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Sample records for climate-development gordian knot

  1. Feedback in clinical education: untying the Gordian knot.

    PubMed

    Weinstein, Debra F

    2015-05-01

    Feedback is essential to clinical education, especially in the era of competencies, milestones, and entrustable professional activities. It is, however, an area where medical educators often fall short. Although educational leaders and faculty supervisors provide feedback in a variety of clinical settings, surveys show important gaps in medical student and resident satisfaction with the feedback received, suggesting lost opportunities to identify performance problems as well as to help each learner reach his or her greatest potential.In this issue of Academic Medicine, Telio and colleagues extend the empirically validated concept of a "therapeutic alliance" to propose the "educational alliance" as a framework for enhancing feedback in medical education. They highlight the importance of source credibility, which depends on the teacher-learner relationship and alignment of values, the teacher's understanding of the learner's role and goals, the teacher's direct observation of the learner, and the learner's perception of the teacher's good intentions. The author of this Commentary suggests that the educational alliance framework should prompt medical educators to reconsider feedback and explore opportunities for optimizing it. Most medical schools and graduate medical education programs are not designed in a way that supports the education alliance model, but the Commentary author offers suggestions for cultivating educational alliances, including rethinking supervisor selection criteria. Such interventions should be combined with ongoing faculty development and efforts to improve coaching and mentoring for students, residents, and fellows. Untying the Gordian knot of effective feedback will require innovative approaches, exchange of successful strategies, and continued research.

  2. Hemoglobinopathies: Slicing the Gordian Knot of Plasmodium falciparum Malaria Pathogenesis

    PubMed Central

    Taylor, Steve M.; Cerami, Carla; Fairhurst, Rick M.

    2013-01-01

    Plasmodium falciparum malaria kills over 500,000 children every year and has been a scourge of humans for millennia. Owing to the co-evolution of humans and P. falciparum parasites, the human genome is imprinted with polymorphisms that not only confer innate resistance to falciparum malaria, but also cause hemoglobinopathies. These genetic traits—including hemoglobin S (HbS), hemoglobin C (HbC), and α-thalassemia—are the most common monogenic human disorders and can confer remarkable degrees of protection from severe, life-threatening falciparum malaria in African children: the risk is reduced 70% by homozygous HbC and 90% by heterozygous HbS (sickle-cell trait). Importantly, this protection is principally present for severe disease and largely absent for P. falciparum infection, suggesting that these hemoglobinopathies specifically neutralize the parasite's in vivo mechanisms of pathogenesis. These hemoglobin variants thus represent a “natural experiment” to identify the cellular and molecular mechanisms by which P. falciparum produces clinical morbidity, which remain partially obscured due to the complexity of interactions between this parasite and its human host. Multiple lines of evidence support a restriction of parasite growth by various hemoglobinopathies, and recent data suggest this phenomenon may result from host microRNA interference with parasite metabolism. Multiple hemoglobinopathies mitigate the pathogenic potential of parasites by interfering with the export of P. falciparum erythrocyte membrane protein 1 (PfEMP1) to the surface of the host red blood cell. Few studies have investigated their effects upon the activation of the innate and adaptive immune systems, although recent murine studies suggest a role for heme oxygenase-1 in protection. Ultimately, the identification of mechanisms of protection and pathogenesis can inform future therapeutics and preventive measures. Hemoglobinopathies slice the “Gordian knot” of host and parasite

  3. Animal abolitionism meets moral abolitionism : cutting the Gordian knot of applied ethics.

    PubMed

    Marks, Joel

    2013-12-01

    The use of other animals for human purposes is as contentious an issue as one is likely to find in ethics. And this is so not only because there are both passionate defenders and opponents of such use, but also because even among the latter there are adamant and diametric differences about the bases of their opposition. In both disputes, the approach taken tends to be that of applied ethics, by which a position on the issue is derived from a fundamental moral commitment. This commitment in turn depends on normative ethics, which investigates the various moral theories for the best fit to our moral intuitions. Thus it is that the use of animals in biomedical research is typically defended by appeal to a utilitarian theory, which legitimates harm to some for the greater good of others; while the opposition condemns that use either by appeal to the same theory, but disagreeing about the actual efficacy of animal experimentation, or by appeal to an alternative theory, such as the right of all sentient beings not to be exploited. Unfortunately, the normative issue seems likely never to be resolved, hence leaving the applied issue in limbo. The present essay seeks to circumvent this impasse by dispensing altogether with any moral claim or argument, thereby cutting the Gordian knot of animal ethics with a meta-ethical sword. The alternative schema defended is simply to advance relevant considerations, whereupon "there is nothing left but to feel." In a word, motivation replaces justification. PMID:24092403

  4. Animal abolitionism meets moral abolitionism : cutting the Gordian knot of applied ethics.

    PubMed

    Marks, Joel

    2013-12-01

    The use of other animals for human purposes is as contentious an issue as one is likely to find in ethics. And this is so not only because there are both passionate defenders and opponents of such use, but also because even among the latter there are adamant and diametric differences about the bases of their opposition. In both disputes, the approach taken tends to be that of applied ethics, by which a position on the issue is derived from a fundamental moral commitment. This commitment in turn depends on normative ethics, which investigates the various moral theories for the best fit to our moral intuitions. Thus it is that the use of animals in biomedical research is typically defended by appeal to a utilitarian theory, which legitimates harm to some for the greater good of others; while the opposition condemns that use either by appeal to the same theory, but disagreeing about the actual efficacy of animal experimentation, or by appeal to an alternative theory, such as the right of all sentient beings not to be exploited. Unfortunately, the normative issue seems likely never to be resolved, hence leaving the applied issue in limbo. The present essay seeks to circumvent this impasse by dispensing altogether with any moral claim or argument, thereby cutting the Gordian knot of animal ethics with a meta-ethical sword. The alternative schema defended is simply to advance relevant considerations, whereupon "there is nothing left but to feel." In a word, motivation replaces justification.

  5. Unravelling the Gordian knot! Key processes impacting overwintering larval survival and growth: A North Sea herring case study

    NASA Astrophysics Data System (ADS)

    Hufnagl, Marc; Peck, Myron A.; Nash, Richard D. M.; Dickey-Collas, Mark

    2015-11-01

    factors can form a Gordian knot of marine fish recruitment processes. We highlight gaps in process knowledge and recommend specific field, laboratory and modelling studies which, in our opinion, are most likely to unravel the dominant processes and advance predictive capacity of the environmental regulation of recruitment in autumn and winter-spawned fishes in temperate areas such as herring in the North Sea.

  6. Chance and time: Cutting the Gordian knot

    NASA Astrophysics Data System (ADS)

    Hagar, Amit

    One of the recurrent problems in the foundations of physics is to explain why we rarely observe certain phenomena that are allowed by our theories and laws. In thermodynamics, for example, the spontaneous approach towards equilibrium is ubiquitous yet the time-reversal-invariant laws that presumably govern thermal behaviour in the microscopic level equally allow spontaneous approach away from equilibrium to occur. Why are the former processes frequently observed while the latter are almost never reported? Another example comes from quantum mechanics where the formalism, if considered complete and universally applicable, predicts the existence of macroscopic superpositions---monstrous Schrodinger cats---and these are never observed: while electrons and atoms enjoy the cloudiness of waves, macroscopic objects are always localized to definite positions. A well-known explanatory framework due to Ludwig Boltzmann traces the rarity of "abnormal" thermodynamic phenomena to the scarcity of the initial conditions that lead to it. After all, physical laws are no more than algorithms and these are expected to generate different results according to different initial conditions, hence Boltzmann's insight that violations of thermodynamic laws are possible but highly improbable. Yet Boltzmann introduces probabilities into this explanatory scheme, and since the latter is couched in terms of classical mechanics, these probabilities must be interpreted as a result of ignorance of the exact state the system is in. Quantum mechanics has taught us otherwise. Here the attempts to explain why we never observe macroscopic superpositions have led to different interpretations of the formalism and to different solutions to the quantum measurement problem. These solutions introduce additional interpretations to the meaning of probability over and above ignorance of the definite state of the physical system: quantum probabilities may result from pure chance. Notwithstanding the success of the Boltzmannian framework in explaining the thermodynamic arrow in time it leaves us with a foundational puzzle: how can ignorance play a role in scientific explanation of objective reality? In turns out that two opposing solutions to the quantum measurement problem in which probabilities arise from the stochastic character of the underlying dynamics may scratch this explanatory itch. By offering a dynamical justification to the probabilities employed in classical statistical mechanics these two interpretations complete the Boltzmannian explanatory scheme and allow us to exorcize ignorance from scientific explanations of unobserved phenomena. In this thesis I argue that the puzzle of the thermodynamic arrow in time is closely related to the problem of interpreting quantum mechanics, i.e., to the measurement problem. We may solve one by fiat and thus solve the other, but it seems unwise to try solving them independently. I substantiate this claim by presenting two possible interpretations to non-relativistic quantum mechanics. Differing as they do on the meaning of the probabilities they introduce into the otherwise deterministic dynamics, these interpretations offer alternative explanatory schemes to the standard Boltzmannian statistical mechanical explanation of thermodynamic approach to equilibrium. I then show how notwithstanding their current empirical equivalence, the two approaches diverge at the continental divide between scientific realism and anti-realism.

  7. Cutting Gordian Knots: Reducing Prejudice Through Attachment Security.

    PubMed

    Saleem, Muniba; Prot, Sara; Cikara, Mina; Lam, Ben C P; Anderson, Craig A; Jelic, Margareta

    2015-11-01

    The positive role of secure attachment in reducing intergroup biases has been suggested in prior studies. We extend this work by testing the effects of secure attachment primes on negative emotions and aggressive behaviors toward outgroup members across four experiments. Results from Studies 1A and 1B reveal that secure attachment prime, relative to neutral, can reduce negative outgroup emotions. In addition, Studies 1B and 3 results rule out positive mood increase as an alternative explanation for the observed effects. Results from Studies 2 and 3 reveal that secure attachment primes can reduce aggressive behavior toward an outgroup member. The effect of secure attachment primes on outgroup harm was found to be fully mediated by negative emotions in Studies 2 and 3. An interaction between secure attachment primes and ingroup identification in Study 2 indicated that the positive effects of secure attachment in reducing outgroup harm may be especially beneficial for highly identified ingroup members. PMID:26338854

  8. Metagenomics for studying unculturable microorganisms: cutting the Gordian knot

    PubMed Central

    Schloss, Patrick D; Handelsman, Jo

    2005-01-01

    More than 99% of prokaryotes in the environment cannot be cultured in the laboratory, a phenomenon that limits our understanding of microbial physiology, genetics, and community ecology. One way around this problem is metagenomics, the culture-independent cloning and analysis of microbial DNA extracted directly from an environmental sample. Recent advances in shotgun sequencing and computational methods for genome assembly have advanced the field of metagenomics to provide glimpses into the life of uncultured microorganisms. PMID:16086859

  9. Cutting the Gordian Knot: Taking Control of Assessment

    ERIC Educational Resources Information Center

    Luff, Ian

    2016-01-01

    Ian Luff recognised that in a post-levels world efforts to devise new assessment systems risked replicating old problems or creating new ones. Drawing on his many years' experience of teaching and school leadership Luff argues that for assessment in history to be truly useful to teachers and pupils it needs to be both holistic and authentic to the…

  10. Cutting Gordian Knots: Reducing Prejudice Through Attachment Security.

    PubMed

    Saleem, Muniba; Prot, Sara; Cikara, Mina; Lam, Ben C P; Anderson, Craig A; Jelic, Margareta

    2015-11-01

    The positive role of secure attachment in reducing intergroup biases has been suggested in prior studies. We extend this work by testing the effects of secure attachment primes on negative emotions and aggressive behaviors toward outgroup members across four experiments. Results from Studies 1A and 1B reveal that secure attachment prime, relative to neutral, can reduce negative outgroup emotions. In addition, Studies 1B and 3 results rule out positive mood increase as an alternative explanation for the observed effects. Results from Studies 2 and 3 reveal that secure attachment primes can reduce aggressive behavior toward an outgroup member. The effect of secure attachment primes on outgroup harm was found to be fully mediated by negative emotions in Studies 2 and 3. An interaction between secure attachment primes and ingroup identification in Study 2 indicated that the positive effects of secure attachment in reducing outgroup harm may be especially beneficial for highly identified ingroup members.

  11. The Gordian Knot of dysbiosis, obesity and NAFLD.

    PubMed

    Mehal, Wajahat Z

    2013-11-01

    The development of obesity and NAFLD is known to be determined by host genetics, diet and lack of exercise. In addition, the gut microbiota has been identified to influence the development of both obesity and NAFLD. Evidence for the role of the gut microbiota has been shown by preclinical studies of transfer of gut microbiota from lean and obese individuals, with the recipient developing the metabolic features of the donor. Many bidirectional interactions of the gut microbiota, including with food, bile and the intestinal epithelium, have been identified. These interactions might contribute to the distinct steps in the progression from lean to obese states, and to steatosis, steatohepatitis and eventually fibrosis. The predominant steps are efficient caloric extraction from the diet, intestinal epithelial damage and greater entry of bacterial components into the portal circulation. These steps result in activation of the innate immune system, liver inflammation and fibrosis. Fortunately, therapeutic interventions might not require a full understanding of these complex interactions. Although antibiotics are too unselective in their action, probiotics have shown efficacy in reversing obesity and NASH in experimental systems, and are under investigation in humans. PMID:23958600

  12. Systematic Weighting and Ranking: Cutting the Gordian Knot.

    ERIC Educational Resources Information Center

    Davis, Charles H.; McKim, Geoffrey W.

    1999-01-01

    Describes SWEAR (Systematic Weighting and Ranking), a powers-of-two algorithm that can be used for searching the World Wide Web or any large database that automatically creates discrete, well-defined result sets and displays them in decreasing order of likely relevance. Also discusses fuzzy sets. (Author/LRW)

  13. A Midsummer Knot's Dream

    ERIC Educational Resources Information Center

    Henrich, A.; MacNaughton, N.; Narayan, S.; Pechenik, O.; Silversmith, R.; Townsend, J.

    2011-01-01

    We introduce playing games on the shadows of knots and demonstrate two novel games, namely, "To Knot or Not to Knot" and "Much Ado about Knotting." We discuss winning strategies for these games on certain families of knot shadows and go on to suggest variations of these games for further study.

  14. Untying the Gordian knot of creation: metaphors for the Human Genome Project in Greek newspapers.

    PubMed

    Gogorosi, Eleni

    2005-12-01

    This article studies the metaphorical expressions used by newspapers to present the near completion of the Human Genome Project (HGP) to the Greek public in the year 2000. The analysis, based on cognitive metaphor theory, deals with the most frequent or captivating metaphors used to refer to the human genome, which give rise to both conventional and novel expressions. The majority of creative metaphorical expressions participate in the discourse of hope and promise propagated by the Greek media in an attempt to present the HGP and its outcome in a favorable light. Instances of the competing discourse of fear and danger are much rarer but can also be found in creative metaphorical expressions. Metaphors pertaining to the Greek culture or to ancient Greek mythology tend to carry a special rhetorical force. However, it will be shown that the Greek press strategically used most of the metaphors that circulated globally at the time, not only culture specific ones.

  15. Procedural vs. substantive in the NEPA law: Cutting the Gordian knot

    SciTech Connect

    Boggs, J.P. . Dept. of Anthropology)

    1993-01-01

    The debate whether the National Environmental Policy Act (NEPA) is procedural or substantive has become central both to agency implementation of the act and to court review of agency compliance. While NEPA mandates both procedural and substantive reform as a means to improve environmental quality, NEPA also focuses on cognitive reform--the improved utilization of knowledge in public affairs. Choices about what knowledge to base public decisions on, and how that knowledge will be used, build the social realities that shape lives. Thus, NEPA's mandates for the creation and use of public knowledge activate fundamentally conflicting values and visions of social order. However, debate about the procedural and substantive provisions of NEPA cannot resolve the conflict about values that actually motivates the debate, and this constrictive debate impoverishes public discussion about NEPA implementation and judicial review. This paper links the present debate with the values issues that underlie it, suggesting a more direct language for characterizing NEPA and a broader framework of legal theory for debating the issues it raises. This paper also finds that environmental and social science practitioners are strategically positioned to contribute materially to the issues raised by a NEPA properly understood as law that mandates knowledge utilization.

  16. Haeckel or Hennig? The Gordian Knot of Characters, Development, and Procedures in Phylogeny.

    ERIC Educational Resources Information Center

    Dupuis, Claude

    1984-01-01

    Discusses the conditions for validating customary phylogenetic procedures. Concludes that the requisites of homogeneity and completeness for proved short lineages seem satisfied by the Hennigian but not the Haeckelian procedure. The epistemological antinomy of the two procedures is emphasized for the first time. (Author/RH)

  17. Disentangling Tfr cells from Treg cells and Tfh cells: How to untie the Gordian knot.

    PubMed

    Amiezer, Mayan; Phan, Tri Giang

    2016-05-01

    T follicular regulatory (Tfr) cells are a subpopulation of Treg cells that have adopted the T follicular helper cell program to localize to the B-cell follicle. Because of the difficulties in generating mouse models in which Tfr cells are selectively affected, determining where and how Tfr cells regulate the germinal center response remains to be resolved. In this issue of the European Journal of Immunology, Dent and colleagues [Eur. J. Immunol. 2016. 46: 1152-1161] describe a simple, elegant mouse model to conditionally delete Tfr cells without impacting on the Treg- and Tfh-cell populations. Their initial studies suggest that Tfr cells have a more complex role than previously thought, particularly with respect to the regulation of immunoglobulin isotype switching to IgA. PMID:27109022

  18. Proliferation and Polarity in Breast Cancer: Untying the GordianKnot

    SciTech Connect

    Liu, Hong; Radisky, Derek C.; Bissell, Mina J.

    2005-05-09

    Epithelial cancers are associated with genomic instability and alterations in signaling pathways that affect proliferation, apoptosis, and integrity of tissue structure. Overexpression of a number of oncogenic protein kinases has been shown to malignantly transform cells in culture and to cause tumors in vivo, but the interconnected signaling events induced by transformation still awaits detailed dissection. We propose that the network of cellular signaling pathways can be classified into functionally distinct branches, and that these pathways are rewired in transformed cells and tissues after they lose tissue-specific architecture to favor tumor expansion and invasion. Using three-dimensional (3D) culture systems, we recently demonstrated that polarity and proliferation of human mammary epithelial cancer cells were separable consequences of signaling pathways downstream of PI3 kinase.These, and results from a number of other laboratories are beginning to provide insight into how different signaling pathways may become interconnected in normal tissues to allow homeostasis, and how they are disrupted during malignant progression.

  19. Disentangling Tfr cells from Treg cells and Tfh cells: How to untie the Gordian knot.

    PubMed

    Amiezer, Mayan; Phan, Tri Giang

    2016-05-01

    T follicular regulatory (Tfr) cells are a subpopulation of Treg cells that have adopted the T follicular helper cell program to localize to the B-cell follicle. Because of the difficulties in generating mouse models in which Tfr cells are selectively affected, determining where and how Tfr cells regulate the germinal center response remains to be resolved. In this issue of the European Journal of Immunology, Dent and colleagues [Eur. J. Immunol. 2016. 46: 1152-1161] describe a simple, elegant mouse model to conditionally delete Tfr cells without impacting on the Treg- and Tfh-cell populations. Their initial studies suggest that Tfr cells have a more complex role than previously thought, particularly with respect to the regulation of immunoglobulin isotype switching to IgA.

  20. Unravelling the Gordian knot: diagnostic dilemma in an HIV-positive patient with neurological involvement

    PubMed Central

    Chakraborty, Avirup; Siddhanta, Sattik; Bhattacharyya, Kuntal; Das, Amit; Banerjee, Siwalik; Sarkar, Rathindra Nath; Datta, Utpal Kumar; Chakraborty, Nilanjan

    2013-01-01

    We report a case of a 40-year-old seropositive-HIV patient with a CD4 count of 120 who presented with fever, severe headache and neck stiffness. Suspecting a case of tubercular meningitis (TBM; as tuberculosis is the commonest opportunistic infection in HIV/AIDS patients in India), a lumbar puncture was performed and a cerebrospinal fluid study revealed TBM. The patient was started on combination antitubercular drug therapy from directly observed treatment, short course (DOTS) (Cat 1 regimen) along with pyridoxine 40 mg/day and adjunctive corticosteroid therapy. However, despite adequate antitubercular therapy for 4 weeks, the patient did not show any improvement in his clinical condition. On the contrary, in the process he developed cytomegalovirus (CMV) retinitis. So we question our learned readers if the coinfection of Mycobacterium tuberculosis and CMV should be implicated for the failure to respond to isolated antitubercular therapy contrary to our expectation. PMID:23616316

  1. Biomarkers of head and neck cancer, tools or a gordian knot?

    PubMed Central

    Lampri, Evangeli S; Chondrogiannis, Georgios; Ioachim, Elli; Varouktsi, Anna; Mitselou, Antigoni; Galani, Aggeliki; Briassoulis, Evangelos; Kanavaros, Panagiotis; Galani, Vasiliki

    2015-01-01

    Head and neck tumors comprise a wide spectrum of heterogeneous neoplasms for which biomarkers are needed to aid in earlier diagnosis, risk assessment and therapy response. Personalized medicine based on predictive markers linked to drug response, it is hoped, will lead to improvements in outcomes and avoidance of unnecessary treatment in carcinoma of the head and neck. Because of the heterogeneity of head and neck tumors, the integration of multiple selected markers in association with the histopathologic features is advocated for risk assessment. Validation of each biomarker in the context of clinical trials will be required before a specific marker can be incorporated into daily practice. Furthermore, we will give evidence that some proteins implicated in cell-cell interaction, such as CD44 may be involved in the multiple mechanism of the development and progression of laryngeal lesions and may help to predict the risk of transformation of the benign or precancerous lesions to cancer. PMID:26379825

  2. Parity in knot theory

    SciTech Connect

    Manturov, Vassily O

    2010-06-29

    In this work we study knot theories with a parity property for crossings: every crossing is declared to be even or odd according to a certain preassigned rule. If this rule satisfies a set of simple axioms related to the Reidemeister moves, then certain simple invariants solving the minimality problem can be defined, and invariant maps on the set of knots can be constructed. The most important example of a knot theory with parity is the theory of virtual knots. Using the parity property arising from Gauss diagrams we show that even a gross simplification of the theory of virtual knots, namely, the theory of free knots, admits simple and highly nontrivial invariants. This gives a solution to a problem of Turaev, who conjectured that all free knots are trivial. In this work we show that free knots are generally not invertible, and provide invariants which detect the invertibility of free knots. The passage to ordinary virtual knots allows us to strengthen known invariants (such as the Kauffman bracket) using parity considerations. We also discuss other examples of knot theories with parity. Bibliography: 27 items.

  3. Tying quantum knots

    NASA Astrophysics Data System (ADS)

    Hall, D. S.; Ray, M. W.; Tiurev, K.; Ruokokoski, E.; Gheorghe, A. H.; Möttönen, M.

    2016-05-01

    As topologically stable objects in field theories, knots have been put forward to explain various persistent phenomena in systems ranging from atoms and molecules to cosmic textures in the universe. Recent experiments have reported the observation of knots in different classical contexts. However, no experimental observation of knots has yet been reported in quantum matter. Here we demonstrate the experimental creation and detection of knot solitons in the order parameter of a spinor Bose-Einstein condensate. The observed texture corresponds to a topologically nontrivial element of the third homotopy group and exhibits the celebrated Hopf fibration, which unites many seemingly unrelated physical phenomena. Our work calls for future studies of the stability and dynamics knot solitons in the quantum regime.

  4. Protein knot server: detection of knots in protein structures.

    PubMed

    Kolesov, Grigory; Virnau, Peter; Kardar, Mehran; Mirny, Leonid A

    2007-07-01

    KNOTS (http://knots.mit.edu) is a web server that detects knots in protein structures. Several protein structures have been reported to contain intricate knots. The physiological role of knots and their effect on folding and evolution is an area of active research. The user submits a PDB id or uploads a 3D protein structure in PDB or mmCIF format. The current implementation of the server uses the Alexander polynomial to detect knots. The results of the analysis that are presented to the user are the location of the knot in the structure, the type of the knot and an interactive visualization of the knot. The results can also be downloaded and viewed offline. The server also maintains a regularly updated list of known knots in protein structures.

  5. Knot Theory with Young Children

    ERIC Educational Resources Information Center

    Handa, Yuichi; Mattman, Thomas

    2008-01-01

    There are many interesting explorations that can be done in knot theory, the study of mathematical knots. This article offers some knot theory activities that are appropriate for elementary grade children. These activities teach some basic concepts from knot theory as a natural extension of commonly-taught geometric ideas. (Contains 10 figures.)

  6. Sedimentation of knotted polymers

    NASA Astrophysics Data System (ADS)

    Piili, J.; Marenduzzo, D.; Kaski, K.; Linna, R. P.

    2013-01-01

    We investigate the sedimentation of knotted polymers by means of stochastic rotation dynamics, a molecular dynamics algorithm that takes hydrodynamics fully into account. We show that the sedimentation coefficient s, related to the terminal velocity of the knotted polymers, increases linearly with the average crossing number nc of the corresponding ideal knot. This provides direct computational confirmation of this relation, postulated on the basis of sedimentation experiments by Rybenkov [J. Mol. Biol.10.1006/jmbi.1996.0876 267, 299 (1997)]. Such a relation was previously shown to hold with simulations for knot electrophoresis. We also show that there is an accurate linear dependence of s on the inverse of the radius of gyration Rg-1, more specifically with the inverse of the Rg component that is perpendicular to the direction along which the polymer sediments. When the polymer sediments in a slab, the walls affect the results appreciably. However, Rg-1 remains to a good precision linearly dependent on nc. Therefore, Rg-1 is a good measure of a knot's complexity.

  7. Cutting the Gordian Knot: Identifiability of anaplerotic reactions in Corynebacterium glutamicum by means of (13) C-metabolic flux analysis.

    PubMed

    Kappelmann, Jannick; Wiechert, Wolfgang; Noack, Stephan

    2016-03-01

    Corynebacterium glutamicum is the major workhorse for the microbial production of several amino and organic acids. As long as these derive from tricarboxylic acid cycle intermediates, the activity of anaplerotic reactions is pivotal for a high biosynthetic yield. To determine single anaplerotic activities (13) C-Metabolic Flux Analysis ((13) C-MFA) has been extensively used for C. glutamicum, however with different network topologies, inconsistent or poorly determined anaplerotic reaction rates. Therefore, in this study we set out to investigate whether a focused isotopomer model of the anaplerotic node can at all admit a unique solution for all fluxes. By analyzing different scenarios of active anaplerotic reactions, we show in full generality that for C. glutamicum only certain anaplerotic deletion mutants allow to uniquely determine the anaplerotic fluxes from (13) C-isotopomer data. We stress that the result of this analysis for different assumptions on active enzymes is directly transferable to other compartment-free organisms. Our results demonstrate that there exist biologically relevant metabolic network topologies for which the flux distribution cannot be inferred by classical (13) C-MFA. PMID:26375179

  8. Sampling and analysis validates acceptable knowledge on LANL transuranic, heterogeneous, debris waste, or ``Cutting the Gordian knot that binds WIPP``

    SciTech Connect

    Kosiewicz, S.T.; Triay, I.R.; Souza, L.A.; Michael, D.I.; Black, P.K.

    1999-02-01

    Through sampling and toxicity characteristic leaching procedure (TCLP) analyses, LANL and the DOE validated that a LANL transuranic (TRU) waste (TA-55-43, Lot No. 01) was not a Resource Recovery and Conservation Act (RCRA) hazardous waste. This paper describes the sampling and analysis project as well as the statistical assessment of the analytical results. The analyses were conducted according to the requirements and procedures in the sampling and analysis plan approved by the New Mexico Environmental Department. The plan used a statistical approach that was consistent with the stratified, random sampling requirements of SW-846. LANL adhered to the plan during sampling and chemical analysis of randomly selected items of the five major types of materials in this heterogeneous, radioactive, debris waste. To generate portions of the plan, LANL analyzed a number of non-radioactive items that were representative of the mix of items present in the waste stream. Data from these cold surrogates were used to generate means and variances needed to optimize the design. Based on statistical arguments alone, only two samples from the entire waste stream were deemed necessary, however a decision was made to analyze at least two samples of each of the five major waste types. To obtain these samples, nine TRU waste drums were opened. Sixty-six radioactively contaminated and four non-radioactive grab samples were collected. Portions of the samples were composited for chemical analyses. In addition, a radioactively contaminated sample of rust-colored powder of interest to the New Mexico Environment Department (NMED) was collected and qualitatively identified as rust.

  9. k/not theory.

    PubMed

    Chowdhry, M

    2000-01-01

    SUMMARY This paper discusses the role of the personal experience in the writing process. Using a personal/journal writing style the author charts the journey of a recent play Skin into Rainbows from first draft to production. The author plays with the constructs of writing and juxtapositions these against a form of Knot Theory to measure their value, playing with math and language techniques in a search for truth.

  10. k/not theory.

    PubMed

    Chowdhry, M

    2000-01-01

    SUMMARY This paper discusses the role of the personal experience in the writing process. Using a personal/journal writing style the author charts the journey of a recent play Skin into Rainbows from first draft to production. The author plays with the constructs of writing and juxtapositions these against a form of Knot Theory to measure their value, playing with math and language techniques in a search for truth. PMID:24802683

  11. Knot probabilities in random diagrams

    NASA Astrophysics Data System (ADS)

    Cantarella, Jason; Chapman, Harrison; Mastin, Matt

    2016-10-01

    We consider a natural model of random knotting—choose a knot diagram at random from the finite set of diagrams with n crossings. We tabulate diagrams with 10 and fewer crossings and classify the diagrams by knot type, allowing us to compute exact probabilities for knots in this model. As expected, most diagrams with 10 and fewer crossings are unknots (about 78% of the roughly 1.6 billion 10 crossing diagrams). For these crossing numbers, the unknot fraction is mostly explained by the prevalence of ‘tree-like’ diagrams which are unknots for any assignment of over/under information at crossings. The data shows a roughly linear relationship between the log of knot type probability and the log of the frequency rank of the knot type, analogous to Zipf’s law for word frequency. The complete tabulation and all knot frequencies are included as supplementary data.

  12. Metastable Tight Knots in DNA

    NASA Astrophysics Data System (ADS)

    Dai, Liang; Renner, C. Benjamin; Doyle, Patrick

    2015-03-01

    Knotted structures can spontaneously occur in polymers such as DNA and proteins, and the formation of knots affects biological functions, mechanical strength and rheological properties. In this work, we calculate the equilibrium size distribution of trefoil knots in linear DNA using off-lattice simulations. We observe metastable knots on DNA, as predicted by Grosberg and Rabin. Furthermore, we extend their theory to incorporate the finite width of chains and show an agreement between our simulations and the modified theory for real chains. Our results suggest localized knots spontaneously occur in long DNA and the contour length in the knot ranges from 600 to 1800 nm. This research was supported by the National Research Foundation Singapore through the Singapore MIT Alliance for Research and Technology's research program in BioSystems and Micromechanics, the National Science Foundation (Grant No. 1335938).

  13. Naughty knot: a case of nasogastric tube knotting.

    PubMed

    Ravind, Rahul; Prameela, Chelakkot G; Gurram, Bharath Chandra; Dinesh, Makuny

    2015-10-13

    Nasogastric intubation is a common procedure for enteral nutritional support in medical practice. Random spontaneous true knot formation in the tube is rarely encountered and is a cause of unanticipated trauma. This is a case of a true knot formation diagnosed with fluoroscopy and managed without untoward trauma.

  14. How superfluid vortex knots untie

    NASA Astrophysics Data System (ADS)

    Kleckner, Dustin; Kauffman, Louis H.; Irvine, William T. M.

    2016-07-01

    Knots and links often occur in physical systems, including shaken strands of rope and DNA (ref. ), as well as the more subtle structure of vortices in fluids and magnetic fields in plasmas. Theories of fluid flows without dissipation predict these tangled structures persist, constraining the evolution of the flow much like a knot tied in a shoelace. This constraint gives rise to a conserved quantity known as helicity, offering both fundamental insights and enticing possibilities for controlling complex flows. However, even small amounts of dissipation allow knots to untie by means of `cut-and-splice’ operations known as reconnections. Despite the potentially fundamental role of these reconnections in understanding helicity--and the stability of knotted fields more generally--their effect is known only for a handful of simple knots. Here we study the evolution of 322 elemental knots and links in the Gross-Pitaevskii model for a superfluid, and find that they universally untie. We observe that the centreline helicity is partially preserved even as the knots untie, a remnant of the perfect helicity conservation predicted for idealized fluids. Moreover, we find that the topological pathways of untying knots have simple descriptions in terms of minimal two-dimensional knot diagrams, and tend to concentrate in states which are twisted in only one direction. These results have direct analogies to previous studies of simple knots in several systems, including DNA recombination and classical fluids. This similarity in the geometric and topological evolution suggests there are universal aspects in the behaviour of knots in dissipative fields.

  15. Knots and Preons

    NASA Astrophysics Data System (ADS)

    Finkelstein, Robert J.

    It is shown that the four quantum trefoil solitons that are described by the irreducible representations { D}3/2mm' of the quantum algebra SLq(2) [and that may be identified with the four families of elementary fermions (e, μ, τ νeνμντd, s, b; u, c, t)] may be built out of three preons, chosen from two charged preons with charges (1/3, -1/3) and two neutral preons. These preons are fermions and are described by the { D}1/2mm' representation of SLq(2). There are also four bosonic preons described by the { D}1mm^' and { D}000 representations of SLq(2). The knotted standard theory may be replicated at the preon level and the conjectured particles are in principle indirectly observable.

  16. Periodic forces trigger knot untying during translocation of knotted proteins

    NASA Astrophysics Data System (ADS)

    Szymczak, Piotr

    2016-03-01

    Proteins need to be unfolded when translocated through the pores in mitochondrial and other cellular membranes. Knotted proteins, however, might get stuck during this process, jamming the pore, since the diameter of the pore is smaller than the size of maximally tightened knot. The jamming probability dramatically increases as the magnitude of the driving force exceeds a critical value, Fc. In this numerical study, we show that for deep knots Fc lies below the force range over which molecular import motors operate, which suggest that in these cases the knots will tighten and block the pores. Next, we show how such topological traps might be prevented by using a pulling protocol of a repetitive, on-off character. Such a repetitive pulling is biologically relevant, since the mitochondrial import motor, like other molecular motors transforms chemical energy into directed motions via nucleotide-hydrolysis-mediated conformational changes, which are cyclic in character.

  17. Periodic forces trigger knot untying during translocation of knotted proteins

    PubMed Central

    Szymczak, Piotr

    2016-01-01

    Proteins need to be unfolded when translocated through the pores in mitochondrial and other cellular membranes. Knotted proteins, however, might get stuck during this process, jamming the pore, since the diameter of the pore is smaller than the size of maximally tightened knot. The jamming probability dramatically increases as the magnitude of the driving force exceeds a critical value, Fc. In this numerical study, we show that for deep knots Fc lies below the force range over which molecular import motors operate, which suggest that in these cases the knots will tighten and block the pores. Next, we show how such topological traps might be prevented by using a pulling protocol of a repetitive, on-off character. Such a repetitive pulling is biologically relevant, since the mitochondrial import motor, like other molecular motors transforms chemical energy into directed motions via nucleotide-hydrolysis-mediated conformational changes, which are cyclic in character. PMID:26996878

  18. Periodic forces trigger knot untying during translocation of knotted proteins.

    PubMed

    Szymczak, Piotr

    2016-01-01

    Proteins need to be unfolded when translocated through the pores in mitochondrial and other cellular membranes. Knotted proteins, however, might get stuck during this process, jamming the pore, since the diameter of the pore is smaller than the size of maximally tightened knot. The jamming probability dramatically increases as the magnitude of the driving force exceeds a critical value, Fc. In this numerical study, we show that for deep knots Fc lies below the force range over which molecular import motors operate, which suggest that in these cases the knots will tighten and block the pores. Next, we show how such topological traps might be prevented by using a pulling protocol of a repetitive, on-off character. Such a repetitive pulling is biologically relevant, since the mitochondrial import motor, like other molecular motors transforms chemical energy into directed motions via nucleotide-hydrolysis-mediated conformational changes, which are cyclic in character. PMID:26996878

  19. Effects of Knots on Protein Folding Properties

    PubMed Central

    Soler, Miguel A.; Faísca, Patrícia F. N.

    2013-01-01

    This work explores the impact of knots, knot depth and motif of the threading terminus in protein folding properties (kinetics, thermodynamics and mechanism) via extensive Monte Carlo simulations of lattice models. A knotted backbone has no effect on protein thermodynamic stability but it may affect key aspects of folding kinetics. In this regard, we found clear evidence for a functional advantage of knots: knots enhance kinetic stability because a knotted protein unfolds at a distinctively slower rate than its unknotted counterpart. However, an increase in knot deepness does not necessarily lead to more effective changes in folding properties. In this regard, a terminus with a non-trivial conformation (e.g. hairpin) can have a more dramatic effect in enhancing kinetic stability than knot depth. Nevertheless, our results suggest that the probability of the denatured ensemble to keep knotted is higher for proteins with deeper knots, indicating that knot depth plays a role in determining the topology of the denatured state. Refolding simulations starting from denatured knotted conformations show that not every knot is able to nucleate folding and further indicate that the formation of the knotting loop is a key event in the folding of knotted trefoils. They also show that there are specific native contacts within the knotted core that are crucial to keep a native knotting loop in denatured conformations which otherwise have no detectable structure. The study of the knotting mechanism reveals that the threading of the knotting loop generally occurs towards late folding in conformations that exhibit a significant degree of structural consolidation. PMID:24023962

  20. Knots in finite memory walks

    NASA Astrophysics Data System (ADS)

    Horwath, Eric; Clisby, Nathan; Virnau, Peter

    2016-09-01

    We investigate the occurrence and size of knots in a continuum polymer model with finite memory via Monte Carlo simulations. Excluded volume interactions are local and extend only to a fixed number of successive beads along the chain, ensuring that at short length scales the excluded volume effect dominates, while at longer length scales the polymer behaves like a random walk. As such, this model may be useful for understanding the behavior of polymers in a melt or semi-dilute solution, where exactly the same crossover is believed to occur. In particular, finite memory walks allow us to investigate the role of local interactions in the transition from highly knotted ideal polymers to almost unknotted self-avoiding polymers. Even though knotting decreases substantially when a few next-nearest neighbor interactions are considered, we find that the knotting probability of a polymer chain of modest length of 500 steps only decays slowly as a function of the range of the excluded volume interaction. In this context, we also find evidence that for length scales up to the interaction length the knotting behavior of the finite memory walk resembles that of a self-avoiding walk (effectively suppressing small knots), while for larger length scales it resembles that of a random walk.

  1. On ambiguity in knot polynomials for virtual knots

    NASA Astrophysics Data System (ADS)

    Morozov, A.; Morozov, And.; Popolitov, A.

    2016-06-01

    We claim that HOMFLY polynomials for virtual knots, defined with the help of the matrix-model recursion relations, contain more parameters, than just the usual q and A =qN. These parameters preserve topological invariance and do not show up in the case of ordinary (non-virtual) knots and links. They are most conveniently observed in the hypercube formalism: then they substitute q-dimensions of certain fat graphs, which are not constrained by recursion and can be chosen arbitrarily. The number of these new topological invariants seems to grow fast with the number of non-virtual crossings: 0, 1, 1, 5, 15, 91, 784, 9160, ... This number can be decreased by imposing the factorization requirement for composites, in addition to topological invariance - still freedom remains. None of these new parameters, however, appears in HOMFLY for Kishino unknot, which thus remains unseparated from the ordinary unknots even by this enriched set of knot invariants.

  2. Spontaneous knotting of an agitated string.

    PubMed

    Raymer, Dorian M; Smith, Douglas E

    2007-10-16

    It is well known that a jostled string tends to become knotted; yet the factors governing the "spontaneous" formation of various knots are unclear. We performed experiments in which a string was tumbled inside a box and found that complex knots often form within seconds. We used mathematical knot theory to analyze the knots. Above a critical string length, the probability P of knotting at first increased sharply with length but then saturated below 100%. This behavior differs from that of mathematical self-avoiding random walks, where P has been proven to approach 100%. Finite agitation time and jamming of the string due to its stiffness result in lower probability, but P approaches 100% with long, flexible strings. We analyzed the knots by calculating their Jones polynomials via computer analysis of digital photos of the string. Remarkably, almost all were identified as prime knots: 120 different types, having minimum crossing numbers up to 11, were observed in 3,415 trials. All prime knots with up to seven crossings were observed. The relative probability of forming a knot decreased exponentially with minimum crossing number and Möbius energy, mathematical measures of knot complexity. Based on the observation that long, stiff strings tend to form a coiled structure when confined, we propose a simple model to describe the knot formation based on random "braid moves" of the string end. Our model can qualitatively account for the observed distribution of knots and dependence on agitation time and string length.

  3. Hidden structures of knot invariants

    NASA Astrophysics Data System (ADS)

    Sleptsov, Alexey

    2014-11-01

    We discuss a connection of HOMFLY polynomials with Hurwitz covers and represent a generating function for the HOMFLY polynomial of a given knot in all representations as Hurwitz partition function, i.e. the dependence of the HOMFLY polynomials on representation R is naturally captured by symmetric group characters (cut-and-join eigenvalues). The genus expansion and the loop expansion through Vassiliev invariants explicitly demonstrate this phenomenon. We study the genus expansion and discuss its properties. We also consider the loop expansion in details. In particular, we give an algorithm to calculate Vassiliev invariants, give some examples and discuss relations among Vassiliev invariants. Then we consider superpolynomials for torus knots defined via double affine Hecke algebra. We claim that the superpolynomials are not functions of Hurwitz type: symmetric group characters do not provide an adequate linear basis for their expansions. Deformation to superpolynomials is, however, straightforward in the multiplicative basis: the Casimir operators are beta-deformed to Hamiltonians of the Calogero-Moser-Sutherland system. Applying this trick to the genus and Vassiliev expansions, we observe that the deformation is fully straightforward only for the thin knots. Beyond the family of thin knots additional algebraically independent terms appear in the Vassiliev expansions. This can suggest that the superpolynomials do in fact contain more information about knots than the colored HOMFLY and Kauffman polynomials.

  4. Relation between strings and ribbon knots

    NASA Astrophysics Data System (ADS)

    Ahmed, E.; El-Rifai, E. A.; Abdellatif, R. A.

    1991-02-01

    A ribbon knot can be represented as the propagation of an open string in (Euclidean) space-time. By imposing physical conditions plus an ansatz on the string scattering amplitude, we get invariant polynomials of ribbon knots which correspond to Jones and Wadati et al. polynomials for ordinary knots. Motivated by the string scattering vertices, we derive an algebra which is a generalization of Hecke and Murakami-Birman-Wenzel (BMW) algebras of knots.

  5. Knotted stents: Case report and outcome analysis

    PubMed Central

    Lee, Ha Na; Hwang, Hokyeong

    2015-01-01

    A knotted ureteral stent is an extremely rare condition, with fewer than 20 cases reported in the literature; however, it is difficult to treat. We report a case in which a folded Terumo guidewire was successfully used to remove a knotted stent percutaneously without anesthesia. We also review the current literature on predisposing factors and management strategies for knotted ureteral stents. PMID:25964843

  6. Second IBEX Map Unties the Knot

    NASA Video Gallery

    One of the clear features visible in the IBEX maps is an apparent knot in the ribbon. The second map showed that the knot in the ribbon somehow spread out. It is as if the knot in the ribbon was li...

  7. POST Quantum Cryptography from Mutant Prime Knots

    NASA Astrophysics Data System (ADS)

    Marzuoli, Annalisa; Palumbo, Giandomenico

    By resorting to basic features of topological knot theory we propose a (classical) cryptographic protocol based on the `difficulty' of decomposing complex knots generated as connected sums of prime knots and their mutants. The scheme combines an asymmetric public key protocol with symmetric private ones and is intrinsecally secure against quantum eavesdropper attacks.

  8. The elusive quest for RNA knots

    PubMed Central

    Burton, Aaron S.; Di Stefano, Marco; Lehman, Niles; Orland, Henri; Micheletti, Cristian

    2016-01-01

    ABSTRACT Physical entanglement, and particularly knots arise spontaneously in equilibrated polymers that are sufficiently long and densely packed. Biopolymers are no exceptions: knots have long been known to occur in proteins as well as in encapsidated viral DNA. The rapidly growing number of RNA structures has recently made it possible to investigate the incidence of physical knots in this type of biomolecule, too. Strikingly, no knots have been found to date in the known RNA structures. In this Point of View Article we discuss the absence of knots in currently available RNAs and consider the reasons why knots in RNA have not yet been found, despite the expectation that they should exist in Nature. We conclude by singling out a number of RNA sequences that, based on the properties of their predicted secondary structures, are good candidates for knotted RNAs. PMID:26828280

  9. Biomechanical evaluation of the Nice knot

    PubMed Central

    Hill, Shannon W.; Chapman, Christopher R.; Adeeb, Samer; Duke, Kajsa; Beaupre, Lauren; Bouliane, Martin J.

    2016-01-01

    Background: The Nice knot is a bulky double-stranded knot. Biomechanical data supporting its use as well as the number of half hitches required to ensure knot security is lacking. Materials and Methods: Nice knots with, one, two, or three half-hitches were compared with the surgeon's and Tennessee slider knots with three half hitches. Each knot was tied 10 times around a fixed diameter using four different sutures: FiberWire (Arthrex, Naples, FL), Ultrabraid (Smith and Nephew, Andover, MA), Hi-Fi (ConMed Linvatec, Largo, FL) and Force Fiber (Teleflex Medical OEM, Gurnee, IL). Cyclic testing was performed for 10 min between 10N and 45N, resulting in approximately 1000 cycles. Displacement from an initial 10N load was recorded. Knots surviving cyclic testing were subjected to a load to failure test at a rate of 60 mm/min. Load at clinical failure: 3 mm slippage or opening of the suture loop was recorded. Bulk, mode of ultimate failure, opening of the loop past clinical failure, was also recorded. Results: During cyclic testing, the Nice knots with one or more half-hitches performed the best, slipping significantly less than the surgeon's and Tennessee Slider (P < 0.002). After one half-hitch, the addition of half-hitches did not significantly improve Nice knot performance during cyclic testing (P > 0.06). The addition of half-hitches improved the strength of the Nice knot during the force to failure test, however after two half-hitches, increase of strength was not significant (P = 0.59). While FiberWire was the most bulky of the sutures tested, it also performed the best, slipping the least. Conclusion: The Nice knot, especially using FiberWire, is biomechanically superior to the surgeon's and Tennessee slider knots. Two half hitches are recommended to ensure adequate knot security. PMID:26980985

  10. KnotProt: a database of proteins with knots and slipknots

    PubMed Central

    Jamroz, Michal; Niemyska, Wanda; Rawdon, Eric J.; Stasiak, Andrzej; Millett, Kenneth C.; Sułkowski, Piotr; Sulkowska, Joanna I.

    2015-01-01

    The protein topology database KnotProt, http://knotprot.cent.uw.edu.pl/, collects information about protein structures with open polypeptide chains forming knots or slipknots. The knotting complexity of the cataloged proteins is presented in the form of a matrix diagram that shows users the knot type of the entire polypeptide chain and of each of its subchains. The pattern visible in the matrix gives the knotting fingerprint of a given protein and permits users to determine, for example, the minimal length of the knotted regions (knot's core size) or the depth of a knot, i.e. how many amino acids can be removed from either end of the cataloged protein structure before converting it from a knot to a different type of knot. In addition, the database presents extensive information about the biological functions, families and fold types of proteins with non-trivial knotting. As an additional feature, the KnotProt database enables users to submit protein or polymer chains and generate their knotting fingerprints. PMID:25361973

  11. Knots "Choke Off" Polymers upon Stretching.

    PubMed

    Stauch, Tim; Dreuw, Andreas

    2016-01-11

    Long polymer chains inevitably get tangled into knots. Like macroscopic ropes, polymer chains are substantially weakened by knots and the rupture point is always located at the "entry" or "exit" of the knot. However, these phenomena are only poorly understood at a molecular level. Here we show that when a knotted polyethylene chain is tightened, most of the stress energy is stored in torsions around the curved part of the chain. The torsions act as "work funnels" that effectively localize mechanical stress in the immediate vicinity of the knot. As a result, the knot "chokes" the chain at its entry or exit, thus leading to bond rupture at much lower forces than those needed to break a linear, unknotted chain. Our work not only explains the weakening of the polymer chain and the position of the rupture point, but more generally demonstrates that chemical bonds do not have to be extensively stretched to be broken. PMID:26629964

  12. Vortex knots in tangled quantum eigenfunctions

    NASA Astrophysics Data System (ADS)

    Taylor, Alexander J.; Dennis, Mark R.

    2016-07-01

    Tangles of string typically become knotted, from macroscopic twine down to long-chain macromolecules such as DNA. Here, we demonstrate that knotting also occurs in quantum wavefunctions, where the tangled filaments are vortices (nodal lines/phase singularities). The probability that a vortex loop is knotted is found to increase with its length, and a wide gamut of knots from standard tabulations occur. The results follow from computer simulations of random superpositions of degenerate eigenstates of three simple quantum systems: a cube with periodic boundaries, the isotropic three-dimensional harmonic oscillator and the 3-sphere. In the latter two cases, vortex knots occur frequently, even in random eigenfunctions at relatively low energy, and are constrained by the spatial symmetries of the modes. The results suggest that knotted vortex structures are generic in complex three-dimensional wave systems, establishing a topological commonality between wave chaos, polymers and turbulent Bose-Einstein condensates.

  13. Vortex knots in tangled quantum eigenfunctions

    PubMed Central

    Taylor, Alexander J.; Dennis, Mark R.

    2016-01-01

    Tangles of string typically become knotted, from macroscopic twine down to long-chain macromolecules such as DNA. Here, we demonstrate that knotting also occurs in quantum wavefunctions, where the tangled filaments are vortices (nodal lines/phase singularities). The probability that a vortex loop is knotted is found to increase with its length, and a wide gamut of knots from standard tabulations occur. The results follow from computer simulations of random superpositions of degenerate eigenstates of three simple quantum systems: a cube with periodic boundaries, the isotropic three-dimensional harmonic oscillator and the 3-sphere. In the latter two cases, vortex knots occur frequently, even in random eigenfunctions at relatively low energy, and are constrained by the spatial symmetries of the modes. The results suggest that knotted vortex structures are generic in complex three-dimensional wave systems, establishing a topological commonality between wave chaos, polymers and turbulent Bose–Einstein condensates. PMID:27468801

  14. Vortex knots in tangled quantum eigenfunctions.

    PubMed

    Taylor, Alexander J; Dennis, Mark R

    2016-01-01

    Tangles of string typically become knotted, from macroscopic twine down to long-chain macromolecules such as DNA. Here, we demonstrate that knotting also occurs in quantum wavefunctions, where the tangled filaments are vortices (nodal lines/phase singularities). The probability that a vortex loop is knotted is found to increase with its length, and a wide gamut of knots from standard tabulations occur. The results follow from computer simulations of random superpositions of degenerate eigenstates of three simple quantum systems: a cube with periodic boundaries, the isotropic three-dimensional harmonic oscillator and the 3-sphere. In the latter two cases, vortex knots occur frequently, even in random eigenfunctions at relatively low energy, and are constrained by the spatial symmetries of the modes. The results suggest that knotted vortex structures are generic in complex three-dimensional wave systems, establishing a topological commonality between wave chaos, polymers and turbulent Bose-Einstein condensates. PMID:27468801

  15. Untying the gordian knot: what we do and don't know about gender-specific medicine-keynote address for the 2014 Academic Emergency Medicine Consensus Conference.

    PubMed

    Legato, Marianne

    2014-12-01

    Over the past two decades, a burgeoning interest in women's health, the direct consequence of the feminist movement, has inspired a worldwide interest in the differences between the normal function of men and women and their unique experiences of the same illnesses. The scope and significance of what we have discovered and continue to find has fundamentally changed the way we prevent, diagnose, and treat diseases. Important questions remain, however, and deserve specific investigation and analysis.

  16. Amoralist rationalism? A response to Joel Marks: commentary on "Animal abolitionism meets moral abolitionism: cutting the Gordian knot of applied ethics" by Joel Marks.

    PubMed

    Lederman, Zohar

    2014-06-01

    In a recent article, Joel Marks presents the amoralist argument against vivisection, or animal laboratory experimentation. He argues that ethical theories that seek to uncover some universal morality are in fact useless and unnecessary for ethical deliberations meant to determine what constitutes an appropriate action in a specific circumstance. I agree with Marks' conclusion. I too believe that vivisection is indefensible, both from a scientific and philosophical perspective. I also believe that we should become vegan (unfortunately, like the two philosophers mentioned by Marks, I too am still struggling to reduce my meat and dairy consumption). However, I am in the dark as to Marks' vision of normative deliberations in the spirit of amoralism and desirism.

  17. Knots and nonorientable surfaces in chiral nematics

    PubMed Central

    Machon, Thomas; Alexander, Gareth P.

    2013-01-01

    Knots and knotted fields enrich physical phenomena ranging from DNA and molecular chemistry to the vortices of fluid flows and textures of ordered media. Liquid crystals provide an ideal setting for exploring such topological phenomena through control of their characteristic defects. The use of colloids in generating defects and knotted configurations in liquid crystals has been demonstrated for spherical and toroidal particles and shows promise for the development of novel photonic devices. Extending this existing work, we describe the full topological implications of colloids representing nonorientable surfaces and use it to construct torus knots and links of type (p,2) around multiply twisted Möbius strips. PMID:23940365

  18. Knots, BPS States, and Algebraic Curves

    NASA Astrophysics Data System (ADS)

    Garoufalidis, Stavros; Kucharski, Piotr; Sułkowski, Piotr

    2016-08-01

    We analyze relations between BPS degeneracies related to Labastida-Mariño-Ooguri-Vafa (LMOV) invariants and algebraic curves associated to knots. We introduce a new class of such curves, which we call extremal A-polynomials, discuss their special properties, and determine exact and asymptotic formulas for the corresponding (extremal) BPS degeneracies. These formulas lead to nontrivial integrality statements in number theory, as well as to an improved integrality conjecture, which is stronger than the known M-theory integrality predictions. Furthermore, we determine the BPS degeneracies encoded in augmentation polynomials and show their consistency with known colored HOMFLY polynomials. Finally, we consider refined BPS degeneracies for knots, determine them from the knowledge of super-A-polynomials, and verify their integrality. We illustrate our results with twist knots, torus knots, and various other knots with up to 10 crossings.

  19. A pseudo-haptic knot diagram interface

    NASA Astrophysics Data System (ADS)

    Zhang, Hui; Weng, Jianguang; Hanson, Andrew J.

    2011-01-01

    To make progress in understanding knot theory, we will need to interact with the projected representations of mathematical knots which are of course continuous in 3D but significantly interrupted in the projective images. One way to achieve such a goal would be to design an interactive system that allows us to sketch 2D knot diagrams by taking advantage of a collision-sensing controller and explore their underlying smooth structures through a continuous motion. Recent advances of interaction techniques have been made that allow progress to be made in this direction. Pseudo-haptics that simulates haptic effects using pure visual feedback can be used to develop such an interactive system. This paper outlines one such pseudo-haptic knot diagram interface. Our interface derives from the familiar pencil-and-paper process of drawing 2D knot diagrams and provides haptic-like sensations to facilitate the creation and exploration of knot diagrams. A centerpiece of the interaction model simulates a "physically" reactive mouse cursor, which is exploited to resolve the apparent conflict between the continuous structure of the actual smooth knot and the visual discontinuities in the knot diagram representation. Another value in exploiting pseudo-haptics is that an acceleration (or deceleration) of the mouse cursor (or surface locator) can be used to indicate the slope of the curve (or surface) of whom the projective image is being explored. By exploiting these additional visual cues, we proceed to a full-featured extension to a pseudo-haptic 4D visualization system that simulates the continuous navigation on 4D objects and allows us to sense the bumps and holes in the fourth dimension. Preliminary tests of the software show that main features of the interface overcome some expected perceptual limitations in our interaction with 2D knot diagrams of 3D knots and 3D projective images of 4D mathematical objects.

  20. Molecular knots in biology and chemistry

    NASA Astrophysics Data System (ADS)

    Lim, Nicole C. H.; Jackson, Sophie E.

    2015-09-01

    Knots and entanglements are ubiquitous. Beyond their aesthetic appeal, these fascinating topological entities can be either useful or cumbersome. In recent decades, the importance and prevalence of molecular knots have been increasingly recognised by scientists from different disciplines. In this review, we provide an overview on the various molecular knots found in naturally occurring biological systems (DNA, RNA and proteins), and those created by synthetic chemists. We discuss the current knowledge in these fields, including recent developments in experimental and, in some cases, computational studies which are beginning to shed light into the complex interplay between the structure, formation and properties of these topologically intricate molecules.

  1. Spontaneous knotting of self-trapped waves

    PubMed Central

    Desyatnikov, Anton S.; Buccoliero, Daniel; Dennis, Mark R.; Kivshar, Yuri S.

    2012-01-01

    We describe theory and simulations of a spinning optical soliton whose propagation spontaneously excites knotted and linked optical vortices. The nonlinear phase of the self-trapped light beam breaks the wave front into a sequence of optical vortex loops around the soliton, which, through the soliton's orbital angular momentum and spatial twist, tangle on propagation to form links and knots. We anticipate similar spontaneous knot topology to be a universal feature of waves whose phase front is twisted and nonlinearly modulated, including superfluids and trapped matter waves. PMID:23105969

  2. Knot theory realizations in nematic colloids.

    PubMed

    Čopar, Simon; Tkalec, Uroš; Muševič, Igor; Žumer, Slobodan

    2015-02-10

    Nematic braids are reconfigurable knots and links formed by the disclination loops that entangle colloidal particles dispersed in a nematic liquid crystal. We focus on entangled nematic disclinations in thin twisted nematic layers stabilized by 2D arrays of colloidal particles that can be controlled with laser tweezers. We take the experimentally assembled structures and demonstrate the correspondence of the knot invariants, constructed graphs, and surfaces associated with the disclination loop to the physically observable features specific to the geometry at hand. The nematic nature of the medium adds additional topological parameters to the conventional results of knot theory, which couple with the knot topology and introduce order into the phase diagram of possible structures. The crystalline order allows the simplified construction of the Jones polynomial and medial graphs, and the steps in the construction algorithm are mirrored in the physics of liquid crystals.

  3. Knot theory realizations in nematic colloids

    PubMed Central

    Čopar, Simon; Tkalec, Uroš; Muševič, Igor; Žumer, Slobodan

    2015-01-01

    Nematic braids are reconfigurable knots and links formed by the disclination loops that entangle colloidal particles dispersed in a nematic liquid crystal. We focus on entangled nematic disclinations in thin twisted nematic layers stabilized by 2D arrays of colloidal particles that can be controlled with laser tweezers. We take the experimentally assembled structures and demonstrate the correspondence of the knot invariants, constructed graphs, and surfaces associated with the disclination loop to the physically observable features specific to the geometry at hand. The nematic nature of the medium adds additional topological parameters to the conventional results of knot theory, which couple with the knot topology and introduce order into the phase diagram of possible structures. The crystalline order allows the simplified construction of the Jones polynomial and medial graphs, and the steps in the construction algorithm are mirrored in the physics of liquid crystals. PMID:25624467

  4. Vortex knot cascade in polynomial skein relations

    NASA Astrophysics Data System (ADS)

    Ricca, Renzo L.

    2016-06-01

    The process of vortex cascade through continuous reduction of topological complexity by stepwise unlinking, that has been observed experimentally in the production of vortex knots (Kleckner & Irvine, 2013), is shown to be reproduced in the branching of the skein relations of knot polynomials (Liu & Ricca, 2015) used to identify topological complexity of vortex systems. This observation can be usefully exploited for predictions of energy-complexity estimates for fluid flows.

  5. Absence of knots in known RNA structures

    PubMed Central

    Micheletti, Cristian; Di Stefano, Marco; Orland, Henri

    2015-01-01

    The ongoing effort to detect and characterize physical entanglement in biopolymers has so far established that knots are present in many globular proteins and also, abound in viral DNA packaged inside bacteriophages. RNA molecules, however, have not yet been systematically screened for the occurrence of physical knots. We have accordingly undertaken the systematic profiling of the several thousand RNA structures present in the Protein Data Bank (PDB). The search identified no more than three deeply knotted RNA molecules. These entries are rRNAs of about 3,000 nt solved by cryo-EM. Their genuine knotted state is, however, doubtful based on the detailed structural comparison with homologs of higher resolution, which are all unknotted. Compared with the case of proteins and viral DNA, the observed incidence of knots in available RNA structures is, therefore, practically negligible. This fact suggests that either evolutionary selection or thermodynamic and kinetic folding mechanisms act toward minimizing the entanglement of RNA to an extent that is unparalleled by other types of biomolecules. A possible general strategy for designing synthetic RNA sequences capable of self-tying in a twist-knot fold is finally proposed. PMID:25646433

  6. Statistics of knots, geometry of conformations, and evolution of proteins.

    PubMed

    Lua, Rhonald C; Grosberg, Alexander Y

    2006-05-01

    Like shoelaces, the backbones of proteins may get entangled and form knots. However, only a few knots in native proteins have been identified so far. To more quantitatively assess the rarity of knots in proteins, we make an explicit comparison between the knotting probabilities in native proteins and in random compact loops. We identify knots in proteins statistically, applying the mathematics of knot invariants to the loops obtained by complementing the protein backbone with an ensemble of random closures, and assigning a certain knot type to a given protein if and only if this knot dominates the closure statistics (which tells us that the knot is determined by the protein and not by a particular method of closure). We also examine the local fractal or geometrical properties of proteins via computational measurements of the end-to-end distance and the degree of interpenetration of its subchains. Although we did identify some rather complex knots, we show that native conformations of proteins have statistically fewer knots than random compact loops, and that the local geometrical properties, such as the crumpled character of the conformations at a certain range of scales, are consistent with the rarity of knots. From these, we may conclude that the known "protein universe" (set of native conformations) avoids knots. However, the precise reason for this is unknown--for instance, if knots were removed by evolution due to their unfavorable effect on protein folding or function or due to some other unidentified property of protein evolution.

  7. Statistics of knots, geometry of conformations, and evolution of proteins.

    PubMed

    Lua, Rhonald C; Grosberg, Alexander Y

    2006-05-01

    Like shoelaces, the backbones of proteins may get entangled and form knots. However, only a few knots in native proteins have been identified so far. To more quantitatively assess the rarity of knots in proteins, we make an explicit comparison between the knotting probabilities in native proteins and in random compact loops. We identify knots in proteins statistically, applying the mathematics of knot invariants to the loops obtained by complementing the protein backbone with an ensemble of random closures, and assigning a certain knot type to a given protein if and only if this knot dominates the closure statistics (which tells us that the knot is determined by the protein and not by a particular method of closure). We also examine the local fractal or geometrical properties of proteins via computational measurements of the end-to-end distance and the degree of interpenetration of its subchains. Although we did identify some rather complex knots, we show that native conformations of proteins have statistically fewer knots than random compact loops, and that the local geometrical properties, such as the crumpled character of the conformations at a certain range of scales, are consistent with the rarity of knots. From these, we may conclude that the known "protein universe" (set of native conformations) avoids knots. However, the precise reason for this is unknown--for instance, if knots were removed by evolution due to their unfavorable effect on protein folding or function or due to some other unidentified property of protein evolution. PMID:16710448

  8. Origin of metastable knots in single flexible chains.

    PubMed

    Dai, Liang; Renner, C Benjamin; Doyle, Patrick S

    2015-01-23

    Recent theoretical progress has explained the physics of knotting of semiflexible polymers, yet knotting of flexible polymers is relatively unexplored. We herein develop a new theory for the size distribution of knots on a flexible polymer and the existence of metastable knots. We show the free energy of a flexible molecule in a tube can be mapped to quantitatively reproduce the free energy distribution of a knot on a flexible chain. The size distribution of knots on flexible chains is expected to be universal and might be observed at a macroscopic scale, such as a string of hard balls. PMID:25659023

  9. Comparing models of Red Knot population dynamics

    USGS Publications Warehouse

    McGowan, Conor

    2015-01-01

    Predictive population modeling contributes to our basic scientific understanding of population dynamics, but can also inform management decisions by evaluating alternative actions in virtual environments. Quantitative models mathematically reflect scientific hypotheses about how a system functions. In Delaware Bay, mid-Atlantic Coast, USA, to more effectively manage horseshoe crab (Limulus polyphemus) harvests and protect Red Knot (Calidris canutus rufa) populations, models are used to compare harvest actions and predict the impacts on crab and knot populations. Management has been chiefly driven by the core hypothesis that horseshoe crab egg abundance governs the survival and reproduction of migrating Red Knots that stopover in the Bay during spring migration. However, recently, hypotheses proposing that knot dynamics are governed by cyclical lemming dynamics garnered some support in data analyses. In this paper, I present alternative models of Red Knot population dynamics to reflect alternative hypotheses. Using 2 models with different lemming population cycle lengths and 2 models with different horseshoe crab effects, I project the knot population into the future under environmental stochasticity and parametric uncertainty with each model. I then compare each model's predictions to 10 yr of population monitoring from Delaware Bay. Using Bayes' theorem and model weight updating, models can accrue weight or support for one or another hypothesis of population dynamics. With 4 models of Red Knot population dynamics and only 10 yr of data, no hypothesis clearly predicted population count data better than another. The collapsed lemming cycle model performed best, accruing ~35% of the model weight, followed closely by the horseshoe crab egg abundance model, which accrued ~30% of the weight. The models that predicted no decline or stable populations (i.e. the 4-yr lemming cycle model and the weak horseshoe crab effect model) were the most weakly supported.

  10. On the universality of knot probability ratios

    NASA Astrophysics Data System (ADS)

    Janse van Rensburg, E. J.; Rechnitzer, A.

    2011-04-01

    Let pn denote the number of self-avoiding polygons of length n on a regular three-dimensional lattice, and let pn(K) be the number which have knot type K. The probability that a random polygon of length n has knot type K is pn(K)/pn and is known to decay exponentially with length (Sumners and Whittington 1988 J. Phys. A: Math. Gen. 21 1689-94, Pippenger 1989 Discrete Appl. Math. 25 273-8). Little is known rigorously about the asymptotics of pn(K), but there is substantial numerical evidence (Orlandini et al 1988 J. Phys. A: Math. Gen. 31 5953-67, Marcone et al 2007 Phys. Rev. E 75 41105, Rawdon et al 2008 Macromolecules 41 4444-51, Janse van Rensburg and Rechnitzer 2008 J. Phys. A: Math. Theor. 41 105002) that pn(K) grows as p_n(K) \\simeq C_K \\mu _\\emptyset ^n n^{\\alpha -3+N_K}, \\qquad as\\quad n \\rightarrow \\infty, where NK is the number of prime components of the knot type K. It is believed that the entropic exponent, α, is universal, while the exponential growth rate, μ∅, is independent of the knot type but varies with the lattice. The amplitude, CK, depends on both the lattice and the knot type. The above asymptotic form implies that the relative probability of a random polygon of length n having prime knot type K over prime knot type L is \\frac{p_n(K)/p_n}{p_n(L)/p_n} = \\frac{p_n(K)}{p_n(L)} \\simeq \\left[ \\frac{C_K}{C_L} \\right].\\\\[-8pt] In the thermodynamic limit this probability ratio becomes an amplitude ratio; it should be universal and depend only on the knot types K and L. In this communication we examine the universality of these probability ratios for polygons in the simple cubic, face-centred cubic and body-centred cubic lattices. Our results support the hypothesis that these are universal quantities. For example, we estimate that a long random polygon is approximately 28 times more likely to be a trefoil than be a figure-eight, independent of the underlying lattice, giving an estimate of the intrinsic entropy associated with knot

  11. Symmetries in proteins: A knot theory approach

    NASA Astrophysics Data System (ADS)

    Chen, Shi-Jie; Dill, Ken A.

    1996-04-01

    Whereas the symmetries of small molecules are described by the methods of group theory, there is no corresponding way to describe the complex symmetries in proteins. We develop a quantitative method to define and classify symmetries in compact polymers, based on the mathematical theory of graphs and knots. We represent different chain folds by their ``polymer graphs,'' equivalent to contact maps. We transform those graphs into mathematical knots to give a parsing of different possible chain folds into conformational taxonomies. We use Alexander-Conway knot polynomials to characterize the knots. We find that different protein structures with the same tertiary fold, e.g., a βαβ motif with different lengths of α helix and β sheet, can be described in terms of the different powers of the propagation matrices of the knot polynomial. This identifies a fundamental type of topological length invariance in proteins, ``elongatable'' symmetries. For example, ``helix,'' ``sheet,'' ``helix-turn-helix,'' and other secondary, supersecondary, and tertiary structures define structures of any chain length. Possibly the nine superfolds identified by Thornton et al. have elongatable symmetries.

  12. Nonlinear electrodynamics is skilled with knots

    NASA Astrophysics Data System (ADS)

    Goulart, E.

    2016-07-01

    The aim of this letter is threefold: First is to show that nonlinear generalizations of electrodynamics support various types of knotted solutions in vacuum. The solutions are universal in the sense that they do not depend on the specific Lagrangian density, at least if the latter gives rise to a well-posed theory. Second, is to describe the interaction between probe waves and knotted background configurations. We show that the qualitative behaviour of this interaction may be described in terms of Robinson congruences, which appear explicitly in the causal structure of the theory. Finally, we argue that optical arrangements endowed with intense background fields could be the natural place to look for the knots experimentally.

  13. IUE observations of NGC 1068 - The extremely luminous starburst knots

    NASA Technical Reports Server (NTRS)

    Bruhweiler, F. C.; Truong, K. Q.; Altner, B.

    1991-01-01

    A complete investigation of the UV characteristics of the starburst knots in the inner 3 kpc region of NGC 1068 mapped by the IUE is presented. It is noted that these knots probably represent the most luminous H II regions yet studied at optical and UV wavelengths. Comparisons suggest that the brightest knot, knot 1, is 30 times brighter than NGC 604 in M33 and has a total luminosity of not less than 10 to the 43rd ergs/s.

  14. Are there p-adic knot invariants?

    NASA Astrophysics Data System (ADS)

    Morozov, A. Yu.

    2016-04-01

    We suggest using the Hall-Littlewood version of the Rosso-Jones formula to define the germs of p-adic HOMFLY-PT polynomials for torus knots [ m, n] as coefficients of superpolynomials in a q-expansion. In this form, they have at least the [ m, n] ↔ [ n, m] topological invariance. This opens a new possibility to interpret superpolynomials as p-adic deformations of HOMFLY polynomials and poses a question of generalizing to other knot families, which is a substantial problem for several branches of modern theory.

  15. A deeply knotted protein structure and how it might fold

    NASA Astrophysics Data System (ADS)

    Taylor, William R.

    2000-08-01

    The search for knots in protein has uncovered little that would cause Alexander the Great to reach for his sword. Excluding knots formed by post-translational crosslinking, the few proteins considered to be knotted form simple trefoil knots with one end of the chain extending through a loop by only a few residues, ten in the `best' example. A knot in an open chain (as distinct from a closed circle) is not rigorously defined and many weak protein knots disappear if the structure is viewed from a different angle. Here I describe a computer algorithm to detect knots in open chains that is not sensitive to viewpoint and that can define the region of the chain giving rise to the knot. It characterizes knots in proteins by the number of residues that must be removed from each end to abolish the knot. I applied this algorithm to the protein structure database and discovered a deep, figure-of-eight knot in the plant protein acetohydroxy acid isomeroreductase. I propose a protein folding pathway that may explain how such a knot is formed.

  16. A deeply knotted protein structure and how it might fold.

    PubMed

    Taylor, W R

    2000-08-24

    The search for knots in protein has uncovered little that would cause Alexander the Great to reach for his sword. Excluding knots formed by post-translational crosslinking, the few proteins considered to be knotted form simple trefoil knots with one end of the chain extending through a loop by only a few residues, ten in the 'best' example. A knot in an open chain (as distinct from a closed circle) is not rigorously defined and many weak protein knots disappear if the structure is viewed from a different angle. Here I describe a computer algorithm to detect knots in open chains that is not sensitive to viewpoint and that can define the region of the chain giving rise to the knot. It characterizes knots in proteins by the number of residues that must be removed from each end to abolish the knot. I applied this algorithm to the protein structure database and discovered a deep, figure-of-eight knot in the plant protein acetohydroxy acid isomeroreductase. I propose a protein folding pathway that may explain how such a knot is formed.

  17. Knotted proteins: A tangled tale of Structural Biology

    PubMed Central

    Faísca, Patrícia F.N.

    2015-01-01

    Knotted proteins have their native structures arranged in the form of an open knot. In the last ten years researchers have been making significant efforts to reveal their folding mechanism and understand which functional advantage(s) knots convey to their carriers. Molecular simulations have been playing a fundamental role in this endeavor, and early computational predictions about the knotting mechanism have just been confirmed in wet lab experiments. Here we review a collection of simulation results that allow outlining the current status of the field of knotted proteins, and discuss directions for future research. PMID:26380658

  18. The constrictor knot is the best ligature

    PubMed Central

    Taylor, H

    2014-01-01

    Introduction An ideal ligature should tighten readily and remain tight. Ligature failure can be a critical complication of invasive procedures in human and veterinary surgical practice. Previous studies have tested various knots but not the constrictor knot. Methods A new test bench was employed to compare six ligatures using four suture materials. As tension in a ligature is not readily measured, the study employed a surrogate measurement: the force required to slide a ligature along a rod. Benchmark values tested each suture material wrapped around the rod to establish the ratio between this force and the ligature tension for each material. Each ligature was tested first during tightening and then again afterwards. The benchmark ratios were employed to calculate the tensions to evaluate which ligature and which suture material retained tension best. Results The model provided consistent linear relationships between the tension in the suture and the force required to pull the ligature along the rod. The constrictor knot retained tension in the ligature best (55–107% better than the next best ligature). Among the suture materials, polydioxanone had the greatest ability to retain the tension in a ligature and polyglactin the least. Conclusions The constrictor knot showed superior characteristics for use as a ligature, and should be introduced into teaching and clinical practice for human and veterinary surgery. The new test bench is recommended for future testing of ligatures as well as objective comparison of suture materials. PMID:24780665

  19. Spontaneous Intravesical Knotting of Urethral Catheter

    PubMed Central

    2011-01-01

    Infant feeding tubes (IFT) have been universally used as urethral catheters in neonates and children for several decades. Though generally a safe procedure, it may cause significant morbidity if the catheter spontaneously knots inside the bladder. We report this complication in three children including a neonate. PMID:22953288

  20. Endoscopic Suturing and Knot Tying: Theory Into Practice

    PubMed Central

    Murphy, Donald L.

