and gene duplication within different gene groups. NRs in p...

  14. The effect of crack branching on the residual lifetime of machine components containing stress corrosion cracks

    International Nuclear Information System (INIS)

    Magdowski, R.M.; Uggowitzer, P.J.; Speidel, M.O.

    1985-01-01

    A comparison is presented of theoretical, numerical and experimental investigations concerning the effect of crack branching on the reduction of stress intensity at the tip of single cracks. The results indicate that the division of a single crack into n branches reduces the stress intensity at the branch tips by a factor of about 1/√n. This permits branched cracks to grow to larger depths before becoming critical. The implication is that longer residual lifetimes and longer operating times between inspections can be calculated for machine components with growing branched stress corrosion cracks. (author)

  15. Fishing drives declines in fish parasite diversity and has variable effects on parasite abundance.

    Science.gov (United States)

    Wood, Chelsea L; Sandin, Stuart A; Zgliczynski, Brian; Guerra, Ana Sofía; Micheli, Fiorenza

    2014-07-01

    Despite the ubiquity and ecological importance of parasites, relatively few studies have assessed their response to anthropogenic environmental change. Heuristic models have predicted both increases and decreases in parasite abundance in response to human disturbance, with empirical support for both. However, most studies focus on one or a few selected parasite species. Here, we assess the abundance of parasites of seven species of coral reef fishes collected from three fished and three unfished islands of the Line Islands archipelago in the central equatorial Pacific. Because we chose fish hosts that spanned different trophic levels, taxonomic groups, and body sizes, we were able to compare parasite responses across a broad cross section of the total parasite community in the presence and absence of fishing, a major human impact on marine ecosystems. We found that overall parasite species richness was substantially depressed on fished islands, but that the response of parasite abundance varied among parasite taxa: directly transmitted parasites were significantly more abundant on fished than on unfished islands, while the reverse was true for trophically transmitted parasites. This probably arises because trophically transmitted parasites require multiple host species, some of which are the top predators most sensitive to fishing impacts. The increase in directly transmitted parasites appeared to be due to fishing-driven compensatory increases in the abundance of their hosts. Together, these results provide support for the predictions of both heuristic models, and indicate that the direction of fishing's impact on parasite abundance is mediated by parasite traits, notably parasite transmission strategies.

  16. Parasites as prey in aquatic food webs: implications for predator infection and parasite transmission

    NARCIS (Netherlands)

    Thieltges, D.W.; Amundsen, P.-A.; Hechinger, R.F.; Johnson, P.T.J.; Lafferty, K.D.; Mouritsen, K.N.; Preston, D.L.; Reise, K.; Zander, C.D.; Poulin, R.

    2013-01-01

    While the recent inclusion of parasites into food-web studies has highlighted the role of parasites as consumers, there is accumulating evidence that parasites can also serve as prey for predators. Here we investigated empirical patterns of predation on parasites and their relationships with

  17. Parasites of mammals species abundance near zone Chernobyl

    International Nuclear Information System (INIS)

    Pen'kevich, V.A.

    2014-01-01

    In wildlife reserve parasitize various types of parasites: arachnids (mites) parasitic insects (horseflies, keds, mosquitoes, gnats, midges), helminths (trematodes, cestodes, nematodes and acanthocephalans) and parasitic protozoa. In quantity: 3 (beaver) to 25 species (wolf). (authors)

  18. Preferential transcription of conserved rif genes in two phenotypically distinct Plasmodium falciparum parasite lines

    DEFF Research Database (Denmark)

    Wang, Christian W; Magistrado, Pamela A; Nielsen, Morten A

    2009-01-01

    transcribed in the VAR2CSA-expressing parasite line. In addition, two rif genes were found transcribed at early and late intra-erythrocyte stages independently of var gene transcription. Rif genes are organised in groups and inter-genomic conserved gene families, suggesting that RIFIN sub-groups may have......Plasmodium falciparum variant surface antigens (VSA) are targets of protective immunity to malaria. Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) and repetitive interspersed family (RIFIN) proteins are encoded by the two variable multigene families, var and rif genes, respectively...... novel rif gene groups, rifA1 and rifA2, containing inter-genomic conserved rif genes, were identified. All rifA1 genes were orientated head-to-head with a neighbouring Group A var gene whereas rifA2 was present in all parasite genomes as a single copy gene with a unique 5' untranslated region. Rif...

  19. Distributed crack analysis of ceramic inlays

    NARCIS (Netherlands)

    Peters, M.C.R.B.; Vree, de J.H.P.; Brekelmans, W.A.M.

    1993-01-01

    In all-ceramic restorations, crack formation and propagation phenomena are of major concern, since they may result in intra-oral fracture. The objective of this study was calculation of damage in porcelain MOD inlays by utilization of a finite-element (FE) implementation of the distributed crack

  20. In-reactor fatigue crack propagation

    International Nuclear Information System (INIS)

    Ermi, A.M.; Mervyn, D.A.; Straalsund, J.L.

    1979-08-01

    An in-reactor fatigue experiment is being designed to determine the effect of dynamic irradiation on the fatigue crack propagation (FCP) behavior of candidate fusion first wall materials. This investigation has been prompted by studies which show gross differences in crack growth characteristics of creep rupture specimens testing by postirradiation versus dynamic in-reactor methods. The experiment utilizes miniature center-cracked-tension specimens developed specifically for in-reactor studies. In the test, a chain of eight specimens, precracked to various initial crack lengths, is stressed during irradiation to determine crack growth rate as a function of stress intensity. Load levels were chosen which result in small crack growth rates encompassing a regime of the crack growth curve not previously investigated during irradiation studies of FCP. The test will be conducted on 20% cold worked 316 stainless steel at a temperature of 425 0 C, in a sodium environment, and at a frequency of 1 cycle/min. Irradiation will occur in the Oak Ridge Research Reactor, resulting in a He/dpa ratio similar to that expected at the first wall in a fusion reactor. Detailed design of the experiment is presented, along with crack growth data obtained from prototypic testing of the experimental apparatus. These results are compared to data obtained under similar conditions generated by conventional test methods

  1. Crack Tip Mechanics in Distortion Gradient Plasticity

    DEFF Research Database (Denmark)

    Fuentes-Alonso, Sandra; Martínez Pañeda, Emilio

    2017-01-01

    Gradient Plasticity (DGP), the influence on crack tip mechanics of DGP's distinguishing features that entail superior modelling capabilities has not been investigated yet. In this work crack tip fields are thoroughly examined by implementing the higher order theory of DGP in an implicit finite element...

  2. Entering a Crack: An Encounter with Gossip

    Science.gov (United States)

    Henderson, Linda

    2014-01-01

    In this paper, I enter a crack to think otherwise about the concept "gossip". Drawing on previous scholarship engaging with Deleuzian concepts to inform research methodologies, this paper builds on this body of work. Following Deleuze and Guattari, the paper undertakes a mapping of gossip, subsequent to an encounter with a crack.…

  3. 46 CFR 59.10-5 - Cracks.

    Science.gov (United States)

    2010-10-01

    ..., DEPARTMENT OF HOMELAND SECURITY (CONTINUED) MARINE ENGINEERING REPAIRS TO BOILERS, PRESSURE VESSELS AND... consecutive cracked ligaments nor more than a total of six cracked ligaments in any one girth joint. (c... ligaments may be repaired by welding. (n) Welding repairs to drums of power boilers, except as otherwise...

  4. Crack velocity measurement by induced electromagnetic radiation

    International Nuclear Information System (INIS)

    Frid, V.; Rabinovitch, A.; Bahat, D.

    2006-01-01

    Our model of electromagnetic radiation (EMR) emanated from fracture implies that EMR amplitude is proportional to crack velocity. Soda lime glass samples were tested under uniaxial tension. Comparison of crack velocity observed by Wallner line analysis and the peak amplitude of EMR signals registered during the test, showed very good correlation, validating this proportionality

  5. Crack velocity measurement by induced electromagnetic radiation

    Energy Technology Data Exchange (ETDEWEB)

    Frid, V. [Deichmann Rock Mechanics Laboratory of the Negev, Geological and Environmental Sciences Department, Ben Gurion University of the Negev, Beer Sheva (Israel)]. E-mail: vfrid@bgu.ac.il; Rabinovitch, A. [Deichmann Rock Mechanics Laboratory of the Negev, Physics Department, Ben Gurion University of the Negev, Beer Sheva (Israel); Bahat, D. [Deichmann Rock Mechanics Laboratory of the Negev, Geological and Environmental Sciences Department, Ben Gurion University of the Negev, Beer Sheva (Israel)

    2006-07-31

    Our model of electromagnetic radiation (EMR) emanated from fracture implies that EMR amplitude is proportional to crack velocity. Soda lime glass samples were tested under uniaxial tension. Comparison of crack velocity observed by Wallner line analysis and the peak amplitude of EMR signals registered during the test, showed very good correlation, validating this proportionality.

  6. Positioning Community Art Practices in Urban Cracks

    Science.gov (United States)

    Verschelden, Griet; Van Eeghem, Elly; Steel, Riet; De Visscher, Sven; Dekeyrel, Carlos

    2012-01-01

    This article addresses the position of community art practices and the role of practitioners in urban cracks. Community art practices raise possibilities for a reconceptualisation of the concept of community and an extension of the concept of art in public space. Urban cracks are conceptualised as spatial, temporal and relational manifestations of…

  7. Corrosion and Cracking of Reinforced Concrete

    DEFF Research Database (Denmark)

    Thoft-Christensen, Palle

    Modelling of the deterioration of reinforced concrete has in recent years changed from being a deterministic modelling based on experience to be stochastic modelling based on sound and consistent physical, chemical and mechanical principles. In this paper is presented a brief review of modern mod...... for time to initial corrosion, time to initial cracking, and time to a given crack width may be obtained....

  8. Mechanism for iodine cracking of zirconium claddings

    International Nuclear Information System (INIS)

    Novikov, V.V.

    1991-01-01

    The mechanism of iodine cracking of zirconium cladding is analyzed taking into account the effect of stresses on diffusion. A decisive effect of the stress gradiemt on crack propagation in an agressive medium is shown. The experimental data are compared with the proposed model

  9. Crack Formation in Grouted Annular Composite

    DEFF Research Database (Denmark)

    Sørensen, Eigil V.

    The objective of the present analysis is to identify the reason for extensive crack formation which occurred during an annulus grouting performance test, to evaluate possible consequences of the cracking, and to recommend measures to be taken in order to avoid similar problems in the future....

  10. Quenching cracks - formation and possible causes

    International Nuclear Information System (INIS)

    Macherauch, E.; Mueller, H.; Voehringer, O.

    1976-01-01

    The most important principles controlling the martensitic hardening of steels containing carbon are presented, and their effects on the cracks formed by tempering are discussed. Micro-crack formation, influenced by any increase in the carbon content, is dependent on the variations of martensitic morphology; this factor is of decisive importance. Apart from micro residual stresses, macro residual stresses become increasingly involved in the crack development. This is dependent on the given content of carbon and increase in the dimensions of the samples. Based on the empirical values gained from experience about cracks formed by tempering and using a schematic diagram, the constructive influences on the propensity to cracks formed by tempering, with regard to materials and processing, are evaluated. Also the effects of thermic, mechanical and chemical after-treatments upon the propensity to tempering cracks are discussed. In conclusion, the problem of the formation of cracks in hardened parts, i.e. the elongation of the cracks under static stress, is treated briefly. (orig.) [de

  11. Crack Monitoring of Operational Wind Turbine Foundations.

    Science.gov (United States)

    Perry, Marcus; McAlorum, Jack; Fusiek, Grzegorz; Niewczas, Pawel; McKeeman, Iain; Rubert, Tim

    2017-08-21

    The degradation of onshore, reinforced-concrete wind turbine foundations is usually assessed via above-ground inspections, or through lengthy excavation campaigns that suspend wind power generation. Foundation cracks can and do occur below ground level, and while sustained measurements of crack behaviour could be used to quantify the risk of water ingress and reinforcement corrosion, these cracks have not yet been monitored during turbine operation. Here, we outline the design, fabrication and field installation of subterranean fibre-optic sensors for monitoring the opening and lateral displacements of foundation cracks during wind turbine operation. We detail methods for in situ sensor characterisation, verify sensor responses against theoretical tower strains derived from wind speed data, and then show that measured crack displacements correlate with monitored tower strains. Our results show that foundation crack opening displacements respond linearly to tower strain and do not change by more than ±5 μ m. Lateral crack displacements were found to be negligible. We anticipate that the work outlined here will provide a starting point for real-time, long-term and dynamic analyses of crack displacements in future. Our findings could furthermore inform the development of cost-effective monitoring systems for ageing wind turbine foundations.

