Backbone cyclization of a recombinant cystine-knot peptide by engineered Sortase A.
Stanger, Karen; Maurer, Till; Kaluarachchi, Harini; Coons, Mary; Franke, Yvonne; Hannoush, Rami N
2014-11-28
Cyclotides belong to the family of cyclic cystine-knot peptides and have shown promise as scaffolds for protein engineering and pharmacological modulation of cellular protein activity. Cyclotides are characterized by a cystine-knotted topology and a head-to-tail cyclic polypeptide backbone. While they are primarily produced in plants, cyclotides have also been obtained by chemical synthesis. However, there is still a need for methods to generate cyclotides in high yields to near homogeneity. Here, we report a biomimetic approach which utilizes an engineered version of the enzyme Sortase A to catalyze amide backbone cyclization of the recombinant cyclotide MCoTI-II, thereby allowing the efficient production of active homogenous species in high yields. Our results provide proof of concept for using engineered Sortase A to produce cyclic MCoTI-II and should be generally applicable to generating other cyclic cystine-knot peptides.
Structural characterization of the cyclic cystine ladder motif of θ-defensins.
Conibear, Anne C; Rosengren, K Johan; Harvey, Peta J; Craik, David J
2012-12-04
The θ-defensins are, to date, the only known ribosomally synthesized cyclic peptides in mammals, and they have promising antimicrobial bioactivities. The characteristic structural motif of the θ-defensins is the cyclic cystine ladder, comprising a cyclic peptide backbone and three parallel disulfide bonds. In contrast to the cyclic cystine knot, which characterizes the plant cyclotides, the cyclic cystine ladder has not been as well described as a structural motif. Here we report the solution structures and nuclear magnetic resonance relaxation properties in aqueous solution of three representative θ-defensins from different species. Our data suggest that the θ-defensins are more rigid and structurally defined than previously thought. In addition, all three θ-defensins were found to self-associate in aqueous solution in a concentration-dependent and reversible manner, a property that might have a role in their mechanism of action. The structural definition of the θ-defensins and the cyclic cystine ladder will help to guide exploitation of these molecules as structural frameworks for the design of peptide drugs.
Novel inhibitor cystine knot peptides from Momordica charantia.
Directory of Open Access Journals (Sweden)
Wen-Jun He
Full Text Available 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.
Allotides: Proline-Rich Cystine Knot α-Amylase Inhibitors from Allamanda cathartica.
Nguyen, Phuong Q T; Luu, Thuy T; Bai, Yang; Nguyen, Giang K T; Pervushin, Konstantin; Tam, James P
2015-04-24
Cystine knot α-amylase inhibitors belong to a knottin family of peptidyl inhibitors of 30-32 residues and contain two to four prolines. Thus far, only four members of the group of cystine knot α-amylase inhibitors have been characterized. Herein, the discovery and characterization of five cystine knot α-amylase inhibitors, allotides C1-C5 (Ac1-Ac5) (1-5), from the medicinal plant Allamanda cathartica are reported using both proteomic and genomic methods. Proteomic analysis showed that 1-5 are 30 amino acids in length with three or four proline residues. NMR determination of 4 revealed that it has two cis- and one trans-proline residues and adopts two equally populated conformations in solution. Determination of disulfide connectivity of 2 by differential S-reduction and S-alkylation provided clues of its unfolding process. Genomic analysis showed that allotide precursors contain a three-domain arrangement commonly found in plant cystine knot peptides with conserved residues flanking the processing sites of the mature allotide domain. This work expands the number of known cystine knot α-amylase inhibitors and furthers the understanding of both the structural and biological diversity of this type of knottin family.
A cactus-derived toxin-like cystine knot Peptide with selective antimicrobial activity.
Aboye, Teshome L; Strömstedt, Adam A; Gunasekera, Sunithi; Bruhn, Jan G; El-Seedi, Hesham; Rosengren, K Johan; Göransson, Ulf
2015-05-04
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.
DEFF Research Database (Denmark)
Eliasen, Rasmus; Andresen, Thomas L.; Conde-Frieboes, Kilian W.
2012-01-01
Gurmarin is a 35 amino acid peptide with three disulfide bridges in an inhibitor cystine knot. It is found in the plant Gymnema sylvestre, and has been identified as a sweet taste inhibitor in rodents. In this article we provide an efficient route for the synthesis of gurmarin by a controlled...
Amide Rotation Hindrance Predicts Proteolytic Resistance of Cystine-Knot Peptides.
Zhou, Yanzi; Xie, Daiqian; Zhang, Yingkai
2016-04-07
Cystine-knot peptides have remarkable stability against protease degradation and are attractive scaffolds for peptide-based therapeutic and diagnostic agents. In this work, by studying the hydrolysis reaction of a cystine-knot inhibitor MCTI-A and its variants with ab initio QM/MM molecular dynamics simulations, we have elucidated an amide rotation hindrance mechanism for proteolysis resistance: The proteolysis of MCTI-A is retarded due to the higher free energy cost during the rotation of NH group around scissile peptide bond at the tetrahedral intermediate of acylation, and covalent constraint provided by disulfide bonds is the key factor to hinder this rotation. A nearly linear correlation has been revealed between free energy barriers of the peptide hydrolysis reaction and the amide rotation free energy changes at the protease-peptide Michaelis complex state. This suggests that amide rotation hindrance could be one useful feature to estimate peptide proteolysis stability.
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
Modeling the human intestinal mucin (MUC2) C-terminal cystine knot dimer.
Sadasivan, Vatsala D; Narpala, Sandeep R; Budil, David E; Sacco, Albert; Carrier, Rebecca L
2011-11-01
Intestinal mucus, a viscous secretion that lines the mucosa, is believed to be a barrier to absorption of many therapeutic compounds and carriers, and is known to play an important physiological role in controlling pathogen invasion. Nevertheless, there is as yet no clear understanding of the barrier properties of mucus, such as the nature of the molecular interactions between drug molecules and mucus components as well as those that govern gel formation. Secretory mucins, large and complex glycoprotein molecules, are the principal determinants of the viscoelastic properties of intestinal mucus. Despite the important role that mucins play in controlling transport and in diseases such as cystic fibrosis, their structures remain poorly characterized. The major intestinal secretory mucin gene, MUC2, has been identified and fully sequenced. The present study was undertaken to determine a detailed structure of the cysteine-rich region within the C-terminal end of human intestinal mucin (MUC2) via homology modeling, and explore possible configurations of a dimer of this cysteine-rich region, which may play an important role in governing mucus gel formation. Based on sequence-structure alignments and three-dimensional modeling, a cystine knot tertiary structure homologous to that of human chorionic gonadotropin (HCG) is predicted at the C-terminus of MUC2. Dimers of this C-terminal cystine knot (CTCK) were modeled using sequence alignment based on HCG and TGF-beta, followed by molecular dynamics and simulated annealing. Results support the formation of a cystine knot dimer with a structure analogous to that of HCG.
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. Copyright © 2014 Elsevier B.V. All rights reserved.
A new family of cystine knot peptides from the seeds of Momordica cochinchinensis.
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. Copyright © 2012 Elsevier Inc. All rights reserved.
NI, WENQIN; Lin, Melanie; Salinas, Paul; Savickas, Philip; Karger, Barry L.; Wu, Shiaw-Lin
2012-01-01
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...
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
Functional evolution of scorpion venom peptides with an inhibitor cystine knot fold.
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.
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.
Werle, M; Kafedjiiski, K; Kolmar, H; Bernkop-Schnürch, A
2007-03-06
Cystine-knot microproteins exhibit several properties that make them highly interesting as scaffolds for oral peptide drug delivery. It was therefore the aim of the study to evaluate the novel clinically relevant cystine-knot microprotein McoEeTI regarding its potential for oral delivery. Additionally, based on the gained results, important features of McoEeTI were improved. Enzymatic degradation was caused by chymotrypsin, trypsin and porcine small intestinal juice whereas McoEeTI was stable towards elastase, membrane bound proteases, pepsin and porcine gastric juice. Only minor McoEeTI degradation was observed during a 24h incubation period in rat plasma. In the presence of various physiological ions about 50% of McoEeTI formed di- and/or trimers. P(app) value of McoEeTI was determined to be (7.4+/-0.4)x10(-6)cm/s. Sodium caprate and polycarbophil-cysteine (PCP-Cys) had no beneficial effect on McoEeTI permeation, whereas the utilization of a chitosan-thiobutylamidine (Chito-TBA) system improved McoEeTI permeation 3-fold. Enzymatic stability could be strongly improved by the utilization of Bowman-Birk-Inhibitor (BBI) as well as PCP-Cys. In conclusion, this study indicates that McoEeTI represents a promising candidate as a novel scaffold for oral peptide drug delivery.
National Research Council Canada - National Science Library
Ni, Wenqin; Lin, Melanie; Salinas, Paul; Savickas, Philip; Wu, Shiaw-Lin; Karger, Barry L
2013-01-01
...). 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...
Boschert, Verena; van Dinther, Maarten; Weidauer, Stella; van Pee, Katharina; Muth, Eva-Maria; Ten Dijke, Peter; Mueller, Thomas D
2013-01-01
The cystine-knot containing protein Sclerostin is an important negative regulator of bone growth and therefore represents a promising therapeutic target. It exerts its biological task by inhibiting the Wnt (wingless and int1) signaling pathway, which participates in bone formation by promoting the differentiation of mesenchymal stem cells to osteoblasts. The core structure of Sclerostin consists of three loops with the first and third loop (Finger 1 and Finger 2) forming a structured β-sheet and the second loop being unstructured and highly flexible. Biochemical data showed that the flexible loop is important for binding of Sclerostin to Wnt co-receptors of the low-density lipoprotein related-protein family (LRP), by interacting with the Wnt co-receptors LRP5 or -6 it inhibits Wnt signaling. To further examine the structural requirements for Wnt inhibition, we performed an extensive mutational study within all three loops of the Sclerostin core domain involving single and multiple mutations as well as truncation of important regions. By this approach we could confirm the importance of the second loop and especially of amino acids Asn92 and Ile94 for binding to LRP6. Based on a Sclerostin variant found in a Turkish family suffering from Sclerosteosis we generated a Sclerostin mutant with cysteines 84 and 142 exchanged thereby removing the third disulfide bond of the cystine-knot. This mutant binds to LRP6 with reduced binding affinity and also exhibits a strongly reduced inhibitory activity against Wnt1 thereby showing that also elements outside the flexible loop are important for inhibition of Wnt by Sclerostin. Additionally, we examined the effect of the mutations on the inhibition of two different Wnt proteins, Wnt3a and Wnt1. We could detect clear differences in the inhibition of these proteins, suggesting that the mechanism by which Sclerostin antagonizes Wnt1 and Wnt3a is fundamentally different.
Directory of Open Access Journals (Sweden)
Verena Boschert
Full Text Available The cystine-knot containing protein Sclerostin is an important negative regulator of bone growth and therefore represents a promising therapeutic target. It exerts its biological task by inhibiting the Wnt (wingless and int1 signaling pathway, which participates in bone formation by promoting the differentiation of mesenchymal stem cells to osteoblasts. The core structure of Sclerostin consists of three loops with the first and third loop (Finger 1 and Finger 2 forming a structured β-sheet and the second loop being unstructured and highly flexible. Biochemical data showed that the flexible loop is important for binding of Sclerostin to Wnt co-receptors of the low-density lipoprotein related-protein family (LRP, by interacting with the Wnt co-receptors LRP5 or -6 it inhibits Wnt signaling. To further examine the structural requirements for Wnt inhibition, we performed an extensive mutational study within all three loops of the Sclerostin core domain involving single and multiple mutations as well as truncation of important regions. By this approach we could confirm the importance of the second loop and especially of amino acids Asn92 and Ile94 for binding to LRP6. Based on a Sclerostin variant found in a Turkish family suffering from Sclerosteosis we generated a Sclerostin mutant with cysteines 84 and 142 exchanged thereby removing the third disulfide bond of the cystine-knot. This mutant binds to LRP6 with reduced binding affinity and also exhibits a strongly reduced inhibitory activity against Wnt1 thereby showing that also elements outside the flexible loop are important for inhibition of Wnt by Sclerostin. Additionally, we examined the effect of the mutations on the inhibition of two different Wnt proteins, Wnt3a and Wnt1. We could detect clear differences in the inhibition of these proteins, suggesting that the mechanism by which Sclerostin antagonizes Wnt1 and Wnt3a is fundamentally different.
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
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.
Directory of Open Access Journals (Sweden)
Volker Herzig
2015-10-01
Full Text Available 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.
Institute of Scientific and Technical Information of China (English)
邓宇晨; 顾嘉伟; 聂菲; 肖良
2016-01-01
胱氨酸结（cystine knot ，CK）模体是由两对二硫键及其相连的肽链骨架形成的一个内部环以及从环中穿过的第三对二硫键组成的球形结构，广泛存在于真菌、植物、海洋软体动物、昆虫以及蜘蛛等生物的毒素多肽和蛋白质中。CK多肽结构非常稳定、生物活性多样，是一类在药物设计和分子工程研究中的理想模型分子。本文综述了抑制剂胱氨酸结（inhibitor cystine knot ，ICK）多肽和环形胱氨酸结（cyclic cystine knot ，CCK）多肽两类主要CK毒素的氨基酸序列、拓扑结构、排列组合、人工合成以及空间折叠等特征，并进一步阐述了其在药物设计与分子工程中的应用前景。%The cystine knot (CK) motif comprises an internal ring formed by two disulfide bonds and their connecting backbone segments which is threaded by a third disulfide bond .It is present in peptides and proteins of a variety of species ,in-cluding fungi ,plants ,marine molluscs ,insects and spiders .CK polypeptide is one of the ideal model molecules for drug design and molecular engineering research because of its stable structure and variety of bioactivities .Here we summarized the main structural features of both inhibitor cystine knot (ICK) peptide and cyclic cystine knot (CCK) peptide ,including primary se-quence ,topology ,permutation ,synthesis and folding characteristics ,as well as its applications on drug design and molecular engineering .
Institute of Scientific and Technical Information of China (English)
Liya; Pi; Pei-Yu; Chung; Sriniwas; Sriram; Masmudur; M; Rahman; Wen-Yuan; Song; Edward; W; Scott; Bryon; E; Petersen; Gregory; S; Schultz
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 en-dothelial 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 Lex A operators and a lac Z reporter plasmid(p80plac Z) containing eight high affinity Lex A 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 Lex A. Yeast cotransformants 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(P < 0
18F-fluorobenzoate-labeled cystine knot peptides for PET imaging of integrin αvβ6.
Hackel, Benjamin J; Kimura, Richard H; Miao, Zheng; Liu, Hongguang; Sathirachinda, Ataya; Cheng, Zhen; Chin, Frederick T; Gambhir, Sanjiv S
2013-07-01
Integrin αvβ6 is a cell surface receptor minimally expressed by healthy tissue but elevated in lung, colon, skin, ovarian, cervical, and pancreatic cancers. A molecular PET agent for integrin αvβ6 could provide significant clinical utility by facilitating both cancer staging and treatment monitoring to more rapidly identify an effective therapeutic approach. Here, we evaluated 2 cystine knot peptides, R01 and S02, previously engineered with a 3-6 nM affinity for integrin αvβ6, for (18)F radiolabeling and PET imaging of BxPC3 pancreatic adenocarcinoma xenografts in mice. Cystine knot peptides were labeled with N-succinimidyl-4-(18)F-fluorobenzoate and evaluated for binding affinity and serum stability. Peptides conjugated with (18)F-fluorobenzoate (2-3 MBq) were injected via the tail vein into nude mice xenografted with BxPC3 (integrin αvβ6-positive) or 293 (integrin αvβ6-negative) tumors. Small-animal PET scans were acquired at 0.5, 1, and 2 h after injection. Ex vivo γ-counting of dissected tissues was performed at 0.5 and 2 h. (18)F-fluorobenzoate peptides were produced in 93% ((18)F-fluorobenzoate-R01) and 99% ((18)F-fluorobenzoate-S02) purity. (18)F-fluorobenzoate-R01 and (18)F-fluorobenzoate-S02 had affinities of 1.1 ± 0.2 and 0.7 ± 0.4 nM, respectively, and were 87% and 94%, respectively, stable in human serum at 37°C for 2 h. (18)F-fluorobenzoate-R01 and (18)F-fluorobenzoate-S02 exhibited 2.3 ± 0.6 and 1.3 ± 0.4 percentage injected dose per gram (%ID/g), respectively, in BxPC3 xenografted tumors at 0.5 h (n = 4-5). Target specificity was confirmed by low tumor uptake in integrin αvβ6-negative 293 tumors (1.4 ± 0.6 and 0.5 ± 0.2 %ID/g, respectively, for (18)F-fluorobenzoate-R01 and (18)F-fluorobenzoate-S02; both P < 0.05; n = 3-4) and low muscle uptake (3.1 ± 1.0 and 2.7 ± 0.4 tumor to muscle for (18)F-fluorobenzoate-R01 and (18)F-fluorobenzoate-S02, respectively). Small-animal PET data were corroborated by ex vivo γ-counting of
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
Energy Technology Data Exchange (ETDEWEB)
Hoffmann, Anita; Neumann, Piotr [Institut für Biochemie und Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, Abteilung Physikalische Biotechnologie, Kurt-Mothes-Strasse 3, 06120 Halle (Saale) (Germany); Schierhorn, Angelika [Max-Planck-Institut für Proteinfaltung, Abteilung Massenspektrometrie, Kurt-Mothes-Strasse 3, 06120 Halle (Saale) (Germany); Stubbs, Milton T., E-mail: stubbs@biochemtech.uni-halle.de [Institut für Biochemie und Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, Abteilung Physikalische Biotechnologie, Kurt-Mothes-Strasse 3, 06120 Halle (Saale) (Germany); Mitteldeutsches Zentrum für Struktur und Dynamik der Proteine (MZP), Martin-Luther-Universität Halle-Wittenberg (Germany)
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.
Pi, Liya; Chung, Pei-Yu; Sriram, Sriniwas; Rahman, Masmudur M; Song, Wen-Yuan; Scott, Edward W; Petersen, Bryon E; Schultz, Gregory S
2015-11-26
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. 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. 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 (P rabbit corneal
Smith, Jennifer J.; Hill, Justine M.; Little, Michelle J.; Nicholson, Graham M.; King, Glenn F.; Alewood, Paul F.
2011-01-01
The three-disulfide inhibitor cystine knot (ICK) motif is a fold common to venom peptides from spiders, scorpions, and aquatic cone snails. Over a decade ago it was proposed that the ICK motif is an elaboration of an ancestral two-disulfide fold coined the disulfide-directed β-hairpin (DDH). Here we report the isolation, characterization, and structure of a novel toxin [U1-liotoxin-Lw1a (U1-LITX-Lw1a)] from the venom of the scorpion Liocheles waigiensis that is the first example of a native peptide that adopts the DDH fold. U1-LITX-Lw1a not only represents the discovery of a missing link in venom protein evolution, it is the first member of a fourth structural fold to be adopted by scorpion-venom peptides. Additionally, we show that U1-LITX-Lw1a has potent insecticidal activity across a broad range of insect pest species, thereby providing a unique structural scaffold for bioinsecticide development. PMID:21670253
Smith, Jennifer J; Hill, Justine M; Little, Michelle J; Nicholson, Graham M; King, Glenn F; Alewood, Paul F
2011-06-28
The three-disulfide inhibitor cystine knot (ICK) motif is a fold common to venom peptides from spiders, scorpions, and aquatic cone snails. Over a decade ago it was proposed that the ICK motif is an elaboration of an ancestral two-disulfide fold coined the disulfide-directed β-hairpin (DDH). Here we report the isolation, characterization, and structure of a novel toxin [U(1)-liotoxin-Lw1a (U(1)-LITX-Lw1a)] from the venom of the scorpion Liocheles waigiensis that is the first example of a native peptide that adopts the DDH fold. U(1)-LITX-Lw1a not only represents the discovery of a missing link in venom protein evolution, it is the first member of a fourth structural fold to be adopted by scorpion-venom peptides. Additionally, we show that U(1)-LITX-Lw1a has potent insecticidal activity across a broad range of insect pest species, thereby providing a unique structural scaffold for bioinsecticide development.
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.
Zhang, Chao; Kimura, Richard; Abou-Elkacem, Lotfi; Levi, Jelena; Xu, Lingyun; Gambhir, Sanjiv Sam
2016-10-01
Photoacoustic imaging is a nonionizing biomedical imaging modality with higher resolution and imaging depth than fluorescence imaging, which has greater sensitivity. The combination of the 2 imaging modalities could improve the detection of cancer. Integrin αvβ6 is a cell surface marker overexpressed in many different cancers. Here, we report the development and evaluation of a dye-labeled cystine knot peptide, which selectively recognizes integrin αvβ6 with high affinity, for photoacoustic and fluorescence imaging. The new dual-modality probe may find clinical application in cancer diagnosis and intraoperative imaging of integrin αvβ6-positive tumors.
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Sarah J Moore
Full Text Available 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
Conibear, Anne C; Rosengren, K Johan; Daly, Norelle L; Henriques, Sónia Troeira; Craik, David J
2013-04-12
θ-Defensins are ribosomally synthesized cyclic peptides found in the leukocytes of some primate species and have promising applications as antimicrobial agents and scaffolds for peptide drugs. The cyclic cystine ladder motif, comprising a cyclic peptide backbone and three parallel disulfide bonds, is characteristic of θ-defensins. In this study, we explore the role of the cyclic peptide backbone and cystine ladder in the structure, stability, and activity of θ-defensins. θ-Defensin analogues with different numbers and combinations of disulfide bonds were synthesized and characterized in terms of their NMR solution structures, serum and thermal stabilities, and their antibacterial and membrane-binding activities. Whereas the structures and stabilities of the peptides were primarily dependent on the number and position of the disulfide bonds, their antibacterial and membrane-binding properties were dependent on the cyclic backbone. The results provide insights into the mechanism of action of θ-defensins and illustrate the potential of θ-defensin analogues as scaffolds for peptide drug design.