    2001-01-01

    Objective To advance modern surgical techniques of endoscopic knot tying, encompassing a new appreciation of knot-tying theory and the application of second-generation, purpose-designed instruments. Summary Background Data During open surgery, surgeons automatically create the surgical half-hitch by using either instrument or hand/finger knot-tying methods (figure 4). Each of these methods, which are mirror images of each other, forms the same result, the half-hitch. Two opposing half-hitches are needed to form a square knot. There are many ways for new-generation instruments to create a secure square knot during endoscopic surgery. An overview of the current endoscopic knot-tying methods is presented. Methods The author presents a theoretical analysis of square knot-tying techniques as applied during instrument and hand/finger movements. The application of a mirror-image concept was considered in the analysis of these two contrasting methods. Results There are 12 ways to create a square knot, some of which have previously not been described or needed in open surgery. Some of these methods have particular application in endoscopic surgery. Conclusions A new understanding of knot-tying theory has been developed, with innovative methods being defined for tissue approximation during endoscopic surgery. These ergonomic, efficient, and contrasting methods of knot tying are described using second-generation endoscopic instruments. The new techniques have direct and broad application in many fields of minimally invasive surgery. PMID:11685022

  1. Towards effective topological field theory for knots

    NASA Astrophysics Data System (ADS)

    Mironov, A.; Morozov, A.

    2015-10-01

    Construction of (colored) knot polynomials for double-fat graphs is further generalized to the case when "fingers" and "propagators" are substituting R-matrices in arbitrary closed braids with m-strands. Original version of [25] corresponds to the case m = 2, and our generalization sheds additional light on the structure of those mysterious formulas. Explicit expressions are now combined from Racah matrices of the type R ⊗ R ⊗ R bar ⟶ R bar and mixing matrices in the sectors R⊗3 ⟶ Q. Further extension is provided by composition rules, allowing to glue two blocks, connected by an m-strand braid (they generalize the product formula for ordinary composite knots with m = 1).

  2. Parity and cobordism of free knots

    SciTech Connect

    Manturov, Vassily O

    2012-02-28

    A simple invariant is constructed which obstructs a free knot to be truncated. In particular, this invariant provides an obstruction to the truncatedness of curves immersed in two-dimensional surfaces. A curve on an oriented two-dimensional surface S{sub g} is referred to as truncated (null-cobordant) if there exists a three-dimensional manifold M with boundary S{sub g} and a smooth proper map of a two-disc to M such that the image of the boundary of the disc coincides with the curve. The problem of truncatedness for free knots is solved in this paper using the notion of parity recently introduced by the author. Bibliography: 12 titles.

  3. Cometary Knots Around A Dying Star

    NASA Technical Reports Server (NTRS)

    1994-01-01

    These gigantic, tadpole-shaped objects are probably the result of a dying star's last gasps. Dubbed 'cometary knots' because their glowing heads and gossamer tails resemble comets, the gaseous objects probably were formed during a star's final stages of life. Hubble astronomer C. Robert O'Dell and graduate student Kerry P. Handron of Rice University in Houston, Texas discovered thousands of these knots with the Hubble Space Telescope while exploring the Helix nebula, the closest planetary nebula to Earth at 450 light-years away in the constellation Aquarius. Although ground-based telescopes have revealed such objects, astronomers have never seen so many of them. The most visible knots all lie along the inner edge of the doomed star's ring, trillions of miles away from the star's nucleus. Although these gaseous knots appear small, they're actually huge. Each gaseous head is at least twice the size of our solar system; each tail stretches for 100 billion miles, about 1,000 times the distance between the Earth and the Sun. Astronomers theorize that the doomed star spews hot, lower-density gas from its surface, which collides with cooler, higher-density gas that had been ejected 10,000 years before. The crash fragments the smooth cloud surrounding the star into smaller, denser finger-like droplets, like dripping paint. This image was taken in August, 1994 with Hubble's Wide Field Planetary Camera 2. The red light depicts nitrogen emission ([NII] 6584A); green, hydrogen (H-alpha, 6563A); and blue, oxygen (5007A).

  4. Stretching Response of Knotted and Unknotted Polymer Chains

    NASA Astrophysics Data System (ADS)

    Caraglio, Michele; Micheletti, Cristian; Orlandini, Enzo

    2015-10-01

    Recent theoretical and experimental advances have clarified the major effects of knotting on the properties of stretched chains. Yet, how knotted chains respond to weak mechanical stretching and how this behavior differs from the unknotted case are still open questions and we address them here by profiling the complete stretching response of chains of hundreds of monomers and different topology. We find that the ratio of the knotted and unknotted chain extensions varies nonmonotonically with the applied force. This surprising feature is shown to be a signature of the crossover between the well-known high-force stretching regime and the previously uncharacterized low-force one. The observed differences of knotted and unknotted chain response increases with knot complexity and are sufficiently marked that they could be harnessed in single-molecule contexts to infer the presence and complexity of physical knots in micron-long biomolecules.

  5. Escape of a knot from a DNA molecule in flow

    NASA Astrophysics Data System (ADS)

    Renner, Benjamin; Doyle, Patrick

    2014-03-01

    Macroscale knots are an everyday occurrence when trying to unravel an unorganized flexible string (e.g. an iPhone cord taken out of your pocket). In nature, knots are found in proteins and viral capsid DNA, and the properties imbued by their topologies are thought to have biological significance. Unlike their macroscale counterparts, thermal fluctuations greatly influence the dynamics of polymer knots. Here, we use Brownian Dynamics simulations to study knot diffusion along a linear polymer chain. The model is parameterized to dsDNA, a model polymer used in previous simulation and experimental studies of knot dynamics. We have used this model to study the process of knot escape and transport along a dsDNA strand extended by an elongational flow. For a range of knot topologies and flow strengths, we show scalings that result in collapse of the data onto a master curve. We show a topologically mediated mode of transport coincides with observed differences in rates of knot transport, and we provide a simple mechanistic explanation for its effect. We anticipate these results will build on the growing body of fundamental studies of knotted polymers and inform future experimental study. This work is supported by the Singapore-MIT Alliance for Research and Technology (SMART) and National Science Foundation (NSF) grant CBET-0852235.

  6. A comparison of ultrasonic suture welding and traditional knot tying.

    PubMed

    Richmond, J C

    2001-01-01

    The slippage of knots and the technical challenge of tying them securely are potential impediments to certain arthroscopic procedures. Ultrasonic energy delivered at 70 kHz can be used to weld No. 2 polypropylene suture. This method was compared with a traditional knot (surgeon's knot with four alternating half hitches) tied with an open technique to determine whether welding of sutures is comparable, in mechanical properties, to hand-tied knots. Both loops were fashioned around a 0.25-inch mandrel and then tested. The load to reach 3-mm elongation (point of likely biologic failure of a repair) was significantly greater for welded sutures than for knots. The elongation at ultimate failure was significantly less for welded sutures than for knots. The number of cycles to failure and the creep after initial displacement were similar for both welded and knotted suture loops. The ultimate load to failure was significantly greater for the knotted than for the welded suture. The welding of suture for the repair of musculoskeletal soft tissue presents an attractive alternative to traditional knot tying, particularly for arthroscopic applications.

  7. Optical knots and contact geometry II. From Ranada dyons to transverse and cosmetic knots

    NASA Astrophysics Data System (ADS)

    Kholodenko, Arkady L.

    2016-08-01

    Some time ago Ranada (1989) obtained new nontrivial solutions of the Maxwellian gauge fields without sources. These were reinterpreted in Kholodenko (2015) [10] (part I) as particle-like (monopoles, dyons, etc.). They were obtained by the method of Abelian reduction of the non-Abelian Yang-Mills functional. The developed method uses instanton-type calculations normally employed for the non-Abelian gauge fields. By invoking the electric-magnetic duality it then becomes possible to replace all known charges/masses by the particle-like solutions of the source-free Abelian gauge fields. To employ these results in high energy physics, it is essential to extend Ranada's results by carefully analyzing and classifying all dynamically generated knotted/linked structures in gauge fields, including those discovered by Ranada. This task is completed in this work. The study is facilitated by the recent progress made in solving the Moffatt conjecture. Its essence is stated as follows: in steady incompressible Euler-type fluids the streamlines could have knots/links of all types. By employing the correspondence between the ideal hydrodynamics and electrodynamics discussed in part I and by superimposing it with the already mentioned method of Abelian reduction, it is demonstrated that in the absence of boundaries only the iterated torus knots and links could be dynamically generated. Obtained results allow to develop further particle-knot/link correspondence studied in Kholodenko (2015) [13].

  8. The Geometry and Physics of Knots

    NASA Astrophysics Data System (ADS)

    Atiyah, Michael

    1990-10-01

    Deals with an area of research that lies at the crossroads of mathematics and physics. The material presented here rests primarily on the pioneering work of Vaughan Jones and Edward Witten relating polynomial invariants of knots to a topological quantum field theory in 2+1 dimensions. Professor Atiyah presents an introduction to Witten's ideas from the mathematical point of view. The book will be essential reading for all geometers and gauge theorists as an exposition of new and interesting ideas in a rapidly developing area.

  9. Ventriculoperitoneal Shunt Peritoneal Catheter Knot Formation

    PubMed Central

    Ul-Haq, Anwar; Al-Otaibi, Faisal; Alshanafey, Saud; Sabbagh, Mohamed Diya; Al Shail, Essam

    2013-01-01

    The ventriculoperitoneal (VP) shunt is a common procedure in pediatric neurosurgery that carries a risk of complications at cranial and abdominal sites. We report on the case of a child with shunt infection and malfunction. The peritoneal catheter was tethered within the abdominal cavity, precluding its removal. Subsequently, laparoscopic exploration identified a knot at the distal end of the peritoneal catheter around the omentum. A new VP shunt was inserted after the infection was healed. This type of complication occurs rarely, so there are a limited number of case reports in the literature. This report is complemented by a literature review. PMID:24109528

  10. Structural recognition and nomenclature standardization in forensic knot analysis.

    PubMed

    Chisnall, Robert Charles

    2016-07-01

    The analysis of knots during civil and criminal investigations is characterized by two fundamental challenges: the precise recognition of all structural nuances and the application of accurate, universally recognized terms. These challenges are exacerbated by inconsistencies, contradictions and regional terminology, which occur in common practice and in mainstream books as well as within forensic science. Some knots bear multiple or value-laden names, even misnomers, and some terms have manifold applications. This can lead to ambiguity and confusion. Additionally, many topological concepts and terms are applicable to practical knot-tying, despite the differences between real-world and theoretical knots, but the esoterica of topology are inaccessible to anyone unfamiliar with that branch of mathematics. To highlight these challenges some examples of knots encountered in case work are presented. Significantly, an overview of a few previously ignored issues is examined and several new concepts are introduced. An emphasis is placed on identifying structural variations, standardized nomenclature is outlined, and recommended terminology is derived from fields such as forensic science, chemistry, archaeology, topology and the textile industry. Greater precision in knot identifications, characterizations and descriptions can assist investigators in linking specific tying practises to potential suspects, analysing the manner in which knotted evidence was tied, and understanding how knots and ligatures perform in given scenarios.

  11. Analysis and physics of laparoscopic intracorporeal square-knot tying.

    PubMed

    Medina, Marelyn

    2005-01-01

    Square knots are often used in open surgery to approximate tissue borders or tie off tubular structures like vessels or ducts. Three common methods are used for surgical square-knot tying: one-hand tying, two-hand tying, and the instrument-tying technique. Two types of suture placements are studied in both the open and laparoscopic surgical fields. The first called equal length has suture segment ends placed at equal distances from the tying site. The second called unequal length has one suture end further away from the tying site than the other. Laparoscopic intracorporeal square-knot tying maneuvers are analyzed herein. Mechanical analysis of square-knot tying movements reveals that regardless of location or method used in construction, all square knots consist of 2 half-knots. For study purposes, these sets of movements are identified in laparoscopy as maneuver A and maneuver B. Further breakout of these maneuvers reveals that they consist of 5 motions. This study reveals that 16 different ways exist to place a square knot by means of the laparoscopic intracorporeal technique. It is likely that difficulty mastering this essential skill is not just the result of poor instrumentation, improper port placement, or the limitations of a 2-dimensional video image. It may also be attributed to mixing up the different square-knot tying techniques during random practice exercises. This is possible if the surgeon is ignorant of the technical variations present in what most people consider a simple task.

  12. The Verbal Facilitation Effect in Learning to Tie Nautical Knots

    ERIC Educational Resources Information Center

    Huff, Markus; Schwan, Stephan

    2012-01-01

    Motor skills are often demonstrated with a combination of verbal information and video demonstration. In this study, participants learned to tie nautical knots with a video clip demonstrating the motor task preceded by a descriptive or a metaphorical, picture-like verbalization. In a control condition participants learned the knots with a video…

  13. Structural recognition and nomenclature standardization in forensic knot analysis.

    PubMed

    Chisnall, Robert Charles

    2016-07-01

    The analysis of knots during civil and criminal investigations is characterized by two fundamental challenges: the precise recognition of all structural nuances and the application of accurate, universally recognized terms. These challenges are exacerbated by inconsistencies, contradictions and regional terminology, which occur in common practice and in mainstream books as well as within forensic science. Some knots bear multiple or value-laden names, even misnomers, and some terms have manifold applications. This can lead to ambiguity and confusion. Additionally, many topological concepts and terms are applicable to practical knot-tying, despite the differences between real-world and theoretical knots, but the esoterica of topology are inaccessible to anyone unfamiliar with that branch of mathematics. To highlight these challenges some examples of knots encountered in case work are presented. Significantly, an overview of a few previously ignored issues is examined and several new concepts are introduced. An emphasis is placed on identifying structural variations, standardized nomenclature is outlined, and recommended terminology is derived from fields such as forensic science, chemistry, archaeology, topology and the textile industry. Greater precision in knot identifications, characterizations and descriptions can assist investigators in linking specific tying practises to potential suspects, analysing the manner in which knotted evidence was tied, and understanding how knots and ligatures perform in given scenarios. PMID:27320402

  14. Factorization of differential expansion for antiparallel double-braid knots

    NASA Astrophysics Data System (ADS)

    Morozov, A.

    2016-09-01

    Continuing the quest for exclusive Racah matrices, which are needed for evaluation of colored arborescent-knot polynomials in Chern-Simons theory, we suggest to extract them from a new kind of a double-evolution — that of the antiparallel double-braids, which is a simple two-parametric family of two-bridge knots, generalizing the one-parametric family of twist knots. In the case of rectangular representations R = [ r s ] we found an evidence that the corresponding differential expansion miraculously factorizes and can be obtained from that for the twist knots. This reduces the problem of rectangular exclusive Racah to constructing the answers for just a few twist knots. We develop a recent conjecture on the structure of differential expansion for the simplest members of this family (the trefoil and the figure-eight knot) and provide the exhaustive answer for the first unknown case of R = [33]. The answer includes HOMFLY of arbitrary twist and double-braid knots and Racah matrices overline{S} and S — what allows to calculate [33]-colored polynomials for arbitrary arborescent (double-fat) knots. For generic rectangular representations fully described are only the contributions of the single-floor pyramids. One step still remains to be done.

  15. Knot Solitons in Spinor Bose-Einstein Condensates

    NASA Astrophysics Data System (ADS)

    Hall, David; Ray, Michael; Tiurev, Konstantin; Ruokokoski, Emmi; Gheorghe, Andrei Horia; Möttönen, Mikko

    2016-05-01

    Knots are familiar entities that appear at a captivating nexus of art, technology, mathematics and science. Following a lengthy period of theoretical investigation and development, they have recently attracted great experimental interest in classical contexts ranging from knotted DNA and nanostructures to vortex knots in fluids. We demonstrate here the controlled creation and detection of knot solitons in the quantum-mechanical order parameter of a spinor Bose-Einstein condensate. Images of the superfluid reveal the circular shape of the soliton core and its associated linked rings. Our observations of the knot soliton establish an experimental foundation for future studies of their stability, dynamics and applications within quantum systems. Supported in part by NSF Grant PHY-1205822.

  16. Design principles for rapid folding of knotted DNA nanostructures.

    PubMed

    Kočar, Vid; Schreck, John S; Čeru, Slavko; Gradišar, Helena; Bašić, Nino; Pisanski, Tomaž; Doye, Jonathan P K; Jerala, Roman

    2016-01-01

    Knots are some of the most remarkable topological features in nature. Self-assembly of knotted polymers without breaking or forming covalent bonds is challenging, as the chain needs to be threaded through previously formed loops in an exactly defined order. Here we describe principles to guide the folding of highly knotted single-chain DNA nanostructures as demonstrated on a nano-sized square pyramid. Folding of knots is encoded by the arrangement of modules of different stability based on derived topological and kinetic rules. Among DNA designs composed of the same modules and encoding the same topology, only the one with the folding pathway designed according to the 'free-end' rule folds efficiently into the target structure. Besides high folding yield on slow annealing, this design also folds rapidly on temperature quenching and dilution from chemical denaturant. This strategy could be used to design folding of other knotted programmable polymers such as RNA or proteins.

  17. UNEXPECTED IONIZATION STRUCTURE IN ETA CARINAE'S ''WEIGELT KNOTS''

    SciTech Connect

    Remmen, Grant N.; Davidson, Kris; Mehner, Andrea

    2013-08-10

    The Weigelt knots, dense slow-moving ejecta near {eta} Carinae, are mysterious in structure as well as in origin. Using spatially dithered spectrograms obtained with the Hubble Space Telescope/Space Telescope Imaging Spectrograph (HST/STIS), we have partially resolved the ionization zones of one knot. Contrary to simple models, higher ionization levels occur on the outer side, i.e., farther from the star. They cannot represent a bow shock, and no satisfying explanation is yet available-though we sketch one qualitative possibility. STIS spectrograms provide far more reliable spatial measurements of the Weigelt knots than HST images do, and this technique can also be applied to the knots' proper motion problem. Our spatial measurement accuracy is about 10 mas, corresponding to a projected linear scale of the order of 30 AU, which is appreciably smaller than the size of each Weigelt knot.

  18. Design principles for rapid folding of knotted DNA nanostructures

    PubMed Central

    Kočar, Vid; Schreck, John S.; Čeru, Slavko; Gradišar, Helena; Bašić, Nino; Pisanski, Tomaž; Doye, Jonathan P. K.; Jerala, Roman

    2016-01-01

    Knots are some of the most remarkable topological features in nature. Self-assembly of knotted polymers without breaking or forming covalent bonds is challenging, as the chain needs to be threaded through previously formed loops in an exactly defined order. Here we describe principles to guide the folding of highly knotted single-chain DNA nanostructures as demonstrated on a nano-sized square pyramid. Folding of knots is encoded by the arrangement of modules of different stability based on derived topological and kinetic rules. Among DNA designs composed of the same modules and encoding the same topology, only the one with the folding pathway designed according to the ‘free-end' rule folds efficiently into the target structure. Besides high folding yield on slow annealing, this design also folds rapidly on temperature quenching and dilution from chemical denaturant. This strategy could be used to design folding of other knotted programmable polymers such as RNA or proteins. PMID:26887681

  19. The genomes of root-knot nematodes.

    PubMed

    Bird, David McK; Williamson, Valerie M; Abad, Pierre; McCarter, James; Danchin, Etienne G J; Castagnone-Sereno, Philippe; Opperman, Charles H

    2009-01-01

    Plant-parasitic nematodes are the most destructive group of plant pathogens worldwide and are extremely challenging to control. The recent completion of two root-knot nematode genomes opens the way for a comparative genomics approach to elucidate the success of these parasites. Sequencing revealed that Meloidogyne hapla, a diploid that reproduces by facultative, meiotic parthenogenesis, encodes approximately 14,200 genes in a compact, 54 Mpb genome. Indeed, this is the smallest metazoan genome completed to date. By contrast, the 86 Mbp Meloidogyne incognita genome encodes approximately 19,200 genes. This species reproduces by obligate mitotic parthenogenesis and exhibits a complex pattern of aneuploidy. The genome includes triplicated regions and contains allelic pairs with exceptionally high degrees of sequence divergence, presumably reflecting adaptations to the strictly asexual reproductive mode. Both root-knot nematode genomes have compacted gene families compared with the free-living nematode Caenorhabditis elegans, and both encode large suites of enzymes that uniquely target the host plant. Acquisition of these genes, apparently via horizontal gene transfer, and their subsequent expansion and diversification point to the evolutionary history of these parasites. It also suggests new routes to their control. PMID:19400640

  20. Knot Invariants from Topological Recursion on Augmentation Varieties

    NASA Astrophysics Data System (ADS)

    Gu, Jie; Jockers, Hans; Klemm, Albrecht; Soroush, Masoud

    2015-06-01

    Using the duality between Wilson loop expectation values of SU( N) Chern-Simons theory on S 3 and topological open-string amplitudes on the local mirror of the resolved conifold, we study knots on S 3 and their invariants encoded in colored HOMFLY polynomials by means of topological recursion. In the context of the local mirror Calabi-Yau threefold of the resolved conifold, we generalize the topological recursion of the remodelled B-model in order to study branes beyond the class of toric Harvey-Lawson special Lagrangians—as required for analyzing non-trivial knots on S 3. The basic ingredients for the proposed recursion are the spectral curve, given by the augmentation variety of the knot, and the calibrated annulus kernel, encoding the topological annulus amplitudes associated to the knot. We present an explicit construction of the calibrated annulus kernel for torus knots and demonstrate the validity of the topological recursion. We further argue that—if an explicit form of the calibrated annulus kernel is provided for any other knot—the proposed topological recursion should still be applicable. We study the implications of our proposal for knot theory, which exhibit interesting consequences for colored HOMFLY polynomials of mutant knots.

  1. Controlling the Motion of Knotted Polymers through Nanopores

    NASA Astrophysics Data System (ADS)

    Narsimhan, Vivek; Renner, C. Benjamin; Doyle, Patrick

    Nanopore sequencing is a technique where DNA moves through a pore and base-pair information is read along the chain as an electric signal. One hurdle facing this technique is that DNA passes too quickly through the pore, rendering the signal to be too noisy. In this talk, we discuss one strategy to control the speed by which polymers move through pores. By tying a knot on a polymer chain, we find that we can jam the polymer at the pore's entrance and halt translocation completely. This idea by itself may not seem useful, but by cycling the field on and off at the relaxation time scale of the knot, we can control the swelling dynamics of the knot at the pore's entrance, and hence ratchet the polymer through the pore. This talk focuses on two parts. First, we will discuss the dynamics of a knot jamming at the pore entrance and determine what sets the critical tension to halt translocation. We will determine how knot topology affects these results and discuss what regimes lead to large fluctuations in the translocation speed. We will then discuss the dynamics of a knot under a time-dependent, periodic force. Lastly, we develop a model to describe the knot's swelling dynamics during relaxation, and use this to explain some of the trends observed in our simulations. Now at Liquiglide.

  2. EJECTA KNOT FLICKERING, MASS ABLATION, AND FRAGMENTATION IN CASSIOPEIA A

    SciTech Connect

    Fesen, Robert A.; Zastrow, Jordan A.; Hammell, Molly C.; Shull, J. Michael; Silvia, Devin W.

    2011-08-01

    Ejecta knot flickering, ablation tails, and fragmentation are expected signatures associated with the gradual dissolution of high-velocity supernova (SN) ejecta caused by their passage through an inhomogeneous circumstellar medium or interstellar medium (ISM). Such phenomena mark the initial stages of the gradual merger of SN ejecta with and the enrichment of the surrounding ISM. Here we report on an investigation of this process through changes in the optical flux and morphology of several high-velocity ejecta knots located in the outskirts of the young core-collapse SN remnant Cassiopeia A using Hubble Space Telescope images. Examination of WFPC2 F675W and combined ACS F625W + F775W images taken between 1999 June and 2004 December of several dozen debris fragments in the remnant's northeast ejecta stream and along the remnant's eastern limb reveal substantial emission variations ('flickering') over timescales as short as nine months. Such widespread and rapid variability indicates knot scale lengths {approx_equal} 10{sup 15} cm and a highly inhomogeneous surrounding medium. We also identify a small percentage of ejecta knots located all around the remnant's outer periphery which show trailing emissions typically 0.''2-0.''7 in length aligned along the knot's direction of motion suggestive of knot ablation tails. We discuss the nature of these trailing emissions as they pertain to ablation cooling, knot disruption, and fragmentation, and draw comparisons to the emission 'strings' seen in {eta} Car. Finally, we identify several tight clusters of small ejecta knots which resemble models of shock-induced fragmentation of larger SN ejecta knots caused by a high-velocity interaction with a lower density ambient medium.

  3. New knotted solutions of Maxwell's equations

    NASA Astrophysics Data System (ADS)

    Hoyos, Carlos; Sircar, Nilanjan; Sonnenschein, Jacob

    2015-06-01

    In this paper we have further developed the study of topologically non-trivial solutions of vacuum electrodynamics. We have discovered a novel method of generating such solutions by applying conformal transformations with complex parameters on known solutions expressed in terms of Bateman's variables. This has enabled us to obtain a wide class of solutions from the basic configuration, such as constant electromagnetic fields and plane-waves. We have introduced a covariant formulation of Bateman's construction and discussed the conserved charges associated with the conformal group as well as a set of four types of conserved helicities. We have also given a formulation in terms of quaternions. This led to a simple map between the electromagnetic knotted and linked solutions into flat connections of SU(2) gauge theory. We have computed the corresponding Chern-Simons charge in a class of solutions and the charge takes integer values.

  4. Ejecta Knot Evolution in Cas A

    NASA Astrophysics Data System (ADS)

    Rutherford, John; Figueroa-Feliciano, E.; Dewey, D.; Trowbridge, S.; Bastien, F.; Sato, K.

    2011-01-01

    Supernova remnants are remarkable laboratories for studying, among other phenomena, explosive nucleosynthesis and plasma dynamics. Time-dependent signatures of such processes can further inform our understanding, and may be found in widely spaced epochs of observation from high spatial and spectral resolution instruments. We investigated the spectral evolution in the X-ray band of the bright ejecta knots in Cassiopeia A over the last decade. Both dispersed and non-dispersed spectra from the Chandra HETG and ACIS instruments were used for this study, helping to better constrain signs of evolution. We present our findings of how such physical properties as the temperature, elemental abundances, velocity, and non-equilibrium ionization age changed over ten years of the several hundred year old remnant's lifetime, along with a careful analysis of the confounding background contamination and model parameter correlations.

  5. Knotted Strings and Leptonic Flavor Structure

    NASA Astrophysics Data System (ADS)

    Kephart, T. W.; Leser, P.; Päs, H.

    2012-12-01

    We propose a third idea for the explanation of the leptonic flavor structure in addition to the prominent approaches based on flavor symmetry and anarchy. Typical flavor patterns can be modeled by using mass spectra obtained from the discrete lengths spectrum of tight knots and links. We assume that a string theory model exists in which this idea can be incorporated via the Majorana mass structure of a type I seesaw model. It is shown by a scan over the parameter space that such a model is able to provide an excellent fit to current neutrino data and that it predicts a normal neutrino mass hierarchy as well as a small mixing angle θ13. Startlingly, such scenarios could be related to the dimensionality of spacetime via an anthropic argument.

  6. Intraoperative wide bore nasogastric tube knotting: A rare incidence.

    PubMed

    Lamba, Sangeeta; Sethi, Surendra K; Khare, Arvind; Saini, Sudheendra

    2016-01-01

    Nasogastric tubes are commonly used in anesthetic practice for gastric decompression in surgical patients intraoperatively. The indications for its use are associated with a number of potential complications. Knotting of small-bore nasogastric tubes is usually common both during insertion and removal as compared to wide bore nasogastric tubes. Knotting of wide bore nasogastric tube is a rare complication and if occurs usually seen in long standing cases. We hereby report a case of incidental knotting of wide bore nasogastric tube that occurred intraoperatively.

  7. Linked and knotted chimera filaments in oscillatory systems.

    PubMed

    Lau, Hon Wai; Davidsen, Jörn

    2016-07-01

    While the existence of stable knotted and linked vortex lines has been established in many experimental and theoretical systems, their existence in oscillatory systems and systems with nonlocal coupling has remained elusive. Here, we present strong numerical evidence that stable knots and links such as trefoils and Hopf links do exist in simple, complex, and chaotic oscillatory systems if the coupling between the oscillators is neither too short ranged nor too long ranged. In this case, effective repulsive forces between vortex lines in knotted and linked structures stabilize curvature-driven shrinkage observed for single vortex rings. In contrast to real fluids and excitable media, the vortex lines correspond to scroll wave chimeras [synchronized scroll waves with spatially extended (tubelike) unsynchronized filaments], a prime example of spontaneous synchrony breaking in systems of identical oscillators. In the case of complex oscillatory systems, this leads to a topological superstructure combining knotted filaments and synchronization defect sheets.

  8. Linked and knotted chimera filaments in oscillatory systems

    NASA Astrophysics Data System (ADS)

    Lau, Hon Wai; Davidsen, Jörn

    2016-07-01

    While the existence of stable knotted and linked vortex lines has been established in many experimental and theoretical systems, their existence in oscillatory systems and systems with nonlocal coupling has remained elusive. Here, we present strong numerical evidence that stable knots and links such as trefoils and Hopf links do exist in simple, complex, and chaotic oscillatory systems if the coupling between the oscillators is neither too short ranged nor too long ranged. In this case, effective repulsive forces between vortex lines in knotted and linked structures stabilize curvature-driven shrinkage observed for single vortex rings. In contrast to real fluids and excitable media, the vortex lines correspond to scroll wave chimeras [synchronized scroll waves with spatially extended (tubelike) unsynchronized filaments], a prime example of spontaneous synchrony breaking in systems of identical oscillators. In the case of complex oscillatory systems, this leads to a topological superstructure combining knotted filaments and synchronization defect sheets.

  9. Linked and knotted chimera filaments in oscillatory systems.

    PubMed

    Lau, Hon Wai; Davidsen, Jörn

    2016-07-01

    While the existence of stable knotted and linked vortex lines has been established in many experimental and theoretical systems, their existence in oscillatory systems and systems with nonlocal coupling has remained elusive. Here, we present strong numerical evidence that stable knots and links such as trefoils and Hopf links do exist in simple, complex, and chaotic oscillatory systems if the coupling between the oscillators is neither too short ranged nor too long ranged. In this case, effective repulsive forces between vortex lines in knotted and linked structures stabilize curvature-driven shrinkage observed for single vortex rings. In contrast to real fluids and excitable media, the vortex lines correspond to scroll wave chimeras [synchronized scroll waves with spatially extended (tubelike) unsynchronized filaments], a prime example of spontaneous synchrony breaking in systems of identical oscillators. In the case of complex oscillatory systems, this leads to a topological superstructure combining knotted filaments and synchronization defect sheets. PMID:27575065

  10. Knots cascade detected by a monotonically decreasing sequence of values

    NASA Astrophysics Data System (ADS)

    Liu, Xin; Ricca, Renzo L.

    2016-04-01

    Due to reconnection or recombination of neighboring strands superfluid vortex knots and DNA plasmid torus knots and links are found to undergo an almost identical cascade process, that tend to reduce topological complexity by stepwise unlinking. Here, by using the HOMFLYPT polynomial recently introduced for fluid knots, we prove that under the assumption that topological complexity decreases by stepwise unlinking this cascade process follows a path detected by a unique, monotonically decreasing sequence of numerical values. This result holds true for any sequence of standardly embedded torus knots T(2, 2n + 1) and torus links T(2, 2n). By this result we demonstrate that the computation of this adapted HOMFLYPT polynomial provides a powerful tool to measure topological complexity of various physical systems.

  11. Knots cascade detected by a monotonically decreasing sequence of values

    PubMed Central

    Liu, Xin; Ricca, Renzo L.

    2016-01-01

    Due to reconnection or recombination of neighboring strands superfluid vortex knots and DNA plasmid torus knots and links are found to undergo an almost identical cascade process, that tend to reduce topological complexity by stepwise unlinking. Here, by using the HOMFLYPT polynomial recently introduced for fluid knots, we prove that under the assumption that topological complexity decreases by stepwise unlinking this cascade process follows a path detected by a unique, monotonically decreasing sequence of numerical values. This result holds true for any sequence of standardly embedded torus knots T(2, 2n + 1) and torus links T(2, 2n). By this result we demonstrate that the computation of this adapted HOMFLYPT polynomial provides a powerful tool to measure topological complexity of various physical systems. PMID:27052386

  12. The beauty of knots at the molecular level.

    PubMed

    Sauvage, Jean-Pierre; Amabilino, David B

    2012-01-01

    What makes a given object look beautiful to the observer, be it in the macroscopic world or at the molecular level? This very general question will be briefly addressed at the beginning of this essay, in relation to contemporary molecular chemistry and biology, leading to the general statement that, most of the time, beauty is tightly connected to function as well as to the cultural background of the observer. The main topic of the present article will be that of topologically non-trivial molecules or molecular ensembles and the fascination that such species have exerted on molecular or solid state chemists. Molecules with a graph identical to Kuratowski's K₅ or K₃,₃ graphs are indeed highly attractive from an aesthetical viewpoint, but perhaps even more fascinating and beautiful are molecular knots. A general discussion will be devoted to these compounds, which are still considered as exotic species because of the very limited number of efficient synthetic strategies leading to their preparation. Particularly efficient are templated approaches based either on transition metals such as copper(I) or on organic groups able to form hydrogen bonds or acceptor-donor stacks. A particularly noteworthy property of knots, and in particular of the trefoil knot, is their topological chirality. The isolation of both enantiomers of the trefoil knot (3₁) could be achieved and showed that such species have fascinating chiroptical properties. Finally, various routes to more complex and beautiful knots than the trefoil knot, which is the simplest non-trivial knot, will be discussed in line with the remarkable ability of transition metals to gather and orient in a very precise fashion several organic components in their coordination spheres, thus leading to synthetic precursors displaying geometries which are perfectly well adapted to the preparation of the desired knots or links.

  13. Shunt insufficiency due to knot formation in the peritoneal catheter.

    PubMed

    Fekete, Gábor; Nagy, Andrea; Pataki, István; Bognar, László; Novák, László

    2013-07-30

    The authors report a rare case of the peripheral obstruction of a ventriculoperitoneal shunt. Premature baby was operated on hydrocephalus due to germinal matrix bleeding. After two months of implantation of venticuloperitoneal shunt peripheral insufficiency of the system was emerged. During the shunt revision extensive knot formation became visible. We simply cut the catheter above the knot and the working shunt was replaced into the abdominal cavity. The postoperative course was uneventful and the baby was free of complaints for more than one year. The pathomechanism of knot formation is not clear thus the discovery of the problem during the operation is an unexpected event. In our opinion tight knot cannot be spontaneously formed intraabdominally. Loose knots can be developed and can reduce the capacity of liquor flow. We think that the knot tightens during pulling out. Longer peritoneal catheters can precipitate multiple looping and/or axial torquations and increase the peripheral resistance of the shunt. In such cases when the pulling out is challenged conversion to laparotomy is suggested.

  14. Probe knots and Hopf insulators with ultracold atoms

    NASA Astrophysics Data System (ADS)

    Deng, Dong-Ling; Wang, Sheng-Tao; Sun, Kai; Duan, Lu-Ming

    2015-05-01

    Knots and links are fascinating and intricate topological objects that have played a prominent role in physical and life sciences. Their influence spans from DNA and molecular chemistry to vortices in superfluid helium, defects in liquid crystals and cosmic strings in the early universe. Here, we show that knotted structures also exist in a peculiar class of three dimensional topological insulators--the Hopf insulators. In particular, we demonstrate that the spin textures of Hopf insulators in momentum space are twisted in a nontrivial way, which implies various knot and link structures. We further illustrate that the knots and nontrivial spin textures can be probed via standard time-of-flight images in cold atoms as preimage contours of spin orientations in stereographic coordinates. The extracted Hopf invariants, knots, and links are validated to be robust to typical experimental imperfections. Our work establishes the existence of knotted structures in cold atoms and may have potential applications in spintronics and quantum information processings. We thank X.-J. Liu and G. Ortiz for helpful discussions. S.T.W., D.L.D., and L.M.D. are supported by the NBRPC 2011CBA00300, the IARPA MUSIQC program, the ARO and the AFOSR MURI program. K.S. acknowledges support from NSF under Grant No. PHY1402971.

  15. Knots and Gamma Classes in Open Topological String Theory

    NASA Astrophysics Data System (ADS)

    Mahowald, Matthew

    This thesis explores some mathematical applications of string dualities in open topological string theory and presents some new techniques for studying and computing open Gromov-Witten invariants. First, we prove a mild generalization of the gamma class formula of [BCR13], and show that it applies in two novel examples: the quintic threefold Q with Lagrangian given by the real quintic QR Q, and for Lagrangians LK ? X = O P1 (--1, --1) obtained from the conormal bundles of (r, s) torus knots K ? S3 via the conifold transition. Disk enumeration on (Q, Q R ) was first considered in [PSW08], and disk enumeration for (X, LK) was studied in winding-1 in [DSV13]. The gamma class formula agrees with the results of [DSV13] and [PSW08], and we generalize the formula of [DSV13] to arbitrary winding. Next we study a relationship between mirror symmetry and knot contact homology described in [AENV14, AV12]. For knots K ? S 3 , large-N duality relates open Gromov-Witten theory on (X, L_K ) to SU (N) Chern-Simons theory on (S3, K). We use the conjecture of [AV12] to compute open Gromov-Witten invariants of (X, L K) through mirror symmetry in many examples, including several non-toric knots. We also find further evidence for this conjecture: for ( r, s) torus knots, we find a formula for the genus-0, 1-boundary-component, degree-d, winding-w open Gromov-Witten invariants of (X, LK ) using localization. This formula agrees with the results of the mirror symmetry calculation. Moreover, using this formula, we describe a method for obtaining the augmentation polynomial of a knot K from the open Gromov-Witten invariants of ( X, LK ). This method is shown to correctly recover the augmentation polynomial for the unknot and (3, 2) torus knot.

  16. To Knot or Not-That is the Question: A Nanofluidic Knot Factory based on Compression of Single DNA Molecules against Slit Barriers in Nanochannels

    NASA Astrophysics Data System (ADS)

    Amin, Susan; Khorshid, Ahmed; Zeng, Lili; Zimny, Philip; Reisner, Walter

    Knots can form during DNA packaging in chromosome and obstruct mapping of DNA in nanochannels. Studies have focused on theoretical and numerical studies of knots, but an efficient and fully controlled means of knotting has not yet been explored. Here, we introduce a knot factory on chip based on pneumatic compression of single T4 DNA against a slit barrier in a nanochannel. The DNA are compressed to a well-defined fraction of their initial equilibrium extension. The pressure is then released and the DNA molecules relax back to their equilibrium extension; knots are present along the relaxed DNA, visualized as sharply localized regions of high intensity. Via repeated compression and relaxation, we can measure the probabilities of forming single and multiple knot states and the distribution of knot sizes as a function of fractional compression and waiting time in the compressed state. We show that the total probability of knot formation increases with greater compression and waiting time.These findings are well described via a knot formation free energy derived from scaling arguments, suggesting that the enhanced knotting probability at high compression arises from avoiding the free energy cost due to self-exclusion interactions that would arise from contour stored in the knot.

  17. YAP overexpression affects tooth morphogenesis and enamel knot patterning.

    PubMed

    Liu, M; Zhao, S; Wang, X P

    2014-05-01

    Teeth develop through distinct morphological stages. At the cap stage, a compactly clustered and concentrically arranged cell mass, the enamel knot, appears at the tip of the enamel organ. Cells in this knot express sets of key molecules, and as such have been proposed to act as a signaling center directing tooth morphogenesis and tooth cusp formation. YAP is a transcriptional co-activator of the Hippo signaling pathway that is essential for the proper regulation of organ growth. In this study, we analyzed the tooth phenotype in transgenic mice that overexpressed a constitutively active form of YAP in the dental epithelium. We found that overexpression of YAP resulted in deformed tooth morphogenesis with widened dental lamina. In addition, the enamel knot was mislocated to the upper portion of the enamel organ, where it remained devoid of proliferating cells and contained apoptotic cells with intense Edar transcripts and reduced E-cadherin expression. Interestingly, some signaling molecules, such as Shh, Fgf4, and Wnt10a, were not expressed in this mislocated enamel knot, but remained at the tip of the enamel organ. Analysis of these data suggests that the signaling center is induced by reciprocal epithelial-mesenchymal interactions, and its induction may be independent of the enamel knot.

  18. Equations on knot polynomials and 3d/5d duality

    SciTech Connect

    Mironov, A.; Morozov, A.

    2012-09-24

    We briefly review the current situation with various relations between knot/braid polynomials (Chern-Simons correlation functions), ordinary and extended, considered as functions of the representation and of the knot topology. These include linear skein relations, quadratic Plucker relations, as well as 'differential' and (quantum) A-polynomial structures. We pay a special attention to identity between the A-polynomial equations for knots and Baxter equations for quantum relativistic integrable systems, related through Seiberg-Witten theory to 5d super-Yang-Mills models and through the AGT relation to the q-Virasoro algebra. This identity is an important ingredient of emerging a 3d- 5d generalization of the AGT relation. The shape of the Baxter equation (including the values of coefficients) depend on the choice of the knot/braid. Thus, like the case of KP integrability, where (some, so far torus) knots parameterize particular points of the Universal Grassmannian, in this relation they parameterize particular points in the moduli space of many-body integrable systems of relativistic type.

  19. Characteristics of oscillations in magnetic knots of solar faculae

    NASA Astrophysics Data System (ADS)

    Chelpanov, A. A.; Kobanov, N. I.; Kolobov, D. Yu.

    2015-10-01

    The characteristics of oscillations of the intensity, magnetic field, andDoppler velocity in facular magnetic knots are compared with those at the facula periphery, where the magnetic field has a moderate intensity. The analysis is based on images in the FeI 6173 Å, 1700 Å, and He II 304 Å lines obtained with the Solar Dynamics Observatory, which are formed in the lower photosphere, upper photosphere, and transition zone, respectively. The spectra of the oscillations of the longitudinal magnetic field in magnetic knots show peaks at a frequency of about 5 mHz, which are not observed at the faculae peripheries. The spectra of the photospheric oscillations of the intensity and Doppler velocity in magnetic knots and in areas of moderate magnetic field are similar, but the oscillation power is a factor of two to four lower in the knots. The maximum spectral peaks in the HeII 304 Å line are mainly distributed in the range 3-6 mHz above magnetic knots and in the range 1.5-3 mHz above periphery regions. It is proposed that this distribution of the oscillations is due to the magnetic-field topologies in faculae: the m

  20. Electrophoretic mobility of supercoiled, catenated and knotted DNA molecules

    PubMed Central

    Cebrián, Jorge; Kadomatsu-Hermosa, Maridian J.; Castán, Alicia; Martínez, Víctor; Parra, Cristina; Fernández-Nestosa, María José; Schaerer, Christian; Martínez-Robles, María-Luisa; Hernández, Pablo; Krimer, Dora B.; Stasiak, Andrzej; Schvartzman, Jorge B.

    2015-01-01

    We systematically varied conditions of two-dimensional (2D) agarose gel electrophoresis to optimize separation of DNA topoisomers that differ either by the extent of knotting, the extent of catenation or the extent of supercoiling. To this aim we compared electrophoretic behavior of three different families of DNA topoisomers: (i) supercoiled DNA molecules, where supercoiling covered the range extending from covalently closed relaxed up to naturally supercoiled DNA molecules; (ii) postreplicative catenanes with catenation number increasing from 1 to ∼15, where both catenated rings were nicked; (iii) knotted but nicked DNA molecules with a naturally arising spectrum of knots. For better comparison, we studied topoisomer families where each member had the same total molecular mass. For knotted and supercoiled molecules, we analyzed dimeric plasmids whereas catenanes were composed of monomeric forms of the same plasmid. We observed that catenated, knotted and supercoiled families of topoisomers showed different reactions to changes of agarose concentration and voltage during electrophoresis. These differences permitted us to optimize conditions for their separation and shed light on physical characteristics of these different types of DNA topoisomers during electrophoresis. PMID:25414338

  1. The northwestern ejecta knot in SN 1006

    NASA Astrophysics Data System (ADS)

    Broersen, S.; Vink, J.; Miceli, M.; Bocchino, F.; Maurin, G.; Decourchelle, A.

    2013-04-01

    Aims: We want to probe the physics of fast collision-less shocks in supernova remnants. We are interested in the non-equilibration of temperatures and particle acceleration. Specifically, we aim to measure the oxygen temperature with regards to the electron temperature. In addition, we search for synchrotron emission in the northwestern thermal rim. Methods: This study is part of a dedicated deep observational project of SN 1006 using XMM-Newton, which provides us with the currently best resolution spectra of the bright northwestern oxygen knot. We aim to use the reflection grating spectrometer to measure the thermal broadening of the O vii line triplet by convolving the emission profile of the remnant with the response matrix. Results: The line broadening was measured as σe = 2.4 ± 0.3 eV, corresponding to an oxygen temperature of 275-63+72 keV. From the EPIC spectra we obtain an electron temperature of 1.35 ± 0.10 keV. The difference in temperature between the species provides further evidence of non-equilibration of temperatures in a shock. In addition, we find evidence of a bow shock that emits X-ray synchrotron radiation, which is at odds with the general idea that because of the magnetic field orientation only in the NE and SW region, X-ray synchrotron radiation should be emitted. We find an unusual Hα and X-ray synchrotron geometry, in that the Hα emission peaks downstream of the synchrotron emission. This may be an indication of a peculiar Hα shock in which the density is lower and the neutral fraction is higher than in other supernova remnants, resulting in a peak in Hα emission further downstream of the shock.

  2. Novel application of an established technique for removing a knotted ureteric stent.

    PubMed

    Tempest, Heidi; Turney, Ben; Kumar, Sunil

    2011-01-01

    This report describes a case whereby a ureteric stent became knotted during removal and lodged within the upper ureter. The authors describe a novel minimally invasive technique to remove the knotted ureteric stent using the holmium laser. PMID:22701009

  3. Topological zoo of free-standing knots in confined chiral nematic fluids

    NASA Astrophysics Data System (ADS)

    Seč, David; Čopar, Simon; Žumer, Slobodan

    2014-01-01

    Knotted fields are an emerging research topic relevant to different areas of physics where topology plays a crucial role. Recent realization of knotted nematic disclinations stabilized by colloidal particles raised a challenge of free-standing knots. Here we demonstrate the creation of free-standing knotted and linked disclination loops in the cholesteric ordering fields, which are confined to spherical droplets with homeotropic surface anchoring. Our approach, using free energy minimization and topological theory, leads to the stabilization of knots via the interplay of the geometric frustration and intrinsic chirality. Selected configurations of the lowest complexity are characterized by knot or link types, disclination lengths and self-linking numbers. When cholesteric pitch becomes short on the confinement scale, the knotted structures change to practically unperturbed cholesteric structures with disclinations expelled close to the surface. The drops with knots could be controlled by optical beams and may be used for photonic elements.

  4. Untangling Knots Via Reaction-Diffusion Dynamics of Vortex Strings.

    PubMed

    Maucher, Fabian; Sutcliffe, Paul

    2016-04-29

    We introduce and illustrate a new approach to the unknotting problem via the dynamics of vortex strings in a nonlinear partial differential equation of reaction-diffusion type. To untangle a given knot, a Biot-Savart construction is used to initialize the knot as a vortex string in the FitzHugh-Nagumo equation. Remarkably, we find that the subsequent evolution preserves the topology of the knot and can untangle an unknot into a circle. Illustrative test case examples are presented, including the untangling of a hard unknot known as the culprit. Our approach to the unknotting problem has two novel features, in that it applies field theory rather than particle mechanics and uses reaction-diffusion dynamics in place of energy minimization. PMID:27176541

  5. Untangling Knots Via Reaction-Diffusion Dynamics of Vortex Strings.

    PubMed

    Maucher, Fabian; Sutcliffe, Paul

    2016-04-29

    We introduce and illustrate a new approach to the unknotting problem via the dynamics of vortex strings in a nonlinear partial differential equation of reaction-diffusion type. To untangle a given knot, a Biot-Savart construction is used to initialize the knot as a vortex string in the FitzHugh-Nagumo equation. Remarkably, we find that the subsequent evolution preserves the topology of the knot and can untangle an unknot into a circle. Illustrative test case examples are presented, including the untangling of a hard unknot known as the culprit. Our approach to the unknotting problem has two novel features, in that it applies field theory rather than particle mechanics and uses reaction-diffusion dynamics in place of energy minimization.

  6. Untangling Knots Via Reaction-Diffusion Dynamics of Vortex Strings

    NASA Astrophysics Data System (ADS)

    Maucher, Fabian; Sutcliffe, Paul

    2016-04-01

    We introduce and illustrate a new approach to the unknotting problem via the dynamics of vortex strings in a nonlinear partial differential equation of reaction-diffusion type. To untangle a given knot, a Biot-Savart construction is used to initialize the knot as a vortex string in the FitzHugh-Nagumo equation. Remarkably, we find that the subsequent evolution preserves the topology of the knot and can untangle an unknot into a circle. Illustrative test case examples are presented, including the untangling of a hard unknot known as the culprit. Our approach to the unknotting problem has two novel features, in that it applies field theory rather than particle mechanics and uses reaction-diffusion dynamics in place of energy minimization.

  7. Classification of knotted tori in 2-metastable dimension

    SciTech Connect

    Cencelj, Matija; Repovs, Dusan; Skopenkov, Mihail B

    2012-11-30

    This paper is devoted to the classical Knotting Problem: for a given manifold N and number m describe the set of isotopy classes of embeddings N{yields}S{sup m}. We study the specific case of knotted tori, that is, the embeddings S{sup p} Multiplication-Sign S{sup q}{yields}S{sup m}. The classification of knotted tori up to isotopy in the metastable dimension range m {>=} p + 3/2q + 2, p{<=}q, was given by Haefliger, Zeeman and A. Skopenkov. We consider the dimensions below the metastable range and give an explicit criterion for the finiteness of this set of isotopy classes in the 2-metastable dimension. Bibliography: 35 titles.

  8. Differential expansion and rectangular HOMFLY for the figure eight knot

    NASA Astrophysics Data System (ADS)

    Morozov, A.

    2016-10-01

    Differential expansion (DE) for a Wilson loop average in representation R is built to respect degenerations of representations for small groups. At the same time it behaves nicely under some changes of the loop, e.g. of some knots in the case of 3d Chern-Simons theory. Especially simple is the relation between the DE for the trefoil 31 and for the figure eight knot 41. Since arbitrary colored HOMFLY for the trefoil are known from the Rosso-Jones formula, it is therefore enough to find their DE in order to make a conjecture for the figure eight. We fulfill this program for all rectangular representation R = [rs ], i.e. make a plausible conjecture for the rectangularly colored HOMFLY of the figure eight knot, which generalizes the old result for totally symmetric and antisymmetric representations.

  9. KNOTS AND RANDOM WALKS IN VIBRATED GRANULAR CHAINS

    SciTech Connect

    E. BEN-NAIM; ET AL

    2000-08-01

    The authors study experimentally statistical properties of the opening times of knots in vertically vibrated granular chains. Our measurements are in good qualitative and quantitative agreement with a theoretical model involving three random walks interacting via hard core exclusion in one spatial dimension. In particular, the knot survival probability follows a universal scaling function which is independent of the chain length, with a corresponding diffusive characteristic time scale. Both the large-exit-time and the small-exit-time tails of the distribution are suppressed exponentially, and the corresponding decay coefficients are in excellent agreement with the theoretical values.

  10. Knots and physics: Old wine in new bottles

    NASA Astrophysics Data System (ADS)

    Hirshfeld, Allen C.

    1998-12-01

    The history of the interplay between physics and mathematics in the theory of knots is briefly reviewed. In particular, Gauss' original definition of the linking number in the context of electromagnetism is presented, along with analytical, algebraical, and geometrical derivations. In a modern context, the linking number appears in the first-order term in the perturbation expansion of a Wilson loop in Chern-Simons quantum field theory. New knot invariants, the Vassiliev numbers, arise in higher-order terms of the expansion, and can be written in a form which shows them to be generalizations of the linking number.

  11. Excitation of knotted vortex lines in matter waves

    NASA Astrophysics Data System (ADS)

    Maucher, F.; Gardiner, S. A.; Hughes, I. G.

    2016-06-01

    We study the creation of knotted ultracold matter waves in Bose–Einstein condensates via coherent two-photon Raman transitions with a Λ level configuration. The Raman transition allows an indirect transfer of atoms from the internal state | a> to the target state | b> via an excited state | e> , that would be otherwise dipole-forbidden. This setup enables us to imprint three-dimensional knotted vortex lines embedded in the probe field to the density in the target state. We elaborate on experimental feasibility as well as on subsequent dynamics of the matter wave.

  12. The Mental Manipulation of 2-D Representations of Knots as Deformable Structures.

    ERIC Educational Resources Information Center

    McLeay, Heather; Piggins, David

    1996-01-01

    Spatial tests involving the comparison of diagrams of interlaced ropes or knots at varying orientations were given to (n=21) subjects, mostly English college undergraduates, to determine an ordering in terms of complexity of tasks involving the mental manipulation of the knots. Certain knot shapes were processed faster than others and greater…

  13. Coaxial rings and H2 knots in Hubble 12

    NASA Astrophysics Data System (ADS)

    Hsia, Chih-Hao; Kwok, Sun; Chau, Wayne; Zhang, Yong

    2016-07-01

    Hubble 12 (Hb 12) is a young planetary nebula (PN) exhibiting nested shells. We present new near-infrared narrow-band imaging observations of Hb 12 using the Canada-France- Hawaii Telescope (CFHT). A number of co-axial rings aligned with the bipolar lobes and two pairs of separate H2 knots with different orientations are detected.

  14. Spontaneous knot; a rare cause of ventriculoperitoneal shunt blockage.

    PubMed

    Mohammed, Wail; Wiig, Ulrikke; Caird, John

    2011-02-01

    A 14-year old X linked congenital hydrocephalus presented with unexplained headaches and vomiting. He had external ventricular drain and intracranial pressure monitoring (ICP). Subsequently, he underwent exploration and removal of previously inserted ventriculoperitoneal (VP) shunts. On retrieval of peritoneal catheters a double knot was noted between his two distal catheters. This case illustrates a rare cause of ventriculoperitoneal shunt malfunction.

  15. Factorization of colored knot polynomials at roots of unity

    NASA Astrophysics Data System (ADS)

    Kononov, Ya.; Morozov, A.

    2015-07-01

    HOMFLY polynomials are the Wilson-loop averages in Chern-Simons theory and depend on four variables: the closed line (knot) in 3d space-time, representation R of the gauge group SU (N) and exponentiated coupling constant q. From analysis of a big variety of different knots we conclude that at q, which is a 2m-th root of unity, q2m = 1, HOMFLY polynomials in symmetric representations [ r ] satisfy recursion identity: Hr+m =Hr ṡHm for any A =qN, which is a generalization of the property Hr = H1r for special polynomials at m = 1. We conjecture a further generalization to arbitrary representation R, which, however, is checked only for torus knots. Next, Kashaev polynomial, which arises from HR at q2 = e 2 πi / | R |, turns equal to the special polynomial with A substituted by A| R |, provided R is a single-hook representations (including arbitrary symmetric) - what provides a q - A dual to the similar property of Alexander polynomial. All this implies non-trivial relations for the coefficients of the differential expansions, which are believed to provide reasonable coordinates in the space of knots - existence of such universal relations means that these variables are still not unconstrained.

  16. Wall-crossing invariants: from quantum mechanics to knots

    SciTech Connect

    Galakhov, D. E-mail: galakhov@physics.rutgers.edu; Mironov, A. Morozov, A.

    2015-03-15

    We offer a pedestrian-level review of the wall-crossing invariants. The story begins from the scattering theory in quantum mechanics where the spectrum reshuffling can be related to permutations of S-matrices. In nontrivial situations, starting from spin chains and matrix models, the S-matrices are operatorvalued and their algebra is described in terms of R- and mixing (Racah) U-matrices. Then the Kontsevich-Soibelman (KS) invariants are nothing but the standard knot invariants made out of these data within the Reshetikhin-Turaev-Witten approach. The R and Racah matrices acquire a relatively universal form in the semiclassical limit, where the basic reshufflings with the change of moduli are those of the Stokes line. Natural from this standpoint are matrices provided by the modular transformations of conformal blocks (with the usual identification R = T and U = S), and in the simplest case of the first degenerate field (2, 1), when the conformal blocks satisfy a second-order Shrödinger-like equation, the invariants coincide with the Jones (N = 2) invariants of the associated knots. Another possibility to construct knot invariants is to realize the cluster coordinates associated with reshufflings of the Stokes lines immediately in terms of check-operators acting on solutions of the Knizhnik-Zamolodchikov equations. Then the R-matrices are realized as products of successive mutations in the cluster algebra and are manifestly described in terms of quantum dilogarithms, ultimately leading to the Hikami construction of knot invariants.

  17. Velocity, energy, and helicity of vortex knots and unknots

    NASA Astrophysics Data System (ADS)

    Maggioni, F.; Alamri, S.; Barenghi, C. F.; Ricca, R. L.

    2010-08-01

    In this paper we determine the velocity, the energy, and estimate writhe and twist helicity contributions of vortex filaments in the shape of torus knots and unknots (as toroidal and poloidal coils) in a perfect fluid. Calculations are performed by numerical integration of the Biot-Savart law. Vortex complexity is parametrized by the winding number w given by the ratio of the number of meridian wraps to that of longitudinal wraps. We find that for w<1 vortex knots and toroidal coils move faster and carry more energy than a reference vortex ring of same size and circulation, whereas for w>1 knots and poloidal coils have approximately same speed and energy of the reference vortex ring. Helicity is dominated by writhe contributions. Finally, we confirm the stabilizing effect of the Biot-Savart law for all knots and unknots tested, found to be structurally stable over a distance of several diameters. Our results also apply to quantized vortices in superfluid H4e .

  18. Velocity, energy, and helicity of vortex knots and unknots.

    PubMed

    Maggioni, F; Alamri, S; Barenghi, C F; Ricca, R L

    2010-08-01

    In this paper we determine the velocity, the energy, and estimate writhe and twist helicity contributions of vortex filaments in the shape of torus knots and unknots (as toroidal and poloidal coils) in a perfect fluid. Calculations are performed by numerical integration of the Biot-Savart law. Vortex complexity is parametrized by the winding number w given by the ratio of the number of meridian wraps to that of longitudinal wraps. We find that for w<1 vortex knots and toroidal coils move faster and carry more energy than a reference vortex ring of same size and circulation, whereas for w>1 knots and poloidal coils have approximately same speed and energy of the reference vortex ring. Helicity is dominated by writhe contributions. Finally, we confirm the stabilizing effect of the Biot-Savart law for all knots and unknots tested, found to be structurally stable over a distance of several diameters. Our results also apply to quantized vortices in superfluid 4He . PMID:20866907

  19. Homochiral and meso figure eight knots and a Solomon link.

    PubMed

    Ponnuswamy, Nandhini; Cougnon, Fabien B L; Pantoş, G Dan; Sanders, Jeremy K M

    2014-06-11

    A homochiral naphthalenediimide-based building block forms in water a disulfide library of macrocycles containing topological isomers. We attempted to identify each of these isomers, and explored the mechanisms leading to their formation. The two most abundant species of the library were assigned as a topologically chiral Solomon link (60% of the library, as measured by high-performance liquid chromatography (HPLC)) and a topologically achiral figure eight knot (18% by HPLC), competing products with formally different geometries but remarkably similar 4-fold symmetries. In contrast, a racemic mixture of building blocks gives the near-quantitative formation of another new and more stable structure, assigned as a meso figure eight knot. Taken together, these results seem to uncover a correlation between the point chirality of the building block used and the topological chirality of the major structure formed. These and the earlier discovery of a trefoil knot also suggest that the number of rigid components in the building block may translate into corresponding knot symmetry and could set the basis of a new strategy for constructing complex topologies. PMID:24831779

  20. Numerical Simulation of Gel Electrophoresis of DNA Knots in Weak and Strong Electric Fields

    PubMed Central

    Weber, C.; Stasiak, A.; De Los Rios, P.; Dietler, G.

    2006-01-01

    Gel electrophoresis allows one to separate knotted DNA (nicked circular) of equal length according to the knot type. At low electric fields, complex knots, being more compact, drift faster than simpler knots. Recent experiments have shown that the drift velocity dependence on the knot type is inverted when changing from low to high electric fields. We present a computer simulation on a lattice of a closed, knotted, charged DNA chain drifting in an external electric field in a topologically restricted medium. Using a Monte Carlo algorithm, the dependence of the electrophoretic migration of the DNA molecules on the knot type and on the electric field intensity is investigated. The results are in qualitative and quantitative agreement with electrophoretic experiments done under conditions of low and high electric fields. PMID:16473912

  1. A Monte Carlo Study of Knots in Long Double-Stranded DNA Chains

    PubMed Central

    Rieger, Florian C.; Virnau, Peter

    2016-01-01

    We determine knotting probabilities and typical sizes of knots in double-stranded DNA for chains of up to half a million base pairs with computer simulations of a coarse-grained bead-stick model: Single trefoil knots and composite knots which include at least one trefoil as a prime factor are shown to be common in DNA chains exceeding 250,000 base pairs, assuming physiologically relevant salt conditions. The analysis is motivated by the emergence of DNA nanopore sequencing technology, as knots are a potential cause of erroneous nucleotide reads in nanopore sequencing devices and may severely limit read lengths in the foreseeable future. Even though our coarse-grained model is only based on experimental knotting probabilities of short DNA strands, it reproduces the correct persistence length of DNA. This indicates that knots are not only a fine gauge for structural properties, but a promising tool for the design of polymer models. PMID:27631891

  2. A Monte Carlo Study of Knots in Long Double-Stranded DNA Chains.

    PubMed

    Rieger, Florian C; Virnau, Peter

    2016-09-01

    We determine knotting probabilities and typical sizes of knots in double-stranded DNA for chains of up to half a million base pairs with computer simulations of a coarse-grained bead-stick model: Single trefoil knots and composite knots which include at least one trefoil as a prime factor are shown to be common in DNA chains exceeding 250,000 base pairs, assuming physiologically relevant salt conditions. The analysis is motivated by the emergence of DNA nanopore sequencing technology, as knots are a potential cause of erroneous nucleotide reads in nanopore sequencing devices and may severely limit read lengths in the foreseeable future. Even though our coarse-grained model is only based on experimental knotting probabilities of short DNA strands, it reproduces the correct persistence length of DNA. This indicates that knots are not only a fine gauge for structural properties, but a promising tool for the design of polymer models. PMID:27631891

  3. Elastic knots of Space-Time may improve QED, QCD

    NASA Astrophysics Data System (ADS)

    Kriske, Richard

    2016-03-01

    This author had previously suggested that the time dimension of Electric fields and Magnetic fields are different. This matter was apparently settled with the Special Theory, in which each Observer, has his own Dimension of Time, that is ``elastic'' with one Dimension of Space. The independence of E and M, when they are not varying with time, leads one wonder if they are the same time. For a moving Observer, the two fields are joined through Faraday and Ampere's law. Particle Physics has made the simple Special Relativity interpretation murky. A photon does not simply become either an Electric field or a Magnetic field when viewed in its ''rest frame''. Because of this all kinds of extra sub theories are used, such as the Photon is quantized, and is massless in its rest frame, and always moves at the velocity of light. As for the Photon of the magnetic, or just the electric field, it is ``off the mass shell''. Perhaps a better theory is that the elasticity of time and the fact the ``Two'' observers show up in the theory, is that there has to be two dimensions of time, tied in a knot, in order for a field to become a Particle. The knot tying in EM is simple, when the E field varies it produces M, and vice-versa. For massive particles the knots are more complicated, more dimensions.

  4. Folding analysis of the most complex Stevedore's protein knot.

    PubMed

    Wang, Iren; Chen, Szu-Yu; Hsu, Shang-Te Danny

    2016-01-01

    DehI is a homodimeric haloacid dehalogenase from Pseudomonas putida that contains the most complex 61 Stevedore's protein knot within its folding topology. To examine how DehI attains such an intricate knotted topology we combined far-UV circular dichroism (CD), intrinsic fluorescence spectroscopy and small angle X-ray scattering (SAXS) to investigate its folding mechanism. Equilibrium unfolding of DehI by chemical denaturation indicated the presence of two highly populated folding intermediates, I and I'. While the two intermediates vary in secondary structure contents and tertiary packing according to CD and intrinsic fluorescence, respectively, their overall dimension and compactness are similar according to SAXS. Three single-tryptophan variants (W34, W53, and W196) were generated to probe non-cooperative unfolding events localized around the three fluorophores. Kinetic fluorescence measurements indicated that the transition from the intermediate I' to the unfolded state is rate limiting. Our multiparametric folding analyses suggest that DehI unfolds through a linear folding pathway with two distinct folding intermediates by initial hydrophobic collapse followed by nucleation condensation, and that knotting precedes the formation of secondary structures. PMID:27527519

  5. Endopathogenic lifestyle of Pseudomonas savastanoi pv. savastanoi in olive knots

    PubMed Central

    Rodríguez‐Moreno, Luis; Jiménez, Antonio J.; Ramos, Cayo

    2009-01-01

    Summary The endophytic phase of Pseudomonas savastanoi pv. savastanoi in olive stems and the structural and ultrastructural histogenesis of olive knots have been studied. Construction of a stable plasmid vector expressing the green fluorescent protein, in combination with the use of in vitro olive plants, allowed real‐time monitoring of P. savastanoi pv. savastanoi infection. The infection process was also examined by bright field and epifluorescence microscopy as well as by scanning and transmission electron microscopy. Hypertrophy of the stem tissue was concomitant with the formation of bacterial aggregates, microcolonies and multilayer biofilms, over the cell surfaces and the interior of plasmolysed cells facing the air‐tissue interface of internal opened fissures, and was followed by invasion of the outer layers of the hypertrophied tissue. Pathogenic invasion of the internal lumen of newly formed xylem vessels, which were connected with the stem vascular system, was also observed in late stages of infection. Ultrastructural analysis of knot sections showed the release of outer membrane vesicles from the pathogen surface, a phenomenon not described before for bacterial phytopathogens during host infection. This is the first real‐time monitoring of P. savastanoi disease development and the first illustrated description of the ultrastructure of P. savastanoi‐induced knots. PMID:21255279

  6. Half-bow sliding knot: modified suture technique for scleral fixation using the corneoscleral pocket.

    PubMed

    Chee, Soon-Phaik

    2011-09-01

    A modified suture technique for precise knot placement in the Hoffman corneoscleral pocket technique of scleral fixation is described. Both loops of the polypropylene suture passing from the intraocular device through the sclera and conjunctiva are retrieved from the pocket. A loop of suture is pulled through 3 suture throws made using the second suture loop, forming a half bow. Centration of the intraocular lens (IOL)-capsular bag is checked. If the suture tension is too tight, the surgeon can easily undo the knot of the half-bow knot by pulling it free and can then retie the sliding knot. When the IOL-capsular bag is centered, the suture loop is cut and the free end removed. The second suture end is retrieved from the pocket, and knot tying is completed without further adjustment to the tension. Posterior pressure on the intraocular device centers it and settles the knot within the sclera at the fixation point.

  7. T7 RNA polymerase cannot transcribe through a highly knotted DNA template.

    PubMed Central

    Portugal, J; Rodríguez-Campos, A

    1996-01-01

    The ability of T7 RNA polymerase to transcribe a plasmid DNA in vitro in its linear, supercoiled, relaxed and knotted forms was analysed. Similar levels of transcription were found on each template with the exception of plasmids showing varying degrees of knotting (obtained using stoichiometric amounts of yeast topoisomerase II). A purified fraction of knotted DNA with a high number of nodes (crosses) was found to be refractory to transcription. The unknotting of the knotted plasmids, using catalytic amounts of topoisomerase II, restored their capacity as templates for transcription to levels similar to those obtained for the other topological forms. These results demonstrate that highly knotted DNA is the only topological form of DNA that is not a template for transcription. We suggest that the regulation of transcription, which depends on the topological state of the template, might be related to the presence of knotted DNA with different number of nodes. PMID:9016657

  8. The Minailo knot: a time-saving and cost-saving technique.

    PubMed

    Brown, John V; Tinnerman-Minailo, Erin J; Rettenmaier, Mark A; Micha, John P; Goldstein, Bram H

    2010-01-01

    Endoscopic knot tying during minimally invasive surgery can be complicated, time consuming, and associated with a protracted learning curve. The Minailo knot seems to be a reasonable option because the technique does not require any specialized instrumentation or skill to perform. In particular, vaginal closure is obtained with the placement of a single intra-corporeal knot. Our initial and successful experience with this knot-tying technique during robotic hysterectomy for treatment of gynecologic disease suggests that the method is safe and feasible. PMID:27628633

  9. A "Firework" of H2 Knots in the Planetary Nebula NGC 7293 (The Helix Nebula)

    NASA Astrophysics Data System (ADS)

    Matsuura, M.; Speck, A. K.; McHunu, B. M.; Tanaka, I.; Wright, N. J.; Smith, M. D.; Zijlstra, A. A.; Viti, S.; Wesson, R.

    2009-08-01

    We present a deep and wide field-of-view (4' × 7') image of the planetary nebula (PN) NGC 7293 (the Helix Nebula) in the 2.12 μm H2 v = 1 → 0 S(1) line. The excellent seeing (0farcs4) at the Subaru Telescope, allows the details of cometary knots to be examined. The knots are found at distances of 2farcm2-6farcm4 from the central star (CS). At the inner edge and in the inner ring (up to 4farcm5 from the CS), the knot often show a "tadpole" shape, an elliptical head with a bright crescent inside and a long tail opposite to the CS. In detail, there are variations in the tadpole shapes, such as narrowing tails, widening tails, meandering tails, or multipeaks within a tail. In the outer ring (4farcm5-6farcm4 from the CS), the shapes are more fractured, and the tails do not collimate into a single direction. The transition in knot morphology from the inner edge to the outer ring is clearly seen. The number density of knots governs the H2 surface brightness in the inner ring: H2 exists only within the knots. Possible mechanisms which contribute to the shaping of the knots are discussed, including photoionization and streaming motions. A plausible interpretation of our images is that inner knots are being overrun by a faster wind, but that this has not (yet) reached the outer knots. Based on H2 formation and destruction rates, H2 gas can survive in knots from formation during the late asymptotic giant branch phase throughout the PN phase. These observations provide new constraints on the formation and evolution of knots, and on the physics of molecular gas embedded within ionized gas. Based on data taken with the Subaru Telescope, National Astronomical Observatory of Japan (proposal ID S07B-054).

  10. The Nature of Cometary Knots in the Helix Nebula

    NASA Astrophysics Data System (ADS)

    Burkert, A.; O'dell, C. R.

    1996-12-01

    Recent HST observations have revealed heretofore unseen fine scale structure in the Helix Nebula. Thousands of well resolved neutral dark cores have been detected in extinction against the background emission of the nebula. These Cometary Knots (CK) have a remarkably uniform appearance with photoionized cusps and tails trailing away from the cusps on almost radial lines. The total mass of the CK is similar to the total mass of the ionized diffuse gas in the ring which means that they represent an important component of the nebula. We discuss the origin and future of the CK in the Helix. It has been suggested that the CK result from Rayleigh-Taylor instabilities arising at the ionization front of the nebula (Capriotti 1973, 1996). Our hydrodynamical simulations indicate that indeed Rayleigh-Taylor instabilities could lead to filamentary structures within planetary nebulae. The substructure of these fingers differs, however, from the observations in important ways. The observed CK therefore must have a different origin. The knots might represent local density fluctuations which remained behind and were compressed as the main ionization front advanced into the neutral material. Another formation scenario is a thin shell instability which results from the interaction of the nebula with a fast stellar wind. Although no stellar wind features have been detected so far, the brightness distribution of the ionized cusps of the knots indicates that this gas is in pressure equilibrium with a high-temperature surrounding gas which could be generated by a shocked stellar wind. If such a wind would have high velocities and low densities it could fall beneath the threshold for spectroscopic detection although it could be important for understanding the formation and structure of the CK. Detailed high-resolution numerical simulations which take into account a fast wind phase as well as the time variation of the Central Star's UV photon flux are presented.

  11. Ball lightning as a force-free magnetic knot

    PubMed

    Ranada; Soler; Trueba

    2000-11-01

    The stability of fireballs in a recent model of ball lightning is studied. It is shown that the balls shine while relaxing in an almost quiescent expansion, and that three effects contribute to their stability: (i) the formation in each one during a process of Taylor relaxation of a force-free magnetic field, a concept introduced in 1954 in order to explain the existence of large magnetic fields and currents in stable configurations of astrophysical plasmas; (ii) the so called Alfven conditions in magnetohydrodynamics; and (iii) the approximate conservation of the helicity integral. The force-free fields that appear are termed "knots" because their magnetic lines are closed and linked.

  12. Racah matrices and hidden integrability in evolution of knots

    NASA Astrophysics Data System (ADS)

    Mironov, A.; Morozov, A.; Morozov, An.; Sleptsov, A.

    2016-09-01

    We construct a general procedure to extract the exclusive Racah matrices S and S bar from the inclusive 3-strand mixing matrices by the evolution method and apply it to the first simple representations R = [ 1 ], [2], [3] and [ 2 , 2 ]. The matrices S and S bar relate respectively the maps (R ⊗ R) ⊗ R bar ⟶ R with R ⊗ (R ⊗ R bar) ⟶ R and (R ⊗ R bar) ⊗ R ⟶ R with R ⊗ (R bar ⊗ R) ⟶ R. They are building blocks for the colored HOMFLY polynomials of arbitrary arborescent (double fat) knots. Remarkably, the calculation realizes an unexpected integrability property underlying the evolution matrices.