  12. Crack initiation under generalized plane strain conditions

    International Nuclear Information System (INIS)

    Shum, D.K.M.; Merkle, J.G.

    1991-01-01

    A method for estimating the decrease in crack-initiation toughness, from a reference plane strain value, due to positive straining along the crack front of a circumferential flaw in a reactor pressure vessel is presented in this study. This method relates crack initiation under generalized plane strain conditions with material failure at points within a distance of a few crack-tip-opening displacements ahead of a crack front, and involves the formulation of a micromechanical crack-initiation model. While this study is intended to address concerns regarding the effects of positive out-of- plane straining on ductile crack initiation, the approach adopted in this work can be extended in a straightforward fashion to examine conditions of macroscopic cleavage crack initiation. Provided single- parameter dominance of near-tip fields exists in the flawed structure, results from this study could be used to examine the appropriateness of applying plane strain fracture toughness to the evaluation of circumferential flaws, in particular to those in ring-forged vessels which have no longitudinal welds. In addition, results from this study could also be applied toward the analysis of the effects of thermal streaming on the fracture resistance of circumferentially oriented flaws in a pressure vessel. 37 refs., 8 figs., 1 tab

  13. Quantitative Analysis of a Parasitic Antiviral Strategy

    OpenAIRE

    Kim, Hwijin; Yin, John

    2004-01-01

    We extended a computer simulation of viral intracellular growth to study a parasitic antiviral strategy that diverts the viral replicase toward parasite growth. This strategy inhibited virus growth over a wide range of conditions, while minimizing host cell perturbations. Such parasitic strategies may inhibit the development of drug-resistant virus strains.

  14. Parasitism and the biodiversity-functioning relationship

    Science.gov (United States)

    Frainer, André; McKie, Brendan G.; Amundsen, Per-Arne; Knudsen, Rune; Lafferty, Kevin D.

    2018-01-01

    Biodiversity affects ecosystem functioning.Biodiversity may decrease or increase parasitism.Parasites impair individual hosts and affect their role in the ecosystem.Parasitism, in common with competition, facilitation, and predation, could regulate BD-EF relationships.Parasitism affects host phenotypes, including changes to host morphology, behavior, and physiology, which might increase intra- and interspecific functional diversity.The effects of parasitism on host abundance and phenotypes, and on interactions between hosts and the remaining community, all have potential to alter community structure and BD-EF relationships.Global change could facilitate the spread of invasive parasites, and alter the existing dynamics between parasites, communities, and ecosystems.Species interactions can influence ecosystem functioning by enhancing or suppressing the activities of species that drive ecosystem processes, or by causing changes in biodiversity. However, one important class of species interactions – parasitism – has been little considered in biodiversity and ecosystem functioning (BD-EF) research. Parasites might increase or decrease ecosystem processes by reducing host abundance. Parasites could also increase trait diversity by suppressing dominant species or by increasing within-host trait diversity. These different mechanisms by which parasites might affect ecosystem function pose challenges in predicting their net effects. Nonetheless, given the ubiquity of parasites, we propose that parasite–host interactions should be incorporated into the BD-EF framework.

  15. 9 CFR 381.88 - Parasites.

    Science.gov (United States)

    2010-01-01

    ... 9 Animals and Animal Products 2 2010-01-01 2010-01-01 false Parasites. 381.88 Section 381.88 Animals and Animal Products FOOD SAFETY AND INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE AGENCY... § 381.88 Parasites. Organs or other parts of carcasses which are found to be infested with parasites, or...

  16. New Laboulbeniales parasitic on endogean ground beetles.

    Science.gov (United States)

    Rossi, Walter; Santamaria, Sergi

    2008-01-01

    Three new species of Laboulbenia occurring on endogean Carabidae are described. These are L. lucifuga, parasitic on Winklerites spp. from Greece, L. magrinii, parasitic on Typloreicheia spp. from Italy, Reicheia spp. from Italy and Corsica and L. vailatii, parasitic on Coecoparvus spp. from Greece. New characters of L. coiffatii and L. endogea are pointed out, and the genus Scalenomyces is synonymized with Laboulbenia.

  17. Corrosion of steel in cracked concrete: a microscale study

    NARCIS (Netherlands)

    Pacheco, J.; Savija, B.; Schlangen, E.; Polder, R.B.

    2014-01-01

    The influence of concrete cracking upon reinforcement corrosion is complex. Cracks allow fast penetration of chlorides, potentially leading to a shorter initiation period of reinforcement corrosion. Structural regulations control acceptable crack width values based on the exposure class of the

  18. Crack growth by micropore coalescence at high temperatures

    International Nuclear Information System (INIS)

    Beere, W.

    1981-01-01

    At high temperatures in the creep regime the stress distribution around a crack is different from the low temperature elastically generated distribution. The stress distribution ahead of the crack is calculated for a crack preceded by an array of growing cavities. The cavities maintain a displacement wedge ahead of the crack. When the displacement wedge is less than one-tenth the crack length the driving force for crack growth is similar to an all elastically loaded crack. When the deforming wedge exceeds the crack length the net section stress controls crack growth. An expression is derived for a crack growing by the growth and coalescence of cavities situated in the crack plane. It is predicted that at high temperatures above a critical stress intensity, the crack propagates in a brittle fashion. (author)

  19. Analysis of 3D crack propagation by microfocus computed tomography

    International Nuclear Information System (INIS)

    Ao Bo; Chen Fuxing; Deng Cuizhen; Zeng Yabin

    2014-01-01

    The three-point bending test of notched specimens of 2A50 forging aluminum was performed by high frequency fatigue tester, and the surface cracks of different stages were analyzed and contrasted by SEM. The crack was reconstructed by microfocus computed tomography, and its size, position and distribution were visually displayed through 3D visualization. The crack propagation behaviors were researched through gray value and position of crack front of 2D CT images in two adjacent stages, and the results show that crack propagation is irregular. The projection image of crack was obtained if crack of two stages projected onto the reference plane respectively, a significant increase of new crack propagation was observed compared with the previous projection of crack, and the distribution curve of crack front of two stages was displayed. The 3D increment distribution of the crack front propagation was obtained through the 3D crack analysis of two stages. (authors)

  20. Mitigation strategies for reflective cracking in pavements : [research project capsule].

    Science.gov (United States)

    2013-12-01

    Refl ection cracks are caused by discontinuities (cracks or joints) in underlying layers, : which propagate through hot-mix asphalt (HMA) overlay due to continuous movement : at the crack prompted by thermal expansion and traffi c loading. If the new...

  1. Unsaturated Seepage Analysis of Cracked Soil including Development Process of Cracks

    Directory of Open Access Journals (Sweden)

    Ling Cao

    2016-01-01

    Full Text Available Cracks in soil provide preferential pathways for water flow and their morphological parameters significantly affect the hydraulic conductivity of the soil. To study the hydraulic properties of cracks, the dynamic development of cracks in the expansive soil during drying and wetting has been measured in the laboratory. The test results enable the development of the relationships between the cracks morphological parameters and the water content. In this study, the fractal model has been used to predict the soil-water characteristic curve (SWCC of the cracked soil, including the developmental process of the cracks. The cracked expansive soil has been considered as a crack-pore medium. A dual media flow model has been developed to simulate the seepage characteristics of the cracked expansive soil. The variations in pore water pressure at different part of the model are quite different due to the impact of the cracks. This study proves that seepage characteristics can be better predicted if the impact of cracks is taken into account.

  2. Estimation of Fatigue Crack Growth Behavior of Cracked Specimen Under Mixed-mode Loads

    International Nuclear Information System (INIS)

    Han, Jeong Woo; Woo, Eun Taek; Han, Seung Ho

    2015-01-01

    To estimate the fatigue crack propagation behavior of compact tension shear (CTS) specimen under mixed-mode loads, crack path prediction theories and Tanaka’s equation were applied. The stress intensity factor at a newly created crack tip was calculated using a finite element method via ANSYS, and the crack path and crack increment were then obtained from the crack path prediction theories, Tanaka’s equation, and the Paris’ equation, which were preprogrammed in Microsoft Excel. A new method called the finite element crack tip updating method (FECTUM) was developed. In this method, the finite element method and Microsoft Excel are used to calculate the stress intensity factors and the crack path, respectively, at the crack tip per each crack increment. The developed FECTUM was applied to simulate the fatigue crack propagation of a single-edge notched bending (SENB) specimen under eccentric three-point bending loads. The results showed that the number of cycles to failure of the specimen obtained experimentally and numerically were in good agreement within an error range of less than 3%

  3. Estimation of Fatigue Crack Growth Behavior of Cracked Specimen Under Mixed-mode Loads

    Energy Technology Data Exchange (ETDEWEB)

    Han, Jeong Woo [KIMM, Daejeon (Korea, Republic of); Woo, Eun Taek; Han, Seung Ho [Dong-A University, Busan (Korea, Republic of)

    2015-07-15

    To estimate the fatigue crack propagation behavior of compact tension shear (CTS) specimen under mixed-mode loads, crack path prediction theories and Tanaka’s equation were applied. The stress intensity factor at a newly created crack tip was calculated using a finite element method via ANSYS, and the crack path and crack increment were then obtained from the crack path prediction theories, Tanaka’s equation, and the Paris’ equation, which were preprogrammed in Microsoft Excel. A new method called the finite element crack tip updating method (FECTUM) was developed. In this method, the finite element method and Microsoft Excel are used to calculate the stress intensity factors and the crack path, respectively, at the crack tip per each crack increment. The developed FECTUM was applied to simulate the fatigue crack propagation of a single-edge notched bending (SENB) specimen under eccentric three-point bending loads. The results showed that the number of cycles to failure of the specimen obtained experimentally and numerically were in good agreement within an error range of less than 3%.

  4. A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs.

    Science.gov (United States)

    Swain, Martin T; Tsai, Isheng J; Assefa, Samual A; Newbold, Chris; Berriman, Matthew; Otto, Thomas D

    2012-06-07

    Genome projects now produce draft assemblies within weeks owing to advanced high-throughput sequencing technologies. For milestone projects such as Escherichia coli or Homo sapiens, teams of scientists were employed to manually curate and finish these genomes to a high standard. Nowadays, this is not feasible for most projects, and the quality of genomes is generally of a much lower standard. This protocol describes software (PAGIT) that is used to improve the quality of draft genomes. It offers flexible functionality to close gaps in scaffolds, correct base errors in the consensus sequence and exploit reference genomes (if available) in order to improve scaffolding and generating annotations. The protocol is most accessible for bacterial and small eukaryotic genomes (up to 300 Mb), such as pathogenic bacteria, malaria and parasitic worms. Applying PAGIT to an E. coli assembly takes ∼24 h: it doubles the average contig size and annotates over 4,300 gene models.

  5. Process and device for magnetic crack testing

    International Nuclear Information System (INIS)

    Seiler, D.; Meili, E.; Fuchs, E.