Conibear, Anne C; Bochen, Alexander; Rosengren, K Johan; Stupar, Petar; Wang, Conan; Kessler, Horst; Craik, David J
2014-02-10
Peptides have the specificity and size required to target the protein-protein interactions involved in many diseases. Some cyclic peptides have been utilised as scaffolds for peptide drugs because of their stability; however, other cyclic peptide scaffolds remain to be explored. θ-Defensins are cyclic peptides from mammals; they are characterised by a cyclic cystine ladder motif and have low haemolytic and cytotoxic activity. Here we demonstrate the potential of the cyclic cystine ladder as a scaffold for peptide drug design by introducing the integrin-binding Arg-Gly-Asp (RGD) motif into the θ-defensin RTD-1. The most active analogue had an IC50 of 18 nM for the αv β3 integrin as well as high serum stability, thus demonstrating that a desired bioactivity can be imparted to the cyclic cystine ladder. This study highlights how θ-defensins can provide a stable and conformationally restrained scaffold for bioactive epitopes in a β-strand or turn conformation. Furthermore, the symmetry of the cyclic cystine ladder presents the opportunity to design peptides with dual bioactive epitopes to increase activity and specificity.
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Jennifer L Lahti
2009-09-01
Full Text Available Cystine-knot miniproteins (knottins are promising molecular scaffolds for protein engineering applications. Members of the knottin family have multiple loops capable of displaying conformationally constrained polypeptides for molecular recognition. While previous studies have illustrated the potential of engineering knottins with modified loop sequences, a thorough exploration into the tolerated loop lengths and sequence space of a knottin scaffold has not been performed. In this work, we used the Ecballium elaterium trypsin inhibitor II (EETI as a model member of the knottin family and constructed libraries of EETI loop-substituted variants with diversity in both amino acid sequence and loop length. Using yeast surface display, we isolated properly folded EETI loop-substituted clones and applied sequence analysis tools to assess the tolerated diversity of both amino acid sequence and loop length. In addition, we used covariance analysis to study the relationships between individual positions in the substituted loops, based on the expectation that correlated amino acid substitutions will occur between interacting residue pairs. We then used the results of our sequence and covariance analyses to successfully predict loop sequences that facilitated proper folding of the knottin when substituted into EETI loop 3. The sequence trends we observed in properly folded EETI loop-substituted clones will be useful for guiding future protein engineering efforts with this knottin scaffold. Furthermore, our findings demonstrate that the combination of directed evolution with sequence and covariance analyses can be a powerful tool for rational protein engineering.
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Gabriela eAyroza
2012-09-01
Full Text Available Abstract The aim of this study was to screen the venom of the theraposid spider Avicularia juruensis for the identification of antimicrobial peptides which could be further used as prototypes for drug development. Eleven antimicrobial peptides, named juruentoxins, with molecular weight ranging from 3.5 to 4.5kDa, were identified by mass spectrometry after the soluble venom was separated by high performance liquid chromatography. Juruentoxins have a putative inhibitory cystine knot 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 antimicrobial peptide, 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.
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Combarnous Yves
2009-08-01
Full Text Available Abstract Background Cystine-knot (cys-knot structure is found in a rather large number of secreted proteins and glycoproteins belonging to the TGFbeta and glycoprotein hormone (GPH superfamilies, many of which are involved in endocrine control of reproduction. In these molecules, the cys-knot is formed by a disulfide (SS bridge penetrating a ring formed by 8, 9 or 10 amino-acid residues among which four are cysteine residues forming two SS bridges. The glycoprotein hormones Follicle-Stimulating Hormone (FSH, Luteinizing Hormone (LH, Thyroid-Stimulating Hormone (TSH and Chorionic Gonadotropin (CG are heterodimers consisting of non-covalently associated alpha and beta subunits that possess cys-knots with 8-amino-acyl (8aa rings. In order to get better insight in the structural evolution of glycoprotein hormones, we examined the number and organization of SS bridges in the sequences of human 8-aa-ring cys-knot proteins having 7 (gremlins, 9 (cerberus, DAN, 10 (GPA2, GPB5, GPHα and 12 (GPHβ cysteine residues in their sequence. Discussion The comparison indicated that the common GPH-alpha subunit exhibits a SS bridge organization ressembling that of DAN and GPA2 but possesses a unique bridge linking an additional cysteine inside the ring to the most N-terminal cysteine residue. The specific GPHbeta subunits also exhibit a SS bridge organization close to that of DAN but it has two additional C-terminal cysteine residues which are involved in the formation of the "seat belt" fastened by a SS "buckle" that ensures the stability of the heterodimeric structure of GPHs. GPA2 and GPB5 exhibit no cys residue potentially involved in interchain SS bridge and GPB5 does not possess a sequence homologous to that of the seatbelt in GPH β-subunits. GPA2 and GPB5 are thus not expected to form a stable heterodimer at low concentration in circulation. Summary The 8-aa cys-knot proteins GPA2 and GPB5 are expected to form a heterodimer only at concentrations above 0
Formation of Cystine Slipknots in Dimeric Proteins
Mateusz Sikora; Marek Cieplak
2013-01-01
We consider mechanical stability of dimeric and monomeric proteins with the cystine knot motif. A structure based dynamical model is used to demonstrate that all dimeric and some monomeric proteins of this kind should have considerable resistance to stretching that is significantly larger than that of titin. The mechanisms of the large mechanostability are elucidated. In most cases, it originates from the induced formation of one or two cystine slipknots. Since there are four termini in a dim...
Geometry of Cyclic Quotients; 1, Knotted Totally Geodesic Submanifolds in Positively Curved Spheres
Reznikov, A G
1994-01-01
We prove that there exists a metric of positive curvature in a three-sphere which admits a given torus knot as a closed geodesic.We also sketch a construction of a metric in a four sphere, very likely of positive curvature, which admits a totally geodesic projective plane with Euler number four. Surpisingly, the technique borrows a lot from the Mostow-Siu-Gromov-Thurston constuction of exotic negatively curved manifolds.
Formation of cystine slipknots in dimeric proteins.
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Mateusz Sikora
Full Text Available We consider mechanical stability of dimeric and monomeric proteins with the cystine knot motif. A structure based dynamical model is used to demonstrate that all dimeric and some monomeric proteins of this kind should have considerable resistance to stretching that is significantly larger than that of titin. The mechanisms of the large mechanostability are elucidated. In most cases, it originates from the induced formation of one or two cystine slipknots. Since there are four termini in a dimer, there are several ways of selecting two of them to pull by. We show that in the cystine knot systems, there is strong anisotropy in mechanostability and force patterns related to the selection. We show that the thermodynamic stability of the dimers is enhanced compared to the constituting monomers whereas machanostability is either lower or higher.
Friedman, Greg
2004-01-01
This is an introduction to the construction of higher-dimensional knots by spinning methods. Simple spinning of classical knots was introduced by E. Artin in 1926, and several generalizations have followed. These include twist spinning, superspinning or p-spinning, frame spinning, roll spinning, and deform spinning. We survey these constructions and some of their most important applications, as well as some newer hybrids due to the author. The exposition, meant to be accessible to a broad aud...
[Cystine-lysinuric lithiasis].
Callís, L; Castelló, F; Vila, A; Pi Ferrer, A
1978-01-01
Cistin-lisinuria is not a unfrequent etiology of lithiasis in children. Six patients have been studied as well as their families, being a total of 45 patients. Lithiasis was present in ten of our patients, and hyperaminoaciduria, without lithiasis in ten, affecting in both cases (with or without litiasis) either all the four amynoacide (cystine, lysine, arginine and ornithine) or only one or two of them. Authors have not found any correlation between clearance of cystine and the presence or absence of lithiasis; on the other hand the best index to correlate the presence of lithiasis is to reach a value, equal or superior to 300 mgr of cystine excreted in the urine per 1 gr of creatinine excreted in urine. The correct treatment in cystinuric patients with lithiasis is to alcalize the urine maintaining a constant urinary pH between 7-8, giving a sufficient dose of sodium bicarbonate per os. In case of resistance to this treatment or if a great calculi is present, D-penicillamine would be an efficient treatment to disolve the calculi. These treatment when carried out under analytical control presents no problems or complications in their experience.
Asteropsin A: an unusual cystine-crosslinked peptide from porifera enhances neuronal Ca2+ influx.
Li, Huayue; Bowling, John J; Fronczek, Frank R; Hong, Jongki; Jabba, Sairam V; Murray, Thomas F; Ha, Nam-Chul; Hamann, Mark T; Jung, Jee H
2013-03-01
Herein we report the discovery of a cystine-crosslinked peptide from Porifera along with high-quality spatial details accompanied by the description of its unique effect on neuronal calcium influx. Asteropsin A (ASPA) was isolated from the marine sponge Asteropus sp., and its structure was independently determined using X-ray crystallography (0.87 angstroms) and solution NMR spectroscopy. An N-terminal pyroglutamate modification, uncommon cis proline conformations, and absence of basic residues helped distinguish ASPA from other cystine-crosslinked knot peptides. ASPA enhanced Ca2+ influx in murine cerebrocortical neuron cells following the addition of the Na+ channel activator veratridine but did not modify the oscillation frequency or amplitude of neuronal Ca2+ currents alone. Allosterism at neurotoxin site 2 was not observed, suggesting an alternative to the known Na+ channel interaction. Together with a distinct biological activity, the origin of ASPA suggests a new subclass of cystine-rich knot peptides associated with Porifera. The discovery of ASPA represents a distinctive addition to an emerging subclass of cystine-crosslinked knot peptides from Porifera.
Cystine dimethylester model of cystinosis: still reliable?
Wilmer, M.J.G.; Willems, P.H.G.M.; Verkaart, S.A.J.; Visch, H.J.; Graaf-Hess, A.C. de; Blom, H.J.; Monnens, L.A.H.; Heuvel, L.P.W.J. van den; Levtchenko, E.N.
2007-01-01
The ability of cystine dimethylester (CDME) to load lysosomes with cystine has been used to establish the basic defect in cystinosis: defective cystine exodus from lysosomes. Using CDME loading, it has been postulated that cystine accumulation in cystinosis affects mitochondrial ATP production, resu
Henrich, Allison; Narayan, Sneha; Pechenik, Oliver; Silversmith, Robert; Townsend, Jennifer
2010-01-01
In this paper, we introduce playing games on shadows of knots. We demonstrate two novel games, namely, To Knot or Not to Knot and Much Ado about Knotting. We also discuss winning strategies for these games on certain families of knot shadows. Finally, we suggest variations of these games for further study.
Steinherz, R; Tietze, F.; Gahl, W A; Triche, T J; Chiang, H.; Modesti, A.; Schulman, J D
1982-01-01
Upon exposure to 0.25 mM cystine dimethyl ester, normal and cystinotic leukocytes accumulate substantially more intracellular cystine than is present endogenously in cystinotic cells. Leukocytes loaded by exposure to cystine dimethyl ester may have abnormally lucent and distended lysosomes, and the cystine is compartmentalized within the granular fraction of the cells. After the cells are exposed to cystine dimethyl ester, cystine clearance from normal leukocytes is much faster than from cyst...
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Douglas Gatte Picchi
2009-01-01
Full Text Available Natural peptides are outstanding as the most promising macromolecules in the search for new drugs, especially those of cyclic nature. The higher plants revealed a very peculiar composition of their cyclic peptides, which distinguish themselves by a "head-to-tail" cyclization. It is possible to define two groups of cyclic peptides from plant biomass. Those called in this review as Eucyclopeptides formed by 2-12 amino acid, and Cyclotides considered as circular polypeptides, composed of 29-37 amino acid that retain three disulfides bridges in an arrangement known as cyclic cystine knot. Searching for plant peptides should form into a subject for scientific research in the forefront of great importance for bioprospecting natural products macromolecular.
2010-04-01
... 21 Food and Drugs 6 2010-04-01 2010-04-01 false Cystine. 582.5273 Section 582.5273 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) ANIMAL DRUGS, FEEDS... § 582.5273 Cystine. (a) Product. Cystine (L- and DL-forms). (b) Conditions of use. This substance...
Practical and ornamental knots
Shaw, George Russell
2008-01-01
For centuries, everyone from sailors, fishermen, and cowboys to explorers, hunters, and mountaineers have known about - and relied on - the indispensable knot. Many of them also knew that the diversity of knot crafting was limited only by the imagination. In this classic guide, George Russell Shaw reveals the unlimited potential of the knot as not only a basic tool, but as a beautiful work of art.Filled with easy-to-follow and accurate instructions on creating scores of useful and decorative knots, 193 hand-drawn illustrations will guide you in creating: Braids Angler Knots Japanese Knots L
Indian Academy of Sciences (India)
Yacov Kantov
2005-06-01
Knots and topological entanglements play an important role in the statistical mechanics of polymers. While topological entanglement is a global property, it is possible to study the size of a knotted region both numerically and analytically. It can be shown that long-range repulsive interactions, as well as entropy favor small knots in dilute systems. However, in dense systems and at the -point in two dimensions the uncontracted knot configuration is the most likely.
Cystine urolithiasis in a caracal (Caracal caracal).
Tordiffe, Adrian Stephen Wolferstan; van der Watt, George Frederick; Reyers, Fred
2012-09-01
In July 2009, a 14-yr-old male caracal (Caracal caracal) at the National Zoological Gardens of South Africa was found, on abdominal ultrasound, to have a single large cystolith. The cystolith was removed, and the composition was determined to be 100% cystine. Blood and urine samples were also collected from three other apparently healthy caracals at the zoo and were submitted, together with the samples from the affected animal, for analysis using gas chromatograph mass spectrometry for cystine, lysine, alanine, and ornithine levels. The cystine levels in the urine, the fractional excretion of cystine, and the normalized excretion of cystine (micromol/g of creatinine) were all higher in the affected caracal than in the healthy animals. Only a single other case of cystine urolithiasis has been previously reported in any wild felid in the literature.
Rolfsen, Dale
2003-01-01
Rolfsen's beautiful book on knots and links can be read by anyone, from beginner to expert, who wants to learn about knot theory. Beginners with a basic background find an inviting introduction to the elements of topology, emphasizing the tools needed for understanding knots, the fundamental group and van Kampen's theorem, for example, which are then applied to concrete problems, such as computing knot groups. For experts, Rolfsen explains advanced topics, such as the connections between knot theory and surgery and how they are useful to understanding three-manifolds. Besides providing a guide
Menasco, William
2005-01-01
This book is a survey of current topics in the mathematical theory of knots. For a mathematician, a knot is a closed loop in 3-dimensional space: imagine knotting an extension cord and then closing it up by inserting its plug into its outlet. Knot theory is of central importance in pure and applied mathematics, as it stands at a crossroads of topology, combinatorics, algebra, mathematical physics and biochemistry.* Survey of mathematical knot theory* Articles by leading world authorities* Clear exposition, not over-technical* Accessible to readers with undergraduate background in mathematics
Molecular jamming—The cystine slipknot mechanical clamp in all-atom simulations
Pepłowski, Łukasz; Sikora, Mateusz; Nowak, Wiesław; Cieplak, Marek
2011-02-01
A recent survey of 17 134 proteins has identified a new class of proteins which are expected to yield stretching induced force peaks in the range of 1 nN. Such high force peaks should be due to forcing of a slip-loop through a cystine ring, i.e., by generating a cystine slipknot. The survey has been performed in a simple coarse grained model. Here, we perform all-atom steered molecular dynamics simulations on 15 cystine knot proteins and determine their resistance to stretching. In agreement with previous studies within a coarse grained structure based model, the level of resistance is found to be substantially higher than in proteins in which the mechanical clamp operates through shear. The large stretching forces arise through formation of the cystine slipknot mechanical clamp and the resulting steric jamming. We elucidate the workings of such a clamp in an atomic detail. We also study the behavior of five top strength proteins with the shear-based mechanostability in which no jamming is involved. We show that in the atomic model, the jamming state is relieved by moving one amino acid at a time and there is a choice in the selection of the amino acid that advances the first. In contrast, the coarse grained model also allows for a simultaneous passage of two amino acids.
Tabulating knot polynomials for arborescent knots
Mironov, A; Morozov, An; Sleptsov, A; Ramadevi, P; Singh, Vivek Kumar
2016-01-01
Arborescent knots are the ones which can be represented in terms of double fat graphs or equivalently as tree Feynman diagrams. This is the class of knots for which the present knowledge is enough for lifting topological description to the level of effective analytical formulas. The paper describes the origin and structure of the new tables of colored knot polynomials, which will be posted at the dedicated site. Even if formal expressions are known in terms of modular transformation matrices, the computation in finite time requires additional ideas. We use the "family" approach, and apply it to arborescent knots in Rolfsen table by developing a Feynman diagram technique, associated with an auxiliary matrix model field theory. Gauge invariance in this theory helps to provide meaning to Racah matrices in the case of non-trivial multiplicities and explains the need for peculiar sign prescriptions in the calculation of [21]-colored HOMFLY polynomials.
Zor, Erhan; Bingol, Haluk; Ramanaviciene, Almira; Ramanavicius, Arunas; Ersoz, Mustafa
2015-01-07
Here, we report a novel enantioselective electrochemical biosensor for the discrimination of cystine enantiomers (d- and l-cystine) using a chiral interface for the specific recognition of d- and l-cystine. The biosensor is based on reduced graphene oxide modified by β-cyclodextrin (rGO/β-CD) at the GCE surface. During the preparation of rGO/β-CD/GCE, the modified electrode surfaces were characterized by cyclic voltammetry (CV), electrochemical impedance spectroscopy (EIS) and scanning electron microscopy (SEM). The electrochemical behaviours of the d- and l-cystine were investigated using the rGO/β-CD/GCE by CV and compared to bare GCE. A clear separation between the oxidation peak potentials of d- and l-cystine was observed at 1.32 and 1.42 V, respectively. The electrochemical discrimination performance of the fabricated chiral sensor was also examined by differential pulse voltammetry (DPV) in a mixed solution of d- and l-cystine. In addition, the DPV technique was used for the determination of d- and l-cystine at low concentration values in the range of 1.0-10.0 μM. To investigate the amperometric response of rGO/β-CD/GCE towards d- and l-cystine, the chronoamperometry technique was used in the concentration range of 10.0-100.0 μM. The interactions of the enantiomers with rGO/β-CD were modelled by molecular docking using AutoDock Vina, and the interaction energies were predicted to be -4.8 and -5.3 kcal mol(-1) for d- and l-cystine, respectively. The corresponding values of binding constants were calculated to be 3.32 × 10(3) and 7.71 × 10(3) M(-1), respectively. The experimental and molecular docking results indicate that the rGO/β-CD/GCE has a different affinity for each enantiomer.
Comparing models of Red Knot population dynamics
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.
Turner, J C
1996-01-01
This book brings together twenty essays on diverse topics in the history and science of knots. It is divided into five parts, which deal respectively with knots in prehistory and antiquity, non-European traditions, working knots, the developing science of knots, and decorative and other aspects of knots.Its authors include archaeologists who write on knots found in digs of ancient sites (one describes the knots used by the recently discovered Ice Man); practical knotters who have studied the history and uses of knots at sea, for fishing and for various life support activities; a historian of l
Zou, L P; Pak, D G
2013-01-01
We consider topological structure of classical vacuum solutions in quantum chromodynamics. Topologically non-equivalent vacuum configurations are classified by non-trivial second and third homotopy groups for coset of the color group SU(N) (N=2,3) under the action of maximal Abelian stability group. Starting with explicit vacuum knot configurations we study possible exact classical solutions as vacuum excitations. Exact analytic non-static knot solution in a simple CP^1 model in Euclidean space-time has been obtained. We construct an ansatz based on knot and monopole topological vacuum structure for searching new solutions in SU(2) and SU(3) QCD. We show that singular knot-like solutions in QCD in Minkowski space-time can be naturally obtained from knot solitons in integrable CP^1 models. A family of Skyrme type low energy effective theories of QCD admitting exact analytic solutions with non-vanishing Hopf charge is proposed.
The Wiese Knot: A Sliding-Locking Arthroscopic Knot.
Parada, Stephen A; Shaw, K Aaron; Eichinger, Josef K; Boykin, Nathan T; Gloystein, David M; Ledford, Cheryl L; Arrington, Edward D; Wiese, Paul T
2017-02-01
Despite recent advances in knotless suture devices for arthroscopic surgical procedures, arthroscopic knot tying remains a necessary skill for the arthroscopic surgeon. Successful completion of arthroscopic knot tying relies on a thorough understanding of the chosen technique, proper suture management, adequate knot tensioning and securement, and the ability to reproducibly create the knot. We introduce a technique that serves as both a sliding and locking knot while being simple to master and reproducible to perform.
Tabulating knot polynomials for arborescent knots
Mironov, A.; Morozov, A.; Morozov, A.; Ramadevi, P.; Singh, Vivek Kumar; Sleptsov, A.
2017-02-01
Arborescent knots are those which can be represented in terms of double fat graphs or equivalently as tree Feynman diagrams. This is the class of knots for which the present knowledge is sufficient for lifting topological description to the level of effective analytical formulas. The paper describes the origin and structure of the new tables of colored knot polynomials, which will be posted at the dedicated site (http://knotebook.org). Even if formal expressions are known in terms of modular transformation matrices, the computation in finite time requires additional ideas. We use the ‘family’ approach, suggested in Mironov and Morozov (2015 Nucl. Phys. B 899 395–413), and apply it to arborescent knots in the Rolfsen table by developing a Feynman diagram technique, associated with an auxiliary matrix model field theory. Gauge invariance in this theory helps to provide meaning to Racah matrices in the case of non-trivial multiplicities and explains the need for peculiar sign prescriptions in the calculation of [21]-colored HOMFLY-PT polynomials.
Combinatorial Maps with Normalized Knot
Zeps, Dainis
2010-01-01
We consider combinatorial maps with fixed combinatorial knot numbered with augmenting numeration called normalized knot. We show that knot's normalization doesn't affect combinatorial map what concerns its generality. Knot's normalization leads to more concise numeration of corners in maps, e.g., odd or even corners allow easy to follow distinguished cycles in map caused by the fixation of the knot. Knot's normalization may be applied to edge structuring knot too. If both are normalized then one is fully and other partially normalized mutually.