  13. Long-term safety of polypropylene knots under scleral flaps for transsclerally sutured posterior chamber lenses.

    PubMed Central

    Van Meter, W S

    1997-01-01

    PURPOSE: To evaluate the safety of polypropylene knots used in TS-SPCL combined with PK and AV over time. METHOD: A retrospective review of 26 consecutive cases of TS-SPCL by one surgeon (WSVM) with at least 12 months follow-up (mean 26, range 12-62). All patients had a double strand polypropylene knot buried under partial thickness scleral flaps at 2 and 8 o'clock. Knots were rotated into the globe (R) in 10 cases, and could not be buried (N) in 13 cases, and in 3 cases 1 knot was buried. RESULTS: No cases of suture erosion occurred in R or N. One or more polypropylene sutures were visible in 17 patients (8 R, 9 T) at last exam. Twenty-three of 52 knots were rotated into the globe, and 70% of rotated knots were not even visible at the slit lamp at final visit. There was no evidence of conjunctival erosion in any patient. There was no lens dislocation and no endophthalmitis. CONCLUSION: The combination of partial thickness scleral flaps with double strand polypropylene knots reduces the incidence of suture erosion through the conjunctive if knots cannot be rotated into the globe. Images FIGURE 1 FIGURE 2 FIGURE 3 PMID:9440177

  14. Percutaneous Retrieval of a Pulmonary Artery Catheter Knot in Pacing Electrodes

    SciTech Connect

    Valenzuela-Garcia, Luis Felipe Almendro-Delia, Manuel; Gonzalez-Valdayo, Miguel; Munoz-Campos, Juan; Dorado-Garcia, Jose C.; Gomez-Rosa, Francisco; Vazquez-Garcia, Rafael; Calderon-Leal, Jose M.

    2007-09-15

    To illustrate a successful approach to resolving a pulmonary artery catheter knot in the pacing leads of a cardiac resynchronization device. When planning invasive monitoring for patients having right chamber electrodes, fluoroscopic-guided catheter insertion and extraction is advisable. In the event of coiling or knotting, an interventional radiologist should be contacted as soon as possible to avoid serious complications.

  15. Translocation dynamics of knotted polymers under a constant or periodic external field.

    PubMed

    Narsimhan, Vivek; Renner, C Benjamin; Doyle, Patrick S

    2016-06-14

    We perform Brownian dynamics simulations to examine how knots alter the dynamics of polymers moving through nanopores under an external field. In the first part of this paper, we study the situation when the field is constant. Here, knots halt translocation above a critical force with jamming occurring at smaller forces for twist topologies compared to non-twist topologies. Slightly below the jamming transition, the polymer's transit times exhibit large fluctuations. This phenomenon is an example of the knot's molecular individualism since the conformation of the knot plays a large role in the chain's subsequent dynamics. In the second part of the paper, we study the motion of the chain when one cycles the field on and off. If the off time is comparable to the knot's relaxation time, one can adjust the swelling of the knot at the pore and hence design strategies to ratchet the polymer in a controllable fashion. We examine how the off time affects the ratcheting dynamics. We also examine how this strategy alters the fluctuations in the polymer's transit time. We find that cycling the force field can reduce fluctuations near the knot's jamming transition, but can enhance the fluctuations at very high forces since knots get trapped in metastable states during the relaxation process. The latter effect appears to be more prominent for non-torus topologies than torus ones. We conclude by discussing the feasibility of this approach to control polymer motion in biotechnology applications such as sequencing. PMID:27181288

  16. Ethnomathematics in Arfak (West Papua-Indonesia): Hidden Mathematics on Knot of Rumah Kaki Seribu

    ERIC Educational Resources Information Center

    Haryanto; Nusantara, Toto; Subanji; Abadyo

    2016-01-01

    This ethnomathematics article focused on the models of knot which is used in the frame of "Rumah Kaki Seribu." The knot model itself was studied mathematically. The results of this study revealed the way Arfak tribal communities think mathematically. This article uses exploration, documentation, interview, experiments and literature…

  17. Introduction of "Papazian Pusher: " A Modified-Design Knot Pusher for Surgical Repair of Cleft Palates.

    PubMed

    Papazian, Nazareth J; Chahine, Fadl; Atiyeh, Bishara; Deeba, Samer; Zgheib, Elias; Abu-Sittah, Ghassan

    2015-09-01

    Tying sutures is an integral aspect of any surgery and reliable instruments are essential for hassle-free procedures including craniofacial surgeries. Knot pushers have been widely known for their application in various laparoscopic, arthroscopic, and anal surgeries. The literature reveals numerous articles pertaining to knot pushers, as well as improvements on existing designs. Nevertheless, no application of knot pushers in the surgical repair of cleft palates has been described. We describe a new knot pusher "Papazian Pusher" (PP) finely designed for application in oral surgeries in general and repair of cleft palates in particular. The instrument was used satisfactorily in repair of cleft palate surgeries and no complications were encountered. The PP was found, overall, to be easy to use, and helps in performing faster, stronger, smooth, and secure knots. PMID:26355980

  18. High Proteolytic Resistance of Spider-Derived Inhibitor Cystine Knots

    PubMed Central

    Kikuchi, Kyoko; Sugiura, Mika; Kimura, Tadashi

    2015-01-01

    Proteolytic stability in gastrointestinal tract and blood plasma is the major obstacle for oral peptide drug development. Inhibitor cystine knots (ICKs) are linear cystine knot peptides which have multifunctional properties and could become promising drug scaffolds. ProTx-I, ProTx-II, GTx1-15, and GsMTx-4 were spider-derived ICKs and incubated with pepsin, trypsin, chymotrypsin, and elastase in physiological conditions to find that all tested peptides were resistant to pepsin, and ProTx-II, GsMTx-4, and GTx1-15 showed resistance to all tested proteases. Also, no ProTx-II degradation was observed in rat blood plasma for 24 hours in vitro and ProTx-II concentration in circulation decreased to half in 40 min, indicating absolute stability in plasma and fast clearance from the system. So far, linear peptides are generally thought to be unsuitable in vivo, but all tested ICKs were not degraded by pepsin and stomach could be selected for the alternative site of drug absorption for fast onset of the drug action. Since spider ICKs are selective inhibitors of various ion channels which are related to the pathology of many diseases, engineered ICKs will make a novel class of peptide medicines which can treat variety of bothering symptoms. PMID:26843868

  19. An Indwelling Urethral Catheter Knotted Around a Double-J Ureteral Stent: An Unusual Complication after Kidney Transplantation

    PubMed Central

    Warmerdam, E. G.; Toorop, R. J.; Abrahams, A. C.; Berger, P.

    2011-01-01

    Urethral catheterization is a common procedure with a relatively low complication rate. Knotting of an indwelling urethral catheter is a very rare complication, and there are only a few case reports on knotted catheters, most of them concerning children. We report an especially rare case where a urethral catheter formed a knot around a double-J ureteral stent after a kidney transplantation. We will discuss the various risk factors for knotting of a catheter and the methods to untangle a knot. PMID:24533194

  20. Effects of horseshoe crab harvest in delaware bay on red knots: Are harvest restrictions working?

    USGS Publications Warehouse

    Niles, L.J.; Bart, J.; Sitters, H.P.; Dey, A.D.; Clark, K.E.; Atkinson, P.W.; Baker, A.J.; Bennett, K.A.; Kalasz, K.S.; Clark, N.A.; Clark, J.; Gillings, S.; Gates, A.S.; Gonzalez, P.M.; Hernandez, D.E.; Minton, C.D.T.; Morrison, R.I.G.; Porter, R.R.; Ross, R.K.; Veitch, C.R.

    2009-01-01

    Each May, red knots (Calidris canutus rufa) congregate in Delaware Bay during their northward migration to feed on horseshoe crab eggs (Limulus polyphemus) and refuel for breeding in the Arctic. During the 1990s, the Delaware Bay harvest of horseshoe crabs for bait increased 10-fold, leading to a more than 90% decline in the availability of their eggs for knots. The proportion of knots achieving weights of more than 180 grams by 26-28 May, their main departure period, dropped from 0.6-0.8 to 0.14-0.4 over 1997-2007. During the same period, the red knot population stopping in Delaware Bay declined by more than 75%, in part because the annual survival rate of adult knots wintering in Tierra del Fuego declined. Despite restrictions, the 2007 horseshoe crab harvest was still greater than the 1990 harvest, and no recovery of knots was detectable. We propose an adaptive management strategy with recovery goals and annual monitoring that, if adopted, will both allow red knot and horseshoe crab populations to recover and permit a sustainable harvest of horseshoe crabs.

  1. Ball lightning as a force-free magnetic knot

    PubMed

    Ranada; Soler; Trueba

    2000-11-01

    The stability of fireballs in a recent model of ball lightning is studied. It is shown that the balls shine while relaxing in an almost quiescent expansion, and that three effects contribute to their stability: (i) the formation in each one during a process of Taylor relaxation of a force-free magnetic field, a concept introduced in 1954 in order to explain the existence of large magnetic fields and currents in stable configurations of astrophysical plasmas; (ii) the so called Alfven conditions in magnetohydrodynamics; and (iii) the approximate conservation of the helicity integral. The force-free fields that appear are termed "knots" because their magnetic lines are closed and linked. PMID:11102074

  2. Discretized knot motion on a tensioned fiber induced by transverse waves.

    PubMed

    Potestio, Raffaello; Tubiana, Luca

    2016-01-21

    Topological entanglement is a ubiquitous feature of many biological as well as artificial polymers and fibers. While the equilibrium properties of entangled chains have been the subject of several studies, little is known about their out-of-equilibrium behavior. Here, we address the problem of a stretched knotted fiber driven by a periodic force applied to one of its termini. We show that the onset of standing waves kinetically traps the knot in spatially localized states where the amplitude of the oscillations is maximal, while the knot normal diffusive dynamics is replaced by a discrete jump dynamics. PMID:26510521

  3. Discretized knot motion on a tensioned fiber induced by transverse waves.

    PubMed

    Potestio, Raffaello; Tubiana, Luca

    2016-01-21

    Topological entanglement is a ubiquitous feature of many biological as well as artificial polymers and fibers. While the equilibrium properties of entangled chains have been the subject of several studies, little is known about their out-of-equilibrium behavior. Here, we address the problem of a stretched knotted fiber driven by a periodic force applied to one of its termini. We show that the onset of standing waves kinetically traps the knot in spatially localized states where the amplitude of the oscillations is maximal, while the knot normal diffusive dynamics is replaced by a discrete jump dynamics.

  4. Tightening slip knots in raw and degummed silk to increase toughness without losing strength

    NASA Astrophysics Data System (ADS)

    Pantano, Maria F.; Berardo, Alice; Pugno, Nicola M.

    2016-02-01

    Knots are fascinating topological elements, which can be found in both natural and artificial systems. While in most of the cases, knots cannot be loosened without breaking the strand where they are tightened, herein, attention is focused on slip or running knots, which on the contrary can be unfastened without compromising the structural integrity of their hosting material. Two different topologies are considered, involving opposite unfastening mechanisms, and their influence on the mechanical properties of natural fibers, as silkworm silk raw and degummed single fibers, is investigated and quantified. Slip knots with optimized shape and size result in a significant enhancement of fibers energy dissipation capability, up to 300-400%, without affecting their load bearing capacity.

  5. Tightening slip knots in raw and degummed silk to increase toughness without losing strength.

    PubMed

    Pantano, Maria F; Berardo, Alice; Pugno, Nicola M

    2016-01-01

    Knots are fascinating topological elements, which can be found in both natural and artificial systems. While in most of the cases, knots cannot be loosened without breaking the strand where they are tightened, herein, attention is focused on slip or running knots, which on the contrary can be unfastened without compromising the structural integrity of their hosting material. Two different topologies are considered, involving opposite unfastening mechanisms, and their influence on the mechanical properties of natural fibers, as silkworm silk raw and degummed single fibers, is investigated and quantified. Slip knots with optimized shape and size result in a significant enhancement of fibers energy dissipation capability, up to 300-400%, without affecting their load bearing capacity. PMID:26868855

  6. Folding of small knotted proteins: Insights from a mean field coarse-grained model

    SciTech Connect

    Najafi, Saeed; Potestio, Raffaello

    2015-12-28

    A small but relevant number of proteins whose native structure is known features nontrivial topology, i.e., they are knotted. Understanding the process of folding from a swollen unknotted state to the biologically relevant native conformation is, for these proteins, particularly difficult, due to their rate-limiting topological entanglement. To shed some light into this conundrum, we introduced a structure-based coarse-grained model of the protein, where the information about the folded conformation is encoded in bonded angular interactions only, which do not favor the formation of native contacts. A stochastic search scheme in parameter space is employed to identify a set of interactions that maximizes the probability to attain the knotted state. The optimal knotting pathways of the two smallest knotted proteins, obtained through this approach, are consistent with the results derived by means of coarse-grained as well as full atomistic simulations.

  7. Tightening slip knots in raw and degummed silk to increase toughness without losing strength

    PubMed Central

    Pantano, Maria F.; Berardo, Alice; Pugno, Nicola M.

    2016-01-01

    Knots are fascinating topological elements, which can be found in both natural and artificial systems. While in most of the cases, knots cannot be loosened without breaking the strand where they are tightened, herein, attention is focused on slip or running knots, which on the contrary can be unfastened without compromising the structural integrity of their hosting material. Two different topologies are considered, involving opposite unfastening mechanisms, and their influence on the mechanical properties of natural fibers, as silkworm silk raw and degummed single fibers, is investigated and quantified. Slip knots with optimized shape and size result in a significant enhancement of fibers energy dissipation capability, up to 300–400%, without affecting their load bearing capacity. PMID:26868855

  8. Management of root-knot nematode (Meloidogyne incognita) in bottle gourd using different botanicals in pots.

    PubMed

    Singh, Tulika; Patel, B A

    2015-09-01

    A pot experiment was conducted to study the efficacy of different botanicals in varying doses for management of root-knot nematode, M. incognita in bottle gourd. The results exhibited that madar (Calotropis procera) and neem (Azadirachta indica) leaves application proved to be more effective in improving plant growth characters and reducing root-knot index and final nematode population. Among the doses tested, higher dose of 1.5 % (w/w) was more effective than lower ones. PMID:26345048

  9. AN ASYMMETRICAL SYNCHROTRON MODEL FOR KNOTS IN THE 3C 273 JET

    SciTech Connect

    Liu, Wen-Po; Chen, Y. J.; Wang, Chun-Cheng

    2015-06-20

    To interpret the emission of knots in the 3C 273 jet from radio to X-rays, we propose a synchrotron model in which, owing to the shock compression effect, the injection spectra from a shock into the upstream and downstream emission regions are asymmetric. Our model could well explain the spectral energy distributions of knots in the 3C 273 jet, and predictions regarding the knots’ spectra could be tested by future observations.

  10. An eddy-current-based sensor for preventing knots in metallic wire drawing processes

    NASA Astrophysics Data System (ADS)

    Esteban, Bernat; Riba, Jordi-Roger; Baquero, Grau; Ferrater, Cèsar

    2011-06-01

    During metallic wire drawing processes, the presence of knots and the failure to detect them can lead to long production interruptions, significant economic losses and a lower quality of final product. Consequently, there is a pressing need to develop methods for real-time detection and prevention of this fault. In this paper, a sensor to prevent the formation of knots during the metallic wire drawing process is presented and evaluated by means of experimental data. This fast, inexpensive, non-contact sensor is based on electromagnetic principles such as eddy current induction, magnetic reluctance variations and magnetic coupling. The proposed sensor without direct contact can detect knots in a target metallic wire by measuring the impedance variations of a calibrated sensing coil caused by either a knot or an unwound loop rising from a wire rod. The incorporation of this type of sensor into a wire-drawing machine can avoid the tightening of the knot, thereby reducing downtime and increasing the security and reliability of the process. Experiments were conducted using a scale model of the above proposed system. This allowed highlighting the sensor's potential by carrying out an automatic, real-time knot detection during steel wire drawing.

  11. Knotted Vortices: Entropic Lattice Boltzmann Method for Simulation of Vortex dynamics

    NASA Astrophysics Data System (ADS)

    Boesch, Fabian; Chikatamarla, Shyam; Karlin, Ilya

    2013-11-01

    Knotted and interlinked vortex structures in real fluids are conjectured to play a major role in hydrodynamic flow dissipation. Much interest lies in determining their temporal stability and the mechanism through which knots dissolve. Kleckner and Irvine recently have shown the existence of such knotted vortices experimentally by accelerating hydrofoils in water. In the present work we employ the entropic lattice Boltzmann method (ELBM) to perform DNS simulations of the creation and dynamics of knotted vortex rings inspired by the experimental setup in. ELBM renders LBM scheme unconditionally stable by restoring the second law of thermodynamics (the Boltzmann H-theorem), and thus enables simulations of large domains and high Reynolds numbers with DNS quality. The results presented in this talk provide an in-depth study of the dynamics of knotted vortices and vortex reconnection events and confirm the existence of trefoil knots in silicio for the first time. This work was supported by a grant from the Swiss National Supercomputing Centre (CSCS) under project ID s347.

  12. Folding Pathways of a Knotted Protein with a Realistic Atomistic Force Field

    PubMed Central

    a Beccara, Silvio; Škrbić, Tatjana; Covino, Roberto; Micheletti, Cristian; Faccioli, Pietro

    2013-01-01

    We report on atomistic simulation of the folding of a natively-knotted protein, MJ0366, based on a realistic force field. To the best of our knowledge this is the first reported effort where a realistic force field is used to investigate the folding pathways of a protein with complex native topology. By using the dominant-reaction pathway scheme we collected about 30 successful folding trajectories for the 82-amino acid long trefoil-knotted protein. Despite the dissimilarity of their initial unfolded configuration, these trajectories reach the natively-knotted state through a remarkably similar succession of steps. In particular it is found that knotting occurs essentially through a threading mechanism, involving the passage of the C-terminal through an open region created by the formation of the native -sheet at an earlier stage. The dominance of the knotting by threading mechanism is not observed in MJ0366 folding simulations using simplified, native-centric models. This points to a previously underappreciated role of concerted amino acid interactions, including non-native ones, in aiding the appropriate order of contact formation to achieve knotting. PMID:23555232

  13. A DECADE-BASELINE STUDY OF THE PLASMA STATES OF EJECTA KNOTS IN CASSIOPEIA A

    SciTech Connect

    Rutherford, John; Dewey, Daniel; Figueroa-Feliciano, Enectali; Heine, Sarah N. T.; Canizares, C. R.; Bastien, Fabienne A.; Sato, Kosuke E-mail: jmrv@mit.edu

    2013-05-20

    We present the analysis of 21 bright X-ray knots in the Cassiopeia A supernova remnant from observations spanning 10 yr. We performed a comprehensive set of measurements to reveal the kinematic and thermal state of the plasma in each knot, using a combined analysis of two high energy resolution High Energy Transmission Grating (HETG) and four medium energy resolution Advanced CCD Imaging Spectrometer (ACIS) sets of spectra. The ACIS electron temperature estimates agree with the HETG-derived values for approximately half of the knots studied, yielding one of the first comparisons between high resolution temperature estimates and ACIS-derived temperatures. We did not observe the expected spectral evolution-predicted from the ionization age and density estimates for each knot-in all but three of the knots studied. The incompatibility of these measurements with our assumptions has led us to propose a dissociated ejecta model, with the metals unmixed inside the knots, which could place strong constraints on supernova mixing models.

  14. Evaluation of the effect of 4 types of knots on the mechanical properties of 4 types of suture material used in small animal practice.

    PubMed

    Avoine, Xytilis; Lussier, Bertrand; Brailovski, Vladimir; Inaekyan, Karine; Beauchamp, Guy

    2016-04-01

    The influence of the type of material used, knot configuration, and use of an additional throw on the tensile force at failure, the elongation, and the mode of failure of different configurations of linear sutures and knotted suture loops was evaluated in this in-vitro mechanical study. We hypothesized that all types of knots would significantly influence the initial force and elongation of suture materials and would influence the force and elongation at which the knotted loops break, but not their mode of failure. A total of 432 samples of 4 types of size 3-0 suture material (polydioxanone, polyglecaprone 25, polyglactin 910, and nylon), representing 9 configurations, were tested in a tensiometer. The configurations were 1 linear suture without a knot and the following loops: square (SQ) knot; surgeon's (SU) knot; granny (GR) knot; and sliding half-hitch (SHH) knot using either 4 and 5 or 3 and 4 throws, depending on the material. For polydioxanone, SQ and SU knots did not decrease the initial force at failure of the suture. Granny (GR) and SHH knots decreased the tensile force at failure and elongation by premature failure of the loop. For polyglecaprone 25, all knots decreased the initial force at failure of the suture, with SHH being weaker than the other knots. For coated polyglactin 910, all knots decreased the initial force at failure of the suture and slippage increased significantly compared with the other 3 sutures. The use of SQ knots with 3 throws did not result in a safe knot. For nylon, knots did not alter the original mechanics of the suture. In conclusion, all knots and types of suture material do not necessarily have the same effect on the initial tensile force at failure of suture materials. PMID:27127344

  15. Optical vortex knots – one photon at a time

    NASA Astrophysics Data System (ADS)

    Tempone-Wiltshire, Sebastien J.; Johnstone, Shaun P.; Helmerson, Kristian

    2016-04-01

    Feynman described the double slit experiment as “a phenomenon which is impossible, absolutely impossible, to explain in any classical way and which has in it the heart of quantum mechanics”. The double-slit experiment, performed one photon at a time, dramatically demonstrates the particle-wave duality of quantum objects by generating a fringe pattern corresponding to the interference of light (a wave phenomenon) from two slits, even when there is only one photon (a particle) at a time passing through the apparatus. The particle-wave duality of light should also apply to complex three dimensional optical fields formed by multi-path interference, however, this has not been demonstrated. Here we observe particle-wave duality of a three dimensional field by generating a trefoil optical vortex knot – one photon at a time. This result demonstrates a fundamental physical principle, that particle-wave duality implies interference in both space (between spatially distinct modes) and time (through the complex evolution of the superposition of modes), and has implications for topologically entangled single photon states, orbital angular momentum multiplexing and topological quantum computing.

  16. Temperature Sensing in Seawater Based on Microfiber Knot Resonator

    PubMed Central

    Yang, Hongjuan; Wang, Shanshan; Wang, Xin; Liao, Yipeng; Wang, Jing

    2014-01-01

    Ocean internal-wave phenomena occur with the variation in seawater vertical temperature, and most internal-wave detections are dependent on the measurement of seawater vertical temperature. A seawater temperature sensor based on a microfiber knot resonator (MKR) is designed theoretically and demonstrated experimentally in this paper. Especially, the dependences of sensing sensitivity on fiber diameter and probing wavelength are studied. Calculated results show that sensing sensitivity increases with the increasing microfiber diameter with the range of 2.30–3.91 μm and increases with the increasing probing wavelength, which reach good agreement with results obtained by experiments. By choosing the appropriate parameters, the maximum sensitivity measured can reach to be 22.81 pm/°C. The seawater temperature sensor demonstrated here shows advantages of small size, high sensitivity, easy fabrication, and easy integration with fiber systems, which may offer a new optical method to detect temperature of seawater or ocean internal-wave phenomenon and offer valuable reference for assembling micro sensors used for other parameters related to seawater, such as salinity, refractive index, concentration of NO3− and so on. PMID:25299951

  17. Optical vortex knots – one photon at a time

    PubMed Central

    Tempone-Wiltshire, Sebastien J.; Johnstone, Shaun P.; Helmerson, Kristian

    2016-01-01

    Feynman described the double slit experiment as “a phenomenon which is impossible, absolutely impossible, to explain in any classical way and which has in it the heart of quantum mechanics”. The double-slit experiment, performed one photon at a time, dramatically demonstrates the particle-wave duality of quantum objects by generating a fringe pattern corresponding to the interference of light (a wave phenomenon) from two slits, even when there is only one photon (a particle) at a time passing through the apparatus. The particle-wave duality of light should also apply to complex three dimensional optical fields formed by multi-path interference, however, this has not been demonstrated. Here we observe particle-wave duality of a three dimensional field by generating a trefoil optical vortex knot – one photon at a time. This result demonstrates a fundamental physical principle, that particle-wave duality implies interference in both space (between spatially distinct modes) and time (through the complex evolution of the superposition of modes), and has implications for topologically entangled single photon states, orbital angular momentum multiplexing and topological quantum computing. PMID:27087642

  18. The magnetic resonance appearance of surfers' knots: a case report.

    PubMed

    McManus, Luke J; Thomson, Andrew; Whan, Andrew

    2016-09-01

    Athletes are at increased risk of developing soft-tissue lesions of the lower limbs. Although the majority of these will be benign, the differential diagnosis is broad and increasingly, doctors are turning to magnetic resonance imaging (MRI) as a first-line investigation when presented with these sorts of lesions, both to narrow the differential diagnosis and exclude malignancy. We report the case of a 28-year-old Caucasian man who presented with 2 soft-tissue lesions of the right foot. History and examination of the nodules fitted with a diagnosis of surfers' knots, an unusual form of acquired, benign, connective tissue nodule that may appear over the tibial tuberosities, dorsum of the feet, and occasionally on the chest of surfers in association with repetitive microtrauma during surfing. MRI findings were consistent with this diagnosis with both lesions exhibiting T1 hypointensity and speckled T2 hypointensity with no significant blooming artifact on gradient echo imaging. When imaged with gadolinium, they demonstrated only mild contrast enhancement. MRI is a valuable tool when investigating athletes with soft-tissue lesions over the lower limbs where the possibility of malignancy must be addressed. In selected cases, MRI may be sufficient to permit a conservative approach to the management of these patients. PMID:27594950

  19. Novel Inhibitor Cystine Knot Peptides from Momordica charantia

    PubMed Central

    Clark, Richard J.; Tang, Jun; Zeng, Guang-Zhi; Franco, Octavio L.; Cantacessi, Cinzia; Craik, David J.; Daly, Norelle L.; Tan, Ning-Hua

    2013-01-01

    Two new peptides, MCh-1 and MCh-2, along with three known trypsin inhibitors (MCTI-I, MCTI-II and MCTI-III), were isolated from the seeds of the tropical vine Momordica charantia. The sequences of the peptides were determined using mass spectrometry and NMR spectroscopy. Using a strategy involving partial reduction and stepwise alkylation of the peptides, followed by enzymatic digestion and tandem mass spectrometry sequencing, the disulfide connectivity of MCh-1 was elucidated to be CysI-CysIV, CysII-CysV and CysIII-CysVI. The three-dimensional structures of MCh-1 and MCh-2 were determined using NMR spectroscopy and found to contain the inhibitor cystine knot (ICK) motif. The sequences of the novel peptides differ significantly from peptides previously isolated from this plant. Therefore, this study expands the known peptide diversity in M. charantia and the range of sequences that can be accommodated by the ICK motif. Furthermore, we show that a stable two-disulfide intermediate is involved in the oxidative folding of MCh-1. This disulfide intermediate is structurally homologous to the proposed ancestral fold of ICK peptides, and provides a possible pathway for the evolution of this structural motif, which is highly prevalent in nature. PMID:24116036

  20. Optical vortex knots - one photon at a time.

    PubMed

    Tempone-Wiltshire, Sebastien J; Johnstone, Shaun P; Helmerson, Kristian

    2016-01-01

    Feynman described the double slit experiment as "a phenomenon which is impossible, absolutely impossible, to explain in any classical way and which has in it the heart of quantum mechanics". The double-slit experiment, performed one photon at a time, dramatically demonstrates the particle-wave duality of quantum objects by generating a fringe pattern corresponding to the interference of light (a wave phenomenon) from two slits, even when there is only one photon (a particle) at a time passing through the apparatus. The particle-wave duality of light should also apply to complex three dimensional optical fields formed by multi-path interference, however, this has not been demonstrated. Here we observe particle-wave duality of a three dimensional field by generating a trefoil optical vortex knot - one photon at a time. This result demonstrates a fundamental physical principle, that particle-wave duality implies interference in both space (between spatially distinct modes) and time (through the complex evolution of the superposition of modes), and has implications for topologically entangled single photon states, orbital angular momentum multiplexing and topological quantum computing. PMID:27087642

  1. Optical vortex knots - one photon at a time.

    PubMed

    Tempone-Wiltshire, Sebastien J; Johnstone, Shaun P; Helmerson, Kristian

    2016-04-18

    Feynman described the double slit experiment as "a phenomenon which is impossible, absolutely impossible, to explain in any classical way and which has in it the heart of quantum mechanics". The double-slit experiment, performed one photon at a time, dramatically demonstrates the particle-wave duality of quantum objects by generating a fringe pattern corresponding to the interference of light (a wave phenomenon) from two slits, even when there is only one photon (a particle) at a time passing through the apparatus. The particle-wave duality of light should also apply to complex three dimensional optical fields formed by multi-path interference, however, this has not been demonstrated. Here we observe particle-wave duality of a three dimensional field by generating a trefoil optical vortex knot - one photon at a time. This result demonstrates a fundamental physical principle, that particle-wave duality implies interference in both space (between spatially distinct modes) and time (through the complex evolution of the superposition of modes), and has implications for topologically entangled single photon states, orbital angular momentum multiplexing and topological quantum computing.

  2. Optical vortex knots - one photon at a time

    NASA Astrophysics Data System (ADS)

    Tempone-Wiltshire, Sebastien J.; Johnstone, Shaun P.; Helmerson, Kristian

    2016-04-01

    Feynman described the double slit experiment as “a phenomenon which is impossible, absolutely impossible, to explain in any classical way and which has in it the heart of quantum mechanics”. The double-slit experiment, performed one photon at a time, dramatically demonstrates the particle-wave duality of quantum objects by generating a fringe pattern corresponding to the interference of light (a wave phenomenon) from two slits, even when there is only one photon (a particle) at a time passing through the apparatus. The particle-wave duality of light should also apply to complex three dimensional optical fields formed by multi-path interference, however, this has not been demonstrated. Here we observe particle-wave duality of a three dimensional field by generating a trefoil optical vortex knot - one photon at a time. This result demonstrates a fundamental physical principle, that particle-wave duality implies interference in both space (between spatially distinct modes) and time (through the complex evolution of the superposition of modes), and has implications for topologically entangled single photon states, orbital angular momentum multiplexing and topological quantum computing.

  3. BRIGHT KNOT APPEARS IN SUPERNOVA 1987A RING

    NASA Technical Reports Server (NTRS)

    2002-01-01

    [RIGHT] - This NASA Hubble Space Telescope Wide Field and Planetary Camera 2 image shows the glowing gas ring around supernova 1987A, as it appeared in 1994. The gas, excited by light from the explosion, has been fading for a decade. [LEFT] - Recent Hubble telescope observations show a brightening knot on the upper right side of the ring. This is the site of a powerful collision between an outward moving blast wave and the innermost parts of the circumstellar ring. The collision heats the gas and has caused it to brighten in recent months. This is likely to be the first sign of a dramatic and violent collision that will take place over the next few years, rejuvenating SN1987A as a powerful source of X-ray and radio emissions. The white sickle-shaped material in the center is the visible part of the shredded star, rushing outward at 3,000 kilometers per second, which is heated by radioactive elements created in the supernova explosion. The bright dot in the lower left is a star, which is the same direction as SN1987A, but is not physically part of the system. Both images were made from separate images taken in blue light, visual light and the narrow emission from glowing hydrogen. Computer image processing techniques were used to enhance details in the ring. Credit: Peter Garnavich (Harvard-Smithsonian Center for Astrophysics), and NASA

  4. Helicity, topology, and Kelvin waves in reconnecting quantum knots

    NASA Astrophysics Data System (ADS)

    Clark di Leoni, P.; Mininni, P. D.; Brachet, M. E.

    2016-10-01

    Helicity is a topological invariant that measures the linkage and knottedness of lines, tubes, and ribbons. As such, it has found myriads of applications in astrophysics, fluid dynamics, atmospheric sciences, and biology. In quantum flows, where topology-changing reconnection events are a staple, helicity appears as a key quantity to study. However, the usual definition of helicity is not well posed in quantum vortices, and its computation based on counting links and crossings of centerline vorticity can be downright impossible to apply in complex and turbulent scenarios. We present a definition of helicity which overcomes these problems and which gives the expected result in the large-scale limit. With it, we show that certain reconnection events can excite Kelvin waves and other complex motions of the centerline vorticity, which slowly deplete helicity as they interact nonlinearly, thus linking the theory of vortex knots with observations of quantum fluids. This process also results in the depletion of helicity in a fully turbulent quantum flow, in a way reminiscent of the decay of helicity in classical fluids.

  5. Characterization of the Inner Knot of the Crab: The Site of the Gamma-Ray Flares?

    NASA Astrophysics Data System (ADS)

    Rudy, Alexander; Horns, Dieter; DeLuca, Andrea; Kolodziejczak, Jeffery; Tennant, Allyn; Yuan, Yajie; Buehler, Rolf; Arons, Jonathon; Blandford, Roger; Caraveo, Patrizia; Costa, Enrico; Funk, Stephan; Hays, Elizabeth; Lobanov, Andrei; Max, Claire; Mayer, Michael; Mignani, Roberto; O'Dell, Stephen L.; Romani, Roger; Tavani, Marco; Weisskopf, Martin C.

    2015-09-01

    A particularly intriguing recent result from γ-ray astronomy missions is the detection of powerful flares from the Crab Nebula, which challenges the current understanding of pulsar wind nebulae and acceleration mechanisms. To search for the production site(s) of these flares, we conducted a multi-wavelength observing campaign using Keck, the Hubble Space Telescope (HST), and the Chandra X-ray Observatory. As the short timescales of the γ-ray flares (≲ 1 day) suggest a small emitting region, the Crab’s inner knot (about 0.6 arcsec from the pulsar) is a candidate site for such flaring. This paper describes observations of the inner knot, seeking to understand its nature and possible relationship with γ-ray flares. Using singular-value decomposition, analysis of the HST images yielded results consistent with traditional methods while substantially reducing some uncertainties. These analyses show that the knot’s intrinsic properties (especially size and brightness) are correlated with its (projected) separation from the pulsar. This characterization of the inner knot helps in constraining standard shock model parameters, under the assumption that the knot lies near the shocked surface. While the standard shock model gives good agreement in several respects, two puzzles persist: (a) the observed angular size of the knot relative to the pulsar-knot separation is much smaller than expected; and (b) the variable high degree of polarization (reported by others) is difficult to reconcile with a highly relativistic downstream flow. However, the IR-optical flux of the inner knot is marginally consistent with the shock accelerating most of the Nebula’s optical-emitting particles.

  6. Bounds for the minimum step number of knots confined to slabs in the simple cubic lattice

    NASA Astrophysics Data System (ADS)

    Ishihara, K.; Scharein, R.; Diao, Y.; Arsuaga, J.; Vazquez, M.; Shimokawa, K.

    2012-02-01

    Volume confinement is a key determinant of the topology and geometry of a polymer. However, the direct relationship between the two is not fully understood. For instance, recent experimental studies have constructed P4 cosmids, i.e. P4 bacteriophages whose genome sequence and length have been artificially engineered and have shown that upon extraction their DNA knot distribution differs from that of wild-type bacteriophage P4. In particular, it was observed that the complexity of the knots decreases sharply with the length of the packed genome. This problem is the motivation of this paper. Here, a polymer is modeled as a self-avoiding polygon on the simple cubic lattice and the confining condition is such that the polygon is bounded between two parallel planes (i.e. bounded within a slab). We estimate the minimum length required for such a polygon to realize a knot type. Our numerical simulations show that in order to realize a prime knot (with up to ten crossings) in a 1-slab (i.e. a slab of height 1), one needs a polygon of length strictly longer than the minimum length needed to realize the same knot when there is no confining condition. In the case of the trefoil knot, we can in fact establish this result analytically by proving that the minimum length required to tie a trefoil in the 1-slab is 26, which is greater than 24, the known minimum length required to tie a trefoil without a confinement condition. Additionally, we find that in the 1-slab not all geometrical realizations of a given knot type are equivalent under BFACF moves. This suggests that in certain confined volumes, knowing the topology of a polymer is not enough to describe all its states.

  7. Knots in rings. The circular knotted protein Momordica cochinchinensis trypsin inhibitor-II folds via a stable two-disulfide intermediate.

    PubMed

    Cemazar, Masa; Daly, Norelle L; Häggblad, Sara; Lo, Kai Pong; Yulyaningsih, Ernie; Craik, David J

    2006-03-24

    The aim of this work was to elucidate the oxidative folding mechanism of the macrocyclic cystine knot protein MCoTI-II. We aimed to investigate how the six-cysteine residues distributed on the circular backbone of the reduced unfolded peptide recognize their correct partner and join up to form a complex cystine-knotted topology. To answer this question, we studied the oxidative folding of the naturally occurring peptide using a range of spectroscopic methods. For both oxidative folding and reductive unfolding, the same disulfide intermediate species was prevalent and was characterized to be a native-like two-disulfide intermediate in which the Cys1-Cys18 disulfide bond was absent. Overall, the folding pathway of this head-to-tail cyclized protein was found to be similar to that of linear cystine knot proteins from the squash family of trypsin inhibitors. However, the pathway differs in an important way from that of the cyclotide kalata B1, in that the equivalent two-disulfide intermediate in that case is not a direct precursor of the native protein. The size of the embedded ring within the cystine knot motif appears to play a crucial role in the folding pathway. Larger rings contribute to the independence of disulfides and favor an on-pathway native-like intermediate that has a smaller energy barrier to cross to form the native fold. The fact that macrocyclic proteins are readily able to fold to a complex knotted structure in vitro in the absence of chaperones makes them suitable as protein engineering scaffolds that have remarkable stability. PMID:16547012

  8. Knots in rings. The circular knotted protein Momordica cochinchinensis trypsin inhibitor-II folds via a stable two-disulfide intermediate.

    PubMed

    Cemazar, Masa; Daly, Norelle L; Häggblad, Sara; Lo, Kai Pong; Yulyaningsih, Ernie; Craik, David J

    2006-03-24

    The aim of this work was to elucidate the oxidative folding mechanism of the macrocyclic cystine knot protein MCoTI-II. We aimed to investigate how the six-cysteine residues distributed on the circular backbone of the reduced unfolded peptide recognize their correct partner and join up to form a complex cystine-knotted topology. To answer this question, we studied the oxidative folding of the naturally occurring peptide using a range of spectroscopic methods. For both oxidative folding and reductive unfolding, the same disulfide intermediate species was prevalent and was characterized to be a native-like two-disulfide intermediate in which the Cys1-Cys18 disulfide bond was absent. Overall, the folding pathway of this head-to-tail cyclized protein was found to be similar to that of linear cystine knot proteins from the squash family of trypsin inhibitors. However, the pathway differs in an important way from that of the cyclotide kalata B1, in that the equivalent two-disulfide intermediate in that case is not a direct precursor of the native protein. The size of the embedded ring within the cystine knot motif appears to play a crucial role in the folding pathway. Larger rings contribute to the independence of disulfides and favor an on-pathway native-like intermediate that has a smaller energy barrier to cross to form the native fold. The fact that macrocyclic proteins are readily able to fold to a complex knotted structure in vitro in the absence of chaperones makes them suitable as protein engineering scaffolds that have remarkable stability.

  9. Long-slit spectrophotometry of the multiple knots of the polar ring galaxy IIZw71

    NASA Astrophysics Data System (ADS)

    Pérez-Montero, E.; García-Benito, R.; Díaz, A. I.; Pérez, E.; Kehrig, C.

    2009-04-01

    Aims: The blue compact dwarf galaxy IIZw71 is catalogued as a probable polar-ring galaxy, and along its long axis it has several very luminous knots showing recent episodes of star formation. Our main aim is to study the physical properties, the stellar content, and the kinematics in the brightest knots of the polar ring. Methods: We carried out long-slit spectroscopic observations of the polar ring in the spectral range 3500-10 000 Å taken with the William Herschel Telescope (WHT). The spectroscopic observations complemented by the available photometry of the galaxy in narrow Hα filters. Results: We measured the rotation curve of the ring, from which we infer a ratio M/LB ≈ 3.9 inside the star-forming ring. We measured the auroral [Oiii] line in the two brightest knots, allowing us to measure oxygen, sulphur, nitrogen, argon, and neon chemical abundances following the direct method. Different empirical calibrators were used to estimate the oxygen abundance in the two faintest knots where the temperature sensitive lines could not be measured. The metallicities obtained are very similar for all the knots, but lower than previously reported in the literature from integrated spectra. The N/O abundance, as derived from the N2O2 parameter (the ratio of the [Nii] and [Oii] intensities), is remarkably constant over the ring, indicating that local polution processes are not conspicuous. Using synthetic stellar populations (SSPs) calculated with the code STARLIGHT, we studied the age distribution of the stellar populations in each knot, finding that in all of them there is a combination of a very young population with less than 10 Myr, responsible for the ionisation of the gas, with other populations older than 100 Myr, probably responsible for the chemical evolution of the knots. The small differences in metallicity and the age distributions among the different knots are indicative of a common chemical evolution, probably related to the process of interaction with the

  10. DNA knots reveal a chiral organization of DNA in phage capsids

    NASA Astrophysics Data System (ADS)

    Arsuaga, Javier; Vazquez, Mariel; McGuirk, Paul; Trigueros, Sonia; Sumners, De Witt; Roca, Joaquim

    2005-06-01

    Icosahedral bacteriophages pack their double-stranded DNA genomes to near-crystalline density and achieve one of the highest levels of DNA condensation found in nature. Despite numerous studies, some essential properties of the packaging geometry of the DNA inside the phage capsid are still unknown. We present a different approach to the problems of randomness and chirality of the packed DNA. We recently showed that most DNA molecules extracted from bacteriophage P4 are highly knotted because of the cyclization of the linear DNA molecule confined in the phage capsid. Here, we show that these knots provide information about the global arrangement of the DNA inside the capsid. First, we analyze the distribution of the viral DNA knots by high-resolution gel electrophoresis. Next, we perform Monte Carlo computer simulations of random knotting for freely jointed polygons confined to spherical volumes. Comparison of the knot distributions obtained by both techniques produces a topological proof of nonrandom packaging of the viral DNA. Moreover, our simulations show that the scarcity of the achiral knot 41 and the predominance of the torus knot 51 over the twist knot 52 observed in the viral distribution of DNA knots cannot be obtained by confinement alone but must include writhe bias in the conformation sampling. These results indicate that the packaging geometry of the DNA inside the viral capsid is writhe-directed. Author contributions: D.W.S. and J.R. designed research; J.A. and J.R. performed research; J.A., M.V., P.M., S.T., and J.R. contributed new reagents/analytic tools; J.A., M.V., P.M., and J.R. analyzed data; and D.W.S. and J.R. wrote the paper.This paper was submitted directly (Track II) to the PNAS office.‡Present address: Department of Mathematics and Center for Computation in the Life Sciences, San Francisco State University, San Francisco, CA 94132.

  11. Particle on a torus knot: Constrained dynamics and semi-classical quantization in a magnetic field

    NASA Astrophysics Data System (ADS)

    Das, Praloy; Pramanik, Souvik; Ghosh, Subir

    2016-11-01

    Kinematics and dynamics of a particle moving on a torus knot poses an interesting problem as a constrained system. In the first part of the paper we have derived the modified symplectic structure or Dirac brackets of the above model in Dirac's Hamiltonian framework, both in toroidal and Cartesian coordinate systems. This algebra has been used to study the dynamics, in particular small fluctuations in motion around a specific torus. The spatial symmetries of the system have also been studied. In the second part of the paper we have considered the quantum theory of a charge moving in a torus knot in the presence of a uniform magnetic field along the axis of the torus in a semiclassical quantization framework. We exploit the Einstein-Brillouin-Keller (EBK) scheme of quantization that is appropriate for multidimensional systems. Embedding of the knot on a specific torus is inherently two dimensional that gives rise to two quantization conditions. This shows that although the system, after imposing the knot condition reduces to a one dimensional system, even then it has manifested non-planar features which shows up again in the study of fractional angular momentum. Finally we compare the results obtained from EBK (multi-dimensional) and Bohr-Sommerfeld (single dimensional) schemes. The energy levels and fractional spin depend on the torus knot parameters that specifies its non-planar features. Interestingly, we show that there can be non-planar corrections to the planar anyon-like fractional spin.

  12. Hippo pathway/Yap regulates primary enamel knot and dental cusp patterning in tooth morphogenesis.

    PubMed

    Kwon, Hyuk-Jae Edward; Li, Liwen; Jung, Han-Sung

    2015-11-01

    The shape of an individual tooth crown is primarily determined by the number and arrangement of its cusps, i.e., cusp patterning. Enamel knots that appear in the enamel organ during tooth morphogenesis have been suggested to play important roles in cusp patterning. Animal model studies have shown that the Hippo pathway effector Yap has a critical function in tooth morphogenesis. However, the role of the Hippo pathway/Yap in cusp patterning has not been well documented and its specific roles in tooth morphogenesis remain unclear. Here, we provide evidence that Yap is a key mediator in tooth cusp patterning. We demonstrate a correlation between Yap localization and cell proliferation in developing tooth germs. We also show that, between the cap stage and bell stage, Yap is crucial for the suppression of the primary enamel knot and for the patterning of secondary enamel knots, which are the future cusp regions. When Yap expression is stage-specifically knocked down during the cap stage, the activity of the primary enamel knot persists into the bell-stage tooth germ, leading to ectopic cusp formation. Our data reveal the importance of the Hippo pathway/Yap in enamel knots and in the proper patterning of tooth cusps.

  13. Ileosigmoid knotting in patients under 25 years of age: A report of two cases☆

    PubMed Central

    Igwe, Patrick Okechukwu; Jebbin, Nze Jephet; Dodiyi-Manuel, Amabra; Adotey, Jacob Molai

    2014-01-01

    INTRODUCTION Ileosigmoid knotting is a rare cause of acute abdomen with high morbidity and mortality. Its diagnosis is infrequently made before surgery because of its varying ways of presentation and rarity. PRESENTATION OF CASE The first was a 21-year-old male who presented with a history of sudden generalized abdominal pain and progressive abdominal distension. He was pale and severely dehydrated. His extremities were cold and clammy. His pulse rate was 110 per minute and blood pressure was 90/50 mmHg. The second case was 20-year-old male who presented with similar symptoms as above. He was not pale but mildly dehydrated. His pulse rate was 92 per minute and blood pressure 110/70 mmHg. Both patients were resuscitated and had exploratory laparotomy a few hours after presentation. The first patient was found to have ileosigmoid knotting with gangrenous sigmoid colon and terminal ileum. He had Hartmann's procedure and right hemicolectomy with ileo-transverse anastomosis. The second patient was found to have ileosigmoid knotting with viable loops of bowel. He had careful detorsion, sigmoidectomy with primary anastomosis. Both patients’ have good outcome. DISCUSSION This is to report two cases of ileosigmoid knotting in two male patients aged 21 and 20 years, respectively, with the hope of increasing awareness. CONCLUSION Ileosigmoid knotting though more common in fourth or fifth decade of life, can also occur in the 2nd decade. Early diagnosis, careful resuscitation and skilful surgical intervention will improve outcome. PMID:25462043

  14. Multispecies modeling for adaptive management of horseshoe crabs and red knots in the delaware bay

    USGS Publications Warehouse

    McGowan, C.P.; Smith, D.R.; Sweka, J.A.; Martin, J.; Nichols, J.D.; Wong, R.; Lyons, J.E.; Niles, L.J.; Kalasz, K.; Brust, J.; Klopfer, M.; Spear, B.

    2011-01-01

    Adaptive management requires that predictive models be explicit and transparent to improve decisions by comparing management actions, directing further research and monitoring, and facilitating learning. The rufa subspecies of red knots (Calidris canutus rufa), which has recently exhibited steep population declines, relies on horseshoe crab (Limulus polyphemus) eggs as their primary food source during stopover in Delaware Bay during spring migration. We present a model with two different parameterizations for use in the adaptive management of horseshoe crab harvests in the Delaware Bay that links red knot mass gain, annual survival, and fecundity to horseshoe crab dynamics. The models reflect prevailing hypotheses regarding ecological links between these two species. When reported crab harvest from 1998 to 2008 was applied, projections corresponded to the observed red knot population abundances depending on strengths of the demographic relationship between these species. We compared different simulated horseshoe crab harvest strategies to evaluate whether, given this model, horseshoe crab harvest management can affect red knot conservation and found that restricting harvest can benefit red knot populations. Our model is the first to explicitly and quantitatively link these two species and will be used within an adaptive management framework to manage the Delaware Bay system and learn more about the specific nature of the linkage between the two species. ?? 2011 Wiley Periodicals, Inc.

  15. Multispecies modeling for adaptive management of horseshoe crabs and red knots in the Delaware Bay

    USGS Publications Warehouse

    McGowan, Conor P.; Smith, David; Sweka, John A.; Martin, Julien; Nichols, James D.; Wong, Richard; Lyons, James E.; Niles, Lawrence J.; Kalasz, Kevin; Brust, Jeffrey; Klopfer, Michelle; Spear, Braddock

    2011-01-01

    Adaptive management requires that predictive models be explicit and transparent to improve decisions by comparing management actions, directing further research and monitoring, and facilitating learning. The rufa subspecies of red knots (Calidris canutus rufa), which has recently exhibited steep population declines, relies on horseshoe crab (Limulus polyphemus) eggs as their primary food source during stopover in Delaware Bay during spring migration. We present a model with two different parameterizations for use in the adaptive management of horseshoe crab harvests in the Delaware Bay that links red knot mass gain, annual survival, and fecundity to horseshoe crab dynamics. The models reflect prevailing hypotheses regarding ecological links between these two species. When reported crab harvest from 1998 to 2008 was applied, projections corresponded to the observed red knot population abundances depending on strengths of the demographic relationship between these species. We compared different simulated horseshoe crab harvest strategies to evaluate whether, given this model, horseshoe crab harvest management can affect red knot conservation and found that restricting harvest can benefit red knot populations. Our model is the first to explicitly and quantitatively link these two species and will be used within an adaptive management framework to manage the Delaware Bay system and learn more about the specific nature of the linkage between the two species.

  16. A 'FIREWORK' OF H{sub 2} KNOTS IN THE PLANETARY NEBULA NGC 7293 (THE HELIX NEBULA)

    SciTech Connect

    Matsuura, M.; Speck, A. K.; McHunu, B. M.; Tanaka, I.; Wright, N. J.; Viti, S.; Wesson, R.; Smith, M. D.; Zijlstra, A. A. E-mail: mikako@star.ucl.ac.uk

    2009-08-01

    We present a deep and wide field-of-view (4' x 7') image of the planetary nebula (PN) NGC 7293 (the Helix Nebula) in the 2.12 {mu}m H{sub 2} v = 1 {yields} 0 S(1) line. The excellent seeing (0.''4) at the Subaru Telescope, allows the details of cometary knots to be examined. The knots are found at distances of 2.'2-6.'4 from the central star (CS). At the inner edge and in the inner ring (up to 4.'5 from the CS), the knot often show a 'tadpole' shape, an elliptical head with a bright crescent inside and a long tail opposite to the CS. In detail, there are variations in the tadpole shapes, such as narrowing tails, widening tails, meandering tails, or multipeaks within a tail. In the outer ring (4.'5-6.'4 from the CS), the shapes are more fractured, and the tails do not collimate into a single direction. The transition in knot morphology from the inner edge to the outer ring is clearly seen. The number density of knots governs the H{sub 2} surface brightness in the inner ring: H{sub 2} exists only within the knots. Possible mechanisms which contribute to the shaping of the knots are discussed, including photoionization and streaming motions. A plausible interpretation of our images is that inner knots are being overrun by a faster wind, but that this has not (yet) reached the outer knots. Based on H{sub 2} formation and destruction rates, H{sub 2} gas can survive in knots from formation during the late asymptotic giant branch phase throughout the PN phase. These observations provide new constraints on the formation and evolution of knots, and on the physics of molecular gas embedded within ionized gas.

  17. Supercoiling, knotting and replication fork reversal in partially replicated plasmids

    PubMed Central

    Olavarrieta, L.; Martínez-Robles, M. L.; Sogo, J. M.; Stasiak, A.; Hernández, P.; Krimer, D. B.; Schvartzman, J. B.

    2002-01-01

    To study the structure of partially replicated plasmids, we cloned the Escherichia coli polar replication terminator TerE in its active orientation at different locations in the ColE1 vector pBR18. The resulting plasmids, pBR18-TerE@StyI and pBR18-TerE@EcoRI, were analyzed by neutral/neutral two-dimensional agarose gel electrophoresis and electron microscopy. Replication forks stop at the Ter–TUS complex, leading to the accumulation of specific replication intermediates with a mass 1.26 times the mass of non-replicating plasmids for pBR18-TerE@StyI and 1.57 times for pBR18-TerE@EcoRI. The number of knotted bubbles detected after digestion with ScaI and the number and electrophoretic mobility of undigested partially replicated topoisomers reflect the changes in plasmid topology that occur in DNA molecules replicated to different extents. Exposure to increasing concentrations of chloroquine or ethidium bromide revealed that partially replicated topoisomers (CCCRIs) do not sustain positive supercoiling as efficiently as their non-replicating counterparts. It was suggested that this occurs because in partially replicated plasmids a positive ΔLk is absorbed by regression of the replication fork. Indeed, we showed by electron microscopy that, at least in the presence of chloroquine, some of the CCCRIs of pBR18-Ter@StyI formed Holliday-like junction structures characteristic of reversed forks. However, not all the positive supercoiling was absorbed by fork reversal in the presence of high concentrations of ethidium bromide. PMID:11809877

  18. Avian influenza virus antibodies in Pacific Coast Red Knots (Calidris canutus rufa)

    USGS Publications Warehouse

    Johnson, James A.; DeCicco, Lucas H.; Ruthrauff, Daniel R.; Krauss, Scott; Hall, Jeffrey S.

    2014-01-01

    Prevalence of avian influenza virus (AIV) antibodies in the western Atlantic subspecies of Red Knot (Calidris canutus rufa) is among the highest for any shorebird. To assess whether the frequency of detection of AIV antibodies is high for the species in general or restricted only to C. c. rufa, we sampled the northeastern Pacific Coast subspecies of Red Knot (Calidris canutus roselaari) breeding in northwestern Alaska. Antibodies were detected in 90% of adults and none of the chicks sampled. Viral shedding was not detected in adults or chicks. These results suggest a predisposition of Red Knots to AIV infection. High antibody titers to subtypes H3 and H4 were detected, whereas low to intermediate antibody levels were found for subtypes H10 and H11. These four subtypes have previously been detected in shorebirds at Delaware Bay (at the border of New Jersey and Delaware) and in waterfowl along the Pacific Coast of North America.

  19. Ventriculoperitoneal shunt disconnection associated with spontaneous knot formation in the peritoneal catheter.

    PubMed

    Lo, William B; Ramirez, Roberto; Rodrigues, Desiderio; Solanki, Guirish A

    2013-01-01

    A 10-year-old girl underwent distal ventriculoperitoneal (VP) shunt revision 3 weeks earlier and developed further shunt malfunction. During the current shunt revision, a disconnection at the straight connector site in the cervical subcutaneous tissue was confirmed and a knot was identified in the peritoneal catheter. Postoperatively, the patient made a rapid neurological recovery and was discharged 48 h later. This is the first case of VP shunt disconnection associated with a spontaneous distal knot formation. The likely mechanism was that the spontaneously formed knot acted as an anchor at the peritoneal wall, preventing free relative movement of the distal catheter. The resultant tension led to failure at the weakest point of the system, resulting in a disconnection at the proximal straight connector site.

  20. Slip knots and unfastening topologies enhance toughness without reducing strength of silk fibroin fibres.

    PubMed

    Berardo, Alice; Pantano, Maria F; Pugno, Nicola M

    2016-02-01

    The combination of high strength and high toughness is a desirable feature that structural materials should display. However, while in the past, engineers had to compromise on either strength or toughness depending on the requested application, nowadays, new toughening strategies are available to provide strong materials with high toughness. In this paper, we focus on one of such strategy, which requires no chemical treatment, but the implementation of slip knots with optimized shape and size in the involved material, which is silkworm silk in this case. In particular, a variety of slip knot topologies with different unfastening mechanisms are investigated, including even complex knots usually used in the textile industry, and their efficiency in enhancing toughness of silk fibres is discussed. PMID:26855750

  1. Slip knots and unfastening topologies enhance toughness without reducing strength of silk fibroin fibres.

    PubMed

    Berardo, Alice; Pantano, Maria F; Pugno, Nicola M

    2016-02-01

    The combination of high strength and high toughness is a desirable feature that structural materials should display. However, while in the past, engineers had to compromise on either strength or toughness depending on the requested application, nowadays, new toughening strategies are available to provide strong materials with high toughness. In this paper, we focus on one of such strategy, which requires no chemical treatment, but the implementation of slip knots with optimized shape and size in the involved material, which is silkworm silk in this case. In particular, a variety of slip knot topologies with different unfastening mechanisms are investigated, including even complex knots usually used in the textile industry, and their efficiency in enhancing toughness of silk fibres is discussed.

  2. A cactus-derived toxin-like cystine knot Peptide with selective antimicrobial activity.

    PubMed

    Aboye, Teshome L; Strömstedt, Adam A; Gunasekera, Sunithi; Bruhn, Jan G; El-Seedi, Hesham; Rosengren, K Johan; Göransson, Ulf

    2015-05-01

    Naturally occurring cystine knot peptides show a wide range of biological activity, and as they have inherent stability they represent potential scaffolds for peptide-based drug design and biomolecular engineering. Here we report the discovery, sequencing, chemical synthesis, three-dimensional solution structure determination and bioactivity of the first cystine knot peptide from Cactaceae (cactus) family: Ep-AMP1 from Echinopsis pachanoi. The structure of Ep-AMP1 (35 amino acids) conforms to that of the inhibitor cystine knot (or knottin) family but represents a novel diverse sequence; its activity was more than 500 times higher against bacterial than against eukaryotic cells. Rapid bactericidal action and liposome leakage implicate membrane permeabilisation as the mechanism of action. Sequence homology places Ec-AMP1 in the plant C6-type of antimicrobial peptides, but the three dimensional structure is highly similar to that of a spider neurotoxin.

  3. Avian influenza virus antibodies in Pacific Coast Red Knots (Calidris canutus roselaari).

    PubMed

    Johnson, James A; DeCicco, Lucas H; Ruthrauff, Daniel R; Krauss, Scott; Hall, Jeffrey S

    2014-07-01

    Prevalence of avian influenza virus (AIV) antibodies in the western Atlantic subspecies of Red Knot (Calidris canutus rufa) is among the highest for any shorebird. To assess whether the frequency of detection of AIV antibodies is high for the species in general or restricted only to C. c. rufa, we sampled the northeastern Pacific Coast subspecies of Red Knot (Calidris canutus roselaari) breeding in northwestern Alaska. Antibodies were detected in 90% of adults and none of the chicks sampled. Viral shedding was not detected in adults or chicks. These results suggest a predisposition of Red Knots to AIV infection. High antibody titers to subtypes H3 and H4 were detected, whereas low to intermediate antibody levels were found for subtypes H10 and H11. These four subtypes have previously been detected in shorebirds at Delaware Bay (at the border of New Jersey and Delaware) and in waterfowl along the Pacific Coast of North America.

  4. First results from the Goddard High-Resolution Spectrograph - Ultraviolet spectra of a starburst knot in NGC 1068

    SciTech Connect

    Hutchings, J.B.; Bruhweiler, F.; Truong, K.Q.; Boggess, A.; Heap, S.R.; Ebbets, D.; Beaver, E.; Rosenblatt, E.; Perez, M. Catholic Univ. of America, Washington, DC NASA, Goddard Space Flight Center, Greenbelt, MD Ball Aerospace Systems Group, Boulder, CO California Univ., La Jolla NASA, Goddard Space Flight Center Computer Sciences Corp., Greenbelt, MD )

    1991-08-01

    This paper presents UV spectroscopy of a circumnuclear starburst knot in the Seyfert 2 galaxy NGC 1068, a close-by active galaxy which has some of the most luminous known starburst knots. The spectrum shows the presence of several thousand O and B stars which appear to have formed about 3 million years ago. 19 refs.

  5. First results from the Goddard High-Resolution Spectrograph - Ultraviolet spectra of a starburst knot in NGC 1068

    NASA Technical Reports Server (NTRS)

    Hutchings, J. B.; Bruhweiler, F.; Truong, K. Q.; Boggess, A.; Heap, S. R.; Ebbets, D.; Beaver, E.; Rosenblatt, E.; Perez, M.

    1991-01-01

    This paper presents UV spectroscopy of a circumnuclear starburst knot in the Seyfert 2 galaxy NGC 1068, a close-by active galaxy which has some of the most luminous known starburst knots. The spectrum shows the presence of several thousand O and B stars which appear to have formed about 3 million years ago.

  6. Characterization of the Inner Knot of the Crab: The Site of the Gamma-ray Flares?

    NASA Astrophysics Data System (ADS)

    Weisskopf, Martin C.; Chandra/HST/Keck gamma-ray flare Team

    2015-01-01

    One of the most intriguing recent discoveries has been the detection of powerful γ-ray flares from the Crab Nebula. Such events, with a recurrence time of about once per year, can be so dramatic to make the system the brightest source in the gamma-ray sky as occurred, e.g. in April 2011. These flares challenge our understanding of how pulsar wind nebulae work and defy current astrophysical models for particle acceleration. We present here our study of the inner knot located within a fraction of an arcsecond from the pulsar with the aim of characterizing the feature and asking if this might be the site of the origin of the γ-ray flares. We took data using Keck, HST, and Chandra obtained as part of our multi-wavelength campaign to identify the source of the enigmatic flares. We set an upper limit as to the x-ray flux from the knot. We also find that the dimensions, surface brightness, flux, etc. of the optical and infrared knot are all correlated with distance of from the pulsar. This distance, in turn, varies with time. In addition to this most thorough characterization of the inner knot's properties, we examine the hypothesis that the knot may be the site of the flares by examining the knot separation versus the Fermi/LAT γ-ray flux. Finally, as part of this research, we make use of a new approach employing singular value decomposition (SVD) for analyzing time series of images and compare the approach to more traditional methods. Our conclusions are only refined but not impacted by using the new approach.

  7. Unfolding knots by proteasome-like systems: simulations of the behaviour of folded and neurotoxic proteins.

    PubMed

    Wojciechowski, Michał; Gómez-Sicilia, Àngel; Carrión-Vázquez, Mariano; Cieplak, Marek

    2016-08-16

    Knots in proteins have been proposed to resist proteasomal degradation. Ample evidence associates proteasomal degradation with neurodegeneration. One interesting possibility is that indeed knotted conformers stall this machinery leading to toxicity. However, although the proteasome is known to unfold mechanically its substrates, at present there are no experimental methods to emulate this particular traction geometry. Here, we consider several dynamical models of the proteasome in which the complex is represented by an effective potential with an added pulling force. This force is meant to induce the translocation of a protein or a polypeptide into the catalytic chamber. The force is either constant or applied periodically. The translocated proteins are modelled in a coarse-grained fashion. We do comparative analysis of several knotted globular proteins and the transiently knotted polyglutamine tracts of length 60 alone and fused in exon 1 of the huntingtin protein. Huntingtin is associated with Huntington's disease, a well-known genetically determined neurodegenerative disease. We show that the presence of a knot hinders and sometimes even jams translocation. We demonstrate that the probability to do so depends on the protein, the model of the proteasome, the magnitude of the pulling force, and the choice of the pulled terminus. In any case, the net effect would be a hindrance in the proteasomal degradation process in the cell. This would then yield toxicity via two different mechanisms: one through toxic monomers compromising degradation and another by the formation of toxic oligomers. Our work paves the way for the mechanistic investigation of the mechanical unfolding of knotted structures by the proteasome and its relation to toxicity and disease. PMID:27425826

  8. Demographic consequences of migratory stopover: linking red knot survival to horseshoe crab spawning abundance

    USGS Publications Warehouse

    McGowan, Conor P.; Hines, James E.; Nichols, James D.; Lyons, James E.; Smith, David; Kalasz, Kevin S.; Niles, Lawrence J.; Dey, Amanda D.; Clark, Nigel A.; Atkinson, Philip W.; Minton, Clive D.T.; Kendall, William

    2011-01-01

    Understanding how events during one period of the annual cycle carry over to affect survival and other fitness components in other periods is essential to understanding migratory bird demography and conservation needs. Previous research has suggested that western Atlantic red knot (Calidris canutus rufa) populations are greatly affected by horseshoe crab (Limulus polyphemus) egg availability at Delaware Bay stopover sites during their spring northward migration. We present a mass-based multistate, capturerecapture/resighting model linking (1) red knot stopover mass gain to horseshoe crab spawning abundance and (2) subsequent apparent annual survival to mass state at the time of departure from the Delaware Bay stopover area. The model and analysis use capture-recapture/resighting data with over 16,000 individual captures and 13,000 resightings collected in Delaware Bay over a 12 year period from 1997–2008, and the results are used to evaluate the central management hypothesis that red knot populations can be influenced by horseshoe crab harvest regulations as part of a larger adaptive management effort. Model selection statistics showed support for a positive relationship between horseshoe crab spawning abundance during the stopover and the probability of red knots gaining mass (parameter coefficient from the top model b = 1.71, SE = 0.46). Our analyses also supported the link between red knot mass and apparent annual survival, although average estimates for the two mass classes differed only slightly. The addition of arctic snow depth as a covariate influencing apparent survival improved the fit of the data to the models (parameter coefficient from the top model b = 0.50, SE = 0.08). Our results indicate that managing horseshoe crab resources in the Delaware Bay has the potential to improve red knot population status.

  9. Characterization of the Inner Knot of the Crab: the Site of the Gamma-ray Flares?

    NASA Technical Reports Server (NTRS)

    Weisskopf, Martin C.

    2015-01-01

    One of the most intriguing recent discoveries has been the detection of powerful gamma-ray flares from the Crab Nebula. Such events, with a recurrence time of about once per year, can be so dramatic to make the system the brightest source in the gamma-ray sky as occurred, e.g. in April 2011. These flares challenge our understanding of how pulsar wind nebulae work and defy current astrophysical models for particle acceleration. We present here our study of the inner knot located within a fraction of an arcsecond from the pulsar with the aim of characterizing the feature and asking if this might be the site of the origin of the gamma-ray flares. We took data using Keck, HST, and Chandra obtained as part of our multi-wavelength campaign to identify the source of the enigmatic flares. We set an upper limit as to the gamma-ray flux from the knot. We also find that the dimensions, surface brightness, flux, etc. of the optical and infrared knot are all correlated with distance from the pulsar. This distance, in turn, varies with time. In addition to this most thorough characterization of the inner knot's properties, we examine the hypothesis that the knot may be the site of the flares by examining the knot separation versus the Fermi/LAT gamma-ray flux. Finally, as part of this research, we make use of a new approach employing singular value decomposition (SVD) for analyzing time series of images and compare the approach to more traditional methods. Our conclusions are only refined but not impacted by using the new approach.

  10. Knot Stent”: An Unusual Cause of Acute Renal Failure in Solitary Kidney

    PubMed Central

    Moufid, Kamal; Touiti, Driss; Mohamed, Lezrek

    2012-01-01

    The insertion of indwelling ureteric stents is a routine procedure in urology practice. Complications secondary to the insertion of these stents have also increased, such as stent encrustation, stent fragmentation, stone formation, and recurrent urinary tract infections. Knot formation within the renal pelvis or in the coiled portion of the ureteral stent is an extremely rare condition, with less than 15 cases reported in literature. The authors report a rare case of knotted stent, complicated by an obstructive acute renal failure and urosepsis, in a patient with a solitary functioning kidney. PMID:22919550

  11. Design considerations for attaining 250-knot test velocities at the aircraft landing dynamics facility

    NASA Technical Reports Server (NTRS)

    Gray, C. E., Jr.; Snyder, R. E.; Taylor, J. T.; Cires, A.; Fitzgerald, A. L.; Armistead, M. F.

    1980-01-01

    Preliminary design studies are presented which consider the important parameters in providing 250 knot test velocities at the Aircraft Landing Dynamics Facility. Four major components of this facility are: the hydraulic jet catapult, the test carriage structure, the reaction turning bucket, and the wheels. Using the hydraulic-jet catapult characteristics, a target design point was selected and a carriage structure was sized to meet the required strength requirements. The preliminary design results indicate that to attain 250 knot test velocities for a given hydraulic jet catapult system, a carriage mass of 25,424 kg (56,000 lbm.) cannot be exceeded.

  12. On the implications of recent observations of the inner knot in the Crab nebula

    NASA Astrophysics Data System (ADS)

    Yuan, Yajie; Blandford, Roger D.

    2015-12-01

    Recent observations of the Crab nebula (Rudy et al.) have maintained its reputation for high-energy astrophysical enlightenment and its use as a test-bed for theories of the behaviour of magnetized, relativistic plasma. In particular, new observations of the inner knot located 0.65 arcsec SE from the pulsar confirm that it is compact, elongated transversely to the symmetry axis and curved concave towards the pulsar. 60 per cent polarization has been measured along the symmetry axis (Moran et al.). The knot does not appear to be involved in the gamma-ray flares. The new observations both reinforce the interpretation of the knot as dissipation of the pulsar wind at a strong shock and challenge the details of existing models of this process. In particular, it is argued that the compactness, high polarization, and curvature are difficult to reconcile with simple relativistic shock models. Alternative possibilities include deflection of the outflow ahead of the shock and spatial variation in which the knot is interpreted as a caustic. Some future observations are proposed and new theoretical investigations are suggested.

  13. Managing Root-knot on Tobacco in the Southeastern United States

    PubMed Central

    Johnson, Charles S.

    1989-01-01

    Root-knot nematodes suppress yields of flue-cured tobacco an estimated 0.1 to 4.8% annually in the southeastern United States, even though nematode management practices have been widely adopted. Although Meloidogyne incognita races 1 and 3 have predominated, M. arenaria, M. javanica, and M. incognita races 2 and 4 are increasingly important. Seventy-five percent of the flue-cured tobacco hectarage in North Carolina and Virginia is rotated on 2-year or 3-year intervals. Over half of the hectarage in the southeastern United States was planted with tobacco cultivars resistant to M. incognita races 1 and 3 in 1986. Resistance to other species or races of root-knot nematodes is not available in commercially available flue-cured tobacco cultivars. Most producers plow and (or) disc-out flue-cured tobacco roots and stalks after harvest. Nematicide use ranges from virtually 100% in Florida and Georgia to 60% in Virginia. Continued research is needed to develop management strategies for mixed populations of root-knot nematodes and to incorporate resistance to more root-knot nematode species and races into tobacco cultivars. Nematode advisory programs that allow producers to optimize nematicide use from an economical and ecological point of view are also needed. PMID:19287655

  14. Black knot [Apiosporina morbosa (Schw.)] resistance in imported and domestic Prunus domestica L. germplasm and cultivars

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Black knot (BK) Apisporina morbosa (Schw.) is an important fungal disease of Prunus domestica and other Prunus species in North America. BK causes economic losses in the plum growing regions of northern and eastern U.S. and eastern Canada. Relatively few P. domestica commercial cultivars are resis...

  15. Resistant Citrullus lanatus var. citroides Rootstocks for Managing Root-knot Nematodes in Grafted Watermelon

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Southern root-knot nematode (RKN), Meloidogyne incognita, is an important re-emerging pest of watermelon. Several factors have contributed to re-emergence of RKN including: 1) ban of methyl bromide for soil fumigation; 2) reduced land area for crop rotation; and 3) continuous cropping of cucurbits u...

  16. Tomato susceptibility to root-knot nematodes requires an intact jasmonic Acid signaling pathway

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Response of tomato (Solanum lycopersicum) to root-knot nematode (RKN; Meloidogyne spp.) infection was monitored using TOM1 cDNA microarray with resistant (‘Motelle’; Mi-1) and susceptible (‘Moneymaker’; mi) tomato at 24 h after RKN infection. The array analysis identified 1497 genes and 750 genes d...

  17. Transcriptome analysis of resistant and susceptible alfalfa cultivars infected with root-knot nematode Meloidogyne incognita

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Nematodes are one of the major limiting factors in alfalfa production. Root knot nematodes (RKN, Meloidogyne spp.) are widely distributed and economically important sedentary endoparasites of agricultural crops (Castagnone-Sereno et al. 2013) and they may inflict significant damage to alfalfa fields...

  18. Field level risk assessment for root-knot nematodes in lima beans

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Southern Root-Knot Nematode (RKN), Meloidogyne incognita, is a major yield limiting pest in lima beans (Phaseolus lunatus). RKN are not evenly distributed through fields and population dynamics are fluid making whole field management challenging. The objectives of this research were to characterize ...

  19. Is Grafting Useful for Managing Root-Knot Nematodes in Watermelon?

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Five Citrullus lanatus var. citroides germplasm lines, four Lagenaria siceraria cultivars, one Cucurbita moschata x C. maxima hybrid, and one commercial wild watermelon (Citrullus lanatus spp.) cultivar were evaluated as rootstocks for watermelon in a field infested with the southern root-knot nemat...

  20. Wormholes in chemical space connecting torus knot and torus link pi-electron density topologies.

    PubMed

    Rzepa, Henry S

    2009-03-01

    Möbius aromaticities can be considered as deriving from cyclic delocalized pi-electron densities rho(r)(pi) which have the topological form of either a two-component torus link or a single-component torus knot. These two topological forms are distinguished by their (non-zero) linking number L(k), which describes how many times the two components of a torus link cross each other or the single component of a torus knot crosses with itself. The special case of Hückel or benzenoid aromaticity is associated with a pi-electron density that takes the form of a two-component torus link for which the linking number is zero. A class of molecule has been identified which here is termed a Janus aromatic, and which bears the characteristics of both a two-component torus link and a single-component torus knot in the topology of the pi-electron density. This is achieved by the formation of one (or more) wormholes or throats in the pi-electron density connecting the two torus forms, which can impart a Janus-like dual personality to the aromaticity of the system. The impact of such wormholes on the overall pi-delocalized aromaticity of such molecules is approximately estimated using a NICS(rcp) index, and subdivides into two types; those where the forms of aromaticity associated with a torus link and a torus knot cooperate and those where they oppose.

  1. Mustard seed meal for management of root-knot nematode and weeds in tomato production

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Mustard seed meals of indian mustard [InM (Brassica juncea)] and yellow mustard [YeM (Sinapis alba)], alone and combined, were tested for effects on tomato (Solanum lycopersicum) plants and for suppression of southern root-knot nematode [RKN (Meloidogyne incognita)] and weed populations. In the gree...