    1983-01-01

    There is a problem of sufficient crack depth discrimination to suppress fault signals or pictures due to unevenness not caused by cracks. To solve this, when magnetising in the preferred direction of adhesion, the effect depending on the direction of the crack, before magnetic powder detection, magnetic powder is blown on, showing the fault and for the comparison of the adhesion effect crack direction characteristics it is blown on parallel to the preferred direction, or if one wants to stress the directional characteristic, it is blown on transversely to the preferred direction. In both cases one blows with the same force, without removing the magnetic powder remnants relevant to faults in the intended crack areas. This strong blowing removes the magnetic powder remnants relevant to interference and not relevant to faults. (orig./HP) [de

  6. Strain rate effects in stress corrosion cracking

    Energy Technology Data Exchange (ETDEWEB)

    Parkins, R.N. (Newcastle upon Tyne Univ. (UK). Dept. of Metallurgy and Engineering Materials)

    1990-03-01

    Slow strain rate testing (SSRT) was initially developed as a rapid, ad hoc laboratory method for assessing the propensity for metals an environments to promote stress corrosion cracking. It is now clear, however, that there are good theoretical reasons why strain rate, as opposed to stress per se, will often be the controlling parameter in determining whether or not cracks are nucleated and, if so, are propagated. The synergistic effects of the time dependence of corrosion-related reactions and microplastic strain provide the basis for mechanistic understanding of stress corrosion cracking in high-pressure pipelines and other structures. However, while this may be readily comprehended in the context of laboratory slow strain tests, its extension to service situations may be less apparent. Laboratory work involving realistic stressing conditions, including low-frequency cyclic loading, shows that strain or creep rates give good correlation with thresholds for cracking and with crack growth kinetics.

  7. Compliance characteristics of cracked UO2 pellets

    International Nuclear Information System (INIS)

    Williford, R.E.; Mohr, C.L.; Lanning, D.D.

    1981-01-01

    The thermally induced cracking of UO 2 fuel pellets causes simultaneous reductions of the bulk (extrinsic) fuel thermal conductivity and elastic moduli to values significantly less than those for solid pellets. The magnitude of these bulk properly reductions was found to be primarily dependent on the amount of crack area in the transverse plane of the fuel. The model described herein uses a simple description of the crack geometry to couple the fuel rod thermal and mechanical behaviors by relating in-reactor data to Hooke's Law and a crack compliance model. Data from the NRC/PNL Halden experiment IFA-432 show that for a typical helium-filled BWR-design rod at 30 kW/m, the effective thermal conductivity and elastic moduli of the cracked fuel are 4/5 and 1/40 of that for solid pellets, respectively

  8. Single-copy nuclear genes place haustorial Hydnoraceae within piperales and reveal a cretaceous origin of multiple parasitic angiosperm lineages.

    Directory of Open Access Journals (Sweden)

    Julia Naumann

    Full Text Available Extreme haustorial parasites have long captured the interest of naturalists and scientists with their greatly reduced and highly specialized morphology. Along with the reduction or loss of photosynthesis, the plastid genome often decays as photosynthetic genes are released from selective constraint. This makes it challenging to use traditional plastid genes for parasitic plant phylogenetics, and has driven the search for alternative phylogenetic and molecular evolutionary markers. Thus, evolutionary studies, such as molecular clock-based age estimates, are not yet available for all parasitic lineages. In the present study, we extracted 14 nuclear single copy genes (nSCG from Illumina transcriptome data from one of the "strangest plants in the world", Hydnora visseri (Hydnoraceae. A ~15,000 character molecular dataset, based on all three genomic compartments, shows the utility of nSCG for reconstructing phylogenetic relationships in parasitic lineages. A relaxed molecular clock approach with the same multi-locus dataset, revealed an ancient age of ~91 MYA for Hydnoraceae. We then estimated the stem ages of all independently originated parasitic angiosperm lineages using a published dataset, which also revealed a Cretaceous origin for Balanophoraceae, Cynomoriaceae and Apodanthaceae. With the exception of Santalales, older parasite lineages tend to be more specialized with respect to trophic level and have lower species diversity. We thus propose the "temporal specialization hypothesis" (TSH implementing multiple independent specialization processes over time during parasitic angiosperm evolution.

  9. Crack shape developments and leak rates for circumferential complex-cracked pipes

    Energy Technology Data Exchange (ETDEWEB)

    Brickstad, B.; Bergman, M. [SAQ Inspection Ltd., Stockholm (Sweden)

    1997-04-01

    A computerized procedure has been developed that predicts the growth of an initial circumferential surface crack through a pipe and further on to failure. The crack growth mechanism can either be fatigue or stress corrosion. Consideration is taken to complex crack shapes and for the through-wall cracks, crack opening areas and leak rates are also calculated. The procedure is based on a large number of three-dimensional finite element calculations of cracked pipes. The results from these calculations are stored in a database from which the PC-program, denoted LBBPIPE, reads all necessary information. In this paper, a sensitivity analysis is presented for cracked pipes subjected to both stress corrosion and vibration fatigue.

  10. Fully plastic crack opening analyses of complex-cracked pipes for Ramberg-Osgood materials

    International Nuclear Information System (INIS)

    Jeong, Jae Uk; Choi, Jae Boong; Huh, Nam Su; Kim, Yun Jae

    2016-01-01

    The plastic influence functions for calculating fully plastic Crack opening displacement (COD) of complex-cracked pipes were newly proposed based on systematic 3-dimensional (3-D) elastic-plastic Finite element (FE) analyses using Ramberg-Osgood (R-O) relation, where global bending moment, axial tension and internal pressure are considered separately as a loading condition. Then, crack opening analyses were performed based on GE/EPRI concept by using the new plastic influence functions for complex-cracked pipes made of SA376 TP304 stainless steel, and the predicted CODs were compared with FE results based on deformation plasticity theory of tensile material behavior. From the comparison, the confidence of the proposed fully plastic crack opening solutions for complex-cracked pipes was gained. Therefore, the proposed engineering scheme for COD estimation using the new plastic influence functions can be utilized to estimate leak rate of a complex-cracked pipe for R-O material.

  11. Optimisation of the Crack Pattern in Continuously Reinforced Concrete Pavements

    OpenAIRE

    Ren, D.

    2015-01-01

    Recent field investigations on several new Continuously Reinforced Concrete Pavements (CRCP) in Belgium indicate that its crack pattern is characterized by low mean crack spacing along with a high percentage of clusters of closely spaced cracks. Field surveys also indicate that it is difficult to significantly reduce the probability of a non-uniform crack pattern - such as closely spaced cracks, meandering, and Y-cracks - by only slightly adjusting the amount of longitudinal steel. Non-unifor...

  12. Footprints of directional selection in wild Atlantic salmon populations: evidence for parasite-driven evolution?

    Science.gov (United States)

    Zueva, Ksenia J; Lumme, Jaakko; Veselov, Alexey E; Kent, Matthew P; Lien, Sigbjørn; Primmer, Craig R

    2014-01-01

    Mechanisms of host-parasite co-adaptation have long been of interest in evolutionary biology; however, determining the genetic basis of parasite resistance has been challenging. Current advances in genome technologies provide new opportunities for obtaining a genome-scale view of the action of parasite-driven natural selection in wild populations and thus facilitate the search for specific genomic regions underlying inter-population differences in pathogen response. European populations of Atlantic salmon (Salmo salar L.) exhibit natural variance in susceptibility levels to the ectoparasite Gyrodactylus salaris Malmberg 1957, ranging from resistance to extreme susceptibility, and are therefore a good model for studying the evolution of virulence and resistance. However, distinguishing the molecular signatures of genetic drift and environment-associated selection in small populations such as land-locked Atlantic salmon populations presents a challenge, specifically in the search for pathogen-driven selection. We used a novel genome-scan analysis approach that enabled us to i) identify signals of selection in salmon populations affected by varying levels of genetic drift and ii) separate potentially selected loci into the categories of pathogen (G. salaris)-driven selection and selection acting upon other environmental characteristics. A total of 4631 single nucleotide polymorphisms (SNPs) were screened in Atlantic salmon from 12 different northern European populations. We identified three genomic regions potentially affected by parasite-driven selection, as well as three regions presumably affected by salinity-driven directional selection. Functional annotation of candidate SNPs is consistent with the role of the detected genomic regions in immune defence and, implicitly, in osmoregulation. These results provide new insights into the genetic basis of pathogen susceptibility in Atlantic salmon and will enable future searches for the specific genes involved.

  13. Cracks assessment using ultrasonic technology

    Energy Technology Data Exchange (ETDEWEB)

    Martinez, Maria Pia; Tomasella, Marcelo [OLDELVAL S.A. Oleoductos del Valle, Rio Negro (Argentina). Pipeline Integrity Dept.

    2005-07-01

    The goal of Oldelval Integrity Program is to prevent ruptures and leaks, developing strategies for a better handling of the integrity of our pipelines. In order to achieve it we have studied and modeled each process that involved in the integrity pipeline. Those processes are mainly based on defects reported by an internal inspection tool and supplied with field inspection and monitoring data. Years of evaluation, study and the continuous effort overturned towards a phenomenon that worries to the industry, as it is the SCC. Since 1998 up to 2004 SCC was included in the integrity program with some preventive maintenance programs. The accomplishment of the inspection based on ultrasound tools, is the culmination of years of evaluation and investigations supported by field digs and materials susceptibility. This paper describes Oldelval's results with ultrasonic crack detection tool, and how it can be reliably to detect SCC. (author)

  14. Diagnostic problems with parasitic and non-parasitic splenic cysts

    Directory of Open Access Journals (Sweden)

    Adas Gokhan

    2009-05-01

    Full Text Available Abstract Background The splenic cysts constitute a very rare clinical entity. They may occur secondary to trauma or even being more seldom due to parasitic infestations, mainly caused by ecchinocccus granulosus. Literature lacks a defined concencus including the treatment plans and follow up strategies, nor long term results of the patients. In the current study, we aimed to evaluate the diagnosis, management of patients with parasitic and non-parasitic splenic cysts together with their long term follow up progresses. Methods Twenty-four patients with splenic cysts have undergone surgery in our department over the last 9 years. Data from eighteen of the twenty-four patients were collected prospectively, while data from six were retrospectively collected. All patients were assessed in terms of age, gender, hospital stay, preoperative diagnosis, additional disease, serology, ultrasonography, computed tomography (CT, cyst recurrences and treatment. Results In this study, the majority of patients presented with abdominal discomfort and palpable swelling in the left hypochondrium. All patients were operated on electively. The patients included 14 female and 10 male patients, with a mean age of 44.77 years (range 20–62. Splenic hydatid cysts were present in 16 patients, one of whom also had liver hydatid cysts (6.25%. Four other patients were operated on for a simple cyst (16% two patients for an epithelial cyst, and the last two for splenic lymphangioma. Of the 16 patients diagnosed as having splenic hydatit cysts, 11 (68.7% were correctly diagnosed. Only two of these patients were administered benzimidazole therapy pre-operatively because of the risk of multicystic disease The mean follow-up period was 64 months (6–108. There were no recurrences of splenic cysts. Conclusion Surgeons should keep in mind the possibility of a parasitic cyst when no definitive alternative diagnosis can be made. In the treatment of splenic hydatidosis, benzimidazole

  15. Nuclear techniques in the study of parasitic infections

    International Nuclear Information System (INIS)

    1982-01-01

    Out of 57 papers published, 47 fall within the INIS subject scope. Seven main topics were covered: resistance to infections with protozoan parasites; resistance to infections with African trypanosomes and helminths of ruminant animals; resistance to infections with filarial parasites and schistosomes; pathology of parasitic infections; epidemiology and diagnosis of parasitic infections; physiology and biochemistry of parasitic organisms; pharmacodynamics of anti-parasitic agents

  16. Smart Parasitic Nematodes Use Multifaceted Strategies to Parasitize Plants

    Directory of Open Access Journals (Sweden)

    Muhammad A. Ali

    2017-10-01

    Full Text Available Nematodes are omnipresent in nature including many species which are parasitic to plants and cause enormous economic losses in various crops. During the process of parasitism, sedentary phytonematodes use their stylet to secrete effector proteins into the plant cells to induce the development of specialized feeding structures. These effectors are used by the nematodes to develop compatible interactions with plants, partly by mimicking the expression of host genes. Intensive research is going on to investigate the molecular function of these effector proteins in the plants. In this review, we have summarized which physiological and molecular changes occur when endoparasitic nematodes invade the plant roots and how they develop a successful interaction with plants using the effector proteins. We have also mentioned the host genes which are induced by the nematodes for a compatible interaction. Additionally, we discuss how nematodes modulate the reactive oxygen species (ROS and RNA silencing pathways in addition to post-translational modifications in their own favor for successful parasitism in plants.