Banagl, Markus
2011-01-01
The present volume grew out of the Heidelberg Knot Theory Semester, organized by the editors in winter 2008/09 at Heidelberg University. The contributed papers bring the reader up to date on the currently most actively pursued areas of mathematical knot theory and its applications in mathematical physics and cell biology. Both original research and survey articles are presented; numerous illustrations support the text. The book will be of great interest to researchers in topology, geometry, and mathematical physics, graduate students specializing in knot theory, and cell biologists interested
Nawata, Satoshi
2015-01-01
We provide various formulations of knot homology that are predicted by string dualities. In addition, we also explain the rich algebraic structure of knot homology which can be understood in terms of geometric representation theory in these formulations. These notes are based on lectures in the workshop "Physics and Mathematics of Link Homology" at Centre de Recherches Math\\'ematiques, Universit\\'e de Montr\\'eal.
Aneziris, Charilaos N
1999-01-01
One of the most significant unsolved problems in mathematics is the complete classification of knots. The main purpose of this book is to introduce the reader to the use of computer programming to obtain the table of knots. The author presents this problem as clearly and methodically as possible, starting from the very basics. Mathematical ideas and concepts are extensively discussed, and no advanced background is required.
Proteins analysed as virtual knots
Alexander, Keith; Dennis, Mark R
2016-01-01
Long, flexible physical filaments are naturally tangled and knotted, from macroscopic string down to long-chain molecules. The existence of knotting in a filament naturally affects its configuration and properties, and may be very stable or disappear rapidly under manipulation and interaction. Knotting has been previously identified in protein backbone chains, for which these mechanical constraints are of fundamental importance to their molecular functionality, despite their being open curves in which the knots are not mathematically well defined; knotting can only be identified by closing the termini of the chain somehow. We introduce a new method for resolving knotting in open curves using virtual knots, a wider class of topological objects that do not require a classical closure and so naturally capture the topological ambiguity inherent in open curves. We describe the results of analysing proteins in the Protein Data Bank by this new scheme, recovering and extending previous knotting results, and identify...
Rational-slice Knots via Strongly Negative-amphicheiral Knots
Institute of Scientific and Technical Information of China (English)
KAWAUCHI AKIO
2009-01-01
We show that certain satellite knots of every strongly negative-amphicheiral rational knot are rational-slice knots. This proof also shows that the 0-surgery man-ifold of a certain strongly negative amphicheiral knot such as the figure-eight knot bounds a compact oriented smooth 4-manifold homotopy equivalent to the 2-sphere such that a second homology class of the 4-manifold is represented by a smoothly embedded 2-sphere if and only if the modulo two reduction of it is zero.
Knot theory in modern chemistry.
Horner, Kate E; Miller, Mark A; Steed, Jonathan W; Sutcliffe, Paul M
2016-11-21
Knot theory is a branch of pure mathematics, but it is increasingly being applied in a variety of sciences. Knots appear in chemistry, not only in synthetic molecular design, but also in an array of materials and media, including some not traditionally associated with knots. Mathematics and chemistry can now be used synergistically to identify, characterise and create knots, as well as to understand and predict their physical properties. This tutorial review provides a brief introduction to the mathematics of knots and related topological concepts in the context of the chemical sciences. We then survey the broad range of applications of the theory to contemporary research in the field.
Sedimentation of Knotted Polymers
Piili, Joonas; Kaski, Kimmo; Linna, Riku
2012-01-01
We investigate the sedimentation of knotted polymers by means of the stochastic rotation dynamics, a molecular dynamics algorithm which 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 n_c of the corresponding ideal knot. To the best of our knowledge, this provides the first direct computational confirmation of this relation, postulated on the basis of experiments in "The effect of ionic conditions on the conformations of supercoiled DNA. I. sedimentation analysis" by Rybenkov et al., for the case of sedimentation. 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 R_g^-1, more specifically with the inverse of the R_g component that is perpendicular to the direction along which the polymer sediments. Intriguingly, the linear de...
Proteins analysed as virtual knots
Alexander, Keith; Taylor, Alexander J.; Dennis, Mark R.
2017-02-01
Long, flexible physical filaments are naturally tangled and knotted, from macroscopic string down to long-chain molecules. The existence of knotting in a filament naturally affects its configuration and properties, and may be very stable or disappear rapidly under manipulation and interaction. Knotting has been previously identified in protein backbone chains, for which these mechanical constraints are of fundamental importance to their molecular functionality, despite their being open curves in which the knots are not mathematically well defined; knotting can only be identified by closing the termini of the chain somehow. We introduce a new method for resolving knotting in open curves using virtual knots, which are a wider class of topological objects that do not require a classical closure and so naturally capture the topological ambiguity inherent in open curves. We describe the results of analysing proteins in the Protein Data Bank by this new scheme, recovering and extending previous knotting results, and identifying topological interest in some new cases. The statistics of virtual knots in protein chains are compared with those of open random walks and Hamiltonian subchains on cubic lattices, identifying a regime of open curves in which the virtual knotting description is likely to be important.
Proteins analysed as virtual knots
Alexander, Keith; Taylor, Alexander J.; Dennis, Mark R.
2017-01-01
Long, flexible physical filaments are naturally tangled and knotted, from macroscopic string down to long-chain molecules. The existence of knotting in a filament naturally affects its configuration and properties, and may be very stable or disappear rapidly under manipulation and interaction. Knotting has been previously identified in protein backbone chains, for which these mechanical constraints are of fundamental importance to their molecular functionality, despite their being open curves in which the knots are not mathematically well defined; knotting can only be identified by closing the termini of the chain somehow. We introduce a new method for resolving knotting in open curves using virtual knots, which are a wider class of topological objects that do not require a classical closure and so naturally capture the topological ambiguity inherent in open curves. We describe the results of analysing proteins in the Protein Data Bank by this new scheme, recovering and extending previous knotting results, and identifying topological interest in some new cases. The statistics of virtual knots in protein chains are compared with those of open random walks and Hamiltonian subchains on cubic lattices, identifying a regime of open curves in which the virtual knotting description is likely to be important. PMID:28205562
Knotted vs. unknotted proteins: evidence of knot-promoting loops.
Directory of Open Access Journals (Sweden)
Raffaello Potestio
Full Text Available Knotted proteins, because of their ability to fold reversibly in the same topologically entangled conformation, are the object of an increasing number of experimental and theoretical studies. The aim of the present investigation is to assess, on the basis of presently available structural data, the extent to which knotted proteins are isolated instances in sequence or structure space, and to use comparative schemes to understand whether specific protein segments can be associated to the occurrence of a knot in the native state. A significant sequence homology is found among a sizeable group of knotted and unknotted proteins. In this family, knotted members occupy a primary sub-branch of the phylogenetic tree and differ from unknotted ones only by additional loop segments. These "knot-promoting" loops, whose virtual bridging eliminates the knot, are found in various types of knotted proteins. Valuable insight into how knots form, or are encoded, in proteins could be obtained by targeting these regions in future computational studies or excision experiments.
Determining Knots by Minimizing Energy
Institute of Scientific and Technical Information of China (English)
Cai-Ming Zhang; Hui-Jian Han; Fuhua Frank Cheng
2006-01-01
A new method for determining knots to construct polynomial curves is presented. At each data point, a quadric curve which passes three consecutive points is constructed. The knots for constructing the quadric curve are determined by minimizing the internal strain energy, which can be regarded as a function of the angle. The function of the angle is expanded as a Taylor series with two terms, then the two knot intervals between the three consecutive points are defined by linear expression. Between the two consecutive points, there are two knot intervals, and the combination of the two knot intervals is used to define the final knot interval. A comparison of the new method with several existing methods is included.
Knot probabilities in random diagrams
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.
Untangling of knotted urethral catheters
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Sambrook, Andrew J. [Aberdeen Royal Infirmary, Department of Radiology, Aberdeen (United Kingdom); Todd, Alistair [Raigmore Hospital, Inverness (United Kingdom)
2007-04-15
Intravesical catheter knotting during micturating cystourethrography is a rare but recognized complication of the procedure. We were able to untangle a knot utilizing a fluoroscopically guided vascular guidewire. Following this success, a small study was performed using a model. Various types of guidewires and techniques were tested for different diameters of knots in order to predict the likelihood of success in this type of situation. (orig.)
Untangling of knotted urethral catheters.
Sambrook, Andrew J; Todd, Alistair
2007-04-01
Intravesical catheter knotting during micturating cystourethrography is a rare but recognized complication of the procedure. We were able to untangle a knot utilizing a fluoroscopically guided vascular guidewire. Following this success, a small study was performed using a model. Various types of guidewires and techniques were tested for different diameters of knots in order to predict the likelihood of success in this type of situation.
Iwao Ohtsu; Yusuke Kawano; Marina Suzuki; Susumu Morigasaki; Kyohei Saiki; Shunsuke Yamazaki; Gen Nonaka; Hiroshi Takagi
2015-01-01
Intracellular thiols like L-cystine and L-cystine play a critical role in the regulation of cellular processes. Here we show that Escherichia coli has two L-cystine transporters, the symporter YdjN and the ATP-binding cassette importer FliY-YecSC. These proteins import L-cystine, an oxidized product of L-cystine from the periplasm to the cytoplasm. The symporter YdjN, which is expected to be a new member of the L-cystine regulon, is a low affinity L-cystine transporter (K m = 1.1 μM) that is ...
Naughty knot: a case of nasogastric tube knotting.
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.
How superfluid vortex knots untie
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.
On knots in overtwisted contact structures
Etnyre, John B
2010-01-01
We prove that each overtwisted contact structure has knot types that are represented by infinitely many distinct transverse knots all with the same self-linking number. In some cases, we can even classify all such knots. We also show similar results for Legendrian knots and prove a "folk" result concerning loose transverse and Legendrian knots (that is knots with overtwisted complements) which says that such knots are determined by their classical invariants (up to contactomorphism). Finally we discuss how these results partially fill in our understanding of the "geography" and "botany"' problems for Legendrian knots in overtwisted contact structures, as well as many open questions regarding these problems.
Zhao, Xin
2013-05-01
Elastic rods have been studied intensively since the 18th century. Even now the theory of elastic rods is still developing and enjoying popularity in computer graphics and physical-based simulation. Elastic rods also draw attention from architects. Architectural structures, NODUS, were constructed by elastic rods as a new method of form-finding. We study discrete models of elastic rods and NODUS structures. We also develop computational tools to find the equilibria of elastic rods and the shape of NODUS. Applications of elastic rods in forming torus knot and closing Bishop frame are included in this thesis.
Ham, J.-Y.; Lee, J.
2016-09-01
We calculate the Chern-Simons invariants of twist-knot orbifolds using the Schläfli formula for the generalized Chern-Simons function on the family of twist knot cone-manifold structures. Following the general instruction of Hilden, Lozano, and Montesinos-Amilibia, we here present concrete formulae and calculations. We use the Pythagorean Theorem, which was used by Ham, Mednykh and Petrov, to relate the complex length of the longitude and the complex distance between the two axes fixed by two generators. As an application, we calculate the Chern-Simons invariants of cyclic coverings of the hyperbolic twist-knot orbifolds. We also derive some interesting results. The explicit formulae of the A-polynomials of twist knots are obtained from the complex distance polynomials. Hence the edge polynomials corresponding to the edges of the Newton polygons of the A-polynomials of twist knots can be obtained. In particular, the number of boundary components of every incompressible surface corresponding to slope -4n+2 turns out to be 2. Bibliography: 39 titles.
Conrad, Marcus; Sato, Hideyo
2012-01-01
The oxidative stress-inducible cystine/glutamate exchange system, system x (c) (-) , transports one molecule of cystine, the oxidized form of cysteine, into cells and thereby releases one molecule of glutamate into the extracellular space. It consists of two protein components, the 4F2 heavy chain, necessary for membrane location of the heterodimer, and the xCT protein, responsible for transport activity. Previously, system x (c) (-) has been regarded to be a mere supplier of cysteine to cells for the synthesis of proteins and the antioxidant glutathione (GSH). In that sense, oxygen, electrophilic agents, and bacterial lipopolysaccharide trigger xCT expression to accommodate with increased oxidative stress by stimulating GSH biosynthesis. However, emerging evidence established that system x (c) (-) may act on its own as a GSH-independent redox system by sustaining a redox cycle over the plasma membrane. Hallmarks of this cycle are cystine uptake, intracellular reduction to cysteine and secretion of the surplus of cysteine into the extracellular space. Consequently, increased levels of extracellular cysteine provide a reducing microenvironment required for proper cell signaling and communication, e.g. as already shown for the mechanism of T cell activation. By contrast, the enhanced release of glutamate in exchange with cystine may trigger neurodegeneration due to glutamate-induced cytotoxic processes. This review aims to provide a comprehensive picture from the early days of system x (c) (-) research up to now.
Nullification of knots and links
Diao, Yuanan; Montemayor, Anthony
2011-01-01
In this paper, we study a geometric/topological measure of knots and links called the nullification number. The nullification of knots/links is believed to be biologically relevant. For example, in DNA topology, one can intuitively regard it as a way to measure how easily a knotted circular DNA can unknot itself through recombination of its DNA strands. It turns out that there are several different ways to define such a number. These definitions lead to nullification numbers that are related, but different. Our aim is to explore the mathematical properties of these nullification numbers. First, we give specific examples to show that the nullification numbers we defined are different. We provide detailed analysis of the nullification numbers for the well known 2-bridge knots and links. We also explore the relationships among the three nullification numbers, as well as their relationships with other knot invariants. Finally, we study a special class of links, namely those links whose general nullification numbe...
Directory of Open Access Journals (Sweden)
Iwao Ohtsu
Full Text Available Intracellular thiols like L-cystine and L-cystine play a critical role in the regulation of cellular processes. Here we show that Escherichia coli has two L-cystine transporters, the symporter YdjN and the ATP-binding cassette importer FliY-YecSC. These proteins import L-cystine, an oxidized product of L-cystine from the periplasm to the cytoplasm. The symporter YdjN, which is expected to be a new member of the L-cystine regulon, is a low affinity L-cystine transporter (Km = 1.1 μM that is mainly involved in L-cystine uptake from outside as a nutrient. E. coli has only two L-cystine importers because ΔydjNΔyecS mutant cells are not capable of growing in the minimal medium containing L-cystine as a sole sulfur source. Another protein YecSC is the FliY-dependent L-cystine transporter that functions cooperatively with the L-cystine transporter YdeD, which exports L-cystine as reducing equivalents from the cytoplasm to the periplasm, to prevent E. coli cells from oxidative stress. The exported L-cystine can reduce the periplasmic hydrogen peroxide to water, and then generated L-cystine is imported back into the cytoplasm via the ATP-binding cassette transporter YecSC with a high affinity to L-cystine (Km = 110 nM in a manner dependent on FliY, the periplasmic L-cystine-binding protein. The double disruption of ydeD and fliY increased cellular levels of lipid peroxides. From these findings, we propose that the hydrogen peroxide-inducible L-cystine/L-cystine shuttle system plays a role of detoxification of hydrogen peroxide before lipid peroxidation occurs, and then might specific prevent damage to membrane lipids.
Ohtsu, Iwao; Kawano, Yusuke; Suzuki, Marina; Morigasaki, Susumu; Saiki, Kyohei; Yamazaki, Shunsuke; Nonaka, Gen; Takagi, Hiroshi
2015-01-01
Intracellular thiols like L-cystine and L-cystine play a critical role in the regulation of cellular processes. Here we show that Escherichia coli has two L-cystine transporters, the symporter YdjN and the ATP-binding cassette importer FliY-YecSC. These proteins import L-cystine, an oxidized product of L-cystine from the periplasm to the cytoplasm. The symporter YdjN, which is expected to be a new member of the L-cystine regulon, is a low affinity L-cystine transporter (Km = 1.1 μM) that is mainly involved in L-cystine uptake from outside as a nutrient. E. coli has only two L-cystine importers because ΔydjNΔyecS mutant cells are not capable of growing in the minimal medium containing L-cystine as a sole sulfur source. Another protein YecSC is the FliY-dependent L-cystine transporter that functions cooperatively with the L-cystine transporter YdeD, which exports L-cystine as reducing equivalents from the cytoplasm to the periplasm, to prevent E. coli cells from oxidative stress. The exported L-cystine can reduce the periplasmic hydrogen peroxide to water, and then generated L-cystine is imported back into the cytoplasm via the ATP-binding cassette transporter YecSC with a high affinity to L-cystine (Km = 110 nM) in a manner dependent on FliY, the periplasmic L-cystine-binding protein. The double disruption of ydeD and fliY increased cellular levels of lipid peroxides. From these findings, we propose that the hydrogen peroxide-inducible L-cystine/L-cystine shuttle system plays a role of detoxification of hydrogen peroxide before lipid peroxidation occurs, and then might specific prevent damage to membrane lipids.
Arrayás, M.; Bouwmeester, D.; Trueba, J. L.
2017-01-01
Maxwell equations in vacuum allow for solutions with a non-trivial topology in the electric and magnetic field line configurations at any given moment in time. One example is a space filling congruence of electric and magnetic field lines forming circles lying on the surfaces of nested tori. In this example the electric, magnetic and Poynting vector fields are orthogonal everywhere. As time evolves the electric and magnetic fields expand and deform without changing the topology and energy, while the Poynting vector structure remains unchanged while propagating with the speed of light. The topology is characterized by the concept of helicity of the field configuration. Helicity is an important fundamental concept and for massless fields it is a conserved quantity under conformal transformations. We will review several methods by which linked and knotted electromagnetic (spin-1) fields can be derived. A first method, introduced by A. Rañada, uses the formulation of the Maxwell equations in terms of differential forms combined with the Hopf map from the three-sphere S3 to the two-sphere S2. A second method is based on spinor and twistor theory developed by R. Penrose in which elementary twistor functions correspond to the family of electromagnetic torus knots. A third method uses the Bateman construction of generating null solutions from complex Euler potentials. And a fourth method uses special conformal transformations, in particular conformal inversion, to generate new linked and knotted field configurations from existing ones. This fourth method is often accompanied by shifting singularities in the field to complex space-time points. Of course the various methods must be closely related to one another although they have been developed largely independently and they suggest different directions in which to expand the study of topologically non-trivial field configurations. It will be shown how the twistor formulation allows for a direct extension to massless
Mechanical Normal Forms of Knots and Flat Knots
Sossinsky, A B
2010-01-01
A new type of knot energy is presented via real life experiments involving a thin resilient metallic tube. Knotted in different ways, the device mechanically acquires a uniquely determined (up to isometry) normal form at least when the original knot diagram has a small number of crossings, thus outperforming the famous M\\"obius energy due to Jun O'Hara and studied by Michael Freedman et al. Various properties of the device are described (under certain conditions it does the Reidemeister and Markov moves, it beautifully performs the Whitney trick by uniformizing its own local curvature). If the device is constrained between two parallel planes (e.g. glass panes), it yields a real life model of a flat knot (class of knot diagrams equivalent under Reidemeister $\\Omega_2$ and $\\Omega_3$ moves) also leading to uniquely determined "flat normal forms" (for a small number of crossing points of the given flat knot diagram). The paper concludes with two mathematical theorems, one reducing the knot recognition problem t...
TOF-SIMS study of cystine and cholesterol stones.
Ghumman, C A A; Moutinho, A M C; Santos, A; Tolstogouzov, A; Teodoro, O M N D
2012-05-01
Two different human stones, cystine and cholesterol from the kidney and gall bladder, were examined by time-of-flight secondary ion mass spectrometry using Ga(+) primary ions as bombarding particles. The mass spectra of kidney stone were compared with those measured for the standard compounds, cystine and cysteine. Similar spectra were obtained for the stone and cystine. The most important identification was based on the existence of the protonated molecules [M + H](+) and deprotonated molecules [M-H](-). The presence of cystine salt was also revealed in the stone through the sodiated cystine [M + Na](+) and the associated fragments, which might be due to the patient treatment history. In the gallstone, the deprotonated molecules [M-H](+) of cholesterol along with relatively intense characteristic fragments [M-OH](+) were detected.
Energy of knots and conformal geometry
O'Hara, Jun
2003-01-01
Energy of knots is a theory that was introduced to create a "canonical configuration" of a knot - a beautiful knot which represents its knot type. This book introduces several kinds of energies, and studies the problem of whether or not there is a "canonical configuration" of a knot in each knot type. It also considers this problems in the context of conformal geometry. The energies presented in the book are defined geometrically. They measure the complexity of embeddings and have applications to physical knotting and unknotting through numerical experiments. Contents: In Search of the "Optima
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.
Knot invariants from Virasoro related representation and pretzel knots
Galakhov, D; Mironov, A; Morozov, A
2015-01-01
We remind the method to calculate colored Jones polynomials for the plat representations of knot diagrams from the knowledge of modular transformation (monodromies) of Virasoro conformal blocks with insertions of degenerate fields. As an illustration we use a rich family of pretzel knots, lying on a surface of arbitrary genus g, which was recently analyzed by the evolution method. Further generalizations can be to generic Virasoro modular transformations, provided by integral kernels, which can lead to the Hikami invariants.
Cosmetic crossings of genus one knots
Balm, Cheryl
2011-01-01
We show that for genus one knots the Alexander polynomial and the homology of the double cover branching over the knot provide obstructions to cosmetic crossings. As an application we prove the nugatory crossing conjecture for the negatively twisted, positive Whitehead doubles of all knots. We also verify the conjecture for several families of pretzel knots and all genus one knots with up to 10 crossings.
Oxidative stress response of Deinococcus geothermalis via a cystine importer.