  2. A knotted1-like homeobox protein regulates abscission in tomato by modulating the auxin pathway

    Technology Transfer Automated Retrieval System (TEKTRAN)

    KD1, a gene encoding a KNOTTED1-LIKE HOMEOBOX transcription factor is known to be involved, in tomato, in ontogeny of the compound leaf. KD1 is also highly expressed in both leaf and flower abscission zones. Reducing abundance of transcripts of this gene in tomato, using both virus induced gene sile...

  3. Comparison of ultrasonic suture welding and traditional knot tying in a rabbit rotator cuff repair model.

    PubMed

    Nho, Shane J; Cole, Brian J; Mazzocca, Augustus D; Williams, James M; Romeo, Anthony A; Bush-Joseph, Charles A; Bach, Bernard R; Hallab, Nadim J

    2006-01-01

    The purpose of this study is to evaluate ultrasonic suture welding of monofilament suture in an animal model of rotator cuff repair with biomechanical and histologic analyses. We randomly assigned 46 shoulders in 23 rabbits to 1 of 3 treatment groups: sham-operated (n = 15), knotted (n = 15), and welded (n = 16). Supraspinatus defects were surgically created and acutely repaired with suture anchors loaded with either No. 2-0 Ethibond for knotted group or No. 2-0 nylon for welded shoulders. Eighteen weeks postoperatively, all animals were killed, and the shoulders underwent either biomechanical testing or histologic analysis. The maximum stress of the sham-operated group (20.6 N/mm2) was significantly greater than that of both the knotted (10.2 N/mm2) and welded (8.3 N/mm2) groups (P < .05), but no differences were observed between the knotted and welded groups. Although some histologic changes were noted, none was considered to be significant to distinguish either group.

  4. Phytotoxicity of Clove Oil to Vegetable Crop Seedlings and Nematotoxicity to Root-knot Nematodes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Clove oil derived from the plant Syzygium aromaticum is active against various soilborne plant pathogens, and therefore has potential for use as a biobased pesticide. A clove oil formulation previously found to be toxic to the root-knot nematode Meloidogyne incognita in laboratory assays was invest...

  5. Evidence for a disease complex between Pythium aphanidermatum and root-knot nematodes in cucumber

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A field trial in 2012 indicated a possible disease complex between Pythium aphanidermatum and the root-knot nematode (RKN) Meloidogyne incognita in cucumber. Two growth chamber trials were conducted to investigate this potential disease complex. Treatments included inoculating nine-day-old cucumbe...

  6. Southern root-knot nematode affects common cocklebur (Xanthium strumarium) interference with cotton

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Southern root-knot nematode and common cocklebur will both interfere with cotton growth and yield. A greater understanding of the interaction of these pests on cotton growth and yield is needed for effective IPM (integrated pest management). An additive design was used in outdoor micro-plots with fi...

  7. Splitting, linking, knotting, and solitonic escape of topological defects in nematic drops with handles.

    PubMed

    Tasinkevych, Mykola; Campbell, Michael G; Smalyukh, Ivan I

    2014-11-18

    Topologically nontrivial field excitations, including solitonic, linked, and knotted structures, play important roles in physical systems ranging from classical fluids and liquid crystals, to electromagnetism, classic, and quantum field theories. These excitations can appear spontaneously during symmetry-breaking phase transitions. For example, in cosmological theories, cosmic strings may have formed knotted configurations influencing the Early Universe development, whereas in liquid crystals transient tangled defect lines were observed during isotropic-nematic transitions, eventually relaxing to defect-free states. Knotted and solitonic fields and defects were also obtained using optical manipulation, complex-shaped colloids, and frustrated cholesterics. Here we use confinement of nematic liquid crystal by closed surfaces with varied genus and perpendicular boundary conditions for a robust control of appearance and stability of such field excitations. Theoretical modeling and experiments reveal structure of defect lines as a function of the surface topology and material and geometric parameters, establishing a robust means of controlling solitonic, knotted, linked, and other field excitations. PMID:25369931

  8. Splitting, linking, knotting, and solitonic escape of topological defects in nematic drops with handles

    PubMed Central

    Tasinkevych, Mykola; Campbell, Michael G.; Smalyukh, Ivan I.

    2014-01-01

    Topologically nontrivial field excitations, including solitonic, linked, and knotted structures, play important roles in physical systems ranging from classical fluids and liquid crystals, to electromagnetism, classic, and quantum field theories. These excitations can appear spontaneously during symmetry-breaking phase transitions. For example, in cosmological theories, cosmic strings may have formed knotted configurations influencing the Early Universe development, whereas in liquid crystals transient tangled defect lines were observed during isotropic–nematic transitions, eventually relaxing to defect-free states. Knotted and solitonic fields and defects were also obtained using optical manipulation, complex-shaped colloids, and frustrated cholesterics. Here we use confinement of nematic liquid crystal by closed surfaces with varied genus and perpendicular boundary conditions for a robust control of appearance and stability of such field excitations. Theoretical modeling and experiments reveal structure of defect lines as a function of the surface topology and material and geometric parameters, establishing a robust means of controlling solitonic, knotted, linked, and other field excitations. PMID:25369931

  9. Percutaneous Untying of a Knot in a Retained Swan-Ganz Catheter

    SciTech Connect

    Bhatti, Waqar A.; Sinha, Sankar; Rowlands, Peter

    2000-03-15

    A patient was referred to us with a tightly knotted Swan-Ganz catheter. The catheter could not be removed by conventional simple methods. We describe a minimally invasive means of removal of the catheter using an Amplatz gooseneck snare and an angioplasty balloon. This allowed the catheter to be removed without trauma.

  10. Pierced Lasso Bundles Are a New Class of Knot-like Motifs

    PubMed Central

    Haglund, Ellinor; Sulkowska, Joanna I.; Noel, Jeffrey K.; Lammert, Heiko; Onuchic, José N.; Jennings, Patricia A.

    2014-01-01

    A four-helix bundle is a well-characterized motif often used as a target for designed pharmaceutical therapeutics and nutritional supplements. Recently, we discovered a new structural complexity within this motif created by a disulphide bridge in the long-chain helical bundle cytokine leptin. When oxidized, leptin contains a disulphide bridge creating a covalent-loop through which part of the polypeptide chain is threaded (as seen in knotted proteins). We explored whether other proteins contain a similar intriguing knot-like structure as in leptin and discovered 11 structurally homologous proteins in the PDB. We call this new helical family class the Pierced Lasso Bundle (PLB) and the knot-like threaded structural motif a Pierced Lasso (PL). In the current study, we use structure-based simulation to investigate the threading/folding mechanisms for all the PLBs along with three unthreaded homologs as the covalent loop (or lasso) in leptin is important in folding dynamics and activity. We find that the presence of a small covalent loop leads to a mechanism where structural elements slipknot to thread through the covalent loop. Larger loops use a piercing mechanism where the free terminal plugs through the covalent loop. Remarkably, the position of the loop as well as its size influences the native state dynamics, which can impact receptor binding and biological activity. This previously unrecognized complexity of knot-like proteins within the helical bundle family comprises a completely new class within the knot family, and the hidden complexity we unraveled in the PLBs is expected to be found in other protein structures outside the four-helix bundles. The insights gained here provide critical new elements for future investigation of this emerging class of proteins, where function and the energetic landscape can be controlled by hidden topology, and should be take into account in ab initio predictions of newly identified protein targets. PMID:24945798

  11. The characteristics and evolution of dense knots in the Supernova Remnant, Cas A

    NASA Astrophysics Data System (ADS)

    Tielens, Alexander

    2014-10-01

    Supernovae are key drivers of the evolution of the interstellar medium of galaxies as they are main sources of freshly synthesized elements, dust and kinetic energy. Dense Fast Moving Knots (FMKs) are an important component of supernova remnants as they may be prime sites for dust formation and their high densities protect this dust against the destructive action of the reverse shock. Herschel, Spitzer, Akari, and ground-based IR studies of dense clumps in the Cas A supernova remnant have revealed large column densities (4E19 per square cm) of warm (500-1000K) dense (1E5 to 1E6 particles per cc) CO gas. This dense environment is very conducive to dust formation and protection. However, the relationship of the molecular and ionic gas is unclear and the derived large column densities are much larger than shock models predict, indicating the importance of energy conduction by electrons from the surrounding hot plasma into the knot. Conduction is a key process in the evolution of knots and drives the overall morphology of supernova remnants and their interaction with the interstellar medium. We propose to observe three CO-rich knots in the [OIII] 52&88 and [OI] 63 fine-structure lines with FIFI-LS/SOFIA. We will compare the distribution of these atomic lines with that of CO and derive the physical conditions and column densities. A pilot program in Cycle 2 has demonstrated the feasibility of this project. The proposed observations will address the key questions: "Can FMKs protect dust ?", "Are the observed variations in the mid-IR CO emission related to variations in the pre-shock density, column density, or the presence of additional heating sources for the gas?", and "What is the importance of electron energy conduction for the heating of the gas and how do these knots dissolve and merge with the SNR/ISM?"

  12. X-Wing RSRA - 80 Knot Taxi Test

    NASA Technical Reports Server (NTRS)

    1987-01-01

    The Rotor Systems Research Aircraft/X-Wing, a vehicle that was used to demonstrate an advanced rotor/fixed wing concept called X-Wing, is shown here during high-speed taxi tests at NASA's Ames-Dryden Flight Research Facility (later redesignated Dryden Flight Research Center), Edwards, California, on 4 November 1987. During these tests, the vehicle made three taxi tests at speeds of up to 138 knots. On the third run, the RSRA/X-Wing lifted off the runway to a 25-foot height for about 16 seconds. This liftoff maneuver was pre-planned as an aid to evaluations for first flight. At the controls were NASA pilot G. Warren Hall and Sikorsky pilot W. Faull. The unusual aircraft that resulted from the Ames Research Center/Army X-Wing Project was flown at the Ames-Dryden Flight Research Facility (now Dryden Flight Research Center), Edwards, California, beginning in the spring of 1984, with a follow-on program beginning in 1986. The program, was conceived to provide an efficient combination of the vertical lift characteristic of conventional helicopters and the high cruise speed of fixed-wing aircraft. It consisted of a hybrid vehicle called the NASA/Army Rotor Systems Research Aircraft (RSRA), which was equipped with advanced X-wing rotor systems. The program began in the early 1970s to investigate ways to increase the speed of rotor aircraft, as well as their performance, reliability, and safety . It also sought to reduce the noise, vibration, and maintenance costs of helicopters. Sikorsky Aircraft Division of United Technologies Laboratories built two RSRA aircraft. NASA's Langley Research Center, Hampton, Virginia, did some initial testing and transferred the program to Ames Research Center, Mountain View, California, for an extensive flight research program conducted by Ames and the Army. The purpose of the 1984 tests was to demonstrate the fixed-wing capability of the helicopter/airplane hybrid research vehicle and explore its flight envelope and flying qualities. These

  13. 78 FR 60023 - Endangered and Threatened Wildlife and Plants; Proposed Threatened Status for the Rufa Red Knot...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-30

    ... review published in the Federal Register on July 1, 1994 (59 FR 34270), we have sought the expert... knots make one of the longest distance migrations known in the animal kingdom, traveling up to...

  14. Accomplishments of a 10-year initiative to develop host plant resistance to root-knot and reniform nematodes in cotton

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In 2003 Cotton Incorporated initiated a Beltwide research program to develop host plant resistance against root-knot (Meloidogyne incognita) and reniform (Rotylenchulus reniformis) nematodes. Objectives formulated at a coordinating meeting in 2003 that included participants from public institutions...

  15. The olive knot disease as a model to study the role of interspecies bacterial communities in plant disease

    PubMed Central

    Buonaurio, Roberto; Moretti, Chiaraluce; da Silva, Daniel Passos; Cortese, Chiara; Ramos, Cayo; Venturi, Vittorio

    2015-01-01

    There is an increasing interest in studying interspecies bacterial interactions in diseases of animals and plants as it is believed that the great majority of bacteria found in nature live in complex communities. Plant pathologists have thus far mainly focused on studies involving single species or on their interactions with antagonistic competitors. A bacterial disease used as model to study multispecies interactions is the olive knot disease, caused by Pseudomonas savastanoi pv. savastanoi (Psv). Knots caused by Psv in branches and other aerial parts of the olive trees are an ideal niche not only for the pathogen but also for many other plant-associated bacterial species, mainly belonging to the genera Pantoea, Pectobacterium, Erwinia, and Curtobacterium. The non-pathogenic bacterial species Erwinia toletana, Pantoea agglomerans, and Erwinia oleae, which are frequently isolated inside the olive knots, cooperate with Psv in modulating the disease severity. Co-inoculations of these species with Psv result in bigger knots and better bacterial colonization when compared to single inoculations. Moreover, harmless bacteria co-localize with the pathogen inside the knots, indicating the formation of stable bacterial consortia that may facilitate the exchange of quorum sensing signals and metabolites. Here we discuss the possible role of bacterial communities in the establishment and development of olive knot disease, which we believe could be taking place in many other bacterial plant diseases. PMID:26113855

  16. The olive knot disease as a model to study the role of interspecies bacterial communities in plant disease.

    PubMed

    Buonaurio, Roberto; Moretti, Chiaraluce; da Silva, Daniel Passos; Cortese, Chiara; Ramos, Cayo; Venturi, Vittorio

    2015-01-01

    There is an increasing interest in studying interspecies bacterial interactions in diseases of animals and plants as it is believed that the great majority of bacteria found in nature live in complex communities. Plant pathologists have thus far mainly focused on studies involving single species or on their interactions with antagonistic competitors. A bacterial disease used as model to study multispecies interactions is the olive knot disease, caused by Pseudomonas savastanoi pv. savastanoi (Psv). Knots caused by Psv in branches and other aerial parts of the olive trees are an ideal niche not only for the pathogen but also for many other plant-associated bacterial species, mainly belonging to the genera Pantoea, Pectobacterium, Erwinia, and Curtobacterium. The non-pathogenic bacterial species Erwinia toletana, Pantoea agglomerans, and Erwinia oleae, which are frequently isolated inside the olive knots, cooperate with Psv in modulating the disease severity. Co-inoculations of these species with Psv result in bigger knots and better bacterial colonization when compared to single inoculations. Moreover, harmless bacteria co-localize with the pathogen inside the knots, indicating the formation of stable bacterial consortia that may facilitate the exchange of quorum sensing signals and metabolites. Here we discuss the possible role of bacterial communities in the establishment and development of olive knot disease, which we believe could be taking place in many other bacterial plant diseases. PMID:26113855

  17. A knot in the catheter--an unusual cause of ventriculo-peritoneal shunt blockage.

    PubMed

    Chopra, I; Gnanalingham, K; Pal, D; Peterson, D

    2004-09-01

    A 25-year-old woman, who was 25 weeks pregnant, underwent insertion of a VP shunt for hydrocephalus, secondary to a bithalamic glioma. Two months later, she represented with symptoms of raised intracranial pressure and MR scan revealed increased ventricular size. On exploration of the shunt, manometry with saline confirmed blockage of the catheter distal to the valve. On re-opening the abdominal wound, the peritoneal catheter was found to be knotted, 2 cm from the end. This segment of the catheter was replaced, with resolution of symptoms, post-operatively. The present case illustrates that a knot in the peritoneal catheter is an extremely rare cause of shunt malfunction. Possible mechanisms underlying it are discussed.

  18. An easy technique for removal of knotted catheter in the bladder: percutaneous suprapubic cystoscopic intervention.

    PubMed

    Ozkan, Aybars; Okur, Mesut; Kaya, Murat; Büyükkaya, Ramazan; Katranci, Ali Osman; Kucuk, Adem

    2013-01-01

    Uncontaminated urine samples are indispensable to precisely diagnose urinary tract infections in new-borns or infants. Among many clinical interventions for urine collection are described, the most common noninvasive practice is using sterile bags, associated with significant contamination of samples. In children, however, invasive methods i.e. catheterization, are generally needed for reliable urine specimens. Almost always all the inserted catheters are easily drawn back, nevertheless, might not work as expected, and lead to considerable problems that cannot be overcome. Herein, a case of a female newborn treated with a successful percutaneous suprapubic cystoscopic procedure for extracting knotted urinary catheter in the bladder is presented. The least invasive and easiest technic is suggested to be used when catheter is knotted in the bladder, as elaborately stated.

  19. Engineered cystine knot miniproteins as potent inhibitors of human mast cell tryptase beta.

    PubMed

    Sommerhoff, Christian P; Avrutina, Olga; Schmoldt, Hans-Ulrich; Gabrijelcic-Geiger, Dusica; Diederichsen, Ulf; Kolmar, Harald

    2010-01-01

    Here we report the design, chemical and recombinant synthesis, and functional properties of a series of novel inhibitors of human mast cell tryptase beta, a protease of considerable interest as a therapeutic target for the treatment of allergic asthma and inflammatory disorders. These inhibitors are derived from a linear variant of the cyclic cystine knot miniprotein MCoTI-II, originally isolated from the seeds of Momordica cochinchinensis. A synthetic cyclic miniprotein that bears additional positive charge in the loop connecting the N- and C-termini inhibits all monomers of the tryptase beta tetramer with an overall equilibrium dissociation constant K(i) of 1 nM and thus is one of the most potent proteinaceous inhibitors of tryptase beta described to date. These cystine knot miniproteins may therefore become valuable scaffolds for the design of a new generation of tryptase inhibitors. PMID:19852971

  20. Optical knots and contact geometry I. From Arnol'd inequality to Ranada's dyons

    NASA Astrophysics Data System (ADS)

    Kholodenko, Arkady L.

    2016-06-01

    Recently there had been a great deal of activity associated with various schemes of designing both analytic and experimental methods describing knotted structures in electrodynamics and in hydrodynamics. The majority of works in electrodynamics were inspired by the influential paper by Ranada (Lett Math Phys 18:97-106, 1989) and its subsequent refinements. In this work and in its companion we analyze Ranada's results using methods of contact geometry and topology. Not only our analysis allows us to reproduce his major results but in addition, it provides opportunities for considerably extending the catalog of the known/obtained knot types. In addition, it allows to reinterpret both the electric and magnetic charges purely geometrically thus opening the possibility of treatment of masses and charges in Yang-Mills and gravitational fields purely geometrically.

  1. Engineered cystine knot miniproteins as potent inhibitors of human mast cell tryptase beta.

    PubMed

    Sommerhoff, Christian P; Avrutina, Olga; Schmoldt, Hans-Ulrich; Gabrijelcic-Geiger, Dusica; Diederichsen, Ulf; Kolmar, Harald

    2010-01-01

    Here we report the design, chemical and recombinant synthesis, and functional properties of a series of novel inhibitors of human mast cell tryptase beta, a protease of considerable interest as a therapeutic target for the treatment of allergic asthma and inflammatory disorders. These inhibitors are derived from a linear variant of the cyclic cystine knot miniprotein MCoTI-II, originally isolated from the seeds of Momordica cochinchinensis. A synthetic cyclic miniprotein that bears additional positive charge in the loop connecting the N- and C-termini inhibits all monomers of the tryptase beta tetramer with an overall equilibrium dissociation constant K(i) of 1 nM and thus is one of the most potent proteinaceous inhibitors of tryptase beta described to date. These cystine knot miniproteins may therefore become valuable scaffolds for the design of a new generation of tryptase inhibitors.

  2. SU(2)/ SL(2) knot invariants and Kontsevich-Soibelman monodromies

    NASA Astrophysics Data System (ADS)

    Galakhov, D. M.; Mironov, A. D.; Morozov, A. Yu.

    2016-05-01

    We review the Reshetikhin-Turaev approach for constructing noncompact knot invariants involving Rmatrices associated with infinite-dimensional representations, primarily those constructed from the Faddeev quantum dilogarithm. The corresponding formulas can be obtained from modular transformations of conformal blocks as their Kontsevich-Soibelman monodromies and are presented in the form of transcendental integrals, where the main issue is working with the integration contours. We discuss possibilities for extracting more explicit and convenient expressions that can be compared with the ordinary (compact) knot polynomials coming from finite-dimensional representations of simple Lie algebras, with their limits and properties. In particular, the quantum A-polynomials and difference equations for colored Jones polynomials are the same as in the compact case, but the equations in the noncompact case are homogeneous and have a nontrivial right-hand side for ordinary Jones polynomials.

  3. Oxidative folding of peptides with cystine-knot architectures: kinetic studies and optimization of folding conditions.

    PubMed

    Reinwarth, Michael; Glotzbach, Bernhard; Tomaszowski, Michael; Fabritz, Sebastian; Avrutina, Olga; Kolmar, Harald

    2013-01-01

    Bioactive peptides often contain several disulfide bonds that provide the main contribution to conformational rigidity and structural, thermal, or biological stability. Among them, cystine-knot peptides-commonly named "knottins"-make up a subclass with several thousand natural members. Hence, they are considered promising frameworks for peptide-based pharmaceuticals. Although cystine-knot peptides are available through chemical and recombinant synthetic routes, oxidative folding to afford the bioactive isomers still remains a crucial step. We therefore investigated the oxidative folding of ten protease-inhibiting peptides from two knottin families, as well as that of an HIV entry inhibitor and of aprotinin, under two conventional sets of folding conditions and by a newly developed procedure. Kinetic studies identified folding conditions that resulted in correctly folded miniproteins with high rates of conversion even for highly hydrophobic and aggregation-prone peptides in concentrated solutions. PMID:23229141

  4. An easy technique for removal of knotted catheter in the bladder: percutaneous suprapubic cystoscopic intervention

    PubMed Central

    Özkan, Aybars; Okur, Mesut; Kaya, Murat; Büyükkaya, Ramazan; Katranci, Ali Osman; Kucuk, Adem

    2013-01-01

    Uncontaminated urine samples are indispensable to precisely diagnose urinary tract infections in new-borns or infants. Among many clinical interventions for urine collection are described, the most common noninvasive practice is using sterile bags, associated with significant contamination of samples. In children, however, invasive methods i.e. catheterization, are generally needed for reliable urine specimens. Almost always all the inserted catheters are easily drawn back, nevertheless, might not work as expected, and lead to considerable problems that cannot be overcome. Herein, a case of a female newborn treated with a successful percutaneous suprapubic cystoscopic procedure for extracting knotted urinary catheter in the bladder is presented. The least invasive and easiest technic is suggested to be used when catheter is knotted in the bladder, as elaborately stated. PMID:23936602

  5. Spontaneous knotting of a pigtail ureteric stent in the ureter requiring percutaneous removal.

    PubMed

    Braslis, K G; Joyce, G

    1992-10-01

    Insertion of a ureteric stent is a common procedure in urologic practice. Ureteric stenting may be performed for: ureteric obstruction, benign or malignant: to prevent ureteric obstruction from stone fragments after extracorporeal shockwave lithotripsy (ESWL); or to prevent leakage from the upper urinary tract. A case of spontaneous knotting of a ureteric stent in situ is reported. Although this complication has been reported previously it is rare.

  6. Comparative pathogenicity of reniform nematode on root-knot resistant and susceptible bidi tobacco.

    PubMed

    Bairwa, Aarti; Patel, H R

    2016-09-01

    Comparative pathogenicity of reniform nematode on root-knot resistant ABT 10 and susceptible bidi tobacco A119 revealed that ABT 10 was found significantly superior to A119 with respect to plant growth characters and as good as A119 with respect to multiplication of reniform nematode. Initial inoculum of 1,000 J4 of the nematode found damaging to both ABT 10 and A119 varieties of bidi tobacco. PMID:27605772

  7. Os2 -Os4 Switch Controls DNA Knotting and Anticancer Activity.

    PubMed

    Fu, Ying; Romero, María J; Salassa, Luca; Cheng, Xi; Habtemariam, Abraha; Clarkson, Guy J; Prokes, Ivan; Rodger, Alison; Costantini, Giovanni; Sadler, Peter J

    2016-07-25

    Dinuclear trihydroxido-bridged osmium-arene complexes are inert and biologically inactive, but we show here that linking dihydroxido-bridged Os(II) -arene fragments by a bridging di-imine to form a metallacycle framework results in strong antiproliferative activity towards cancer cells and distinctive knotting of DNA. The shortened spacer length reduces biological activity and stability in solution towards decomposition to biologically inactive dimers. Significant differences in behavior toward plasmid DNA condensation are correlated with biological activity. PMID:27240103

  8. Stability of small-amplitude torus knot solutions of the localized induction approximation

    NASA Astrophysics Data System (ADS)

    Calini, Annalisa; Ivey, Thomas

    2011-08-01

    We study the linear stability of small-amplitude torus knot solutions of the localized induction approximation equation for the motion of a thin vortex filament in an ideal fluid. Such solutions can be constructed analytically through the connection with the focusing nonlinear Schrödinger equation using the method of isoperiodic deformations. We show that these (p, q) torus knots are generically linearly unstable for p < q, while we provide examples of neutrally stable (p, q) torus knots with p > q, in contrast with an earlier linear stability study by Ricca (1993 Chaos 3 83-95 1995 Chaos 5 346; 1995 Small-scale Structures in Three-dimensional Hydro and Magneto-dynamics Turbulence (Lecture Notes in Physics vol 462) (Berlin: Springer)). We also provide an interpretation of the original perturbative calculation in Ricca (1995), and an explanation of the numerical experiments performed by Ricca et al (1999 J. Fluid Mech. 391 29-44), in light of our results.

  9. Folding analysis of the most complex Stevedore’s protein knot

    PubMed Central

    Wang, Iren; Chen, Szu-Yu; Hsu, Shang-Te Danny

    2016-01-01

    DehI is a homodimeric haloacid dehalogenase from Pseudomonas putida that contains the most complex 61 Stevedore’s protein knot within its folding topology. To examine how DehI attains such an intricate knotted topology we combined far-UV circular dichroism (CD), intrinsic fluorescence spectroscopy and small angle X-ray scattering (SAXS) to investigate its folding mechanism. Equilibrium unfolding of DehI by chemical denaturation indicated the presence of two highly populated folding intermediates, I and I’. While the two intermediates vary in secondary structure contents and tertiary packing according to CD and intrinsic fluorescence, respectively, their overall dimension and compactness are similar according to SAXS. Three single-tryptophan variants (W34, W53, and W196) were generated to probe non-cooperative unfolding events localized around the three fluorophores. Kinetic fluorescence measurements indicated that the transition from the intermediate I’ to the unfolded state is rate limiting. Our multiparametric folding analyses suggest that DehI unfolds through a linear folding pathway with two distinct folding intermediates by initial hydrophobic collapse followed by nucleation condensation, and that knotting precedes the formation of secondary structures. PMID:27527519

  10. Combinatorial optimization of cystine-knot peptides towards high-affinity inhibitors of human matriptase-1.

    PubMed

    Glotzbach, Bernhard; Reinwarth, Michael; Weber, Niklas; Fabritz, Sebastian; Tomaszowski, Michael; Fittler, Heiko; Christmann, Andreas; Avrutina, Olga; Kolmar, Harald

    2013-01-01

    Cystine-knot miniproteins define a class of bioactive molecules with several thousand natural members. Their eponymous motif comprises a rigid structured core formed by six disulfide-connected cysteine residues, which accounts for its exceptional stability towards thermic or proteolytic degradation. Since they display a remarkable sequence tolerance within their disulfide-connected loops, these molecules are considered promising frameworks for peptide-based pharmaceuticals. Natural open-chain cystine-knot trypsin inhibitors of the MCoTI (Momordica cochinchinensis trypsin inhibitor) and SOTI (Spinacia oleracea trypsin inhibitor) families served as starting points for the generation of inhibitors of matriptase-1, a type II transmembrane serine protease with possible clinical relevance in cancer and arthritic therapy. Yeast surface-displayed libraries of miniproteins were used to select unique and potent matriptase-1 inhibitors. To this end, a knowledge-based library design was applied that makes use of detailed information on binding and folding behavior of cystine-knot peptides. Five inhibitor variants, four of the MCoTI family and one of the SOTI family, were identified, chemically synthesized and oxidatively folded towards the bioactive conformation. Enzyme assays revealed inhibition constants in the low nanomolar range for all candidates. One subnanomolar binder (Ki = 0.83 nM) with an inverted selectivity towards trypsin and matriptase-1 was identified. PMID:24146945

  11. Physical experience leads to enhanced object perception in parietal cortex: insights from knot tying.

    PubMed

    Cross, Emily S; Cohen, Nichola Rice; Hamilton, Antonia F de C; Ramsey, Richard; Wolford, George; Grafton, Scott T

    2012-12-01

    What does it mean to "know" what an object is? Viewing objects from different categories (e.g., tools vs. animals) engages distinct brain regions, but it is unclear whether these differences reflect object categories themselves or the tendency to interact differently with objects from different categories (grasping tools, not animals). Here we test how the brain constructs representations of objects that one learns to name or physically manipulate. Participants learned to name or tie different knots and brain activity was measured whilst performing a perceptual discrimination task with these knots before and after training. Activation in anterior intraparietal sulcus, a region involved in object manipulation, was specifically engaged when participants viewed knots they learned to tie. This suggests that object knowledge is linked to sensorimotor experience and its associated neural systems for object manipulation. Findings are consistent with a theory of embodiment in which there can be clear overlap in brain systems that support conceptual knowledge and control of object manipulation. PMID:23022108

  12. Characterization of a Root-Knot Nematode Population of Meloidogyne arenaria from Tupungato (Mendoza, Argentina)

    PubMed Central

    Evangelina García, Laura; Sánchez-Puerta, María Virginia

    2012-01-01

    Root-knot nematodes (Meloidogyne spp.) are polyphagous plant parasites of global importance. Successful host infection depends on the particular interaction between a specific nematode species and race and a specific plant species and cultivar. Accurate diagnosis of nematode species is relevant to effective agricultural management; and benefits further from understanding the variability within a single nematode species. Here, we described a population of M. arenaria race 2 from Mendoza (Argentina). This study represents the first morphometric, morphological, biochemical, reproductive, molecular, and host range characterization of a root-knot nematode species from Argentina. Even after gathering morphological and morphometric data of this population and partially sequencing its rRNA, an unequivocal taxonomic assignment could not be achieved. The most decisive data was provided by esterase phenotyping and molecular methods using SCARs. These results highlight the importance of taking a multidimensional approach for Meloidogyne spp. diagnosis. This study contributes to the understanding of the variability of morphological, reproductive and molecular traits of M. arenaria, and provides data on the identification of root-knot nematodes on tomato cultivars from Argentina. PMID:23481918

  13. [Controlling effect of antagonist bioorganic fertilizer on tomato root-knot nematode].

    PubMed

    Zhu, Zhen; Chen, Fang; Xiao, Tong-jian; Wang, Xiao-hui; Ran, Wei; Yang, Xing-ming; Shen, Qi-rong

    2011-04-01

    Indoor in vitro culture experiment and greenhouse pot experiment were conducted to evaluate the capabilities of three bacterial strains XZ-173 (Bacillus amyloliquefaciens), SL-25 (B. gibsonii), and KS-62 (Paenibacillus polymyxa) that can hydrolyze collagen protein in controlling tomato root-knot nematode. In the in vitro culture experiment, suspensions of XZ-173, SL-25, and KS-62 induced a mortality rate of 75.9%, 66.7%, and 50.0% to the second-stage junior nematode within 24 h, and decreased the egg hatching rate to 17.8%, 28.9% and 37.6% after 7-day incubation, respectively, in contrast to the 17.4% mortality rate and 53.6% egg hatching rate in the control (sterilized water). In the greenhouse pot experiment, the bioorganic fertilizer mixed with equal parts of fermented XZ-173, SL-25, and KS-62 gained the best result, with the root-knot nematode population in rhizosphere soil decreased by 84.0% as compared with the control. The bioorganic fertilizer also decreased the numbers of galls and eggs on tomato roots significantly, and increased the underground and aboveground biomass of tomato. Therefore, antagonist bioorganic fertilizer has promising potential in controlling root-knot nematode. PMID:21774329

  14. The chemical abundances of the Cassiopeia A fast-moving knots - Explosive nucleosynthesis on a minicomputer

    NASA Technical Reports Server (NTRS)

    Johnston, M. D.; Joss, P. C.

    1980-01-01

    A simplified nuclear reaction network for explosive nucleosynthesis calculations is described in which only the most abundant nuclear species and the most important reactions linking these species are considered. This scheme permits the exploration of many cases without excessive computational effort. Good agreement with previous calculations employing more complex reaction networks is obtained. This scheme is applied to the observed chemical abundances of the fast-moving knots in the supernova remnant Cassiopeia A and it is found that a wide range of initial conditions could yield the observed abundances. The abundances of four of the knots with significant and different amounts of elements heavier than oxygen are consistent with an origin in material of the same initial composition but processed at different peak temperatures and densities. Despite the observed high oxygen abundances and low abundances of light elements in the knots, they did not necessarily undergo incomplete oxygen burning; in fact, it is not even necessary that oxygen have been present in the initial composition. The agreement between the calculated and observed chemical abundances in Cas A and similar supernova remnants depends primarily upon the relevant nuclear physics and does not provide strong evidence in favor of any particular model of the supernova event.

  15. DotKnot: pseudoknot prediction using the probability dot plot under a refined energy model

    PubMed Central

    Sperschneider, Jana; Datta, Amitava

    2010-01-01

    RNA pseudoknots are functional structure elements with key roles in viral and cellular processes. Prediction of a pseudoknotted minimum free energy structure is an NP-complete problem. Practical algorithms for RNA structure prediction including restricted classes of pseudoknots suffer from high runtime and poor accuracy for longer sequences. A heuristic approach is to search for promising pseudoknot candidates in a sequence and verify those. Afterwards, the detected pseudoknots can be further analysed using bioinformatics or laboratory techniques. We present a novel pseudoknot detection method called DotKnot that extracts stem regions from the secondary structure probability dot plot and assembles pseudoknot candidates in a constructive fashion. We evaluate pseudoknot free energies using novel parameters, which have recently become available. We show that the conventional probability dot plot makes a wide class of pseudoknots including those with bulged stems manageable in an explicit fashion. The energy parameters now become the limiting factor in pseudoknot prediction. DotKnot is an efficient method for long sequences, which finds pseudoknots with higher accuracy compared to other known prediction algorithms. DotKnot is accessible as a web server at http://dotknot.csse.uwa.edu.au. PMID:20123730

  16. Combinatorial Optimization of Cystine-Knot Peptides towards High-Affinity Inhibitors of Human Matriptase-1

    PubMed Central

    Weber, Niklas; Fabritz, Sebastian; Tomaszowski, Michael; Fittler, Heiko; Christmann, Andreas; Avrutina, Olga; Kolmar, Harald

    2013-01-01

    Cystine-knot miniproteins define a class of bioactive molecules with several thousand natural members. Their eponymous motif comprises a rigid structured core formed by six disulfide-connected cysteine residues, which accounts for its exceptional stability towards thermic or proteolytic degradation. Since they display a remarkable sequence tolerance within their disulfide-connected loops, these molecules are considered promising frameworks for peptide-based pharmaceuticals. Natural open-chain cystine-knot trypsin inhibitors of the MCoTI (Momordica cochinchinensis trypsin inhibitor) and SOTI (Spinacia oleracea trypsin inhibitor) families served as starting points for the generation of inhibitors of matriptase-1, a type II transmembrane serine protease with possible clinical relevance in cancer and arthritic therapy. Yeast surface-displayed libraries of miniproteins were used to select unique and potent matriptase-1 inhibitors. To this end, a knowledge-based library design was applied that makes use of detailed information on binding and folding behavior of cystine-knot peptides. Five inhibitor variants, four of the MCoTI family and one of the SOTI family, were identified, chemically synthesized and oxidatively folded towards the bioactive conformation. Enzyme assays revealed inhibition constants in the low nanomolar range for all candidates. One subnanomolar binder (Ki = 0.83 nM) with an inverted selectivity towards trypsin and matriptase-1 was identified. PMID:24146945

  17. Combinatorial optimization of cystine-knot peptides towards high-affinity inhibitors of human matriptase-1.

    PubMed

    Glotzbach, Bernhard; Reinwarth, Michael; Weber, Niklas; Fabritz, Sebastian; Tomaszowski, Michael; Fittler, Heiko; Christmann, Andreas; Avrutina, Olga; Kolmar, Harald

    2013-01-01

    Cystine-knot miniproteins define a class of bioactive molecules with several thousand natural members. Their eponymous motif comprises a rigid structured core formed by six disulfide-connected cysteine residues, which accounts for its exceptional stability towards thermic or proteolytic degradation. Since they display a remarkable sequence tolerance within their disulfide-connected loops, these molecules are considered promising frameworks for peptide-based pharmaceuticals. Natural open-chain cystine-knot trypsin inhibitors of the MCoTI (Momordica cochinchinensis trypsin inhibitor) and SOTI (Spinacia oleracea trypsin inhibitor) families served as starting points for the generation of inhibitors of matriptase-1, a type II transmembrane serine protease with possible clinical relevance in cancer and arthritic therapy. Yeast surface-displayed libraries of miniproteins were used to select unique and potent matriptase-1 inhibitors. To this end, a knowledge-based library design was applied that makes use of detailed information on binding and folding behavior of cystine-knot peptides. Five inhibitor variants, four of the MCoTI family and one of the SOTI family, were identified, chemically synthesized and oxidatively folded towards the bioactive conformation. Enzyme assays revealed inhibition constants in the low nanomolar range for all candidates. One subnanomolar binder (Ki = 0.83 nM) with an inverted selectivity towards trypsin and matriptase-1 was identified.

  18. Cellular uptake of a cystine-knot peptide and modulation of its intracellular trafficking

    PubMed Central

    Gao, Xinxin; Stanger, Karen; Kaluarachchi, Harini; Maurer, Till; Ciepla, Paulina; Chalouni, Cecile; Franke, Yvonne; Hannoush, Rami N.

    2016-01-01

    Cyclotides or cyclic cystine-knot peptides have emerged as a promising class of pharmacological ligands that modulate protein function. Interestingly, very few cyclotides have been shown to enter into cells. Yet, it remains unknown whether backbone cyclization is required for their cellular internalization. In this report, we studied the cellular behavior of EETI-II, a model acyclic cystine-knot peptide. Even though synthetic methods have been used to generate EETI-II, recombinant methods that allow efficient large scale biosynthesis of EETI-II have been lagging. Here, we describe a novel protocol for recombinant generation of folded EETI-II in high yields and to near homogeneity. We also uncover that EETI-II is efficiently uptaken via an active endocytic pathway to early endosomes in mammalian cells, eventually accumulating in late endosomes and lysosomes. Notably, co-incubation with a cell-penetrating peptide enhanced the cellular uptake and altered the trafficking of EETI-II, leading to its evasion of lysosomes. Our results demonstrate the feasibility of modulating the subcellular distribution and intracellular targeting of cystine-knot peptides, and hence enable future exploration of their utility in drug discovery and delivery. PMID:27734922

  19. Erwinia oleae sp. nov., isolated from olive knots caused by Pseudomonas savastanoi pv. savastanoi.

    PubMed

    Moretti, Chiaraluce; Hosni, Taha; Vandemeulebroecke, Katrien; Brady, Carrie; De Vos, Paul; Buonaurio, Roberto; Cleenwerck, Ilse

    2011-11-01

    Three endophytic bacterial isolates were obtained in Italy from olive knots caused by Pseudomonas savastanoi pv. savastanoi. Phenotypic tests in combination with 16S rRNA gene sequence analysis indicated a phylogenetic position for these isolates in the genera Erwinia or Pantoea, and revealed two other strains with highly similar 16S rRNA gene sequences (>99 %), CECT 5262 and CECT 5264, obtained in Spain from olive knots. Rep-PCR DNA fingerprinting of the five strains from olive knots with BOX, ERIC and REP primers revealed three groups of profiles that were highly similar to each other. Multilocus sequence analysis (MLSA) based on concatenated partial atpD, gyrB, infB and rpoB gene sequences indicated that the strains constituted a single novel species in the genus Erwinia. The strains showed general phenotypic characteristics typical of the genus Erwinia and whole genome DNA-DNA hybridization data confirmed that they represented a single novel species of the genus Erwinia. The strains showed DNA G+C contents ranging from 54.7 to 54.9 mol%. They could be discriminated from phylogenetically related species of the genus Erwinia by their ability to utilize potassium gluconate, l-rhamnose and d-arabitol, but not glycerol, inositol or d-sorbitol. The name Erwinia oleae sp. nov. (type strain DAPP-PG 531(T)= LMG 25322(T) = DSM 23398(T)) is proposed for this novel taxon.

  20. Application of lariat lock catch knot suture in the achilles tendon rupture

    PubMed Central

    Wang, Baocang; Feng, Xiaona; Yan, Ming; Wang, Hui; Li, Yong

    2015-01-01

    The aim of this study was to summarize the clinical experience of repairing the Achilles tendon rupture by lariat lock catch knot suture. Between January 2011 and February, 2014, 32 cases of the Achilles tendon rupture were treated by lariat lock catch knot suture. There were 26 males and 6 females, with the average age of 39 years (range 17-53 years), including 13 left knees and 19 right knees. 29 wounds healed by first intention, and 3 cases who were performed local flap transfer due to necrosis of skin were healed by second intention. Thirty-two cases were followed up 10-25 months (13 months on average). No re-rupture of Achilles tendon or deep infection occurred during follow-up period. According to Arner-Lindholm assessment standard, the results were excellent in 19 cases and good in 13 cases, the excellent and good rate was 100%. Lariat lock catch knot suture is a safe and effective method for repairing Achilles tendon. PMID:26770612

  1. The properties of conformal blocks, the AGT hypothesis, and knot polynomials

    NASA Astrophysics Data System (ADS)

    Morozov, A. A.

    2016-09-01

    Various properties of correlators of the two-dimensional conformal field theory are discussed. Specifically, their relation to the partition function of the four-dimensional supersymmetric theory is analyzed. In addition to being of interest in its own right, this relation is of practical importance. For example, it is much easier to calculate the known expressions for the partition function of supersymmetric theory than to calculate directly the expressions for correlators in conformal theory. The examined representation of conformal theory correlators as a matrix model serves the same purpose. The integral form of these correlators allows one to generalize the obtained results for the Virasoro algebra to more complicated cases of the W algebra or the quantum Virasoro algebra. This provides an opportunity to examine more complex configurations in conformal field theory. The three-dimensional Chern-Simons theory is discussed in the second part of the present review. The current interest in this theory stems largely from its relation to the mathematical knot theory (a rather well-developed area of mathematics known since the 17th century). The primary objective of this theory is to develop an algorithm that allows one to distinguish different knots (closed loops in three-dimensional space). The basic way to do this is by constructing the so-called knot invariants.

  2. High and Low Throughput Screens with Root-knot Nematodes Meloidogyne spp.

    PubMed Central

    Atamian, Hagop S.; Roberts, Philip A.; Kaloshian, Isgouhi

    2012-01-01

    Root-knot nematodes (genus Meloidogyne) are obligate plant parasites. They are extremely polyphagous and considered one of the most economically important plant parasitic nematodes. The microscopic second-stage juvenile (J2), molted once in the egg, is the infective stage. The J2s hatch from the eggs, move freely in the soil within a film of water, and locate root tips of suitable plant species. After penetrating the plant root, they migrate towards the vascular cylinder where they establish a feeding site and initiate feeding using their stylets. The multicellular feeding site is comprised of several enlarged multinuclear cells called 'giant cells' which are formed from cells that underwent karyokinesis (repeated mitosis) without cytokinesis. Neighboring pericycle cells divide and enlarge in size giving rise to a typical gall or root knot, the characteristic symptom of root-knot nematode infection. Once feeding is initiated, J2s become sedentary and undergo three additional molts to become adults. The adult female lays 150-250 eggs in a gelatinous matrix on or below the surface of the root. From the eggs new infective J2s hatch and start a new cycle. The root-knot nematode life cycle is completed in 4-6 weeks at 26-28°C. Here we present the traditional protocol to infect plants, grown in pots, with root-knot nematodes and two methods for high-throughput assays. The first high-throughput method is used for plants with small seeds such as tomato while the second is for plants with large seeds such as cowpea and common bean. Large seeds support extended seedling growth with minimal nutrient supplement. The first high throughput assay utilizes seedlings grown in sand in trays while in the second assay plants are grown in pouches in the absence of soil. The seedling growth pouch is made of a 15.5 x 12.5cm paper wick, folded at the top to form a 2-cm-deep trough in which the seed or seedling is placed. The paper wick is contained inside a transparent plastic pouch

  3. Foraging in a tidally structured environment by Red Knots (Calidris canutus): ideal, but not free.

    PubMed

    van Gils, Jan A; Spaans, Bernard; Dekinga, Anne; Piersma, Theunis

    2006-05-01

    Besides the "normal" challenge of obtaining adequate intake rates in a patchy and dangerous world, shorebirds foraging in intertidal habitats face additional environmental hurdles. The tide forces them to commute between a roosting site and feeding grounds, twice a day. Moreover, because intertidal food patches are not all available at the same time, shorebirds should follow itineraries along the best patches available at a given time. Finally, shorebirds need additional energy stores in order to survive unpredictable periods of bad weather, during which food patches are covered by extreme tides. In order to model such tide-specific decisions, we applied stochastic dynamic programming in a spatially explicit context. Two assumptions were varied, leading to four models. First, birds had either perfect (ideal) or no (non-ideal) information about the intake rate at each site. Second, traveling between sites was either for free or incurred time and energy costs (non-free). Predictions were generated for three aspects of foraging: area use, foraging routines, and energy stores. In general, non-ideal foragers should feed most intensely and should maintain low energy stores. If traveling for such birds is free, they should feed at a random site; otherwise, they should feed close to their roost. Ideal foragers should concentrate their feeding around low tide (especially when free) and should maintain larger energy stores (especially when non-free). If traveling for such birds is free, they should feed at the site offering the highest intake rate; otherwise, they should trade off travel costs and intake rate. Models were parameterized for Red Knots (Calidris canutus) living in the Dutch Wadden Sea in late summer, an area for which detailed, spatially explicit data on prey densities and tidal heights are available. Observations of radio-marked knots (area use) and unmarked knots (foraging routines, energy stores) showed the closest match with the ideal/non-free model. We

  4. Foraging in a tidally structured environment by Red Knots (Calidris canutus): ideal, but not free.

    PubMed

    van Gils, Jan A; Spaans, Bernard; Dekinga, Anne; Piersma, Theunis

    2006-05-01

    Besides the "normal" challenge of obtaining adequate intake rates in a patchy and dangerous world, shorebirds foraging in intertidal habitats face additional environmental hurdles. The tide forces them to commute between a roosting site and feeding grounds, twice a day. Moreover, because intertidal food patches are not all available at the same time, shorebirds should follow itineraries along the best patches available at a given time. Finally, shorebirds need additional energy stores in order to survive unpredictable periods of bad weather, during which food patches are covered by extreme tides. In order to model such tide-specific decisions, we applied stochastic dynamic programming in a spatially explicit context. Two assumptions were varied, leading to four models. First, birds had either perfect (ideal) or no (non-ideal) information about the intake rate at each site. Second, traveling between sites was either for free or incurred time and energy costs (non-free). Predictions were generated for three aspects of foraging: area use, foraging routines, and energy stores. In general, non-ideal foragers should feed most intensely and should maintain low energy stores. If traveling for such birds is free, they should feed at a random site; otherwise, they should feed close to their roost. Ideal foragers should concentrate their feeding around low tide (especially when free) and should maintain larger energy stores (especially when non-free). If traveling for such birds is free, they should feed at the site offering the highest intake rate; otherwise, they should trade off travel costs and intake rate. Models were parameterized for Red Knots (Calidris canutus) living in the Dutch Wadden Sea in late summer, an area for which detailed, spatially explicit data on prey densities and tidal heights are available. Observations of radio-marked knots (area use) and unmarked knots (foraging routines, energy stores) showed the closest match with the ideal/non-free model. We

  5. Slow knot formation by suppressed self-reptation in a collapsed polymer chain

    NASA Astrophysics Data System (ADS)

    Nakata, Mitsuo; Nakamura, Yoshiki; Sasaki, Naoki; Maki, Yasuyuki

    2012-02-01

    Chain-expansion processes from knotted globules have been measured for poly(methyl methacrylate) (PMMA) in the mixed solvent tert-butyl alcohol (TBA) + water (2.5 vol %) by static light scattering. The solution was quenched from the Θ temperature of 41.5 ∘C to 37.0 ∘C, aged there for a time period tp, and then returned rapidly to the Θ temperature. The chain-expansion process was determined as a time evolution of the expansion factor α2 after the temperature increase. The measurement was carried out by changing the aging time tp from 240 to 7200 min, and the molecular weight from Mw = 4.0 × 106 to 1.5 × 107, by taking advantage of the extremely slow chain aggregation in the solution. The chain-expansion process obtained for Mw = 1.22 × 107 became slow with increasing tp, which revealed the knot formation in single globules. The characteristic time of the chain expansion from globules aged for tp = 7200 min was found to depend on the molecular weight as Mw2.7. This exponent, which is close to 3, demonstrated a disentanglement process due to self-reptation. The present data were compared with the previous data of the chain expansion from compact globules aged at 25.0 ∘C. The comparison made at Mw = 1.22 × 107 and at the same values of tp revealed that the chain expansion from the globules aged at 25.0 ∘C was much faster than that from the globules at 37.0 ∘C, indicating a lower knot density in the more compact globules. It was conjectured that the knot formation due to self-reptation would be suppressed in a compact globule because an entire conformational change required by knot formation would become difficult to occur in the confined space of high segment concentration, particularly for a long polymer chain. The chain collapse of PMMA in the mixed solvent has been observed to occur extremely slowly at the later stage. This slow process was explained by the suppressed self-reptation.

  6. EXPANSION OF HYDROGEN-POOR KNOTS IN THE BORN-AGAIN PLANETARY NEBULAE A30 AND A78

    SciTech Connect

    Fang, X.; Guerrero, M. A.; Marquez-Lugo, R. A.; Toalá, J. A.; Chu, Y.-H.; Gruendl, R. A.; Blair, W. P.; Hamann, W.-R.; Oskinova, L. M.; Todt, H.

    2014-12-20

    We analyze the expansion of hydrogen-poor knots and filaments in the born-again planetary nebulae A30 and A78 based on Hubble Space Telescope (HST) images obtained almost 20 yr apart. The proper motion of these features generally increases with distance to the central star, but the fractional expansion decreases, i.e., the expansion is not homologous. As a result, there is not a unique expansion age, which is estimated to be 610-950 yr for A30 and 600-1140 yr for A78. The knots and filaments have experienced complex dynamical processes: the current fast stellar wind is mass loaded by the material ablated from the inner knots; the ablated material is then swept up until it shocks the inner edges of the outer, hydrogen-rich nebula. The angular expansion of the outer filaments shows a clear dependence on position angle, indicating that the interaction of the stellar wind with the innermost knots channels the wind along preferred directions. The apparent angular expansion of the innermost knots seems to be dominated by the rocket effect of evaporating gas and by the propagation of the ionization front inside them. Radiation-hydrodynamical simulations show that a single ejection of material followed by a rapid onset of the stellar wind and ionizing flux can reproduce the variety of clumps and filaments at different distances from the central star found in A30 and A78.

  7. Identification of Sources of Resistance to Four Species of Root-knot Nematodes in Tobacco

    PubMed Central

    Ng'ambi, Tenson B. S.; Rufty, Rebeca C.; Barker, Kenneth R.; Melton, Thomas A.

    1999-01-01

    Resistance to the southern root-knot nematode, Meloidogyne incognita races 1 and 3, has been identified, incorporated, and deployed into commercial cultivars of tobacco, Nicotiana tabacum. Cultivars with resistance to other economically important root-knot nematode species attacking tobacco, M. arenaria, M. hapla, M. javanica, and other host-specific races of M. incognita, are not available in the United States. Twenty-eight tobacco genotypes of diverse origin and two standard cultivars, NC 2326 (susceptible) and Speight G 28 (resistant to M. incognita races 1 and 3), were screened for resistance to eight root-knot nematode populations of North Carolina origin. Based on root gall indices at 8 to 12 weeks after inoculation, all genotypes except NC 2326 and Okinawa were resistant to M. arenaria race 1, and races 1 and 3 of M. incognita. Except for slight root galling, genotypes resistant to M. arenaria race 1 responded similarly to races 1 and 3 of M. incognita. All genotypes except NC 2326, Okinawa, and Speight G 28 showed resistance to M. javanica. Okinawa, while supporting lower reproduction of M. javanica than NC 2326, was rated as moderately susceptible. Tobacco breeding lines 81-R-617A, 81-RL- 2K, SA 1213, SA 1214, SA 1223, and SA 1224 were resistant to M. arenaria race 2, and thus may be used as sources of resistance to this pathogen. No resistance to M. hapla and only moderate resistance to races 2 and 4 of M. incognita were found in any of the tobacco genotypes. Under natural field infestations of M. arenaria race 2, nematode development on resistant tobacco breeding lines 81-RL-2K, SA 1214, and SA 1215 was similar to a susceptible cultivar with some nematicide treatments; however, quantity and quality of yield were inferior compared to K 326 plus nematicides. PMID:19270897

  8. Polymer Uncrossing and Knotting in Protein Folding, and Their Role in Minimal Folding Pathways

    PubMed Central

    Mohazab, Ali R.; Plotkin, Steven S.

    2013-01-01

    We introduce a method for calculating the extent to which chain non-crossing is important in the most efficient, optimal trajectories or pathways for a protein to fold. This involves recording all unphysical crossing events of a ghost chain, and calculating the minimal uncrossing cost that would have been required to avoid such events. A depth-first tree search algorithm is applied to find minimal transformations to fold , , , and knotted proteins. In all cases, the extra uncrossing/non-crossing distance is a small fraction of the total distance travelled by a ghost chain. Different structural classes may be distinguished by the amount of extra uncrossing distance, and the effectiveness of such discrimination is compared with other order parameters. It was seen that non-crossing distance over chain length provided the best discrimination between structural and kinetic classes. The scaling of non-crossing distance with chain length implies an inevitable crossover to entanglement-dominated folding mechanisms for sufficiently long chains. We further quantify the minimal folding pathways by collecting the sequence of uncrossing moves, which generally involve leg, loop, and elbow-like uncrossing moves, and rendering the collection of these moves over the unfolded ensemble as a multiple-transformation “alignment”. The consensus minimal pathway is constructed and shown schematically for representative cases of an , , and knotted protein. An overlap parameter is defined between pathways; we find that proteins have minimal overlap indicating diverse folding pathways, knotted proteins are highly constrained to follow a dominant pathway, and proteins are somewhere in between. Thus we have shown how topological chain constraints can induce dominant pathway mechanisms in protein folding. PMID:23365638

  9. True knot of umbilical cord: Case report and review of literat.

    PubMed

    Khan, Momna; Zahiruddin, Sana; Iftikhar, Maria

    2016-08-01

    True knot of umbilical cord (TKUC) is a rare abnormality. When it becomes tight, it may lead to the obstruction of the foetal circulation and intrauterine death (IUD). We present two cases of TKUC managed at The Aga Khan University Hospital with two extreme outcomes. A 22 years old primigravida was diagnosed with unexplained intrauterine foetal demise at 28th week gestation. She delivered vaginally after induction and tight TKUC was identified as a cause of IUD. The second patient delivered an alive healthy male baby vaginally who was found to have a lose TKUC. PMID:27524546

  10. All-fiber magnetic-field sensor based on microfiber knot resonator and magnetic fluid.

    PubMed

    Li, Xianli; Ding, Hui

    2012-12-15

    All-fiber magnetic-field sensor based on a device consisting of a microfiber knot resonator and magnetic fluid is proposed for the first time in this Letter. Sensor principles and package technology are introduced in detail. Experimental results show that the resonance wavelength of the proposed sensor regularly varies with changes to the applied magnetic field. When the magnetic field is increased to 600 Oe, the wavelength shift reaches nearly 100 pm. Moreover, the sensor responding to the 50 Hz alternating magnetic field is also experimentally investigated, and a minimal detectable magnetic-field strength of 10 Oe is successfully achieved.

  11. The classical and quantum mechanics of a particle on a knot

    SciTech Connect

    Sreedhar, V.V.

    2015-08-15

    A free particle is constrained to move on a knot obtained by winding around a putative torus. The classical equations of motion for this system are solved in a closed form. The exact energy eigenspectrum, in the thin torus limit, is obtained by mapping the time-independent Schrödinger equation to the Mathieu equation. In the general case, the eigenvalue problem is described by the Hill equation. Finite-thickness corrections are incorporated perturbatively by truncating the Hill equation. Comparisons and contrasts between this problem and the well-studied problem of a particle on a circle (planar rigid rotor) are performed throughout.

  12. Os2–Os4 Switch Controls DNA Knotting and Anticancer Activity

    PubMed Central

    Fu, Ying; Romero, María J.; Salassa, Luca; Cheng, Xi; Habtemariam, Abraha; Clarkson, Guy J.; Prokes, Ivan; Rodger, Alison; Costantini, Giovanni

    2016-01-01

    Abstract Dinuclear trihydroxido‐bridged osmium–arene complexes are inert and biologically inactive, but we show here that linking dihydroxido‐bridged OsII–arene fragments by a bridging di‐imine to form a metallacycle framework results in strong antiproliferative activity towards cancer cells and distinctive knotting of DNA. The shortened spacer length reduces biological activity and stability in solution towards decomposition to biologically inactive dimers. Significant differences in behavior toward plasmid DNA condensation are correlated with biological activity. PMID:27240103

  13. Effect of tea dust residues to control root-knot nematode of tomato.

    PubMed

    Fathi, G H; Eshtiaghi, H; Kheiri, A; Okhovat, M

    2004-01-01

    In this research, control of tomato root- knot nematode (Meloidogyne incognita) was conducted using tea dust residues at different rates. First, the species and race of nematode were identified by employing diagnostic keys. Then, with 5 replications in complete randomized design. Tea dust residues were used at 9 treatments (0, 5, 10, 15, 20, 25, 30, 35 and 40 g/kg of soil). Statistical analysis on mean treatments rates showed that treatment with 25 g/kg soil economically was effective in growth rates and reduction in gall index. PMID:15759440

  14. Understanding the light curves of the HST-1 knot in M87 with internal relativistic shock waves along its jet

    NASA Astrophysics Data System (ADS)

    Coronado, Y.; López-Corona, O.; Mendoza, S.

    2016-10-01

    Knots or blobs observed in astrophysical jets are commonly interpreted as shock waves moving along them. Long-time observations of the HST-1 knot inside the jet of the galaxy M87 have produced detailed multiwavelength light curves. In this paper, we model these light curves using the semi-analytical approach developed by Mendoza et al. This model was developed to account for the light curves produced by working surfaces (blobs) moving along relativistic jets. These working surfaces are generated by periodic oscillations of the injected flow velocity and mass ejection rates at the base of the jet. Using genetic algorithms to fit the parameters of the model, we are able to explain the outbursts observed in the light curves of the HST-1 knot with an accuracy greater than a 2σ statistical confidence level.

  15. 14 CFR 61.327 - How do I obtain privileges to operate a light-sport aircraft that has a VH greater than 87 knots...

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... light-sport aircraft that has a VH greater than 87 knots CAS? 61.327 Section 61.327 Aeronautics and...: PILOTS, FLIGHT INSTRUCTORS, AND GROUND INSTRUCTORS Sport Pilots § 61.327 How do I obtain privileges to operate a light-sport aircraft that has a VH greater than 87 knots CAS? If you hold a sport...

  16. Potential of Leguminous Cover Crops in Management of a Mixed Population of Root-knot Nematodes (Meloidogyne spp.)

    PubMed Central

    Osei, Kingsley; Gowen, Simon R.; Pembroke, Barbara; Brandenburg, Rick L.; Jordan, David L.

    2010-01-01

    Root-knot nematode is an important pest in agricultural production worldwide. Crop rotation is the only management strategy in some production systems, especially for resource poor farmers in developing countries. A series of experiments was conducted in the laboratory with several leguminous cover crops to investigate their potential for managing a mixture of root-knot nematodes (Meloidogyne arenaria, M. incognita, M. javanica). The root-knot nematode mixture failed to multiply on Mucuna pruriens and Crotalaria spectabilis but on Dolichos lablab the population increased more than 2- fold when inoculated with 500 and 1,000 nematodes per plant. There was no root-galling on M. pruriens and C. spectabilis but the gall rating was noted on D. lablab. Greater mortality of juvenile root-knot nematodes occurred when exposed to eluants of roots and leaves of leguminous crops than those of tomato; 48.7% of juveniles died after 72 h exposure to root eluant of C. spectabilis. The leaf eluant of D. lablab was toxic to nematodes but the root eluant was not. Thus, different parts of a botanical contain different active ingredients or different concentrations of the same active ingredient. The numbers of root-knot nematode eggs that hatched in root exudates of M. pruriens and C. spectabilis were significantly lower (20% and 26%) than in distilled water, tomato and P. vulgaris root exudates (83%, 72% and 89%) respectively. Tomato lacks nematotoxic compounds found in M. pruriens and C. spectabilis. Three months after inoculating plants with 1,000 root-knot nematode juveniles the populations in pots with M. pruriens, C. spectabilis and C. retusa had been reduced by approximately 79%, 85% and 86% respectively; compared with an increase of 262% nematodes in pots with Phaseolus vulgaris. There was significant reduction of 90% nematodes in fallow pots with no growing plant. The results from this study demonstrate that some leguminous species contain compounds that either kill root-knot

  17. SLA and the Literature Classroom: Fostering Dialogues. Issues in Language Program Direction: A Series of Annual Volumes.

    ERIC Educational Resources Information Center

    Scott, Virginia M., Ed.; Tucker, Holly, Ed.

    This monograph offers eight papers in four sections. Section 1, "Renewed Debates," includes "The Gordian Knot: Language, Literature, and Critical Thinking" (Jean Marie Schultz). Section 2, "Colleagues in Dialogue," includes "Developing Literacy and Literary Competence: Challenges for Foreign Language Departments" (Heidi Byrnes and Susanne Kord)…

  18. Changing Conceptions of Reading: Literacy Learning Instruction. Seventh Yearbook of the American Reading Forum.

    ERIC Educational Resources Information Center

    Lumpkin, Donavon, Ed.; And Others

    Articles in this yearbook contribute to a broad perspective of changing concepts of reading, each focusing attention on an area of major factors exercising current impact on reading and on the education of reading teachers. The articles and their authors are as follows: "Learning from Text" (T. Estes); "Untying the Gordian Knot" (W. Blanton and G.…

  19. Anterior Cruciate Ligament Remnant–Preserving Reconstruction Using a “Lasso-Loop” Knot Configuration

    PubMed Central

    Boutsiadis, Achilleas; Karampalis, Christos; Tzavelas, Anastasios; Vraggalas, Vasileios; Christodoulou, Pavlos; Bisbinas, Ilias

    2015-01-01

    Anterior cruciate ligament (ACL) rupture predisposes to altered kinematics and possible knee joint degeneration. Graft fiber maturation and ligamentization may eliminate this risk during ACL reconstruction procedures. ACL remnant–sparing techniques support the theory that the preserved tissue enhances revascularization, preserves the mechanoreceptors, and leads to anatomic remodeling. The purpose of this article is to present a simple and reproducible technique of tensioning the preserved ACL remnant over the femur. A nonabsorbable suture is passed through the ACL remnant with a “lasso-loop” technique using a curved rotator cuff hook. Femoral and tibial tunnel preparation is performed according to a standard surgical technique for the EndoButton device (Smith & Nephew Endoscopy, Andover, MA). The free ends of the ACL remnant suture are retrieved through the tibial tunnel and passed through each outside hole of the EndoButton device. The hamstring graft is passed through the tibial and femoral tunnels and fixed to the femoral cortex by flipping the EndoButton and to the tibia by an interference screw. Finally, non-sliding half-stitch locking knots are made to secure the ACL remnant suture on the EndoButton device, by use of a knot pusher. This technique offers simple and secure tensioning of the ACL remnant on the fixation device. PMID:26870656

  20. The enigma of the rise of angiosperms: can we untie the knot?

    PubMed

    Augusto, L; Davies, T J; Delzon, S; De Schrijver, A

    2014-10-01

    Multiple hypotheses have been put forward to explain the rise of angiosperms to ecological dominance following the Cretaceous. A unified scheme incorporating all these theories appears to be an inextricable knot of relationships, processes and plant traits. Here, we revisit these hypotheses, categorising them within frameworks based on plant carbon economy, resistance to climatic stresses, nutrient economy, biotic interactions and diversification. We maintain that the enigma remains unresolved partly because our current state of knowledge is a result of the fragmentary nature of palaeodata. This lack of palaeodata limits our ability to draw firm conclusions. Nonetheless, based on consistent results, some inferences may be drawn. Our results indicate that a complex multidriver hypothesis may be more suitable than any single-driver theory. We contend that plant carbon economy and diversification may have played an important role during the early stages of gymnosperms replacement by angiosperms in fertile tropical sites. Plant tolerance to climatic stresses, plant nutrition, biotic interactions and diversification may have played a role in later stages of angiosperm expansion within temperate and harsh environments. The angiosperm knot remains partly tied, but to unravel it entirely will only be feasible if new discoveries are made by scientific communities.

  1. Effect of Mulch Surface Color on Root-knot of Tomato Grown in Simulated Planting Beds

    PubMed Central

    Fortnum, B. A.; Kasperbauer, M. J.; Decoteau, D. R.

    2000-01-01

    The effect of different-colored polyethylene mulches on quantity and spectra of reflected light, plant morphology, and root-knot disease was studied in tomato (Lycopersicon esculentum) grown in simulated planting beds. Tomato plants were inoculated with Meloidogyne incognita at initial populations (Pi) of 0, 1,000, 10,000, or 50,000 eggs/plant, and grown in a greenhouse for 50 days over white, red, or black mulch. Soil temperature was kept constant among the mulch treatments by placing an insulation barrier between the colored mulch and the soil surface. Soil temperature varied less than 0.5 °C between soil chambers at solar noon. Tomatoes grown over white mulch received more reflected photosynthetic light and had greater shoot weights (27%), root weights (32%), and leaf area (20%) than plants grown over black mulch. Plants grown over red mulch received a higher far-red-to-red ratio in the reflected light. Mulch color altered the plant's response to root-knot nematode infection by changing the distribution of mass in axillary shoots. At high Pi, axillary leaf area and leaf weight were greater in tomato grown over white mulch than when grown over red mulch. The root-gall index was lower for plants grown over white mulch than similar plants grown over red mulch. PMID:19270954

  2. Anterior Cruciate Ligament Remnant-Preserving Reconstruction Using a "Lasso-Loop" Knot Configuration.

    PubMed

    Boutsiadis, Achilleas; Karampalis, Christos; Tzavelas, Anastasios; Vraggalas, Vasileios; Christodoulou, Pavlos; Bisbinas, Ilias

    2015-12-01

    Anterior cruciate ligament (ACL) rupture predisposes to altered kinematics and possible knee joint degeneration. Graft fiber maturation and ligamentization may eliminate this risk during ACL reconstruction procedures. ACL remnant-sparing techniques support the theory that the preserved tissue enhances revascularization, preserves the mechanoreceptors, and leads to anatomic remodeling. The purpose of this article is to present a simple and reproducible technique of tensioning the preserved ACL remnant over the femur. A nonabsorbable suture is passed through the ACL remnant with a "lasso-loop" technique using a curved rotator cuff hook. Femoral and tibial tunnel preparation is performed according to a standard surgical technique for the EndoButton device (Smith & Nephew Endoscopy, Andover, MA). The free ends of the ACL remnant suture are retrieved through the tibial tunnel and passed through each outside hole of the EndoButton device. The hamstring graft is passed through the tibial and femoral tunnels and fixed to the femoral cortex by flipping the EndoButton and to the tibia by an interference screw. Finally, non-sliding half-stitch locking knots are made to secure the ACL remnant suture on the EndoButton device, by use of a knot pusher. This technique offers simple and secure tensioning of the ACL remnant on the fixation device. PMID:26870656

  3. A baseline correction algorithm for Raman spectroscopy by adaptive knots B-spline

    NASA Astrophysics Data System (ADS)

    Wang, Xin; Fan, Xian-guang; Xu, Ying-jie; Wang, Xiu-fen; He, Hao; Zuo, Yong

    2015-11-01

    The Raman spectroscopy technique is a powerful and non-invasive technique for molecular fingerprint detection which has been widely used in many areas, such as food safety, drug safety, and environmental testing. But Raman signals can be easily corrupted by a fluorescent background, therefore we presented a baseline correction algorithm to suppress the fluorescent background in this paper. In this algorithm, the background of the Raman signal was suppressed by fitting a curve called a baseline using a cyclic approximation method. Instead of the traditional polynomial fitting, we used the B-spline as the fitting algorithm due to its advantages of low-order and smoothness, which can avoid under-fitting and over-fitting effectively. In addition, we also presented an automatic adaptive knot generation method to replace traditional uniform knots. This algorithm can obtain the desired performance for most Raman spectra with varying baselines without any user input or preprocessing step. In the simulation, three kinds of fluorescent background lines were introduced to test the effectiveness of the proposed method. We showed that two real Raman spectra (parathion-methyl and colza oil) can be detected and their baselines were also corrected by the proposed method.

  4. Initial speed of knots in the plasma tail of C/2013 R1(Lovejoy)

    SciTech Connect

    Yagi, Masafumi; Furusho, Reiko; Terai, Tsuyoshi; Watanabe, Jun-Ichi; Koda, Jin; Fujiwara, Hideaki

    2015-03-01

    We report short-time variations in the plasma tail of C/2013 R1(Lovejoy). A series of short (2–3 minutes) exposure images with the 8.2 m Subaru telescope shows faint details of filaments and their motions over a 24 minute observing duration. We identified rapid movements of two knots in the plasma tail near the nucleus (∼3×10{sup 5} km). Their speeds are 20 and 25 km s{sup −1} along the tail and 3.8 and 2.2 km s{sup −1} across it, respectively. These measurements set a constraint on an acceleration model of plasma tail and knots as they set the initial speed just after their formation. We also found a rapid narrowing of the tail. After correcting the motion along the tail, the narrowing speed is estimated to be ∼8 km s{sup −1}. These rapid motions suggest the need for high time-resolution studies of comet plasma tails with a large telescope.

  5. The Knotted Sky I: Planck constraints on the primordial power spectrum

    SciTech Connect

    Aslanyan, Grigor; Price, Layne C.; Easther, Richard; Abazajian, Kevork N. E-mail: lpri691@aucklanduni.ac.nz E-mail: r.easther@auckland.ac.nz

    2014-08-01

    Using the temperature data from Planck we search for departures from a power-law primordial power spectrum, employing Bayesian model-selection and posterior probabilities. We parametrize the spectrum with n knots located at arbitrary values of logk, with both linear and cubic splines. This formulation recovers both slow modulations and sharp transitions in the primordial spectrum. The power spectrum is well-fit by a featureless, power-law at wavenumbers k>10{sup -3} Mpc{sup -1}. A modulated primordial spectrum yields a better fit relative to ΛCDM at large scales, but there is no strong evidence for a departure from a power-law spectrum. Moreover, using simulated maps we show that a local feature at k ∼ 10{sup -3} Mpc{sup -1} can mimic the suppression of large-scale power. With multi-knot spectra we see only small changes in the posterior distributions for the other free parameters in the standard ΛCDM universe. Lastly, we investigate whether the hemispherical power asymmetry is explained by independent features in the primordial power spectrum in each ecliptic hemisphere, but find no significant differences between them.

  6. Resistance of upland-rice lines to root-knot nematode, Meloidogyne incognita.

    PubMed

    Souza, D C T; Botelho, F B S; Rodrigues, C S; Furtini, I V; Smiderle, E C; de Matos, D L; Bruzi, A T

    2015-01-01

    Despite the benefits of crop rotation, occurrence of nematodes is a common problem for almost all crops within the Cerrado biome, especially for rice. The use of resistant cultivars is one of the main methods for control of nematodes. Thus, the present study aimed to evaluate the reaction of 36 upland-rice lines, with desirable agronomic characteristics, according to their resistance to root-knot nematodes (Meloidogyne incognita). The experimental design was entirely randomized with four replications. Each plot of land consisted of two rice plants in a 3-L vase. The plants were inoculated with 1000 eggs and eventual juveniles of the respective nematodes. Fifty-five days after the inoculation, the roots and the aerial part of the plant were weighed and the egg mass (EM) as well as the reproduction factor (Rf) were estimated. It was determined that the isolated use of EM was not beneficial in selecting rice lines resistant to the root-knot nematode. This procedure must, therefore, take into account the egg counting and the Rf, in order to improve the reliability of the selection. In our study, 30 evaluated lines were observed to be resistant. Among the recommended cultivars, only BRS Monarca had its performance susceptible to the studied nematode species. PMID:26782379

  7. Kalata B8, a novel antiviral circular protein, exhibits conformational flexibility in the cystine knot motif.

    PubMed

    Daly, Norelle L; Clark, Richard J; Plan, Manuel R; Craik, David J

    2006-02-01

    The cyclotides are a family of circular proteins with a range of biological activities and potential pharmaceutical and agricultural applications. The biosynthetic mechanism of cyclization is unknown and the discovery of novel sequences may assist in achieving this goal. In the present study, we have isolated a new cyclotide from Oldenlandia affinis, kalata B8, which appears to be a hybrid of the two major subfamilies (Möbius and bracelet) of currently known cyclotides. We have determined the three-dimensional structure of kalata B8 and observed broadening of resonances directly involved in the cystine knot motif, suggesting flexibility in this region despite it being the core structural element of the cyclotides. The cystine knot motif is widespread throughout Nature and inherently stable, making this apparent flexibility a surprising result. Furthermore, there appears to be isomerization of the peptide backbone at an Asp-Gly sequence in the region involved in the cyclization process. Interestingly, such isomerization has been previously characterized in related cyclic knottins from Momordica cochinchinensis that have no sequence similarity to kalata B8 apart from the six conserved cysteine residues and may result from a common mechanism of cyclization. Kalata B8 also provides insight into the structure-activity relationships of cyclotides as it displays anti-HIV activity but lacks haemolytic activity. The 'uncoupling' of these two activities has not previously been observed for the cyclotides and may be related to the unusual hydrophilic nature of the peptide. PMID:16207177

  8. The Circumstellar Medium of Cassiopeia A Inferred from the Outer Ejecta Knot Properties

    NASA Technical Reports Server (NTRS)

    Hwang, Una; Laming, J. Martin

    2009-01-01

    We investigate the effect of the circumstellar medium density profile on the X-ray emission from outer ejecta knots in the Cassiopeia A supernova remnant using the 1 Ms Chandra observation. The spectra of a number of radial series of ejecta knots at various positions around the remnant are analyzed using techniques similar to those devised in previous papers. We can obtain a reasonable match to our data for a circumstellar density profile proportional to r(sup -2) as would arise from the steady dense wind of a red supergiant, but the agreement is improved if we introduce a central cavity around the progenitor into our models. Such a profile might arise if the progenitor emitted a, fast tenuous stellar wind for a short period immediately prior to explosion. We review other lines of evidence supporting this conclusion. The spectra also indicate the widespread presence of Fe-enriched plasma that was presumably formed by complete Si burning during the explosion, possibly via alpha-rich freezeout. This component is typically associated with hotter and more highly ionized gas than the bulk of the O- and Si-rich ejecta.