  17. Parasitic infections of the external eye.

    Science.gov (United States)

    Pahuja, Shivani; Puranik, Charuta; Jelliti, Bechir; Khairallah, Moncef; Sangwan, Virender S

    2013-08-01

    To review the published literature on parasitic infections of external eye. Published articles and case reports on parasitic infections of external eye were reviewed and relevant information was collected. Parasitic infections of the eye are rare. However, being more commonly seen in developing nations, they require active measures for screening, diagnosis, and therapy. Parasites of importance causing external ocular disease are protozoan parasites, such as Leishmania; metazoans, such as nematodes (roundworms), cestodes (tapeworms), and trematodes (flatworms); or ectoparasites, such as Phthirus pubis and Demodex.

  18. Homologous Recombination in Protozoan Parasites and Recombinase Inhibitors

    Directory of Open Access Journals (Sweden)

    Andrew A. Kelso

    2017-09-01

    Full Text Available Homologous recombination (HR is a DNA double-strand break (DSB repair pathway that utilizes a homologous template to fully repair the damaged DNA. HR is critical to maintain genome stability and to ensure genetic diversity during meiosis. A specialized class of enzymes known as recombinases facilitate the exchange of genetic information between sister chromatids or homologous chromosomes with the help of numerous protein accessory factors. The majority of the HR machinery is highly conserved among eukaryotes. In many protozoan parasites, HR is an essential DSB repair pathway that allows these organisms to adapt to environmental conditions and evade host immune systems through genetic recombination. Therefore, small molecule inhibitors, capable of disrupting HR in protozoan parasites, represent potential therapeutic options. A number of small molecule inhibitors were identified that disrupt the activities of the human recombinase RAD51. Recent studies have examined the effect of two of these molecules on the Entamoeba recombinases. Here, we discuss the current understandings of HR in the protozoan parasites Trypanosoma, Leishmania, Plasmodium, and Entamoeba, and we review the small molecule inhibitors known to disrupt human RAD51 activity.

  19. Molecular genetic transfection of the coccidian parasite Sarcocystis neurona.

    Science.gov (United States)

    Gaji, Rajshekhar Y; Zhang, Deqing; Breathnach, Cormac C; Vaishnava, Shipra; Striepen, Boris; Howe, Daniel K

    2006-11-01

    Sarcocystis neurona is an apicomplexan parasite that is the major cause of equine protozoal myeloencephalitis (EPM). The biology of this pathogen remains poorly understood in part due to unavailability of molecular genetic tools. Hence, with an objective to develop DNA transfection capabilities for S. neurona, the 5' flanking region of the SnSAG1 gene was isolated from a genomic library and used to construct expression plasmids. In transient assays, the reporter molecules beta-galactosidase (beta-gal) and yellow fluorescent protein (YFP) could be detected in electroporated S. neurona, thereby confirming the feasibility of transgene expression in this organism. Stable transformation of S. neurona was achieved using a mutant dihydrofolate reductase thymidylate synthase (DHFR-TS) gene of Toxoplasma gondii that confers resistance to pyrimethamine. This selection system was used to create transgenic S. neurona that stably express beta-gal and YFP. As shown in this study, these transgenic clones can be useful for analyzing growth rate of parasites in vitro and for assessing drug sensitivities. More importantly, the DNA transfection methods described herein should greatly facilitate studies examining intracellular parasitism by this important coccidian pathogen.

  20. Insect antimicrobial peptides act synergistically to inhibit a trypanosome parasite.

    Science.gov (United States)

    Marxer, Monika; Vollenweider, Vera; Schmid-Hempel, Paul

    2016-05-26

    The innate immune system provides protection from infection by producing essential effector molecules, such as antimicrobial peptides (AMPs) that possess broad-spectrum activity. This is also the case for bumblebees, Bombus terrestris, when infected by the trypanosome, Crithidia bombi Furthermore, the expressed mixture of AMPs varies with host genetic background and infecting parasite strain (genotype). Here, we used the fact that clones of C. bombi can be cultivated and kept as strains in medium to test the effect of various combinations of AMPs on the growth rate of the parasite. In particular, we used pairwise combinations and a range of physiological concentrations of three AMPs, namely Abaecin, Defensin and Hymenoptaecin, synthetized from the respective genomic sequences. We found that these AMPs indeed suppress the growth of eight different strains of C. bombi, and that combinations of AMPs were typically more effective than the use of a single AMP alone. Furthermore, the most effective combinations were rarely those consisting of maximum concentrations. In addition, the AMP combination treatments revealed parasite strain specificity, such that strains varied in their sensitivity towards the same mixtures. Hence, variable expression of AMPs could be an alternative strategy to combat highly variable infections.This article is part of the themed issue 'Evolutionary ecology of arthropod antimicrobial peptides'. © 2016 The Author(s).

  1. Passive transfer of leishmania lipopolysaccharide confers parasite survival in macrophages

    International Nuclear Information System (INIS)

    Handman, E.; Schnur, L.F.; Spithill, T.W.; Mitchell, G.F.

    1986-01-01

    Infection of macrophages by the intracellular protozoan parasite Leishmania involves specific attachment to the host membrane, followed by phagocytosis and intracellular survival and growth. Two parasite molecules have been implicated in the attachment event: Leishmania lipopolysaccharide (L-LPS) and a glycoprotein (gp63). This study was designed to clarify the role of L-LPS in infection and the stage in the process of infection at which it operates. The authors have recently identified a Leishmania major strain (LRC-L119) which lacks the L-LPS molecule and is not infective for hamsters or mice. This parasite was isolated from a gerbil in Kenya and was identified phenotypically as L. major by isoenzyme and fatty acid analysis. In this study they have confirmed at the genotype level that LRC-L119 is L. major by analyzing and comparing the organization of cloned DNA sequences in the genome of different strains of L. major. Here they show that LRC-L119 promastigotes are phagocytosed rapidly by macrophages in vitro, but in contrast to virulent strains of L. major, they are then killed over a period of 18 hr. In addition, they show that transfer of purified L-LPS from a virulent clone of L. major (V121) into LRC-L119 promastigotes confers on them the ability to survive in macrophages in vitro

  2. The role of moulting in parasite defence.

    Science.gov (United States)

    Duneau, David; Ebert, Dieter

    2012-08-07

    Parasitic infections consist of a succession of steps during which hosts and parasites interact in specific manners. At each step, hosts can use diverse defence mechanisms to counteract the parasite's attempts to invade and exploit them. Of these steps, the penetration of parasites into the host is a key step for a successful infection and the epithelium is the first line of host defence. The shedding of this protective layer (moulting) is a crucial feature in the life cycle of several invertebrate and vertebrate taxa, and is generally considered to make hosts vulnerable to parasites and predators. Here, we used the crustacean Daphnia magna to test whether moulting influences the likelihood of infection by the castrating bacterium Pasteuria ramosa. This parasite is known to attach to the host cuticula before penetrating into its body. We found that the likelihood of successful parasite infection is greatly reduced if the host moults within 12 h after parasite exposure. Thus, moulting is beneficial for the host being exposed to this parasite. We further show that exposure to the parasite does not induce hosts to moult earlier. We discuss the implications of our findings for host and parasite evolution and epidemiology.

  3. Parasites in Forensic Science: a historic perspective

    Science.gov (United States)

    Cardoso, Rita; Alves, Helena; Richter, Joachim; Botelho, Monica C

    Parasites show a great potential to Forensic Science. Forensic Science is the application of any science and methodology to the legal system. The forensic scientist collects and analyses the physical evidence and produce a report of the results to the court. A parasite is an organism that lives at the expense of another and they exist in any ecosystem. Parasites are the cause of many important diseases. The forensic scientists can use the parasites to identify a crime scene, to determine the murder weapon or simply identify an individual. The applications for parasites in the Forensic Science can be many and more studies should be made in Forensic Parasitology. The most important parasites in Forensic Science are helminths specifically schistosomes. Through history there are many cases where schistosomes were described in autopsies and it was related to the cause of death. Here we review the applications of parasites in Forensic Science and its importance to the forensic scientist.

  4. The adaptive significance of inquiline parasite workers

    DEFF Research Database (Denmark)

    Sumner, Seirian; Nash, David R; Boomsma, Jacobus J

    2003-01-01

    Social parasites exploit the socially managed resources of their host's society. Inquiline social parasites are dependent on their host throughout their life cycle, and so many of the traits inherited from their free-living ancestor are removed by natural selection. One trait that is commonly lost...... is the worker caste, the functions of which are adequately fulfilled by host workers. The few inquiline parasites that have retained a worker caste are thought to be at a transitional stage in the evolution of social parasitism, and their worker castes are considered vestigial and non-adaptive. However...... a vital role in ensuring the parasite's fitness. We show that the presence of these parasite workers has a positive effect on the production of parasite sexuals and a negative effect on the production of host sexuals. This suggests that inquiline workers play a vital role in suppressing host queen...

  5. The mitochondrial genome of Toxocara canis.

    Science.gov (United States)

    Jex, Aaron R; Waeschenbach, Andrea; Littlewood, D Timothy J; Hu, Min; Gasser, Robin B

    2008-08-06

    Toxocara canis (Ascaridida: Nematoda), which parasitizes (at the adult stage) the small intestine of canids, can be transmitted to a range of other mammals, including humans, and can cause the disease toxocariasis. Despite its significance as a pathogen, the genetics, epidemiology and biology of this parasite remain poorly understood. In addition, the zoonotic potential of related species of Toxocara, such as T. cati and T. malaysiensis, is not well known. Mitochondrial DNA is known to provide genetic markers for investigations in these areas, but complete mitochondrial genomic data have been lacking for T. canis and its congeners. In the present study, the mitochondrial genome of T. canis was amplified by long-range polymerase chain reaction (long PCR) and sequenced using a primer-walking strategy. This circular mitochondrial genome was 14162 bp and contained 12 protein-coding, 22 transfer RNA, and 2 ribosomal RNA genes consistent for secementean nematodes, including Ascaris suum and Anisakis simplex (Ascaridida). The mitochondrial genome of T. canis provides genetic markers for studies into the systematics, population genetics and epidemiology of this zoonotic parasite and its congeners. Such markers can now be used in prospecting for cryptic species and for exploring host specificity and zoonotic potential, thus underpinning the prevention and control of toxocariasis in humans and other hosts.

  6. The mitochondrial genome of Toxocara canis.

    Directory of Open Access Journals (Sweden)

    Aaron R Jex

    2008-08-01

    Full Text Available Toxocara canis (Ascaridida: Nematoda, which parasitizes (at the adult stage the small intestine of canids, can be transmitted to a range of other mammals, including humans, and can cause the disease toxocariasis. Despite its significance as a pathogen, the genetics, epidemiology and biology of this parasite remain poorly understood. In addition, the zoonotic potential of related species of Toxocara, such as T. cati and T. malaysiensis, is not well known. Mitochondrial DNA is known to provide genetic markers for investigations in these areas, but complete mitochondrial genomic data have been lacking for T. canis and its congeners. In the present study, the mitochondrial genome of T. canis was amplified by long-range polymerase chain reaction (long PCR and sequenced using a primer-walking strategy. This circular mitochondrial genome was 14162 bp and contained 12 protein-coding, 22 transfer RNA, and 2 ribosomal RNA genes consistent for secementean nematodes, including Ascaris suum and Anisakis simplex (Ascaridida. The mitochondrial genome of T. canis provides genetic markers for studies into the systematics, population genetics and epidemiology of this zoonotic parasite and its congeners. Such markers can now be used in prospecting for cryptic species and for exploring host specificity and zoonotic potential, thus underpinning the prevention and control of toxocariasis in humans and other hosts.