Kim, Minwook; Jeong, Sunwook; Lim, Sangyong; Sim, Jeonggu; Rhie, Ho-Gun; Lee, Sung-Jae
2017-02-01
A cystine-dependent anti-oxidative stress response is characterized in Deinococcus geothermalis for the first time. Nevertheless, the same transcriptional directed Δdgeo_1985F mutant strain was revealed to have an identical phenotype to the wild-type strain, while the reverse transcriptional directed Δdgeo_1985R mutant strain was more resistant to oxidative stress at a certain concentration of H2O2 than the wild-type strain. The wild-type and mutant strains expressed equal levels of superoxide dismutase and catalase under H2O2-induced stress. Although the expression levels of the general DNA-damage response-related genes recA, pprA, ddrA, and ddrB were up-regulated by more than five-fold in the wild-type strain relative to the Δdgeo_1985R mutant strain, the mutant strain had a higher survival rate than the wild-type under H2O2 stress. The Δdgeo_1985R mutant strain highly expressed a cystine-transporter gene (dgeo_1986), at levels 150-fold higher than the wild-type strain, leading to the conclusion that this cystine transporter might be involved in the defensive response to H2O2 stress. In this study, the cystine transporter was identified and characterized through membrane protein expression analysis, a cystine-binding assay, and assays of intracellular H2O2, cysteine, and thiol levels. The genedisrupted mutant strain of the cystine importer revealed high sensitivity to H2O2 and less absorbed cystine, resulting in low concentrations of total thiol. Thus, the absorbed cystine via this cystine-specific importer may be converted into cysteine, which acts as a primitive defense substrate that non-enzymatically scavenges oxidative stress agents in D. geothermalis.
Handbook of knotting and splicing
Hasluck, Paul N
2005-01-01
Clearly written and amply illustrated with 208 figures, this classic guide ranges from simple and useful knots to complex varieties. Additional topics include rope splicing, working cordage, hammock making, more.
Effects of knots on protein folding properties.
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Miguel A Soler
Full Text Available 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.
Weaving knotted vector fields with tunable helicity
Kedia, Hridesh; Dennis, Mark R; Irvine, William T M
2016-01-01
We present a general construction of divergence-free knotted vector fields from complex scalar fields, whose closed field lines encode many kinds of knots and links, including torus knots, their cables, the figure-8 knot and its generalizations. As finite-energy physical fields they represent initial states for fields such as the magnetic field in a plasma, or the vorticity field in a fluid. We give a systematic procedure for calculating the vector potential, starting from complex scalar functions with knotted zero filaments, thus enabling an explicit computation of the helicity of these knotted fields. The construction can be used to generate isolated knotted flux tubes, filled by knots encoded in the lines of the vector field. Lastly we give examples of manifestly knotted vector fields with vanishing helicity. Our results provide building blocks for analytical models and simulations alike.
Universal Racah matrices and adjoint knot polynomials: Arborescent knots
Mironov, A.; Morozov, A.
2016-04-01
By now it is well established that the quantum dimensions of descendants of the adjoint representation can be described in a universal form, independent of a particular family of simple Lie algebras. The Rosso-Jones formula then implies a universal description of the adjoint knot polynomials for torus knots, which in particular unifies the HOMFLY (SUN) and Kauffman (SON) polynomials. For E8 the adjoint representation is also fundamental. We suggest to extend the universality from the dimensions to the Racah matrices and this immediately produces a unified description of the adjoint knot polynomials for all arborescent (double-fat) knots, including twist, 2-bridge and pretzel. Technically we develop together the universality and the "eigenvalue conjecture", which expresses the Racah and mixing matrices through the eigenvalues of the quantum R-matrix, and for dealing with the adjoint polynomials one has to extend it to the previously unknown 6 × 6 case. The adjoint polynomials do not distinguish between mutants and therefore are not very efficient in knot theory, however, universal polynomials in higher representations can probably be better in this respect.
On ambiguity in knot polynomials for virtual knots
Morozov, A; Popolitov, A
2015-01-01
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 $A = q^N$. 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, appear in HOMFLY for Kishino unknot, which thus remains unseparated from the ordinary unknots even by this enriched set of knot invariants.
On ambiguity in knot polynomials for virtual knots
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.
Planar and spherical stick indices of knots
Adams, Colin; Hawkins, Katherine; Sia, Charmaine; Silversmith, Rob; Tshishiku, Bena; 10.1142/S0218216511008954
2011-01-01
The stick index of a knot is the least number of line segments required to build the knot in space. We define two analogous 2-dimensional invariants, the planar stick index, which is the least number of line segments in the plane to build a projection, and the spherical stick index, which is the least number of great circle arcs to build a projection on the sphere. We find bounds on these quantities in terms of other knot invariants, and give planar stick and spherical stick constructions for torus knots and for compositions of trefoils. In particular, unlike most knot invariants,we show that the spherical stick index distinguishes between the granny and square knots, and that composing a nontrivial knot with a second nontrivial knot need not increase its spherical stick index.
Universal Racah matrices and adjoint knot polynomials. I. Arborescent knots
Mironov, A
2015-01-01
By now it is well established that the quantum dimensions of descendants of the adjoint representation can be described in a universal form, independent of a particular family of simple Lie algebras. The Rosso-Jones formula then implies a universal description of the adjoint knot polynomials for torus knots, which in particular unifies the HOMFLY (SU_N) and Kauffman (SO_N) polynomials. For E_8 the adjoint representation is also fundamental. We suggest to extend the universality from the dimensions to the Racah matrices and this immediately produces a unified description of the adjoint knot polynomials for all arborescent (double-fat) knots, including twist, 2-bridge and pretzel. Technically we develop together the universality and the "eigenvalue conjecture", which expresses the Racah and mixing matrices through the eigenvalues of the quantum R-matrix, and for dealing with the adjoint polynomials one has to extend it to the previously unknown 6x6 case. The adjoint polynomials do not distinguish between mutant...
Directory of Open Access Journals (Sweden)
Jessica A. Simpkins
2016-06-01
Full Text Available Cystine and cysteine are important molecules for pathways such as redox signaling and regulation, and thus identifying cellular deficits upon deletion of the Saccharomyces cerevisiae cystine transporter Ers1p allows for a further understanding of cystine homeostasis. Previous complementation studies using the human ortholog suggest yeast Ers1p is a cystine transporter. Human CTNS encodes the protein Cystinosin, a cystine transporter that is embedded in the lysosomal membrane and facilitates the export of cystine from the lysosome. When CTNS is mutated, cystine transport is disrupted, leading to cystine accumulation, the diagnostic hallmark of the lysosomal storage disorder cystinosis. Here, we provide biochemical evidence for Ers1p-dependent cystine transport. However, the accumulation of intracellular cystine is not observed when the ERS1 gene is deleted from ers1-Δ yeast, supporting the existence of modifier genes that provide a mechanism in ers1-Δ yeast that prevents or corrects cystine accumulation. Upon comparison of the transcriptomes of isogenic ERS1+ and ers1-Δ strains of S. cerevisiae by DNA microarray followed by targeted qPCR, sixteen genes were identified as being differentially expressed between the two genotypes. Genes that encode proteins functioning in sulfur regulation, cellular respiration, and general transport were enriched in our screen, demonstrating pleiotropic effects of ers1-Δ. These results give insight into yeast cystine regulation and the multiple, seemingly distal, pathways that involve proper cystine recycling.
Simpkins, Jessica A.; Rickel, Kirby E.; Madeo, Marianna; Ahlers, Bethany A.; Carlisle, Gabriel B.; Nelson, Heidi J.; Cardillo, Andrew L.; Weber, Emily A.; Vitiello, Peter F.; Pearce, David A.
2016-01-01
ABSTRACT Cystine and cysteine are important molecules for pathways such as redox signaling and regulation, and thus identifying cellular deficits upon deletion of the Saccharomyces cerevisiae cystine transporter Ers1p allows for a further understanding of cystine homeostasis. Previous complementation studies using the human ortholog suggest yeast Ers1p is a cystine transporter. Human CTNS encodes the protein Cystinosin, a cystine transporter that is embedded in the lysosomal membrane and facilitates the export of cystine from the lysosome. When CTNS is mutated, cystine transport is disrupted, leading to cystine accumulation, the diagnostic hallmark of the lysosomal storage disorder cystinosis. Here, we provide biochemical evidence for Ers1p-dependent cystine transport. However, the accumulation of intracellular cystine is not observed when the ERS1 gene is deleted from ers1-Δ yeast, supporting the existence of modifier genes that provide a mechanism in ers1-Δ yeast that prevents or corrects cystine accumulation. Upon comparison of the transcriptomes of isogenic ERS1+ and ers1-Δ strains of S. cerevisiae by DNA microarray followed by targeted qPCR, sixteen genes were identified as being differentially expressed between the two genotypes. Genes that encode proteins functioning in sulfur regulation, cellular respiration, and general transport were enriched in our screen, demonstrating pleiotropic effects of ers1-Δ. These results give insight into yeast cystine regulation and the multiple, seemingly distal, pathways that involve proper cystine recycling. PMID:27142334
Electrochemical studies of cystine modified self-assembled monolayer for Escherichia coli detection
Energy Technology Data Exchange (ETDEWEB)
Pandey, Chandra Mouli; Sumana, Gajjala [Department of Science and Technology Centre on Biomolecular Electronics, Biomedical Instrumentation Section, Materials Physics and Engineering Division, National Physical Laboratory (Council of Scientific and Industrial Research), Dr. K. S. Krishnan Marg, New Delhi 110012 (India); Sood, K.N. [Electron Microscope Section, Division of Material Characterization, National Physical Laboratory, Dr. K. S. Krishnan Marg, New Delhi 110012 (India); Malhotra, B.D., E-mail: bansi.malhotra@gmail.co [Department of Science and Technology Centre on Biomolecular Electronics, Biomedical Instrumentation Section, Materials Physics and Engineering Division, National Physical Laboratory (Council of Scientific and Industrial Research), Dr. K. S. Krishnan Marg, New Delhi 110012 (India)
2010-11-30
An electrochemical DNA biosensor based on cystine modified self-assembled monolayer (cys-SAM) onto gold electrode (AuE) has been fabricated for Escherichia coli (E. coli) detection. This biosensing electrode has been characterized using scanning electron microscopy (SEM), FT-IR spectroscopy, cyclic voltammetry (CV), differential pulse voltammetry (DPV) and electrochemical impedance spectroscopy (EIS). Under the optimum conditions, this DNA biosensor can be used to detect complementary target DNA concentration in the range of 1 x 10{sup -6} M to 1 x 10{sup -20} M within 60 s of hybridization time at 25 {sup o}C and has been found to be stable for about four months when stored at 4 {sup o}C.
Directory of Open Access Journals (Sweden)
Eloy Caballo-Ponce
2017-06-01
Full Text Available The study of the molecular basis of tree diseases is lately receiving a renewed attention, especially with the emerging perception that pathogens require specific pathogenicity and virulence factors to successfully colonize woody hosts. Pathosystems involving woody plants are notoriously difficult to study, although the use of model bacterial strains together with genetically homogeneous micropropagated plant material is providing a significant impetus to our understanding of the molecular determinants leading to disease. The gammaproteobacterium Pseudomonas savastanoi belongs to the intensively studied Pseudomonas syringae complex, and includes three pathogenic lineages causing tumorous overgrowths (knots in diverse economically relevant trees and shrubs. As it occurs with many other bacteria, pathogenicity of P. savastanoi is dependent on a type III secretion system, which is accompanied by a core set of at least 20 effector genes shared among strains isolated from olive, oleander, and ash. The induction of knots of wild-type size requires that the pathogen maintains adequate levels of diverse metabolites, including the phytohormones indole-3-acetic acid and cytokinins, as well as cyclic-di-GMP, some of which can also regulate the expression of other pathogenicity and virulence genes and participate in bacterial competitiveness. In a remarkable example of social networking, quorum sensing molecules allow for the communication among P. savastanoi and other members of the knot microbiome, while at the same time are essential for tumor formation. Additionally, a distinguishing feature of bacteria from the P. syringae complex isolated from woody organs is the possession of a 15 kb genomic island (WHOP carrying four operons and three other genes involved in degradation of phenolic compounds. Two of these operons mediate the catabolism of anthranilate and catechol and, together with another operon, are required for the induction of full-size tumors
Introduction to Virtual Knot Theory
Kauffman, Louis H
2011-01-01
This paper is an introduction to virtual knot theory and an exposition of new ideas and constructions, including the parity bracket polynomial, the arrow polynomial, the parity arrow polynomial and categorifications of the arrow polynomial. The paper is relatively self-contained and it describes virtual knot theory both combinatorially and in terms of the knot theory in thickened surfaces. The arrow polynomial (of Dye and Kauffman) is a natural generalization of the Jones polynomial, obtained by using the oriented structure of diagrams in the state sum. The paper discusses uses of parity pioneered by Vassily Manturov and uses his parity bracket polynomial to give a counterexample to a conjecture of Fenn, Kauffman and Manturov. The paper gives an exposition of the categorification of the arrow polynomial due to Dye, Kauffman and Manturov and it gives one example (from many found by Aaron Kaestner) of a pair of virtual knots that are not distinguished by Khovanov homology (mod 2), or by the arrow polynomial, bu...
Duality properties of indicatrices of knots
Adams, Colin; Hawkins, Katherine; Sia, Charmaine; Silversmith, Robert; Tshishiku, Bena
2012-01-01
The bridge index and superbridge index of a knot are important invariants in knot theory. We define the bridge map of a knot conformation, which is closely related to these two invariants, and interpret it in terms of the tangent indicatrix of the knot conformation. Using the concepts of dual and derivative curves of spherical curves as introduced by Arnold, we show that the graph of the bridge map is the union of the binormal indicatrix, its antipodal curve, and some number of great circles. Similarly, we define the inflection map of a knot conformation, interpret it in terms of the binormal indicatrix, and express its graph in terms of the tangent indicatrix. This duality relationship is also studied for another dual pair of curves, the normal and Darboux indicatrices of a knot conformation. The analogous concepts are defined and results are derived for stick knots.
Cystine Plug and Other Novel Mechanisms of Large Mechanical Stability in Dimeric Proteins
Sikora, Mateusz; Cieplak, Marek
2012-11-01
We identify three dimeric proteins whose mechanostability is anisotropic and should exceed 1 nN along some directions. They come with distinct mechanical clamps: either shear-based, or involving a cystine slipknot, or due to dragging of a cystine plug through a cystine ring. The latter two mechanisms are topological in nature; the cystine plug mechanism has not yet been discussed but it turns out to provide the largest resistance to stretching. Its possible applications in elastomers are discussed.
Mickelson, M. N.; Anderson, A J
1984-01-01
Cystine reduction in Streptococcus agalactiae, resulting in sulfhydryl formation, may account for antagonism of the antibacterial effect of lactoperoxidase-thiocyanate-hydrogen peroxide when cystine is present in excess of the amount needed for maximum growth. Accumulation of cystine by S. agalactiae and its reduction to form sulfhydryl compounds were demonstrated. The reduction of cystine appeared to occur by a couple reaction between glutathione reductase and glutathione-disulfide transhydr...
Crystal structure of seleno-l-cystine dihydrochloride
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Carl Henrik Görbitz
2015-06-01
Full Text Available Numerous crystal structures are available for the dimeric amino acid cystine. In proteins it is formed by oxidation of the –SH thiol groups of two closely spaced cysteine residues, resulting in the formation of a familiar disulfide bridge. The title compound [systematic name: (R,R-1,1′-dicarboxy-2,2′-(diselanediyldiethanaminium dichloride], C6H14N2O4Se22+·2Cl−, is the first example of a small molecule structure of the biologically important analogue with a —CH2—Se—Se—CH2— bridging unit. Bond lengths and angles of seleno-l-cystine dihydrochloride and its isotypic sulfur analogue l-cystine dihydrochloride are compared.
Gres, A A; Nitkin, D M; Juraha, T M; Sivakow, A A
2016-08-01
to define the reference value ranges of cystine, lysine and arginine urinary excretion relative to creatinine in the morning urine samples for the metabolic disorders diagnosis leading to the formation of urinary stones. the study involved 695 healthy individuals aged 1-17 and 1564 patients with urolithiasis aged 7-45. The content of cystine in the urine samples was determined by high performance liquid chromatography. The chemical composition of urinary stones was investigated by methods of the qualitative chemical reaction and the crystals microscopy. the reference value ranges of cystine, lysine and arginine urinary excretion relative to creatinine in the morning urine samples were developed in the age aspect. Excess in cystine level in the urine samples of the relatively healthy individuals detected in 1.4% of cases. From 1564 urinary stones submitted for analysis, the frequency of cystine stones was 0.8%. for the objective assessment of the cystine metabolism status the evaluation of the degree of cystinuria is necessary in order to form the risk group for cystine nephrolithiasis. The reference value ranges of cystine urinary excretion developed in the age aspect and "cystine / creatinine index" in morning urine samples will provide the opportunity to identify the state of the cystine exchange from early childhood and develop differentiated program for the prevention of stone formation in the kidneys.
Adams operators and knot decorations
Aiston, A K
1997-01-01
We use an explicit isomorphism from the representation ring of the quantum group U_q(sl(N)) to the Homfly skein of the annulus, to determine an element of the skein which is the image of the mth Adams operator, \\psi_m, on the fundamental representation, c_1. This element is a linear combination of m very simple m-string braids. Using this skein element, we show that the Vassiliev invariant of degree n in the power series expansion of the U_q(sl(N)) quantum invariant of a knot coloured by \\psi_m(c_1) is the canonical Vassiliev invariant with weight system W_n\\psi_m^{(n)} where W_n is the weight system for the Vassiliev invariant of degree n in the expansion of the quantum invariant of the knot coloured by c_1 and \\psi_m^{(n)} is the Adams operator on n-chord diagrams defined by Bar-Natan.
Vortex knots in tangled quantum eigenfunctions
Taylor, Alexander J
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 3-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 3-dimensional wave systems, establishing a topological commonality between wave chaos, polymers and turbulent Bose-Einstein condensates.
Endoscopic Release of Master Knot of Henry.
Lui, Tun Hing
2015-12-01
A post-traumatic partial tear of the flexor hallucis longus tendon at the master knot of Henry and the resultant fibrosis of the knot can result in pain at the medial foot arch or posteromedial ankle pain with trigger hallux. Open debridement of the master knot of Henry is indicated if the symptoms do not improve with nonoperative treatment. The open procedure requires extensive soft-tissue dissection because the master knot of Henry is a deep structure. Endoscopic release of the master knot of Henry is an alternative to the open procedure and has the advantage of less surgical trauma and potential for less chance of recurrence of fibrosis of the master knot of Henry.
The pathogenesis of cystinosis: mechanisms beyond cystine accumulation.
Wilmer, M.J.G.; Emma, F.; Levtchenko, E.N.
2010-01-01
Renal proximal tubules are highly sensitive to ischemic and toxic insults and are affected in diverse genetic disorders, of which nephropathic cystinosis is the most common. The disease is caused by mutations in the CTNS gene, encoding the lysosomal cystine transporter cystinosin, and is characteriz
Evaluation of Medical Cystine Stone Prevention in an Animal Model
Sagi, Sreedhar; Wendt-Nordahl, Gunnar; Alken, Peter; Knoll, Thomas
2007-04-01
Medical treatment for cystinuria aims to decrease the concentration of cystine in the urine, increase its solubility and therefore prevent stone formation. Ascorbic acid and captopril have been recommended as alternatives to thiol drugs, though conflicting data undermining their efficacy has been widely reported, too. The aim of this study was to verify the effects of ascorbic acid and captopril on cystine stone formation in the cystinuria mouse model. A total of 28 male homozygous pebbles mice were used for characterizing the mice on normal diet, ascorbic acid and captopril supplemented diets. The baseline physiological parameters of the mice were determined initially. The normal diet was then replaced with the supplemented diet (ascorbic acid/captopril) for the next 48 weeks and various biochemical parameters in urine and plasma were analyzed. All homozygous mice developed urinary cystine stones during the first year of life. No reduction in the urinary cystine concentration was seen with either of the supplemented diets. The stone mass varied widely in the study and a beneficial effect of ascorbic acid in some of the animals was possible though an overall statistical significance was not seen. Conclusions: The cystinuria mouse model provides an ideal tool for evaluation of stone preventive measures in a standardized environment. This study confirms that ascorbic acid and captopril are not effective in cystinuria.
De behoefte van vleesvarkens aan methionine + cystine, threonine en tryptofaan
Lenis, N.; Diepen, van H.
1990-01-01
Door het Instituut voor Veevoedingsonderzoek is op het Varkensproefbedrijf te Raalte de behoefte van vleesvarkens aan de aminozuren methionine + cystine, threonine en tryptof-aan nader onderzocht. De uitslag was, dat de behoefte aan threonine op het niveau van de Nederlandse praktijksituatie lag.
21 CFR 862.1240 - Cystine test system.
2010-04-01
... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Cystine test system. 862.1240 Section 862.1240 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES CLINICAL CHEMISTRY AND CLINICAL TOXICOLOGY DEVICES Clinical Chemistry Test Systems §...
Knotted solitons in nonlinear magnetic metamaterials.
Rosanov, Nikolay N; Vysotina, Nina V; Shatsev, Anatoly N; Desyatnikov, Anton S; Kivshar, Yuri S
2012-03-30
We demonstrate that nonlinear magnetic metamaterials comprised of a lattice of weakly coupled split-ring resonators driven by an external electromagnetic field may support entirely new classes of spatially localized modes--knotted solitons, which are stable self-localized dissipative structures in the form of closed knotted chains. We demonstrate different topological types of stable knots for the subcritical coupling between resonators and instability-induced breaking of the chains for the supercritical coupling.
Knowledge of knots: shapes in action
Casati, Roberto
2013-01-01
Logic is to natural language what knot theory is to natural knots. Logic is concerned with some cognitive performances; in particular, some natural language inferences are captured by various types of calculi (propositional, predicate, modal, deontic, quantum, probabilistic, etc.), which in turn may generate inferences that are arguably beyond natural logic abilities, or non-well synchronized therewith (eg. ex falso quodlibet, material implication). Mathematical knot theory accounts for some ...
Coherent band pathways between knots and links
Buck, Dorothy
2014-01-01
We categorise coherent band (aka nullification) pathways between knots and 2-component links. Additionally, we characterise the minimal coherent band pathways (with intermediates) between any two knots or 2-component links with small crossing number. We demonstrate these band surgeries for knots and links with small crossing number. We apply these results to place lower bounds on the minimum number of recombinant events separating DNA configurations, restrict the recombination pathways and determine chirality and/or orientation of the resulting recombinant DNA molecules.