  9. Helicity conservation by flow across scales in reconnecting vortex links and knots

    PubMed Central

    Scheeler, Martin W.; Kleckner, Dustin; Kindlmann, Gordon L.; Irvine, William T. M.

    2014-01-01

    The conjecture that helicity (or knottedness) is a fundamental conserved quantity has a rich history in fluid mechanics, but the nature of this conservation in the presence of dissipation has proven difficult to resolve. Making use of recent advances, we create vortex knots and links in viscous fluids and simulated superfluids and track their geometry through topology-changing reconnections. We find that the reassociation of vortex lines through a reconnection enables the transfer of helicity from links and knots to helical coils. This process is remarkably efficient, owing to the antiparallel orientation spontaneously adopted by the reconnecting vortices. Using a new method for quantifying the spatial helicity spectrum, we find that the reconnection process can be viewed as transferring helicity between scales, rather than dissipating it. We also infer the presence of geometric deformations that convert helical coils into even smaller scale twist, where it may ultimately be dissipated. Our results suggest that helicity conservation plays an important role in fluids and related fields, even in the presence of dissipation. PMID:25326419

  10. Kalata B8, a novel antiviral circular protein, exhibits conformational flexibility in the cystine knot motif.

    PubMed

    Daly, Norelle L; Clark, Richard J; Plan, Manuel R; Craik, David J

    2006-02-01

    The cyclotides are a family of circular proteins with a range of biological activities and potential pharmaceutical and agricultural applications. The biosynthetic mechanism of cyclization is unknown and the discovery of novel sequences may assist in achieving this goal. In the present study, we have isolated a new cyclotide from Oldenlandia affinis, kalata B8, which appears to be a hybrid of the two major subfamilies (Möbius and bracelet) of currently known cyclotides. We have determined the three-dimensional structure of kalata B8 and observed broadening of resonances directly involved in the cystine knot motif, suggesting flexibility in this region despite it being the core structural element of the cyclotides. The cystine knot motif is widespread throughout Nature and inherently stable, making this apparent flexibility a surprising result. Furthermore, there appears to be isomerization of the peptide backbone at an Asp-Gly sequence in the region involved in the cyclization process. Interestingly, such isomerization has been previously characterized in related cyclic knottins from Momordica cochinchinensis that have no sequence similarity to kalata B8 apart from the six conserved cysteine residues and may result from a common mechanism of cyclization. Kalata B8 also provides insight into the structure-activity relationships of cyclotides as it displays anti-HIV activity but lacks haemolytic activity. The 'uncoupling' of these two activities has not previously been observed for the cyclotides and may be related to the unusual hydrophilic nature of the peptide.

  11. Nematodetoxic aurovertin-type metabolites from a root-knot nematode parasitic fungus Pochonia chlamydosporia.

    PubMed

    Niu, Xue-Mei; Wang, Yan-Li; Chu, Yan-Sheng; Xue, Hua-Xi; Li, Nan; Wei, Lu-Xia; Mo, Ming-He; Zhang, Ke-Qin

    2010-01-27

    Chemical investigation of one fungal strain P. chlamydosporia YMF 1.00613 isolated from root knots of tobacco infected by Meloidogyne incognita led to the isolation and identification of four aurovertin-type metabolites, which include a new compound, aurovertin I (A1), and three known metabolites, aurovertins E, F and D (A2-A4). Their structures were established by spectroscopic studies such as 1D- and 2D-NMR and MS analysis. Aurovertin I (A1) is the first natural product with an aurovertin skeleton with one less carbon. Compounds A3 and A4 showed the toxicity to the worms of the free-living nematode Panagrellus redivevus with the LC(50) values 88.6 and 41.7 microg/mL at 48 h, respectively. All four aurovertins did not show obvious inhibitory effects on egg hatch of root knot nematode Meloidogyne incognita. The results suggested that the aurovertin-type metabolites produced by P. chlamydosporia might be one of the pathogenic factors involved in the suppression of nematodes.

  12. Response of cucurbit rootstocks for grafted melon (Cucumis melo) to southern root-knot nematode, Meloidogyne incognita

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Root-knot nematodes (RKN) are an important re-emerging pest of melon (Cucumis melo), due largely to the loss of methyl bromide as a pre-plant soil fumigant. Melon is highly susceptible to southern RKN, Meloidogyne incognita, which causes severe root galling and reduced melon fruit yields. Cucurbit...

  13. Large flake graphene oxide fibers with unconventional 100% knot efficiency and highly aligned small flake graphene oxide fibers.

    PubMed

    Xiang, Changsheng; Young, Colin C; Wang, Xuan; Yan, Zheng; Hwang, Chi-Chau; Cerioti, Gabriel; Lin, Jian; Kono, Junichiro; Pasquali, Matteo; Tour, James M

    2013-09-01

    Two types of graphene oxide fibers are spun from high concentration aqueous dopes. Fibers extruded from large flake graphene oxide dope without drawing show unconventional 100% knot efficiency. Fibers spun from small sized graphene oxide dope with stable and continuous drawing yield in good intrinsic alignment with a record high tensile modulus of 47 GPa.

  14. Molecular Characterisation and Diagnosis of Root-Knot Nematodes (Meloidogyne spp.) from Turfgrasses in North Carolina, USA

    PubMed Central

    Ye, Weimin; Zeng, Yongsan; Kerns, James

    2015-01-01

    Root-knot nematodes (Meloidogyne spp.) are the most common and destructive plant-parasitic nematode group worldwide and adversely influence both crop quality and yield. In this study, a total of 51 root-knot nematode populations from turfgrasses were tested, of which 44 were from North Carolina, 6 from South Carolina and 1 from Virginia. Molecular characterisation was performed on these samples by DNA sequencing on the ribosomal DNA 18S, ITS and 28S D2/D3. Species-specific primers were developed to identify turfgrass root-knot nematode through simplex or duplex PCR. Four species were identified, including M. marylandi Jepson & Golden in Jepson, 1987, M. graminis (Sledge & Golden, 1964) Whitehead, 1968, M. incognita (Kofoid & White, 1919) Chitwood, 1949 and M. naasi Franklin, 1965 through a combined analysis of DNA sequencing and PCR by species-specific primers. M. marylandi has been reported from North Carolina and South Carolina for the first time. Molecular diagnosis using PCR by species-specific primers provides a rapid and cheap species identification approach for turfgrass root-knot nematodes. PMID:26599462

  15. Exploitation of intertidal feeding resources by the red knot Calidris canutus under megatidal conditions (Bay of Saint-Brieuc, France)

    NASA Astrophysics Data System (ADS)

    Sturbois, Anthony; Ponsero, Alain; Desroy, Nicolas; Le Mao, Patrick; Fournier, Jérôme

    2015-02-01

    The feeding ecology of the red knot has been widely studied across its wintering range. Red knots mainly select bivalves and gastropods, with differences between sites due to variation in prey availability. The shorebird's diet is also influenced or controlled by the tidal regime. The aim of this paper is to demonstrate the adaptation of foraging red knots to the megatidal environment. The variation in their diet during tidal cycles was studied in the bay of Saint-Brieuc, a functional unit for this species. The method used combined macrofauna, distribution of foraging birds and diet data. Comparative spatial analyses of macrofauna and distribution of foraging red knots have shown that the bay's four benthic assemblages are exploited by birds. By analysing droppings, we highlighted that bivalve molluscs are the main component of their diet, as shown in most overwintering sites. Fifteen types of prey were identified and Donax vittatus was discovered to be a significant prey item. The relative proportion of each main prey item differs significantly depending on the benthic assemblage used to forage. All available benthic assemblages and all potential feeding resources can be used during a single tidal cycle, reflecting an adaptation to megatidal conditions. This approach develops accurate knowledge about the feeding ecology of birds which managers need in order to identify optimal areas for the conservation of waders based on the areas and resources actually used by the birds.

  16. Impact of grapevine (Vitis vinifera) varieties on reproduction of the northern root-knot nematode (Meloidogyne hapla)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Plant-parasitic nematodes are microscopic soil worms that attack the roots of grape plants and cause yield loss. One of the most commonly encountered plant-parasitic nematodes in eastern Washington Vitis vinifera vineyards is Meloidogyne hapla, the northern root-knot nematode. The selection of plant...

  17. 16D10 siRNAs inhibit root-knot nematode infection in transgenic grape hairy roots

    Technology Transfer Automated Retrieval System (TEKTRAN)

    To develop a biotech-based solution for controlling Root-knot nematodes (RKNs) in grapes, we evaluated the efficacy of plant-derived RNA interference (RNAi) silencing of a conserved RKN effector gene, 16D10, for nematode resistance in transgenic grape hairy roots. Two hairpin-based silencing constru...

  18. Cystine-knot peptides targeting cancer-relevant human cytotoxic T lymphocyte-associated antigen 4 (CTLA-4).

    PubMed

    Maaß, Franziska; Wüstehube-Lausch, Joycelyn; Dickgießer, Stephan; Valldorf, Bernhard; Reinwarth, Michael; Schmoldt, Hans-Ulrich; Daneschdar, Matin; Avrutina, Olga; Sahin, Ugur; Kolmar, Harald

    2015-08-01

    Cystine-knot peptides sharing a common fold but displaying a notably large diversity within the primary structure of flanking loops have shown great potential as scaffolds for the development of therapeutic and diagnostic agents. In this study, we demonstrated that the cystine-knot peptide MCoTI-II, a trypsin inhibitor from Momordica cochinchinensis, can be engineered to bind to cytotoxic T lymphocyte-associated antigen 4 (CTLA-4), an inhibitory receptor expressed by T lymphocytes, that has emerged as a target for the treatment of metastatic melanoma. Directed evolution was used to convert a cystine-knot trypsin inhibitor into a CTLA-4 binder by screening a library of variants using yeast surface display. A set of cystine-knot peptides possessing dissociation constants in the micromolar range was obtained; the most potent variant was synthesized chemically. Successive conjugation with neutravidin, fusion to antibody Fc domain or the oligomerization domain of C4b binding protein resulted in oligovalent variants that possessed enhanced (up to 400-fold) dissociation constants in the nanomolar range. Our data indicate that display of multiple knottin peptides on an oligomeric scaffold protein is a valid strategy to improve their functional affinity with ramifications for applications in diagnostics and therapy. PMID:25964162

  19. SSR markers for marker assisted selection of root-knot nematode (Meloidogyne incognita) resistant plants in cotton (Gossypium hirsutum L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cotton (Gossypium hirsutum L) cultivars highly resistant to the southern root-knot nematode (RKN) [Meloidogyne incognita (Kofoid & White) Chitwood] are not available. Recently, molecular markers on chromosomes 11 and 14 have been associated with RKN resistance, thus opening the way for marker assis...

  20. Accomplishments of a 10-year initiative to develop host plant resistance to root-knot and reniform nematodes in cotton

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In 2003 Cotton Incorporated initiated a Beltwide research program to develop host plant resistance to root-knot (Meloidogyne incognita) and reniform (Rotylenchulus reniformis) nematodes. Objectives formulated at a coordinating meeting in 2003 that included participants from public institutions and p...

  1. Dose-response effects of clove oil from Syzygium aromaticum on the root-knot nematode Meloidogyne incognita

    Technology Transfer Automated Retrieval System (TEKTRAN)

    BACKGROUND: Clove oil, derived from the plant Syzygium aromaticum (L.) Merr. & Perry, is active against various organisms, and was prepared in a soy lecithin/detergent formulation to determine concentrations active against the root-knot nematode Meloidogyne incognita (Kofoid and White) Chitwood. RE...

  2. Cystine-knot peptides targeting cancer-relevant human cytotoxic T lymphocyte-associated antigen 4 (CTLA-4).

    PubMed

    Maaß, Franziska; Wüstehube-Lausch, Joycelyn; Dickgießer, Stephan; Valldorf, Bernhard; Reinwarth, Michael; Schmoldt, Hans-Ulrich; Daneschdar, Matin; Avrutina, Olga; Sahin, Ugur; Kolmar, Harald

    2015-08-01

    Cystine-knot peptides sharing a common fold but displaying a notably large diversity within the primary structure of flanking loops have shown great potential as scaffolds for the development of therapeutic and diagnostic agents. In this study, we demonstrated that the cystine-knot peptide MCoTI-II, a trypsin inhibitor from Momordica cochinchinensis, can be engineered to bind to cytotoxic T lymphocyte-associated antigen 4 (CTLA-4), an inhibitory receptor expressed by T lymphocytes, that has emerged as a target for the treatment of metastatic melanoma. Directed evolution was used to convert a cystine-knot trypsin inhibitor into a CTLA-4 binder by screening a library of variants using yeast surface display. A set of cystine-knot peptides possessing dissociation constants in the micromolar range was obtained; the most potent variant was synthesized chemically. Successive conjugation with neutravidin, fusion to antibody Fc domain or the oligomerization domain of C4b binding protein resulted in oligovalent variants that possessed enhanced (up to 400-fold) dissociation constants in the nanomolar range. Our data indicate that display of multiple knottin peptides on an oligomeric scaffold protein is a valid strategy to improve their functional affinity with ramifications for applications in diagnostics and therapy.

  3. EVALUATION OF SPK, A NOVEL COMBINATION OF ORGANIC COMPOUNDS FOR ROOT-KNOT NEMATODE CONTROL IN TOMATO

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Laboratory, greenhouse, and field microplot trials were conducted to evaluate the efficacy of a novel combination of organic compounds, referred to as SPK, for control of root-knot nematode (Meloidogyne incognita) on tomato. SPK has zero ozone depletion potential, has a short half-life in soil (3-7...

  4. Pinpointing genes underlying the quantitative trait loci for root-knot nematode resistance in palaeopolyploid soybean by whole genome resequencing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective of this study was to utilize next-generation sequencing (NGS) technologies to dissect quantitative trait loci (QTL) for southern root-knot nematode (RKN) resistance into individual genes in soybean. Two-hundred forty-six recombinant inbred lines (RIL) derived from a cross between Mage...

  5. A comparative study of extraction methods reveals preferred solvents for cystine knot peptide isolation from Momordica cochinchinensis seeds.

    PubMed

    Mahatmanto, Tunjung; Poth, Aaron G; Mylne, Joshua S; Craik, David J

    2014-06-01

    MCoTI-I and MCoTI-II (short for Momordica cochinchinensis Trypsin Inhibitor-I and -II, respectively) are attractive candidates for developing novel intracellular-targeting drugs because both are exceptionally stable and can internalize into cells. These seed-derived cystine knot peptides are examples of how natural product discovery efforts can lead to biomedical applications. However, discovery efforts are sometimes hampered by the limited availability of seed materials, highlighting the need for efficient extraction methods. In this study, we assessed five extraction methods using M. cochinchinensis seeds, a source of well-characterized cystine knot peptides. The most efficient extraction of nine known cystine knot peptides was achieved by a method based on acetonitrile/water/formic acid (25:24:1), followed by methods based on sodium acetate (20 mM, pH 5.0), ammonium bicarbonate (5 mM, pH 8.0), and boiling water. On average, the yields obtained by these four methods were more than 250-fold higher than that obtained using dichloromethane/methanol (1:1) extraction, a previously applied standard method. Extraction using acetonitrile/water/formic acid (25:24:1) yielded the highest number of reconstructed masses within the majority of plant-derived cystine knot peptide mass range but only accounted for around 50% of the total number of masses, indicating that any single method may result in under-sampling. Applying acetonitrile/water/formic acid (25:24:1), boiling water, and ammonium bicarbonate (5 mM, pH 8.0) extractions either successively or discretely significantly increased the sampling number. Overall, acetonitrile/water/formic acid (25:24:1) can facilitate efficient extraction of cystine-knot peptides from M. cochinchinensis seeds but for discovery purposes the use of a combination of extraction methods is recommended where practical. PMID:24613804

  6. A comparative study of extraction methods reveals preferred solvents for cystine knot peptide isolation from Momordica cochinchinensis seeds.

    PubMed

    Mahatmanto, Tunjung; Poth, Aaron G; Mylne, Joshua S; Craik, David J

    2014-06-01

    MCoTI-I and MCoTI-II (short for Momordica cochinchinensis Trypsin Inhibitor-I and -II, respectively) are attractive candidates for developing novel intracellular-targeting drugs because both are exceptionally stable and can internalize into cells. These seed-derived cystine knot peptides are examples of how natural product discovery efforts can lead to biomedical applications. However, discovery efforts are sometimes hampered by the limited availability of seed materials, highlighting the need for efficient extraction methods. In this study, we assessed five extraction methods using M. cochinchinensis seeds, a source of well-characterized cystine knot peptides. The most efficient extraction of nine known cystine knot peptides was achieved by a method based on acetonitrile/water/formic acid (25:24:1), followed by methods based on sodium acetate (20 mM, pH 5.0), ammonium bicarbonate (5 mM, pH 8.0), and boiling water. On average, the yields obtained by these four methods were more than 250-fold higher than that obtained using dichloromethane/methanol (1:1) extraction, a previously applied standard method. Extraction using acetonitrile/water/formic acid (25:24:1) yielded the highest number of reconstructed masses within the majority of plant-derived cystine knot peptide mass range but only accounted for around 50% of the total number of masses, indicating that any single method may result in under-sampling. Applying acetonitrile/water/formic acid (25:24:1), boiling water, and ammonium bicarbonate (5 mM, pH 8.0) extractions either successively or discretely significantly increased the sampling number. Overall, acetonitrile/water/formic acid (25:24:1) can facilitate efficient extraction of cystine-knot peptides from M. cochinchinensis seeds but for discovery purposes the use of a combination of extraction methods is recommended where practical.

  7. A remarkably easy knot-tying technique for single-incision laparoscopic surgery with the SILS port for gynecologic diseases.

    PubMed

    Endo, Toshiaki; Nagasawa, Kunihiko; Umemura, Kota; Baba, Tsuyoshi; Henmi, Hirofumi; Saito, Tsuyoshi

    2011-01-01

    Single-incision laparoscopic surgery (SILS) has been quickly accepted, especially for women, because the cosmetic benefits may be greater than with ordinary laparoscopic surgery. In gynecologic disease, SILS is appropriate for diagnostic laparoscopy, oophorectomy, and salpingectomy, among other conditions. In addition, the knot-tying process for intracorporeal suturing during SILS is a major rate-limiting step and a key determinant of the popularity of SILS. Although a roticulator instrument is useful for creating the needed operative angle, knot tying is still believed to be difficult. We have devised a remarkably simple knot-tying technique that can be applied during SILS with a SILS Port with a Roticulator and a straight-type needle driver. We determined that, after transfixing the needle, the long tail of the thread should be grasped at around 90 degrees relative to the long axis of tip of the Roticulator, which is articulated at 80 degrees. This automatically forms an ideal C-loop because of gravitation. The needle attached to the long tail should face the distal side from the tip of Roticulator (from the surgeon's perspective). The apex of the C-loop is then toward the proximal side from the tip of the Roticulator (from the perspective of the surgeon). This thread position is important during the knot-tying process. The upper arm of the C-loop should then be entwined by applying a series of axial spinning movements to the rod of the needle driver. At this time, the jaws of the needle driver should be kept open so the thread does not slip off of the rod. The benefit of this technique is that it does not require any special skills; any surgeon able to perform intracorporeal suturing should also be able to easily tie knots during SILS. PMID:21570364

  8. Topological patterns in two-dimensional gel electrophoresis of DNA knots

    PubMed Central

    Michieletto, Davide; Marenduzzo, Davide; Orlandini, Enzo

    2015-01-01

    Gel electrophoresis is a powerful experimental method to probe the topology of DNA and other biopolymers. Although there is a large body of experimental work that allows us to accurately separate different topoisomers of a molecule, a full theoretical understanding of these experiments has not yet been achieved. Here we show that the mobility of DNA knots depends crucially and subtly on the physical properties of the gel and, in particular, on the presence of dangling ends. The topological interactions between these and DNA molecules can be described in terms of an “entanglement number” and yield a nonmonotonic mobility at moderate fields. Consequently, in 2D electrophoresis, gel bands display a characteristic arc pattern; this turns into a straight line when the density of dangling ends vanishes. We also provide a novel framework to accurately predict the shape of such arcs as a function of molecule length and topological complexity, which may be used to inform future experiments. PMID:26351668

  9. A new family of cystine knot peptides from the seeds of Momordica cochinchinensis.

    PubMed

    Chan, Lai Yue; He, Wenjun; Tan, Ninghua; Zeng, Guangzhi; Craik, David J; Daly, Norelle L

    2013-01-01

    Momordica cochinchinensis, a Cucurbitaceae plant commonly found in Southeast Asia, has the unusual property of containing both acyclic and backbone-cyclized trypsin inhibitors with inhibitor cystine knot (ICK) motifs. In the current study we have shown that M. cochinchinensis also contains another family of acyclic ICK peptides. We recently reported two novel peptides from M. cochinchinensis but have now discovered four additional peptides (MCo-3-MCo-6) with related sequences. Together these peptides form a novel family of M. cochinchinensis ICK peptides (MCo-ICK) that do not have sequence homology with other known peptides and are not potent trypsin inhibitors. Otherwise these new peptides MCo-3 to MCo-6 were evaluated for antimalarial activity against Plasmodium falciparum, and cytotoxic activity against the cancer cell line MDA-MB-231. But these peptides were not active. PMID:23127518

  10. Body shrinkage due to Arctic warming reduces red knot fitness in tropical wintering range.

    PubMed

    van Gils, Jan A; Lisovski, Simeon; Lok, Tamar; Meissner, Włodzimierz; Ożarowska, Agnieszka; de Fouw, Jimmy; Rakhimberdiev, Eldar; Soloviev, Mikhail Y; Piersma, Theunis; Klaassen, Marcel

    2016-05-13

    Reductions in body size are increasingly being identified as a response to climate warming. Here we present evidence for a case of such body shrinkage, potentially due to malnutrition in early life. We show that an avian long-distance migrant (red knot, Calidris canutus canutus), which is experiencing globally unrivaled warming rates at its high-Arctic breeding grounds, produces smaller offspring with shorter bills during summers with early snowmelt. This has consequences half a world away at their tropical wintering grounds, where shorter-billed individuals have reduced survival rates. This is associated with these molluscivores eating fewer deeply buried bivalve prey and more shallowly buried seagrass rhizomes. We suggest that seasonal migrants can experience reduced fitness at one end of their range as a result of a changing climate at the other end.

  11. Stable and biocompatible cystine knot peptides from the marine sponge Asteropus sp.

    PubMed

    Su, Mingzhi; Li, Huayue; Wang, Haibo; Kim, Eun La; Kim, Hyung Sik; Kim, Eun-Hee; Lee, Jaewon; Jung, Jee H

    2016-07-01

    Two new cystine knot peptides, asteropsins F (ASPF) and G (ASPG), were isolated from the marine sponge Asteropus sp. ASPF and ASPG are composed of 33 and 32 amino acids, respectively, and contain six cysteines which are involved in three disulfide bonds. They shared the characteristic features of the asteropsin family, such as, N-terminal pyroglutamate modification, incorporation of cis prolines, and the unique anionic profile, which distinguish them from other knottin families. Tertiary structures of the peptides were determined by high resolution NMR. ASPF and ASPG were found to be remarkably resistant not only to digestive enzymes (chymotrypsin, pepsin, elastase, and trypsin) but also to thermal degradation. In addition, these peptides were pharmacologically inert; non-hemolytic to human and fish red blood cells, non-stimulatory to murine macrophage cells, and nontoxic in vitro or in vivo. These observations support their stability and biocompatibility as suitable carrier scaffolds for the design of oral peptide drug. PMID:27189887

  12. Design considerations for attaining 200-knot test velocities at the aircraft landing loads and traction facility

    NASA Technical Reports Server (NTRS)

    Giles, G. L.; Stubbs, S. M.

    1979-01-01

    Design studies are presented which consider the important parameters in providing 200 knot test velocities at the landing loads and traction facility. Two major components of this facility, the hydraulic jet catapult and the test carriage structure, are considered. Suitable factors are determined to correlate analytical data for characteristics of the hydraulic jet catapult with data measured from the existing catapult system. The resulting equations are used to calculate test velocities for a range of jet nozzle diameters and carriage masses with both the current 122 m and an increased 183 m catapult stroke. Using the catapult characteristics, a target design point is selected and a carriage structure is sized to meet the target point strength requirements.

  13. Explosive nucleosynthesis in massive stars - Comparison with the Cassiopeia A fast-moving knots

    NASA Technical Reports Server (NTRS)

    Johnston, M. D.; Yahil, A.

    1984-01-01

    If the ejecta of a Type II supernova do not undergo extensive mixing, then, based on the explosion of current presupernova models, only a small fraction approximately equal to or less than 0.1 solar mass of the mantle of a massive star can yield abundances similar to those observed in the fast-moving knots of Cas A. This is shown to be independent of the detailed structure of the mantle and the supernova energy. Lack of mixing in Cas A is indicated by strong upper limits on the abundance ratios Ne/O, and Fe/O. If this is confirmed by further observations, then either Cas A is not the result of a standard progenitor of approximately equal to or less than 25 solar masses disrupted by a Type II supernova, or the picture of the last stages of stellar evolution in massive stars needs to be modified substantially.

  14. Untargeted Metabolomics of Tomato Plants after Root-Knot Nematode Infestation.

    PubMed

    Eloh, Kodjo; Sasanelli, Nicola; Maxia, Andrea; Caboni, Pierluigi

    2016-07-27

    After 2 months from the infestation of tomato plants with the root-knot nematode (RKN) Meloidogyne incognita, we performed a gas chromatography-mass spectrometry untargeted fingerprint analysis for the identification of characteristic metabolites and biomarkers. Principal component analysis, and orthogonal projections to latent structures discriminant analysis suggested dramatic local changes of the plant metabolome. In the case of tomato leaves, β-alanine, phenylalanine, and melibiose were induced in response to RKN stimuli, while ribose, glycerol, myristic acid, and palmitic acid were reduced. For tomato stems, upregulated metabolites were ribose, sucrose, fructose, and glucose, while fumaric acid and glycine were downregulated. The variation in molecular strategies to the infestation of RKNs may play an important role in how Solanum lycopersicum and other plants adapt to nematode parasitic stress. PMID:27389052

  15. Body shrinkage due to Arctic warming reduces red knot fitness in tropical wintering range.

    PubMed

    van Gils, Jan A; Lisovski, Simeon; Lok, Tamar; Meissner, Włodzimierz; Ożarowska, Agnieszka; de Fouw, Jimmy; Rakhimberdiev, Eldar; Soloviev, Mikhail Y; Piersma, Theunis; Klaassen, Marcel

    2016-05-13

    Reductions in body size are increasingly being identified as a response to climate warming. Here we present evidence for a case of such body shrinkage, potentially due to malnutrition in early life. We show that an avian long-distance migrant (red knot, Calidris canutus canutus), which is experiencing globally unrivaled warming rates at its high-Arctic breeding grounds, produces smaller offspring with shorter bills during summers with early snowmelt. This has consequences half a world away at their tropical wintering grounds, where shorter-billed individuals have reduced survival rates. This is associated with these molluscivores eating fewer deeply buried bivalve prey and more shallowly buried seagrass rhizomes. We suggest that seasonal migrants can experience reduced fitness at one end of their range as a result of a changing climate at the other end. PMID:27174985

  16. A new family of cystine knot peptides from the seeds of Momordica cochinchinensis.

    PubMed

    Chan, Lai Yue; He, Wenjun; Tan, Ninghua; Zeng, Guangzhi; Craik, David J; Daly, Norelle L

    2013-01-01

    Momordica cochinchinensis, a Cucurbitaceae plant commonly found in Southeast Asia, has the unusual property of containing both acyclic and backbone-cyclized trypsin inhibitors with inhibitor cystine knot (ICK) motifs. In the current study we have shown that M. cochinchinensis also contains another family of acyclic ICK peptides. We recently reported two novel peptides from M. cochinchinensis but have now discovered four additional peptides (MCo-3-MCo-6) with related sequences. Together these peptides form a novel family of M. cochinchinensis ICK peptides (MCo-ICK) that do not have sequence homology with other known peptides and are not potent trypsin inhibitors. Otherwise these new peptides MCo-3 to MCo-6 were evaluated for antimalarial activity against Plasmodium falciparum, and cytotoxic activity against the cancer cell line MDA-MB-231. But these peptides were not active.

  17. Bubbles and Knots in the Kinematical Structure of the Bipolar Planetary Nebula NGC 2818

    NASA Astrophysics Data System (ADS)

    Vázquez, Roberto

    2012-06-01

    High-resolution Hubble Space Telescope archive imaging and high-dispersion spectroscopy are used to study the complex morphological and kinematical structure of the planetary nebula, NGC 2818. We analyze narrowband Hα, [O III], [N II], [S II], and He II images, addressing important morphological features. Ground-based long-slit echelle spectra were obtained crossing NGC 2818 at five different positions to precisely determine kinematical features in the structure of the nebula. A distance of 2.5 kpc was used to determine physical scales. Constructing models to fit the data with modern computational tools, we find NGC 2818 is composed of (1) a non-uniform bipolar structure with a semimajor axis of 0.92 pc (75''), possibly deformed by the stellar wind, (2) a 0.17 pc (14'') diameter central region, which is potentially the remnant of an equatorial enhancement, and (3) a great number of cometary knots. These knots are preferentially located inside a radius of 0.24 pc (20'') around the central star. The major axis of the main structure is oriented at i ~= 60° with respect to the line of sight and at P.A. = +89° on the plane of the sky. Expansion velocities of this nebula are V pol = 105 km s-1 and V eq = 20 km s-1, which lead to our estimate of the kinematical age of τk ~= 8400 ± 3400 yr (assuming homologous expansion). Our observations do not support the idea that high-velocity collimated ejections are responsible for the formation of microstructures inside the nebula. We determine the systemic velocity of NGC 2818 to be V HEL = +26 ± 2 km s-1.

  18. Transcriptome Analysis of Resistant and Susceptible Alfalfa Cultivars Infected With Root-Knot Nematode Meloidogyne incognita

    PubMed Central

    Postnikova, Olga A.; Hult, Maria; Shao, Jonathan; Skantar, Andrea; Nemchinov, Lev G.

    2015-01-01

    Nematodes are one of the major limiting factors in alfalfa production. Root-knot nematodes (RKN, Meloidogyne spp.) are widely distributed and economically important sedentary endoparasites of agricultural crops and they may inflict significant damage to alfalfa fields. As of today, no studies have been published on global gene expression profiling in alfalfa infected with RKN or any other plant parasitic nematode. Very little information is available about molecular mechanisms that contribute to pathogenesis and defense responses in alfalfa against these pests and specifically against RKN. In this work, we performed root transcriptome analysis of resistant (cv. Moapa 69) and susceptible (cv. Lahontan) alfalfa cultivars infected with RKN Meloidogyne incognita, widespread root-knot nematode species and a major pest worldwide. A total of 1,701,622,580 pair-end reads were generated on an Illumina Hi-Seq 2000 platform from the roots of both cultivars and assembled into 45,595 and 47,590 transcripts in cvs Moapa 69 and Lahontan, respectively. Bioinformatic analysis revealed a number of common and unique genes that were differentially expressed in susceptible and resistant lines as a result of nematode infection. Although the susceptible cultivar showed a more pronounced defense response to the infection, feeding sites were successfully established in its roots. Characteristically, basal gene expression levels under normal conditions differed between the two cultivars as well, which may confer advantage to one of the genotypes toward resistance to nematodes. Differentially expressed genes were subsequently assigned to known Gene Ontology categories to predict their functional roles and associated biological processes. Real-time PCR validated expression changes in genes arbitrarily selected for experimental confirmation. Candidate genes that contribute to protection against M. incognita in alfalfa were proposed and alfalfa-nematode interactions with respect to resistance

  19. Comparisons of Pathological Responses in Carrot to Root-knot Nematodes

    PubMed Central

    Seo, Yunhee; Kim, Yong Su; Park, Yong; Kim, Young Ho

    2015-01-01

    Carrot (Dacus carota var. sativus) is one of the top-ten most economically important vegetable crops produced worldwide, and the root-knot nematodes, Meloidogyne spp., are one of the most important pests in the carrot. In Korea, M. hapla and M. incognita are presumed to be the major root-knot nematodes distributing mostly in open carrot fields and greenhouses, respectively. In our study, currently-developed and commercial carrot cultivars and the parental lines were examined for their pathological responses to M. incognita and M. hapla 7 weeks after inoculation with about 1,000 second-stage juveniles (J2) of the nematodes. All the carrot cultivars and lines showed susceptible responses to both nematodes with the gall index (GI) of 2.4–4.4, which were always higher on the carrot plants infected with M. incognita than M. hapla. Gall sizes were remarkably larger with more serious reduction of the root growths in the plants infected with M. incognita than M. hapla, suggesting the carrot lines examined in our study were more susceptible to the former than the latter. In the infection sites of the root tissues, giant cells were more extensively formed, occupying larger stellar regions with the prominent destruction of adjacent xylem vessels by M. incognita than M. hapla. All of these results suggest M. incognita affect more seriously on the carrot plants that are grown in greenhouses, compared to M. hapla that has a major distribution in open carrot fields, which would be used for determining cropping systems based on target nematode species, their damage and pathological characteristics. PMID:26675114

  20. Biocontrol of root-knot nematode, Meloidogyne incognita damaging queen palm, Livistona rotundifolia using Trichoderma species.

    PubMed

    Jegathambigai, V; Karunaratne, M D S D; Svinningen, Arne; Mikunthan, G

    2008-01-01

    Livistona rotundifolia is a widely grown queen palm in all the net houses of floriculture industries in Sri Lanka. It is grown to an extent of 10,000 mZ in Green Farms Ltd, Marawilla under shade net house. Root knot nematode is one among the key pests of queen palms and causes heavy loss in the queen palm industry. Queen palm is grown in a coir based compost media under sprinkler irrigation. Management of nematodes using chemicals is impractical due the non availability and selectivity of the nematicides available in the market. This study attempted to evaluate the efficacy of Trichoderma species to control root knot nematode, Meloidogyne incognita that damage L. rotundifolia and caused heavy loss at Green Farms Ltd, Marawilla. Experiments were conducted using organic amendments with T. viride + T. harzianum (1 x 10(10) cfu/ml) to control the nematodes. Carbofuran (3%) (2.5 g/750 ml pot with organic amendments), the only available pesticide with nematicidal property, was used as a standard check. Queen palm naturally infected with M. incognita was treated with Trichoderma species and the effect was compared with the carbofuran treatment. Standard procedures were adopted to count the nematodes in the pre and post treated queen palm plots. The results revealed that the application of mixture of T. viride and T. harzianum at 1 x 10(10) cfu/ml significantly reduced the nematode populations in the media and number of galls in the palms compare to Carbofuran treated palms. Eggs and juveniles of M. incognita were found infected with Trichoderma species under the in-vitro conditions. The population of M. incognita was started declining significantly 3 weeks after the first application of Trichoderma species in the field. The response was apparent in the palms treated with mixture of Trichoderma species and recovered within 3 months as a healthy and quality product with export standards.

  1. Biocontrol of root-knot nematode, Meloidogyne incognita damaging queen palm, Livistona rotundifolia using Trichoderma species.

    PubMed

    Jegathambigai, V; Karunaratne, M D S D; Svinningen, Arne; Mikunthan, G

    2008-01-01

    Livistona rotundifolia is a widely grown queen palm in all the net houses of floriculture industries in Sri Lanka. It is grown to an extent of 10,000 mZ in Green Farms Ltd, Marawilla under shade net house. Root knot nematode is one among the key pests of queen palms and causes heavy loss in the queen palm industry. Queen palm is grown in a coir based compost media under sprinkler irrigation. Management of nematodes using chemicals is impractical due the non availability and selectivity of the nematicides available in the market. This study attempted to evaluate the efficacy of Trichoderma species to control root knot nematode, Meloidogyne incognita that damage L. rotundifolia and caused heavy loss at Green Farms Ltd, Marawilla. Experiments were conducted using organic amendments with T. viride + T. harzianum (1 x 10(10) cfu/ml) to control the nematodes. Carbofuran (3%) (2.5 g/750 ml pot with organic amendments), the only available pesticide with nematicidal property, was used as a standard check. Queen palm naturally infected with M. incognita was treated with Trichoderma species and the effect was compared with the carbofuran treatment. Standard procedures were adopted to count the nematodes in the pre and post treated queen palm plots. The results revealed that the application of mixture of T. viride and T. harzianum at 1 x 10(10) cfu/ml significantly reduced the nematode populations in the media and number of galls in the palms compare to Carbofuran treated palms. Eggs and juveniles of M. incognita were found infected with Trichoderma species under the in-vitro conditions. The population of M. incognita was started declining significantly 3 weeks after the first application of Trichoderma species in the field. The response was apparent in the palms treated with mixture of Trichoderma species and recovered within 3 months as a healthy and quality product with export standards. PMID:19226812

  2. Effect of Soils from Six Management Systems on Root-knot Nematodes and Plant Growth in Greenhouse Assays

    PubMed Central

    Kokalis-Burelle, N.; Chellemi, D. O.; Périès, X.

    2005-01-01

    The effects of soil management systems on root-knot nematode (Meloidogyne incognita) eggs and gall incidence on tomato (Lycopersicon esculentum) and cucumber (Cucumis sativus) following tomato were evaluated. Soil was collected from a replicated field experiment in which six management systems were being assessed for vegetable production. Soil management systems were conventional production, organic production, bahiagrass (Paspalum notatum) pasture, bahiagrass: Stylosanthes (Stylosanthes guianensis) pasture, bare ground fallow, and weed fallow. Soil was collected from field plots and used in greenhouse experiments. Identification of egg-parasitic fungi and the incidence of root-knot nematode galling were assessed both on tomato and cucumber planted in the same pots following the removal of tomato plants. Organic, bare ground fallow and conventional production treatments reduced galling both on tomato and on cucumber following tomato. Although no treatment consistently enhanced egg-parasitic fungi, management system did affect egg viability and the types of fungi isolated from parasitized eggs. PMID:19262892

  3. Structure and dynamics of the plasma tail of comet P/Halley. I - Knot event on December 31, 1985

    NASA Technical Reports Server (NTRS)

    Saito, T.; Yumoto, K.; Hirao, K.; Minami, S.; Saito, K.; Smith, E.

    1987-01-01

    On the basis of about 500 photographs of comet Halley taken by many observers, Saito et al. (1986) classified the detected disturbances of the plasma tail as outstanding rays, streamer, helix, kink, arcade, and disconnection event (DE). In this paper, the interaction of the solar wind with the plasma tail of Comet P/Halley is examined by using results of observations by the Sakigake spacecraft of the December 31, 1985 event, which included various disturbances and one DE-like knot. On the basis of twenty photographs taken on December 31 by Japanese astronomers, the dynamic pressure model proposed by Saito et al. (1986) is examined, and the mechnism of the knot event that appeared in the plasma tail of the comet on December 31, is explained.

  4. Ab-interno scleral suture loop fixation with cow-hitch knot in posterior chamber intraocular lens decentration

    PubMed Central

    Can, Ertuğrul; Koçak, Nurullah; Yücel, Özlem Eşki; Gül, Adem; Öztürk, Hilal Eser; Sayın, Osman

    2016-01-01

    Aim of Study: To describe a simplified ab-interno cow-hitch suture fixation technique for repositioning decentered posterior chamber intraocular lens (PC IOL). Materials and Methods: Two cases are presented with the surgical correction of decentered and subluxated IOL. Ab-interno scleral suture fixation technique with hitch-cow knot in the eye was performed with a ciliary sulcus guide instrument and 1 year follow-up was completed. Results: Both of the patients had well centered lenses postoperatively. Corrected distant and near visual acuities of the patients were improved. There was no significant postoperative complication. In the follow-up period of 1 year, no evidence of suture erosion was found. Conclusions: Ab-interno scleral suture loop fixation with hitch-cow knot in the eye was effective in repositioning decentered or subluxated PC IOLs with excellent postoperative centered lenses and visual outcomes. PMID:27050346

  5. Hi-C analysis in Arabidopsis identifies the KNOT, a structure with similarities to the flamenco locus of Drosophila.

    PubMed

    Grob, Stefan; Schmid, Marc W; Grossniklaus, Ueli

    2014-09-01

    Chromosomes are folded, spatially organized, and regulated by epigenetic marks. How chromosomal architecture is connected to the epigenome is not well understood. We show that chromosomal architecture of Arabidopsis is tightly linked to the epigenetic state. Furthermore, we show how physical constraints, such as nuclear size, correlate with the folding principles of chromatin. We also describe a nuclear structure, termed KNOT, in which genomic regions of all five Arabidopsis chromosomes interact. These KNOT ENGAGED ELEMENT (KEE) regions represent heterochromatic islands within euchromatin. Similar to PIWI-interacting RNA clusters, such as flamenco in Drosophila, KEEs represent preferred landing sites for transposable elements, which may be part of a transposon defense mechanism in the Arabidopsis nucleus. PMID:25132176

  6. Fabrication and characterization of high order filter based on resonance in hybrid multi-knots microfiber structure

    NASA Astrophysics Data System (ADS)

    Nodehi, S.; Mohammed, W. S.; Ahmad, H.; Harun, S. W.

    2016-04-01

    This work proposes a novel design of a hybrid microfiber resonator which can be used as a band-pass and band-stop filter in various applications such as fiber lasers. The structure comprises of two microfiber knot resonators with different sizes which are surrounded by a semi-loop structure with one input and two output ports. Utilization of the Vernier effect in the proposed structure showed an enhancement of the free spectral range (FSR). The finesse has increased by a factor of three compared to a single knot providing a sharper roll-off. The filter bandwidth is adjustable as a result of the manipulation of the coupling length and rings' radii. The performance of the device is explained theoretically using transfer matrix analysis.

  7. Chandra X-ray Observation of a Mature Cloud-Shock Interaction in the Bright Eastern Knot of Puppis A

    NASA Technical Reports Server (NTRS)

    Hwang, Una; Flanagan, Kathryn A.; Petre, Robert

    2005-01-01

    We present Chandra X-ray images and spectra of the most prominent cloud-shock interaction region in the Puppis A supernova remnant. The Bright Eastern Knot (BEK) has two main morphological components: (1) a bright compact knot that lies directly behind the apex of an indentation in the eastern X-ray boundary and (2) lying 1 westward behind the shock, a curved vertical structure (bar) that is separated from a smaller bright cloud (cap) by faint diffuse emission. Based on hardness images and spectra, we identify the bar and cap as a single shocked interstellar cloud. Its morphology strongly resembles the "voided sphere" structures seen at late times in Klein et al. experimental simulat.ions of cloud-shock interactions, when the crushing of the cloud by shear instabilities is well underway. We infer an intera.ction time of roughly cloud-crushing timescales, which translates to 2000-4000 years, based on the X-ray temperature, physical size, and estimated expansion of the shocked cloud. This is the first X-ray identified example of a cloud-shock interaction in this advanced phase. Closer t o the shock front, the X-ray emission of the compact knot in the eastern part of the BEK region implies a recent interaction with relatively denser gas, some of which lies in front of the remnant. The complex spatial relationship of the X-ray emission of the compact knot to optical [O III] emission suggests that there are multiple cloud interactions occurring along the line of sight.

  8. Direct regulation of knot gene expression by Ultrabithorax and the evolution of cis-regulatory elements in Drosophila.

    PubMed

    Hersh, Bradley M; Carroll, Sean B

    2005-04-01

    The regulation of development by Hox proteins is important in the evolution of animal morphology, but how the regulatory sequences of Hox-regulated target genes function and evolve is unclear. To understand the regulatory organization and evolution of a Hox target gene, we have identified a wing-specific cis-regulatory element controlling the knot gene, which is expressed in the developing Drosophila wing but not the haltere. This regulatory element contains a single binding site that is crucial for activation by the transcription factor Cubitus interruptus (Ci), and a cluster of binding sites for repression by the Hox protein Ultrabithorax (UBX). The negative and positive control regions are physically separable, demonstrating that UBX does not repress by competing for occupancy of Ci-binding sites. Although knot expression is conserved among Drosophila species, this cluster of UBX binding sites is not. We isolated the knot wing cis-regulatory element from D. pseudoobscura, which contains a cluster of UBX-binding sites that is not homologous to the functionally defined D. melanogaster cluster. It is, however, homologous to a second D. melanogaster region containing a cluster of UBX sites that can also function as a repressor element. Thus, the knot regulatory region in D. melanogaster has two apparently functionally redundant blocks of sequences for repression by UBX, both of which are widely separated from activator sequences. This redundancy suggests that the complete evolutionary unit of regulatory control is larger than the minimal experimentally defined control element. The span of regulatory sequences upon which selection acts may, in general, be more expansive and less modular than functional studies of these elements have previously indicated.

  9. Discovery and characterization of pseudocyclic cystine-knot α-amylase inhibitors with high resistance to heat and proteolytic degradation.

    PubMed

    Nguyen, Phuong Q T; Wang, Shujing; Kumar, Akshita; Yap, Li J; Luu, Thuy T; Lescar, Julien; Tam, James P

    2014-10-01

    Obesity and type 2 diabetes are chronic metabolic diseases, and those affected could benefit from the use of α-amylase inhibitors to manage starch intake. The pseudocyclics, wrightides Wr-AI1 to Wr-AI3, isolated from an Apocynaceae plant show promise for further development as orally active α-amylase inhibitors. These linear peptides retain the stability known for cystine-knot peptides in the presence of harsh treatment. They are resistant to heat treatment and endopeptidase and exopeptidase degradation, which is characteristic of cyclic cystine-knot peptides. Our NMR and crystallography analysis also showed that wrightides, which are currently the smallest proteinaceous α-amylase inhibitors reported, contain the backbone-twisting cis-proline, which is preceded by a nonaromatic residue rather than a conventional aromatic residue. The modeled structure and a molecular dynamics study of Wr-AI1 in complex with yellow mealworm α-amylase suggested that, despite having a similar structure and cystine-knot fold, the knottin-type α-amylase inhibitors may bind to insect α-amylase via a different set of interactions. Finally, we showed that the precursors of pseudocyclic cystine-knot α-amylase inhibitors and their biosynthesis in plants follow a secretory protein synthesis pathway. Together, our findings provide insights for the use of the pseudocyclic α-amylase inhibitors as useful leads for the development of orally active peptidyl bioactives, as well as an alternative scaffold for cyclic peptides for engineering metabolically stable human α-amylase inhibitors.

  10. Root vs pod infection by root-knot nematodes on aflatoxin contamination of peanut.

    PubMed

    Timper, P; Holbrook, C; Wilson, D

    2007-01-01

    Aflatoxins are potent carcinogens produced by some Aspergillus spp. Infection of peanut (Arachis hypogaea) by root-knot nematodes (Meloidogyne arenaria) can lead to an increase in aflatoxin contamination of kernels when the plants are subjected to drought stress during pod maturation. It is not clear whether the increased aflatoxin contamination is primarily due to greater invasion of the galled pods by toxigenic Aspergillus spp. or whether root galling is also involved. Our objective was to determine the contribution of root and pod galling caused by root-knot nematodes to the increase in aflatoxin contamination in peanut. Two greenhouse experiments were conducted in which pods and roots were physically separated. Pod set was restricted to soil-filled pans (41 cm dia. x 10 cm depth), while the roots grew underneath the pan into a pot. The experiments had a factorial arrangement of treatments: pod zone with and without nematodes, and root zone with and without nematodes. In Experiment 1, 5000 eggs of M. arenaria were added to the root zone14 days after planting (DAP) and 8000 eggs were added to the pod zone 60 and 80 DAP. In Experiment 2, 3000 eggs were added to the root zone 30 DAP and 8000 eggs were added to the pod zone every week starting 60 DAP. The four treatment combinations were replicated 10 to 13 times. Conidia of Aspergillus flavus/A. parasiticus was added to the soil surface (pods zone) at mid bloom. Plants were subjected to drought stress 40 days before harvest. In Experiment 1, adding nematodes to the pod zone had no effect on aflatoxin concentrations in the peanut kernel. However, the lack of an effect may have been to due to the low occurrence of galling on the hulls. In pots where nematodes were added to the root zone, 50 to 80% of the root system was galled. Adding nematodes to the root zone increased aflatoxin concentrations in the peanut kernels from 34 ppb in the control to 71 ppb. In Experiment 2, there was heavy pod galling with galls present

  11. Knotting of a nasogastric feeding tube in a child with head injury: A case report and review of literature.

    PubMed

    Ismail, Nasiru J; Bot, Gyang Markus; Hassan, Ismail; Shilong, Danaan J; Obande, Joseph O; Aliu, Salamat Ahuoiza; Dung, Ezekiel D; Shehu, Bello B

    2014-01-01

    Nasogastric intubation is one of the most common routine nonoperative procedures available for the hospital care of patients. The insertion and removal of this tube is associated with many complications. The complications include trauma, nasal septal abscess and inadvertent entry into the cranial cavity and trachea, ulceration, bleeding from varices and perforation. Knotting of the nasogastric tube is one of the very rare complications of nasogastric intubation particularly in children. To the best of our knowledge there are very few reported cases in children. The technique used in the patient was the application of a steady tug which allows the lower oesophageal sphincter to open, therefore enabling the removal of the nasogastric tube. The possible predispositions to knotting of a nasogastric tube include small bore tubes, excess tube length and gastric surgery. We postulate that reduced gastric tone is another possible predisposing factor with head injury being the most likely reason in the index patient. We also challenge the fact that the small sized stomach is a risk factor for knotting of a feeding tube if the functional status and tone are normal, because of the rarity in children.

  12. Reversible arterial redistribution in a fetus with true umbilical cord knot: case report and review of literature.

    PubMed

    Navolan, Dan Bogdan; Sas, Ioan; Grigoraş, Dorin; Moldovan, Mihaela; Cîrlan, Casius; Angheloiu Rîcă, Daiana Elena; Levai, Codrina Mihaela

    2015-01-01

    Umbilical cord knot (UCK) affects around 1% of pregnancies and tightening of UCK is a very rare and highly unpredictable complication of pregnancy that can lead to fetal demise or neonatal death. The majority of authors agree that very little could be done to prevent fetal deaths in pregnancies with undiagnosed tight UCK. We herein report the case of a 39-year-old, gravidity five, parity three, pregnant woman at 40 weeks and five days age of pregnancy, whose pregnancy evolved without complications and who was admitted to hospital for the management of the birth. Although the last ultrasound examination before birth showed a reversible arterial redistribution in the fetus dependent on the postural status of the pregnant women and other factors associated with umbilical cord knot were present, the diagnosis was missed because of the factors' non-specificity. After a spontaneous labor without complications a dead male fetus, weight 3300 g, without heartbeat, Apgar score 0 was delivered. Macroscopic and microscopic findings confirmed that the cause of neonatal death was asphyxia caused by a tight UCK. The aim of our paper is to present the dramatic outcome of a pregnancy with a fetus with a tight umbilical cord knot (UCK), to bring to attention the signs that suggested the diagnosis, and to review the literature on this subject.

  13. Fragmentation follows structure: top-down mass spectrometry elucidates the topology of engineered cystine-knot miniproteins.

    PubMed

    Reinwarth, Michael; Avrutina, Olga; Fabritz, Sebastian; Kolmar, Harald

    2014-01-01

    Over the last decades the field of pharmaceutically relevant peptides has enormously expanded. Among them, several peptide families exist that contain three or more disulfide bonds. In this context, elucidation of the disulfide patterns is extremely important as these motifs are often prerequisites for folding, stability, and activity. An example of this structure-determining pattern is a cystine knot which comprises three constrained disulfide bonds and represents a core element in a vast number of mechanically interlocked peptidic structures possessing different biological activities. Herein, we present our studies on disulfide pattern determination and structure elucidation of cystine-knot miniproteins derived from Momordica cochinchinensis peptide MCoTI-II, which act as potent inhibitors of human matriptase-1. A top-down mass spectrometric analysis of the oxidised and bioactive peptides is described. Following the detailed sequencing of the peptide backbone, interpretation of the MS(3) spectra allowed for the verification of the knotted topology of the examined miniproteins. Moreover, we found that the fragmentation pattern depends on the knottin's folding state, hence, tertiary structure, which to our knowledge has not been described for a top-down MS approach before. PMID:25303319

  14. Heterogeneous side chain conformation highlights a network of interactions implicated in hysteresis of the knotted protein, Minimal Tied Trefoil (MTTTm)

    PubMed Central

    Capraro, Dominique T.; Jennings, Patricia A.

    2015-01-01

    Hysteresis is a signature for a bistability in the native landscape of a protein with significant transition state barriers for the interconversion of stable species. Large global stability, as in GFP, contributes to the observation of this rare hysteretic phenomenon in folding. The signature for such behavior is non-coincidence in the unfolding and refolding transitions, despite waiting significantly longer than the time necessary for complete denaturation. Our work indicates that hysteresis in the knotted protein, the Minimal Tied Trefoil from Thermotoga maritma (MTTTm), is mediated by a network of side chain interactions within a tightly packed core. These initially identified interactions include proline 62 from a tight β-like turn, phenylalanine 65 at the beginning of the knotting loop, and histidine 114 that initiates the threading element. It is this tightly packed region and the knotting element that we propose is disrupted with prolonged incubation in the denatured state, and is involved in the observed hysteresis. Interestingly, the disruption is not linked to backbone interactions, but rather to the packing of side chains in this critical region. PMID:26291198

  15. Fragmentation follows structure: top-down mass spectrometry elucidates the topology of engineered cystine-knot miniproteins.

    PubMed

    Reinwarth, Michael; Avrutina, Olga; Fabritz, Sebastian; Kolmar, Harald

    2014-01-01

    Over the last decades the field of pharmaceutically relevant peptides has enormously expanded. Among them, several peptide families exist that contain three or more disulfide bonds. In this context, elucidation of the disulfide patterns is extremely important as these motifs are often prerequisites for folding, stability, and activity. An example of this structure-determining pattern is a cystine knot which comprises three constrained disulfide bonds and represents a core element in a vast number of mechanically interlocked peptidic structures possessing different biological activities. Herein, we present our studies on disulfide pattern determination and structure elucidation of cystine-knot miniproteins derived from Momordica cochinchinensis peptide MCoTI-II, which act as potent inhibitors of human matriptase-1. A top-down mass spectrometric analysis of the oxidised and bioactive peptides is described. Following the detailed sequencing of the peptide backbone, interpretation of the MS(3) spectra allowed for the verification of the knotted topology of the examined miniproteins. Moreover, we found that the fragmentation pattern depends on the knottin's folding state, hence, tertiary structure, which to our knowledge has not been described for a top-down MS approach before.

  16. Fragmentation Follows Structure: Top-Down Mass Spectrometry Elucidates the Topology of Engineered Cystine-Knot Miniproteins

    PubMed Central

    Reinwarth, Michael; Avrutina, Olga; Fabritz, Sebastian; Kolmar, Harald

    2014-01-01

    Over the last decades the field of pharmaceutically relevant peptides has enormously expanded. Among them, several peptide families exist that contain three or more disulfide bonds. In this context, elucidation of the disulfide patterns is extremely important as these motifs are often prerequisites for folding, stability, and activity. An example of this structure-determining pattern is a cystine knot which comprises three constrained disulfide bonds and represents a core element in a vast number of mechanically interlocked peptidic structures possessing different biological activities. Herein, we present our studies on disulfide pattern determination and structure elucidation of cystine-knot miniproteins derived from Momordica cochinchinensis peptide MCoTI-II, which act as potent inhibitors of human matriptase-1. A top-down mass spectrometric analysis of the oxidised and bioactive peptides is described. Following the detailed sequencing of the peptide backbone, interpretation of the MS3 spectra allowed for the verification of the knotted topology of the examined miniproteins. Moreover, we found that the fragmentation pattern depends on the knottin’s folding state, hence, tertiary structure, which to our knowledge has not been described for a top-down MS approach before. PMID:25303319

  17. Heterogeneous side chain conformation highlights a network of interactions implicated in hysteresis of the knotted protein, minimal tied trefoil

    NASA Astrophysics Data System (ADS)

    Burban, David J.; Haglund, Ellinor; Capraro, Dominique T.; Jennings, Patricia A.

    2015-09-01

    Hysteresis is a signature for a bistability in the native landscape of a protein with significant transition state barriers for the interconversion of stable species. Large global stability, as in GFP, contributes to the observation of this rare hysteretic phenomenon in folding. The signature for such behavior is non-coincidence in the unfolding and refolding transitions, despite waiting significantly longer than the time necessary for complete denaturation. Our work indicates that hysteresis in the knotted protein, the minimal tied trefoil from Thermotoga maritma (MTTTm), is mediated by a network of side chain interactions within a tightly packed core. These initially identified interactions include proline 62 from a tight β-like turn, phenylalanine 65 at the beginning of the knotting loop, and histidine 114 that initiates the threading element. It is this tightly packed region and the knotting element that we propose is disrupted with prolonged incubation in the denatured state, and is involved in the observed hysteresis. Interestingly, the disruption is not linked to backbone interactions, but rather to the packing of side chains in this critical region.

  18. The Knotted Sky II: does BICEP2 require a nontrivial primordial power spectrum?

    SciTech Connect

    Abazajian, Kevork N.; Aslanyan, Grigor; Easther, Richard; Price, Layne C. E-mail: g.aslanyan@auckland.ac.nz E-mail: lpri691@aucklanduni.ac.nz

    2014-08-01

    An inflationary gravitational wave background consistent with BICEP2 is difficult to reconcile with a simple power-law spectrum of primordial scalar perturbations. Tensor modes contribute to the temperature anisotropies at multipoles with l∼< 100, and this effect — together with a prior on the form of the scalar perturbations — was the source of previous bounds on the tensor-to-scalar ratio. We compute Bayesian evidence for combined fits to BICEP2 and Planck for three nontrivial primordial spectra: a) a running spectral index, b) a cutoff at fixed wavenumber, and c) a spectrum described by a linear spline with a single internal knot. We find no evidence for a cutoff, weak evidence for a running index, and significant evidence for a ''broken'' spectrum. Taken at face-value, the BICEP2 results require two new inflationary parameters in order to describe both the broken scale invariance in the perturbation spectrum and the observed tensor-to-scalar ratio. Alternatively, this tension may be resolved by additional data and more detailed analyses.

  19. Poplar-Root Knot Nematode Interaction: A Model for Perennial Woody Species.

    PubMed

    Baldacci-Cresp, Fabien; Sacré, Pierre-Yves; Twyffels, Laure; Mol, Adeline; Vermeersch, Marjorie; Ziemons, Eric; Hubert, Philippe; Pérez-Morga, David; El Jaziri, Mondher; de Almeida Engler, Janice; Baucher, Marie

    2016-07-01

    Plant root-knot nematode (RKN) interaction studies are performed on several host plant models. Though RKN interact with trees, no perennial woody model has been explored so far. Here, we show that poplar (Populus tremula × P. alba) grown in vitro is susceptible to Meloidogyne incognita, allowing this nematode to penetrate, to induce feeding sites, and to successfully complete its life cycle. Quantitative reverse transcription-polymerase chain reaction analysis was performed to study changes in poplar gene expression in galls compared with noninfected roots. Three genes (expansin A, histone 3.1, and asparagine synthase), selected as gall development marker genes, followed, during poplar-nematode interaction, a similar expression pattern to what was described for other plant hosts. Downregulation of four genes implicated in the monolignol biosynthesis pathway was evidenced in galls, suggesting a shift in the phenolic profile within galls developed on poplar roots. Raman microspectroscopy demonstrated that cell walls of giant cells were not lignified but mainly composed of pectin and cellulose. The data presented here suggest that RKN exercise conserved strategies to reproduce and to invade perennial plant species and that poplar is a suitable model host to study specific traits of tree-nematode interactions. PMID:27135257

  20. Effect of Emamectin Benzoate on Root-Knot Nematodes and Tomato Yield

    PubMed Central

    Cheng, Xingkai; Liu, Xiumei; Wang, Hongyan; Ji, Xiaoxue; Wang, Kaiyun; Wei, Min; Qiao, Kang

    2015-01-01

    Southern root-knot nematode (Meloidogyne incognita) is an obligate, sedentary endoparasite of more than 3000 plant species, that causes heavy economic losses and limit the development of protected agriculture of China. As a biological pesticide, emamectin benzoate has effectively prevented lepidopteran pests; however, its efficacy to control M. incognita remains unknown. The purpose of the present study was to test soil application of emamectin benzoate for management of M. incognita in laboratory, greenhouse and field trials. Laboratory results showed that emamectin benzoate exhibited high toxicity to M. incognita, with LC50 and LC90 values 3.59 and 18.20 mg L-1, respectively. In greenhouse tests, emamectin benzoate soil application offered good efficacy against M. incognita while maintaining excellent plant growth. In field trials, emamectin benzoate provided control efficacy against M. incognita and resulted in increased tomato yields. Compared with the untreated control, there was a 36.5% to 81.3% yield increase obtained from all treatments and the highest yield was received from the highest rate of emamectin benzoate. The results confirmed that emamectin benzoate has enormous potential for the control of M. incognita in tomato production in China. PMID:26509680

  1. Resistance to root-knot nematodes Meloidogyne spp. in woody plants.

    PubMed

    Saucet, Simon Bernard; Van Ghelder, Cyril; Abad, Pierre; Duval, Henri; Esmenjaud, Daniel

    2016-07-01

    I. 42 II. 43 III. 44 IV. 47 V. 49 VI. 50 VII. 50 VIII. 50 IX. 52 52 References 52 SUMMARY: Root-knot nematodes (RKNs) Meloidogyne spp. cause major damage to cultivated woody plants. Among them, Prunus, grapevine and coffee are the crops most infested by worldwide polyphagous species and species with a more limited distribution and/or narrower host range. The identification and characterization of natural sources of resistance are important steps to develop RKN control strategies. In woody crops, resistant rootstocks genetically different from the scion of agronomical interest may be engineered. We describe herein the interactions between RKNs and different woody crops, and highlight the plant species in which resistance and corresponding resistance (R) genes have been discovered. Even though grapevine and, to a lesser extent, coffee have a history of rootstock selection for RKN resistance, few cases of resistance have been documented. By contrast, in Prunus, R genes with different spectra have been mapped in plums, peach and almond and can be pyramided for durable resistance in interspecific rootstocks. We particularly discuss here the Ma Toll/interleukin-1 receptor-like-nucleotide binding-leucine-rich repeat gene from Myrobalan plum, one of the longest plant R genes cloned to date, due to its unique biological and structural properties. RKN R genes in Prunus will enable us to carry out molecular studies aimed at improving our knowledge of plant immunity in woody plants. PMID:27128375

  2. Msp40 effector of root-knot nematode manipulates plant immunity to facilitate parasitism

    PubMed Central

    Niu, Junhai; Liu, Pei; Liu, Qian; Chen, Changlong; Guo, Quanxin; Yin, Junmei; Yang, Guangsui; Jian, Heng

    2016-01-01

    Root-knot nematodes (RKNs) are obligate biotrophic parasites that invade plant roots and engage in prolonged and intimate relationships with their hosts. Nematode secretions, some of which have immunosuppressing activity, play essential roles in successful parasitism; however, their mechanisms of action remain largely unknown. Here, we show that the RKN-specific gene MiMsp40, cloned from Meloidogyne incognita, is expressed exclusively in subventral oesophageal gland cells and is strongly upregulated during early parasitic stages. Arabidopsis plants overexpressing MiMsp40 were more susceptible to nematode infection than were wild type plants. Conversely, the host-derived MiMsp40 RNAi suppressed nematode parasitism and/or reproduction. Moreover, overexpression of MiMsp40 in plants suppressed the deposition of callose and the expression of marker genes for bacterial elicitor elf18-triggered immunity. Transient expression of MiMsp40 prevented Bax-triggered defence-related programmed cell death. Co-agroinfiltration assays indicated that MiMsp40 also suppressed macroscopic cell death triggered by MAPK cascades or by the ETI cognate elicitors R3a/Avr3a. Together, these results demonstrate that MiMsp40 is a novel Meloidogyne-specific effector that is injected into plant cells by early parasitic stages of the nematode and that plays a role in suppressing PTI and/or ETI signals to facilitate RKN parasitism. PMID:26797310

  3. Characterization of the Inner Knot of the Crab: The Site of the Gamma-Ray Flares?

    NASA Technical Reports Server (NTRS)

    Weisskopf, M. C.

    2014-01-01

    Subsequent to the detections AGILE and Fermi/LAT of the gamma-ray flares from the Crab Nebula in the fall of 2010, this team has been monitoring the X-Ray emission from the Crab on a regular basis. Initially X-Ray observations took place once per month when viewing constraints allowed. More recently observations with Chandra and HST have taken place four times per year. There have been notable exceptions, e.g. in April of 2011 and March 2013 when we initiated a set of Chandra Target of opportunity observations in conjunction with bright gamma-ray flares. Often Keck observations were obtained. The aim of this program to characterize, in depth, the X-ray, optical, and infrared variations that take place in the nebula, and, by so doing, determine the regions which contribute to the harder X-ray variations and, if possible, determine the precise location within the Nebula of the origin of the gamma-ray flares. As part of this project members of the team have applied Singular Value Decomposition techniques to sequences of images in order to more accurately characterize features and their behavior. The current status of the project will be discussed highlighting studies of the inner knot and possible correlations with the gamma-ray flares.

  4. The Nematicidal Effect of Camellia Seed Cake on Root-Knot Nematode Meloidogyne javanica of Banana

    PubMed Central

    Yang, Xiujuan; Wang, Xuan; Wang, Kang; Su, Lanxi; Li, Hongmei; Li, Rong; Shen, Qirong

    2015-01-01

    Suppression of root-knot nematodes is crucially important for maintaining the worldwide development of the banana industry. Growing concerns about human and environmental safety have led to the withdrawal of commonly used nematicides and soil fumigants, thus motivating the development of alternative nematode management strategies. In this study, Meloidogyne javanica was isolated, and the nematicidal effect of Camellia seed cake on this pest was investigated. The results showed that in dish experiments, Camellia seed cake extracts under low concentration (2 g/L) showed a strong nematicidal effect. After treatment for 72 h, the eggs of M. javanica were gradually dissolved, and the intestine of the juveniles gradually became indistinct. Nematicidal compounds, including saponins identified by HPLC-ESI-MS and 8 types of volatile compounds identified by GC-MS, exhibited effective nematicidal activities, especially 4-methylphenol. The pot experiments demonstrated that the application of Camellia seed cake suppressed M. javanica, and promoted the banana plant growth. This study explored an effective nematicidal agent for application in soil and revealed its potential mechanism of nematode suppression. PMID:25849382

  5. Shape memory thermoplastic polyurethane (TPU)/poly(ε-caprolactone) (PCL) blends as self-knotting sutures.

    PubMed

    Jing, Xin; Mi, Hao-Yang; Huang, Han-Xiong; Turng, Lih-Sheng

    2016-12-01

    Thermally responsive shape memory polymers have promising applications in many fields, especially in biomedical areas. In this study, a simple method was purposed to prepare thermoplastic polyurethane (TPU)/poly(ε-caprolactone) (PCL) blends that possess shape memory attributes. TPU and PCL were melt compounded via a twin-screw extruder and injection molded at various ratios. Multiple test methods were used to characterize their shape memory properties and reveal the underling mechanism. The blends containing 25% TPU and 75% PCL possessed the best shape memory properties as indicated by a 98% shape fixing ratio and 90% shape recovery ratio. This was attributed to the hybrid crystalline and amorphous regions of PCL and TPU. We also found that PCL and TPU had good miscibility and that the PCL domain in TPU25% had higher crystallinity than neat PCL. The crystalline region in TPU25% could deform and maintain its temporary shape when stretched, which contributed to its high shape fixing attribute, while the rubbery TPU region assisted in the recovery of the sample upon heating by releasing the deformation energy stored. Moreover, the TPU25% string prepared could knot itself in a hot water bath, indicating a potential for suture applications. Lastly, the 3T3 fibroblast cells cultured on the TPU/PCL blends showed high viability and active substrate-cell interactions. PMID:27490212

  6. Redirection of auxin flow in Arabidopsis thaliana roots after infection by root-knot nematodes

    PubMed Central

    Kyndt, Tina; Goverse, Aska; Haegeman, Annelies; Warmerdam, Sonja; Wanjau, Cecilia; Jahani, Mona; Engler, Gilbert; de Almeida Engler, Janice; Gheysen, Godelieve

    2016-01-01

    Plant-parasitic root-knot nematodes induce the formation of giant cells within the plant root, and it has been recognized that auxin accumulates in these feeding sites. Here, we studied the role of the auxin transport system governed by AUX1/LAX3 influx proteins and different PIN efflux proteins during feeding site development in Arabidopsis thaliana roots. Data generated via promoter–reporter line and protein localization analyses evoke a model in which auxin is being imported at the basipetal side of the feeding site by the concerted action of the influx proteins AUX1 and LAX3, and the efflux protein PIN3. Mutants in auxin influx proteins AUX1 and LAX3 bear significantly fewer and smaller galls, revealing that auxin import into the feeding sites is needed for their development and expansion. The feeding site development in auxin export (PIN) mutants was only slightly hampered. Expression of some PINs appears to be suppressed in galls, probably to prevent auxin drainage. Nevertheless, a functional PIN4 gene seems to be a prerequisite for proper nematode development and gall expansion, most likely by removing excessive auxin to stabilize the hormone level in the feeding site. Our data also indicate a role of local auxin peaks in nematode attraction towards the root. PMID:27312670

  7. Free-energy calculations for semi-flexible macromolecules: Applications to DNA knotting and looping

    SciTech Connect

    Giovan, Stefan M.; Scharein, Robert G.; Hanke, Andreas; Levene, Stephen D.

    2014-11-07

    We present a method to obtain numerically accurate values of configurational free energies of semiflexible macromolecular systems, based on the technique of thermodynamic integration combined with normal-mode analysis of a reference system subject to harmonic constraints. Compared with previous free-energy calculations that depend on a reference state, our approach introduces two innovations, namely, the use of internal coordinates to constrain the reference states and the ability to freely select these reference states. As a consequence, it is possible to explore systems that undergo substantially larger fluctuations than those considered in previous calculations, including semiflexible biopolymers having arbitrary ratios of contour length L to persistence length P. To validate the method, high accuracy is demonstrated for free energies of prime DNA knots with L/P = 20 and L/P = 40, corresponding to DNA lengths of 3000 and 6000 base pairs, respectively. We then apply the method to study the free-energy landscape for a model of a synaptic nucleoprotein complex containing a pair of looped domains, revealing a bifurcation in the location of optimal synapse (crossover) sites. This transition is relevant to target-site selection by DNA-binding proteins that occupy multiple DNA sites separated by large linear distances along the genome, a problem that arises naturally in gene regulation, DNA recombination, and the action of type-II topoisomerases.

  8. Aliphatic ketones from Ruta chalepensis (Rutaceae) induce paralysis on root knot nematodes.

    PubMed

    Ntalli, Nikoletta G; Manconi, Francesca; Leonti, Marco; Maxia, Andrea; Caboni, Pierluigi

    2011-07-13

    This paper reports on the use of Ruta chalepensis L. extracts as a potential nematicide against root knot nematodes Meloidogyne incognita and Meloidogyne javanica . The essential oil (REO) and methanol extract (RME) of R. chalepensis were tested against second-stage juveniles, with REO inducing paralysis in both species (EC(50/1d) = 77.5 and 107.3 mg/L) and RME being selective for M. incognita (EC(50/1d) = 1001 mg/L). Chemical characterization of extracts was done by means of GC-MS and LC-MS, revealing mainly aliphatic ketones and coumarins, respectively. The first-ranking volatile nematicidal component in terms of individual activity against both species was 2-undecanone (EC(50) = 20.6 and 22.5 mg/L for M. incognita and M. javanica, respectively). This fact together with its high concentration in the most active extract found in this study, namely, REO (2926 mg/kg), categorizes 2-undecanone among the nematicidal principles of R. chalepensis. On the contrary, coumarins rutin and 8-methoxypsoralen were not found to be nematicidal at concentrations of ≤500 mg/L. Interestingly, M. incognita was found more sensitive than M. javanica.