  7. The Mitochondrial Genome of Toxocara canis

    Science.gov (United States)

    Littlewood, D. Timothy J.; Hu, Min; Gasser, Robin B.

    2008-01-01

    Toxocara canis (Ascaridida: Nematoda), which parasitizes (at the adult stage) the small intestine of canids, can be transmitted to a range of other mammals, including humans, and can cause the disease toxocariasis. Despite its significance as a pathogen, the genetics, epidemiology and biology of this parasite remain poorly understood. In addition, the zoonotic potential of related species of Toxocara, such as T. cati and T. malaysiensis, is not well known. Mitochondrial DNA is known to provide genetic markers for investigations in these areas, but complete mitochondrial genomic data have been lacking for T. canis and its congeners. In the present study, the mitochondrial genome of T. canis was amplified by long-range polymerase chain reaction (long PCR) and sequenced using a primer-walking strategy. This circular mitochondrial genome was 14162 bp and contained 12 protein-coding, 22 transfer RNA, and 2 ribosomal RNA genes consistent for secernentean nematodes, including Ascaris suum and Anisakis simplex (Ascaridida). The mitochondrial genome of T. canis provides genetic markers for studies into the systematics, population genetics and epidemiology of this zoonotic parasite and its congeners. Such markers can now be used in prospecting for cryptic species and for exploring host specificity and zoonotic potential, thus underpinning the prevention and control of toxocariasis in humans and other hosts. PMID:18682828

  8. PARASITIC MITES IN BACKYARD TURKEYS

    Directory of Open Access Journals (Sweden)

    Marco Antonio Camacho-Escobar

    2010-02-01

    Full Text Available To describe the parasitic mites in backyard turkeys, was did this work. The mites were obtain by hand for 30 backyard turkeys in Oaxaca’s Coast region, Mexico; the mites were mount in adhesive paper and wash with the 200X lent in a computer optical microscopy, the parasites size were determinate in the pictures obtained by the microscopy software, the images were sized using a specialist software for it, which relate the number of pixels in the picture with the size of the observation field. Were indentified the species Dermanyssus gallinae, Megninia ginglymura and Ornithonyssus sylviarum, the last two described for first time in backyard turkeys in Mexico. Â

  9. Dislocation model of a subsurface crack

    International Nuclear Information System (INIS)

    Yang, F.; Li, J.C.

    1997-01-01

    A dislocation model of a subsurface crack parallel to the surface is presented. For tensile loading, the results agree with those of previous workers except that we studied the crack very close to the surface and found that K II (mode II stress intensity factor) approaches K I (mode I stress intensity factor) to within about 22% (K II =0.78K I ). (Note that K II is zero when the crack is far away from the surface). Using bending theory for such situations, it is found that both stress intensity factors are inversely proportional to the 3/2 power of the distance between the subsurface crack and the free surface. For shear loading, the crack faces overlap each other for the free traction condition. This indicates the failure of the model. However, there was no overlap for tensile loading even though the stresses in front of the crack oscillate somewhat when the crack is very close to the surface. copyright 1997 American Institute of Physics

  10. Identification of cracks in thick beams with a cracked beam element model

    Science.gov (United States)

    Hou, Chuanchuan; Lu, Yong

    2016-12-01

    The effect of a crack on the vibration of a beam is a classical problem, and various models have been proposed, ranging from the basic stiffness reduction method to the more sophisticated model involving formulation based on the additional flexibility due to a crack. However, in the damage identification or finite element model updating applications, it is still common practice to employ a simple stiffness reduction factor to represent a crack in the identification process, whereas the use of a more realistic crack model is rather limited. In this paper, the issues with the simple stiffness reduction method, particularly concerning thick beams, are highlighted along with a review of several other crack models. A robust finite element model updating procedure is then presented for the detection of cracks in beams. The description of the crack parameters is based on the cracked beam flexibility formulated by means of the fracture mechanics, and it takes into consideration of shear deformation and coupling between translational and longitudinal vibrations, and thus is particularly suitable for thick beams. The identification procedure employs a global searching technique using Genetic Algorithms, and there is no restriction on the location, severity and the number of cracks to be identified. The procedure is verified to yield satisfactory identification for practically any configurations of cracks in a beam.

  11. Successes against insects and parasites

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1967-10-15

    With more and more answers being found to intricate problems which have entailed years of research in many parts of the world, some successes can now be claimed in the fight to control insect threats to crops, animals and human beings. Nuclear techniques are playing an important part in world efforts, and recent reports show that they have been effective in pioneer work against crop pests as well as in finding an answer to some diseases caused by parasites

  12. Parasitic Diseases and Psychiatric Illness

    OpenAIRE

    Weiss, Mitchell Gralnick

    1994-01-01

    Distinguishing parasitic diseases from other infections and tropical medical disorders based on microbiological classification is a matter of convenience. Organic brain syndromes are associated with both protozoan and helminthic infections; side-effects of drugs commonly used to treat parasitoses may impair mood and cause anxiety, agitation or psychosis. Emotional states may in turn affect the experience of medical illness. Psychiatrically significant features of medical illness are determine...

  13. Parasites and chronic renal failure

    OpenAIRE

    Mohammadi Manesh, Reza; Hosseini Safa, Ahmad; Sharafi, Seyedeh Maryam; Jafari, Rasool; Bahadoran, Mehran; Yousefi, Morteza; Nasri, Hamid; Yousofi Darani, Hossein

    2014-01-01

    Suppression of the human immune system results in an increase in susceptibility to infection by various infectious agents. Conditions such as AIDS, organ transplantation and chronic renal insufficiency (CRI) are the most important cause of insufficient immune response against infections. Long term renal disorders result in uremia, which can suppress human immune system. Parasitic infections are one of the most important factors indicating the public health problems of the societies. These inf...

  14. Additive for vanadium and sulfur oxide capture in catalytic cracking

    International Nuclear Information System (INIS)

    Chin, A.A.; Sapre, A.V.; Sarli, M.S.

    1991-01-01

    This patent describes a fluid catalytic cracking process in which a hydrocarbon feedstock. It comprises: a vanadium contaminant in an amount of a least 2 ppmw is cracked under fluid catalytic cracking conditions with a solid, particulate cracking catalyst to produce cracking products of lower molecular weight while depositing carbonaceous material on the particles of cracking catalyst, separating the particles of cracking catalyst from the cracking products in the disengaging zone and oxidatively regenerating the cracking catalyst by burning off the deposited carbonaceous material in a regeneration zone, the improvement comprising reducing the make-up rate of the cracking catalyst by contacting the cracking feed with a particulate additive composition for passivating the vanadium content of the feed, comprising an alkaline earth metal oxide and an alkaline earth metal spinel

  15. Crack embryo formation before crack initiation and growth in high temperature water

    International Nuclear Information System (INIS)

    Arioka, Koji; Yamada, Takuyo; Terachi, Takumi; Miyamoto, Tomoki

    2008-01-01

    Crack growth measurements were performed in high temperature water and in air to examine the role of creep on IGSCC growth using cold rolled non-sensitized Type316(UNS S31600), TT690 alloy, MA600 alloy, and Carbon steel (STPT42). In addition, crack initiation tests were performed also in high temperature water and in air using specially designed CT specimen. The obtained major results are as follows: (1) TT690 did crack in intergranularly in hydrogenated high temperature water if material is cold worked in heavily. (2) Cold worked carbon steel also cracked in intergranularly in dearated high temperature water. (3) Intergranular crack growth was recognized on cold worked 316, TT690, MA600, and carbon steel even in air which might be crack embryo of IGSCC. (4) Simple Arrhenius type temperature dependence was observed on IGSCC in high temperature water and creep crack growth in air. This suggested that intergranular crack growth rate was determined by some thermal activated reaction. (5) Vacancy condensation was recognized at just ahead of the crack tips of IGSCC and creep crack of cold worked steel. This showed that IGSCC and creep crack growth was controlled by same mechanism. (6) Clear evidence of vacancies condensation was recognized at just beneath the surface before crack initiation. This proved that crack did initiate as the result of diffusion of vacancies in the solid. And the incubation time seems to be controlled by the required time for the condensation of vacancies to the stress concentrated zone. (7) Diffusion of subsituational atoms was also driven by stress gradient. This is the important knowledge to evaluate the SCC initiation after long term operation in LWR's. Based on the observed results, IGSCC initiation and growth mechanism were proposed considering the diffusion process of cold worked induced vacancies. (author)

  16. Fauna Europaea: Helminths (Animal Parasitic

    Directory of Open Access Journals (Sweden)

    David Gibson

    2014-09-01

    Full Text Available Fauna Europaea provides a public web-service with an index of scientific names (including important synonyms of all living European land and freshwater animals, their geographical distribution at country level (up to the Urals, excluding the Caucasus region, and some additional information. The Fauna Europaea project covers about 230,000 taxonomic names, including 130,000 accepted species and 14,000 accepted subspecies, which is much more than the originally projected number of 100,000 species. This represents a huge effort by more than 400 contributing specialists throughout Europe and is a unique (standard reference suitable for many users in science, government, industry, nature conservation and education. Helminths parasitic in animals represent a large assemblage of worms, representing three phyla, with more than 200 families and almost 4,000 species of parasites from all major vertebrate and many invertebrate groups. A general introduction is given for each of the major groups of parasitic worms, i.e. the Acanthocephala, Monogenea, Trematoda (Aspidogastrea and Digenea, Cestoda and Nematoda. Basic information for each group includes its size, host-range, distribution, morphological features, life-cycle, classification, identification and recent key-works. Tabulations include a complete list of families dealt with, the number of species in each and the name of the specialist responsible for data acquisition, a list of additional specialists who helped with particular groups, and a list of higher taxa dealt with down to the family level. A compilation of useful references is appended.

  17. Parasitic leiomyoma after laparoscopic myomectomy

    Directory of Open Access Journals (Sweden)

    Srithean Lertvikool

    2015-08-01

    Full Text Available A 31-year-old nulligravid underwent laparoscopic myomectomy and the masses were removed by an electric morcellator. Five years later, this patient suffered from acute pelvic pain and received an operation. During laparoscopic surgery, an 8-cm right-sided multiloculated ovarian cyst with chocolate-like content was seen. After adhesiolysis, two parasitic myomas (each ∼2 cm in diameter were found attached to the right ovarian cyst and the other two parasitic myomas (each ∼1 cm in diameter were found at the right infundibulopelvic ligament and omentum respectively. These tumors were successfully removed by laparoscopic procedure. Histopathological examination confirmed that all masses were leiomyomas and the right ovarian cyst was confirmed to be endometriosis. The formation of parasitic myomas was assumed that myomatous fragments during morcellation at the time of myomectomy may have been left behind unintentionally. Thus, morcellator should be used carefully. With that being said, all of the myomatous fragment should be removed after morcellation.

  18. Eosinophilic fasciitis after parasite infection

    Directory of Open Access Journals (Sweden)

    Marta Oliveira

    2016-03-01

    Full Text Available Eosinophilic fasciitis is a systemic inflammatory disease characterized by symmetrical swelling and skin induration of the distal portions of the arms and/or legs, evolving into a scleroderma-like appearance, accompanied by peripheral blood eosinophilia. It is a rare disease with a poorly understood etiology. Corticosteroid treatment remains the standard therapy, either taken alone or in association with an immunosuppressive drug. This paper presents a case of a male patient with palpebral edema and marked eosinophilia, diagnosed with intestinal parasitic infection in October 2006. He was treated with an antiparasitic drug, but both the swelling and the analytical changes remained. This was followed by a skin and muscle biopsy, which turned out to be compatible with eosinophilic fasciitis. There was progressive worsening of the clinical state, with stiffness of the abdominal wall and elevated inflammatory parameters, and the patient was referred to the Immunology Department, medicated with corticosteroids and methotrexate. Over the years there were therapeutic adjustments and other causes were excluded. Currently the patient continues to be monitored, and there is no evidence of active disease. The case described in this article is interesting because of the diagnosis of eosinophilic fasciitis probably associated/coexisting with a parasite infection. This case report differs from others in that there is an uncommon cause associated with the onset of the disease, instead of the common causes such as trauma, medication, non-parasitic infections or cancer.