Crystal growth inhibitors for the prevention of L-cystine kidney stones through molecular design.
Rimer, Jeffrey D; An, Zhihua; Zhu, Zina; Lee, Michael H; Goldfarb, David S; Wesson, Jeffrey A; Ward, Michael D
2010-10-15
Crystallization of L-cystine is a critical step in the pathogenesis of cystine kidney stones. Treatments for this disease are somewhat effective but often lead to adverse side effects. Real-time in situ atomic force microscopy (AFM) reveals that L-cystine dimethylester (L-CDME) and L-cystine methylester (L-CME) dramatically reduce the growth velocity of the six symmetry-equivalent {100} steps because of specific binding at the crystal surface, which frustrates the attachment of L-cystine molecules. L-CDME and L-CME produce l-cystine crystals with different habits that reveal distinct binding modes at the crystal surfaces. The AFM observations are mirrored by reduced crystal yield and crystal size in the presence of L-CDME and L-CME, collectively suggesting a new pathway to the prevention of L-cystine stones by rational design of crystal growth inhibitors.
Activated human CD4 T cells express transporters for both cysteine and cystine
DEFF Research Database (Denmark)
Levring, Trine Bøegh; Hansen, Ann Kathrine; Nielsen, Bodil Lisbeth;
2012-01-01
Because naïve T cells are unable to import cystine due to the absence of cystine transporters, it has been suggested that T cell activation is dependent on cysteine generated by antigen presenting cells. The aim of this study was to determine at which phases during T cell activation exogenous...... cystine/cysteine is required and how T cells meet this requirement. We found that early activation of T cells is independent of exogenous cystine/cysteine, whereas T cell proliferation is strictly dependent of uptake of exogenous cystine/cysteine. Naïve T cells express no or very low levels of both...... cystine and cysteine transporters. However, we found that these transporters become strongly up-regulated during T cell activation and provide activated T cells with the required amount of cystine/cysteine needed for T cell proliferation. Thus, T cells are equipped with mechanisms that allow T cell...
Crystal Growth Inhibitors for the Prevention of L-Cystine Kidney Stones Through Molecular Design
Energy Technology Data Exchange (ETDEWEB)
Rimer, Jeffrey D.; An, Zhihua; Zhu, Zina; Lee, Michael H.; Goldfarb, David S.; Wesson, Jeffrey A.; Ward, Michael D. (NY Univ.); (MCW)
2010-11-12
Crystallization of L-cystine is a critical step in the pathogenesis of cystine kidney stones. Treatments for this disease are somewhat effective but often lead to adverse side effects. Real-time in situ atomic force microscopy (AFM) reveals that L-cystine dimethylester (L-CDME) and L-cystine methylester (L-CME) dramatically reduce the growth velocity of the six symmetry-equivalent {l_brace}100{r_brace} steps because of specific binding at the crystal surface, which frustrates the attachment of L-cystine molecules. L-CDME and L-CME produce L-cystine crystals with different habits that reveal distinct binding modes at the crystal surfaces. The AFM observations are mirrored by reduced crystal yield and crystal size in the presence of L-CDME and L-CME, collectively suggesting a new pathway to the prevention of L-cystine stones by rational design of crystal growth inhibitors.
The mathematics and physics of knots
Energy Technology Data Exchange (ETDEWEB)
Kauffman, Louis H [Department of Mathematics, Statistics and Computer Science, University of Illinois at Chicago, 851 South Morgan Street, Chicago, IL 60607-7045 (United States)
2005-12-01
This paper is an introduction to relationships between knot theory and theoretical physics. We give an exposition of the theory of polynomial invariants of knots and links, the Witten functional integral formulation of knot and link invariants, and the beginnings of topological quantum field theory, and show how the theory of knots is related to a number of key issues in mathematical physics, including loop quantum gravity and quantum information theory. Along with the references cited in the text below, we also recommend the following as sources of background information.
Increased expression of cystine/glutamate antiporter in multiple sclerosis
Directory of Open Access Journals (Sweden)
Villoslada Pablo
2011-06-01
Full Text Available Abstract Background Glutamate excitotoxicity contributes to oligodendrocyte and tissue damage in multiple sclerosis (MS. Intriguingly, glutamate level in plasma and cerebrospinal fluid of MS patients is elevated, a feature which may be related to the pathophysiology of this disease. In addition to glutamate transporters, levels of extracellular glutamate are controlled by cystine/glutamate antiporter xc-, an exchanger that provides intracellular cystine for production of glutathione, the major cellular antioxidant. The objective of this study was to analyze the role of the system xc- in glutamate homeostasis alterations in MS pathology. Methods Primary cultures of human monocytes and the cell line U-937 were used to investigate the mechanism of glutamate release. Expression of cystine glutamate exchanger (xCT was quantified by quantitative PCR, Western blot, flow cytometry and immunohistochemistry in monocytes in vitro, in animals with experimental autoimmune encephalomyelitis (EAE, the animal model of MS, and in samples of MS patients. Results and discussion We show here that human activated monocytes release glutamate through cystine/glutamate antiporter xc- and that the expression of the catalytic subunit xCT is upregulated as a consequence of monocyte activation. In addition, xCT expression is also increased in EAE and in the disease proper. In the later, high expression of xCT occurs both in the central nervous system (CNS and in peripheral blood cells. In particular, cells from monocyte-macrophage-microglia lineage have higher xCT expression in MS and in EAE, indicating that immune activation upregulates xCT levels, which may result in higher glutamate release and contribution to excitotoxic damage to oligodendrocytes. Conclusions Together, these results reveal that increased expression of the cystine/glutamate antiporter system xc- in MS provides a link between inflammation and excitotoxicity in demyelinating diseases.
Siska, Peter J; Kim, Bumki; Ji, Xiangming; Hoeksema, Megan D; Massion, Pierre P; Beckermann, Kathryn E; Wu, Jianli; Chi, Jen-Tsan; Hong, Jiyong; Rathmell, Jeffrey C
2016-11-01
T and B lymphocytes undergo metabolic re-programming upon activation that is essential to allow bioenergetics, cell survival, and intermediates for cell proliferation and function. To support changes in the activity of signaling pathways and to provide sufficient and necessary intracellular metabolites, uptake of extracellular nutrients increases sharply with metabolic re-programming. One result of increased metabolic activity can be reactive oxygen species (ROS), which can be toxic when accumulated in excess. Uptake of cystine allows accumulation of cysteine that is necessary for glutathione synthesis and ROS detoxification. Cystine uptake is required for T cell activation and function but measurements based on radioactive labeling do not allow analysis on single cell level. Here we show the critical role for cystine uptake in T cells using a method for measurement of cystine uptake using a novel CystineFITC probe. T cell receptor stimulation lead to upregulation of the cystine transporter xCT (SLC7a11) and increased cystine uptake in CD4+ and CD8+ human T cells. Similarly, lipopolysaccharide stimulation increased cystine uptake in human B cells. The CystineFITC probe was not toxic and could be metabolized to prevent cystine starvation induced cell death. Furthermore, blockade of xCT or competition with natural cystine decreased uptake of CystineFITC. CystineFITC is thus a versatile tool that allows measurement of cystine uptake on single cell level and shows the critical role for cystine uptake for T cell ROS regulation and activation.
Differential and symplectic topology of knots and curves
Tabachnikov, S
1999-01-01
This book presents a collection of papers on two related topics: topology of knots and knot-like objects (such as curves on surfaces) and topology of Legendrian knots and links in 3-dimensional contact manifolds. Featured is the work of international experts in knot theory (""quantum"" knot invariants, knot invariants of finite type), in symplectic and contact topology, and in singularity theory. The interplay of diverse methods from these fields makes this volume unique in the study of Legendrian knots and knot-like objects such as wave fronts. A particularly enticing feature of the volume is
Cosmetic surgeries on knots in $S^3$
Ni, Yi
2010-01-01
Two Dehn surgeries on a knot are called {\\it purely cosmetic}, if they yield manifolds that are homeomorphic as oriented manifolds. Using Heegaard Floer homology, we give necessary conditions for the existence of purely cosmetic surgeries on knots in $S^3$. Among other things, we show that the two surgery slopes must be the opposite of each other.
Diagnosis of true umbilical cord knot.
Guzikowski, Wojciech; Kowalczyk, Dariusz; Więcek, Jacek
2014-02-24
Many abnormalities are observed in the morphology and pathology of the umbilical cord. The aim of the study was to assess the role of 3D sonography in pathology of true umbilical cord knots. In our materials we observed 10 cases of true umbilical cord knots in a population of 2,864 deliveries. The 2-dimensional transverse scan of the umbilical cord was shown in 3- and 4-dimensional volume scan in order to get a precise image. Four knots were diagnosed prenatally, 3 knots were not diagnosed before the delivery and in the 3 remaining cases ultrasound examinations were not undertaken because the patients were in the course of delivery. In the pregnant subjects with diagnosed true umbilical cord knot once a week the Doppler blood flow indices were examined in the umbilical cord sections before and after the knot. In the three shown cases there were no signs of constriction or tightening of the knot. Four newborns were delivered spontaneously and five by caesarean section. In none of the cases was a pathological FHR trace an indication for emergency delivery. Four-dimensional and Color Doppler examination is very important to diagnose a true umbilical cord. To make a precise diagnosis a longer observation of the abnormality is necessary and its repeated confirmation by color Doppler and power Doppler. This diagnosis requires strict monitoring of fetal wellbeing during pregnancy and the delivery. Perfection of true umbilical cord knot diagnoses may reduce sudden and unforeseen fetal distress.
Knot strength of nylon-band cerclage.
Kirby, B M; Wilson, J W
1989-12-01
Nylon bands of five sizes were tested to failure using a splint circular jaw mounted on a tensile testing machine. Four treatment groups of each of the five sizes were tested: as supplied by the manufacturer, ethylene oxide sterilized, autoclave sterilized, and saline-soaked. Comparisons were made between groups and to previously reported results of similar testing of stainless steel wire of three sizes. All the bands failed at the lock mechanism. Knot strength increased with increased size of nylon band. There was no difference between untreated and ethylene oxide sterilized bands, whereas bands subjected to autoclaving or saline soaking failed at less force. The knot strength of all the treatment groups in the three smaller sizes of bands was less than twist-knotted 0.8-mm wire cerclage; and when soaked in saline for 24 hours, the knot strength of the two largest size bands dropped to less than 1.2-mm twist-knotted wire.
Star-formation knots in IRAS galaxies
Hutchings, J B
1995-01-01
Images of IRAS galaxies with a range of IR properties are examined for bright knots, both within and outside the galaxy. These are found almost exclusively in galaxies with steep IR spectra, but over a wide range of IR luminosity, and usually without strong nuclear activity. In most cases, the knots are likely to be star-formation induced by tidal interactions, and are seen in the early stages of such interactions. Detailed photometry is presented of knots in six representative galaxies. The knots appear to have a wide range of colour and luminosity, but it is argued that many are heavily reddened. Knots formed outside the parent galaxy may be a new generation of what later become globular clusters, but they appear to have a wide range of luminosities.
A pseudo-haptic knot diagram interface
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.
TREATMENT OF CYSTINE CALCULUS WITH EXTRACORPOREAL SHOCK WAVE LITHOTRIPSY
Institute of Scientific and Technical Information of China (English)
无
2006-01-01
Objective To evaluate the effectiveness of ESWL for treating patients with cystine calculus.Methods Of 31 patients, 20 were subjected to ESWL only, 6 were subjected to combination therapy of PCNL and ESWL, 2 Pneumatic Lithotriptor-ESWL, 3 Laser lithotripsy-ESWL. Results For 14 renal stones, the fragmentation after ESWL monotherapy was 85. 7% and 14.3% after twice ESWL sessions. For 17 ureter calculus, the fragmentation after ESWL monotherapy was 82.3% and 11.7% after twice ESWL sessions. One patient (5. 8% ) failed and changed to open surgery. Conclusion ESWL is an effective and reliable method for treating patients with cystine calculus, however, better effects and shorter treatment time could be obtained by the combination of ESWL with other therapy options.
[Cystinic lithiasis. Current aspects of the urologic treatment].
Dore, B; Irani, J; Marroncle, M; Aubert, J
1990-01-01
On the basis of a series of 9 patients (12 renal units) gathered over 19 years, the authors analyze the current possibilities of treatment of cystine lithiasis. They first describe the characteristics of this litiasis, which is rare but serious, being naturally prone to recurrence because it is caused by a genetic defect. The development of extracorporeal lithotripsy raised great hopes for the treatment of this lithiasis, but it was soon realized that cystine strones were hard to break. However, even the mere fragmentation of the stones improves the dissolving action of the various drugs proposed to modify the pH of urine. The authors consider that open surgery by means of posterior vertical lumbar section still is indicated for larger stones, and percutaneous nephrolithotomy seems to be a very useful technique, either exclusively or as a complement of extracorporeal lithotrity.
Thomas, Ajit G; Sattler, Rita; Tendyke, Karen; Loiacono, Kara A; Hansen, Hans; Sahni, Vishal; Hashizume, Yutaka; Rojas, Camilo; Slusher, Barbara S
2015-01-01
The cystine-glutamate antiporter (system xc-) is a Na+-independent amino acid transporter that exchanges extracellular cystine for intracellular glutamate. It is thought to play a critical role in cellular redox processes through regulation of intracellular glutathione synthesis via cystine uptake. In gliomas, system xc- expression is universally up-regulated while that of glutamate transporters down-regulated, leading to a progressive accumulation of extracellular glutamate and excitotoxic cell death of the surrounding non-tumorous tissue. Additionally, up-regulation of system xc- in activated microglia has been implicated in the pathogenesis of several neurodegenerative disorders mediated by excess glutamate. Consequently, system xc- is a new drug target for brain cancer and neuroinflammatory diseases associated with excess extracellular glutamate. Unfortunately no potent and selective small molecule system xc- inhibitors exist and to our knowledge, no high throughput screening (HTS) assay has been developed to identify new scaffolds for inhibitor design. To develop such an assay, various neuronal and non-neuronal human cells were evaluated as sources of system xc-. Human glioma cells were chosen based on their high system xc- activity. Using these cells, [14C]-cystine uptake and cystine-induced glutamate release assays were characterized and optimized with respect to cystine and protein concentrations and time of incubation. A pilot screen of the LOPAC/NINDS libraries using glutamate release demonstrated that the logistics of the assay were in place but unfortunately, did not yield meaningful pharmacophores. A larger, HTS campaign using the 384-well cystine-induced glutamate release as primary assay and the 96-well 14C-cystine uptake as confirmatory assay is currently underway. Unexpectedly, we observed that the rate of cystine uptake was significantly faster than the rate of glutamate release in human glioma cells. This was in contrast to the same rates of
Rajalakshmi, S.; Shethna, YI
1980-01-01
The effect of the addition of different concentratons of cystine and cysteine on sporulation and parasporal crystal formation in Bacillus thuringiensis var. thuringiensis was studied. The effect was well pronounced when the systine/cysteine additions were made after the stationary phase. Heat stable spores and crystals were formed when the culture was provided with a low concentration of cystine/cysteine (0.05 per cent w/v). At a moderate concentration of cystine or cysteine (0.15%), only ...
Open knot-tying skills: residents skills assessed
van Empel, P.J.; Verdam, M.G.E.; Huirne, J.A.; Bonjer, H.J.; Meijerink, W.J.; Scheele, F.
2013-01-01
Aim: Open knot-tying and suturing skills are fundamental surgical skills, founding many alternative knot-tying techniques. It is therefore mandatory for residents to possess adequate basic open knot-tying skills. The aim of this study was to compare an objective assessment of open knot-tying skills
Phase behaviour of polyethylene knotted ring chains
Institute of Scientific and Technical Information of China (English)
Wen Xiao-Hui; Zhang Lin-Xi; Xia A-Gen; Chen Hong-Ping
2011-01-01
The phase behaviour of polyethylene knotted ring chains is investigated by using molecular dynamics simulations.In this paper, we focus on the collapse of the polyethylene knotted ring chain, and also present the results of linear and ring chains for comparison. At high temperatures, a fully extensive knot structure is observed. The mean-square radius of gyration per bond〈S2〉/(Nb2)and the shape factor(δ*)depend on not only the chain length but also the knot type.With temperature decreasing, chain collapse is observed, and the collapse temperature decreases with the chain length increasing. The actual collapse transition can be determined by the specific heat capacity Cv, and the knotted ring chain undergoes gas-liquid-solid-like transition directly. The phase transition of a knotted ring chain is only one-stage collapse, which is different from the polyethylene linear and ring chains. This investigation can provide some insights into the statistical properties of knotted polymer chains.
On the concordance orders of knots
Collins, Julia
2012-01-01
This thesis develops some general calculational techniques for finding the orders of knots in the topological concordance group C. The techniques currently available in the literature are either too theoretical, applying to only a small number of knots, or are designed to only deal with a specific knot. The thesis builds on the results of Herald, Kirk and Livingston [HKL10] and Tamulis [Tam02] to give a series of criteria, using twisted Alexander polynomials, for determining whether a knot is of infinite order in C. There are two immediate applications of these theorems. The first is to give the structure of the subgroups of the concordance group C and the algebraic concordance group G generated by the prime knots of 9 or fewer crossings. This should be of practical value to the knot-theoretic community, but more importantly it provides interesting examples of phenomena both in the algebraic and geometric concordance groups. The second application is to find the concordance orders of all prime knots with up t...
Canine cystine urolithiasis: A review of 1760 submissions over 35 years (1979-2013).
Hesse, Albrecht; Hoffmann, Jenni; Orzekowsky, Helmut; Neiger, Reto
2016-03-01
This study reports a retrospective evaluation of epidemiological data from cystine stones of dogs submitted to the Urinary Stone Analysis Center Bonn, Germany, over a period of 35 years. Of the 20 316 uroliths submitted from 1979 to 2013, 1760 were cystine stones. In total, 109 breeds were affected with 16 breeds having an odds ratio > 1.0. Most of the cystine uroliths were retrieved from male dogs, with only 19 female dogs (1.1%) being affected. Percentage of submitted cystine stones amongst all stones decreased significantly over 35 years from 38.9% to 4.4%.
Inflammasome activation by cystine crystals: implications for the pathogenesis of cystinosis.
Prencipe, Giusi; Caiello, Ivan; Cherqui, Stephanie; Whisenant, Thomas; Petrini, Stefania; Emma, Francesco; De Benedetti, Fabrizio
2014-06-01
Intralysosomal cystine crystal accumulation, due to mutations in the CTNS gene, is a hallmark of nephropathic cystinosis, but the role of these crystals in disease pathogenesis remains unclear. We hypothesized that, similar to other host-derived crystalline moieties, cystine crystals can induce IL-1β production through inflammasome activation. Thus, we investigated the proinflammatory effects of cystine crystals in primary human PBMCs. LPS-primed PBMCs stimulated with cystine crystals secreted IL-1β in a dose-dependent manner. Similarly to IL-1β secretion induced by other crystalline inflammasome activators, cystine crystal-induced IL-1β secretion required activation of caspase-1. Additionally, exogenous cystine crystals were internalized by monocytes, and inhibition of phagocytosis, cathepsin B leakage, generation of reactive oxygen species, and potassium efflux reduced cystine crystal-induced IL-1β secretion. Patients with cystinosis had higher levels of circulating IL-1β and IL-18 compared with controls. Analysis of inflammasome-related gene expression in PBMCs from patients with cystinosis revealed a significant increase in IL-1β and CASP-1 transcript levels compared with controls. Moreover, knockout of cystinosin in mice led to significant increases in serum IL-18 levels and kidney expression of inflammasome-related genes (Casp-1, Pycard, Il-18, Il18r1, Il1r1, and Il1rl2). Taken together, these data demonstrate that cystine crystals are endogenous inflammasome-activating stimuli, suggesting a novel role for cystine crystals in the pathogenesis of nephropathic cystinosis.
Induction of the Escherichia coli yijE gene expression by cystine.
Yamamoto, Kaneyoshi; Nonaka, Gen; Ozawa, Takahiro; Takumi, Kazuhiro; Ishihama, Akira
2015-01-01
Cystine is formed from two molecules of the cysteine under oxidized conditions, but is reversibly converted to cysteine by reduction. Growth of Escherichia coli is retarded in the presence of excess cystine. Transcriptome analysis showed 11 up-regulated and 26 down-regulated genes upon exposure to excess cystine. The reporter assay confirmed regulation by cystine of the expression of one up-regulated membrane gene, yijE, and two down-regulated membrane genes, yhdT and yihN. In order to identify the as yet unidentified gene encoding cystine efflux transporter, the putative cystine efflux candidate, yijE gene, was over-expressed. Expression of the yijE gene suppressed the slow growth of E. coli in the presence of high concentration of extracellular cystine. In good agreement, the knock-out of yijE gene increased the sensibility to cystine. These observations altogether imply that the yijE gene is involved in response to cystine in E. coli.
Crystal Growth Inhibitors for the Prevention of L-Cystine Kidney Stones through Molecular Design
Rimer, Jeffrey D.; An, Zhihua; Zhu, Zina; Lee, Michael H.; Goldfarb, David S.; Wesson, Jeffrey A.; Ward, Michael D.
2010-01-01
Crystallization of L-cystine is a critical process in the pathogenesis of kidney stone formation in cystinuria, a disorder affecting at least 20,000 U.S. citizens. Current therapeutic treatments for this disease are somewhat effective but often lead to adverse side effects. Real-time in situ atomic force microscopy (AFM) reveals that L-cystine dimethylester (L-CDME) and L-cystine methylester (L-CME) – structural mimics of L-cystine – dramatically reduce the growth velocity of the six symmetry...
α-Lipoic acid treatment prevents cystine urolithiasis in a mouse model of cystinuria.