  9. Redirection of auxin flow in Arabidopsis thaliana roots after infection by root-knot nematodes.

    PubMed

    Kyndt, Tina; Goverse, Aska; Haegeman, Annelies; Warmerdam, Sonja; Wanjau, Cecilia; Jahani, Mona; Engler, Gilbert; de Almeida Engler, Janice; Gheysen, Godelieve

    2016-08-01

    Plant-parasitic root-knot nematodes induce the formation of giant cells within the plant root, and it has been recognized that auxin accumulates in these feeding sites. Here, we studied the role of the auxin transport system governed by AUX1/LAX3 influx proteins and different PIN efflux proteins during feeding site development in Arabidopsis thaliana roots. Data generated via promoter-reporter line and protein localization analyses evoke a model in which auxin is being imported at the basipetal side of the feeding site by the concerted action of the influx proteins AUX1 and LAX3, and the efflux protein PIN3. Mutants in auxin influx proteins AUX1 and LAX3 bear significantly fewer and smaller galls, revealing that auxin import into the feeding sites is needed for their development and expansion. The feeding site development in auxin export (PIN) mutants was only slightly hampered. Expression of some PINs appears to be suppressed in galls, probably to prevent auxin drainage. Nevertheless, a functional PIN4 gene seems to be a prerequisite for proper nematode development and gall expansion, most likely by removing excessive auxin to stabilize the hormone level in the feeding site. Our data also indicate a role of local auxin peaks in nematode attraction towards the root. PMID:27312670

  10. Spontaneous knot formation in the peritoneal catheter: a rare cause of ventriculoperitoneal shunt malfunction.

    PubMed

    Charalambides, Constantinos; Sgouros, Spyros

    2012-01-01

    Ventriculoperitoneal shunt malfunction is a relatively common problem encountered in shunted hydrocephalic patients and is attributed most frequently to mechanical obstruction of the ventricular catheter. We present the case of a rare cause of mechanical obstruction of the peritoneal catheter due to the spontaneous formation of a knot just underneath the abdominal wound. This occurred 1 year after shunt implantation and is thought to have been caused by a combination of plastic material memory and bowel peristaltic movements. This case brings for discussion the role of radiographic investigation of the shunt system in children who present with suspected shunt obstruction. Radiographic investigation is warranted in children who have unusual shunt arrangements (e.g., Y-connectors and multiple catheters) in order to exclude disconnections or those who develop shunt problems years after implantation, to exclude material fracture in the neck or migration of any kind. In shunt systems which have been implanted for shorter time periods, the need for radiographs is less apparent. Some surgeons proclaim that when clinical circumstances fall outside the realms of obvious possible proximal obstruction, radiographic evaluation of the shunt system should be considered. PMID:23816925

  11. Poplar-Root Knot Nematode Interaction: A Model for Perennial Woody Species.

    PubMed

    Baldacci-Cresp, Fabien; Sacré, Pierre-Yves; Twyffels, Laure; Mol, Adeline; Vermeersch, Marjorie; Ziemons, Eric; Hubert, Philippe; Pérez-Morga, David; El Jaziri, Mondher; de Almeida Engler, Janice; Baucher, Marie

    2016-07-01

    Plant root-knot nematode (RKN) interaction studies are performed on several host plant models. Though RKN interact with trees, no perennial woody model has been explored so far. Here, we show that poplar (Populus tremula × P. alba) grown in vitro is susceptible to Meloidogyne incognita, allowing this nematode to penetrate, to induce feeding sites, and to successfully complete its life cycle. Quantitative reverse transcription-polymerase chain reaction analysis was performed to study changes in poplar gene expression in galls compared with noninfected roots. Three genes (expansin A, histone 3.1, and asparagine synthase), selected as gall development marker genes, followed, during poplar-nematode interaction, a similar expression pattern to what was described for other plant hosts. Downregulation of four genes implicated in the monolignol biosynthesis pathway was evidenced in galls, suggesting a shift in the phenolic profile within galls developed on poplar roots. Raman microspectroscopy demonstrated that cell walls of giant cells were not lignified but mainly composed of pectin and cellulose. The data presented here suggest that RKN exercise conserved strategies to reproduce and to invade perennial plant species and that poplar is a suitable model host to study specific traits of tree-nematode interactions.

  12. Expression of a Cystatin Transgene in Eggplant Provides Resistance to Root-knot Nematode, Meloidogyne incognita

    PubMed Central

    Papolu, Pradeep K.; Dutta, Tushar K.; Tyagi, Nidhi; Urwin, Peter E.; Lilley, Catherine J.; Rao, Uma

    2016-01-01

    Root-knot nematodes (RKN) cause substantial yield decline in eggplant and sustainable management options to minimize crop damage due to nematodes are still limited. A number of genetic engineering strategies have been developed to disrupt the successful plant–nematode interactions. Among them, delivery of proteinase inhibitors from the plant to perturb nematode development and reproduction is arguably the most effective strategy. In the present study, transgenic eggplant expressing a modified rice cystatin (OC-IΔD86) gene under the control of the root-specific promoter, TUB-1, was generated to evaluate the genetically modified nematode resistance. Five putative transformants were selected through PCR and genomic Southern blot analysis. Expression of the cystatin transgene was confirmed in all the events using western blotting, ELISA and qPCR assay. Upon challenge inoculation, all the transgenic events exhibited a detrimental effect on RKN development and reproduction. The best transgenic line (a single copy event) showed 78.3% inhibition in reproductive success of RKN. Our results suggest that cystatins can play an important role for improving nematode resistance in eggplant and their deployment in gene pyramiding strategies with other proteinase inhibitors could ultimately enhance crop yield. PMID:27516765

  13. Abell 58 - a Planetary Nebula with an ONe-rich knot: a signature of binary interaction? .

    NASA Astrophysics Data System (ADS)

    Lau, H. H. B.; De Marco, O.; Liu, X.-W.

    We have investigated the possibility that binary evolution is involved in the formation of the planetary nebula Abell 58. In particular, we assume a neon nova is responsible for the observed high oxygen and neon abundances of the central hydrogen-deficient knot of the H-deficient planetary nebula Abell 58 and the ejecta from the explosion are mixed with the planetary nebula. We have investigated different scenarios involving mergers and wind accretion and found that the most promising formation scenario involves a primary SAGB star that ends its evolution as an ONe white dwarf with an AGB companion at a moderately close separation. Mass is deposited on the white dwarf through wind accretion. So neon novae could occur just after the secondary AGB companion undergoes its final flash. However, the initial separation has to be fine-tuned. To estimate the frequency of such systems we evolve a population of binary systems and find that that Abell 58-like objects should indeed be rare and the fraction of Abell-58 planetary nebula is on the order of 10-4, or lower, among all planetary nebulae.

  14. (Homo)glutathione Deficiency Impairs Root-knot Nematode Development in Medicago truncatula

    PubMed Central

    Baldacci-Cresp, Fabien; Chang, Christine; Maucourt, Mickaël; Deborde, Catherine; Hopkins, Julie; Lecomte, Philippe; Bernillon, Stéphane; Brouquisse, Renaud; Moing, Annick; Abad, Pierre; Hérouart, Didier; Puppo, Alain; Favery, Bruno; Frendo, Pierre

    2012-01-01

    Root-knot nematodes (RKN) are obligatory plant parasitic worms that establish and maintain an intimate relationship with their host plants. During a compatible interaction, RKN induce the redifferentiation of root cells into multinucleate and hypertrophied giant cells essential for nematode growth and reproduction. These metabolically active feeding cells constitute the exclusive source of nutrients for the nematode. Detailed analysis of glutathione (GSH) and homoglutathione (hGSH) metabolism demonstrated the importance of these compounds for the success of nematode infection in Medicago truncatula. We reported quantification of GSH and hGSH and gene expression analysis showing that (h)GSH metabolism in neoformed gall organs differs from that in uninfected roots. Depletion of (h)GSH content impaired nematode egg mass formation and modified the sex ratio. In addition, gene expression and metabolomic analyses showed a substantial modification of starch and γ-aminobutyrate metabolism and of malate and glucose content in (h)GSH-depleted galls. Interestingly, these modifications did not occur in (h)GSH-depleted roots. These various results suggest that (h)GSH have a key role in the regulation of giant cell metabolism. The discovery of these specific plant regulatory elements could lead to the development of new pest management strategies against nematodes. PMID:22241996

  15. Dynamics and topology of a flexible chain: knots in steady shear flow

    NASA Astrophysics Data System (ADS)

    Slowicka, Agnieszka; Kuei, Steve; Ekiel-Jezewska, Maria; Wajnryb, Eligiusz; Stone, Howard

    2015-11-01

    Dynamics of particles in a water-base liquid is a very important subject of research from the point of view of biological, medical and industrial applications. Motion of microorganisms, biopolymers, proteins or artificial particles immersed in a flowing liquid is complex and such systems have numerous applications but, on the other hand,the dynamics has not been yet very well understood. I our paper we performed numerical simulations of a bead-spring model chain to investigate the dynamics of long and flexible elastic fibers in a steady shear flow. For a class of rather open conformations and different parameters of flexibility, we identify two district conformational modes with different final size, shape, and orientation. Through further analysis we identify slipknots in the chain. We also analyzed evolution of the fibers which initially form ``open'' trefoils for different chain flexibilities and initial orientations with respect to the flow direction. We found examples, which illustrate that the shear flow can unknot a flexible chain and then knot it again; this phenomenon sometimes repeats several times.

  16. Expression of a Cystatin Transgene in Eggplant Provides Resistance to Root-knot Nematode, Meloidogyne incognita.

    PubMed

    Papolu, Pradeep K; Dutta, Tushar K; Tyagi, Nidhi; Urwin, Peter E; Lilley, Catherine J; Rao, Uma

    2016-01-01

    Root-knot nematodes (RKN) cause substantial yield decline in eggplant and sustainable management options to minimize crop damage due to nematodes are still limited. A number of genetic engineering strategies have been developed to disrupt the successful plant-nematode interactions. Among them, delivery of proteinase inhibitors from the plant to perturb nematode development and reproduction is arguably the most effective strategy. In the present study, transgenic eggplant expressing a modified rice cystatin (OC-IΔD86) gene under the control of the root-specific promoter, TUB-1, was generated to evaluate the genetically modified nematode resistance. Five putative transformants were selected through PCR and genomic Southern blot analysis. Expression of the cystatin transgene was confirmed in all the events using western blotting, ELISA and qPCR assay. Upon challenge inoculation, all the transgenic events exhibited a detrimental effect on RKN development and reproduction. The best transgenic line (a single copy event) showed 78.3% inhibition in reproductive success of RKN. Our results suggest that cystatins can play an important role for improving nematode resistance in eggplant and their deployment in gene pyramiding strategies with other proteinase inhibitors could ultimately enhance crop yield. PMID:27516765

  17. Histopathological response of Lens culinaris roots towards root-knot nematode, Meloidogyne incognito.

    PubMed

    Singh, Swarn; Abbasi; Hisamuddin

    2013-04-01

    Lens culinaris (lentil) is an important pulse crop. The yield of the crop is reduced if grown in root-knot nematode (Meloidogyne incognita) infested field. Meloidogyne incognita caused infection in primary and the secondary roots leading to the anomalies in the affected part of the root. The study revealed that the second stage juveniles (J2) of Meloidogyne incognita entered the growing roots and their branches inter and intracellularly. The immediate response was hypertrophy and hyperplasia in the root tissue near the nematode head. In response to hypertrophy some cells became very large and contained dense and granular cytoplasm. Adjacent to the giant cells, the vascular tissue was found to be disturbed. Shape, size and orientation of the vascular elements was so much altered that it had become difficult to trace the normal course of vascular strands. In various sections vascular strands were found disrupted. The vessel elements had the shapes resembling the shapes of parenchyma cells. Similarly sieve tube elements of the phloem, near the giant cells were shorter and resembled with nearby parenchyma cells. Abnormalities in xylem and phloem favored transport water, minerals and metabolites towards the giant cells. From this study, it might be inferred that alteration in the cells of galled tissue was essential for the sustenance of giant cells and for the survival of the nematode.

  18. The conserved KNOX domain mediates specificity of tobacco KNOTTED1-type homeodomain proteins.

    PubMed Central

    Sakamoto, T; Nishimura, A; Tamaoki, M; Kuba, M; Tanaka, H; Iwahori, S; Matsuoka, M

    1999-01-01

    Overproduction of the tobacco KNOTTED1-type homeodomain proteins NTH1, NTH15, and NTH23 in transgenic tobacco plants causes mild, severe, and no morphological alterations, respectively. The deduced amino acid sequences of the homeodomains and adjacent ELK domains are highly conserved, and the N-terminal KNOX domains also are moderately conserved. To investigate the contributions of both the conserved and divergent regions to the severity of morphological alterations, we generated chimeric proteins by exchanging different regions of NTH1, NTH15, and NTH23. The severity of the abnormal phenotype was dependent upon the synergistic action of both the N terminus, containing the KNOX domain, and the C terminus, containing the ELK homeodomain. Detailed analysis focusing on the C terminus revealed that the C-terminal half of the ELK domain is more effective in inducing the abnormal phenotypes than are the homeodomains. For the N terminus, severe morphological alterations were induced by exchanging a part of the KNOX domain of NTH1 with the corresponding region of NTH15. This limited region in the KNOX domain of all homeodomain proteins includes a predicted alpha-helical region, but only that in NTH15 is predicted to form a typical amphipathic structure. We discuss the possibility, based on these results, that the secondary structure of the KNOX domain is important for the induction of abnormal morphology in transgenic tobacco plants. PMID:10449577

  19. Detection of two fungal biocontrol agents against root-knot nematodes by RAPD markers.

    PubMed

    Zhu, Ming Liang; Mo, Ming He; Xia, Zhen Yuan; Li, Yun Hua; Yang, Shu Jun; Li, Tian Fei; Zhang, Ke Qin

    2006-05-01

    The strain ZK7 of Pochonia chlamydosporia var. chlamydosporia and IPC of Paecilomyces lilacinus are highly effective in the biological control against root-knot nematodes infecting tobacco. When applied, they require a specific monitoring method to evaluate the colonization and dispersal in soil. In this work, the randomly amplified polymorphic DNA (RAPD) technique was used to differentiate between the two individual strains and 95 other isolates, including isolates of the same species and common soil fungi. This approach allowed the selection of specific fragments of 1.2 kb (Vc1200) and 2.0 kb (Vc2000) specific for ZK7, 1.4 kb (P1400) and 0.85 kb (P850) specific for IPC, using the random Primers OPL-02, OPD-05, OPD-05 and OPC-11, respectively. These fragments were cloned, sequenced, and used to design sequence-characterized amplification region (SCAR) primers specific for the two strains. In classical polymerase chain reaction (PCR), with serial dilution of ZK7 and IPC pure culture DNAs template, the detection limits of these oligonucleotide SCAR-PCR primers were found to be 10, 1000, 500, 100 pg, respectively. In the dot blotting, digoxigenin (DIG)-labeled amplicons from these four primers specifically recognized the corresponding fragments in the DNAs template of these two strains. The detection limit of these amplicons were 0.2, 0.2, 0.5, 0.5 mug, respectively.

  20. The nematicidal effect of camellia seed cake on root-knot nematode Meloidogyne javanica of banana.

    PubMed

    Yang, Xiujuan; Wang, Xuan; Wang, Kang; Su, Lanxi; Li, Hongmei; Li, Rong; Shen, Qirong

    2015-01-01

    Suppression of root-knot nematodes is crucially important for maintaining the worldwide development of the banana industry. Growing concerns about human and environmental safety have led to the withdrawal of commonly used nematicides and soil fumigants, thus motivating the development of alternative nematode management strategies. In this study, Meloidogyne javanica was isolated, and the nematicidal effect of Camellia seed cake on this pest was investigated. The results showed that in dish experiments, Camellia seed cake extracts under low concentration (2 g/L) showed a strong nematicidal effect. After treatment for 72 h, the eggs of M. javanica were gradually dissolved, and the intestine of the juveniles gradually became indistinct. Nematicidal compounds, including saponins identified by HPLC-ESI-MS and 8 types of volatile compounds identified by GC-MS, exhibited effective nematicidal activities, especially 4-methylphenol. The pot experiments demonstrated that the application of Camellia seed cake suppressed M. javanica, and promoted the banana plant growth. This study explored an effective nematicidal agent for application in soil and revealed its potential mechanism of nematode suppression. PMID:25849382

  1. RNApdbee—a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs

    PubMed Central

    Antczak, Maciej; Zok, Tomasz; Popenda, Mariusz; Lukasiak, Piotr; Adamiak, Ryszard W.; Blazewicz, Jacek; Szachniuk, Marta

    2014-01-01

    In RNA structural biology and bioinformatics an access to correct RNA secondary structure and its proper representation is of crucial importance. This is true especially in the field of secondary and 3D RNA structure prediction. Here, we introduce RNApdbee—a new tool that allows to extract RNA secondary structure from the pdb file, and presents it in both textual and graphical form. RNApdbee supports processing of knotted and unknotted structures of large RNAs, also within protein complexes. The method works not only for first but also for high order pseudoknots, and gives an information about canonical and non-canonical base pairs. A combination of these features is unique among existing applications for RNA structure analysis. Additionally, a function of converting between the text notations, i.e. BPSEQ, CT and extended dot-bracket, is provided. In order to facilitate a more comprehensive study, the webserver integrates the functionality of RNAView, MC-Annotate and 3DNA/DSSR, being the most common tools used for automated identification and classification of RNA base pairs. RNApdbee is implemented as a publicly available webserver with an intuitive interface and can be freely accessed at http://rnapdbee.cs.put.poznan.pl/. PMID:24771339

  2. Computing with quantum knots: Marjorana modes, non-Abelian anyons, and topological quantum computation

    SciTech Connect

    Das Sarma, Sankar

    2012-10-03

    I will discuss the revolutionary new concept of topological quantum computation, which is fault-tolerant at the hardware level with no need, in principle, of any quantum error correction protocols. Errors simply do not occur since the physical qubits and the computation steps are protected against decoherence by non-local topological correlations in the underlying physical system. The key idea is non-Abelian statistics of the quasiparticles (called 'anyons' as opposed to fermions or bosons), where the space-time braiding of the anyons around each other, i.e. quantum 'knots', form topologically protected quantum gate operations. I will describe in detail the theoretical principles guiding the experimental search for the appropriate topological phases of matter where such non-Abelian anyons, which are low-dimensional solid state versions of the elusive and exotic Majorana fermions hypothesized seventy-five years ago, may exist. I will critically discuss the recent experimental claims of observing the Majorana modes in semiconductor nanowire structures following earlier theoretical proposals, outlining the future developments which would be necessary to eventually build a topological quantum computer.

  3. A prospective randomized trial comparing the harmonic scalpel with conventional knot tying in thyroidectomy.

    PubMed

    Kilic, Mehmet; Keskek, Mehmet; Ertan, Tamer; Yoldas, Omer; Bilgin, Aydin; Koc, Mahmut

    2007-01-01

    Currently, thyroidectomies are performed with very little morbidity. This study was undertaken to investigate whether the use of the harmonic scalpel during thyroid surgery has any advantage over the conventional technique. Eighty patients were randomly assigned to 2 groups. The patients in group 1 (n=40) underwent thyroidectomy performed with conventional knot tying and the electrocautery technique; in patients in group 2 (n=40), the harmonic scalpel was used for the procedure. Significant differences were observed between these 2 surgical techniques in terms of operative time, number of ligatures used, amount of bleeding, average length of incision, total amount of drainage fluid, and cosmetic satisfaction (P<.05). With the harmonic scalpel technique, there was a nearly 18% reduction in operative time. No significant differences were noted between mean hospital stay and postoperative pain (P>.05). No patient in either group had permanent recurrent laryngeal nerve palsy or hypoparathyroidism. The harmonic scalpel significantly shortens the duration of thyroidectomies; it can be used safely and effectively in thyroid surgery with no additional morbidity.

  4. Brassinosteroids suppress rice defense against root-knot nematodes through antagonism with the jasmonate pathway.

    PubMed

    Nahar, Kamrun; Kyndt, Tina; Hause, Bettina; Höfte, Monica; Gheysen, Godelieve

    2013-01-01

    The importance of phytohormone balance is increasingly recognized as central to the outcome of plant-pathogen interactions. Next to their well-known developmental role, brassinosteroids (BR) were recently found to be involved in plant innate immunity. In this study, we examined the role of BR in rice (Oryza sativa) innate immunity during infection with the root-knot nematode Meloidogyne graminicola, and we studied the inter-relationship with the jasmonate (JA) pathway. Exogenous epibrassinolide (BL) supply at low concentrations induced susceptibility in the roots whereas high concentrations of BL enforced systemic defense against this nematode. Upon high exogenous BL supply on the shoot, quantitative reverse-transcription polymerase chain reaction (qRT-PCR) confirmed a strong feedback inhibitory effect, leading to reduced BR biosynthesis in the root. Moreover, we demonstrate that the immune suppressive effect of BR is at least partly due to negative cross-talk with the JA pathway. Mutants in the BR biosynthesis or signaling pathway accumulate slightly higher levels of the immediate JA-precursor 12-oxo-phytodienoic acid, and qRT-PCR data showed that the BR and JA pathway are mutually antagonistic in rice roots. Collectively, these results suggest that the balance between the BR and JA pathway is an effective regulator of the outcome of the rice-M. graminicola interaction.

  5. Comparative analysis of the folding dynamics and kinetics of an engineered knotted protein and its variants derived from HP0242 of Helicobacter pylori

    NASA Astrophysics Data System (ADS)

    Wang, Liang-Wei; Liu, Yu-Nan; Lyu, Ping-Chiang; Jackson, Sophie E.; Hsu, Shang-Te Danny

    2015-09-01

    Understanding the mechanism by which a polypeptide chain thread itself spontaneously to attain a knotted conformation has been a major challenge in the field of protein folding. HP0242 is a homodimeric protein from Helicobacter pylori with intertwined helices to form a unique pseudo-knotted folding topology. A tandem HP0242 repeat has been constructed to become the first engineered trefoil-knotted protein. Its small size renders it a model system for computational analyses to examine its folding and knotting pathways. Here we report a multi-parametric study on the folding stability and kinetics of a library of HP0242 variants, including the trefoil-knotted tandem HP0242 repeat, using far-UV circular dichroism and fluorescence spectroscopy. Equilibrium chemical denaturation of HP0242 variants shows the presence of highly populated dimeric and structurally heterogeneous folding intermediates. Such equilibrium folding intermediates retain significant amount of helical structures except those at the N- and C-terminal regions in the native structure. Stopped-flow fluorescence measurements of HP0242 variants show that spontaneous refolding into knotted structures can be achieved within seconds, which is several orders of magnitude faster than previously observed for other knotted proteins. Nevertheless, the complex chevron plots indicate that HP0242 variants are prone to misfold into kinetic traps, leading to severely rolled-over refolding arms. The experimental observations are in general agreement with the previously reported molecular dynamics simulations. Based on our results, kinetic folding pathways are proposed to qualitatively describe the complex folding processes of HP0242 variants.

  6. A knot in the protein structure - probing the near-infrared fluorescent protein iRFP designed from a bacterial phytochrome.

    PubMed

    Stepanenko, Olesya V; Bublikov, Grigory S; Stepanenko, Olga V; Shcherbakova, Daria M; Verkhusha, Vladislav V; Turoverov, Konstantin K; Kuznetsova, Irina M

    2014-05-01

    The possibility of engineering near-infrared fluorescent proteins and biosensors from bacterial phytochrome photoreceptors (BphPs) has led to substantial interest in this family of proteins. The near-infrared fluorescent proteins have allowed non-invasive bio-imaging of deep tissues and whole organs in living animals. BphPs and derived near-infrared fluorescent proteins contain a structural element, called a knot, in their polypeptide chains. The formation of knot structures in proteins was refuted for a long time. Here, we studied the denaturation and renaturation processes of the near-infrared fluorescent probe iRFP, engineered from RpBphP2, which utilizes a heme-derived tetrapyrrole compound biliverdin as a chromophore. iRFP contains a unique figure-of-eight knot. The denaturation and renaturation curves of the iRFP apoform coincided well, suggesting efficient refolding. However, the iRFP holoform exhibited irreversible unfolding and aggregation associated with the bound chromophore. The knot structure in the apoform did not prevent subsequent binding of biliverdin, resulting in the functional iRFP holoform. We suggest that the irreversibility of protein unfolding is caused by post-translational protein modifications, such as chromophore binding, rather than the presence of the knot. These results are essential for future design of BphP-based near-infrared probes, and add important features to our knowledge of protein folding.

  7. Resistance to Southern Root-knot Nematode (Meloidogyne incognita) in Wild Watermelon (Citrullus lanatus var. citroides)

    PubMed Central

    Thies, Judy A.; Ariss, Jennifer J.; Kousik, Chandrasekar S.; Hassell, Richard L.; Levi, Amnon

    2016-01-01

    Southern root-knot nematode (RKN, Meloidogyne incognita) is a serious pest of cultivated watermelon (Citrullus lanatus var. lanatus) in southern regions of the United States and no resistance is known to exist in commercial watermelon cultivars. Wild watermelon relatives (Citrullus lanatus var. citroides) have been shown in greenhouse studies to possess varying degrees of resistance to RKN species. Experiments were conducted over 2 yr to assess resistance of southern RKN in C. lanatus var. citroides accessions from the U.S. Watermelon Plant Introduction Collection in an artificially infested field site at the U.S. Vegetable Laboratory in Charleston, SC. In the first study (2006), 19 accessions of C. lanatus var. citroides were compared with reference entries of Citrullus colocynthis and C. lanatus var. lanatus. Of the wild watermelon accessions, two entries exhibited significantly less galling than all other entries. Five of the best performing C. lanatus var. citroides accessions were evaluated with and without nematicide at the same field site in 2007. Citrullus lanatus var. citroides accessions performed better than C. lanatus var. lanatus and C. colocynthis. Overall, most entries of C. lanatus var. citroides performed similarly with and without nematicide treatment in regard to root galling, visible egg masses, vine vigor, and root mass. In both years of field evaluations, most C. lanatus var. citroides accessions showed lesser degrees of nematode reproduction and higher vigor and root mass than C. colocynthis and C. lanatus var. lanatus. The results of these two field evaluations suggest that wild watermelon populations may be useful sources of resistance to southern RKN. PMID:27168648

  8. Functional evolution of scorpion venom peptides with an inhibitor cystine knot fold.

    PubMed

    Gao, Bin; Harvey, Peta J; Craik, David J; Ronjat, Michel; De Waard, Michel; Zhu, Shunyi

    2013-06-27

    The ICK (inhibitor cystine knot) defines a large superfamily of polypeptides with high structural stability and functional diversity. Here, we describe a new scorpion venom-derived K+ channel toxin (named λ-MeuKTx-1) with an ICK fold through gene cloning, chemical synthesis, nuclear magnetic resonance spectroscopy, Ca2+ release measurements and electrophysiological recordings. λ-MeuKTx-1 was found to adopt an ICK fold that contains a three-strand anti-parallel β-sheet and a 310-helix. Functionally, this peptide selectively inhibits the Drosophila Shaker K+ channel but is not capable of activating skeletal-type Ca2+ release channels/ryanodine receptors, which is remarkably different from the previously known scorpion venom ICK peptides. The removal of two C-terminal residues of λ-MeuKTx-1 led to the loss of the inhibitory activity on the channel, whereas the C-terminal amidation resulted in the emergence of activity on four mammalian K+ channels accompanied by the loss of activity on the Shaker channel. A combination of structural and pharmacological data allows the recognition of three putative functional sites involved in channel blockade of λ-MeuKTx-1. The presence of a functional dyad in λ-MeuKTx-1 supports functional convergence among scorpion venom peptides with different folds. Furthermore, similarities in precursor organization, exon-intron structure, 3D-fold and function suggest that scorpion venom ICK-type K+ channel inhibitors and Ca2+ release channel activators share a common ancestor and their divergence occurs after speciation between buthidae and non-buthids. The structural and functional characterizations of the first scorpion venom ICK toxin with K+ channel-blocking activity sheds light on functionally divergent and convergent evolution of this conserved scaffold of ancient origin.

  9. Ileo-sigmoid knotting: a review of 61 cases in Kenya

    PubMed Central

    Ooko, Philip Blasto; Saruni, Seno; Oloo, Mark; Topazian, Hillary Mariko; White, Russell

    2016-01-01

    Introduction Ileo-sigmoid knotting (ISK) is a rare cause of bowel obstruction in which the ileum twists around the sigmoid colon. It is associated with rapid bowel gangrene and a high mortality rate. Little has been published about this condition in Kenya. The objective was to determine the presentation, management, and outcome of patients with ISK. Methods A seven year (January 2008-December 2014) retrospective chart review of patients managed for ISK at Tenwek Hospital in Bomet, Kenya. Results A total of 61 cases were identified, with a mean age of 35.8 years (range 2-68), and mean symptom duration of 1.6 days (range 3 hours-7 days). Gangrene was noted to involve both the ileum and colon in 45 patients, the ileum only in 9 patients, and the sigmoid colon only in one. Resection and primary anastomosis was carried out in most cases of gangrenous ileum (48/54, 89%) and gangrenous sigmoid colon (34/46, 74%), while resection and stoma was performed in 8 patients with gangrenous colon. Death occurred in 7 (11.5%) patients due to severe sepsis and multisystem organ failure. Morbidities were noted in 15 (24.6%) patients, including surgical site infection (8, 13.1%), respiratory insufficiency (4, 6.6%), fascial dehiscence (3, 4.9%) and anastomotic leak (2, 3.2%). The mean duration of hospitalization was 8.3 days (range 1-26). Conclusion In this review, though retrospective in nature, ISK was noted to have high rates of bowel gangrene. In the appropriate setting, resection and primary anastomosis can be safely carried out in most cases of gangrenous colon. PMID:27347287

  10. Where the endoplasmic reticulum and the mitochondrion tie the knot: the mitochondria-associated membrane (MAM).

    PubMed

    Raturi, Arun; Simmen, Thomas

    2013-01-01

    More than a billion years ago, bacterial precursors of mitochondria became endosymbionts in what we call eukaryotic cells today. The true significance of the word "endosymbiont" has only become clear to cell biologists with the discovery that the endoplasmic reticulum (ER) superorganelle dedicates a special domain for the metabolic interaction with mitochondria. This domain, identified in all eukaryotic cell systems from yeast to man and called the mitochondria-associated membrane (MAM), has a distinct proteome, specific tethers on the cytosolic face and regulatory proteins in the ER lumen of the ER. The MAM has distinct biochemical properties and appears as ER tubules closely apposed to mitochondria on electron micrographs. The functions of the MAM range from lipid metabolism and calcium signaling to inflammasome formation. Consistent with these functions, the MAM is enriched in lipid metabolism enzymes and calcium handling proteins. During cellular stress situations, like an altered cellular redox state, the MAM alters its set of regulatory proteins and thus alters MAM functions. Notably, this set prominently comprises ER chaperones and oxidoreductases that connect protein synthesis and folding inside the ER to mitochondrial metabolism. Moreover, ER membranes associated with mitochondria also accommodate parts of the machinery that determines mitochondrial membrane dynamics and connect mitochondria to the cytoskeleton. Together, these exciting findings demonstrate that the physiological interactions between the ER and mitochondria are so bilateral that we are tempted to compare their relationship to the one of a married couple: distinct, but inseparable and certainly dependent on each other. In this paradigm, the MAM stands for the intracellular location where the two organelles tie the knot. Resembling "real life", the happy marriage between the two organelles prevents the onset of diseases that are characterized by disrupted metabolism and decreased lifespan

  11. Jet-intracluster medium interaction in Hydra A - I. Estimates of jet velocity from inner knots

    NASA Astrophysics Data System (ADS)

    Nawaz, M. A.; Wagner, A. Y.; Bicknell, G. V.; Sutherland, R. S.; McNamara, B. R.

    2014-10-01

    We present the first stage of an investigation of the interactions of the jets in the radio galaxy Hydra A with the intracluster medium. We consider the jet kinetic power, the galaxy and cluster atmosphere and the inner structure of the radio source. Analysing radio observations of the inner lobes of Hydra A by Taylor et al. we confirm the jet power estimates ˜1045 erg s-1 derived by Wise et al. from dynamical analysis of the X-ray cavities. With this result and a model for the galaxy halo, we explore the jet-intracluster medium interactions occurring on a scale of 10 kpc using two-dimensional, axisymmetric, relativistic pure hydrodynamic simulations. A key feature is that we identify the three bright knots in the northern jet as biconical reconfinement shocks, which result when an overpressured jet starts to come into equilibrium with the galactic atmosphere. Through an extensive parameter space study we deduce that the jet velocity is approximately 0.8c at a distance 0.5 kpc from the black hole. The combined constraints of jet power, the observed jet radius profile along the jet and the estimated jet pressure and jet velocity imply a value of the jet density parameter χ ≈ 13 for the northern jet. We show that for a jet β = 0.8 and θ = 42°, an intrinsic asymmetry in the emissivity of the northern and southern jet is required for a consistent brightness ratio ≈7 estimated from the 6-cm Very Large Array image of Hydra A.

  12. Resistance to Southern Root-knot Nematode (Meloidogyne incognita) in Wild Watermelon (Citrullus lanatus var. citroides).

    PubMed

    Thies, Judy A; Ariss, Jennifer J; Kousik, Chandrasekar S; Hassell, Richard L; Levi, Amnon

    2016-03-01

    Southern root-knot nematode (RKN, Meloidogyne incognita) is a serious pest of cultivated watermelon (Citrullus lanatus var. lanatus) in southern regions of the United States and no resistance is known to exist in commercial watermelon cultivars. Wild watermelon relatives (Citrullus lanatus var. citroides) have been shown in greenhouse studies to possess varying degrees of resistance to RKN species. Experiments were conducted over 2 yr to assess resistance of southern RKN in C. lanatus var. citroides accessions from the U.S. Watermelon Plant Introduction Collection in an artificially infested field site at the U.S. Vegetable Laboratory in Charleston, SC. In the first study (2006), 19 accessions of C. lanatus var. citroides were compared with reference entries of Citrullus colocynthis and C. lanatus var. lanatus. Of the wild watermelon accessions, two entries exhibited significantly less galling than all other entries. Five of the best performing C. lanatus var. citroides accessions were evaluated with and without nematicide at the same field site in 2007. Citrullus lanatus var. citroides accessions performed better than C. lanatus var. lanatus and C. colocynthis. Overall, most entries of C. lanatus var. citroides performed similarly with and without nematicide treatment in regard to root galling, visible egg masses, vine vigor, and root mass. In both years of field evaluations, most C. lanatus var. citroides accessions showed lesser degrees of nematode reproduction and higher vigor and root mass than C. colocynthis and C. lanatus var. lanatus. The results of these two field evaluations suggest that wild watermelon populations may be useful sources of resistance to southern RKN.

  13. Shocks and star formation in Stephan's Quintet. I. Gemini spectroscopy of Hα-bright knots

    SciTech Connect

    Konstantopoulos, I. S.; Cluver, M. E.; Appleton, P. N.; Guillard, P.; Trancho, G.; Bastian, N.; Charlton, J. C.; Fedotov, K.; Gallagher, S. C.; Smith, L. J.; Struck, C. J.

    2014-03-20

    We present a Gemini-GMOS spectroscopic study of Hubble Space Telescope (HST)-selected Hα-emitting regions in Stephan's Quintet (HCG 92), a nearby compact galaxy group, with the aim of disentangling the processes of shock-induced heating and star formation in its intra-group medium. The ≈40 sources are distributed across the system, but most densely concentrated in the ∼kiloparsec-long shock region. Their spectra neatly divide them into narrow- and broad-line emitters, and we decompose the latter into three or more emission peaks corresponding to spatial elements discernible in HST imaging. The emission-line ratios of the two populations of Hα-emitters confirm their nature as H II regions (90% of the sample) or molecular gas heated by a shock front propagating at ≲300 km s{sup –1}. Their redshift distribution reveals interesting three-dimensional structure with respect to gas-phase baryons, with no H II regions associated with shocked gas, no shocked regions in the intruder galaxy NGC 7318B, and a sharp boundary between shocks and star formation. We conclude that star formation is inhibited substantially, if not entirely, in the shock region. Attributing those H II regions projected against the shock to the intruder, we find a lopsided distribution of star formation in this galaxy, reminiscent of pileup regions in models of interacting galaxies. The Hα luminosities imply mass outputs, star formation rates, and efficiencies similar to nearby star-forming regions. Two large knots are an exception to this, being comparable in stellar output to the prolific 30 Doradus region. We also examine Stephan's Quintet in the context of compact galaxy group evolution, as a paradigm for intermittent star formation histories in the presence of a rich, X-ray-emitting intra-group medium. All spectra are provided as supplemental materials.

  14. Enhancement of the Forbidden Line in the Southwestern Knot of the Cygnus Loop

    NASA Astrophysics Data System (ADS)

    Uchida, Hiroyuki; Tanaka, Takaaki; Katsuda, Satoru; Mori, Koji; Koyama, Katsuji; Tsunemi, Hiroshi

    We observed the southwestern knot (SW-K) of the Cygnus Loop supernova remnant with XMM-Newton RGS. The SW-K is one of the brightest and the most compact region in this remnant. The high energy resolution of RGS enables us to resolve details of the line complex of SW-K below ˜1 keV. We particularly focus on the OVII triplet in which the forbidden line is significantly enhanced relative to the resonance line. The measured forbidden-to-resonance line ratio is 1.75±0.13 which can not be explained by standard thermal plasma models such as collisional ionization equilibrium or ionizing plasmas. Recently, our comprehensive study of the Cygnus Loop with Suzaku XIS has found a possible sign of charge exchange (CX) from some points of its rim; their spectra always show a strong excess at ˜0.7 keV whose origin is likely a complex of cascade lines of He-like Oxygen (Kgamma+delta+epsilon). Since the SW-K is one of these regions, the RGS spectrum provides a conclusive information about the presence of the CX emission. It will also resolve a problem of the abundance inhomogeneity which is extensively seen in the Cygnus Loop and more importantly, will give us direct evidence for an interaction between ambient neutrals and ionized materials existing behind the shock. In this talk, we will also discuss other important possibilities such as the recombination or the resonance scattering for the SW-K spectrum. The RGS observation will cast a new light on the X-ray studies of shock-cloud interactions in SNRs ahead of the ASTRO-H era.

  15. Response of five lettuce cultivars to root-knot nematode, Meloidogyne incognita.

    PubMed

    Pedroche, Nordalyn B; Villanueva, Luciana M; De Dirk, Waele

    2007-01-01

    The root-knot nematode, Meloidogyne incognito (Kofoid et White) Chitwood is an important pathogen of vegetables. Five commercial cultivars of lettuce (Lactuca sativa L.) were evaluated under greenhouse conditions for resistance to Meloidogyne incognita, Benguet population. Plants were inoculated with 1000 eggs collected from 'Apollo' tomato (Lycopersicon esculentum) roots. The degree of galling and number of egg masses were assessed 4 and 8 weeks after inoculation. Host plant response was classified as immune, highly resistant, resistant, moderately resistant, intermediate, moderately susceptible, and highly susceptible based on the resistance index of Kouamè et at., 1998 [RI = (gall2 + egg2)]. Inoculation of 1000 eggs/plant significantly affected the growth and yield of the five lettuce cultivars 4 and 8 weeks after inoculation. A significant interaction was observed between treatment and cultivar during the two evaluation periods in terms of marketable and non-marketable yield, plant height, root weight, number of galls and number of egg masses. A reduction in growth and yield was observed in the cultivars Ballon, Lollo Rosa and Red Wave. Significant differences were noted in the number of galls and egg masses among the different cultivars tested. The highest average number of galls was obtained from the cultivars Red Wave, Ballon and Lollo Rosa. Cultivar Ballon had the highest average number of recovered nematode while Gilaben had the lowest with 15 and 4 per roots, respectively after 4 weeks inoculation. After 8 weeks, nematode was highest in cultivar Red Wave (615) and lowest in Great Lakes (70). Based on the host response, cultivars Great Lakes and Gilaben were rated highly resistant and resistant, respectively, while Red Wave, Ballon and Lollo Rosa were rated intermediate. PMID:18399501

  16. Resistance to Southern Root-knot Nematode (Meloidogyne incognita) in Wild Watermelon (Citrullus lanatus var. citroides).

    PubMed

    Thies, Judy A; Ariss, Jennifer J; Kousik, Chandrasekar S; Hassell, Richard L; Levi, Amnon

    2016-03-01

    Southern root-knot nematode (RKN, Meloidogyne incognita) is a serious pest of cultivated watermelon (Citrullus lanatus var. lanatus) in southern regions of the United States and no resistance is known to exist in commercial watermelon cultivars. Wild watermelon relatives (Citrullus lanatus var. citroides) have been shown in greenhouse studies to possess varying degrees of resistance to RKN species. Experiments were conducted over 2 yr to assess resistance of southern RKN in C. lanatus var. citroides accessions from the U.S. Watermelon Plant Introduction Collection in an artificially infested field site at the U.S. Vegetable Laboratory in Charleston, SC. In the first study (2006), 19 accessions of C. lanatus var. citroides were compared with reference entries of Citrullus colocynthis and C. lanatus var. lanatus. Of the wild watermelon accessions, two entries exhibited significantly less galling than all other entries. Five of the best performing C. lanatus var. citroides accessions were evaluated with and without nematicide at the same field site in 2007. Citrullus lanatus var. citroides accessions performed better than C. lanatus var. lanatus and C. colocynthis. Overall, most entries of C. lanatus var. citroides performed similarly with and without nematicide treatment in regard to root galling, visible egg masses, vine vigor, and root mass. In both years of field evaluations, most C. lanatus var. citroides accessions showed lesser degrees of nematode reproduction and higher vigor and root mass than C. colocynthis and C. lanatus var. lanatus. The results of these two field evaluations suggest that wild watermelon populations may be useful sources of resistance to southern RKN. PMID:27168648

  17. Ventriculoperitoneal shunt with a rare twist: small-bowel ischemia and necrosis secondary to knotting of peritoneal catheter.

    PubMed

    Tan, Lee A; Kasliwal, Manish K; Moftakhar, Roham; Munoz, Lorenzo F

    2014-09-01

    Small-bowel ischemia and necrosis due to knotting of the peritoneal catheter is an extremely rare complication related to a ventriculoperitoneal shunt (VPS). A 3-month-old girl, with a history of Chiari II malformation and myelomeningocele (MM) after undergoing right occipital VPS insertion and MM repair at birth, presented to the emergency department with a high-grade fever. Examination of a CSF sample obtained via shunt tap raised suspicion for the presence of infection. Antibiotic therapy was initiated, and subsequently the VPS was removed and an external ventricular drain was placed. Intraoperatively, as attempts at pulling the distal catheter from the scalp incision were met with resistance, the distal catheter was cut and left in the abdomen while the remainder of the shunt system was successfully removed. While the patient was awaiting definitive shunt revision surgery to replace the VPS, she developed abdominal distension due to small-bowel obstruction. An emergency exploratory laparotomy revealed a knot in the distal catheter looping around and strangulating the distal ileum, causing small-bowel ischemia and necrosis in addition to the obstruction. A small-bowel resection with ileostomy was performed, with subsequent placement of ventriculoatrial shunt for treatment of hydrocephalus. The authors report this exceedingly rare clinical scenario to highlight the fact that any retained distal catheter must be carefully managed with immediate abdominal exploration to remove the distal catheter to avoid bowel necrosis as pulling of a knotted peritoneal catheter may strangulate the bowel and cause ischemia, with significant clinical morbidity and possible mortality.

  18. High yield production and refolding of the double-knot toxin, an activator of TRPV1 channels.

    PubMed

    Bae, Chanhyung; Kalia, Jeet; Song, Inhye; Yu, JeongHeon; Kim, Ha Hyung; Swartz, Kenton J; Kim, Jae Il

    2012-01-01

    A unique peptide toxin, named double-knot toxin (DkTx), was recently purified from the venom of the tarantula Ornithoctonus huwena and was found to stably activate TRPV1 channels by targeting the outer pore domain. DkTx has been shown to consist of two inhibitory cysteine-knot (ICK) motifs, referred to as K1 and K2, each containing six cysteine residues. Beyond this initial characterization, however, the structural and functional details about DkTx remains elusive in large part due to the lack of a high yielding methodology for the synthesis and folding of this cysteine-rich peptide. Here, we overcome this obstacle by generating pure DkTx in quantities sufficient for structural and functional analyses. Our methodology entails expression of DkTx in E. coli followed by oxidative folding of the isolated linear peptide. Upon screening of various oxidative conditions for optimizing the folding yield of the toxin, we observed that detergents were required for efficient folding of the linear peptide. Our synthetic DkTx co-eluted with the native toxin on HPLC, and irreversibly activated TRPV1 in a manner identical to native DkTx. Interestingly, we find that DkTx has two interconvertible conformations present in a 1∶6 ratio at equilibrium. Kinetic analysis of DkTx folding suggests that the K1 and K2 domains influence each other during the folding process. Moreover, the CD spectra of the toxins shows that the secondary structures of K1 and K2 remains intact even after separating the two knots. These findings provide a starting point for detailed studies on the structural and functional characterization of DkTx and utilization of this toxin as a tool to explore the elusive mechanisms underlying the polymodal gating of TRPV1. PMID:23240036

  19. How salinity and temperature combine to affect physiological state and performance in red knots with contrasting non-breeding environments.

    PubMed

    Gutiérrez, Jorge S; Soriano-Redondo, Andrea; Dekinga, Anne; Villegas, Auxiliadora; Masero, José A; Piersma, Theunis

    2015-08-01

    Migratory shorebirds inhabit environments that may yield contrasting salinity-temperature regimes-with widely varying osmoregulatory demands, even within a given species-and the question is: by which physiological means and at which organisational level do they show adjustments with respect to these demands? Red knots Calidris canutus winter in coastal areas over a range of latitudes. The nominal subspecies winters in salty areas in the tropics, whereas the subspecies Calidris canutus islandica winters in north-temperate regions of comparatively lower salinities and temperatures. In this study, both subspecies of red knot were acclimated to different salinity (28/40‰)-temperature (5/35 °C) combinations for 2-week periods. We then measured food/salt intakes, basal metabolic rate (BMR), body mass and temperature, fat and salt gland scores, gizzard mass, heat-shock proteins, heterophils/lymphocytes (H/L) ratio and plasma Na(+) to assess the responses of each taxon to osmoregulatory challenges. High salinity (HS)-warm-acclimated birds reduced food/salt intake, BMR, body mass, fat score and gizzard mass, showing that salt/heat loads constrained energy acquisition rates. Higher salt gland scores in saltier treatments indicated that its size was adjusted to higher osmoregulatory demands. Elevated plasma Na(+) and H/L ratio in high-salinity-warm-acclimated birds indicated that salt/heat loads might have a direct effect on the water-salt balance and stress responses of red knots. Subspecies had little or no effect on most measured parameters, suggesting that most adjustments reflect phenotypic flexibility rather than subspecific adaptations. Our results demonstrate how salinity and temperature affect various phenotypic traits in a migrant shorebird, highlighting the importance of considering these factors jointly when evaluating the environmental tolerances of air-breathing marine taxa. PMID:25851406

  20. The Combined “Double Pulley”–Simple Knot Technique for Arthroscopic Shoulder Posterior Labral Repair and Capsular Shift

    PubMed Central

    Parnes, Nata; Carey, Paul; Morman, Monica; Carr, Brian

    2016-01-01

    Posterior shoulder instability is more prevalent than traditionally believed. Surgical repairs of posterior shoulder instability have overall good success rates. However, in elite overhead and throwing athletes, a low rate of return to the preinjury level of play after repair remains a challenge. The 2 goals of posterior shoulder stabilization surgery are secure fixation of the labrum to the glenoid and retensioning of the posterior capsulolabral complex. Recent studies have shown significant advantages of arthroscopic anatomic repair over open nonanatomic techniques. We report a combined double pulley–simple knot technique for arthroscopic fixation of posterior labral tears and capsular shift. The technique incorporates several advantages of this hybrid fixation method. PMID:27069863

  1. Hopf-Ranãda linked and knotted light beam solution viewed as a null electromagnetic field.

    PubMed

    Besieris, Ioannis M; Shaarawi, Amr M

    2009-12-15

    The Hopf-Ranãda linked and knotted light beam solution, which has been interpreted physically and extended analytically by Irvine and Bouwmeester recently, is viewed in this Letter as a null electromagnetic field. It is shown, in particular, that the Hopf-Ranãda solution is a variant of a luminal null electromagnetic wave due originally to Robinson and Troutman and reported by Bialynicki-Birula recently. This analogy is motivated by means of a method due to Whittaker and Bateman, and a relationship to well-known scalar luminal localized waves is examined. PMID:20016647

  2. Initial description of primate-specific cystine-knot Prometheus genes and differential gene expansions of D-dopachrome tautomerase genes.

    PubMed

    Premzl, Marko

    2015-06-01

    Using eutherian comparative genomic analysis protocol and public genomic sequence data sets, the present work attempted to update and revise two gene data sets. The most comprehensive third party annotation gene data sets of eutherian adenohypophysis cystine-knot genes (128 complete coding sequences), and d-dopachrome tautomerases and macrophage migration inhibitory factor genes (30 complete coding sequences) were annotated. For example, the present study first described primate-specific cystine-knot Prometheus genes, as well as differential gene expansions of D-dopachrome tautomerase genes. Furthermore, new frameworks of future experiments of two eutherian gene data sets were proposed. PMID:25941635

  3. Solanum torvum responses to the root-knot nematode Meloidogyne incognita

    PubMed Central

    2013-01-01

    Background Solanum torvum Sw is worldwide employed as rootstock for eggplant cultivation because of its vigour and resistance/tolerance to the most serious soil-borne diseases as bacterial, fungal wilts and root-knot nematodes. The little information on Solanum torvum (hereafter Torvum) resistance mechanisms, is mostly attributable to the lack of genomic tools (e.g. dedicated microarray) as well as to the paucity of database information limiting high-throughput expression studies in Torvum. Results As a first step towards transcriptome profiling of Torvum inoculated with the nematode M. incognita, we built a Torvum 3’ transcript catalogue. One-quarter of a 454 full run resulted in 205,591 quality-filtered reads. De novo assembly yielded 24,922 contigs and 11,875 singletons. Similarity searches of the S. torvum transcript tags catalogue produced 12,344 annotations. A 30,0000 features custom combimatrix chip was then designed and microarray hybridizations were conducted for both control and 14 dpi (day post inoculation) with Meloidogyne incognita-infected roots samples resulting in 390 differentially expressed genes (DEG). We also tested the chip with samples from the phylogenetically-related nematode-susceptible eggplant species Solanum melongena. An in-silico validation strategy was developed based on assessment of sequence similarity among Torvum probes and eggplant expressed sequences available in public repositories. GO term enrichment analyses with the 390 Torvum DEG revealed enhancement of several processes as chitin catabolism and sesquiterpenoids biosynthesis, while no GO term enrichment was found with eggplant DEG. The genes identified from S. torvum catalogue, bearing high similarity to known nematode resistance genes, were further investigated in view of their potential role in the nematode resistance mechanism. Conclusions By combining 454 pyrosequencing and microarray technology we were able to conduct a cost-effective global transcriptome profiling

  4. Complexity of bioindicator selection for ecological, human, and cultural health: Chinook salmon and red knot as case studies.

    PubMed

    Burger, Joanna; Gochfeld, Michael; Niles, Lawrence; Powers, Charles; Brown, Kevin; Clarke, James; Dey, Amanda; Kosson, David

    2015-03-01

    There is considerable interest in developing bioindicators of ecological health that are also useful indicators for human health. Yet, human health assessment usually encompasses physical/chemical exposures and not cultural well-being. In this paper, we propose that bioindicators can be selected for all three purposes. We use Chinook or king salmon (Oncorhynchus tshawytscha) and red knot (Calidris canutus rufa, a sandpiper) as examples of indicators that can be used to assess human, ecological, and cultural health. Even so, selecting endpoints or metrics for each indicator species is complex and is explored in this paper. We suggest that there are several endpoint types to examine for a given species, including physical environment, environmental stressors, habitat, life history, demography, population counts, and cultural/societal aspects. Usually cultural endpoints are economic indicators (e.g., number of days fished, number of hunting licenses), rather than the importance of a fishing culture. Development of cultural/societal endpoints must include the perceptions of local communities, cultural groups, and tribal nations, as well as governmental and regulatory communities (although not usually so defined, the latter have cultures as well). Endpoint selection in this category is difficult because the underlying issues need to be identified and used to develop endpoints that tribes and stakeholders themselves see as reasonable surrogates of the qualities they value. We describe several endpoints for salmon and knots that can be used for ecological, human, and cultural/societal health.

  5. Gall-forming root-knot nematodes hijack key plant cellular functions to induce multinucleate and hypertrophied feeding cells.

    PubMed

    Favery, Bruno; Quentin, Michaël; Jaubert-Possamai, Stéphanie; Abad, Pierre

    2016-01-01

    Among plant-parasitic nematodes, the root-knot nematodes (RKNs) of the Meloidogyne spp. are the most economically important genus. RKN are root parasitic worms able to infect nearly all crop species and have a wide geographic distribution. During infection, RKNs establish and maintain an intimate relationship with the host plant. This includes the creation of a specialized nutritional structure composed of multinucleate and hypertrophied giant cells, which result from the redifferentiation of vascular root cells. Giant cells constitute the sole source of nutrients for the nematode and are essential for growth and reproduction. Hyperplasia of surrounding root cells leads to the formation of the gall or root-knot, an easily recognized symptom of plant infection by RKNs. Secreted effectors produced in nematode salivary glands and injected into plant cells through a specialized feeding structure called the stylet play a critical role in the formation of giant cells. Here, we describe the complex interactions between RKNs and their host plants. We highlight progress in understanding host plant responses, focusing on how RKNs manipulate key plant processes and functions, including cell cycle, defence, hormones, cellular scaffold, metabolism and transport.

  6. Microfluidic Fabrication of Bio-Inspired Microfibers with Controllable Magnetic Spindle-Knots for 3D Assembly and Water Collection.

    PubMed

    He, Xiao-Heng; Wang, Wei; Liu, Ying-Mei; Jiang, Ming-Yue; Wu, Fang; Deng, Ke; Liu, Zhuang; Ju, Xiao-Jie; Xie, Rui; Chu, Liang-Yin

    2015-08-12

    A simple and flexible approach is developed for controllable fabrication of spider-silk-like microfibers with tunable magnetic spindle-knots from biocompatible calcium alginate for controlled 3D assembly and water collection. Liquid jet templates with volatile oil drops containing magnetic Fe3O4 nanoparticles are generated from microfluidics for fabricating spider-silk-like microfibers. The structure of jet templates can be precisely adjusted by simply changing the flow rates to tailor the structures of the resultant spider-silk-like microfibers. The microfibers can be well manipulated by external magnetic fields for controllably moving, and patterning and assembling into different 2D and 3D structures. Moreover, the dehydrated spider-silk-like microfibers, with magnetic spindle-knots for collecting water drops, can be controllably assembled into spider-web-like structures for excellent water collection. These spider-silk-like microfibers are promising as functional building blocks for engineering complex 3D scaffolds for water collection, cell culture, and tissue engineering.

  7. Microfluidic Fabrication of Bio-Inspired Microfibers with Controllable Magnetic Spindle-Knots for 3D Assembly and Water Collection.

    PubMed

    He, Xiao-Heng; Wang, Wei; Liu, Ying-Mei; Jiang, Ming-Yue; Wu, Fang; Deng, Ke; Liu, Zhuang; Ju, Xiao-Jie; Xie, Rui; Chu, Liang-Yin

    2015-08-12

    A simple and flexible approach is developed for controllable fabrication of spider-silk-like microfibers with tunable magnetic spindle-knots from biocompatible calcium alginate for controlled 3D assembly and water collection. Liquid jet templates with volatile oil drops containing magnetic Fe3O4 nanoparticles are generated from microfluidics for fabricating spider-silk-like microfibers. The structure of jet templates can be precisely adjusted by simply changing the flow rates to tailor the structures of the resultant spider-silk-like microfibers. The microfibers can be well manipulated by external magnetic fields for controllably moving, and patterning and assembling into different 2D and 3D structures. Moreover, the dehydrated spider-silk-like microfibers, with magnetic spindle-knots for collecting water drops, can be controllably assembled into spider-web-like structures for excellent water collection. These spider-silk-like microfibers are promising as functional building blocks for engineering complex 3D scaffolds for water collection, cell culture, and tissue engineering. PMID:26192108

  8. Complexity of bioindicator selection for ecological, human, and cultural health: Chinook salmon and red knot as case studies.

    PubMed

    Burger, Joanna; Gochfeld, Michael; Niles, Lawrence; Powers, Charles; Brown, Kevin; Clarke, James; Dey, Amanda; Kosson, David

    2015-03-01

    There is considerable interest in developing bioindicators of ecological health that are also useful indicators for human health. Yet, human health assessment usually encompasses physical/chemical exposures and not cultural well-being. In this paper, we propose that bioindicators can be selected for all three purposes. We use Chinook or king salmon (Oncorhynchus tshawytscha) and red knot (Calidris canutus rufa, a sandpiper) as examples of indicators that can be used to assess human, ecological, and cultural health. Even so, selecting endpoints or metrics for each indicator species is complex and is explored in this paper. We suggest that there are several endpoint types to examine for a given species, including physical environment, environmental stressors, habitat, life history, demography, population counts, and cultural/societal aspects. Usually cultural endpoints are economic indicators (e.g., number of days fished, number of hunting licenses), rather than the importance of a fishing culture. Development of cultural/societal endpoints must include the perceptions of local communities, cultural groups, and tribal nations, as well as governmental and regulatory communities (although not usually so defined, the latter have cultures as well). Endpoint selection in this category is difficult because the underlying issues need to be identified and used to develop endpoints that tribes and stakeholders themselves see as reasonable surrogates of the qualities they value. We describe several endpoints for salmon and knots that can be used for ecological, human, and cultural/societal health. PMID:25666646

  9. Tomato transgenic plants expressing hairpin construct of a nematode protease gene conferred enhanced resistance to root-knot nematodes

    PubMed Central

    Dutta, Tushar K.; Papolu, Pradeep K.; Banakar, Prakash; Choudhary, Divya; Sirohi, Anil; Rao, Uma

    2015-01-01

    Root-knot nematodes (Meloidogyne incognita) cause substantial yield losses in vegetables worldwide, and are difficult to manage. Continuous withdrawal of environmentally-harmful nematicides from the global market warrants the need for novel nematode management strategies. Utility of host-delivered RNAi has been demonstrated in several plants (Arabidopsis, tobacco, and soybean) that exhibited resistance against root-knot and cyst nematodes. Herein, a M. incognita-specific protease gene, cathepsin L cysteine proteinase (Mi-cpl-1), was targeted to generate tomato transgenic lines to evaluate the genetically modified nematode resistance. In vitro knockdown of Mi-cpl-1 gene led to the reduced attraction and penetration of M. incognita in tomato, suggesting the involvement of Mi-cpl-1 in nematode parasitism. Transgenic expression of the RNAi construct of Mi-cpl-1 gene resulted in 60–80% reduction in infection and multiplication of M. incognita in tomato. Evidence for in vitro and in vivo silencing of Mi-cpl-1 was confirmed by expression analysis using quantitative PCR. Our study demonstrates that Mi-cpl-1 plays crucial role during plant-nematode interaction and plant-mediated downregulation of this gene elicits detrimental effect on M. incognita development, reinforcing the potential of RNAi technology for management of phytonematodes in crop plants. PMID:25883594

  10. Complexity of bioindicator selection for ecological, human, and cultural health: Chinook salmon and red knot as case studies

    PubMed Central

    Burger, Joanna; Gochfeld, Michael; Niles, Lawrence; Powers, Charles; Brown, Kevin; Clarke, James; Dey, Amanda; Kosson, David

    2015-01-01

    There is considerable interest in developing bioindicators of ecological health that are also useful indicators for human health. Yet, human health assessment usually encompasses physical/chemical exposures and not cultural well-being. In this paper, we propose that bioindicators can be selected for all three purposes. We use Chinook or king salmon (Oncorhynchus tshawytscha) and red knot (Calidris canutus rufa, a sandpiper) as examples of indicators that can be used to assess human, ecological, and cultural health. Even so, selecting endpoints or metrics for each indicator species is complex and is explored in this paper. We suggest that there are several endpoint types to examine for a given species, including physical environment, environmental stressors, habitat, life history, demography, population counts, and cultural/societal aspects. Usually cultural endpoints are economic indicators (e.g., number of days fished, number of hunting licenses), rather than the importance of a fishing culture. Development of cultural/societal endpoints must include the perceptions of local communities, cultural groups, and tribal nations, as well as governmental and regulatory communities (although not usually so defined, the latter have cultures as well). Endpoint selection in this category is difficult because the underlying issues need to be identified and used to develop endpoints that tribes and stakeholders themselves see as reasonable surrogates of the qualities they value. We describe several endpoints for salmon and knots that can be used for ecological, human, and cultural/societal health. PMID:25666646

  11. The Mutliple Lobes and Geometric Model of Hubble 12: A Young Planetary Nebula with two pairs of H2 Knots

    NASA Astrophysics Data System (ADS)

    Hsia, Chih-Hao; Chau, Wayne; Zhang, Yong; Kwok, Sun

    2015-08-01

    Hubble 12 (Hb 12) is a member of the rare group of planetary nebulae (PNs) exhibiting nested shells. Its intrinsic structures and shaping mechanism are still not fully understood. We present new near-infrared narrow-band imaging observations of Hb 12 using Wide-field InfraRed Camera on the Canada-France-Hawaii Telescope (CFHT). Combining Hubble Space Telescope optical imaging and CFHT observations, we find a number of co-axial rings aligned with the bipolar lobes and two pairs of separate knots with different orientations. These rings are thought to be the manifestation of a time-variable, collimated fast wind of bipolar lobes interacting with surrounding asymptotic giant branch circumstellar medium. The existence of knots with different orientations suggests that this PN hosts a bipolar, rotating, episodic jet (BRET). We construct a three-dimensional model that allows the visualization of the nebula viewed from different orientations, and infer that this PN might have intrinsic structures similar to the young multipolar PNs, Hen 2-320 and M 2-9.

  12. Evaluation of the effect of ecologic on root knot nematode, Meloidogyne incognita, and tomato plant, Lycopersicon esculenum.

    PubMed

    Ladner, Debora C; Tchounwou, Paul B; Lawrence, Gary W

    2008-06-01

    Nonchemical methods and strategies for nematode management including cultural methods and engineered measures have been recommended as an alternative to methyl bromide (a major soil fumigant), due to its role in the depletion of the ozone layer. Hence, an international agreement has recently been reached calling for its reduced consumption and complete phasing out. This present research evaluates the potential of Ecologic, a biological, marine shell meal chitin material, as a soil amendment management agent for root knot nematode, Meloidogyne incognita, control, and its effect on the growth of Floradel tomato plant, Lycopersicon esculentum. To accomplish this goal, studies were conducted during which, experimental pots were set up in greenhouse environments using sterilized soil inoculated with 5,000 root-knot eggs per 1500 g soil. There were 4 treatments and 5 replications. Treatments were: No chitin; 50 g chitin; 100 g chitin; and 200 g chitin. A two-week wait period following Ecologic amendment preceded Floradel tomato planting to allow breakdown of the chitin material into the soil. Fresh and dry weights of shoot and root materials were taken as growth end-points. A statistically significant difference (p < or = 0.05) was obtained with regard to the growth rate of L. esculentum at 100 g chitin treatment compared to the control with no chitin. Mean fresh weights of Floradel tomato were 78.0 +/- 22.3 g, 81.0 +/- 20.3 g, 109.0 +/- 25.4 g and 102.0 +/- 33.3 g at 0, 50, 100 and 200 g chitin, respectively. The analysis of root knot nematode concentrations indicated a substantial effect on reproduction rate associated with chitin amendment. Study results showed a significant decrease in both root knot nematode eggs and juveniles (J2) at 100g and 200 g Ecologic chitin levels, however, an increase in nematode concentrations was recorded at the 50 g Ecologic chitin level (p < or = 0.05). The mean amounts of J2 population, as expressed per 1500 cm3 soil, were 49

  13. Evaluation of the Effect of Ecologic on Root Knot Nematode, Meloidogyne incognita, and Tomato Plant, Lycopersicon esculenum

    PubMed Central

    Ladner, Debora C.; Tchounwou, Paul B.; Lawrence, Gary W.

    2008-01-01

    Nonchemical methods and strategies for nematode management including cultural methods and engineered measures have been recommended as an alternative to methyl bromide (a major soil fumigant), due to its role in the depletion of the ozone layer. Hence, an international agreement has recently been reached calling for its reduced consumption and complete phasing out. This present research evaluates the potential of Ecologic, a biological, marine shell meal chitin material, as a soil amendment management agent for root knot nematode, Meloidogyne incognita, control, and its effect on the growth of Floradel tomato plant, Lycopersicon esculentum. To accomplish this goal, studies were conducted during which, experimental pots were set up in greenhouse environments using sterilized soil inoculated with 5,000 root-knot eggs per 1500 g soil. There were 4 treatments and 5 replications. Treatments were: No chitin; 50 g chitin; 100 g chitin; and 200 g chitin. A two-week wait period following Ecologic amendment preceded Floradel tomato planting to allow breakdown of the chitin material into the soil. Fresh and dry weights of shoot and root materials were taken as growth end-points. A statistically significant difference (p ≤ 0.05) was obtained with regard to the growth rate of L. esculentum at 100 g chitin treatment compared to the control with no chitin. Mean fresh weights of Floradel tomato were 78.0 ± 22.3g, 81.0 ± 20.3g, 109.0 ± 25.4g and 102.0 ± 33.3g at 0, 50, 100 and 200g chitin, respectively. The analysis of root knot nematode concentrations indicated a substantial effect on reproduction rate associated with chitin amendment. Study results showed a significant decrease in both root knot nematode eggs and juveniles (J2) at 100g and 200g Ecologic chitin levels, however, an increase in nematode concentrations was recorded at the 50g Ecologic chitin level (p ≤ 0.05). The mean amounts of J2 population, as expressed per 1500cm3 soil, were 49,933 ± 38,819, 86,050

  14. Molecular characteristics and efficacy of 16D10 siRNAs in inhibiting root-knot nematode infection in transgenic grape hairy roots

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Root-knot nematodes (RKNs) infect many annual and perennial crops and are the most devastating soil-born pests in vineyards. To develop a biotech-based solution for controlling RKNs in grapes, we evaluated the efficacy of plant-derived RNA interference (RNAi) silencing of a conserved RKN effector ge...

  15. Effects of the Mi-1 and the N root-knot nematode-resistance gene on infection and reproduction of Meloidogyne enterolobii on tomato and pepper cultivars

    PubMed Central

    Dessimoz, Mireille; Franck, Lucie

    2009-01-01

    Meloidogyne enterolobii is widely considered to be an aggressive root-knot nematode species that is able to reproduce on root-knot nematode-resistant tomato and pepper cultivars. In greenhouse experiments, M. enterolobii isolates 1 and 2 from Switzerland were able to reproduce on tomato cultivars carrying the Mi-1 resistance gene as well as an N-carrying pepper cultivar. Reproduction factors (Rf) ranged between 12 and 109 depending on the plant cultivar, with M. enterolobii isolate 2 being more virulent when compared to isolate 1. In contrast, M. arenaria completely failed to reproduce on these resistant tomato and pepper cultivars. Although some variability in virulence and effectiveness of root-knot nematode-resistance genes was detected, none of the plant cultivars showed Rf values less than 1 or less than 10% of the reproduction observed on the susceptible cv. ‘Moneymaker’ (Rf = 23-44) used to characterize resistance. The ability of M. enterolobii to overcome the resistance of tomato and pepper carrying the Mi-1 and the N gene makes it difficult to manage this root-knot nematode species, particularly in organic farming systems where chemical control is not an option. PMID:22661786

  16. From the root to the stem: interaction between the biocontrol root endophyte Pseudomonas fluorescens PICF7 and the pathogen Pseudomonas savastanoi NCPPB 3335 in olive knots.

    PubMed

    Maldonado-González, M Mercedes; Prieto, Pilar; Ramos, Cayo; Mercado-Blanco, Jesús

    2013-05-01

    Olive knot disease, caused by Pseudomonas savastanoi pv. savastanoi, is one of the most important biotic constraints for olive cultivation. Pseudomonas fluorescens PICF7, a natural colonizer of olive roots and effective biological control agent (BCA) against Verticillium wilt of olive, was examined as potential BCA against olive knot disease. Bioassays using in vitro-propagated olive plants were carried out to assess whether strain PICF7 controlled knot development either when co-inoculated with the pathogen in stems or when the BCA (in roots) and the pathogen (in stems) were spatially separated. Results showed that PICF7 was able to establish and persist in stem tissues upon artificial inoculation. While PICF7 was not able to suppress disease development, its presence transiently decreased pathogen population size, produced less necrotic tumours, and sharply altered the localization of the pathogen in the hyperplasic tissue, which may pose epidemiological consequences. Confocal laser scanning microscopy combined with fluorescent tagging of bacteria revealed that when PICF7 was absent the pathogen tended to be localized at the knot surface. However, presence of the BCA seemed to confine P. savastanoi at inner regions of the tumours. This approach has also enabled to prove that the pathogen can moved systemically beyond the hypertrophied tissue.

  17. Draft Genome Sequence of Stenotrophomonas maltophilia Strain B418, a Promising Agent for Biocontrol of Plant Pathogens and Root-Knot Nematode

    PubMed Central

    Wu, Yuanzheng; Wang, Yilian; Li, Jishun; Hu, Jindong; Chen, Kai; Wei, Yanli; Bazhanov, Dmitry P.; Bazhanova, Alesia A.

    2015-01-01

    Stenotrophomonas maltophilia strain B418 was isolated from a barley rhizosphere in China. This bacterium exhibits broad-spectrum inhibitory activities against plant pathogens and root-knot nematode along with growth-promoting effects. Here, we present the draft genome sequence of S. maltophilia B418. PMID:25700397

  18. From the root to the stem: interaction between the biocontrol root endophyte Pseudomonas fluorescens PICF7 and the pathogen Pseudomonas savastanoi NCPPB 3335 in olive knots

    PubMed Central

    Maldonado-González, M Mercedes; Prieto, Pilar; Ramos, Cayo; Mercado-Blanco, Jesús

    2013-01-01

    Olive knot disease, caused by Pseudomonas savastanoi pv. savastanoi, is one of the most important biotic constraints for olive cultivation. Pseudomonas fluorescens PICF7, a natural colonizer of olive roots and effective biological control agent (BCA) against Verticillium wilt of olive, was examined as potential BCA against olive knot disease. Bioassays using in vitro-propagated olive plants were carried out to assess whether strain PICF7 controlled knot development either when co-inoculated with the pathogen in stems or when the BCA (in roots) and the pathogen (in stems) were spatially separated. Results showed that PICF7 was able to establish and persist in stem tissues upon artificial inoculation. While PICF7 was not able to suppress disease development, its presence transiently decreased pathogen population size, produced less necrotic tumours, and sharply altered the localization of the pathogen in the hyperplasic tissue, which may pose epidemiological consequences. Confocal laser scanning microscopy combined with fluorescent tagging of bacteria revealed that when PICF7 was absent the pathogen tended to be localized at the knot surface. However, presence of the BCA seemed to confine P. savastanoi at inner regions of the tumours. This approach has also enabled to prove that the pathogen can moved systemically beyond the hypertrophied tissue. PMID:23425069

  19. Sampling techniques and detection methods for developing risk assessments for root-knot nematode (Meloidogyne incognita) on lima bean (Phaseolus lunatus) in the Mid-Atlantic region

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Lima bean, Phaseolus lunatus, is a cornerstone crop in the Mid-Atlantic region and Meloidogyne incognita, the southern root knot nematode (RKN), causes significant yield loss. The RKN has become more pervasive as toxic nematicides have been removed from the market, and risk evaluation research is ne...

  20. Engineered Cystine-Knot Peptides That Bind αvβ3 Integrin With Antibody-Like Affinities

    PubMed Central

    Silverman, Adam P.; Levin, Aron M.; Lahti, Jennifer L.; Cochran, Jennifer R.

    2010-01-01

    The αvβ3 integrin receptor is an important cancer target due to its overexpression on many solid tumors and the tumor neovasculature, and its role in metastasis and angiogenesis. We used a truncated form of the Agouti-related protein (AgRP), a 4 kDa cystine-knot peptide with four disulfide bonds and four solvent-exposed loops, as a scaffold for engineering peptides that bound to αvβ3 integrins with high affinity and specificity. A yeast-displayed cystine-knot peptide library was generated by substituting a 6-amino acid loop of AgRP with a 9-amino acid loop containing the Arg-Gly-Asp (RGD) integrin recognition motif and randomized flanking residues. Mutant cystine-knot peptides were screened in a high-throughput manner by fluorescence-activated cell sorting (FACS) to identify clones with high affinity to detergent-solubilized αvβ3 integrin receptor. Select integrin-binding peptides were expressed recombinantly in Pichia pastoris and were tested for their ability to bind to human cancer cells expressing various integrin receptors. These studies showed that the engineered AgRP peptides bound to cells expressing αvβ3 integrins with affinities ranging from 15 nM to 780 pM. Furthermore, the engineered peptides were shown bind specifically to αvβ3 integrins, and had only minimal or no binding to αvβ5, α5β1, and αiibβ3 integrins. The engineered AgRP peptides were also shown to inhibit cell adhesion to the extracellular matrix protein vitronectin, which is a naturally-occurring ligand for αvβ3 and other integrins. Next, to evaluate whether the other three loops of AgRP could modulate integrin specificity, we made second generation libraries by individually randomizing these loops in one of the high affinity integrin-binding variants. Screening of these loop-randomized libraries against αvβ3 integrins resulted in peptides that retained high affinities for αvβ3 and had increased specificities for αvβ3 over αiibβ3 integrins. Collectively, these data

  1. Vegetation and climate development on the Atlantic Coastal Plain during the late Mid-Miocene Climatic Optimum (IODP Expedition 313)

    NASA Astrophysics Data System (ADS)

    Prader, Sabine; Kotthoff, Ulrich; McCarthy, Francine; Greenwood, David

    2015-04-01

    which was reminiscent of Oligocene and early Miocene ecosystems analyzed in previous studies (e.g. Kotthoff et al. 2014). The ecosystem was characterized by oak-hickory forests which probably dominated in the lowlands, while frequent occurrence of conifer pollen (Pinus, Picea, Abies, Sciadopitys, and Tsuga canadensis) indicate that conifer forests prevailed in higher altitudes during the MMCO. We assume that the Miocene uplift of the Appalachian Mountains (e.g. Gallen et al., 2013) led to the proliferation of mountainous taxa and thus to an increase of related pollen taxa in the palynological record. References: Gallen, S. F., Wegmann, K. W., Bohnenstieh, D. W. R.: Miocene rejuvenation of topographic relief in the southern Appalachians, GSA Today, 23, 4-10, 2013. Kotthoff, U., McCarthy, F.M.G., Greenwood, D.R., Müller-Navarra, K., Prader, S., Hesselbo, S.P., (2014): Vegetation and climate development on the Atlantic Coastal Plain from 33 to 13 million years ago (IODP expedition 313). Climate of the Past 10, 1523-1539.

  2. A KNOTTED1-LIKE HOMEOBOX Protein Regulates Abscission in Tomato by Modulating the Auxin Pathway1[OPEN

    PubMed Central

    Ma, Chao; Meir, Shimon; Xiao, Langtao; Tong, Jianhua; Liu, Qing; Reid, Michael S.; Jiang, Cai-Zhong

    2015-01-01

    A gene encoding a KNOTTED1-LIKE HOMEOBOX PROTEIN1 (KD1) is highly expressed in both leaf and flower abscission zones. Reducing the abundance of transcripts of this gene in tomato (Solanum lycopersicum) by both virus-induced gene silencing and stable transformation with a silencing construct driven by an abscission-specific promoter resulted in a striking retardation of pedicel and petiole abscission. In contrast, Petroselinum, a semidominant KD1 mutant, showed accelerated pedicel and petiole abscission. Complementary DNA microarray and quantitative reverse transcription-polymerase chain reaction analysis indicated that regulation of abscission by KD1 was associated with changed abundance of genes related to auxin transporters and signaling components. Measurement of auxin content and activity of a DR5::β-glucuronidase auxin reporter assay showed that changes in KD1 expression modulated the auxin concentration and response gradient in the abscission zone. PMID:25560879

  3. Automatic measurement of wood fiber orientation and knot detection using an optical system based on heating conduction.