  19. Trichostatin A effects on gene expression in the protozoan parasite Entamoeba histolytica

    Directory of Open Access Journals (Sweden)

    Singh Upinder

    2007-07-01

    Full Text Available Abstract Background Histone modification regulates chromatin structure and influences gene expression associated with diverse biological functions including cellular differentiation, cancer, maintenance of genome architecture, and pathogen virulence. In Entamoeba, a deep-branching eukaryote, short chain fatty acids (SCFA affect histone acetylation and parasite development. Additionally, a number of active histone modifying enzymes have been identified in the parasite genome. However, the overall extent of gene regulation tied to histone acetylation is not known. Results In order to identify the genome-wide effects of histone acetylation in regulating E. histolytica gene expression, we used whole-genome expression profiling of parasites treated with SCFA and Trichostatin A (TSA. Despite significant changes in histone acetylation patterns, exposure of parasites to SCFA resulted in minimal transcriptional changes (11 out of 9,435 genes transcriptionally regulated. In contrast, exposure to TSA, a more specific inhibitor of histone deacetylases, significantly affected transcription of 163 genes (122 genes upregulated and 41 genes downregulated. Genes modulated by TSA were not regulated by treatment with 5-Azacytidine, an inhibitor of DNA-methyltransferase, indicating that in E. histolytica the crosstalk between DNA methylation and histone modification is not substantial. However, the set of genes regulated by TSA overlapped substantially with genes regulated during parasite development: 73/122 genes upregulated by TSA exposure were upregulated in E. histolytica cysts (p-value = 6 × 10-53 and 15/41 genes downregulated by TSA exposure were downregulated in E. histolytica cysts (p-value = 3 × 10-7. Conclusion This work represents the first genome-wide analysis of histone acetylation and its effects on gene expression in E. histolytica. The data indicate that SCFAs, despite their ability to influence histone acetylation, have minimal effects on gene

  20. RNA Interference: A Novel Source of Resistance to Combat Plant Parasitic Nematodes

    Directory of Open Access Journals (Sweden)

    Sagar Banerjee

    2017-05-01

    Full Text Available Plant parasitic nematodes cause severe damage and yield loss in major crops all over the world. Available control strategies include use of insecticides/nematicides but these have proved detrimental to the environment, while other strategies like crop rotation and resistant cultivars have serious limitations. This scenario provides an opportunity for the utilization of technological advances like RNA interference (RNAi to engineer resistance against these devastating parasites. First demonstrated in the model free living nematode, Caenorhabtidis elegans; the phenomenon of RNAi has been successfully used to suppress essential genes of plant parasitic nematodes involved in parasitism, nematode development and mRNA metabolism. Synthetic neurotransmitants mixed with dsRNA solutions are used for in vitro RNAi in plant parasitic nematodes with significant success. However, host delivered in planta RNAi has proved to be a pioneering phenomenon to deliver dsRNAs to feeding nematodes and silence the target genes to achieve resistance. Highly enriched genomic databases are exploited to limit off target effects and ensure sequence specific silencing. Technological advances like gene stacking and use of nematode inducible and tissue specific promoters can further enhance the utility of RNAi based transgenics against plant parasitic nematodes.

  1. Crack propagation and fracture in silicon carbide

    International Nuclear Information System (INIS)

    Evans, A.G.; Lange, F.F.

    1975-01-01

    Fracture mechanics and strength studies performed on two silicon carbides - a hot-pressed material (with alumina) and a sintered material (with boron) - have shown that both materials exhibit slow crack growth at room temperature in water, but only the hot-pressed material exhibits significant high temperature slow crack growth (1000 to 1400 0 C). A good correlation of the observed fracture behaviour with the crack growth predicted from the fracture mechanics parameters shows that effective failure predictions for this material can be achieved using macro-fracture mechanics data. (author)

  2. Minimizing hydride cracking in zirconium alloys

    International Nuclear Information System (INIS)

    Coleman, C.E.; Cheadle, B.A.; Ambler, J.F.R.; Eadie, R.L.

    1985-01-01

    Zirconium alloy components can fail by hydride cracking if they contain large flaws and are highly stressed. If cracking in such components is suspected, crack growth can be minimized by following two simple operating rules: components should be heated up from at least 30K below any operating temperature above 450K, and when the component requires cooling to room temperature from a high temperature, any tensile stress should be reduced as much and as quickly as is practical during cooling. This paper describes the physical basis for these rules

  3. Signal processing for underclad crack sizing

    International Nuclear Information System (INIS)

    Shankar, R.; Lane, S.S.; Paradiso, T.J.; Quinn, J.R.

    1985-01-01

    The techniques developed in this work provide a means of sizing underclad cracks and quality control methods for assessing the accuracy of the data. Data were collected with a minicomputer (LSI 11-02), a transient recorder (Biomaton 8100) and anti-aliasing filter. Three techniques were developed: the calibration curve, phase velocity and epicentral. The phase reversal characteristic in the data is a strong indication of the nature of the signal source. That is, cracks are clearly seperable from two isolated inclusions on the basis of observed phase reversal. These methods have been implemented on a computer and appear to provide an accurate rapid method to discriminate and size underclad cracks

  4. Stress corrosion crack growth in unirradiated zircaloy

    International Nuclear Information System (INIS)

    Pettersson, K.

    1978-10-01

    Experimental techniques suitable for the determination of stress corrosion crack growth rates in irradiated Zircaloy tube have been developed. The techniques have been tested on unirradiated. Zircaloy and it was found that the results were in good agreement with the results of other investigations. Some of the results were obtained at very low stress intensities and the crack growth rates observed, gave no indication of the existance of a K sub(ISCC) for iodine induced stress corrosion cracking in Zircaloy. This is of importance both for fuel rod behavior after a power ramp and for long term storage of spent Zircaloy-clad fuel. (author)

  5. Fatigue cracking on a steam generator tube

    International Nuclear Information System (INIS)

    Boccanfuso, M.; Lothios, J.; Thebault, Y.; Bruyere, B.; Duisabeau, L.; Herms, E.

    2015-01-01

    A circumferential fatigue crack was observed on a steam generator tube of the unit 2 of the Fessenheim plant. The results of destructive testing and the examination of the fracture surface show that the circumferential crack is linked to a large number of cycles with a very low stress intensity factor. Other aggravating factors like inter-granular corrosion have played a role in the initiating phase of fatigue cracking. The damage has been exacerbated by the lack of support of the tube at the level of the anti-vibration bars. (A.C.)

  6. Process and apparatus for cracking petroleum, etc

    Energy Technology Data Exchange (ETDEWEB)

    1931-04-25

    Process for catalytic cracking of petroleum and similar material at normal pressure, characterized by the oil vaporized in a vaporizer being treated in a first catalyst-chamber and in a separator attached to it, light constituents being separated, and then its being run into a second apparatus-group (vaporizer, catalyst-chamber, and separator), further groups following in series, whereby the catalyst works in a separate catalyst apparatus with ever-increasing activity time on the always lesser but always more difficult to crack material, so that in the whole apparatus a methodical cracking process is effected.

  7. Cause of Damage. Hot cracking; Schadensursache Heissrissigkeit

    Energy Technology Data Exchange (ETDEWEB)

    Wader, Therese [BENTELER Steel/Tube GmbH, Paderborn (Germany). Vorentwicklung Werkstoffe

    2016-10-15

    Under certain conditions, Nb-containing stainless steels are susceptible to hot cracking. Such conditions include low melting phases on the grain boundaries, a coarse-grained microstructure such as cast structures, microstructure orientations towards the main tensile direction and high processing temperatures. The case of damage was characterized using metallographic and microanalytical methods. In the laboratory, the critical temperature range for the formation of hot cracks could furthermore specifically be localized under mechanical stresses by means of a dilatometer aiming at clearly verifying the cause of the damage, namely ''hot cracks''.

  8. Eddy current standards - Cracks versus notches

    Science.gov (United States)

    Hagemaier, D. J.; Collingwood, M. R.; Nguyen, K. H.

    1992-10-01

    Eddy current tests aimed at evaluating cracks and electron-discharge machined (EDM) notches in 7075-T6 aluminum specimens are described. A comparison of the shape and amplitude of recordings made from both transverse and longitudinal scans of small EDM notches and fatigue cracks showd almost identical results. The signal amplitude and phase angle increased with an increase of EDM notch and crak size. It is concluded that equivalent eddy current results obtained from similar-size surface cracks and notches in aluminum can be used to establish a desired sensitivity level for inspection.

  9. Crack Growth Properties of Sealing Glasses

    Science.gov (United States)

    Salem, Jonathan A.; Tandon, R.

    2008-01-01

    The crack growth properties of several sealing glasses were measured using constant stress rate testing in 2% and 95% RH (relative humidity). Crack growth parameters measured in high humidity are systematically smaller (n and B) than those measured in low humidity, and velocities for dry environments are approx. 100x lower than for wet environments. The crack velocity is very sensitivity to small changes in RH at low RH. Confidence intervals on parameters that were estimated from propagation of errors were comparable to those from Monte Carlo simulation.

  10. TEM observations of crack tip: cavity interactions

    International Nuclear Information System (INIS)

    Horton, J.A.; Ohr, S.M.; Jesser, W.A.

    1981-01-01

    Crack tip-cavity interactions have been studied by performing room temperature deformation experiments in a transmission electron microscope on ion-irradiated type 316 stainless steel with small helium containing cavities. Slip dislocations emitted from a crack tip cut, sheared, and thereby elongated cavities without a volume enlargement. As the crack tip approached, a cavity volume enlargement occurred. Instead of the cavities continuing to enlarge until they touch, the walls between the cavities fractured. Fracture surface dimples do not correlate in size or density with these enlarged cavities

  11. Prospective identification of malaria parasite genes under balancing selection.

    Directory of Open Access Journals (Sweden)

    Kevin K A Tetteh

    Full Text Available Endemic human pathogens are subject to strong immune selection, and interrogation of pathogen genome variation for signatures of balancing selection can identify important target antigens. Several major antigen genes in the malaria parasite Plasmodium falciparum have shown such signatures in polymorphism-versus-divergence indices (comparing with the chimpanzee parasite P. reichenowi, and in allele frequency based indices.To compare methods for prospective identification of genes under balancing selection, 26 additional genes known or predicted to encode surface-exposed proteins of the invasive blood stage merozoite were first sequenced from a panel of 14 independent P. falciparum cultured lines and P. reichenowi. Six genes at the positive extremes of one or both of the Hudson-Kreitman-Aguade (HKA and McDonald-Kreitman (MK indices were identified. Allele frequency based analysis was then performed on a Gambian P. falciparum population sample for these six genes and three others as controls. Tajima's D (TjD index was most highly positive for the msp3/6-like PF10_0348 (TjD = 1.96 as well as the positive control ama1 antigen gene (TjD = 1.22. Across the genes there was a strong correlation between population TjD values and the relative HKA indices (whether derived from the population or the panel of cultured laboratory isolates, but no correlation with the MK indices.Although few individual parasite genes show significant evidence of balancing selection, analysis of population genomic and comparative sequence data with the HKA and TjD indices should discriminate those that do, and thereby identify likely targets of immunity.