Zee, Tiffany; Bose, Neelanjan; Zee, Jarcy; Beck, Jennifer N; Yang, See; Parihar, Jaspreet; Yang, Min; Damodar, Sruthi; Hall, David; O'Leary, Monique N; Ramanathan, Arvind; Gerona, Roy R; Killilea, David W; Chi, Thomas; Tischfield, Jay; Sahota, Amrik; Kahn, Arnold; Stoller, Marshall L; Kapahi, Pankaj
2017-03-01
Cystinuria is an incompletely dominant disorder characterized by defective urinary cystine reabsorption that results in the formation of cystine-based urinary stones. Current treatment options are limited in their effectiveness at preventing stone recurrence and are often poorly tolerated. We report that the nutritional supplement α-lipoic acid inhibits cystine stone formation in the Slc3a1(-/-) mouse model of cystinuria by increasing the solubility of urinary cystine. These findings identify a novel therapeutic strategy for the clinical treatment of cystinuria.
Eyraud, Vanessa; Karaki, Lamis; Rahioui, Isabelle; Sivignon, Catherine; Da Silva, Pedro; Rahbé, Yvan; Royer, Corinne; Gressent, Frédéric
2013-01-01
The PA1b (Pea Albumin 1, subunit b) peptide is an entomotoxin extract from Legume seeds with lethal activity on several insect pests, such as mosquitoes, some aphids and cereal weevils. This 37 amino-acid cysteine-rich peptide has been, until now, obtained by biochemical purification or chemical synthesis. In this paper, we present our results for the transient production of the peptide in Nicotiana benthamiana by agro-infiltration, with a yield of about 35 µg/g of fresh leaves and maximum production 8 days after infiltration. PA1b is part of the PA1 gene which, after post-translational modifications, encodes two peptides (PA1b and PA1a). We show that transforming tobacco with the PA1b cDNA alone does not result in production of the toxin and, in fact, the entire cDNA is necessary, raising the question of the role of PA1a. We constructed a PA1-cassette, allowing for the quick "cut/paste" of different PA1b mutants within a conserved PA1 cDNA. This cassette enabled us to produce the six isoforms of PA1b which exist in pea seeds. Biological tests revealed that all the isoforms display similar activity, with the exception of one which is inactive. The lack of activity in this isoform led us to conclude that the amphiphilic nature of the peptide is necessary for activity. The possible applications of this expression system for other cysteine-rich biomolecules are discussed.
Expression and biological activity of the cystine knot bioinsecticide PA1b (Pea Albumin 1 Subunit b.
Directory of Open Access Journals (Sweden)
Vanessa Eyraud
Full Text Available The PA1b (Pea Albumin 1, subunit b peptide is an entomotoxin extract from Legume seeds with lethal activity on several insect pests, such as mosquitoes, some aphids and cereal weevils. This 37 amino-acid cysteine-rich peptide has been, until now, obtained by biochemical purification or chemical synthesis. In this paper, we present our results for the transient production of the peptide in Nicotiana benthamiana by agro-infiltration, with a yield of about 35 µg/g of fresh leaves and maximum production 8 days after infiltration. PA1b is part of the PA1 gene which, after post-translational modifications, encodes two peptides (PA1b and PA1a. We show that transforming tobacco with the PA1b cDNA alone does not result in production of the toxin and, in fact, the entire cDNA is necessary, raising the question of the role of PA1a. We constructed a PA1-cassette, allowing for the quick "cut/paste" of different PA1b mutants within a conserved PA1 cDNA. This cassette enabled us to produce the six isoforms of PA1b which exist in pea seeds. Biological tests revealed that all the isoforms display similar activity, with the exception of one which is inactive. The lack of activity in this isoform led us to conclude that the amphiphilic nature of the peptide is necessary for activity. The possible applications of this expression system for other cysteine-rich biomolecules are discussed.
Torus knots and the rational DAHA
Gorsky, Eugene; Rasmussen, Jacob; Shende, Vivek
2012-01-01
We conjecturally extract the triply graded Khovanov-Rozansky homology of the (m, n) torus knot from the unique finite dimensional simple representation of the rational DAHA of type A, rank n - 1, and central character m/n. The conjectural differentials of Gukov, Dunfield and the third author receive an explicit algebraic expression in this picture, yielding a prescription for the doubly graded Khovanov-Rozansky homologies. We match our conjecture to previous conjectures of the first author relating knot homology to q, t-Catalan numbers, and of the last three authors relating knot homology to Hilbert schemes on singular curves.
Urethral catheter knotting: an avoidable complication
Directory of Open Access Journals (Sweden)
Ismail Burud
2013-03-01
Full Text Available Urethral catheterisation is a common andsafe procedure performed routinely. The small sizeof the urethra in a child necessitates the use of aninfant feeding tube (Size 5 to 8 F for catheterisation.Knotting within the bladder is a rare complication withsignificant morbidity often necessitating surgical orendoscopic removal. Insertion of an excessive lengthof tube contributes to coiling and knotting. We reportan instance of knotting of an infant feeding tube inthe proximal penile urethra of a 4 year-old male childrequiring urethrotomy to remove it. Awareness of therisk and proper technique can reduce this complication.
Knot Invariants from Classical Field Theories
Leal, L C
1999-01-01
We consider the Non-Abelian Chern-Simons term coupled to external particles, in a gauge and diffeomorphism invariant form. The classical equations of motion are perturbativelly studied, and the on-shell action is shown to produce knot-invariants associated with the sources. The first contributions are explicitly calculated, and the corresponding knot-invariants are recognized. We conclude that the interplay between Knot Theory and Topological Field Theories is manifested not only at the quantum level, but in a classical context as well.
Grid homology for knots and links
Ozsváth, Peter S; Szabó, Zoltán
2015-01-01
Knot theory is a classical area of low-dimensional topology, directly connected with the theory of three-manifolds and smooth four-manifold topology. In recent years, the subject has undergone transformative changes thanks to its connections with a number of other mathematical disciplines, including gauge theory; representation theory and categorification; contact geometry; and the theory of pseudo-holomorphic curves. Starting from the combinatorial point of view on knots using their grid diagrams, this book serves as an introduction to knot theory, specifically as it relates to some of the ab
Studying uniform thickness II: Transversely nonsimple iterated torus knots
DEFF Research Database (Denmark)
LaFountain, Douglas
2011-01-01
We prove that an iterated torus knot type in the standard contact 3-sphere fails the uniform thickness property (UTP) if and only if it is formed from repeated positive cablings, which is precisely when an iterated torus knot supports the standard contact structure. This is the first complete UTP...... classification for a large class of knots. We also show that all iterated torus knots that fail the UTP support cabling knot types that are transversely non-simple....
A Partial Order in the Knot Table Ⅱ
Institute of Scientific and Technical Information of China (English)
Teruaki KITANO; Masaaki SUZUKI
2008-01-01
A partial order on the set of the prime knots can be defined by the existence of a surjective homomorphism between knot groups.In the previous paper,we determined the partial order in the knot table.In this paper,we prove that 31 and 41 are minimal elements.Further,we study which surjection a pair of a periodic knot and its quotient knot induces,and which surjection a degree one map can induce.
Zeros of the Jones Polynomial for Torus Knots and 2-bridge Knots
Institute of Scientific and Technical Information of China (English)
HAN You-fa; ZHANG Rong-wei; WANG Lin-lin; MA Xiao-sha
2014-01-01
We study zeros of the Jones polynomial and their distributions for torus knots and 2-bridge knots. We prove that e(2m+1)πi/2 and e(2m+1)πi/4(m is a positive integer) can not be the zeros of Jones polynomial for torus knots Tp,q by the knowledge of the trigonometric function. We elicit the normal form of Jones polynomials of the 2-bridge knot C (−2, 2, · · · , (−1)r 2) by the recursive form and discuss the distribution of their zeros.
Kleckner, Dustin; Irvine, William T M
2013-01-01
The idea that the knottedness (hydrodynamic Helicity) of a fluid flow is conserved has a long history in fluid mechanics. The quintessential example of a knotted flow is a knotted vortex filament, however, owing to experimental difficulties, it has not been possible until recently to directly generate knotted vortices in real fluids. Using 3D printed hydrofoils and high-speed laser scanning tomography, we generate vortex knots and links and measure their subsequent evolution. In both cases, we find that the vortices deform and stretch until a series of vortex reconnections occurs, eventually resulting several disjoint vortex rings. This article accompanies a fluid dynamics video entered into the Gallery of Fluid Motion at the 66th Annual Meeting of the APS Division of Fluid Dynamics.
Cotranslational folding of deeply knotted proteins
Chwastyk, Mateusz
2015-01-01
Proper folding of deeply knotted proteins has a very low success rate even in structure-based models which favor formation of the native contacts but have no topological bias. By employing a structure-based model, we demonstrate that cotranslational folding on a model ribosome may enhance the odds to form trefoil knots for protein YibK without any need to introduce any non-native contacts. The ribosome is represented by a repulsive wall that keeps elongating the protein. On-ribosome folding proceeds through a a slipknot conformation. We elucidate the mechanics and energetics of its formation. We show that the knotting probability in on-ribosome folding is a function of temperature and that there is an optimal temperature for the process. Our model often leads to the establishment of the native contacts without formation of the knot.
Assaf, Sami H
2010-01-01
A classic problem in enumerative combinatorics is to count the number of derangements, that is, permutations with no fixed point. Inspired by a recent generalization to facet derangements of the hypercube by Gordon and McMahon, we generalize this problem to enumerating derangements in the wreath product of any finite cyclic group with the symmetric group. We also give q- and (q, t)-analogs for cyclic derangements, generalizing results of Brenti and Gessel.
The crossing number of composite knots
Lackenby, Marc
2008-01-01
It is a very old conjecture that the crossing number of knots is additive under connected sum. In other words, if K#K' is the connected sum of knots K and K', then does the equality c(K#K') = c(K) + c(K') hold? We prove that c(K#K') is at most c(K) + c(K') and at least (c(K) + c(K'))/152.
On rectangular HOMFLY for twist knots
Kononov, Ya
2016-01-01
As a new step in the study of rectangularly-colored knot polynomials, we reformulate the prescription of arXiv:1606.06015 for twist knots in the double-column representations $R=[rr]$ in terms of skew Schur polynomials. These, however, are mysteriously shifted from the standard topological locus, what makes further generalization to arbitrary $R=[r^s]$ not quite straightforward.
Counting Links and Knots in Complete Graphs
Abrams, Loren
2010-01-01
We investigate the minimal number of links and knots in complete partite graphs. We provide exact values or bounds on the minimal number of links for all complete partite graphs with all but 4 vertices in one partition, or with 9 vertices in total. In particular, we find that the minimal number of links for $K_{4,4,1}$ is 74. We also provide exact values or bounds on the minimal number of knots for all complete partite graphs with 8 vertices.
Twisted Alexander polynomials of hyperbolic knots
Dunfield, Nathan M; Jackson, Nicholas
2011-01-01
We study a twisted Alexander polynomial naturally associated to a hyperbolic knot in an integer homology 3-sphere via a lift of the holonomy representation to SL(2, C). It is an unambiguous symmetric Laurent polynomial whose coefficients lie in the trace field of the knot. It contains information about genus, fibering, and chirality, and moreover is powerful enough to sometimes detect mutation. We calculated this invariant numerically for all 313,209 hyperbolic knots in S^3 with at most 15 crossings, and found that in all cases it gave a sharp bound on the genus of the knot and determined both fibering and chirality. We also study how such twisted Alexander polynomials vary as one moves around in an irreducible component X_0 of the SL(2, C)-character variety of the knot group. We show how to understand all of these polynomials at once in terms of a polynomial whose coefficients lie in the function field of X_0. We use this to help explain some of the patterns observed for knots in S^3, and explore a potential...
Self-assembly of knots and links
Orlandini, Enzo; Polles, Guido; Marenduzzo, Davide; Micheletti, Cristian
2017-03-01
Guiding the self-assembly of identical building blocks towards complex three-dimensional structures with a set of desired properties is a major goal in material science, chemistry and physics. A particularly challenging problem, especially explored in synthetic chemistry, is that of self-assembling closed structures with a target topology starting by simple geometrical templates. Here we overview and revisit recent advancements, based on stochastic simulations, where the geometry of rigid helical templates with functionalised sticky ends has been designed for self-assembling efficiently and reproducibly into a wide range of three-dimensional closed structures. Notably, these include non trivial topologies of links and knots, including the 819 knot that we had predicted to be highly encodable and that has only recently been obtained experimentally. By appropriately tuning the parameters that define the template shape, we show that, for fixed concentration of templates, the assembly process can be directed towards the formation of specific knotted and linked structures such as the trefoils, pentafoil knots, Hopf and Solomon links. More exotic and unexpected knots and links are also found. Our results should be relevant to the design of new protocols that can both increase and broaden the population of synthetise molecular knots and catenanes.
Torus Knots and the Topological Vertex
Jockers, Hans; Soroush, Masoud
2012-01-01
We propose a class of toric Lagrangian A-branes on the resolved conifold that is suitable to describe torus knots on S^3. The key role is played by the SL(2,Z) transformation, which generates a general torus knot from the unknot. Applying the topological vertex to the proposed A-branes, we rederive the colored HOMFLY polynomials for torus knots, in agreement with the Rosso and Jones formula. We show that our A-model construction is mirror symmetric to the B-model analysis of Brini, Eynard and Marino. Comparing to the recent proposal by Aganagic and Vafa for knots on S^3, we demonstrate that the disk amplitude of the A-brane associated to any knot is sufficient to reconstruct the entire B-model spectral curve. Finally, the construction of toric Lagrangian A-branes is generalized to other local toric Calabi-Yau geometries, which paves the road to study knots in other three-manifolds such as lens spaces.
Iglesias, D.M.; El-Kares, R.; Taranta, A.; Bellomo, F.; Emma, F.; Besouw, M.; Levtchenko, E.N.; Toelen, J.; Heuvel, L.P. van den; Chu, L.; Zhao, J.; Young, Y.K.; Eliopoulos, N.; Goodyer, P.
2012-01-01
Cystinosis is a rare disease caused by homozygous mutations of the CTNS gene, encoding a cystine efflux channel in the lysosomal membrane. In Ctns knockout mice, the pathologic intralysosomal accumulation of cystine that drives progressive organ damage can be reversed by infusion of wildtype bone ma
Iglesias, D.M.; El-Kares, R.; Taranta, A.; Bellomo, F.; Emma, F.; Besouw, M.; Levtchenko, E.N.; Toelen, J.; Heuvel, L.P. van den; Chu, L.; Zhao, J.; Young, Y.K.; Eliopoulos, N.; Goodyer, P.
2012-01-01
Cystinosis is a rare disease caused by homozygous mutations of the CTNS gene, encoding a cystine efflux channel in the lysosomal membrane. In Ctns knockout mice, the pathologic intralysosomal accumulation of cystine that drives progressive organ damage can be reversed by infusion of wildtype bone
Crystal structure of seleno-l-cystine dihydrochloride
Carl Henrik Görbitz; Vladimir Levchenko; Jevgenijs Semjonovs; Mohamed Yusuf Sharif
2015-01-01
Numerous crystal structures are available for the dimeric amino acid cystine. In proteins it is formed by oxidation of the –SH thiol groups of two closely spaced cysteine residues, resulting in the formation of a familiar disulfide bridge. The title compound [systematic name: (R,R)-1,1′-dicarboxy-2,2′-(diselanediyl)diethanaminium dichloride], C6H14N2O4Se22+·2Cl−, is the first example of a small molecule structure of the biologically important analogue with a —CH2—Se—Se—CH2— bridging unit. Bon...
Bhatnagar, Akshay; Apostol, Marcin I; Bandyopadhyay, Debashree
2016-11-01
In our previous study, we have shown that the microenvironments around conserved amino acids are also conserved in protein families (Bandyopadhyay and Mehler, Proteins 2008; 72:646-659). In this study, we have hypothesized that amino acids perform similar functions when embedded in a certain type of protein microenvironment. We have tested this hypothesis on the microenvironments around disulfide-bridged cysteines from high-resolution protein crystal structures. Although such cystines mainly play structural role in proteins, in certain enzymes they participate in catalysis and redox reactions. We have performed and report a functional annotation of enzymatically active cystines to their respective microenvironments. Three protein microenvironment clusters were identified: (i) buried-hydrophobic, (ii) exposed-hydrophilic, and (iii) buried-hydrophilic. The buried-hydrophobic cluster encompasses a small group of 22 redox-active cystines, mostly in alpha-helical conformations in a -C-x-x-C- motif from the Oxido-reductase enzyme class. All these cystines have high strain energy and near identical microenvironments. Most of the active cystines in hydrolase enzyme class belong to buried hydrophilic microenvironment cluster. In total there are 34 half-cystines detected in buried hydrophilic cluster from hydrolases, as a part of enzyme active site. Even within the buried hydrophilic cluster, there is clear separation of active half-cystines between surface exposed part of the protein and protein interior. Half-cystines toward the surface exposed region are higher in number compared to those in protein interior. Apart from cystines at the active sites of the enzymes, many more half-cystines were detected in buried hydrophilic cluster those are part of the microenvironment of enzyme active sites. However, no active half-cystines were detected in extremely hydrophilic microenvironment cluster, that is, exposed hydrophilic cluster, indicating that total exposure of cystine
Knots in homology spheres which have simple knot Floer homology are trivial
Eftekhary, Eaman
2010-01-01
We show that if K is a non-trivial knot inside a homology sphere X, the rank of the knot Floer homology group associated with K is strictly bigger than the rank of the Heegaard Floer homology group associated with X.
Sumayao, Rodolfo; McEvoy, Bernadette; Martin-Martin, Natalia; McMorrow, Tara; Newsholme, Philip
2013-10-01
Using the cystine dimethylester (CDME) loading technique to achieve elevated lysosomal cystine levels, ATP depletion has previously been postulated to be responsible for the renal dysfunction in cystinosis, a genetic disorder characterized by an excessive accumulation of cystine in the lysosomes. However, this is unlikely to be the sole factor responsible for the complexity of cell stress associated with cystinosis. Moreover, CDME has been shown to induce a direct toxic effect on mitochondrial ATP generation. Using a human-derived proximal tubular epithelial cell line, we compared the effects of CDME loading with small interfering RNA-mediated cystinosin, lysosomal cystine transporter (CTNS) gene silencing on glutathione redox status, reactive oxygen species levels, oxidative stress index, antioxidant enzyme activities and ATP generating capacity. The CDME-loaded cells displayed increased total glutathione content, extensive superoxide depletion, augmented oxidative stress index, decreased catalase activity, normal superoxide dismutase activity and compromised ATP generation. In contrast, cells subjected to CTNS gene inhibition demonstrated decreased total glutathione content, increased superoxide levels, unaltered oxidative stress index, unaltered catalase activity, induction of superoxide dismutase activity and normal ATP generation. Our data indicate that many CDME-induced effects are independent of lysosomal cystine accumulation, which further underscores the limited value of CDME loading for studying the pathogenesis of cystinosis. CTNS gene inhibition, which results in intracellular cystine accumulation, is a more realistic approach for investigating biochemical alterations in cystinosis.
Legendrian and transverse cables of positive torus knots
DEFF Research Database (Denmark)
Etnyre, John; LaFountain, Douglas; Tosun, Bülent
2012-01-01
In this paper we classify Legendrian and transverse knots in the knot types obtained from positive torus knots by cabling. This classification allows us to demonstrate several new phenomena. Specifically, we show there are knot types that have non-destabilizable Legendrian representatives whose...... Thurston-Bennequin invariant is arbitrarily far from maximal. We also exhibit Legendrian knots requiring arbitrarily many stabilizations before they become Legendrian isotopic. Similar new phenomena are observed for transverse knots. To achieve these results we define and study "partially thickenable" tori...
Origin of Metastable Knots in Single Flexible Chains
Dai, Liang; Renner, C. Benjamin; Doyle, Patrick S.
2015-01-01
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.
Health-related quality of life (HRQoL) in cystine compared with non-cystine stone formers.
Modersitzki, Frank; Pizzi, Laura; Grasso, Michael; Goldfarb, David S
2014-02-01
Cystinuria is a genetic cause of recurrent kidney stones which may be more recurrent and larger than more common non-cystine stones. They may have a greater impact on health-related quality of life (HRQoL). We measured this impact by surveying HRQoL in patients with stones, comparing non-cystine stone formers (NCSF) to cystine stone formers (CYSF) and both groups to normative values of the US population. We used SF-36v2 via an internet instrument. CYSF patients were recruited via cystinuria-related websites, two patient advocacy groups, and an active endourology practice. NCSF patients were recruited from the same practice and by email. Total n surveyed with scorable data: 214 CYSF and 81 NCSF. The participants included 128 men and 161 women. The group of CYSF were significantly younger (39 vs. 54 years) and suffered longer from kidney stones (255 vs. 136 months). CYSF patients had significantly more episodes of stones than NCSF patients in the last year (N = 108 CYSF, N = 20 NCSF). More frequent stones in the last year and mental comorbidities most often predicted worse scores in the individual HRQoL domains. However, cystine stone composition was a significant predictor of worse scores only for role emotional. Better scores in all SF-36 domains were associated with greater time since the last kidney stone event. Although kidney stones are often transient, kidney stone formers, regardless of stone composition, have a worse HRQoL than the standard US population, which has a normative score of 50, such as general health (41.2 ± 12.8), bodily pain (46.5 ± 11.8) and mental health (45.1 ± 12.6). CYSF are more frequent and severe stone formers compared with NCSF with a resulting greater, direct impact on the HRQoL of CYSF patients. Whether preventive strategies for cystinuria are being properly utilized by practitioners, and which strategies are most effective, should be established.
The inner knot of the Crab nebula
Lyutikov, Maxim; Porth, Oliver
2015-01-01
We model the inner knot of the Crab Nebula as a synchrotron emission coming from the non-spherical MHD termination shock of relativistic pulsar wind. The post-shock flow is mildly relativistic; as a result the Doppler-beaming has a strong impact on the shock appearance. The model can reproduce the knot location, size, elongation, brightness distribution, luminosity and polarization provided the effective magnetization of the section of the pulsar wind producing the knot is low, $\\sigma \\leq 1$. In the striped wind model, this implies that the striped zone is rather wide, with the magnetic inclination angle of the Crab pulsar $\\ge 45^\\circ$; this agrees with the previous model-dependent estimate based on the gamma-ray emission of the pulsar. We conclude that the tiny knot is indeed a bright spot on the surface of a quasi-stationary magnetic relativistic shock and that this shock is a site of efficient particle acceleration. On the other hand, the deduced low magnetization of the knot plasma implies that this i...