    PubMed

    Daval, Vincent; Pot, Guillaume; Belkacemi, Mohamed; Meriaudeau, Fabrice; Collet, Robert

    2015-12-28

    In this paper, a new approach to computing the deviation of wood grain is proposed. To do this, the thermal conduction properties of timber are used (higher conduction in the fiber direction). Exciting the surface of the wood with a laser and capturing the thermal conduction using a thermal camera, an ellipse can be observed. Using a method similar to the tracheid effect, it is possible to extract information from this ellipse, such as the slope of grain and the presence of knots. With this method it is therefore possible to extend the mechanical model (assessing the mechanical properties of timber) to take certain singularities into account. Using this approach, the slope of grain can be estimated for any wood species, either hardwood or softwood, which was not possible with the existing tracheid effect. PMID:26832017

  4. Identification of markers tightly linked to tomato yellow leaf curl disease and root-knot nematode resistance by multiplex PCR.

    PubMed

    Chen, S X; Du, J N; Hao, L N; Wang, C Y; Chen, Q; Chang, Y X

    2012-01-01

    Seven different commercial F₁ hybrids and two F₂ populations were evaluated by multiplex PCR to identify plants that are homozygous or heterozygous for Ty-1 and Mi, which confer resistance to tomato yellow leaf curl disease and root-knot nematode, respectively. The Ty-1 and Mi markers were amplified by PCR and identified by digestion of the amplicons with the TaqI enzyme. The hybrids E13 and 288 were found to be Ty/ty heterozygous plants with 398-, 303-, and 95-bp bands, and B08, 314, 198, and A10 were found to be ty/ty homozygous plants with a 398-bp band; whereas 098 did not give any PCR products. The hybrids E13 and 198 were found to be Mi/Mi homozygous plants with 570- and 180-bp bands, and 288 and A10 were found to be Mi/mi heterozygous plants, with 750-, 570- and 180-bp bands, and B08, 109 and 314 were found to be mi/mi homozygous plants with only a 750-bp band. We additionally developed a multiplex PCR technique for JB-1 and Mi, which confer resistance to tomato yellow leaf curl disease and root-knot nematode. The JB-1 marker identified the genotype of the Ty gene, and the plants that produced the 400-bp band were ty/ty homozygous plants, whereas the plants that produced 400- and 500-bp bands were resistant to tomato yellow leaf curl disease. We conclude that multiplex PCRs can be used to reproducibly and efficiently detect these resistance genes. PMID:22869069

  5. The Cystine Knot Is Responsible for the Exceptional Stability of the Insecticidal Spider Toxin ω-Hexatoxin-Hv1a.

    PubMed

    Herzig, Volker; King, Glenn F

    2015-10-26

    The inhibitor cystine knot (ICK) is an unusual three-disulfide architecture in which one of the disulfide bonds bisects a loop formed by the two other disulfide bridges and the intervening sections of the protein backbone. Peptides containing an ICK motif are frequently considered to have high levels of thermal, chemical and enzymatic stability due to cross-bracing provided by the disulfide bonds. Experimental studies supporting this contention are rare, in particular for spider-venom toxins, which represent the largest diversity of ICK peptides. We used ω-hexatoxin-Hv1a (Hv1a), an insecticidal toxin from the deadly Australian funnel-web spider, as a model system to examine the contribution of the cystine knot to the stability of ICK peptides. We show that Hv1a is highly stable when subjected to temperatures up to 75 °C, pH values as low as 1, and various organic solvents. Moreover, Hv1a was highly resistant to digestion by proteinase K and when incubated in insect hemolymph and human plasma. We demonstrate that the ICK motif is essential for the remarkable stability of Hv1a, with the peptide's stability being dramatically reduced when the disulfide bonds are eliminated. Thus, this study demonstrates that the ICK motif significantly enhances the chemical and thermal stability of spider-venom peptides and provides them with a high level of protease resistance. This study also provides guidance to the conditions under which Hv1a could be stored and deployed as a bioinsecticide.

  6. Avascular Villi, Increased Syncytial Knots, and Hypervascular Villi Are Associated with Pregnancies Complicated by Factor V Leiden Mutation

    PubMed Central

    Rogers, Beverly Barton; Momirova, Valerija; Dizon-Townson, Donna; Wenstrom, Katharine; Samuels, Philip; Sibai, Baha; Spong, Catherine; Caritis, Steve N.; Sorokin, Yoram; Miodovnik, Menachem; O’Sullivan, Mary J.; Conway, Deborah; Wapner, Ronald J.

    2011-01-01

    There is controversy about whether pathologic abnormalities are associated with pregnancies complicated by factor V Leiden (FVL) mutation. The purpose of this study was to evaluate 105 placentas delivered to mothers heterozygous for FVL mutation to determine if there are pathologic changes suggestive of hypoxia or thrombosis, which correlate with mutation status. We examined placentas obtained as part of a prospective study of 5188 pregnancies analyzed for the presence of FVL mutation in either the mother or the infant. One hundred five placentas from mothers heterozygous for the mutation were compared with 225 controls matched for maternal age, race, and geographic site. Of the 330 pregnancies, 50 infants were FVL mutation heterozygotes. Maternal FVL heterozygote status was associated with more frequent increased numbers of syncytial knots (13% vs 4%); the difference remained significant after controlling for hypertension, preeclampsia, small-for-gestational-age infants, and delivery prior to 35 weeks of gestation (odds ratio 3.6, 95% confidence interval 1.5–8.7, P = 0.004). Maternal FVL heterozygotes had more hypervascular villi (10% vs 3%), with significance retained controlling for delivery route (odds ratio 3.4, 95% confidence ratio 1.2–9.4, P = 0.018). Placentas from infants heterozygous for FVL mutation had more avascular villi than controls (odds ratio 2.9, 95% confidence interval 1.5–5.6, P = 0.001). Fetal or maternal FVL heterozygosity was not associated with infarcts, small-for-gestational-age placentas, or fetal thrombotic vasculopathy. This analysis demonstrates that pathologic findings associated with placental hypoxia, specifically focal avascular villi, increased numbers of syncytial knots, and hypervascular villi, also correlate with FVL heterozygosity in infants or mothers. PMID:20121426

  7. The Cystine Knot Is Responsible for the Exceptional Stability of the Insecticidal Spider Toxin ω-Hexatoxin-Hv1a

    PubMed Central

    Herzig, Volker; King, Glenn F.

    2015-01-01

    The inhibitor cystine knot (ICK) is an unusual three-disulfide architecture in which one of the disulfide bonds bisects a loop formed by the two other disulfide bridges and the intervening sections of the protein backbone. Peptides containing an ICK motif are frequently considered to have high levels of thermal, chemical and enzymatic stability due to cross-bracing provided by the disulfide bonds. Experimental studies supporting this contention are rare, in particular for spider-venom toxins, which represent the largest diversity of ICK peptides. We used ω-hexatoxin-Hv1a (Hv1a), an insecticidal toxin from the deadly Australian funnel-web spider, as a model system to examine the contribution of the cystine knot to the stability of ICK peptides. We show that Hv1a is highly stable when subjected to temperatures up to 75 °C, pH values as low as 1, and various organic solvents. Moreover, Hv1a was highly resistant to digestion by proteinase K and when incubated in insect hemolymph and human plasma. We demonstrate that the ICK motif is essential for the remarkable stability of Hv1a, with the peptide’s stability being dramatically reduced when the disulfide bonds are eliminated. Thus, this study demonstrates that the ICK motif significantly enhances the chemical and thermal stability of spider-venom peptides and provides them with a high level of protease resistance. This study also provides guidance to the conditions under which Hv1a could be stored and deployed as a bioinsecticide. PMID:26516914

  8. Connective tissue growth factor differentially binds to members of the cystine knot superfamily and potentiates platelet-derived growth factor-B signaling in rabbit corneal fibroblast cells

    PubMed Central

    Pi, Liya; Chung, Pei-Yu; Sriram, Sriniwas; Rahman, Masmudur M; Song, Wen-Yuan; Scott, Edward W; Petersen, Bryon E; Schultz, Gregory S

    2015-01-01

    AIM: To study the binding of connective tissue growth factor (CTGF) to cystine knot-containing ligands and how this impacts platelet-derived growth factor (PDGF)-B signaling. METHODS: The binding strengths of CTGF to cystine knot-containing growth factors including vascular endothelial growth factor (VEGF)-A, PDGF-B, bone morphogenetic protein (BMP)-4, and transforming growth factor (TGF)-β1 were compared using the LexA-based yeast two-hybrid system. EYG48 reporter strain that carried a wild-type LEU2 gene under the control of LexA operators and a lacZ reporter plasmid (p80p-lacZ) containing eight high affinity LexA binding sites were used in the yeast two-hybrid analysis. Interactions between CTGF and the tested growth factors were evaluated based on growth of transformed yeast cells on selective media and colorimetric detection in a liquid β-galactosidase activity assay. Dissociation constants of CTGF to VEGF-A isoform 165 or PDGF-BB homo-dimer were measured in surface plasma resonance (SPR) analysis. CTGF regulation in PDGF-B presentation to the PDGF receptor β (PDGFRβ) was also quantitatively assessed by the SPR analysis. Combinational effects of CTGF protein and PDGF-BB on activation of PDGFRβ and downstream signaling molecules ERK1/2 and AKT were assessed in rabbit corneal fibroblast cells by Western analysis. RESULTS: In the LexA-based yeast two-hybrid system, cystine knot motifs of tested growth factors were fused to the activation domain of the transcriptional factor GAL4 while CTGF was fused to the DNA binding domain of the bacterial repressor protein LexA. Yeast co-transformants containing corresponding fusion proteins for CTGF and all four tested cystine knot motifs survived on selective medium containing galactose and raffinose but lacking histidine, tryptophan, and uracil. In liquid β-galactosidase assays, CTGF expressing cells that were co-transformed with the cystine knot of VEGF-A had the highest activity, at 29.88 ± 0.91 fold above controls

  9. Tying the knot: the cystine signature and molecular-recognition processes of the vascular endothelial growth factor family of angiogenic cytokines.

    PubMed

    Iyer, Shalini; Acharya, K Ravi

    2011-11-01

    The cystine-knot motif, made up of three intertwined disulfide bridges, is a unique feature of several toxins, cyclotides and growth factors, and occurs in a variety of species, including fungi, insects, molluscs and mammals. Growth factor molecules containing the cystine-knot motif serve as ligands for a diverse range of receptors and play an important role in extracellular signalling. This superfamily of polypeptides comprises several homodimeric and heterodimeric molecules that are central characters in both health and disease. Amongst these molecules are a group of proteins that belong to the vascular endothelial growth factor (VEGF) subfamily. The members of this family are known angiogenic factors that regulate processes leading to blood vessel formation in physiological and pathological conditions. The focus of the present review is on the structural characteristics of proteins that belong to the VEGF family and on signal-transduction pathways that become initiated via the VEGF receptors.

  10. Identification of Novel Target Genes for Safer and More Specific Control of Root-Knot Nematodes from a Pan-Genome Mining

    PubMed Central

    Danchin, Etienne G. J.; Perfus-Barbeoch, Laetitia; Magliano, Marc; Rosso, Marie-Noëlle; Da Rocha, Martine; Da Silva, Corinne; Nottet, Nicolas; Labadie, Karine; Guy, Julie; Artiguenave, François; Abad, Pierre

    2013-01-01

    Root-knot nematodes are globally the most aggressive and damaging plant-parasitic nematodes. Chemical nematicides have so far constituted the most efficient control measures against these agricultural pests. Because of their toxicity for the environment and danger for human health, these nematicides have now been banned from use. Consequently, new and more specific control means, safe for the environment and human health, are urgently needed to avoid worldwide proliferation of these devastating plant-parasites. Mining the genomes of root-knot nematodes through an evolutionary and comparative genomics approach, we identified and analyzed 15,952 nematode genes conserved in genomes of plant-damaging species but absent from non target genomes of chordates, plants, annelids, insect pollinators and mollusks. Functional annotation of the corresponding proteins revealed a relative abundance of putative transcription factors in this parasite-specific set compared to whole proteomes of root-knot nematodes. This may point to important and specific regulators of genes involved in parasitism. Because these nematodes are known to secrete effector proteins in planta, essential for parasitism, we searched and identified 993 such effector-like proteins absent from non-target species. Aiming at identifying novel targets for the development of future control methods, we biologically tested the effect of inactivation of the corresponding genes through RNA interference. A total of 15 novel effector-like proteins and one putative transcription factor compatible with the design of siRNAs were present as non-redundant genes and had transcriptional support in the model root-knot nematode Meloidogyne incognita. Infestation assays with siRNA-treated M. incognita on tomato plants showed significant and reproducible reduction of the infestation for 12 of the 16 tested genes compared to control nematodes. These 12 novel genes, showing efficient reduction of parasitism when silenced, constitute

  11. The Single-Knot Running Vesicourethral Anastomosis after Minimally Invasive Prostatectomy: Review of the Technique and Its Modifications, Tips, and Pitfalls.

    PubMed

    Albisinni, Simone; Aoun, Fouad; Peltier, Alexandre; van Velthoven, Roland

    2016-01-01

    The vesicourethral anastomosis represents a step of major difficulty at the end of minimally invasive radical prostatectomy. Over 10 years ago, we have devised the single-knot running vesicourethral anastomosis, which has been widely adopted in urologic departments worldwide. Aim of the current paper is to review the technique, its adaptability in complex situations, its complications, and possible modifications, including the use of barbed sutures. PMID:27340567

  12. Pharmacokinetically Stabilized Cystine Knot Peptides that Bind Alpha-v-Beta-6 Integrin with Single-Digit Nanomolar Affinities for Detection of Pancreatic Cancer

    PubMed Central

    Kimura, Richard H.; Teed, Robert; Hackel, Benjamin J.; Pysz, Marybeth A.; Chuang, Courtney Z.; Sathirachinda, Ataya; Willmann, Jürgen K.; Gambhir, Sanjiv S.

    2012-01-01

    Purpose Detection of pancreatic cancer remains high priority and effective diagnostic tools are needed for clinical applications. Many cancer cells overexpress integrin αvβ6, a cell surface receptor being evaluated as a novel clinical biomarker. Experimental Design To validate this molecular target, several highly stable cystine knot peptides were engineered by directed evolution to bind specifically and with high-affinity (3-6 nM) to integrin αvβ6. The binders don’t cross-react with related integrin αvβ5, integrin α5β1 or tumor-angiogenesis associated integrin, αvβ3. Results Positron emission tomography showed that these disulfide-stabilized peptides rapidly accumulate at tumors expressing integrin αvβ6. Clinically relevant tumor-to-muscle ratios of 7.7 ± 2.4 to 11.3 ± 3.0 were achieved within one hour after radiotracer injection. Minimization of off-target dosing was achieved by reformatting αvβ6-binding activities across various natural and pharmacokinetically-stabilized cystine knot scaffolds with different amino acid content. We demonstrate that a peptide scaffold’s primary sequence directs its pharmacokinetics. Scaffolds with high arginine or glutamic acid content suffered high renal retention of > 75 percent injected dose per gram (%ID/g). Substitution of these amino acids with renally-cleared amino acids, notably serine, led to significant decreases in renal accumulation of < 20 %ID/g 1h post injection (p < 0.05, n=3). Conclusions We have engineered highly stable cystine knot peptides with potent and specific integrin αvβ6 binding activities for cancer detection. Pharmacokinetic engineering of scaffold primary sequence led to significant decreases in off-target radiotracer accumulation. Optimization of binding affinity, specificity, stability and pharmacokinetics will facilitate translation of cystine knots for cancer molecular imaging. PMID:22173551

  13. The Single-Knot Running Vesicourethral Anastomosis after Minimally Invasive Prostatectomy: Review of the Technique and Its Modifications, Tips, and Pitfalls

    PubMed Central

    Albisinni, Simone; Aoun, Fouad; Peltier, Alexandre; van Velthoven, Roland

    2016-01-01

    The vesicourethral anastomosis represents a step of major difficulty at the end of minimally invasive radical prostatectomy. Over 10 years ago, we have devised the single-knot running vesicourethral anastomosis, which has been widely adopted in urologic departments worldwide. Aim of the current paper is to review the technique, its adaptability in complex situations, its complications, and possible modifications, including the use of barbed sutures. PMID:27340567

  14. Landscape context and scale differentially impact coffee leaf rust, coffee berry borer, and coffee root-knot nematodes.

    PubMed

    Avelino, Jacques; Romero-Gurdián, Alí; Cruz-Cuellar, Héctor F; Declerck, Fabrice A J

    2012-03-01

    Crop pest and disease incidences at plot scale vary as a result of landscape effects. Two main effects can be distinguished. First, landscape context provides habitats of variable quality for pests, pathogens, and beneficial and vector organisms. Second, the movements of these organisms are dependent on the connectivity status of the landscape. Most of the studies focus on indirect effects of landscape context on pest abundance through their predators and parasitoids, and only a few on direct effects on pests and pathogens. Here we studied three coffee pests and pathogens, with limited or no pressure from host-specific natural enemies, and with widely varying life histories, to test their relationships with landscape context: a fungus, Hemileia vastatrix, causal agent of coffee leaf rust; an insect, the coffee berry borer, Hypothenemus hampei (Coleoptera: Curculionidae); and root-knot nematodes, Meloidogyne spp. Their incidence was assessed in 29 coffee plots from Turrialba, Costa Rica. In addition, we characterized the landscape context around these coffee plots in 12 nested circular sectors ranging from 50 to 1500 m in radius. We then performed correlation analysis between proportions of different land uses at different scales and coffee pest and disease incidences. We obtained significant positive correlations, peaking at the 150 m radius, between coffee berry borer abundance and proportion of coffee in the landscape. We also found significant positive correlations between coffee leaf rust incidence and proportion of pasture, peaking at the 200 m radius. Even after accounting for plot level predictors of coffee leaf rust and coffee berry borer through covariance analysis, the significance of landscape structure was maintained. We hypothesized that connected coffee plots favored coffee berry borer movements and improved its survival. We also hypothesized that wind turbulence, produced by low-wind-resistance land uses such as pasture, favored removal of coffee

  15. Crystallization of Spätzle, a cystine-knot protein involved in embryonic development and innate immunity in Drosophila melanogaster

    SciTech Connect

    Hoffmann, Anita; Neumann, Piotr; Schierhorn, Angelika; Stubbs, Milton T.

    2008-08-01

    Crystallization of the cystine-knot protein Spätzle occurred following serendipitous limited degradation of the pro-Spätzle propeptide during the crystallization experiment. The Spätzle protein is involved in both the definition of the dorsal–ventral axis during embryonic development and in the adult innate immune response. The disulfide-linked dimeric cystine-knot protein has been expressed as a proprotein in inclusion bodies in Escherichia coli and refolded in vitro by rapid dilution. Initial orthorhombic crystals that diffracted to 7 Å resolution were obtained after three months by the sitting-drop vapour-diffusion method. Optimization of the crystallization conditions resulted in orthorhombic crystals (space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 53.0, b = 59.2, c = 62.5 Å) that diffracted to 2.8 Å resolution in-house. The small volume of the asymmetric unit indicated that it was not possible for the crystals to contain the complete pro-Spätzle dimer. Mass spectrometry, N-terminal sequencing and Western-blot analysis revealed that the crystals contained the C-terminal disulfide-linked cystine-knot dimer. Comparison of various crystallization experiments indicated that degradation of the N-terminal prodomain was dependent on the buffer conditions.

  16. Mitochondrial coding genome analysis of tropical root-knot nematodes (Meloidogyne) supports haplotype based diagnostics and reveals evidence of recent reticulate evolution

    PubMed Central

    Janssen, Toon; Karssen, Gerrit; Verhaeven, Myrtle; Coyne, Danny; Bert, Wim

    2016-01-01

    The polyphagous parthenogenetic root-knot nematodes of the genus Meloidogyne are considered to be the most significant nematode pest in sub-tropical and tropical agriculture. Despite the crucial need for correct diagnosis, identification of these pathogens remains problematic. The traditionally used diagnostic strategies, including morphometrics, host-range tests, biochemical and molecular techniques, now appear to be unreliable due to the recently-suggested hybrid origin of root-knot nematodes. In order to determine a suitable barcode region for these pathogens nine quickly-evolving mitochondrial coding genes were screened. Resulting haplotype networks revealed closely related lineages indicating a recent speciation, an anthropogenic-aided distribution through agricultural practices, and evidence for reticulate evolution within M. arenaria. Nonetheless, nucleotide polymorphisms harbor enough variation to distinguish these closely-related lineages. Furthermore, completeness of lineage sorting was verified by screening 80 populations from widespread geographical origins and variable hosts. Importantly, our results indicate that mitochondrial haplotypes are strongly linked and consistent with traditional esterase isozyme patterns, suggesting that different parthenogenetic lineages can be reliably identified using mitochondrial haplotypes. The study indicates that the barcode region Nad5 can reliably identify the major lineages of tropical root-knot nematodes. PMID:26940543

  17. Management of Root-knot and Reniform Nematodes in Ultra-Narrow Row Cotton with 1,3-Dichloropropene

    PubMed Central

    Kinloch, R. A.; Rich, J. R.

    2001-01-01

    Ultra-narrow row cotton studies were conducted during 1999 at two field sites in northern Florida. One site was naturally infested with Meloidogyne incognita Race 3 and the other with Rotylenchulus reniformis. The fumigant 1,3-dichloropropene (1,3-D) was applied broadcast at rates of 0, 16, 32, 48, 64, 80, and 96 kg ai./ha in replicated plots before planting Delta Pine 655 BRR cotton in 25-cm-wide rows. Post-harvest soil population densities at the root-knot nematode site had a significant (P ≤ 0.01) negative linear relationship to 1,3-D dosage level. Cotton lint yields at this site had a significant (P ≤ 0.01) positive linear relationship to 1,3-D dosage level. At the reniform nematode site, there was no relationship between post-harvest soil population densities of reniform nematodes and 1,3-D dosage level. However, significant (P ≤ 0.01) positive curvilinear relationships were found between both plant heights and lint yield to 1,3-D dosage levels. PMID:19265894

  18. Comparison of harmonic scalpel versus conventional knot tying for transection of short hepatic veins at liver transplantation: prospective randomized study.

    PubMed

    Olmez, A; Karabulut, K; Aydin, C; Kayaalp, C; Yilmaz, S

    2012-01-01

    The objective of this study was to compare harmonic scalpel for short hepatic vein transection with conventional ligation during recipient hepatectomy with caval preservation. Sixteen patients undergoing elective living donor liver transplantation were randomized into 2 groups. We recorded number, diameter, and location of each short hepatic vein, procedure time, central venous pressure, and degree of liver failure (Child-Pugh and Model for End stage Liver Disease scores). As an end point, we observed the intraoperative and postoperative bleeding rates of the transected veins. We transected 144 veins of mean diameter of 2.6 ± 1.8 mm (range, 1-12 mm). Mean number of short hepatic veins in each person was 9 (range, 5-16). Harmonic scalpel was safe for veins with a diameter ≤ 2 mm; these veins were more prone to bleeding with conventional ligation. Bleeding rate was higher after ligation of veins in the upper half than the lower half of the cava (37% vs 21%; P = .04). Both total and per vessel procedure time did not differ between the groups. No postoperative bleeding complications occurred. Transection of veins with a diameter ≤ 2 mm by harmonic scalpel was as safe as conventional ligation. Harmonic scalpel transection of small hepatic veins (≤ 2 mm) can be even safer than conventional control by knot tying, particularly in narrow areas. PMID:22841252

  19. Long-Term In Vitro System for Maintenance and Amplification of Root-Knot Nematodes in Cucumis sativus Roots.

    PubMed

    Díaz-Manzano, Fernando E; Olmo, Rocío; Cabrera, Javier; Barcala, Marta; Escobar, Carolina; Fenoll, Carmen

    2016-01-01

    Root-knot nematodes (RKN) are polyphagous plant-parasitic roundworms that produce large crop losses, representing a relevant agricultural pest worldwide. After infection, they induce swollen root structures called galls containing giant cells (GCs) indispensable for nematode development. Among efficient control methods are biotechnology-based strategies that require a deep knowledge of underlying molecular processes during the plant-nematode interaction. Methods of achieving this knowledge include the application of molecular biology techniques such as transcriptomics (as massive sequencing or microarray hybridization), proteomics or metabolomics. These require aseptic experimental conditions, as undetected contamination with other microorganisms could compromise the interpretation of the results. Herein, we present a simple, efficient and long-term method for nematode amplification on cucumber roots grown in vitro. Amplification of juveniles (J2) from the starting inoculum is around 40-fold. The method was validated for three Meloidogyne species (Meloidogyne javanica, M. incognita, and M. arenaria), producing viable and robust freshly hatched J2s. These J2s can be used for further in vitro infection of different plant species such as Arabidopsis, tobacco and tomato, as well as to maintain and amplify the population. The method allowed maintenance of around 90 Meloidogyne sp. generations (one every 2 months) from a single initial female over 15 years.

  20. Discrete knot ejection from the jet in a nearby low-luminosity active galactic nucleus, M81*

    NASA Astrophysics Data System (ADS)

    King, Ashley L.; Miller, Jon M.; Bietenholz, Michael; Gültekin, Kayhan; Reynolds, Mark T.; Mioduszewski, Amy; Rupen, Michael; Bartel, Norbert

    2016-08-01

    Observational constraints of the relativistic jets from black holes have largely come from the most powerful and extended jets, leaving the nature of the low-luminosity jets a mystery. M81* is one of the nearest low-luminosity jets and it emitted an extremely large radio flare in 2011, allowing us to study compact core emission with unprecedented sensitivity and linear resolution. Using a multiwavelength campaign, we were able to track the flare as it re-brightened and became optically thick. Simultaneous X-ray observations indicated that the radio re-brightening was preceded by a low-energy X-ray flare at least 12 days earlier. Associating the time delay (tdelay) between the two bands with the cooling time in a synchrotron flare, we find that the magnetic field strength was 1.9 < B < 9.2 G, which is consistent with magnetic field estimate from spectral energy distribution modelling, B < 10.2 G. In addition, Very Long Baseline Array observations at 23 GHz clearly illustrate a discrete knot moving at a low relativistic speed of vapp/c = 0.51 +/- 0.17 associated with the initial radio flare. The observations indicate radial jet motions for the first time in M81*. This has profound implications for jet production, as it means radial motion can be observed in even the lowest-luminosity AGN, but at slower velocities and smaller radial extents (≍104 RG).

  1. Transcriptional Changes of the Root-Knot Nematode Meloidogyne incognita in Response to Arabidopsis thaliana Root Signals

    PubMed Central

    Teillet, Alice; Dybal, Katarzyna; Kerry, Brian R.; Miller, Anthony J.; Curtis, Rosane H. C.; Hedden, Peter

    2013-01-01

    Root-knot nematodes are obligate parasites that invade roots and induce the formation of specialized feeding structures. Although physiological and molecular changes inside the root leading to feeding site formation have been studied, very little is known about the molecular events preceding root penetration by nematodes. In order to investigate the influence of root exudates on nematode gene expression before plant invasion and to identify new genes potentially involved in parasitism, sterile root exudates from the model plant Arabidopsis thaliana were produced and used to treat Meloidogyne incognita pre-parasitic second-stage juveniles. After confirming the activity of A. thaliana root exudates (ARE) on M. incognita stylet thrusting, six new candidate genes identified by cDNA-AFLP were confirmed by qRT-PCR as being differentially expressed after incubation for one hour with ARE. Using an in vitro inoculation method that focuses on the events preceding the root penetration, we show that five of these genes are differentially expressed within hours of nematode exposure to A. thaliana roots. We also show that these genes are up-regulated post nematode penetration during migration and feeding site initiation. This study demonstrates that preceding root invasion plant-parasitic nematodes are able to perceive root signals and to respond by changing their behaviour and gene expression. PMID:23593446

  2. Pulling-force-induced elongation and alignment effects on entanglement and knotting characteristics of linear polymers in a melt.

    PubMed

    Panagiotou, E; Kröger, M

    2014-10-01

    We employ a primitive path (PP) algorithm and the Gauss linking integral to study the degree of entanglement and knotting characteristics of linear polymer model chains in a melt under the action of a constant pulling force applied to selected chain ends. Our results for the amount of entanglement, the linking number, the average crossing number, the writhe of the chains and their PPs and the writhe of the entanglement strands all suggest a different response at the length scale of entanglement strands than that of the chains themselves and of the corresponding PPs. Our findings indicate that the chains first stretch at the level of entanglement strands and next the PP (tube) gets oriented with the "flow." These two phases of the extension and alignment of the chains coincide with two phases related to the disentanglement of the chains. Soon after the onset of external force the PPs attain a more entangled conformation, and the number of nontrivially linked end-to-end closed chains increases. Next, the chains disentangle continuously to attain an almost unentangled conformation. Using the linking matrix of the chains in the melt, we furthermore show that these phases are accompanied by a different scaling of the homogeneity of the global entanglement in the system. The homogeneity of the end-to-end closed chains first increases to a maximum and then decreases slowly to a value characterizing a completely unlinked system.

  3. Management of Root-knot Nematodes by Phenamiphos Applied through an Irrigation Simulator with Various Amounts of Water.

    PubMed

    Johnson, A W; Young, J R; Wright, W C

    1986-07-01

    Phenamiphos (6.7 kg a.i./ha) was applied via an irrigation simulator to squash at planting (AP) and 2 weeks after planting (PP), and to corn AP and 1 week PP to manage root-knot nematodes (Meloidogyne incognita). The nematicide was applied with 0.25, 0.64, 1.27, and 1.91 cm surface water/ ha to a Lakeland sand in which the soil moisture was at or near field capacity. Based on efficacy and crop response, no additional benefits resulted when phenamiphos was applied in volumes of water greater than 0.25 crn/ha. The cost of applying each 0.25 cm of water over a hectare is approximately $1.08, or a 92% reduction in nematicide application cost over conventional methods ($13.50/ha). Low root-gall indices and high yields from squash and corn indicate more effective nematode management when phenamiphos was applied AP rather than PP. Results from this method of applying phenamiphos suggest that certain nematicides could be used as salvage alternatives when nematodes are detected in crops soon after planting. For multiple-pest management, nematicides, other compatible biocides, and fertilizers could be applied simultaneously with sprinkler irrigation. PMID:19294192

  4. Mitochondrial Haplotype-based Identification of Root-knot Nematodes (Meloidogyne spp.) on Cut Foliage Crops in Florida

    PubMed Central

    Baidoo, Richard; Joseph, Soumi; Mengistu, Tesfamariam M.; Brito, Janete A.; McSorley, Robert; Stamps, Robert H.; Crow, William T.

    2016-01-01

    Florida accounts for more than 75% of the national cut foliage production. Unfortunately, root-knot nematodes (RKN) (Meloidogyne spp.) are a serious problem on these crops, rendering many farms unproductive. Currently, information on the Meloidogyne spp. occurring on most commonly cultivated cut foliage crops in Florida, and tools for their rapid identification are lacking. The objectives of this study were to (i) identify specific RKN infecting common ornamental cut foliage crops in Florida and (ii) evaluate the feasibility of using the mtDNA haplotype as a molecular diagnostic tool for rapid identification of large samples of RKN. A total of 200 Meloidogyne females were collected from cut foliage plant roots. Meloidogyne spp. were identified by PCR and RFLP of mitochondrial DNA. PCR and RFLP of mitochondrial DNA were effective in discriminating the Meloidogyne spp. present. Meloidogyne incognita is the most dominant RKN on cut foliage crops in Florida and must be a high target for making management decisions. Other Meloidogyne spp. identified include M. javanica, M. hapla, Meloidogyne sp. 1, and Meloidogyne sp. 2. The results for this study demonstrate the usefulness of the mtDNA haplotype-based designation as a valuable molecular tool for identification of Meloidogyne spp. PMID:27765993

  5. Involvement of nitric oxide in the jasmonate-dependent basal defense against root-knot nematode in tomato plants

    PubMed Central

    Zhou, Jie; Jia, Feifei; Shao, Shujun; Zhang, Huan; Li, Guiping; Xia, Xiaojian; Zhou, Yanhong; Yu, Jingquan; Shi, Kai

    2015-01-01

    Jasmonic acid (JA) and nitric oxide (NO) are well-characterized signaling molecules in plant defense responses. However, their roles in plant defense against root-knot nematode (RKN, Meloidogyne incognita) infection are largely unknown. In this study, we found that the transcript levels of the JA- and NO-related biosynthetic and signaling component genes were induced after RKN infection. Application of exogenous JA and sodium nitroprusside (SNP; a NO donor) significantly decreased the number of egg masses in tomato roots after RKN infection and partially alleviated RKN-induced decreases in plant fresh weight and net photosynthetic rate. These molecules also alleviated RKN-induced increases in root electrolyte leakage and membrane peroxidation. Importantly, NO scavenger partially inhibited JA-induced RKN defense. The pharmacological inhibition of JA biosynthesis significantly increased the plants’ susceptibility to RKNs, which was effectively alleviated by SNP application, showing that NO may be involved in the JA-dependent RKN defense pathway. Furthermore, both JA and SNP induced increases in protease inhibitor 2 (PI2) gene expression after RKN infestation. Silencing of PI2 compromised both JA- and SNP-induced RKN defense responses, suggesting that the PI2 gene mediates JA- and NO-induced defense against RKNs. This work will be important for deepening the understanding of the mechanisms involved in basal defense against RKN attack in plants. PMID:25914698

  6. [Effects of adding straw carbon source to root knot nematode diseased soil on soil microbial biomass and protozoa abundance].

    PubMed

    Zhang, Si-Hui; Lian, Jian-Hong; Cao, Zhi-Ping; Zhao, Li

    2013-06-01

    A field experiment with successive planting of tomato was conducted to study the effects of adding different amounts of winter wheat straw (2.08 g x kg(-1), 1N; 4.16 g x kg(-1), 2N; and 8.32 g x kg(-1), 4N) to the soil seriously suffered from root knot nematode disease on the soil microbial biomass and protozoa abundance. Adding straw carbon source had significant effects on the contents of soil microbial biomass carbon (MBC) and microbial biomass nitrogen (MBN) and the abundance of soil protozoa, which all decreased in the order of 4N > 2N > 1N > CK. The community structure of soil protozoa also changed significantly under straw addition. In the treatments with straw addition, the average proportion of fagellate, amoeba, and ciliates accounted for 36.0%, 59.5%, and 4.5% of the total protozoa, respectively. Under the same adding amounts of wheat straw, there was an increase in the soil MBC and MBN contents, MBC/MBN ratio, and protozoa abundance with increasing cultivation period. PMID:24066551

  7. RKN Lethal DB: A database for the identification of Root Knot Nematode (Meloidogyne spp.) candidate lethal genes

    PubMed Central

    Ismail, Ahmed; Matthews, Benjamin F; Alkharouf, Nadim W

    2012-01-01

    Root Knot nematode (RKN; Meloidogyne spp.) is one of the most devastating parasites that infect the roots of hundreds of plant species. RKN cannot live independently from their hosts and are the biggest contributors to the loss of the world's primary foods. RNAi gene silencing studies have demonstrated that there are fewer galls and galls are smaller when RNAi constructs targeted to silence certain RKN genes are expressed in plant roots. We conducted a comparative genomics analysis, comparing RKN genes of six species: Meloidogyne Arenaria, Meloidogyne Chitwoodi, Meloidogyne Hapla, Meloidogyne Incognita, Meloidogyne Javanica, and Meloidogyne Paranaensis to that of the free living nematode Caenorhabditis elegans, to identify candidate genes that will be lethal to RKN when silenced or mutated. Our analysis yielded a number of such candidate lethal genes in RKN, some of which have been tested and proven to be effective in soybean roots. A web based database was built to house and allow scientists to search the data. This database will be useful to scientists seeking to identify candidate genes as targets for gene silencing to confer resistance in plants to RKN. Availability The database can be accessed from http://bioinformatics.towson.edu/RKN/ PMID:23144556

  8. Development of enzyme linked immunosorbent assay (ELISA) for the detection of root-knot nematode Meloidogyne incognita.

    PubMed

    Kapur-Ghai, J; Kaur, M; Goel, P

    2014-09-01

    Root-knot nematodes (Meloidogyne incognita) are obligate, sedentary plant endoparasites that are extremely polyphagous in nature and cause severe economic losses in agriculture. Hence, it is essential to control the parasite at an early stage. For any control strategy to be effective, an early and accurate diagnosis is of paramount importance. Immunoassays have the inherent advantages of sensitivity and specificity; have the potential to identify and quantify these plant-parasitic nematodes. Hence, in the present studies, enzyme-linked immunosorbent assay (ELISA) has been developed for the detection of M.incognita antigens. First an indirect ELISA was developed for detection and titration of anti-M.incognita antibodies. Results indicated as high as 320 K titre of the antisera. Finally competitive inhibition ELISA was developed employing these anti-M.incognita antibodies for detection of M.incognita antigens. Sensitivity of ELISA was 10 fg. Competitive inhibition ELISA developed in the present studies has the potential of being used as an easy, rapid, specific and sensitive diagnostic tool for the detection of M.incognita infection.

  9. Developing objectives with multiple stakeholders: adaptive management of horseshoe crabs and Red Knots in the Delaware Bay

    USGS Publications Warehouse

    McGowan, Conor P.; Lyons, James E.; Smith, David

    2015-01-01

    Structured decision making (SDM) is an increasingly utilized approach and set of tools for addressing complex decisions in environmental management. SDM is a value-focused thinking approach that places paramount importance on first establishing clear management objectives that reflect core values of stakeholders. To be useful for management, objectives must be transparently stated in unambiguous and measurable terms. We used these concepts to develop consensus objectives for the multiple stakeholders of horseshoe crab harvest in Delaware Bay. Participating stakeholders first agreed on a qualitative statement of fundamental objectives, and then worked to convert those objectives to specific and measurable quantities, so that management decisions could be assessed. We used a constraint-based approach where the conservation objectives for Red Knots, a species of migratory shorebird that relies on horseshoe crab eggs as a food resource during migration, constrained the utility of crab harvest. Developing utility functions to effectively reflect the management objectives allowed us to incorporate stakeholder risk aversion even though different stakeholder groups were averse to different or competing risks. While measurable objectives and quantitative utility functions seem scientific, developing these objectives was fundamentally driven by the values of the participating stakeholders.

  10. [Effects of adding straw carbon source to root knot nematode diseased soil on soil microbial biomass and protozoa abundance].

    PubMed

    Zhang, Si-Hui; Lian, Jian-Hong; Cao, Zhi-Ping; Zhao, Li

    2013-06-01

    A field experiment with successive planting of tomato was conducted to study the effects of adding different amounts of winter wheat straw (2.08 g x kg(-1), 1N; 4.16 g x kg(-1), 2N; and 8.32 g x kg(-1), 4N) to the soil seriously suffered from root knot nematode disease on the soil microbial biomass and protozoa abundance. Adding straw carbon source had significant effects on the contents of soil microbial biomass carbon (MBC) and microbial biomass nitrogen (MBN) and the abundance of soil protozoa, which all decreased in the order of 4N > 2N > 1N > CK. The community structure of soil protozoa also changed significantly under straw addition. In the treatments with straw addition, the average proportion of fagellate, amoeba, and ciliates accounted for 36.0%, 59.5%, and 4.5% of the total protozoa, respectively. Under the same adding amounts of wheat straw, there was an increase in the soil MBC and MBN contents, MBC/MBN ratio, and protozoa abundance with increasing cultivation period.

  11. Developing objectives with multiple stakeholders: adaptive management of horseshoe crabs and Red Knots in the Delaware Bay.

    PubMed

    McGowan, Conor P; Lyons, James E; Smith, David R

    2015-04-01

    Structured decision making (SDM) is an increasingly utilized approach and set of tools for addressing complex decisions in environmental management. SDM is a value-focused thinking approach that places paramount importance on first establishing clear management objectives that reflect core values of stakeholders. To be useful for management, objectives must be transparently stated in unambiguous and measurable terms. We used these concepts to develop consensus objectives for the multiple stakeholders of horseshoe crab harvest in Delaware Bay. Participating stakeholders first agreed on a qualitative statement of fundamental objectives, and then worked to convert those objectives to specific and measurable quantities, so that management decisions could be assessed. We used a constraint-based approach where the conservation objectives for Red Knots, a species of migratory shorebird that relies on horseshoe crab eggs as a food resource during migration, constrained the utility of crab harvest. Developing utility functions to effectively reflect the management objectives allowed us to incorporate stakeholder risk aversion even though different stakeholder groups were averse to different or competing risks. While measurable objectives and quantitative utility functions seem scientific, developing these objectives was fundamentally driven by the values of the participating stakeholders. PMID:25537153

  12. On the Determination of Ejecta Structure and Explosion Asymmetry from the X-ray Knots of Cassiopeia A

    NASA Technical Reports Server (NTRS)

    Laming, J. Martin; Hwang, Una

    2003-01-01

    We present a detailed analysis of Chandra X-ray spectra from individual ejecta knots in the supernova remnant Cassiopeia A. The spectra are fitted to give the electron temperature T(sub e), and (single) ionization age n(sub e)t. These quantities are compared with the predictions of self similar hydrodynamic models incorporating time dependent ionization and radiation losses, and Coulomb electron-ion equilibration behind the reverse shock, for a variety of different ejecta density profiles described by a uniform density core and a power law envelope. We find that the ejecta close to the 'jet' region in the NE, but not actually in the jet itself, have a systematically shallower outer envelope than ejecta elsewhere in the remnant, and we interpret this as being due to more energy of the initial explosion being directed in this polar direction as opposed to equatorially. The degree of asymmetry we infer is at the low end of that generally modelled in asymmetric core-collapse simulations, and may be used to rule out highly asymmetric explosion models.

  13. Host genetic resistance to root-knot nematodes, Meloidogyne spp., in Solanaceae: from genes to the field.

    PubMed

    Barbary, Arnaud; Djian-Caporalino, Caroline; Palloix, Alain; Castagnone-Sereno, Philippe

    2015-12-01

    Root-knot nematodes (RKNs) heavily damage most solanaceous crops worldwide. Fortunately, major resistance genes are available in a number of plant species, and their use provides a safe and economically relevant strategy for RKN control. From a structural point of view, these genes often harbour NBS-LRR motifs (i.e. a nucleotide binding site and a leucine rich repeat region near the carboxy terminus) and are organised in syntenic clusters in solanaceous genomes. Their introgression from wild to cultivated plants remains a challenge for breeders, although facilitated by marker-assisted selection. As shown with other pathosystems, the genetic background into which the resistance genes are introgressed is of prime importance to both the expression of the resistance and its durability, as exemplified by the recent discovery of quantitative trait loci conferring quantitative resistance to RKNs in pepper. The deployment of resistance genes at a large scale may result in the emergence and spread of virulent nematode populations able to overcome them, as already reported in tomato and pepper. Therefore, careful management of the resistance genes available in solanaceous crops is crucial to avoid significant reduction in the duration of RKN genetic control in the field. From that perspective, only rational management combining breeding and cultivation practices will allow the design and implementation of innovative, sustainable crop production systems that protect the resistance genes and maintain their durability.

  14. Involvement of nitric oxide in the jasmonate-dependent basal defense against root-knot nematode in tomato plants.

    PubMed

    Zhou, Jie; Jia, Feifei; Shao, Shujun; Zhang, Huan; Li, Guiping; Xia, Xiaojian; Zhou, Yanhong; Yu, Jingquan; Shi, Kai

    2015-01-01

    Jasmonic acid (JA) and nitric oxide (NO) are well-characterized signaling molecules in plant defense responses. However, their roles in plant defense against root-knot nematode (RKN, Meloidogyne incognita) infection are largely unknown. In this study, we found that the transcript levels of the JA- and NO-related biosynthetic and signaling component genes were induced after RKN infection. Application of exogenous JA and sodium nitroprusside (SNP; a NO donor) significantly decreased the number of egg masses in tomato roots after RKN infection and partially alleviated RKN-induced decreases in plant fresh weight and net photosynthetic rate. These molecules also alleviated RKN-induced increases in root electrolyte leakage and membrane peroxidation. Importantly, NO scavenger partially inhibited JA-induced RKN defense. The pharmacological inhibition of JA biosynthesis significantly increased the plants' susceptibility to RKNs, which was effectively alleviated by SNP application, showing that NO may be involved in the JA-dependent RKN defense pathway. Furthermore, both JA and SNP induced increases in protease inhibitor 2 (PI2) gene expression after RKN infestation. Silencing of PI2 compromised both JA- and SNP-induced RKN defense responses, suggesting that the PI2 gene mediates JA- and NO-induced defense against RKNs. This work will be important for deepening the understanding of the mechanisms involved in basal defense against RKN attack in plants.

  15. Intraspecific variability of the facultative meiotic parthenogenetic root-knot nematode (Meloidogyne graminicola) from rice fields in Vietnam.

    PubMed

    Bellafiore, Stéphane; Jougla, Claire; Chapuis, Élodie; Besnard, Guillaume; Suong, Malyna; Vu, Phong Nguyen; De Waele, Dirk; Gantet, Pascal; Thi, Xuyen Ngo

    2015-07-01

    Twenty years ago, the facultative meiotic parthenogenetic root-knot nematode (RKN), Meloidogyne graminicola, was recognised as an important rice pathogen in South Vietnam. Although this country is one of the most important rice exporters worldwide, a comprehensive picture of the occurrence of M. graminicola in Vietnamese rice fields is still not available. Therefore a nematode survey was carried out with the aim of better understanding the geographical distribution, and the pathogenic and genetic variability of the RKN in Vietnam. From the fields surveyed in a range of ecosystems, 21 RKN populations were recovered from infected rice roots. A diagnostic SCAR marker was developed showing that all Vietnamese populations belong to M. graminicola. Furthermore, sequencing of the Internal Transcribed Spacer (ITS) of the rDNA genes confirmed this identification. These populations were then characterised using morphometrics and pathogenicity tests (host plant range diversity, reproduction and virulence diversity) revealing intraspecific variability. We showed that morphometric traits are mainly genetically heritable characters with significant differences among the studied populations. Finally, a distinctive trait signature was found for the populations isolated from the upland rice cultures. All together, our study reveals the prevalence of M. graminicola populations in Vietnamese rice. Further investigations need to be developed to explore the population dynamics and evolutionary history of this species in South East Asia.

  16. Whole-mount confocal imaging of nuclei in giant feeding cells induced by root-knot nematodes in Arabidopsis.

    PubMed

    Vieira, Paulo; Engler, Gilbert; de Almeida Engler, Janice

    2012-07-01

    • Excellent visualization of nuclei was obtained here using a whole-mount procedure adapted to provide high-resolution images of large, irregularly shaped nuclei. The procedure is based on tissue clearing, and fluorescent staining of nuclear DNA with the dye propidium iodide. • The method developed for standard confocal imaging was applied to large multicellular root swellings, named galls, induced in plant hosts by the root-knot nematode Meloidogyne incognita. • Here, we performed a functional analysis, and examined the nuclear structure in giant feeding cells overexpressing the cell cycle inhibitor Kip-related protein 4 (KRP4). Ectopic KRP4 expression in galls led to aberrant nuclear structure, disturbing giant cell expansion and nematode reproduction. In vivo live-cell imaging of GFP-KRP4 demonstrated that this protein co-localizes to chromosomes from prophase to late anaphase during cell cycle progression. • The data presented here suggest the involvement of KRP4 during mitotic progression in plant cells. The detailed results obtained using confocal analysis also demonstrate the potential utility of a rapid, easy-to-use clearing method for the analysis of the nuclei of certain Arabidopsis mutants and other complex plant nuclei.

  17. High conservation of the differentially amplified MPA2 satellite DNA family in parthenogenetic root-knot nematodes.

    PubMed

    Mestrović, Nevenka; Castagnone-Sereno, Philippe; Plohl, Miroslav

    2006-07-19

    Sequence variability and distribution of a newly characterized MPA2 satellite DNA family are described in five root-knot nematode species of the genus Meloidogyne, the mitotic parthenogens M. paranaensis, M. incognita, M. arenaria and M. javanica, and the meiotic/mitotic M. hapla (isolates A and B, respectively). The lack of distinctive mutations and the considerable contribution (40.8%) of ancestral changes disclose an ancient satellite DNA which existed in the common ancestor of extant parthenogenetic species in the same or similar form and remained preserved for a period of at least 43 My. Nonuniformly distributed polymorphic sites along the satellite monomer suggest differences in constraints acting on particular sequence segments. Sequence diversity is clearly unaffected by significant differences in genomic abundance of the MPA2 satellite DNA in the examined species. Observed results suggest that the dynamics of this satellite DNA family might be in the first instance a consequence of characteristics of its nucleotide sequence and possible constraints imposed on it. Under conditions of mitotic and meiotic parthenogenesis, slow accumulation of mutations and slow replacement of old MPA2 sequence variants with new ones may be equivalent to the dynamics of some satellite DNA sequences conserved for extremely long evolutionary periods in sexual species.

  18. Long-Term In Vitro System for Maintenance and Amplification of Root-Knot Nematodes in Cucumis sativus Roots

    PubMed Central

    Díaz-Manzano, Fernando E.; Olmo, Rocío; Cabrera, Javier; Barcala, Marta; Escobar, Carolina; Fenoll, Carmen

    2016-01-01

    Root-knot nematodes (RKN) are polyphagous plant-parasitic roundworms that produce large crop losses, representing a relevant agricultural pest worldwide. After infection, they induce swollen root structures called galls containing giant cells (GCs) indispensable for nematode development. Among efficient control methods are biotechnology-based strategies that require a deep knowledge of underlying molecular processes during the plant-nematode interaction. Methods of achieving this knowledge include the application of molecular biology techniques such as transcriptomics (as massive sequencing or microarray hybridization), proteomics or metabolomics. These require aseptic experimental conditions, as undetected contamination with other microorganisms could compromise the interpretation of the results. Herein, we present a simple, efficient and long-term method for nematode amplification on cucumber roots grown in vitro. Amplification of juveniles (J2) from the starting inoculum is around 40-fold. The method was validated for three Meloidogyne species (Meloidogyne javanica, M. incognita, and M. arenaria), producing viable and robust freshly hatched J2s. These J2s can be used for further in vitro infection of different plant species such as Arabidopsis, tobacco and tomato, as well as to maintain and amplify the population. The method allowed maintenance of around 90 Meloidogyne sp. generations (one every 2 months) from a single initial female over 15 years. PMID:26941745

  19. Disulfide assignment of the C-terminal cysteine knot of agouti-related protein (AGRP) by direct sequencing analysis.

    PubMed

    Young, Y; Zeni, L; Rosenfeld, R D; Stark, K L; Rohde, M F; Haniu, M

    1999-12-01

    We have assigned the disulfide structure of Md-65 agouti-related protein (Md65-AGRP) using differential reduction and alkylation followed by direct sequencing analysis. The mature human AGRP is a single polypeptide chain of 112 amino acid residues, consisting of an N-terminal acidic region and a unique C-terminal cysteine-rich domain. The C-terminal domain, a 48 amino acid peptide named Md65-AGRP, was expressed in Escherichia coil cells and refolded under different conditions from the mature recombinant protein. The disulfide bonds in the cystine knot structure of Md65-AGRP were partially reduced using tris(2-carboxyethyl) phosphine (TCEP) under acidic conditions, followed by alkylation with N-ethylmaleimide (NEM). The procedure generated several isoforms with varying degrees of NEM alkylation. The multiple forms of Md65-AGRP generated by partial reduction and NEM modification were then completely reduced and carboxymethylated to identify unreactive disulfide bonds. Differentially labeled Md65-AGRP were directly sequenced and analyzed by MALDI mass spectrometry. The results confirmed that Md65-AGRP contained the same disulfide structure as that of Md5-AGRP reported previously [Bures, E. J., Hui, J. O., Young, Y. et al. (1998) Biochemistry 37, 12172-12177].

  20. Influence of root-knot nematode infestation on antioxidant enzymes, chlorophyll content and growth in Pogostemon cablin (Blanco) Benth.

    PubMed

    Bhau, B S; Borah, Bitupon; Ahmed, Reshma; Phukon, P; Gogoi, Barbi; Sarmah, D K; Lal, M; Wann, S B

    2016-04-01

    Plants adapt themselves to overcome adverse environmental conditions, and this involves a plethora of concurrent cellular activities. Physiological experiments or metabolic profiling can quantify this response. Among several diseases of Pogostemon cablin (Blanco) Benth. (Patchouli), root-knot nematode infection caused by Meloidogyne incognita (Kofoid and White) Chitwood causes severe damage to the plant and hence, the oil production. In the present study, we identified M. incognita morphologically and at molecular level using sequenced characterized amplified region marker (SCAR). M. incognita was artificially inoculated at different levels of second stage juveniles (J₂) to examine the effect on Patchouli plant growth parameters. Peroxidase and polyphenol oxidase enzyme activity and changes in the total phenol and chlorophyll contents in M. incognita was also evaluated in response to infection. The results have demonstrated that nematode infestation leads to increased peroxidase activities in the leaves of the patchouli plants and thereby, increase in phenolic content as a means of defence against nematode infestation. Chlorophyll content was also found decreased but no changes in polyphenol oxidase enzyme activity.

  1. Developing Objectives with Multiple Stakeholders: Adaptive Management of Horseshoe Crabs and Red Knots in the Delaware Bay

    NASA Astrophysics Data System (ADS)

    McGowan, Conor P.; Lyons, James E.; Smith, David R.

    2015-04-01

    Structured decision making (SDM) is an increasingly utilized approach and set of tools for addressing complex decisions in environmental management. SDM is a value-focused thinking approach that places paramount importance on first establishing clear management objectives that reflect core values of stakeholders. To be useful for management, objectives must be transparently stated in unambiguous and measurable terms. We used these concepts to develop consensus objectives for the multiple stakeholders of horseshoe crab harvest in Delaware Bay. Participating stakeholders first agreed on a qualitative statement of fundamental objectives, and then worked to convert those objectives to specific and measurable quantities, so that management decisions could be assessed. We used a constraint-based approach where the conservation objectives for Red Knots, a species of migratory shorebird that relies on horseshoe crab eggs as a food resource during migration, constrained the utility of crab harvest. Developing utility functions to effectively reflect the management objectives allowed us to incorporate stakeholder risk aversion even though different stakeholder groups were averse to different or competing risks. While measurable objectives and quantitative utility functions seem scientific, developing these objectives was fundamentally driven by the values of the participating stakeholders.

  2. Developing objectives with multiple stakeholders: adaptive management of horseshoe crabs and Red Knots in the Delaware Bay.

    PubMed

    McGowan, Conor P; Lyons, James E; Smith, David R

    2015-04-01

    Structured decision making (SDM) is an increasingly utilized approach and set of tools for addressing complex decisions in environmental management. SDM is a value-focused thinking approach that places paramount importance on first establishing clear management objectives that reflect core values of stakeholders. To be useful for management, objectives must be transparently stated in unambiguous and measurable terms. We used these concepts to develop consensus objectives for the multiple stakeholders of horseshoe crab harvest in Delaware Bay. Participating stakeholders first agreed on a qualitative statement of fundamental objectives, and then worked to convert those objectives to specific and measurable quantities, so that management decisions could be assessed. We used a constraint-based approach where the conservation objectives for Red Knots, a species of migratory shorebird that relies on horseshoe crab eggs as a food resource during migration, constrained the utility of crab harvest. Developing utility functions to effectively reflect the management objectives allowed us to incorporate stakeholder risk aversion even though different stakeholder groups were averse to different or competing risks. While measurable objectives and quantitative utility functions seem scientific, developing these objectives was fundamentally driven by the values of the participating stakeholders.

  3. Influence of root-knot nematode infestation on antioxidant enzymes, chlorophyll content and growth in Pogostemon cablin (Blanco) Benth.

    PubMed

    Bhau, B S; Borah, Bitupon; Ahmed, Reshma; Phukon, P; Gogoi, Barbi; Sarmah, D K; Lal, M; Wann, S B

    2016-04-01

    Plants adapt themselves to overcome adverse environmental conditions, and this involves a plethora of concurrent cellular activities. Physiological experiments or metabolic profiling can quantify this response. Among several diseases of Pogostemon cablin (Blanco) Benth. (Patchouli), root-knot nematode infection caused by Meloidogyne incognita (Kofoid and White) Chitwood causes severe damage to the plant and hence, the oil production. In the present study, we identified M. incognita morphologically and at molecular level using sequenced characterized amplified region marker (SCAR). M. incognita was artificially inoculated at different levels of second stage juveniles (J₂) to examine the effect on Patchouli plant growth parameters. Peroxidase and polyphenol oxidase enzyme activity and changes in the total phenol and chlorophyll contents in M. incognita was also evaluated in response to infection. The results have demonstrated that nematode infestation leads to increased peroxidase activities in the leaves of the patchouli plants and thereby, increase in phenolic content as a means of defence against nematode infestation. Chlorophyll content was also found decreased but no changes in polyphenol oxidase enzyme activity. PMID:27295922

  4. Intraspecific variability of the facultative meiotic parthenogenetic root-knot nematode (Meloidogyne graminicola) from rice fields in Vietnam.

    PubMed

    Bellafiore, Stéphane; Jougla, Claire; Chapuis, Élodie; Besnard, Guillaume; Suong, Malyna; Vu, Phong Nguyen; De Waele, Dirk; Gantet, Pascal; Thi, Xuyen Ngo

    2015-07-01

    Twenty years ago, the facultative meiotic parthenogenetic root-knot nematode (RKN), Meloidogyne graminicola, was recognised as an important rice pathogen in South Vietnam. Although this country is one of the most important rice exporters worldwide, a comprehensive picture of the occurrence of M. graminicola in Vietnamese rice fields is still not available. Therefore a nematode survey was carried out with the aim of better understanding the geographical distribution, and the pathogenic and genetic variability of the RKN in Vietnam. From the fields surveyed in a range of ecosystems, 21 RKN populations were recovered from infected rice roots. A diagnostic SCAR marker was developed showing that all Vietnamese populations belong to M. graminicola. Furthermore, sequencing of the Internal Transcribed Spacer (ITS) of the rDNA genes confirmed this identification. These populations were then characterised using morphometrics and pathogenicity tests (host plant range diversity, reproduction and virulence diversity) revealing intraspecific variability. We showed that morphometric traits are mainly genetically heritable characters with significant differences among the studied populations. Finally, a distinctive trait signature was found for the populations isolated from the upland rice cultures. All together, our study reveals the prevalence of M. graminicola populations in Vietnamese rice. Further investigations need to be developed to explore the population dynamics and evolutionary history of this species in South East Asia. PMID:26026576

  5. Ectopic expression of AtPAD4 broadens resistance of soybean to soybean cyst and root-knot nematodes

    PubMed Central

    2013-01-01

    Background The gene encoding PAD4 (PHYTOALEXIN-DEFICIENT4) is required in Arabidopsis for expression of several genes involved in the defense response to Pseudomonas syringae pv. maculicola. AtPAD4 (Arabidopsis thaliana PAD4) encodes a lipase-like protein that plays a regulatory role mediating salicylic acid signaling. Results We expressed the gene encoding AtPAD4 in soybean roots of composite plants to test the ability of AtPAD4 to deter plant parasitic nematode development. The transformed roots were challenged with two different plant parasitic nematode genera represented by soybean cyst nematode (SCN; Heterodera glycines) and root-knot nematode (RKN; Meloidogyne incognita). Expression of AtPAD4 in soybean roots decreased the number of mature SCN females 35 days after inoculation by 68 percent. Similarly, soybean roots expressing AtPAD4 exhibited 77 percent fewer galls when challenged with RKN. Conclusions Our experiments show that AtPAD4 can be used in an economically important crop, soybean, to provide a measure of resistance to two different genera of nematodes. PMID:23617694

  6. The Potential of Five Winter-grown Crops to Reduce Root-knot Nematode Damage and Increase Yield of Tomato

    PubMed Central

    López-Pérez, Jose Antonio; Roubtsova, Tatiana; de Cara García, Miguel

    2010-01-01

    Broccoli (Brassica oleracea), carrot (Daucus carota), marigold (Tagetes patula), nematode-resistant tomato (Solanum lycopersicum), and strawberry (Fragaria ananassa) were grown for three years during the winter in a root-knot nematode (Meloidogyne incognita) infested field in Southern California. Each year in the spring, the tops of all crops were shredded and incorporated in the soil. Amendment with poultry litter was included as a sub-treatment. The soil was then covered with clear plastic for six weeks and M. incognita-susceptible tomato was grown during the summer season. Plastic tarping raised the average soil temperature at 13 cm depth by 7°C.The different winter-grown crops or the poultry litter did not affect M. incognita soil population levels. However, root galling on summer tomato was reduced by 36%, and tomato yields increased by 19% after incorporating broccoli compared to the fallow control. This crop also produced the highest amount of biomass of the five winter-grown crops. Over the three-year trial period, poultry litter increased tomato yields, but did not affect root galling caused by M. incognita. We conclude that cultivation followed by soil incorporation of broccoli reduced M. incognita damage to tomato. This effect is possibly due to delaying or preventing a portion of the nematodes to reach the host roots. We also observed that M. incognita populations did not increase under a host crop during the cool season when soil temperatures remained low (< 18°C). PMID:22736848

  7. The Power of Omics to Identify Plant Susceptibility Factors and to Study Resistance to Root-knot Nematodes.

    PubMed

    Cabrera, Javier; Barcala, Marta; Fenoll, Carmen; Escobar, Carolina

    2016-01-01

    Technology has contributed to the advances on the genomic, transcriptomic, metabolomic and proteomic analyses of the plant-root-knot nematode (RKN) interaction. Holistic approaches to obtain expression profiles, such as cDNA libraries, differential display, q-PCR, microarray hybridization, massive sequencing, etc., have increased our knowledge on the molecular aspects of the interaction and have triggered the development of biotechnological tools to control this plague. An important limitation, however, has been the difficulty of cross-comparative analysis of these data. The construction of a database, NEMATIC, compiling microarray data available in Arabidopsis of the interaction with plant endoparasitic nematodes facilitated the in silico analysis, but is not sufficient for the handling of 'omic' information of different plant species. Omics combined with cell isolation techniques have shed some light on the heterogeneous expression signatures of nematode induced gall tissues, i.e., plant defences are specifically inhibited in giant cells within the gall aiding the nematode for a successful establishment. The natural resistance against RKNs varies from an early hypersensitive reaction before the establishment of the nematode, to the arrest of gall growth. The molecular bases of these mechanisms, not fully understood yet, could disclose powerful targets for the development of biotechnology based tools for nematode control.

  8. Transcription profile of soybean-root-knot nematode interaction reveals a key role of phythormones in the resistance reaction

    PubMed Central

    2013-01-01

    Background Root-knot nematodes (RKN– Meloidogyne genus) present extensive challenges to soybean crop. The soybean line (PI 595099) is known to be resistant against specific strains and races of nematode species, thus its differential gene expression analysis can lead to a comprehensive gene expression profiling in the incompatible soybean-RKN interaction. Even though many disease resistance genes have been studied, little has been reported about phytohormone crosstalk on modulation of ROS signaling during soybean-RKN interaction. Results Using 454 technology to explore the common aspects of resistance reaction during both parasitism and resistance phases it was verified that hormone, carbohydrate metabolism and stress related genes were consistently expressed at high levels in infected roots as compared to mock control. Most noteworthy genes include those encoding glycosyltransferases, peroxidases, auxin-responsive proteins and gibberellin-regulated genes. Our data analysis suggests the key role of glycosyltransferases, auxins and components of gibberellin signal transduction, biosynthesis and deactivation pathways in the resistance reaction and their participation in jasmonate signaling and redox homeostasis in mediating aspects of plant growth and responses to biotic stress. Conclusions Based on this study we suggest a reasonable model regarding to the complex mechanisms of crosstalk between plant hormones, mainly gibberellins and auxins, which can be crucial to modulate the levels of ROS in the resistance reaction to nematode invasion. The model also includes recent findings concerning to the participation of DELLA-like proteins and ROS signaling controlling plant immune or stress responses. Furthermore, this study provides a dataset of potential candidate genes involved in both nematode parasitism and resistance, which can be tested further for their role in this biological process using functional genomics approaches. PMID:23663436

  9. A Reliable Protocol for In situ microRNAs Detection in Feeding Sites Induced by Root-Knot Nematodes.

    PubMed

    Díaz-Manzano, Fernando E; Barcala, Marta; Engler, Gilbert; Fenoll, Carmen; de Almeida-Engler, Janice; Escobar, Carolina

    2016-01-01

    Galls induced by Meloidogyne spp. in plant roots are a complex organ formed by heterogeneous tissues; within them there are 5-8 giant cells (GCs) that root-knot nematodes use for their own nurturing. Subtle regulatory mechanisms likely mediate the massive gene repression described at early infection stages in galls, particularly in giant cells. Some of these mechanisms are mediated by microRNAs (miRNAs); hence we describe a reliable protocol to detect miRNAs abundance within the gall tissues induced by Meloidogyne spp. Some methods are available to determine the abundance of specific miRNAs in different plant parts; however, galls are complex organs formed by different tissues. Therefore, detection of miRNAs at the cellular level is particularly important to understand specific regulatory mechanisms operating within the GCs. In situ hybridization (ISH) is a classical, robust and accurate method that allows the localization of specific RNAs directly on plant tissues. We present for the first time an adapted and standardized ISH protocol to detect miRNAs in GCs induced by nematodes based on tissue embedded in paraffin and on-slide ISH of miRNAs. It can be adapted to any laboratory with no more requirements than a microtome and an optical microscope and it takes 10 days to perform once plant material has been collected. It showed to be very valuable for a quick detection of miRNAs expression pattern in tomato. We tested the protocol for miR390, as massive sequencing analysis showed that miR390 was induced at 3 dpi (days post-infection) in Arabidopsis galls and miR390 is 100% conserved between Arabidopsis and tomato. Successful localization of miR390 in tomato GCs constitutes a validation of this method that could be easily extended to other crops and/or syncytia induced by cyst nematodes. Finally, the protocol also includes guidance on troubleshooting.

  10. Bacterial Antagonists of Fungal Pathogens Also Control Root-Knot Nematodes by Induced Systemic Resistance of Tomato Plants

    PubMed Central

    Adam, Mohamed; Heuer, Holger; Hallmann, Johannes

    2014-01-01

    The potential of bacterial antagonists of fungal pathogens to control the root-knot nematode Meloidogyne incognita was investigated under greenhouse conditions. Treatment of tomato seeds with several strains significantly reduced the numbers of galls and egg masses compared with the untreated control. Best performed Bacillus subtilis isolates Sb4-23, Mc5-Re2, and Mc2-Re2, which were further studied for their mode of action with regard to direct effects by bacterial metabolites or repellents, and plant mediated effects. Drenching of soil with culture supernatants significantly reduced the number of egg masses produced by M. incognita on tomato by up to 62% compared to the control without culture supernatant. Repellence of juveniles by the antagonists was shown in a linked twin-pot set-up, where a majority of juveniles penetrated roots on the side without inoculated antagonists. All tested biocontrol strains induced systemic resistance against M. incognita in tomato, as revealed in a split-root system where the bacteria and the nematodes were inoculated at spatially separated roots of the same plant. This reduced the production of egg masses by up to 51%, while inoculation of bacteria and nematodes in the same pot had only a minor additive effect on suppression of M. incognita compared to induced systemic resistance alone. Therefore, the plant mediated effect was the major reason for antagonism rather than direct mechanisms. In conclusion, the bacteria known for their antagonistic potential against fungal pathogens also suppressed M. incognita. Such “multi-purpose” bacteria might provide new options for control strategies, especially with respect to nematode-fungus disease complexes that cause synergistic yield losses. PMID:24587352

  11. A Novel Cysteine Knot Protein for Enhancing Sperm Motility That Might Facilitate the Evolution of Internal Fertilization in Amphibians

    PubMed Central

    Yokoe, Misato; Takayama-Watanabe, Eriko; Saito, Yoko; Kutsuzawa, Megumi; Fujita, Kosuke; Ochi, Haruki; Nakauchi, Yuni; Watanabe, Akihiko

    2016-01-01

    Internal fertilization ensures successful reproduction of tetrapod vertebrates on land, although how this mode of reproduction evolved is unknown. Here, we identified a novel gene encoding sperm motility-initiating substance (SMIS), a key protein for the internal fertilization of the urodele Cynops pyrrhogaster by Edman degradation of an isolated protein and subsequent reverse transcription polymerase chain reaction. The SMIS gene encoded a 150 amino-acid sequence including the cysteine knot (CK) motif. No gene with substantial similarity to the SMIS was in the data bank of any model organisms. An active site of the SMIS was in the C-terminal region of the 2nd loop of CK motif. A synthetic peptide including the active site sequence bound to the midpiece and initiated/enhanced the circular motion of C. pyrrhogaster sperm, which allows penetration of the egg jelly specialized for the internal fertilization of this species. The synthetic peptide bound to whole sperm of Rhacophorus arboreus and enhanced the rotary motion, which is adapted to propel the sperm through egg coat matrix specialized for arboreal reproduction, while it bound to the tip of head and tail of Bufo japonicus sperm, and enhanced the vibratory motion, which is suited to sperm penetration through the egg jelly specialized for the reproduction of that species in freshwater. The polyclonal antibody against the active site of the SMIS specifically bound to egg coat matrix of R. arboreus. These findings suggest that diversification of amphibian reproductive modes accompanies the specialization of egg coat and the adaptation of sperm motility to penetrate the specialized egg coat, and SMIS acts as the sperm motility enhancer of anurans and urodeles that might facilitate to adaptively optimize sperm motility for allowing the establishment of internal fertilization. PMID:27579691

  12. Stage-Wise Identification and Analysis of miRNA from Root-Knot Nematode Meloidogyne incognita

    PubMed Central

    Subramanian, Parthiban; Choi, In-Chan; Mani, Vimalraj; Park, Junhyung; Subramaniyam, Sathiyamoorthy; Choi, Kang-Hyun; Sim, Joon-Soo; Lee, Chang-Muk; Koo, Ja Choon; Hahn, Bum-Soo

    2016-01-01

    In this study, we investigated global changes in miRNAs of Meloidogyne incognita throughout its life cycle. Small RNA sequencing resulted in approximately 62, 38, 38, 35, and 39 Mb reads in the egg, J2, J3, J4, and female stages, respectively. Overall, we identified 2724 known and 383 novel miRNAs (read count > 10) from all stages, of which 169 known and 13 novel miRNA were common to all the five stages. Among the stage-specific miRNAs, miR-286 was highly expressed in eggs, miR-2401 in J2, miR-8 and miR-187 in J3, miR-6736 in J4, and miR-17 in the female stages. These miRNAs are reported to be involved in embryo and neural development, muscular function, and control of apoptosis. Cluster analysis indicated the presence of 91 miRNA clusters, of which 36 clusters were novel and identified in this study. Comparison of miRNA families with other nematodes showed 17 families to be commonly absent in animal parasitic nematodes and M. incognita. Validation of 43 predicted common and stage-specific miRNA by quantitative PCR (qPCR) indicated their expression in the nematode. Stage-wise exploration of M. incognita miRNAs has not been carried out before and this work presents information on common and stage-specific miRNAs of the root-knot nematode. PMID:27775666

  13. Identification and overexpression of a knotted1-like transcription factor in switchgrass (Panicum virgatum L.) for lignocellulosic feedstock improvement

    DOE PAGES

    Wuddineh, Wegi A.; Mazarei, Mitra; Zhang, Ji -Yi; Turner, Geoffrey B.; Sykes, Robert W.; Decker, Stephen R.; Davis, Mark F.; Udvardi, Michael K.; C. Neal Stewart, Jr.

    2016-04-28

    High biomass production and wide adaptation has made switchgrass (Panicum virgatum L.) an important candidate lignocellulosic bioenergy crop. One major limitation of this and other lignocellulosic feedstocks is the recalcitrance of complex carbohydrates to hydrolysis for conversion to biofuels. Lignin is the major contributor to recalcitrance as it limits the accessibility of cell wall carbohydrates to enzymatic breakdown into fermentable sugars. Therefore, genetic manipulation of the lignin biosynthesis pathway is one strategy to reduce recalcitrance. Here, we identified a switchgrass Knotted1 transcription factor, PvKN1, with the aim of genetically engineering switchgrass for reduced biomass recalcitrance for biofuel production. Gene expressionmore » of the endogenous PvKN1 gene was observed to be highest in young inflorescences and stems. Ectopic overexpression of PvKN1 in switchgrass altered growth, especially in early developmental stages. Transgenic lines had reduced expression of most lignin biosynthetic genes accompanied by a reduction in lignin content suggesting the involvement of PvKN1 in the broad regulation of the lignin biosynthesis pathway. Moreover, the reduced expression of the Gibberellin 20-oxidase (GA20ox) gene in tandem with the increased expression of Gibberellin 2-oxidase (GA2ox) genes in transgenic PvKN1 lines suggest that PvKN1 may exert regulatory effects via modulation of GA signaling. Furthermore, overexpression of PvKN1 altered the expression of cellulose and hemicellulose biosynthetic genes and increased sugar release efficiency in transgenic lines. Our findings demonstrated that switchgrass PvKN1 is a putative ortholog of maize KN1 that is linked to plant lignification and cell wall and development traits as a major regulatory gene. Therefore, targeted overexpression of PvKN1 in bioenergy feedstocks may provide one feasible strategy for reducing biomass recalcitrance and simultaneously improving plant growth characteristics.« less

  14. The expression and phylogenetics of the Inhibitor Cysteine Knot peptide OCLP1 in the honey bee Apis mellifera.

    PubMed

    Bloch, Guy; Cohen, Mira

    2014-06-01

    Small cysteine-rich peptides have diverse functions in insects including antimicrobial defense, phenoloxidase activity regulation, and toxic inhibition of ion channels of prey or predator. We combined bioinformatics and measurements of transcript abundance to start characterizing AmOCLP1, a recently discovered Inhibitor Cysteine Knot peptide in the honey bee Apis mellifera. We found that the genomes of ants, bees, and the wasp Nasonia vitripennis encode orthologous sequences indicating that OCLP1 is a conserved peptide and not unique to the honey bee. Search of available EST libraries and quantitative real time PCR analyses indicate that the transcript of AmOCLP1 is ubiquitous with expression in life stages ranging from embryos to adults and in all tested tissues. In worker honey bees AmOCLP1 expression was not associated with age or task and did not show clear enrichment in any of the tested tissues. There was however a consistent trend toward higher transcript levels in the abdomen of foragers relative to levels in the head or thorax, and compared to levels in the abdomen of younger worker bees. By contrast, in drones AmOCLP1 transcript levels appeared higher in the head relative to the abdomen. Finer analyses of the head and abdomen indicated that the AmOCLP1 transcript is not enriched in the stinger and the associated venom sac or in cephalic exocrine glands. The evolutionary conservation in the Hymenoptera, the ubiquitous expression, and the lack of enrichment in the venom gland, stinger, exocrine glands, and the brain are not consistent with the hypotheses that OCLP1 is a secreted honeybee toxin or an endotoxin acting in the central nervous system. Rather we hypothesize that OCLP1 is a conserved antimicrobial or phenoloxidase inhibitor peptide.