  12. Protease-associated cellular networks in malaria parasite Plasmodium falciparum

    Directory of Open Access Journals (Sweden)

    Lilburn Timothy G

    2011-12-01

    Full Text Available Abstract Background Malaria continues to be one of the most severe global infectious diseases, responsible for 1-2 million deaths yearly. The rapid evolution and spread of drug resistance in parasites has led to an urgent need for the development of novel antimalarial targets. Proteases are a group of enzymes that play essential roles in parasite growth and invasion. The possibility of designing specific inhibitors for proteases makes them promising drug targets. Previously, combining a comparative genomics approach and a machine learning approach, we identified the complement of proteases (degradome in the malaria parasite Plasmodium falciparum and its sibling species 123, providing a catalog of targets for functional characterization and rational inhibitor design. Network analysis represents another route to revealing the role of proteins in the biology of parasites and we use this approach here to expand our understanding of the systems involving the proteases of P. falciparum. Results We investigated the roles of proteases in the parasite life cycle by constructing a network using protein-protein association data from the STRING database 4, and analyzing these data, in conjunction with the data from protein-protein interaction assays using the yeast 2-hybrid (Y2H system 5, blood stage microarray experiments 678, proteomics 9101112, literature text mining, and sequence homology analysis. Seventy-seven (77 out of 124 predicted proteases were associated with at least one other protein, constituting 2,431 protein-protein interactions (PPIs. These proteases appear to play diverse roles in metabolism, cell cycle regulation, invasion and infection. Their degrees of connectivity (i.e., connections to other proteins, range from one to 143. The largest protease-associated sub-network is the ubiquitin-proteasome system which is crucial for protein recycling and stress response. Proteases are also implicated in heat shock response, signal peptide

  13. The initiation of environmentally-assisted cracking in semi-elliptical surface cracks

    International Nuclear Information System (INIS)

    James, L.A.

    1997-01-01

    A criterion to predict under what conditions EAC would Initiate In cracks In a high-sulfur steel in contact with low-oxygen water was recently proposed by Wire and U. This EAC Initiation Criterion was developed using transient analyses for the diffusion of sulfides plus experimental test results. The experiments were conducted mainly on compact tension-type specimens with initial crack depths of about 2.54 mm. The present paper expands upon the work of Wire and U by presenting results for significantly deeper initial semi-elliptical surface cracks. In addition, in one specimen, the surface crack penetrated weld-deposited cladding into the high-sulfur steel. The results for the semi-elliptical surface cracks agreed quite well with the EAC Initiation Criterion, and provide confirmation of the applicability of the criterion to crack configurations with more restricted access to water

  14. Genome Imprinting

    Indian Academy of Sciences (India)

    the cell nucleus (mitochondrial and chloroplast genomes), and. (3) traits governed ... tively good embryonic development but very poor development of membranes and ... Human homologies for the type of situation described above are naturally ..... imprint; (b) New modifications of the paternal genome in germ cells of each ...

  15. Baculovirus Genomics

    NARCIS (Netherlands)

    Oers, van M.M.; Vlak, J.M.

    2007-01-01

    Baculovirus genomes are covalently closed circles of double stranded-DNA varying in size between 80 and 180 kilobase-pair. The genomes of more than fourty-one baculoviruses have been sequenced to date. The majority of these (37) are pathogenic to lepidopteran hosts; three infect sawflies

  16. Genomic Testing

    Science.gov (United States)

    ... this database. Top of Page Evaluation of Genomic Applications in Practice and Prevention (EGAPP™) In 2004, the Centers for Disease Control and Prevention launched the EGAPP initiative to establish and test a ... and other applications of genomic technology that are in transition from ...

  17. Ancient genomes

    OpenAIRE

    Hoelzel, A Rus

    2005-01-01

    Ever since its invention, the polymerase chain reaction has been the method of choice for work with ancient DNA. In an application of modern genomic methods to material from the Pleistocene, a recent study has instead undertaken to clone and sequence a portion of the ancient genome of the cave bear.

  18. Application of small RNA technology for improved control of parasitic helminths.

    Science.gov (United States)

    Britton, Collette; Winter, Alan D; Marks, Neil D; Gu, Henry; McNeilly, Tom N; Gillan, Victoria; Devaney, Eileen

    2015-08-15

    Over the last decade microRNAs (miRNAs) and small interfering RNAs (siRNAs) have emerged as important regulators of post-transcriptional gene expression. miRNAs are short, non-coding RNAs that regulate a variety of processes including cancer, organ development and immune function. This class of small RNAs bind with partial complementarity to their target mRNA sequences, most often in the 3'UTR, to negatively regulate gene expression. In parasitic helminths, miRNAs are being increasingly studied for their potential roles in development and host-parasite interactions. The availability of genome data, combined with small RNA sequencing, has paved the way to profile miRNAs expressed at particular developmental stages for many parasitic helminths. While some miRNAs are conserved across species, others appear to be unique to specific parasites, suggesting important roles in adaptation and survival in the host environment. Some miRNAs are released from parasites, in exosomes or in protein complexes, and the potential effects of these on host immune function are being increasingly studied. In addition, release of miRNAs from schistosome and filarial parasites into host plasma can be exploited for the development of specific and sensitive diagnostic biomarkers of infection. Interfering with miRNA function, as well as silencing key components of the pathways they regulate, will progress our understanding of parasite development and provide a novel approach to therapeutic control. RNA interference (RNAi) by siRNAs has proven to be inconsistent in parasitic nematodes. However, the recent successes reported for schistosome and liver fluke RNAi, encourage further efforts to enhance delivery of RNA and improve in vitro culture systems and assays to monitor phenotypic effects in nematodes. These improvements are important for the establishment of reliable functional genomic platforms for novel drug and vaccine development. In this review we focus on the important roles of mi

  19. Fatigue cracks in Eurofer 97 steel: Part II. Comparison of small and long fatigue crack growth

    Czech Academy of Sciences Publication Activity Database

    Kruml, Tomáš; Hutař, Pavel; Náhlík, Luboš; Seitl, Stanislav; Polák, Jaroslav

    2011-01-01

    Roč. 412, 1 (2011), s. 7-12 ISSN 0022-3115 R&D Projects: GA ČR GA106/09/1954; GA ČR GA101/09/0867 Institutional research plan: CEZ:AV0Z20410507 Keywords : ferritic-martensitic steel * long crack growth * small crack growth * crack closure Subject RIV: JL - Materials Fatigue, Friction Mechanics Impact factor: 2.052, year: 2011

  20. Cracking the code of change.

    Science.gov (United States)

    Beer, M; Nohria, N

    2000-01-01

    Today's fast-paced economy demands that businesses change or die. But few companies manage corporate transformations as well as they would like. The brutal fact is that about 70% of all change initiatives fail. In this article, authors Michael Beer and Nitin Nohria describe two archetypes--or theories--of corporate transformation that may help executives crack the code of change. Theory E is change based on economic value: shareholder value is the only legitimate measure of success, and change often involves heavy use of economic incentives, layoffs, downsizing, and restructuring. Theory O is change based on organizational capability: the goal is to build and strengthen corporate culture. Most companies focus purely on one theory or the other, or haphazardly use a mix of both, the authors say. Combining E and O is directionally correct, they contend, but it requires a careful, conscious integration plan. Beer and Nohria present the examples of two companies, Scott Paper and Champion International, that used a purely E or purely O strategy to create change--and met with limited levels of success. They contrast those corporate transformations with that of UK-based retailer ASDA, which has successfully embraced the paradox between the opposing theories of change and integrated E and O. The lesson from ASDA? To thrive and adapt in the new economy, companies must make sure the E and O theories of business change are in sync at their own organizations.

  1. Crack imaging by pulsed laser spot thermography

    International Nuclear Information System (INIS)

    Li, T; Almond, D P; Rees, D A S; Weekes, B

    2010-01-01

    A surface crack close to a spot heated by a laser beam impedes lateral heat flow and produces alterations to the shape of the thermal image of the spot that can be monitored by thermography. A full 3D simulation has been developed to simulate heat flow from a laser heated spot in the proximity of a crack. The modelling provided an understanding of the ways that different parameters affect the thermal images of laser heated spots. It also assisted in the development of an efficient image processing strategy for extracting the scanned cracks. Experimental results show that scanning pulsed laser spot thermography has considerable potential as a remote, non-contact crack imaging technique.

  2. Cracking Advanced Encryption Standard-A Review

    Directory of Open Access Journals (Sweden)

    Jashnil Kumar

    2017-07-01

    Full Text Available Password protection is a major security concern the world is facing today. While there are many publications available that discuss ways to protect passwords and data how widely user from around the world adhere to these rules are unknown. The novelty of this study is that this is the first time a review is done on software tools that can be used to crack Advanced Encryption Standards. Firstly the study does a review on top 10 software tools that are available to crack Advanced Encryption Standards. After which an analysis on two software tools was performed to see how long each software tool took to crack a password. The result of the study gives Advanced Encryption Standard researcher Network security researcher and the general public helpful information on how to strengthen advanced encryption standards and strengthen passwords that are hard for the software tools discussed above to crack.

  3. Photoelastic Analysis of Cracked Thick Walled Cylinders

    Science.gov (United States)

    Pastramă, Ştefan Dan

    2017-12-01

    In this paper, the experimental determination of the stress intensity factor in thick walled cylinders subject to uniform internal pressure and having longitudinal non-penetrating cracks is presented. Photoelastic measurements were used together with the expressions of the stress field near the crack tip for Mode I crack extension and a specific methodology for stress intensity factor determination. Two types of longitudinal cracks - internal and external - were considered. Four plane models were manufactured and analyzed in a plane polariscope at different values of the applied internal pressure. The values of the normalized stress intensity factor were calculated and the results were compared to those reported by other authors. A good accuracy was noticed, showing the reliability of the experimental procedure.

  4. Internal shear cracking in bulk metal forming

    DEFF Research Database (Denmark)

    Christiansen, Peter; Nielsen, Chris Valentin; Bay, Niels Oluf

    2017-01-01

    This paper presents an uncoupled ductile damage criterion for modelling the opening and propagation of internal shear cracks in bulk metal forming. The criterion is built upon the original work on the motion of a hole subjected to shear with superimposed tensile stress triaxiality and its overall...... performance is evaluated by means of side-pressing formability tests in Aluminium AA2007-T6 subjected to different levels of pre-strain. Results show that the new proposed criterionis able to combine simplicity with efficiency for predicting the onset of fracture and the crack propagation path for the entire...... cracking to internal cracks formed undert hree-dimensional states of stress that are typical of bulk metal forming....

  5. Purifying oils, cracking oils, catalysts. [British Patent

    Energy Technology Data Exchange (ETDEWEB)

    1936-02-05

    Hydrocarbon oils are refined by treating while substantially in the liquid phase between 200/sup 0/ and 400/sup 0/C with a phosphoric acid catalyst deposited on metallurgical coke, a suitable blast furnace slag, silica gel or other carrier with similar properties, until the objectionable components are converted into innocuous substances by polymerization cracking, isomerization and/or alkylation. By this treatment the bromine number is reduced, the end-point of the A.S.T.M. distillation is increased, the octane number is raised, mercaptans are converted to hydrogen sulphide and olefines, thioethers and thiophenes are converted to mereaptans, and the initial boiling point is lowered. The process is applicable to gasoline, cracked distillate, kerosine and lubricating oil, obtained by distilling or cracking petroleum, shale and hydrogenated oils; and is particularly applicable for stabilizing cracked distillates.

  6. Crack identification by artificial neural network

    Energy Technology Data Exchange (ETDEWEB)

    Hwu, C.B.; Liang, Y.C. [National Cheng Kung Univ., Tainan (Taiwan, Province of China). Inst. of Aeronaut. and Astronaut.

    1998-04-01

    In this paper, a most popular artificial neural network called the back propagation neural network (BPN) is employed to achieve an ideal on-line identification of the crack embedded in a composite plate. Different from the usual dynamic estimate, the parameters used for the present crack identification are the strains of static deformation. It is known that the crack effects are localized which may not be clearly reflected from the boundary information especially when the data is from static deformation only. To remedy this, we use data from multiple-loading modes in which the loading modes may include the opening, shearing and tearing modes. The results show that our method for crack identification is always stable and accurate no matter how far-away of the test data from its training set. (orig.) 8 refs.