The inner knot of the Crab nebula
Lyutikov, Maxim; Komissarov, Serguei S.; Porth, Oliver
2016-02-01
We model the inner knot of the Crab nebula as a synchrotron emission coming from the non-spherical MHD termination shock of relativistic pulsar wind. The post-shock flow is mildly relativistic; as a result the Doppler beaming has a strong impact on the shock appearance. The model can reproduce the knot location, size, elongation, brightness distribution, luminosity and polarization provided the effective magnetization of the section of the pulsar wind producing the knot is low, σ ≤ 1. In the striped wind model, this implies that the striped zone is rather wide, with the magnetic inclination angle of the Crab pulsar ≥45°; this agrees with the previous model-dependent estimate based on the gamma-ray emission of the pulsar. We conclude that the tiny knot is indeed a bright spot on the surface of a quasi-stationary magnetic relativistic shock and that this shock is a site of efficient particle acceleration. On the other hand, the deduced low magnetization of the knot plasma implies that this is an unlikely site for the Crab's gamma-ray flares, if they are related to the fast relativistic magnetic reconnection events.
Symmetries in proteins: A knot theory approach
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.
Evans, Dennis H.; And Others
1983-01-01
Cyclic voltammetry is a simple experiment that has become popular in chemical research because it can provide useful information about redox reactions in a form which is easily obtained and interpreted. Discusses principles of the method and illustrates its use in the study of four electrode reactions. (Author/JN)
Evans, Dennis H.; And Others
1983-01-01
Cyclic voltammetry is a simple experiment that has become popular in chemical research because it can provide useful information about redox reactions in a form which is easily obtained and interpreted. Discusses principles of the method and illustrates its use in the study of four electrode reactions. (Author/JN)
The recurrent true umbilical cord knots: a case report
Directory of Open Access Journals (Sweden)
I Naghi
2012-11-01
Full Text Available Background: True umbilical cord knot is one of the abnormalities of the umbilical cord. Active fetal movements create cord knotting. True umbilical cord knots are rare but may be associated with fetal distress and stillbirth. True umbilical cord knots are capable of impeding blood flow to the fetus.Case presentation: A 26-year old primigravid woman was first treated for genital herpes simplex virus (HSV type 2 at 36 weeks of gestational age. She received oral acyclovir (400 mg three times daily for 10 days. At the gestational age of 38 weeks and 5 days, fetal activity decreased and NST was nonreactive. She was delivered by cesarean section and a true umbilical cord knot was found. Four years later, in her second pregnancy, another true knot was seen.Conclusion: Excessively long umbilical cords are more likely to be associated with true knots. Genetics has an important role in determining cord length and occurrence of true knots.
Representations of Knot Groups and Twisted Alexander Polynomials
Institute of Scientific and Technical Information of China (English)
Xiao Song LIN
2001-01-01
We present a twisted version of the Alexander polynomial associated with a matrix representation of the knot group. Examples of two knots with the same Alexander module but differenttwisted Alexander polynomials are given.
Activated human CD4+ T cells express transporters for both cysteine and cystine.
Levring, Trine Bøegh; Hansen, Ann Kathrine; Nielsen, Bodil Lisbeth; Kongsbak, Martin; von Essen, Marina Rode; Woetmann, Anders; Odum, Niels; Bonefeld, Charlotte Menné; Geisler, Carsten
2012-01-01
Because naïve T cells are unable to import cystine due to the absence of cystine transporters, it has been suggested that T cell activation is dependent on cysteine generated by antigen presenting cells. The aim of this study was to determine at which phases during T cell activation exogenous cystine/cysteine is required and how T cells meet this requirement. We found that early activation of T cells is independent of exogenous cystine/cysteine, whereas T cell proliferation is strictly dependent of uptake of exogenous cystine/cysteine. Naïve T cells express no or very low levels of both cystine and cysteine transporters. However, we found that these transporters become strongly up-regulated during T cell activation and provide activated T cells with the required amount of cystine/cysteine needed for T cell proliferation. Thus, T cells are equipped with mechanisms that allow T cell activation and proliferation independently of cysteine generated by antigen presenting cells.
Knot solitons in the AFZ model
Institute of Scientific and Technical Information of China (English)
Ren Ji-Rong; Mo Shu-Fan; Zhu Tao
2009-01-01
This paper studies the topological properties of knotted solitons in the (3 + 1)-dimensional Aratyn-Ferreira-Zimerman (AFZ) model. Topologically, these solitons are characterized by the Hopf invariant I, which is an integral class in the homotopy group π3(S3)= Z. By making use of the decomposition of U(1) gauge potential theory and Duan's topological current theory, it is shown that the invariant is just the total sum of all the self-linking and linking numbers of the knot family while only linking numbers are considered in other papers. Furthermore, it is pointed out that this invariant is preserved in the branch processes (splitting, merging and intersection) of these knot vortex lines.
Nonlinear electrodynamics is skilled with knots
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.
Nonlinear electrodynamics is skilled with knots
Goulart, E
2016-01-01
The aims of this letter are three-fold: 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.
On the concordance genus of topologically slice knots
Hom, Jennifer
2012-01-01
The concordance genus of a knot K is the minimum Seifert genus of all knots smoothly concordant to K. Concordance genus is bounded below by the 4-ball genus and above by the Seifert genus. We give a lower bound for the concordance genus of K coming from the knot Floer complex of K. As an application, we prove that there are topologically slice knots with 4-ball genus equal to one and arbitrarily large concordance genus.
Knot invariants and higher representation theory II: the categorification of quantum knot invariants
Webster, Ben
2010-01-01
We construct knot invariants categorifying the quantum knot variants for all representations of quantum groups. We show that these invariants coincide with previous invariants defined by Khovanov for sl_2 and sl_3 and by Mazorchuk-Stroppel and Sussan for sl_n. We also suggest an approach to showing that these knot homologies are functorial. Our technique uses categorifications of the tensor products of integrable representations of Kac-Moody algebras and quantum groups, constructed a prequel to this paper. In particular, we construct functors on these categorifying the action of the braiding and duality of quantum group representations. These categories are based on the pictorial approach of Khovanov and Lauda.
A principle for ideal torus knots
DEFF Research Database (Denmark)
Olsen, Kasper Wibeck; Bohr, Jakob
2013-01-01
Using bent-helix embeddings, we investigate simple and knotted torus windings that are made of tubes of finite thickness. Knots which have the shortest rope length are often denoted as ideal structures. Conventionally, the ideal structures are found by rope shortening routines. It is shown...... that alternatively they can be directly determined as maximally twisted structures. In many cases these structures are also structures with zero strain-twist coupling, i.e. structures that neither rotate one or the other way under strain. We use this principle to implement rapid numerical calculations of the ideal...
On Chebyshev polynomials and torus knots
Gavrilik, A. M.; Pavlyuk, A. M.
2009-01-01
In this work we demonstrate that the q-numbers and their two-parameter generalization, the q,p-numbers, can be used to obtain some polynomial invariants for torus knots and links. First, we show that the q-numbers, which are closely connected with the Chebyshev polynomials, can also be related with the Alexander polynomials for the class T(s,2) of torus knots, s being an odd integer, and used for finding the corresponding skein relation. Then, we develop this procedure in order to obtain, wit...
Knotted strings and leptonic flavor structure
Kephart, Thomas W; Päs, Heinrich
2011-01-01
Tight knots and links arising in the infrared limit of string theories may provide an interesting alternative to flavor symmetries for explaining the observed flavor patterns in the leptonic sector. As an example we consider a type I seesaw model where the Majorana mass structure is based on the discrete length spectrum of tight knots and links. It is shown 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 $\\theta_{13}$.
Universal Form of Renormalizable Knots in Symbolic Dynamics
Institute of Scientific and Technical Information of China (English)
GAO Wen; PENG Shou-Li
2005-01-01
@@ The knot structure of three-dimensional flow has been constructed based on minimal braid assumption [Chin. Phys. Lett. 20 (2003) 1444]. Here we provide a new universal form of renormalizable knots. From this universal form an arbitrary renormalizable knot can be decomposed into a unique set of elementary templates.
Knotcraft the practical and entertaining art of tying knots
Macfarlan, Allan and Paulette
1983-01-01
Comprehensive reference work explains how to tie hundreds of practical (and decorative) knots in clear illustrations and precisely worded written instructions. Ideal for boaters and campers. Also covers knots in history, knot mystery and magic, and games, stunts and tricks with rope. Introduction. Index. 166 black-and-white illustrations.
On slope genera of knotted tori in the 4-space
Liu, Yi; Sun, Hongbin; Wang, Shicheng
2011-01-01
In this note, we investigate genera for the slopes of a knotted torus in the 4-sphere analogous to the genus of a classical knot. We compare various formulations of this notion, and use this notion to study the extendable subgroup of the mapping class group of the knotted torus.
A facile method to produce highly monodispersed nanospheres of cystine aggregates
Han, Hongliang; Wang, Chungang; Ma, Zhanfang; Su, Zhongmin
2006-10-01
Multiple shapes of nano- and micro-structured cystine aggregates, including spheres, rods, spindles, dendrites, and multipods, were easily synthesized just by adjusting the concentrations and pH values of L-Cysteine solutions under ultrasonic irritation. Importantly, highly monodispersed nanospheres of cystine aggregates 225 nm in diameter without any other shapes were easily obtained for the system of 0.1 M L-Cysteine with pH 8. This will provide a very simple and effective approach to produce monodispersed cystine microspheres, which could promote new possibilities for future applications in biosensor, drug delivery, medicine, and the production of nanomaterials.
A facile method to produce highly monodispersed nanospheres of cystine aggregates
Energy Technology Data Exchange (ETDEWEB)
Han Hongliang; Wang Chungang; Ma Zhanfang; Su Zhongmin [Chemistry Department, Northeast Normal University, Changchun 130024 (China)
2006-10-28
Multiple shapes of nano- and micro-structured cystine aggregates, including spheres, rods, spindles, dendrites, and multipods, were easily synthesized just by adjusting the concentrations and pH values of L-Cysteine solutions under ultrasonic irritation. Importantly, highly monodispersed nanospheres of cystine aggregates 225 nm in diameter without any other shapes were easily obtained for the system of 0.1 M L-Cysteine with pH 8. This will provide a very simple and effective approach to produce monodispersed cystine microspheres, which could promote new possibilities for future applications in biosensor, drug delivery, medicine, and the production of nanomaterials.
Marosek, Konrad; Balcerzak, Adam
2015-01-01
Starting with the idea of regularization of singularities due to the variability of the fundamental constants in cosmology we first study the cyclic universe models. We find two models of oscillating mass density and pressure regularized by varying gravitational constant $G$. Then, we extend this idea onto the multiverse containing cyclic individual universes with either growing or decreasing entropy though leaving the net entropy constant. In order to get the key idea, we consider the doubleverse with the same geometrical evolution of the two "parallel" universes with their physical evolution (physical coupling constants $c(t)$ and $G(t)$) being different. An interesting point is that there is a possibility to exchange the universes at the point of maximum expansion -- the fact which was already noticed in quantum cosmology. Similar scenario is also possible within the framework of Brans-Dicke theory.
Refined large N duality for torus knots
DEFF Research Database (Denmark)
Nawata, Satoshi; Kameyama, Masaya
We formulate large N duality of U(N) refined Chern-Simons theory with a torus knot/link in S³. By studying refined BPS states in M-theory, we provide the explicit form of low-energy effective actions of Type IIA string theory with D4-branes on the Ω-background. This form enables us to relate...
Four-manifolds, geometries and knots
Hillman, Jonathan A
2007-01-01
The goal of this book is to characterize algebraically the closed 4-manifolds that fibre nontrivially or admit geometries in the sense of Thurston, or which are obtained by surgery on 2-knots, and to provide a reference for the topology of such manifolds and knots. The first chapter is purely algebraic. The rest of the book may be divided into three parts: general results on homotopy and surgery (Chapters 2-6), geometries and geometric decompositions (Chapters 7-13), and 2-knots (Chapters 14-18). In many cases the Euler characteristic, fundamental group and Stiefel-Whitney classes together form a complete system of invariants for the homotopy type of such manifolds, and the possible values of the invariants can be described explicitly. The strongest results are characterizations of manifolds which fibre homotopically over S^1 or an aspherical surface (up to homotopy equivalence) and infrasolvmanifolds (up to homeomorphism). As a consequence 2-knots whose groups are poly-Z are determined up to Gluck reconstruc...
Kontsevich integral for knots and Vassiliev invariants
Dunin-Barkowski, P.; Sleptsov, A.; Smirnov, A.
2013-01-01
We review quantum field theory approach to the knot theory. Using holomorphic gauge, we obtain the Kontsevich integral. It is explained how to calculate Vassiliev invariants and coefficients in Kontsevich integral in a combinatorial way which can be programmed on a computer. We discuss experimental
The constrictor knot is the best ligature.
Taylor, H; Grogono, A W
2014-03-01
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. 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. 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. 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.
Refined large N duality for torus knots
DEFF Research Database (Denmark)
Nawata, Satoshi; Kameyama, Masaya
We formulate large N duality of U(N) refined Chern-Simons theory with a torus knot/link in S³. By studying refined BPS states in M-theory, we provide the explicit form of low-energy effective actions of Type IIA string theory with D4-branes on the Ω-background. This form enables us to relate...
A preliminary design of a knot undulator.
Xi, Fuchun; Shi, Tan; Fan, Qingyan; Prestemon, Soren; Wan, Weishi; An, Zhenghua; Qiao, S
2013-01-01
The magnetic field configuration of the previously proposed knot undulator [Qiao et al. (2009). Rev. Sci. Instrum. 80, 085108] is realised in the design of a hybridized elliptically polarized undulator, which is presented. Although the details of the field distribution are not the same as those in the theoretical proposal, it is demonstrated that the practical knot undulator could work perfectly. In order to understand the minor discrepancies of the two, mathematical formulae of the synchrotron radiation are derived based on the Fourier transform of the magnetic field. From the results of calculations by simulation program, the discrepancies could be well interpreted by the corresponding formulae. The results show the importance of optimization of the end sections of the knot undulator to suppress the on-axis heat load. Furthermore, a study of the impact of the undulator on beam dynamics of the storage ring was conducted using the Shanghai Synchrotron Radiation Facility as an example and the results show that the knot undulator has little effect on the beam.
Colored HOMFLY polynomials can distinguish mutant knots
Nawata, Satoshi; Singh, Vivek Kumar
2015-01-01
We illustrate from the viewpoint of braiding operations on WZNW conformal blocks how colored HOMFLY polynomials with multiplicity structure can detect mutations. As an example, we explicitly evaluate the (2,1)-colored HOMFLY polynomials that distinguish a famous mutant pair, Kinoshita-Terasaka and Conway knot.
Chang, Hung-Ju; Yang, An-Suei
2014-01-01
Cystine-stabilized mini-proteins are important scaffolds in the combinatorial search of binders for molecular recognition. The structural determinants of a cystine-stabilized scaffold are the critical residues determining the formation of the native disulfide-bonding configuration, and thus should remain unchanged in the combinatorial libraries so as to allow a large portion of the library sequences to be compatible with the scaffold structure. A high-throughput molecular evolution procedure has been developed to select and screen for the polypeptide sequences folding into a specific cystine-stabilized structure. Patterns of sequence preference that emerge from the resultant sequence profiles provide structural determinant information, which facilitates the designs of combinatorial libraries for combinatorial approaches as in phage display. This methodology enables artificial cystine-stabilized proteins to be engineered with enhanced folding and binding properties.
Death by Cystine: an Adverse Emergent Property from a Beneficial Series of Reactions.
Reitzer, Larry
2015-12-01
In this issue of the Journal of Bacteriology, Chonoles Imlay et al. (K. R. Chonoles Imlay, S. Korshunov, and J. A. Imlay, J Bacteriol 197:3629-3644, 2015, http://dx.doi.org/10.1128/JB.00277-15) show that oxidative stress kills sulfur-restricted Escherichia coli grown with sublethal H2O2 when challenged with cystine. Killing requires rapid and seemingly unregulated cystine transport and equally rapid cystine reduction to cysteine. Cysteine export completes an energy-depleting futile cycle. Each reaction of the cycle could be beneficial. Together, a cystine-mediated vulnerability emerges during the transition from a sulfur-restricted to a sulfur-replete environment, perhaps because of complexities of sulfur metabolism.
Radio continuum emission from knots in the DG Tau jet
Rodriguez, L F; Raga, A C; Canto, J; Riera, A; Loinard, L; Dzib, S A; Zapata, L A
2011-01-01
Context: HH 158, the jet from the young star DG Tau, is one of the few sources of its type where jet knots have been detected at optical and X-ray wavelengths. Aims: To search, using Very Large Array observations of this source, radio knots and if detected, compare them with the optical and X-ray knots. To model the emission from the radio knots. Methods: We analyzed archive data and also obtained new Very Large Array observations of this source, as well as an optical image, to measure the present position of the knots. We also modeled the radio emission from the knots in terms of shocks in a jet with intrinsically time-dependent ejection velocities. Results: We detected radio knots in the 1996.98 and 2009.62 VLA data. These radio knots are,within error, coincident with optical knots. We also modeled satisfactorily the observed radio flux densities as shock features from a jet with intrinsic variability. All the observed radio, optical, and X-ray knot positions can be intepreted as four successive knots, ejec...
Effect of knots on binding of intercalators to DNA
Medalion, Shlomi; Rabin, Yitzhak
2014-05-01
We study the effect of knots in circular dsDNA molecules on the binding of intercalating ligands. Using Monte Carlo simulations we show that depending on their handedness, the presence of knots can either suppress or enhance intercalation in supercoiled DNA. When the occupancy of intercalators on DNA is low, the effect of knots on intercalation can be captured by introducing a shift in the mean writhe of the chain that accounts for the writhe of the corresponding ideal knot. In the limit of high intercalator occupancy, the writhe distribution of different knots is strongly affected by excluded volume effects and therefore by salt concentration. Based on the finding that different knots yield well-separated probability distributions of bound intercalators, we propose a new experimental approach to determine DNA topology by monitoring the intensity of fluorescence emitted by dye molecules intercalated into knotted DNA molecules.
The reduction of l-cystine in hydrochloric acid at mercury drop electrodes
Ralph, T.R.; Hitchman, M.L.; Millington, J.P.; Walsh, F.C.
2006-01-01
The reduction of L-cystine in 0.1 mol dm3 HCl at 298 K has been studied at mercury electrodes. Dropping mercury electrode (DME), static mercury drop electrode (SMDE) and hanging mercury drop electrode (HMDE) modes were used with normal, sampled d.c. and differential pulse polarographic detection. The charge transfer kinetics for the irreversible reduction of L-cystine were complicated by reactant and product adsorption, by the formation of cysteinate complexes between mercury and the product ...
DEFF Research Database (Denmark)
Halse, Sven
2014-01-01
an enthusiastic worshipping of life, one that holds youth, health, strength and beauty as its primary attributes, and which was prevalent in all aspects of cultural life around 1900. But even the post war founders of the Vitalist re-conceptualisation of this era, Wolfdietrich Rasch and Gunter Martens, warned...... that also encompasses notions of destruction, decay and death. “All life symbols in literature around 1900 are at the same time symbols of death”. (Rasch, W. 1967:24) Through the analyses of three poems, this article aims to show concrete examples of how cyclic Vitalist thinking is embedded in poetry...
Digestible methionine + cystine requirement for Nile tilapia from 550 to 700 g
Directory of Open Access Journals (Sweden)
Mariana Michelato
2013-01-01
Full Text Available This trial was conducted to determine the dietary digestible methionine + cystine requirement of Nile tilapia (550 to 700 g based on the ideal protein concept. Six hundred fish were distributed in a completely randomized design with five treatments and four replicates, with 30 fish per experimental unit. The fish were fed diets containing approximately 262 g of digestible protein/kg, 3,040 kcal of digestible energy/kg and 7.90, 9.40, 10.90, 12.40 or 13.90 g of methionine + cystine/kg. The fish were hand-fed three times a day until apparent satiation for 30 days. No effects of dietary methionine + cystine on feed conversion ratio, daily protein deposition, whole body moisture, fillet moisture, crude protein, ether extract and ash, plasmatic HDL and LDL cholesterol were observed. Dietary methionine resulted in a linear increase in whole body protein and linear reduction in lipid deposition rate, hepatosomatic index, whole body ether extract and ash, plasmatic total cholesterol, plasmatic total lipids and plasmatic triglycerides. According to the Linear Response Plateau, the daily weight gain and fillet yield increased up to a level of 9.00 and 9.90 g methionine + cystine/kg of diet, respectively. The digestible methionine + cystine requirement of Nile tilapia is 9.00 g/kg for weight gain and 9.90 g/kg for fillet yield, corresponding to methionine + cystine:lysine ratios of 0.60 and 0.66, respectively.
Marosek, Konrad; Dąbrowski, Mariusz P.; Balcerzak, Adam
2016-09-01
Using the idea of regularization of singularities due to the variability of the fundamental constants in cosmology we study the cyclic universe models. We find two models of oscillating and non-singular mass density and pressure (`non-singular' bounce) regularized by varying gravitational constant G despite the scale factor evolution is oscillating and having sharp turning points (`singular' bounce). Both violating (big-bang) and non-violating (phantom) null energy condition models appear. Then, we extend this idea on to the multiverse containing cyclic individual universes with either growing or decreasing entropy though leaving the net entropy constant. In order to get an insight into the key idea, we consider the doubleverse with the same geometrical evolution of the two `parallel' universes with their physical evolution [physical coupling constants c(t) and G(t)] being different. An interesting point is that there is a possibility to exchange the universes at the point of maximum expansion - the fact which was already noticed in quantum cosmology. Similar scenario is also possible within the framework of Brans-Dicke theory where varying G(t) is replaced by the dynamical Brans-Dicke field φ(t) though these theories are slightly different.