  15. A Reliable Protocol for In situ microRNAs Detection in Feeding Sites Induced by Root-Knot Nematodes

    PubMed Central

    Díaz-Manzano, Fernando E.; Barcala, Marta; Engler, Gilbert; Fenoll, Carmen; de Almeida-Engler, Janice; Escobar, Carolina

    2016-01-01

    Galls induced by Meloidogyne spp. in plant roots are a complex organ formed by heterogeneous tissues; within them there are 5–8 giant cells (GCs) that root-knot nematodes use for their own nurturing. Subtle regulatory mechanisms likely mediate the massive gene repression described at early infection stages in galls, particularly in giant cells. Some of these mechanisms are mediated by microRNAs (miRNAs); hence we describe a reliable protocol to detect miRNAs abundance within the gall tissues induced by Meloidogyne spp. Some methods are available to determine the abundance of specific miRNAs in different plant parts; however, galls are complex organs formed by different tissues. Therefore, detection of miRNAs at the cellular level is particularly important to understand specific regulatory mechanisms operating within the GCs. In situ hybridization (ISH) is a classical, robust and accurate method that allows the localization of specific RNAs directly on plant tissues. We present for the first time an adapted and standardized ISH protocol to detect miRNAs in GCs induced by nematodes based on tissue embedded in paraffin and on-slide ISH of miRNAs. It can be adapted to any laboratory with no more requirements than a microtome and an optical microscope and it takes 10 days to perform once plant material has been collected. It showed to be very valuable for a quick detection of miRNAs expression pattern in tomato. We tested the protocol for miR390, as massive sequencing analysis showed that miR390 was induced at 3 dpi (days post-infection) in Arabidopsis galls and miR390 is 100% conserved between Arabidopsis and tomato. Successful localization of miR390 in tomato GCs constitutes a validation of this method that could be easily extended to other crops and/or syncytia induced by cyst nematodes. Finally, the protocol also includes guidance on troubleshooting. PMID:27458466

  16. Identification and Overexpression of a Knotted1-Like Transcription Factor in Switchgrass (Panicum virgatum L.) for Lignocellulosic Feedstock Improvement

    PubMed Central

    Wuddineh, Wegi A.; Mazarei, Mitra; Zhang, Ji-Yi; Turner, Geoffrey B.; Sykes, Robert W.; Decker, Stephen R.; Davis, Mark F.; Udvardi, Michael K.; Stewart, C. Neal

    2016-01-01

    High biomass production and wide adaptation has made switchgrass (Panicum virgatum L.) an important candidate lignocellulosic bioenergy crop. One major limitation of this and other lignocellulosic feedstocks is the recalcitrance of complex carbohydrates to hydrolysis for conversion to biofuels. Lignin is the major contributor to recalcitrance as it limits the accessibility of cell wall carbohydrates to enzymatic breakdown into fermentable sugars. Therefore, genetic manipulation of the lignin biosynthesis pathway is one strategy to reduce recalcitrance. Here, we identified a switchgrass Knotted1 transcription factor, PvKN1, with the aim of genetically engineering switchgrass for reduced biomass recalcitrance for biofuel production. Gene expression of the endogenous PvKN1 gene was observed to be highest in young inflorescences and stems. Ectopic overexpression of PvKN1 in switchgrass altered growth, especially in early developmental stages. Transgenic lines had reduced expression of most lignin biosynthetic genes accompanied by a reduction in lignin content suggesting the involvement of PvKN1 in the broad regulation of the lignin biosynthesis pathway. Moreover, the reduced expression of the Gibberellin 20-oxidase (GA20ox) gene in tandem with the increased expression of Gibberellin 2-oxidase (GA2ox) genes in transgenic PvKN1 lines suggest that PvKN1 may exert regulatory effects via modulation of GA signaling. Furthermore, overexpression of PvKN1 altered the expression of cellulose and hemicellulose biosynthetic genes and increased sugar release efficiency in transgenic lines. Our results demonstrated that switchgrass PvKN1 is a putative ortholog of maize KN1 that is linked to plant lignification and cell wall and development traits as a major regulatory gene. Therefore, targeted overexpression of PvKN1 in bioenergy feedstocks may provide one feasible strategy for reducing biomass recalcitrance and simultaneously improving plant growth characteristics. PMID:27200006

  17. Three-dimensional printed knotted reactors enabling highly sensitive differentiation of silver nanoparticles and ions in aqueous environmental samples.

    PubMed

    Su, Cheng-Kuan; Hsieh, Meng-Hsuan; Sun, Yuh-Chang

    2016-03-31

    Whether silver nanoparticles (AgNPs) persist or release silver ions (Ag(+)) when discharged into a natural environment has remained an unresolved issue. In this study, we employed a low-cost stereolithographic three-dimensional printing (3DP) technology to fabricate the angle-defined knotted reactors (KRs) to construct a simple differentiation scheme for quantitative assessment of Ag(+) ions and AgNPs in municipal wastewater samples. We chose xanthan/phosphate-buffered saline as a dispersion medium for in situ stabilization of the two silver species, while also facilitating their extraction from complicated wastewater matrices. After method optimization, we measured extraction efficiencies of 54.5 and 32.3% for retaining Ag(+) ions and AgNPs, respectively, in the printed KR (768-turn), with detection limits (DLs) of 0.86 and 0.52 ng L(-1) when determining Ag(+) ions and AgNPs, respectively (sample run at pH 11 without a rinse solution), and 0.86 ng L(-1) when determining Ag(+) ions alone (sample run at pH 12 with a 1.5-mL rinse solution). The proposed scheme is tolerant of the wastewater matrix and provides more reliable differentiation between Ag(+)/AgNPs than does a conventional filtration method. The concept and applicability of adopting 3DP technology to renew traditional KR devices were evidently proven by means of these significantly improved analytical performance. Our analytical data suggested that the concentrations of Ag(+) ions and AgNPs in the tested industrial wastewater sample were both higher than those in domestic wastewater, implying that industrial activity might be a main source of environmental silver species, rather than domestic discharge from AgNP-containing products.

  18. A study of interaction between Verticillium wilt Verticillium dahliae and root-knot nematode Meloidogyne javanica in olive cultivars.

    PubMed

    Saeedizadeh, Ayatollah; Kheiri, Ahmad; Zad, Javad; Etebarian, Hasan Reza; Bandani, Ali Reza; Nasiri, Mohammad Bagher

    2009-01-01

    Second stage juvenile (J2) of root-knot nematode, Meloidogyne javanica, and microsclerotia of verticillium wilt, Verticillium dahliae, were used as the source of inoculum for nematode and fungus respectively. One-year-old seedlings of olive cultivars, Zard, Roghani, Koroneiki and Manzanilla, were transplanted to pots containing 2000g of sterilized sandy loam soil. Experiment was conducted in completely randomized design with 32 treatments and five replications. Treatments were as follows: control, nematode alone, fungus alone and fungus + nematode. Pots were inoculated with (0, 2000, 3000, 4000) J2 of nematode and/or (10 no/g soil) microsclerotia of fungus according to the treatments. Experiment was terminated after 10 months and fallowing parameters were determined i.e., fresh weight of root and stem, number of galls and egg masses per root system, and percentage of incidence of symptom on aerial parts, browning of vascular tissue, decrease of seedling height and stem/root tissue colonization by fungus. Results showed that presence of nematode caused reduction on colonization of the fungus in the root and stem and vice versa i.e. presence of fungus caused reduction on number of galls and egg masses produced by the nematode. Severe fungus wilt on aerial parts of Manzanilla cultivar was observed when both pathogens were inoculated and mild fungus wilt was observed in fungus alone treatments of Koroneiki cultivar. Galling and egg mass production in root system were reduced in cvs Manzanilla, Zard, Roghani and Koroneiki, respectively (p < or = 0/05). Based on the results obtained in this study, verticilliosis symptoms and galling of nematode in olive seedlings were be less on cvs Koroneiki, Roghani, Zard and Manzanilla, respectively (p < or = 0/05). PMID:20222619

  19. A Novel Cysteine Knot Protein for Enhancing Sperm Motility That Might Facilitate the Evolution of Internal Fertilization in Amphibians.

    PubMed

    Yokoe, Misato; Takayama-Watanabe, Eriko; Saito, Yoko; Kutsuzawa, Megumi; Fujita, Kosuke; Ochi, Haruki; Nakauchi, Yuni; Watanabe, Akihiko

    2016-01-01

    Internal fertilization ensures successful reproduction of tetrapod vertebrates on land, although how this mode of reproduction evolved is unknown. Here, we identified a novel gene encoding sperm motility-initiating substance (SMIS), a key protein for the internal fertilization of the urodele Cynops pyrrhogaster by Edman degradation of an isolated protein and subsequent reverse transcription polymerase chain reaction. The SMIS gene encoded a 150 amino-acid sequence including the cysteine knot (CK) motif. No gene with substantial similarity to the SMIS was in the data bank of any model organisms. An active site of the SMIS was in the C-terminal region of the 2nd loop of CK motif. A synthetic peptide including the active site sequence bound to the midpiece and initiated/enhanced the circular motion of C. pyrrhogaster sperm, which allows penetration of the egg jelly specialized for the internal fertilization of this species. The synthetic peptide bound to whole sperm of Rhacophorus arboreus and enhanced the rotary motion, which is adapted to propel the sperm through egg coat matrix specialized for arboreal reproduction, while it bound to the tip of head and tail of Bufo japonicus sperm, and enhanced the vibratory motion, which is suited to sperm penetration through the egg jelly specialized for the reproduction of that species in freshwater. The polyclonal antibody against the active site of the SMIS specifically bound to egg coat matrix of R. arboreus. These findings suggest that diversification of amphibian reproductive modes accompanies the specialization of egg coat and the adaptation of sperm motility to penetrate the specialized egg coat, and SMIS acts as the sperm motility enhancer of anurans and urodeles that might facilitate to adaptively optimize sperm motility for allowing the establishment of internal fertilization. PMID:27579691

  20. The expression and phylogenetics of the Inhibitor Cysteine Knot peptide OCLP1 in the honey bee Apis mellifera.

    PubMed

    Bloch, Guy; Cohen, Mira

    2014-06-01

    Small cysteine-rich peptides have diverse functions in insects including antimicrobial defense, phenoloxidase activity regulation, and toxic inhibition of ion channels of prey or predator. We combined bioinformatics and measurements of transcript abundance to start characterizing AmOCLP1, a recently discovered Inhibitor Cysteine Knot peptide in the honey bee Apis mellifera. We found that the genomes of ants, bees, and the wasp Nasonia vitripennis encode orthologous sequences indicating that OCLP1 is a conserved peptide and not unique to the honey bee. Search of available EST libraries and quantitative real time PCR analyses indicate that the transcript of AmOCLP1 is ubiquitous with expression in life stages ranging from embryos to adults and in all tested tissues. In worker honey bees AmOCLP1 expression was not associated with age or task and did not show clear enrichment in any of the tested tissues. There was however a consistent trend toward higher transcript levels in the abdomen of foragers relative to levels in the head or thorax, and compared to levels in the abdomen of younger worker bees. By contrast, in drones AmOCLP1 transcript levels appeared higher in the head relative to the abdomen. Finer analyses of the head and abdomen indicated that the AmOCLP1 transcript is not enriched in the stinger and the associated venom sac or in cephalic exocrine glands. The evolutionary conservation in the Hymenoptera, the ubiquitous expression, and the lack of enrichment in the venom gland, stinger, exocrine glands, and the brain are not consistent with the hypotheses that OCLP1 is a secreted honeybee toxin or an endotoxin acting in the central nervous system. Rather we hypothesize that OCLP1 is a conserved antimicrobial or phenoloxidase inhibitor peptide. PMID:24721445

  1. Knock-down of heat-shock protein 90 and isocitrate lyase gene expression reduced root-knot nematode reproduction.

    PubMed

    Lourenço-Tessutti, Isabela Tristan; Souza Junior, José Dijair Antonino; Martins-de-Sa, Diogo; Viana, Antônio Américo Barbosa; Carneiro, Regina Maria Dechechi Gomes; Togawa, Roberto Coiti; de Almeida-Engler, Janice; Batista, João Aguiar Nogueira; Silva, Maria Cristina Mattar; Fragoso, Rodrigo Rocha; Grossi-de-Sa, Maria Fatima

    2015-05-01

    Crop losses caused by nematode infections are estimated to be valued at USD 157 billion per year. Meloidogyne incognita, a root-knot nematode (RKN), is considered to be one of the most important plant pathogens due to its worldwide distribution and the austere damage it can cause to a large variety of agronomically important crops. RNA interference (RNAi), a gene silencing process, has proven to be a valuable biotechnology alternative method for RKN control. In this study, the RNAi approach was applied, using fragments of M. incognita genes that encode for two essential molecules, heat-shock protein 90 (HSP90) and isocitrate lyase (ICL). Plant-mediated RNAi of these genes led to a significant level of resistance against M. incognita in the transgenic Nicotiana tabacum plants. Bioassays of plants expressing HSP90 dsRNA demonstrated a delay in gall formation and up to 46% reduction in eggs compared with wild-type plants. A reduction in the level of HSP90 transcripts was observed in recovered eggs from plants expressing dsRNA, indicating that gene silencing persisted and was passed along to first progeny. The ICL knock-down had no clear effect on gall formation but resulted in up to 77% reduction in egg oviposition compared with wild-type plants. Our data suggest that both genes may be involved in RKN development and reproduction. Thus, in this paper, we describe essential candidate genes that could be applied to generate genetically modified crops, using the RNAi strategy to control RKN parasitism.

  2. Geostatistical modeling of the spatial variability and risk areas of southern root-knot nematodes in relation to soil properties

    PubMed Central

    Ortiz, B.V.; Perry, C.; Goovaerts, P.; Vellidis, G.; Sullivan, D.

    2010-01-01

    Identifying the spatial variability and risk areas for southern root-knot nematode [Meloidogyne incognita (Kofoid & White) Chitwood] (RKN) is key for site-specific management (SSM) of cotton (Gossypium hirsutum L.) fields. The objectives of this study were to: (i) determine the soil properties that influence RKN occurrence at different scales; and (ii) delineate risk areas of RKN by indicator kriging. The study site was a cotton field located in the southeastern coastal plain region of the USA. Nested semivariograms indicated that RKN samples, collected from a 50×50 m grid, exhibited a local and regional scale of variation describing small and large clusters of RKN population density. Factorial kriging decomposed RKN and soil properties variability into different spatial components. Scale dependent correlations between RKN data showed that the areas with high RKN population remained stable though the growing season. RKN data were strongly correlated with slope (SL) at local scale and with apparent soil electrical conductivity deep (ECa-d) at both local and regional scales, which illustrate the potential of these soil physical properties as surrogate data for RKN population. The correlation between RKN data and soil chemical properties was soil texture mediated. Indicator kriging (IK) maps developed using either RKN, the relation between RKN and soil electrical conductivity or a combination of both, depicted the probability for RKN population to exceed the threshold of 100 second stage juveniles/100 cm3 of soil. Incorporating ECa-d as soft data improved predictions favoring the reduction of the number of RKN observations required to map areas at risk for high RKN population. PMID:20717481

  3. Identification and Overexpression of a Knotted1-Like Transcription Factor in Switchgrass (Panicum virgatum L.) for Lignocellulosic Feedstock Improvement.

    PubMed

    Wuddineh, Wegi A; Mazarei, Mitra; Zhang, Ji-Yi; Turner, Geoffrey B; Sykes, Robert W; Decker, Stephen R; Davis, Mark F; Udvardi, Michael K; Stewart, C Neal

    2016-01-01

    High biomass production and wide adaptation has made switchgrass (Panicum virgatum L.) an important candidate lignocellulosic bioenergy crop. One major limitation of this and other lignocellulosic feedstocks is the recalcitrance of complex carbohydrates to hydrolysis for conversion to biofuels. Lignin is the major contributor to recalcitrance as it limits the accessibility of cell wall carbohydrates to enzymatic breakdown into fermentable sugars. Therefore, genetic manipulation of the lignin biosynthesis pathway is one strategy to reduce recalcitrance. Here, we identified a switchgrass Knotted1 transcription factor, PvKN1, with the aim of genetically engineering switchgrass for reduced biomass recalcitrance for biofuel production. Gene expression of the endogenous PvKN1 gene was observed to be highest in young inflorescences and stems. Ectopic overexpression of PvKN1 in switchgrass altered growth, especially in early developmental stages. Transgenic lines had reduced expression of most lignin biosynthetic genes accompanied by a reduction in lignin content suggesting the involvement of PvKN1 in the broad regulation of the lignin biosynthesis pathway. Moreover, the reduced expression of the Gibberellin 20-oxidase (GA20ox) gene in tandem with the increased expression of Gibberellin 2-oxidase (GA2ox) genes in transgenic PvKN1 lines suggest that PvKN1 may exert regulatory effects via modulation of GA signaling. Furthermore, overexpression of PvKN1 altered the expression of cellulose and hemicellulose biosynthetic genes and increased sugar release efficiency in transgenic lines. Our results demonstrated that switchgrass PvKN1 is a putative ortholog of maize KN1 that is linked to plant lignification and cell wall and development traits as a major regulatory gene. Therefore, targeted overexpression of PvKN1 in bioenergy feedstocks may provide one feasible strategy for reducing biomass recalcitrance and simultaneously improving plant growth characteristics. PMID:27200006

  4. Effects of temperature on the life-history traits of Sancassania (Caloglyphus) berlesei (Acari: Astigmatina: Acaridae) feeding on root-knot nematodes, Meloidogyne spp. (Nematoda: Meloidogynidae).

    PubMed

    Abou El-Atta, Doaa Abd El-Maksoud; Ghazy, Noureldin Abuelfadl; Osman, Mohamed Ali

    2014-11-01

    Sancassania (Caloglyphus) berlesei (Michael) is a cosmopolitan and free-living mite that inhabits soil as well as laboratory colonies of insects and fungi and may have a role as a biocontrol agent of nematodes. In this study, we investigated the effects of temperature on the development, reproduction, and food consumption of S. berlesei fed egg masses of root-knot nematodes, Meloidogyne spp., an important group of agricultural pests. Mites were reared at 20, 25 or 30 °C in the dark. The mites could feed on the nematode egg masses, and their developmental time decreased at higher temperatures. Time from the egg to adult was similar in females and males reared at the same temperature. Adult females lived longer than males at 25 °C, but not at 20 or 30 °C. Generally, females showed a higher rate of food consumption than males. Females laid the largest number of eggs at 20 and 25 °C (199.7 and 189.8 eggs/female, respectively), but the intrinsic rate of natural increase was highest at 30 °C (r m = 0.29). In comparing our data with previous reports, we noted that S. berlesei that fed on egg masses of root-knot nematodes showed a longer developmental time and a lower reproductive rate than Sancassania mites that fed on other diets. Nonetheless, the relatively high value of r m (e.g., at 25 and 30 °C) suggests that this mite may have certain advantages as a biocontrol agent of root-knot nematodes.

  5. Complete Mapping of a Cystine Knot and Nested Disulfides of Recombinant Human Arylsulfatase A by Multi-Enzyme Digestion and LC-MS Analysis Using CID and ETD

    NASA Astrophysics Data System (ADS)

    Ni, Wenqin; Lin, Melanie; Salinas, Paul; Savickas, Philip; Wu, Shiaw-Lin; Karger, Barry L.

    2013-01-01

    Cystine knots or nested disulfides are structurally difficult to characterize, despite current technological advances in peptide mapping with high-resolution liquid chromatography coupled with mass spectrometry (LC-MS). In the case of recombinant human arylsulfatase A (rhASA), there is one cystine knot at the C-terminal, a pair of nested disulfides at the middle, and two out of three unpaired cysteines in the N-terminal region. The statuses of these cysteines are critical structure attributes for rhASA function and stability that requires precise examination. We used a unique approach to determine the status and linkage of each cysteine in rhASA, which was comprised of multi-enzyme digestion strategies (from Lys-C, trypsin, Asp-N, pepsin, and PNGase F) and multi-fragmentation methods in mass spectrometry using electron transfer dissociation (ETD), collision induced dissociation (CID), and CID with MS3 (after ETD). In addition to generating desired lengths of enzymatic peptides for effective fragmentation, the digestion pH was optimized to minimize the disulfide scrambling. The disulfide linkages, including the cystine knot and a pair of nested cysteines, unpaired cysteines, and the post-translational modification of a cysteine to formylglycine, were all determined. In the assignment, the disulfide linkages were Cys138-Cys154, Cys143-Cys150, Cys282-Cys396, Cys470-Cys482, Cys471-Cys484, and Cys475-Cys481. For the unpaired cysteines, Cys20 and Cys276 were free cysteines, and Cys51 was largely converted to formylglycine (>70 %). A successful methodology has been developed, which can be routinely used to determine these difficult-to-resolve disulfide linkages, ensuring drug function and stability.

  6. Effects of temperature on the life-history traits of Sancassania (Caloglyphus) berlesei (Acari: Astigmatina: Acaridae) feeding on root-knot nematodes, Meloidogyne spp. (Nematoda: Meloidogynidae).

    PubMed

    Abou El-Atta, Doaa Abd El-Maksoud; Ghazy, Noureldin Abuelfadl; Osman, Mohamed Ali

    2014-11-01

    Sancassania (Caloglyphus) berlesei (Michael) is a cosmopolitan and free-living mite that inhabits soil as well as laboratory colonies of insects and fungi and may have a role as a biocontrol agent of nematodes. In this study, we investigated the effects of temperature on the development, reproduction, and food consumption of S. berlesei fed egg masses of root-knot nematodes, Meloidogyne spp., an important group of agricultural pests. Mites were reared at 20, 25 or 30 °C in the dark. The mites could feed on the nematode egg masses, and their developmental time decreased at higher temperatures. Time from the egg to adult was similar in females and males reared at the same temperature. Adult females lived longer than males at 25 °C, but not at 20 or 30 °C. Generally, females showed a higher rate of food consumption than males. Females laid the largest number of eggs at 20 and 25 °C (199.7 and 189.8 eggs/female, respectively), but the intrinsic rate of natural increase was highest at 30 °C (r m = 0.29). In comparing our data with previous reports, we noted that S. berlesei that fed on egg masses of root-knot nematodes showed a longer developmental time and a lower reproductive rate than Sancassania mites that fed on other diets. Nonetheless, the relatively high value of r m (e.g., at 25 and 30 °C) suggests that this mite may have certain advantages as a biocontrol agent of root-knot nematodes. PMID:24923664

  7. Study on interaction between root-knot nematode Meloidogyne javanica and wilt fungus Verticillium dahliae on olive seedlings in greenhouse.

    PubMed

    Saeedizadeh, A; Kheiri, A; Okhovat, M; Hoseininejad, A

    2003-01-01

    Verticillium dahliae has been reported as a limiting factor in cotton, olive, potato and tomato fields from several countries in the world. Root-knot nematodes Meloidogyne javanica causes considerable damage to olive groves in olive growing areas. Since the presence of these two pathogens in olive trees and seedlings were confirmed in Golestan Province, this study was proposed to find the mode of their action and interaction with olive seedlings in greenhouse. The non-defoliant strain of the fungus (SS-4) was isolated from olive groves showing symptom in Golestan Province. M. javanica was also recovered from the infested olive seedlings. After species identification, it was reared on tomato seedlings var. Rutgers. The larvae were used as a source of inoculum. Conidia and microsclerotia of V. dahliae were used as a source of inoculum for pathogenesis in this study. Stem cuttings of olive cultivar Zard were transplanted in different sets of pots containing 720 ml. of sterilized loamy soil and sandy soil. Experiment was conducted in Completely Randomized Design with 6 treatments and 8 replicates including control, nematode alone, fungus alone, nematode and fungus simultaneously, nematode and fungus concomitantly, fungus two weeks prior to nematode, nematode and fungus concomitantly, nematode two weeks prior to fungus. Pots were inoculated with 1500 larvae of nematodes and 7200 microsclerotia of V. dahliae. Experiment was terminated after 9 months and following parameters were determined i.e. fresh weight of roots, number of galls and females, per root system and discoloration of leaf and root tissues. Presence of nematode prior to fungus caused reduction in colonization of fungus in the roots and the stems and vis presence of fungus prior to nematode caused reduction in number of galls produced by nematode. Sever symptom on aerial parts of plant was observed when both pathogens were inoculated simultaneously. However fresh weight of roots was reduced in all treatments

  8. Study on interaction between root-knot nematode Meloidogyne javanica and wilt fungus Verticillium dahliae on olive seedlings in greenhouse.

    PubMed

    Saeedizadeh, A; Kheiri, A; Okhovat, M; Hoseininejad, A

    2003-01-01

    Verticillium dahliae has been reported as a limiting factor in cotton, olive, potato and tomato fields from several countries in the world. Root-knot nematodes Meloidogyne javanica causes considerable damage to olive groves in olive growing areas. Since the presence of these two pathogens in olive trees and seedlings were confirmed in Golestan Province, this study was proposed to find the mode of their action and interaction with olive seedlings in greenhouse. The non-defoliant strain of the fungus (SS-4) was isolated from olive groves showing symptom in Golestan Province. M. javanica was also recovered from the infested olive seedlings. After species identification, it was reared on tomato seedlings var. Rutgers. The larvae were used as a source of inoculum. Conidia and microsclerotia of V. dahliae were used as a source of inoculum for pathogenesis in this study. Stem cuttings of olive cultivar Zard were transplanted in different sets of pots containing 720 ml. of sterilized loamy soil and sandy soil. Experiment was conducted in Completely Randomized Design with 6 treatments and 8 replicates including control, nematode alone, fungus alone, nematode and fungus simultaneously, nematode and fungus concomitantly, fungus two weeks prior to nematode, nematode and fungus concomitantly, nematode two weeks prior to fungus. Pots were inoculated with 1500 larvae of nematodes and 7200 microsclerotia of V. dahliae. Experiment was terminated after 9 months and following parameters were determined i.e. fresh weight of roots, number of galls and females, per root system and discoloration of leaf and root tissues. Presence of nematode prior to fungus caused reduction in colonization of fungus in the roots and the stems and vis presence of fungus prior to nematode caused reduction in number of galls produced by nematode. Sever symptom on aerial parts of plant was observed when both pathogens were inoculated simultaneously. However fresh weight of roots was reduced in all treatments

  9. Engineering Agatoxin, a Cystine-Knot Peptide from Spider Venom, as a Molecular Probe for In Vivo Tumor Imaging

    PubMed Central

    Norton, Heidi K.; Cochran, Jennifer R.

    2013-01-01

    Background Cystine-knot miniproteins, also known as knottins, have shown great potential as molecular scaffolds for the development of targeted therapeutics and diagnostic agents. For this purpose, previous protein engineering efforts have focused on knottins based on the Ecballium elaterium trypsin inhibitor (EETI) from squash seeds, the Agouti-related protein (AgRP) neuropeptide from mammals, or the Kalata B1 uterotonic peptide from plants. Here, we demonstrate that Agatoxin (AgTx), an ion channel inhibitor found in spider venom, can be used as a molecular scaffold to engineer knottins that bind with high-affinity to a tumor-associated integrin receptor. Methodology/Principal Findings We used a rational loop-grafting approach to engineer AgTx variants that bound to αvβ3 integrin with affinities in the low nM range. We showed that a disulfide-constrained loop from AgRP, a structurally-related knottin, can be substituted into AgTx to confer its high affinity binding properties. In parallel, we identified amino acid mutations required for efficient in vitro folding of engineered integrin-binding AgTx variants. Molecular imaging was used to evaluate in vivo tumor targeting and biodistribution of an engineered AgTx knottin compared to integrin-binding knottins based on AgRP and EETI. Knottin peptides were chemically synthesized and conjugated to a near-infrared fluorescent dye. Integrin-binding AgTx, AgRP, and EETI knottins all generated high tumor imaging contrast in U87MG glioblastoma xenograft models. Interestingly, EETI-based knottins generated significantly lower non-specific kidney imaging signals compared to AgTx and AgRP-based knottins. Conclusions/Significance In this study, we demonstrate that AgTx, a knottin from spider venom, can be engineered to bind with high affinity to a tumor-associated receptor target. This work validates AgTx as a viable molecular scaffold for protein engineering, and further demonstrates the promise of using tumor

  10. A genome-wide association study of a global rice panel reveals resistance in Oryza sativa to root-knot nematodes

    PubMed Central

    Dimkpa, Stanley O. N.; Lahari, Zobaida; Shrestha, Roshi; Douglas, Alex; Gheysen, Godelieve; Price, Adam H.

    2016-01-01

    The root-knot nematode Meloidogyne graminicola is one of the most serious nematode pests worldwide and represents a major constraint on rice production. While variation in the susceptibility of Asian rice (Oryza sativa) exists, so far no strong and reliable resistance has been reported. Quantitative trait loci for partial resistance have been reported but no underlying genes have been tagged or cloned. Here, 332 accessions of the Rice Diversity Panel 1 were assessed for gall formation, revealing large variation across all subpopulations of rice and higher susceptibility in temperate japonica accessions. Accessions Khao Pahk Maw and LD 24 appeared to be resistant, which was confirmed in large pot experiments where no galls were observed. Detailed observations on these two accessions revealed no nematodes inside the roots 2 days after inoculation and very few females after 17 days (5 in Khao Pahk Maw and <1 in LD 24, in comparison with >100 in the susceptible controls). These two cultivars appear ideal donors for breeding root-knot nematode resistance. A genome-wide association study revealed 11 quantitative trait loci, two of which are close to epistatic loci detected in the Bala x Azucena population. The discussion highlights a small number of candidate genes worth exploring further, in particular many genes with lectin domains and genes on chromosome 11 with homology to the Hordeum Mla locus. PMID:26552884

  11. Observations on the suppression of root-knot nematode (Meloidogyne arenaria) on tomato by incorporation of cyanobacterial powder (Oscillatoria chlorina) into potting field soil.

    PubMed

    Khan, Z; Kim, Y H; Kim, S G; Kim, H W

    2007-01-01

    Experiments were carried out to investigate the nematicidal potential of a cyanobacterium, Oscillatoria chlorina, against the root-knot nematode, Meloidogyne arenaria on tomato plants grown in pots filled with 500 cm3 of field soil infested with 12-s stage juveniles (J2)/cm3 soil. Incorporation of freeze-dried cyanobacterial powder into potted field soil at the rate of 0.2%, 0.4%, 0.6%, 0.8% and 1.0% (w/w) 5 days prior to tomato planting, reduced root galling, final population of M. arenaria and increased vegetative growth of tomato plants and root-mass production, compared with untreated control (P > or = 0.05). The beneficial effect of adding cyanobacterial powder into infested potted field soil increased exponentially with concentration up to 0.8%. Root galling and nematode population decreased by 68.9% and 97.6%, respectively at the highest dose (1%) of cyanobacterial powder compared with the untreated control. Addition of cyanobacterial powder into infested potted field soil at 5 days before planting was the most effective followed by 2 days before and at the time of tomato planting. We conclude that application rate and timing are important factors in the control of root-knot nematodes with O. chlorina.

  12. Phytotoxicity analysis of extracts from compost and their ability to inhibit soil-borne pathogenic fungi and reduce root-knot nematodes.

    PubMed

    Xu, Dabing; Raza, Waseem; Yu, Guanghui; Zhao, Qingyun; Shen, Qirong; Huang, Qiwei

    2012-03-01

    Compost extracts are novel organic amendments, typically applied to suppress soil-borne diseases. This research evaluated the phytotoxicity of compost extracts and analyzed their ability to inhibit pathogenic fungal growth and reduce root-knot nematodes. The physical, chemical and biological characteristics of extracts from a pig manure and straw compost were analyzed. Three types of extracts were tested: direct extracts of compost (DEC), aerated fermentation extracts of compost (AFEC) and non-aerated fermentation extracts of compost (NAFEC). All compost extracts showed low phytotoxicity against lettuce and cress, but AFEC and NAFEC were more phytotoxic than DEC. All compost extracts significantly inhibited pathogenic fungal growth except for the fungus Rhizoctonia solania AG4. For two seasons, tomato root biomass of three compost extracts was 1.25-5.67 times greater than CK (water control), and AFEC and NAFEC showed the best tomato root growth promotion. The reduction ratio of root egg mass and density of soil nematodes were 34.51-87.77% and 30.92-51.37%, when applied with three compost extracts. The microbial population in compost extracts was considered to be the most significant factor of inhibition pathogenic fungal growth. No markedly correlations among bacterial community diversity, the inhibition of pathogenic fungal growth and the reduction of root-knot nematodes were observed. This information adds to the understanding of the growth-promoting and suppression effects of compost extracts and will help to enhance crop production.

  13. The diverse nematicidal properties and biocontrol efficacy of Bacillus thuringiensis Cry6A against the root-knot nematode Meloidogyne hapla.

    PubMed

    Yu, Ziquan; Xiong, Jing; Zhou, Qiaoni; Luo, Haiyan; Hu, Shengbiao; Xia, Liqiu; Sun, Ming; Li, Lin; Yu, Ziniu

    2015-02-01

    Cry6A toxin from Bacillus thuringiensis is a representative nematicidal crystal protein with a variety of nematicidal properties to free-living nematode Caenorhabditis elegans. Cry6A shares very low homology and different structure with Cry5B, another representative nematicidal crystal protein, and probably acts in a distinct pathway. All these strongly indicate that Cry6A toxin is likely a potent candidate for nematicide. The present study dealt with global investigation to determine the detrimental impacts of Cry6Aa2 toxin on Meloidogyne hapla, a root-knot nematode, and evaluated its biocontrol efficacy in pot experiment. Obtained results indicated that Cry6Aa2 toxin exhibits obvious toxicity to second-stage juvenile of M. hapla, and significantly inhibits egg hatch, motility, and penetration to host plant. Pot experiment suggested that soil drenching with spore-crystal mixture of Cry6Aa2 can clearly lighten the disease of root-knot nematode, including reduction of galling index and egg masses on host plant root, decreasing final population of nematode in soil. Moreover, application of Cry6Aa2 can obviously promote plant growth. These results demonstrated that Cry6Aa2 toxin is a promising nematicidal agent, and possesses great potential in plant-parasitic nematode management and construction of transgenic crop with constant resistance to nematode.

  14. Three-Phase Fuel Deposition in a Long-Distance Migrant, the Red Knot (Calidris canutus piersmai), before the Flight to High Arctic Breeding Grounds

    PubMed Central

    Hua, Ning; Piersma, Theunis; Ma, Zhijun

    2013-01-01

    Refuelling by migratory birds before take-off on long flights is generally considered a two-phase process, with protein accumulation preceding rapid fat deposition. The first phase expresses the demands for a large digestive system for nutrient storage after shrinkage during previous flights, the second phase the demands for fat stores to fuel the subsequent flight. At the last staging site in northward migration, this process may include expression of selection pressures both en route to and after arrival at the breeding grounds, which remains unascertained. Here we investigated changes in body composition during refuelling of High Arctic breeding red knots (Calidris canutus piersmai) in the northern Yellow Sea, before their flight to the tundra. These red knots followed a three-phase fuel deposition pattern, with protein being stored in the first and last phases, and fat being deposited mainly in the second phase. Thus, they did not shrink nutritional organs before take-off, and even showed hypertrophy of the nutritional organs. These suggest the build up of strategic protein stores before departure to cope with a protein shortage upon arrival on the breeding grounds. Further comparative studies are warranted to examine the degree to which the deposition of stores by migrant birds generally reflects a balance between concurrent and upcoming environmental selection pressures. PMID:23638114

  15. Phytotoxicity analysis of extracts from compost and their ability to inhibit soil-borne pathogenic fungi and reduce root-knot nematodes.

    PubMed

    Xu, Dabing; Raza, Waseem; Yu, Guanghui; Zhao, Qingyun; Shen, Qirong; Huang, Qiwei

    2012-03-01

    Compost extracts are novel organic amendments, typically applied to suppress soil-borne diseases. This research evaluated the phytotoxicity of compost extracts and analyzed their ability to inhibit pathogenic fungal growth and reduce root-knot nematodes. The physical, chemical and biological characteristics of extracts from a pig manure and straw compost were analyzed. Three types of extracts were tested: direct extracts of compost (DEC), aerated fermentation extracts of compost (AFEC) and non-aerated fermentation extracts of compost (NAFEC). All compost extracts showed low phytotoxicity against lettuce and cress, but AFEC and NAFEC were more phytotoxic than DEC. All compost extracts significantly inhibited pathogenic fungal growth except for the fungus Rhizoctonia solania AG4. For two seasons, tomato root biomass of three compost extracts was 1.25-5.67 times greater than CK (water control), and AFEC and NAFEC showed the best tomato root growth promotion. The reduction ratio of root egg mass and density of soil nematodes were 34.51-87.77% and 30.92-51.37%, when applied with three compost extracts. The microbial population in compost extracts was considered to be the most significant factor of inhibition pathogenic fungal growth. No markedly correlations among bacterial community diversity, the inhibition of pathogenic fungal growth and the reduction of root-knot nematodes were observed. This information adds to the understanding of the growth-promoting and suppression effects of compost extracts and will help to enhance crop production. PMID:22805840

  16. Three-phase fuel deposition in a long-distance migrant, the red knot (Calidris canutus piersmai), before the flight to high Arctic breeding grounds.

    PubMed

    Hua, Ning; Piersma, Theunis; Ma, Zhijun

    2013-01-01

    Refuelling by migratory birds before take-off on long flights is generally considered a two-phase process, with protein accumulation preceding rapid fat deposition. The first phase expresses the demands for a large digestive system for nutrient storage after shrinkage during previous flights, the second phase the demands for fat stores to fuel the subsequent flight. At the last staging site in northward migration, this process may include expression of selection pressures both en route to and after arrival at the breeding grounds, which remains unascertained. Here we investigated changes in body composition during refuelling of High Arctic breeding red knots (Calidris canutus piersmai) in the northern Yellow Sea, before their flight to the tundra. These red knots followed a three-phase fuel deposition pattern, with protein being stored in the first and last phases, and fat being deposited mainly in the second phase. Thus, they did not shrink nutritional organs before take-off, and even showed hypertrophy of the nutritional organs. These suggest the build up of strategic protein stores before departure to cope with a protein shortage upon arrival on the breeding grounds. Further comparative studies are warranted to examine the degree to which the deposition of stores by migrant birds generally reflects a balance between concurrent and upcoming environmental selection pressures.

  17. Identification of novel virulence genes and metabolic pathways required for full fitness of Pseudomonas savastanoi pv. savastanoi in olive (Olea europaea) knots.

    PubMed

    Matas, Isabel M; Lambertsen, Lotte; Rodríguez-Moreno, Luis; Ramos, Cayo

    2012-12-01

    Comparative genomics and functional analysis of Pseudomonas syringae and related pathogens have mainly focused on diseases of herbaceous plants; however, there is a general lack of knowledge about the virulence and pathogenicity determinants required for infection of woody plants. Here, we applied signature-tagged mutagenesis (STM) to Pseudomonas savastanoi pv. savastanoi during colonization of olive (Olea europaea) knots, with the goal of identifying the range of genes linked to growth and symptom production in its plant host. A total of 58 different genes were identified, and most mutations resulted in hypovirulence in woody olive plants. Sequence analysis of STM mutations allowed us to identify metabolic pathways required for full fitness of P. savastanoi in olive and revealed novel mechanisms involved in the virulence of this pathogen, some of which are essential for full colonization of olive knots by the pathogen and for the lysis of host cells. This first application of STM to a P. syringae-like pathogen provides confirmation of functional capabilities long believed to play a role in the survival and virulence of this group of pathogens but not adequately tested before, and unravels novel factors not correlated previously with the virulence of other plant or animal bacterial pathogens.

  18. Tracing the Southwest African climate development during the Miocene - changes in elemental distribution and clay mineral composition at DSDP Site 530A (southeastern Angola Basin)

    NASA Astrophysics Data System (ADS)

    Roters, B.

    2009-04-01

    During the middle and late Miocene the climatic system in Southwest Africa was reorganized leading to generally drier conditions as known from today. The reason for this was the cooling of the coastal-near ocean by the initialization of the Benguela Current. Thus the temperature difference between the continent and the sea increased and a system of seaward blowing winds developed. This lead to (1) the development of the Benguela Upwelling System in front of the Namibian coast and (2) it prevented the landward flow of humid air masses. The Mid-Miocene climate change in SW-Africa has been shown by data-sets from the Cape Basin and the Walvis Ridge (Kastanja et al., 2006; Westerhold et al., 2005; Diester-Haass et al., 2002; Roters & Henrich, in press). The DSDP Site 530A is situated in the SE corner of the Walvis Basin at the toe of the Walvis Ridge in a water depth of 4629 m. Today the distance to the coast is about 285 km. The idea is to trace the climatic development between 19 and 9 Myr with the help of (1) a clay mineral record and (2) the results of XRF-scanning of the core. The sediment is carbonate-depleted, which, inversely, enriches the terrigenous components. On the other hand mass accumulation rates are low and the age control of the sediments is difficult. XRF scanning was done on the archive cores at the MARUM, Bremen in a resolution of about 10 kyr, while the clay mineral contents were measured in the isolated clay fraction (< 2µm) on a XRD machine at the AWI, Bremerhaven in a 100 kyr resolution. By grain size analysis it was found that the content of clays (fraction < 2µm) of the sediments averages out to about 75%. The most prominent clays found in the samples are Illites. The remaining material is nearly completely composed of silt. The sediments could have been transported to site 530A by three different processes: (1) in the sediment load of the Kunene River and onwards by surface ocean currents, (2) with the dust load from the African continent

  19. Coupling of MIC-3 overexpression with the chromosome 11 and 14 root-knot nematode (RKN) (Meloidogyne incognita) resistance QTLs provides insights into the regulation of the RKN resistance response in Upland cotton...

    Technology Transfer Automated Retrieval System (TEKTRAN)

    High levels of resistance to root-knot nematode (RKN) (Meloidogyne incognita) in Upland cotton (Gossypium hirsutum) is mediated by two major quantitative trait loci (QTL) located on chromosomes 11 and 14. We had previously determined that MIC-3 expression played a direct role in suppressing RKN egg...

  20. Evidence for cross-linking DNA by bis-intercalators with rigid and extended linkers is provided by knotting and catenation.

    PubMed Central

    Annan, N K; Cook, P R; Mullins, S T; Lowe, G

    1992-01-01

    A new series of DNA bis-intercalators is reported in which acridine moieties are connected by rigid and extended pyridine-based linkers of varied length. Cross-linking of DNA by bis-intercalation is inferred from the unwinding and folding of linear DNA induced by the compounds; after ligation and removal of the bis-intercalator, superhelical circles, catenanes and knots that bear a residual imprint of the bis-intercalator are observed. These novel bis-intercalators are of interest because they can be used to probe the spatial organization of DNA, especially near sites of replication, recombination or topoisomerase action where two duplexes must be in close proximity. Preliminary results on the effects of the various compounds on the cloning efficiency of bacteria and replication by permeabilized human cells are also presented. Images PMID:1549510

  1. Studies on the management of root-knot nematode, Meloidogyne incognita-wilt fungus, Fusarium oxysporum disease complex of green gram, Vigna radiata cv ML-1108

    PubMed Central

    Haseeb, Akhtar; Sharma, Anita; Shukla, Prabhat Kuma

    2005-01-01

    Studies were conducted under pot conditions to determine the comparative efficacy of carbofuran at 1 mg a.i./kg soil, bavistin at 1 mg a.i./kg soil, neem (Azadirachta indica) seed powder at 50 mg/kg soil, green mould (Trichoderma harzianum) at 50.0 ml/kg soil, rhizobacteria (Pseudomonas fluorescens) at 50.0 ml/kg soil against root-knot nematode, Meloidogyne incognita–wilt fungus, Fusarium oxysporum disease complex on green gram, Vigna radiata cv ML-1108. All the treatments significantly improved the growth of the plants as compared to untreated inoculated plants. Analysis of data showed that carbofuran and A. indica seed powder increased plant growth and yield significantly more in comparison to bavistin and P. fluorescens. Carbofuran was highly effective against nematode, bavistin against fungus, A. indica seed powder against both the pathogens and both the bioagents were moderately effective against both the pathogens. PMID:16052706

  2. The plant cell inhibitor KRP6 is involved in multinucleation and cytokinesis disruption in giant-feeding cells induced by root-knot nematodes.

    PubMed

    Vieira, Paulo; de Almeida Engler, Janice

    2015-01-01

    The plant cell cycle inhibitor gene KRP6 has been investigated in roots infected by plant-parasitic root-knot nematodes (Meloidogyne spp.). Unexpectedly, KRP6 overexpressing lines revealed a distinct role for this specific KRP as an activator of the mitotic cell cycle. This function was confirmed in Arabidopsis thaliana suspension cultures ectopically expressing KRP6. A blockage in the mitotic exit was observed in cell suspensions and in giant cells resulted in the appearance of multi-nucleated cells. KRP6 expression during nematode infection and the similarity in phenotypes among KRP6 overexpressing cell cultures and giant-cell morphology strongly suggest that KRP6 is involved in multinucleation and acytokinesis occurring in giant-cells. Once again nematodes have been shown to manipulate the plant cell cycle machinery in order to promote gall establishment.

  3. The plant cell inhibitor KRP6 is involved in multinucleation and cytokinesis disruption in giant-feeding cells induced by root-knot nematodes

    PubMed Central

    Vieira, Paulo; Engler, Janice de Almeida

    2015-01-01

    The plant cell cycle inhibitor gene KRP6 has been investigated in roots infected by plant-parasitic root-knot nematodes (Meloidogyne spp.). Unexpectedly, KRP6 overexpressing lines revealed a distinct role for this specific KRP as an activator of the mitotic cell cycle. This function was confirmed in Arabidopsis thaliana suspension cultures ectopically expressing KRP6. A blockage in the mitotic exit was observed in cell suspensions and in giant cells resulted in the appearance of multi-nucleated cells. KRP6 expression during nematode infection and the similarity in phenotypes among KRP6 overexpressing cell cultures and giant-cell morphology strongly suggest that KRP6 is involved in multinucleation and acytokinesis occurring in giant-cells. Once again nematodes have been shown to manipulate the plant cell cycle machinery in order to promote gall establishment. PMID:25915833

  4. Norrie disease pedigree carrying the novel mutation C65Y, predicted to disrupt the cystine knot growth factor motif, analyzed by RasI restriction digestion

    SciTech Connect

    Strasberg, P.M.; Liede, H.A.; Stein, T.

    1994-09-01

    Norrie disease (MIM 310600; ND) is an X-linked (Xp11.2-11.3) neurodevelopmental disorder characterized by congenital blindness, retinal dysplasia with pseudoglioma formation, and often associated with progressive mental retardation and deafness. The ND gene, comprised of 3 exons, codes for an evolutionarily conserved protein of 133 amino acids. We have analyzed 8 pedigrees segregating Norrie disease. Although microdeletions have been detected in several typical ND patients, Southern blot analysis with probes L1.28, MAO-A, MAO-B, TIMP-3.9X, pTak8, and M27{beta} failed to detect such deletions in these 8 ND pedigrees. With the cloning of the ND gene, PCR analysis of all 3 exons likewise did not reveal any insertions or deletions. SSCP analysis ({sup 35}S-dNTP PCR) on PCR products of exon 3 showed a band shift for 1 patient. Repeat `cold` SSCP on minigels (3 inches x 4 inches) followed by liver staining was confirmatory. Direct sequencing revealed a G{r_arrow}A transition at nucleotide 610 corresponding to amino acid 65, changing Cys to Tyr. The mutation created an RsaI site, such that the uncut, normal, and mutant PCR products (using the same PCR primers) were 297 bp, 243 and 54 bp, and 177, 72 and 54 bp respectively. Affected males in the relevant pedigree had restricted PCR products of 177, 72 and 54 bp, carrier mothers 243, 177, 72, and 54 bp, and normals, including 30 unrelated individuals, 243 and 54 bp. Recent evidence indicates that the ND gene has a C-terminal domain homologous to that of TGF{beta}, thus identifying it as putative peptide growth factor, providing a monogenic disease model for the family of cystine knot growth factors. This is the first report of a mutation in Cys 2, critical for crosslinking to Cys 5 forming a disulphide bridge which holds the cystine knot growth factor tertiary structure together.

  5. The Mi-9 Gene from Solanum arcanum Conferring Heat-Stable Resistance to Root-Knot Nematodes Is a Homolog of Mi-11[W][OA

    PubMed Central

    Jablonska, Barbara; Ammiraju, Jetty S.S.; Bhattarai, Kishor K.; Mantelin, Sophie; de Ilarduya, Oscar Martinez; Roberts, Philip A.; Kaloshian, Isgouhi

    2007-01-01

    Resistance conferred by the Mi-1 gene from Solanum peruvianum is effective and widely used for limiting root-knot nematode (Meloidogyne spp.) yield loss in tomato (Solanum lycopersicum), but the resistance is ineffective at soil temperatures above 28°C. Previously, we mapped the heat-stable resistance gene Mi-9 in Solanum arcanum accession LA2157 to the short arm of chromosome 6, in a genetic interval as Mi-1 and the Cladosporium fulvum resistance gene Cf2. We developed a fine map of the Mi-9 region by resistance and marker screening of an F2 population and derived F3 families from resistant LA2157 × susceptible LA392. Mi-1 intron 1 flanking primers were designed to amplify intron 1 and fingerprint Mi-1 homologs. Using these primers, we identified seven Mi-1 homologs in the mapping parents. Cf-2 and Mi-1 homologs were mapped on chromosome 6 using a subset of the F2. Cf-2 homologs did not segregate with Mi-9 resistance, but three Mi-1 homologs (RH1, RH2, and RH4) from LA2157 and one (SH1) from LA392 colocalized to the Mi-9 region. Reverse transcriptase-polymerase chain reaction analysis indicated that six Mi-1 homologs are expressed in LA2157 roots. We targeted transcripts of Mi-1 homologs for degradation with tobacco (Nicotiana tabacum) rattle virus (TRV)-based virus-induced gene silencing using Agrobacterium infiltration with a TRV-Mi construct. In most LA2157 plants infiltrated with the TRV-Mi construct, Mi-9-meditated heat-stable root-knot nematode resistance was compromised at 32°C, indicating that the heat-stable resistance is mediated by a homolog of Mi-1. PMID:17172289

  6. Percutaneous retrieval of centrally embolized fragments of central venous access devices or knotted Swan-Ganz catheters. Clinical report of 14 retrievals with detailed angiographic analysis and review of procedural aspects

    PubMed Central

    Chmielak, Zbigniew; Dębski, Artur; Kępka, Cezary; Rudziński, Piotr N.; Bujak, Sebastian; Skwarek, Mirosław; Kurowski, Andrzej; Dzielińska, Zofia; Demkow, Marcin

    2016-01-01

    Introduction Totally implantable venous access systems (TIVAS), Swan-Ganz (SG) and central venous catheters (CVC) allow easy and repetitive entry to the central cardiovascular system. Fragments of them may be released inadvertently into the cardiovascular system during their insertion or as a result of mechanical complications encountered during long-term utilization. Aim To present results of percutaneous retrieval of embolized fragments of central venous devices or knotted SG and review the procedural aspects with a series of detailed angiographies. Material and methods Between January 2003 and December 2012 there were 14 (~0.025%) successful retrievals in 13 patients (44 ±16 years, 15% females) of embolized fragments of TIVAS (n = 10) or CVC (n = 1) or of dislodged guide-wires (n = 2) or knotted SG (n = 1). Results Foreign bodies with the forward end located in the right ventricle (RV), as well as those found in the pulmonary artery (PA), often required repositioning with a pigtail catheter as compared to those catheter fragments which were located in the right atrium (RA) and/or great vein and possessed an accessible free end allowing their direct ensnarement with the loop snare (57.0% (4/7) vs. 66.7% (2/3) vs. 0.0% (0/3); p = 0.074 respectively). Procedure duration was 2–3 times longer among catheters retrieved from the PA than among those with the forward edge located in the RV or RA (30 (18–68) vs. 13.5 (11–37) vs. 8 min (8–13); p = 0.054 respectively). The SG catheter knotted in the vena cava superior (VCS) was encircled with the loop snare introduced transfemorally, subsequently cut at its skin entrance and then pulled down inside the 14 Fr vascular sheath. Conclusions By using the pigtail catheter and the loop snare, it is feasible to retrieve centrally embolized fragments or knotted central venous access devices. PMID:27279874

  7. Fatty Acid-and Retinol-Binding Protein, Mj-FAR-1 Induces Tomato Host Susceptibility to Root-Knot Nematodes

    PubMed Central

    Iberkleid, Ionit; Vieira, Paulo; de Almeida Engler, Janice; Firester, Kalia; Spiegel, Yitzhak; Horowitz, Sigal Brown

    2013-01-01

    Plant-parasitic nematodes produce at least one structurally unique class of small helix-rich retinol- and fatty-acid-binding proteins that have no counterparts in their plant hosts. Herein we describe a protein of the plant-parasitic root-knot nematode Meloidogyne javanica, which is a member of the nematode-specific fatty-acid- and retinol-binding (Mj-FAR-1) family of proteins. The mj-far-1 mRNA was detected through M. javanica pre-parasitic J2s, migratory and sedentary parasitic stages by quantitative reverse transcriptase polymerase chain reaction (qRT-PCR). Immunolocalization assays demonstrate that the FAR protein of Meloidogyne is secreted during sedentary stages, as evidenced by the accumulation of FAR at the nematode cuticle surface and along the adjacent host root tissues. Tomato roots constitutively expressing mj-far-1 demonstrated an increased susceptibility to root-knot nematodes infection as observed by accelerated gall induction and expansion, accompanied by a higher percentage of nematodes developing into mature females compared to control roots. RNA interference assays that expressed double-stranded RNA complementary to mj-far-1 in transgenic tomato lines specifically reduced nematode infection levels. Histological analysis of nematode-infested roots indicated that in roots overexpressing mj-far-1, galls contained larger feeding cells and might support a faster nematode development and maturation. Roots overexpressing mj-far-1 suppressed jasmonic acid responsive genes such as the proteinase inhibitor (Pin2) and γ-thionin, illustrating the possible role of Mj-FAR-1 in manipulating the lipid based signaling in planta. This data, suggests that Meloidogyne FAR might have a strategic function during the interaction of the nematode with its plant host. Our study present the first demonstration of an in planta functional characterization and localization of FAR proteins secreted by plant-parasitic nematodes. It provides evidence that Mj-FAR-1 facilitates

  8. Preliminary study of the green algae chlorella (Chlorella vulgaris) for control on the root-knot nematode (Meloidogyne arenaria) in tomato plants and ectoparasite Xiphinema indexin grape seedlings.

    PubMed

    Choleva, B; Bileva, T; Tzvetkov, Y; Barakov, P

    2005-01-01

    The alternative ecological methods require investigation of many organo-biological means for plant protection against dangerous root parasites such as root-knot nematode Meloidogyne arenaria and some ectoparasites (Xiphinema index). The Bulgarian organic product - dry extract of green alga Chlorella vulgaris ("The Golden Apple"-Plamen Barakov) is the latest product, which in comparative aspect gives the best results. Series of laboratory and pot experiments are carried out with tomato (cv. Bele and cv. Ideal) and grape seedlings (cv. Cabernet Sauvignon). Different dosages of Chlorella from 0.5 g to 2 g per plant/pot are investigated. The first results show that even low dosages had double effect - on the one hand they suppress the parasite development and on the other hand they strongly stimulate plant growing. The very important conclusion is that Chlorella vulgaris ignores the negative influence of M. arenaria and X. index. These results give us opportunity for future model and field investigations of Chlorella vulgaris with the aim of its practical application.

  9. Pyramiding taro cystatin and fungal chitinase genes driven by a synthetic promoter enhances resistance in tomato to root-knot nematode Meloidogyne incognita.

    PubMed

    Chan, Yuan-Li; He, Yong; Hsiao, Tsen-Tsz; Wang, Chii-Jeng; Tian, Zhihong; Yeh, Kai-Wun

    2015-02-01

    Meloidogyne incognita, one of the major root-knot nematode (RKN) species in agriculture, attacks many plant species, causing severe economic losses. Genetic engineering of plants with defense-responsive genes has been demonstrated to control RKN. These studies, however, focused on controlling RKN at certain growth stages. In the present study, a dual gene overexpression system, utilizing a plant cysteine proteinase inhibitor (CeCPI) and a fungal chitinase (PjCHI-1), was used to transform tomato (Solanum lycopersicum) in order to provide protection from all growth stages of RKN. A synthetic promoter, pMSPOA, containing NOS-like and SP8a elements, was employed to drive the expression of introduced genes. Gall formation and the proportion of female nematodes in the population, as well as effects on the reproduction of RKN, were monitored in both transgenic and control plants. RKN eggs collected from transgenic plants displayed reduced chitin content and retardation in embryogenesis. The results demonstrated that transgenic plants had inhibitory effects on RKN that were superior to plants transformed with a single gene. The pyramiding expression system produced synergistic effects by the two defense-responsive genes, leading to a detrimental effect on all growth stages of RKN. PMID:25575993

  10. Evidence of Differences between the Communities of Arbuscular Mycorrhizal Fungi Colonizing Galls and Roots of Prunus persica Infected by the Root-Knot Nematode Meloidogyne incognita▿

    PubMed Central

    Alguacil, Maria del Mar; Torrecillas, Emma; Lozano, Zenaida; Roldán, Antonio

    2011-01-01

    Arbuscular mycorrhizal fungi (AMF) play important roles as plant protection agents, reducing or suppressing nematode colonization. However, it has never been investigated whether the galls produced in roots by nematode infection are colonized by AMF. This study tested whether galls produced by Meloidogyne incognita infection in Prunus persica roots are colonized by AMF. We also determined the changes in AMF composition and biodiversity mediated by infection with this root-knot nematode. DNA from galls and roots of plants infected by M. incognita and from roots of noninfected plants was extracted, amplified, cloned, and sequenced using AMF-specific primers. Phylogenetic analysis using the small-subunit (SSU) ribosomal DNA (rDNA) data set revealed 22 different AMF sequence types (17 Glomus sequence types, 3 Paraglomus sequence types, 1 Scutellospora sequence type, and 1 Acaulospora sequence type). The highest AMF diversity was found in uninfected roots, followed by infected roots and galls. This study indicates that the galls produced in P. persica roots due to infection with M. incognita were colonized extensively by a community of AMF, belonging to the families Paraglomeraceae and Glomeraceae, that was different from the community detected in roots. Although the function of the AMF in the galls is still unknown, we hypothesize that they act as protection agents against opportunistic pathogens. PMID:21984233

  11. Metagenomic insights into communities, functions of endophytes, and their associates with infection by root-knot nematode, Meloidogyne incognita, in tomato roots.

    PubMed

    Tian, Bao-Yu; Cao, Yi; Zhang, Ke-Qin

    2015-11-25

    Endophytes are known to play important roles in plant's health and productivity. In this study, we investigated the root microbiome of tomato in association with infection by root knot nematodes. Our objectives were to observe the effects and response of the bacterial endophytes before nematode attacks and to reveal the functional attributes of microbes in plant health and nematode pathogenesis. Community analysis of root-associated microbiomes in healthy and nematode-infected tomatoes indicated that nematode infections were associated with variation and differentiation of the endophyte and rhizosphere bacterial populations in plant roots. The community of the resident endophytes in tomato root was significantly affected by nemato-pathogenesis. Remarkably, some bacterial groups in the nematode feeding structure, the root gall, were specifically enriched, suggesting an association with nematode pathogenesis. Function-based metagenomic analysis indicated that the enriched bacterial populations in root gall harbored abundant genes related to degradation of plant polysaccharides, carbohydrate and protein metabolism, and biological nitrogen fixation. Our data indicated that some of the previously assumed beneficial endophytes or bacterial associates with nematode might be involved in nematode infections of the tomato roots.

  12. BEL1-LIKE HOMEODOMAIN6 and KNOTTED ARABIDOPSIS THALIANA7 interact and regulate secondary cell wall formation via repression of REVOLUTA.

    PubMed

    Liu, Yuanyuan; You, Shijun; Taylor-Teeples, Mallorie; Li, Wenhua L; Schuetz, Mathias; Brady, Siobhan M; Douglas, Carl J

    2014-12-01

    The TALE homeodomain transcription factor KNOTTED ARABIDOPSIS THALIANA7 (KNAT7) is part of a regulatory network governing the commitment to secondary cell wall biosynthesis of Arabidopsis thaliana, where it contributes to negative regulation of this process. Here, we report that BLH6, a BELL1-LIKE HOMEODOMAIN protein, specifically interacts with KNAT7, and this interaction influences secondary cell wall development. BLH6 is a transcriptional repressor, and BLH6-KNAT7 physical interaction enhances KNAT7 and BLH6 repression activities. The overlapping expression patterns of BLH6 and KNAT7 and phenotypes of blh6, knat7, and blh6 knat7 loss-of-function mutants are consistent with the existence of a BLH6-KNAT7 heterodimer that represses commitment to secondary cell wall biosynthesis in interfascicular fibers. BLH6 and KNAT7 overexpression results in thinner interfascicular fiber secondary cell walls, phenotypes that are dependent on the interacting partner. A major impact of the loss of BLH6 and KNAT7 function is enhanced expression of the homeodomain-leucine zipper transcription factor REVOLUTA/INTERFASCICULAR FIBERLESS1 (REV/IFL1). BLH6 and KNAT7 bind to the REV promoter and repress REV expression, while blh6 and knat7 interfascicular fiber secondary cell wall phenotypes are suppressed in blh6 rev and knat7 rev double mutants, suggesting that BLH6/KNAT7 signaling acts through REV as a direct target.

  13. Comparing the defence-related gene expression changes upon root-knot nematode attack in susceptible versus resistant cultivars of rice

    PubMed Central

    Kumari, Chanchal; Dutta, Tushar K.; Banakar, Prakash; Rao, Uma

    2016-01-01

    Rice is one of the major staple food crops in the world and an excellent model system for studying monocotyledonous plants. Diseases caused by nematodes in rice are well documented and among them, root-knot nematode (RKN), Meloidogyne graminicola, causes extensive yield decline. It is therefore necessary to identify novel sources of natural resistance to RKN in rice and to investigate the rice-RKN interaction in detail to understand the basal plant defence mechanisms and nematode manipulation of the host physiology. To this end, six different cultivars of rice were initially screened for RKN infection and development; Pusa 1121 and Vandana were found to be most susceptible and resistant to RKN infection, respectively. In order to investigate the role of major hormone-regulated plant defence pathways in compatible/incompatible rice-RKN interaction, some well-identified marker genes involved in salicylate/jasmonate/ethylene pathway were evaluated for their differential expression through qRT-PCR. In general, our study shows a remarkable discrepancy in the expression pattern of those genes between compatible and incompatible rice-RKN interaction. As most information on the molecular interplay between plants and nematodes were generated on dicotyledonous plants, the current study will strengthen our basic understanding of plant-nematode interaction in the monocot crops, which will aid in defining future strategies for best plant health measures. PMID:26961568

  14. BEL1-LIKE HOMEODOMAIN6 and KNOTTED ARABIDOPSIS THALIANA7 Interact and Regulate Secondary Cell Wall Formation via Repression of REVOLUTA[C][W

    PubMed Central

    Liu, Yuanyuan; You, Shijun; Taylor-Teeples, Mallorie; Li, Wenhua L.; Schuetz, Mathias; Brady, Siobhan M.; Douglas, Carl J.

    2014-01-01

    The TALE homeodomain transcription factor KNOTTED ARABIDOPSIS THALIANA7 (KNAT7) is part of a regulatory network governing the commitment to secondary cell wall biosynthesis of Arabidopsis thaliana, where it contributes to negative regulation of this process. Here, we report that BLH6, a BELL1-LIKE HOMEODOMAIN protein, specifically interacts with KNAT7, and this interaction influences secondary cell wall development. BLH6 is a transcriptional repressor, and BLH6-KNAT7 physical interaction enhances KNAT7 and BLH6 repression activities. The overlapping expression patterns of BLH6 and KNAT7 and phenotypes of blh6, knat7, and blh6 knat7 loss-of-function mutants are consistent with the existence of a BLH6-KNAT7 heterodimer that represses commitment to secondary cell wall biosynthesis in interfascicular fibers. BLH6 and KNAT7 overexpression results in thinner interfascicular fiber secondary cell walls, phenotypes that are dependent on the interacting partner. A major impact of the loss of BLH6 and KNAT7 function is enhanced expression of the homeodomain-leucine zipper transcription factor REVOLUTA/INTERFASCICULAR FIBERLESS1 (REV/IFL1). BLH6 and KNAT7 bind to the REV promoter and repress REV expression, while blh6 and knat7 interfascicular fiber secondary cell wall phenotypes are suppressed in blh6 rev and knat7 rev double mutants, suggesting that BLH6/KNAT7 signaling acts through REV as a direct target. PMID:25490916

  15. Juruin: an antifungal peptide from the venom of the Amazonian Pink Toe spider, Avicularia juruensis, which contains the inhibitory cystine knot motif.

    PubMed

    Ayroza, Gabriela; Ferreira, Ivan L C; Sayegh, Raphael S R; Tashima, Alexandre K; da Silva Junior, Pedro I

    2012-01-01

    The aim of this study was to screen the venom of the theraposid spider Avicularia juruensis for the identification of antimicrobial peptides (AMPs) which could be further used as prototypes for drug development. Eleven AMPs, named juruentoxins, with molecular weight ranging from 3.5 to 4.5 kDa, were identified by mass spectrometry after the soluble venom was separated by high performance liquid chromatography. Juruentoxins have a putative inhibitory cystine knot (ICK) motif, generally found in neurotoxins, which are also resistant to proteolysis. One juruentoxin that has 38 amino acid residues and three disulfide bonds were characterized, to which we proposed the name Juruin. Based on liquid growth inhibition assays, it has potent antifungal activity in the micromolar range. Importantly, Juruin lacks haemolytic activity on human erythrocytes at the antimicrobial concentrations. Based on the amino acid sequence, it is highly identical to the insecticidal peptides from the theraposid spiders Selenocosmia huwena, Chilobrachys jingzhao, and Haplopelma schmidti from China, indicating they belong to a group of conserved toxins which are likely to inhibit voltage-gated ion channels. Juruin is a cationic AMP, and Lys22 and Lys23 show maximum positive charge localization that might be important for receptor recognition. Although it shows marked sequence similarity to neurotoxic peptides, Juruin is a novel exciting molecule with potent antifungal activity, which could be used as a novel template for development of drugs against clinical resistant fungi strains. PMID:22973266

  16. Elucidating the molecular bases of epigenetic inheritance in non-model invertebrates: the case of the root-knot nematode Meloidogyne incognita

    PubMed Central

    Perfus-Barbeoch, Laetitia; Castagnone-Sereno, Philippe; Reichelt, Michael; Fneich, Sara; Roquis, David; Pratx, Loris; Cosseau, Céline; Grunau, Christoph; Abad, Pierre

    2014-01-01

    Root-knot nematodes of the genus Meloidogyne are biotrophic plant parasites that exhibit different life cycles and reproduction modes, ranging from classical amphimixis to obligatory mitotic parthenogenesis (apomixis), depending on the species. Meloidogyne incognita, an apomictic species, exhibits a worldwide distribution and a wide host range affecting more than 3000 plant species. Furthermore, evidences suggest that apomixis does not prevent M. incognita from adapting to its environment in contrast to what is expected from mitotic parthenogenesis that should theoretically produce clonal progenies. This raises questions about mechanisms of genome plasticity leading to genetic variation and adaptive evolution in apomictic animals. We reasoned that epigenetic mechanisms might in part be responsible for the generation of phenotypic variants that provide potential for rapid adaptation. We established therefore a pipeline to investigate the principal carriers of epigenetic information, DNA methylation and post-translational histone modifications. Even if M. incognita possesses the epigenetic machinery i.e., chromatin modifying enzymes, 5-methyl-cytosine and 5-hydroxy-methyl-cytosine content is absent or very weak. In contrast, we demonstrated that the canonical histone modifications are present and chromatin shows typical nucleosome structure. This work is the first characterization of carriers of epigenetic information in M. incognita and constitutes a preamble to further investigate if M. incognita development and its adaptation to plant hosts are under epigenetic control. Our pipeline should allow performing similar types of studies in any non-model organism. PMID:24936189

  17. Molecular and biochemical characterization of the β-1,4-endoglucanase gene Mj-eng-3 in the root-knot nematode Meloidogyne javanica.

    PubMed

    Hu, Lili; Cui, Ruqiang; Sun, Longhua; Lin, Borong; Zhuo, Kan; Liao, Jinling

    2013-09-01

    This study describes the molecular and biochemical characterization of the β-1,4-endoglucanase gene (Mj-eng-3) from the root knot nematode Meloidogyne javanica. A 2156-bp genomic DNA sequence of Mj-eng-3 containing six introns was obtained. Mj-eng-3 was localized in the subventral esophageal glands of M. javanica juveniles by in situ hybridization. Real-time RT-PCR assay showed that the highest transcriptional level of Mj-eng-3 occurred in pre-parasitic second-stage juveniles, and this high expression persisted in parasitic second-stage juveniles. Recombinant MJ-ENG-3 degraded carboxymethylcellulose and optimum enzyme activity at 40°C and pH 8.0. EDTA, Mg(2+), Mn(2+), Ca(2+), Co(2+), and Cu(2+) did not affect the activity of MJ-ENG-3; however, Zn(2+) and Fe(2+) inhibited MJ-ENG-3 enzyme activity. In planta Mj-eng-3 RNAi assay displayed a reduction in the number of nematodes and galls in transgenic tobacco roots. These results suggested that MJ-ENG-3 could be secreted by M. javanica to degrade the cellulose of plant cell walls to facilitate its entry and migration during the early stages of parasitism.

  18. Pyramiding taro cystatin and fungal chitinase genes driven by a synthetic promoter enhances resistance in tomato to root-knot nematode Meloidogyne incognita.

    PubMed

    Chan, Yuan-Li; He, Yong; Hsiao, Tsen-Tsz; Wang, Chii-Jeng; Tian, Zhihong; Yeh, Kai-Wun

    2015-02-01

    Meloidogyne incognita, one of the major root-knot nematode (RKN) species in agriculture, attacks many plant species, causing severe economic losses. Genetic engineering of plants with defense-responsive genes has been demonstrated to control RKN. These studies, however, focused on controlling RKN at certain growth stages. In the present study, a dual gene overexpression system, utilizing a plant cysteine proteinase inhibitor (CeCPI) and a fungal chitinase (PjCHI-1), was used to transform tomato (Solanum lycopersicum) in order to provide protection from all growth stages of RKN. A synthetic promoter, pMSPOA, containing NOS-like and SP8a elements, was employed to drive the expression of introduced genes. Gall formation and the proportion of female nematodes in the population, as well as effects on the reproduction of RKN, were monitored in both transgenic and control plants. RKN eggs collected from transgenic plants displayed reduced chitin content and retardation in embryogenesis. The results demonstrated that transgenic plants had inhibitory effects on RKN that were superior to plants transformed with a single gene. The pyramiding expression system produced synergistic effects by the two defense-responsive genes, leading to a detrimental effect on all growth stages of RKN.

  19. Characterization of LeMir, a root-knot nematode-induced gene in tomato with an encoded product secreted from the root.

    PubMed

    Brenner, E D; Lambert, K N; Kaloshian, I; Williamson, V M

    1998-09-01

    A tomato gene that is induced early after infection of tomato (Lycopersicon esculentum Mill.) with root-knot nematodes (Meloidogyne javanica) encodes a protein with 54% amino acid identity to miraculin, a flavorless protein that causes sour substances to be perceived as sweet. This gene was therefore named LeMir (L. esculentum miraculin). Sequence similarity places the encoded protein in the soybean trypsin-inhibitor family (Kunitz). LeMir mRNA is found in root, hypocotyl, and flower tissues, with the highest expression in the root. Rapid induction of expression upon nematode infection is localized to root tips. In situ hybridization shows that LeMir is expressed constitutively in the root-cap and root-tip epidermis. The LeMir protein product (LeMir) was produced in the yeast Pichia pastoris for generation of antibodies. Western-blot analysis showed that LeMir expression is up-regulated by nematode infection and by wounding. LeMir is also expressed in tomato callus tissue. Immunoprint analysis revealed that LeMir is expressed throughout the seedling root, but that levels are highest at the root/shoot junction. Analysis of seedling root exudates revealed that LeMir is secreted from the root into the surrounding environment, suggesting that it may interact with soil-borne microorganisms. PMID:9733543

  20. Metagenomic insights into communities, functions of endophytes, and their associates with infection by root-knot nematode, Meloidogyne incognita, in tomato roots

    PubMed Central

    Tian, Bao-Yu; Cao, Yi; Zhang, Ke-Qin

    2015-01-01

    Endophytes are known to play important roles in plant’s health and productivity. In this study, we investigated the root microbiome of tomato in association with infection by root knot nematodes. Our objectives were to observe the effects and response of the bacterial endophytes before nematode attacks and to reveal the functional attributes of microbes in plant health and nematode pathogenesis. Community analysis of root-associated microbiomes in healthy and nematode-infected tomatoes indicated that nematode infections were associated with variation and differentiation of the endophyte and rhizosphere bacterial populations in plant roots. The community of the resident endophytes in tomato root was significantly affected by nemato-pathogenesis. Remarkably, some bacterial groups in the nematode feeding structure, the root gall, were specifically enriched, suggesting an association with nematode pathogenesis. Function-based metagenomic analysis indicated that the enriched bacterial populations in root gall harbored abundant genes related to degradation of plant polysaccharides, carbohydrate and protein metabolism, and biological nitrogen fixation. Our data indicated that some of the previously assumed beneficial endophytes or bacterial associates with nematode might be involved in nematode infections of the tomato roots. PMID:26603211