  7. Distinct genomic architecture of Plasmodium falciparum populations from South Asia.

    Science.gov (United States)

    Kumar, Shiva; Mudeppa, Devaraja G; Sharma, Ambika; Mascarenhas, Anjali; Dash, Rashmi; Pereira, Ligia; Shaik, Riaz Basha; Maki, Jennifer N; White, John; Zuo, Wenyun; Tuljapurkar, Shripad; Duraisingh, Manoj T; Gomes, Edwin; Chery, Laura; Rathod, Pradipsinh K

    Previous whole genome comparisons of Plasmodium falciparum populations have not included collections from the Indian subcontinent, even though two million Indians contract malaria and about 50,000 die from the disease every year. Stratification of global parasites has revealed spatial relatedness of parasite genotypes on different continents. Here, genomic analysis was further improved to obtain country-level resolution by removing var genes and intergenic regions from distance calculations. P. falciparum genomes from India were found to be most closely related to each other. Their nearest neighbors were from Bangladesh and Myanmar, followed by Thailand. Samples from the rest of Southeast Asia, Africa and South America were increasingly more distant, demonstrating a high-resolution genomic-geographic continuum. Such genome stratification approaches will help monitor variations of malaria parasites within South Asia and future changes in parasite populations that may arise from in-country and cross-border migrations. Copyright © 2016 The Author(s). Published by Elsevier B.V. All rights reserved.

  8. WormBase 2016: expanding to enable helminth genomic research.

    Science.gov (United States)

    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

    2016-01-04

    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. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  9. Fatigue crack growth retardation in spot heated mild steel sheet

    Indian Academy of Sciences (India)

    A fatigue crack can be effectively retarded by heating a spot near the crack tip under nil remote stress condition. The subcritical spot heating at a proper position modifies the crack growth behaviour in a way, more or less, similar to specimen subjected to overload spike. It is observed that the extent of crack growth retardation ...

  10. Investigation of the fatigue crack opening under low cyclic loading

    International Nuclear Information System (INIS)

    Daunys, M.; Taraskevicius, A.

    2003-01-01

    Low cycle loading crack opening under various load levels were investigated. Analytical method of the fatigue crack opening investigation was described using relations of crack surface displacements. Calculated results of the crack surface displacement were compared with the experimental results. (author)

  11. A numerical study of non-linear crack tip parameters

    Directory of Open Access Journals (Sweden)

    F.V. Antunes

    2015-07-01

    Full Text Available Crack closure concept has been widely used to explain different issues of fatigue crack propagation. However, different authors have questioned the relevance of crack closure and have proposed alternative concepts. The main objective here is to check the effectiveness of crack closure concept by linking the contact of crack flanks with non-linear crack tip parameters. Accordingly, 3D-FE numerical models with and without contact were developed for a wide range of loading scenarios and the crack tip parameters usually linked to fatigue crack growth, namely range of cyclic plastic strain, crack tip opening displacement, size of reversed plastic zone and total plastic dissipation per cycle, were investigated. It was demonstrated that: i LEFM concepts are applicable to the problem under study; ii the crack closure phenomenon has a great influence on crack tip parameters decreasing their values; iii the Keff concept is able to explain the variations of crack tip parameters produced by the contact of crack flanks; iv the analysis of remote compliance is the best numerical parameter to quantify the crack opening level; v without contact there is no effect of stress ratio on crack tip parameters. Therefore it is proved that the crack closure concept is valid.

  12. Analysis of cracking in glass molds made of cast iron

    Science.gov (United States)

    Leushin, I. O.; Chistyakov, D. G.

    2014-09-01

    The cracking in the parts of cast iron molds intended for glass is considered, and this cracking substantially affects the operation of glass-blowing equipment, maintainability, and the replacement of mold sets. The processes that cause cracking in the parts of glass molds and initiate crack growth are studied.

  13. Hydride effect on crack instability of Zircaloy cladding

    Energy Technology Data Exchange (ETDEWEB)

    Tseng, Che-Chung, E-mail: cctseng@iner.gov.tw [Institute of Nuclear Energy Research, No. 1000, Wunhua Road, Jiaan Village, Lungtan, Township, Taoyuan County 32546, Taiwan (China); Sun, Ming-Hung [Institute of Nuclear Energy Research, No. 1000, Wunhua Road, Jiaan Village, Lungtan, Township, Taoyuan County 32546, Taiwan (China); Chao, Ching-Kong [Department of Mechanical Engineering, National Taiwan University of Science and Technology, 43 Keelung Road, Section 4, Taipei 106, Taiwan (China)

    2014-04-01

    Highlights: • Radial hydrides near the crack tip had a significant effect on crack propagation. • For radial hydrides off the crack line vertically, the effect on crack propagation was notably reduced. • The longer hydride platelet resulted in a remarkable effect on crack propagation. • A long split in the radial hydride precipitate would enhance crack propagation. • The presence of circumferential hydride among radial hydrides may play an important role in crack propagation. - Abstract: A methodology was proposed to investigate the effect of hydride on the crack propagation in fuel cladding. The analysis was modeled based on an outside-in crack with radial hydrides located near its crack tip. The finite element method was used in the calculation; both stress intensity factor K{sub I} and J integral were applied to evaluate the crack stability. The parameters employed in the analysis included the location of radial hydride, hydride dimensions, number of hydrides, and the presence of circumferential hydride, etc. According to our study, the effective distance between a radial hydride and the assumed cladding surface crack for the enhancement of crack propagation proved to be no greater than 0.06 mm. For a hydride not on the crack line, it would induce a relatively minor effect on crack propagation if the vertical distance was beyond 0.05 mm. However, a longer hydride precipitate as well as double radial hydrides could have a remarkable effect on crack propagation. A combined effect of radial and circumferential hydrides was also discussed.

  14. Fatigue crack threshold relevant to stress ratio, crack wake and loading histories

    International Nuclear Information System (INIS)

    Okazaki, Masakazu; Iwasaki, Akira; Kasahara, Naoto

    2013-01-01

    Fatigue crack propagation behavior was investigated in a low alloy steel which experienced several kind of loading histories. Both the effects of stress ratio, test temperature on the fatigue crack threshold, and the change in the threshold depending on the thermo-mechanical loading histories, were experimentally investigated. It was shown that the thermo-mechanical loading history left its effect along the prior fatigue crack wake resulting in the change of fatigue crack threshold. Some discussions are made on how this type of loading history effect should be treated from engineering point of view. (author)

  15. On the transition of short cracks into long fatigue cracks in reactor pressure vessel steels

    Directory of Open Access Journals (Sweden)

    Singh Rajwinder

    2018-01-01

    Full Text Available Short fatigue cracks, having dimension less than 1 mm, propagate at much faster rates (da/dN even at lower stress intensity factor range (da/dN as compared to the threshold stress intensity factor range obtained from long fatigue crack growth studies. These short cracks originate at the sub-grain level and some of them ultimately transit into critical long cracks over time. Therefore, designing the components subjected to fatigue loading merely on the long crack growth data and neglecting the short crack growth behavior can overestimate the component’s life. This aspect of short fatigue cracks become even more critical for materials used for safety critical applications such as reactor pressure vessel (RPV steel in nuclear plants. In this work, the transition behaviour of short fatigue crack gowth into long fatigue crack is studied in SA508 Grade 3 Class I low alloy steel used in RPVs. In-situ characterization of initiation, propagation and transition of short fatigue cracks is performed using fatigue stage for Scanning Electron Microscope (SEM in addition to digital microscopes fitted over a servo-hydraulic fatigue machine and correlated with the microtructural information obtained using electron backscatter diffraction (EBSD. SA508 steel having an upper bainitic microstructure have several microstructural interfaces such as phase and grain boundaries that play a significant role in controlling the short fatigue crack propagation. Specially designed and prepared short fatigue specimens (eletro-polished with varying initial crack lengths of the order of tens of microns are used in this study. The transition of such short initial cracks into long cracks is then tracked to give detailed insight into the role of each phase and phase/grain boundary with an objective of establishing Kitagawa-Takahashi diagram for the given RPV steel. The behavior of the transited long cracks is then compared with the crack propagation behavior obtained using

  16. Probabilistic fracture mechanics of nuclear structural components: consideration of transition from embedded crack to surface crack

    International Nuclear Information System (INIS)

    Yagawa, G.; Yoshimura, S.

    1999-01-01

    This paper describes a probabilistic fracture mechanics (PFM) analysis of aged nuclear reactor pressure vessel (RPV) material. New interpolation formulas of three-dimensional stress intensity factors are presented for both embedded elliptical surface cracks and semi-elliptical surface cracks. To investigate effects of transition from embedded crack to surface crack in PFM analyses, one of the PFM round-robin problems set by JSME-RC111 committee (i.e. aged RPV under normal and upset operating conditions) is solved, employing the interpolation formulas. (orig.)

  17. Terahertz non-destructive imaging of cracks and cracking in structures of cement-based materials

    Directory of Open Access Journals (Sweden)

    Shujie Fan

    2017-11-01

    Full Text Available Cracks and crack propagation in cement-based materials are key factors leading to failure of structures, affecting safety in construction engineering. This work investigated the application of terahertz (THz non-destructive imaging to inspections on structures of cement-based materials, so as to explore the potential of THz imaging in crack detection. Two kinds of disk specimens made of plain cement mortar and UHMWPE fiber concrete were prepared respectively. A mechanical expansion load device was deployed to generate cracks and control the whole process of cracking. Experimental tests were carried out on cracked specimens by using a commercial THz time domain spectroscopy (THz-TDS during loading. The results show that crack opening and propagation could be examined by THz clearly and the material factors influence the ability of crack resistance significantly. It was found that the THz imaging of crack initiation and propagation agrees with the practical phenomenon and supplies more information about damage of samples. It is demonstrated that the damage behavior of structures of cement-based materials can be successfully detected by THz imaging.

  18. Terahertz non-destructive imaging of cracks and cracking in structures of cement-based materials

    Science.gov (United States)

    Fan, Shujie; Li, Tongchun; Zhou, Jun; Liu, Xiaoqing; Liu, Xiaoming; Qi, Huijun; Mu, Zhiyong

    2017-11-01

    Cracks and crack propagation in cement-based materials are key factors leading to failure of structures, affecting safety in construction engineering. This work investigated the application of terahertz (THz) non-destructive imaging to inspections on structures of cement-based materials, so as to explore the potential of THz imaging in crack detection. Two kinds of disk specimens made of plain cement mortar and UHMWPE fiber concrete were prepared respectively. A mechanical expansion load device was deployed to generate cracks and control the whole process of cracking. Experimental tests were carried out on cracked specimens by using a commercial THz time domain spectroscopy (THz-TDS) during loading. The results show that crack opening and propagation could be examined by THz clearly and the material factors influence the ability of crack resistance significantly. It was found that the THz imaging of crack initiation and propagation agrees with the practical phenomenon and supplies more information about damage of samples. It is demonstrated that the damage behavior of structures of cement-based materials can be successfully detected by THz imaging.

  19. A probabilistic approach to crack instability

    Science.gov (United States)

    Chudnovsky, A.; Kunin, B.

    1989-01-01

    A probabilistic model of brittle fracture is examined with reference to two-dimensional problems. The model is illustrated by using experimental data obtained for 25 macroscopically identical specimens made of short-fiber-reinforced composites. It is shown that the model proposed here provides a predictive formalism for the probability distributions of critical crack depth, critical loads, and crack arrest depths. It also provides similarity criteria for small-scale testing.

  20. Radioactive tracers and the cracking modelings

    International Nuclear Information System (INIS)

    Bettens, B.

    1982-01-01

    The use of tracers (3H and 14 C) labelled in specific positions is an intensive contribution to the understanding and the revealing of the very often complex cracking modeling. The pyrolytic decay of the phenol and the cresols, of the aniline, of the phenantrene and its hydrogenated derived products were investigated and are presented as examples. The decay mechanisms give a theoretical knowledge of the thermal cracking and allow to handle the results on an industrial scale. (AF)