A process for the preparation of cysteine from cystine
Chang, Shih-Ger; Liu, David K.; Griffiths, Elizabeth A.; Littlejohn, David
1989-01-01
The present invention in one aspect relates to a process for the simultaneous removal of NO.sub.x and SO.sub.2 from a fluid stream comprising mixtures thereof and in another aspect relates to the separation, use and/or regeneration of various chemicals contaminated or spent in the process and which includes the steps of: (A) contacting the fluid stream at a temperature of between about 105.degree. and 180.degree. C. with a liquid aqueous slurry or solution comprising an effective amount of an iron chelate of an amino acid moiety having at least one --SH group; (B) separating the fluid stream from the particulates formed in step (A) comprising the chelate of the amino acid moiety and fly ash; (C) washing and separating the particulates of step (B) with an aqeous solution having a pH value of between about 5 to 8; (D) subsequently washing and separating the particulates of step (C) with a strongly acidic aqueous solution having a pH value of between about 1 to 3; (E) washing and separating the particulates of step (D) with an basic aqueous solution having a pH value of between about 9 to 12; (F) optionally adding additional amino acid moiety, iron (II) and alkali to the aqueous liquid from step (D) to produce an aqueous solution or slurry similar to that in step (A) having a pH value of between about 4 to 12; and (G) recycling the aqueous slurry of step (F) to the contacting zone of step (A). Steps (D) and (E) can be carried out in the reverse sequence, however the preferred order is (D) and then (E). In a preferred embodiment the present invention provides an improved process for the preparation (regeneration) of cysteine from cystine, which includes reacting an aqueous solution of cystine at a pH of between about 9 to 13 with a reducing agent selected from hydrogen sulfide or alkali metal sulfides, sulfur dioxide, an alkali metal sulfite or mixtures thereof for a time and at a temperature effective to cleave and reduce the cystine to cysteine with subsequent
Mandal, Nabarun; Bhattacharjee, Debojyoti; Rout, Jayanta Kumar; Dasgupta, Anindya; Bhattacharya, Gorachand; Sarkar, Chandan; Gangopadhyaya, Prasanta Kumar
2016-10-01
Wilson's disease is a disease of abnormal copper metabolism in which free serum copper level is raised. The objective of the study was to determine, whether in Wilson disease, l-cysteine/l-cystine influx into RBC was decreased or not and the specific amino acid transporter affected by copper in normal human RBC. For l-cysteine/l-cystine influx, ten untreated cases, ten treated cases and ten age and sex matched healthy controls were recruited. To study the effect of copper on l-cysteine/l-cystine influx in RBC, 15 healthy subjects were selected. RBC GSH and l-cysteine/l-cystine influx were estimated by Beautler's and Yildiz's method respectively. In untreated cases, l-cysteine/l-cystine influx and erythrocyte GSH level were decreased showing that elevated level of free copper in serum or media decreased l-cysteine/l-cystine influx in human RBC. Copper treatment inhibited L amino acid transporter in normal RBC specifically.
Surface-knots in 4-space an introduction
Kamada, Seiichi
2017-01-01
This introductory volume provides the basics of surface-knots and related topics, not only for researchers in these areas but also for graduate students and researchers who are not familiar with the field. Knot theory is one of the most active research fields in modern mathematics. Knots and links are closed curves (one-dimensional manifolds) in Euclidean 3-space, and they are related to braids and 3-manifolds. These notions are generalized into higher dimensions. Surface-knots or surface-links are closed surfaces (two-dimensional manifolds) in Euclidean 4-space, which are related to two-dimensional braids and 4-manifolds. Surface-knot theory treats not only closed surfaces but also surfaces with boundaries in 4-manifolds. For example, knot concordance and knot cobordism, which are also important objects in knot theory, are surfaces in the product space of the 3-sphere and the interval. Included in this book are basics of surface-knots and the related topics of classical knots, the motion picture method, surf...
DEFF Research Database (Denmark)
Halse, Sven
2014-01-01
of taking such a unilateral view of what constituted a Vitalist concept of life. It could lead to a misunderstanding of Vitalist way of thinking, Rasch said, if the focus were only set upon the enthusiastic surplus, the worshipping of youth and health. To Vitalists, life is more than that. It is a totality...... that also encompasses notions of destruction, decay and death. “All life symbols in literature around 1900 are at the same time symbols of death”. (Rasch, W. 1967:24) Through the analyses of three poems, this article aims to show concrete examples of how cyclic Vitalist thinking is embedded in poetry...... of the era. The analyses include a further sub-categorisation to capture the different types of Life Force dealt with in the texts. By way of an introduction, Vitalism is discussed within the context of the scientific and social developments of the 19th Century....
On Chebyshev polynomials and torus knots
Gavrilik, A M
2009-01-01
In this work we demonstrate that the q-numbers and their two-parameter generalization, the q,p-numbers, can be used to obtain some polynomial invariants for torus knots and links. First, we show that the q-numbers, which are closely connected with the Chebyshev polynomials, can also be related with the Alexander polynomials for the class T(s,2) of torus knots, s being an odd integer, and used for finding the corresponding skein relation. Then, we develop this procedure in order to obtain, with the help of q,p-numbers, the generalized two-variable Alexander polynomials, and prove their direct connection with the HOMFLY polynomials and the skein relation of the latter.
Towards effective topological field theory for knots
Mironov, A
2015-01-01
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 arXiv:1504.00371 corresponds to the case m=2, and our generalizations sheds additional light on the structure of those mysterious formulas. Explicit expressions are now combined from Racah matrices of the type $R\\otimes R\\otimes\\bar R\\longrightarrow \\bar R$ and mixing matrices in the sectors $R^{\\otimes 3}\\longrightarrow Q$. 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).
Induction effects of torus knots and unknots
Oberti, Chiara; Ricca, Renzo L.
2017-09-01
Geometric and topological aspects associated with induction effects of field lines in the shape of torus knots/unknots are examined and discussed in detail. Knots are assumed to lie on a mathematical torus of circular cross-section and are parametrized by standard equations. The induced field is computed by direct integration of the Biot-Savart law. Field line patterns of the induced field are obtained and several properties are examined for a large family of knots/unknots up to 51 crossings. The intensity of the induced field at the origin of the reference system (center of the torus) is found to depend linearly on the number of toroidal coils and reaches maximum values near the boundary of the mathematical torus. New analytical estimates and bounds on energy and helicity are established in terms of winding number and minimum crossing number. These results find useful applications in several contexts when the source field is either vorticity, electric current or magnetic field, from vortex dynamics to astrophysics and plasma physics, where highly braided magnetic fields and currents are present.
Modeling the Effects of Knots in Structural Timber
DEFF Research Database (Denmark)
Foley, Christina
was established, which describes variations of radial growth direction and fiber orientation related to knots in timber. The adaptability of the paradigm allows practically any softwood knot and its effect on surrounding wood material to be modeled with an accuracy that is limited only by input data. The knot......The main purpose of the pursued research presented in this thesis is to increase knowledge of the effects of knots in structural timber so that characteristics of weaker timber may be determined and applied to improve current grading techniques. In the process, a three-dimensional fiber paradigm...... are given to Shigo's knot formation theory, and thus predicts two separate patterns of fiber direction within annual growth layers related to live knots. In order to determine the possibility to practically and non destructively predict local material directions in structural timber with the three...
Factorization of differential expansion for antiparallel double-braid knots
Morozov, A
2016-01-01
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,-- but manage to guess the full answer only for contributions of single-floor pyramids. One step still remains to be done.
Cocycle Knot Invariants, Quandle Extensions, and Alexander Matrices
2002-01-01
The theory of quandle (co)homology and cocycle knot invariants is rapidly being developed. We begin with a summary of these recent advances. One such advance is the notion of a dynamical cocycle. We show how dynamical cocycles can be used to color knotted surfaces that are obtained from classical knots by twist-spinning. We also demonstrate relations between cocycle invariants and Alexander matrices.
Zhou, Ping; Wu, Yan-Guang; Wei, De-Li; Li, Qing; Wang, Gang; Zhang, Jie; Luo, Ming-Jiu; Tan, Jing-He
2010-04-01
Our objectives were to study how cysteamine, cystine, and cumulus cells (CCs), as well as oocytes interact to increase oocyte intracellular glutathione (GSH) and thereby to establish an efficient in vitro maturation system for cumulus-denuded oocytes (DOs). Using M16 that contained no thiol as maturation medium, we showed that when supplemented alone, neither cystine nor cysteamine promoted GSH synthesis of mouse DOs, but they did when used together. Although goat CCs required either cysteamine or cystine to promote GSH synthesis, mouse CCs required both. In the presence of cystine, goat CCs produced cysteine but mouse CCs did not. Cysteamine reduced cystine to cysteine in cell-free M16. When TCM-199 that contained 83 microM cystine was used as maturation medium, supplementation with cysteamine alone had no effect, but supplementation with 100 microM cysteamine and 200 microM cystine increased blastulation of DOs matured with CC coculture to a level as high as achieved in cumulus-surrounded oocytes (COCs). Similar numbers of young were produced after two-cell embryos from mouse COCs or CC-cocultured DOs matured with optimal thiol supplementation were transferred to pseudopregnant recipients. It is concluded that 1) mouse CCs can use neither cysteamine nor cystine to promote GSH synthesis, but goat CCs can use either one; 2) goat CCs promote mouse oocyte GSH synthesis by reducing cystine to cysteine, but how they use cysteamine requires further investigation; and 3) mouse DOs can use neither cystine nor cysteamine for GSH synthesis, but they restore developmental capacity completely when matured in the presence of optimum supplementation of cysteamine, cystine, and CCs.
Large N duality, lagrangian cycles, and algebraic knots
Diaconescu, D -E; Vafa, C
2011-01-01
We consider knot invariants in the context of large $N$ transitions of topological strings. In particular we consider aspects of Lagrangian cycles associated to knots in the conifold geometry. We show how these can be explicity constructed in the case of algebraic knots. We use this explicit construction to explain a recent conjecture relating study of stable pairs on algebraic curves with HOMFLY polynomials. Furthermore, for torus knots, using the explicit construction of the Lagrangian cycle, we also give a direct A-model computation and recover the HOMFLY polynomial for this case.
Large N Duality, Lagrangian Cycles, and Algebraic Knots
Diaconescu, D.-E.; Shende, V.; Vafa, C.
2013-05-01
We consider knot invariants in the context of large N transitions of topological strings. In particular we consider aspects of Lagrangian cycles associated to knots in the conifold geometry. We show how these can be explicitly constructed in the case of algebraic knots. We use this explicit construction to explain a recent conjecture relating study of stable pairs on algebraic curves with HOMFLY polynomials. Furthermore, for torus knots, using the explicit construction of the Lagrangian cycle, we also give a direct A-model computation and recover the HOMFLY polynomial for this case.
Classical invariants of Legendrian knots in the 3-dimensional torus
SJ, Paul A. Schweitzer; Souza, Fábio S.
2014-01-01
All knots in $R^3$ possess Seifert surfaces, and so the classical Thurston-Bennequin and rotation (or Maslov) invariants for Legendrian knots in a contact structure on $R^3$ can be defined. The definitions extend easily to null-homologous knots in any $3$-manifold $M$ endowed with a contact structure $\\xi$. We generalize the definition of Seifert surfaces and use them to define these invariants for all Legendrian knots, including those that are not null-homologous, in a contact structure on t...
Mandal, Trinanjana; Ward, Michael D
2013-04-17
The pathogenesis of L-cystine kidney stones involves four critical steps: nucleation, crystal growth, crystal aggregation, and crystal adhesion to cells. Although inhibition of crystal growth by L-cystine "imposters" at L-cystine crystal surfaces has been suggested as a plausible route for the suppression of stones, understanding the factors that govern crystal-crystal aggregation and adhesion of crystals to epithelial cells also is essential for devising strategies to mitigate L-cystine stone formation. Chemical force microscopy performed with atomic force microscope tips decorated with functional groups commonly found in urinary constituents that likely mediate aggregation and attachment (e.g., COOH, NH2, SH, CH3, OH) revealed signatures that reflect differences in the chemical affinity of these groups for the (001) and {100} faces of the naturally occurring hexagonal form of L-cystine single crystals and the {110} faces of the non-native tetragonal form. These signatures can be explained by the different chemical compositions of the crystal faces, and they reveal a remarkable binding specificity of the thiol group for the sulfur-rich {100} and {110} faces of the hexagonal and tetragonal forms, respectively. Collectively, these observations suggest that alterations of the crystal habit and polymorph by crystal growth inhibitors may not affect crystal aggregation or adhesion to cells significantly.
Lee, Michael H; Sahota, Amrik; Ward, Michael D; Goldfarb, David S
2015-05-01
Cystinuria is a genetic disease marked by recurrent kidney stone formation, usually at a young age. It frequently leads to chronic kidney disease. Treatment options for cystinuria have been limited despite comprehensive understanding of its genetic pathophysiology. Currently available therapies suffer from either poor clinical adherence to the regimen or potentially serious adverse effects. Recently, we employed atomic force miscopy (AFM) to identify L-cystine dimethylester (CDME) as an effective molecular imposter of L-cystine, capable of inhibiting crystal growth in vitro. More recently, we demonstrated CDME's efficacy in inhibiting L-cystine crystal growth in vivo utilizing a murine model of cystinuria. The application of AFM to discover inhibitors of crystal growth through structural mimicry suggests a novel approach to preventing and treating crystal diseases.
Nanowire Oriented On-Surface Growth of Chiral Cystine Crystalline Nanosheets.
Zhang, Shenxiang; Zhang, Feng; Qin, Haili; Hu, Liang; Jin, Jian
2015-08-18
Exploration of an effective route to achieve the controlled growth of two-dimensional (2D) molecular crystal is of scientific significance yet greatly underdeveloped due to the complexity of weak intermolecular interactions, thus leading to difficulty of inducing anisotropic 2D growth. We report here a facile nanowire oriented on-surface growth strategy for the fabrication of cystine crystalline nanosheets with finely controlled thickness (1.1, 1.9, 2.9, and 4.8 nm which correspond to one layer, two layers, three layers, and five layers of crystal cystine, respectively) and large areas (>100 μm(2)). The cystine crystalline nanosheets display chirality delivered by chiral cysteine monomers, either l-cysteine or d-cysteine. The chiral nanosheets with structural precision and chemical diversity could serve as a novel 2D platform for constructing advanced hybrid materials.
Meggiato, Luca; Cattaneo, Francesco; Zattoni, Fabio; Dal Moro, Fabrizio; Beltrami, Paolo; Zattoni, Filiberto
2017-02-18
Cystinuria, a rare autosomal recessive disease characterized by a defect in cystine renal reabsorption, can often determine complex cystine renal calculi, leading to important complications such as urinary obstruction, urinary infections, and impaired kidney function. Complex kidney stones can have a difficult management and can be very arduous to treat. We present the case of a 20-year-old Jeowah's witness woman with complex cystine renal stones treated with combined robot-assisted laparoscopic pyelolithotomy and intraoperative renoscopy. The combination of robot-assisted laparoscopic pyelolithotomy and intraoperative renoscopy can be useful to achieve an immediate high stone clearance rate also in complex renal stones. This combined technique could be indicated to minimize intraoperative bleeding. Moreover, it can also be used in pediatric cases or when there is no ureteral compliance. However, this strategy can be performed only in hospital referral centers by expert surgeons.
Optical knots and contact geometry II. From Ranada dyons to transverse and cosmetic knots
Energy Technology Data Exchange (ETDEWEB)
Kholodenko, Arkady L., E-mail: string@clemson.edu
2016-08-15
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].
Optical knots and contact geometry II. From Ranada dyons to transverse and cosmetic knots
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].
Mass spectrometry and potentiometry studies of Pb(II)-, Cd(II)- and Zn(II)-cystine complexes.
Furia, Emilia; Aiello, Donatella; Di Donna, Leonardo; Mazzotti, Fabio; Tagarelli, Antonio; Thangavel, Hariprasad; Napoli, Anna; Sindona, Giovanni
2014-01-21
Cd(II)-, Pb(II)- and Zn(II)-cystine complexes were investigated by potentiometric and different mass spectrometric (MS) methodologies. Laser desorption mass spectrometry has provided both the composition and structure of metal-cystine complexes according to the speciation models proposed on the basis of the potentiometric data. Detection of neutral complexes was achieved by protonation or electrochemical reduction during mass spectrometric experiments. The redox activity of metal-cystine complexes was confirmed by laser desorption and charge transfer matrix assisted laser assisted MS experiments, which allowed us to observe the formation of complexes with a reduction of cystine. The stoichiometry of Cd(II)-, Pb(II)- and Zn(II)-cystine complexes was defined by observing the isotopic pattern of the investigated compound. The results suggest that interaction occurs through the carboxylate group of the ligand.
Synthesis of L-cystine nanotubes by alkalinization of L-cysteine in the presence of gallium nitride
Arizaga, Gregorio Guadalupe Carbajal
2013-12-01
The alkaline oxidation of L-cysteine (L-Cys) was conducted in aqueous media forming the insoluble L-cystine dimer as confirmed by X-ray diffraction. In another experiment, a gallium nitride film was added to the L-Cys solution and the L-cystine crystals presented a preferential growth. The transmission electron microscopy images showed the formation of single- and multi-wall L-cystine nanotubes. The infrared and high resolution electron microscopy data suggested that the growth of the tubes resulted from the successive staking of L-cystine dimers onto the (0 0 1) family of planes, which was a consequence of the ionic assembly between L-cystine over a layer of L-Cys molecules previously grafted to the gallium nitride particles.
DEFF Research Database (Denmark)
Zhang, Jingdong; Chi, Qijin; Nielsen, Jens Ulrik;
2000-01-01
Microscopic structures for molecular monolayers of L-cysteine and L-cystine assembled on Au(111) have been disclosed by employing electrochemistry and in situ scanning tunneling microscopy (STM). HighresolutionSTMimages show that the adlayers of both cyteine and cystine exhibit highly......-ordered networklike clusters with (3x3 6)R30° structure. By combining the surface coverage estimated from voltammetric data, each cluster is demonstrated to include six individual cysteine molecules or three cystine molecules. As a comparison, no cluster structure is observed for the 1-butanethiol adlayer prepared...... and examined under the same conditions as those for cysteine and cystine. This suggests that intermolecular and intramolecular hydrogen bonds among adsorbed cysteine or cystine molecules could be responsible for the origin of the cluster-network structures for the adlayers. Several models are proposed and used...
Knot polynomial identities and quantum group coincidences
Morrison, Scott; Snyder, Noah
2010-01-01
We construct link invariants using the D_2n subfactor planar algebras, and use these to prove new identities relating certain specializations of colored Jones polynomials to specializations of other quantum knot polynomials. These identities can also be explained by coincidences between small modular categories involving the even parts of the D_2n planar algebras. We discuss the origins of these coincidences, explaining the role of SO level-rank duality, Kirby-Melvin symmetry, and properties of small Dynkin diagrams. One of these coincidences involves G_2 and does not appear to be related to level-rank duality.
Gutierrez Millet, V; Praga, M; Miranda, B; Bello, I; Ruilope, L; Diaz Gonzalez, R; Leyva, O; Alcazar, J M; Barrientos, A; Rodicio, J L
1985-03-01
We report a case of cystinuria with staghorn renal lithiasis in a solitary right kidney and chronic renal failure. Right nephropyelolithotomy was performed and although 29 renal calculi were extracted many stones remained in situ. A permanent nephrostomy was left in the kidney. Several months later the urine was infected chronically with a ureolytic Citrobacter freundii bacteria and urinary pH oscillated between 8.0 and 9.2. Spontaneous dissolution of the cystine calculi was observed and many tiny fragments of cystine were expulsed through the nephrostomy, following which renal function improved. Despite the conditions favoring struvite calculi, formation did not occur.
Kinetics and Mechanism of Oxidation of L-Cystine by Hexacyanoferrate(III in Alkaline Medium
Directory of Open Access Journals (Sweden)
Annapurna Nowduri
2009-01-01
Full Text Available Kinetics of oxidation of L-cystine by hexacyanoferrate(III was studied in alkaline medium at 30 °C. The reaction was followed spectrophotometrically at λmax = 420 nm. The reaction was found to be first order dependence each on [HCF(III] and [cystine]. It was found that the rate of the reaction increases with increase in [OH-]. The oxidation product of the reaction was found to be cysteic acid. A plausible mechanism has been proposed to account for the experimental results.
Root-knot nematode resistant rootstocks for grafted watermelon
Rootstock lines of wild watermelon (Citrullus lanatus var. citroides) with resistance to root-knot nematodes (RKN) were developed by our team at the U.S. Vegetable Laboratory. Rootstock lines RKVL 301, RKVL 316, and RKVL 318 (RKVL = Root Knot Vegetable Laboratory) were compared to wild tinda (Praec...
Correspondence Between Bell Bases and Oriented Links in Knot Theory
Institute of Scientific and Technical Information of China (English)
QIAN ShangWu; GU ZhiYu
2002-01-01
From the comparison of correlation tensor in the theory of quantum network, the Alexander relation matrix in the theory of knot crystals and the identical inversion relations under the action of Pauli matrices, we show that there is a one to one correspondence between four Bell bases and four oriented links of the linkage 41 in knot theory.
Detection of Chirality and Mutations of Knots and Links
Pichai, Ramadevi
2011-01-01
In this brief presentation, we would like to present our attempts of detecting chirality and mutations from Chern-Simons gauge theory. The results show that the generalised knot invariants, obtained from Chern-Simons gauge theory, are more powerful than Jones, HOMFLYPT and Kauffman polynomials. However the classification problem of knots and links is still an open challenging problem.
Legendrian and transverse cables of positive torus knots
DEFF Research Database (Denmark)
B. Etnyre, John; la Fountain, Douglas James; Tosun, Bulent
Thurston-Bennequin invariant is arbitrarily far from maximal. We also exhibit Legendrian knots requiring arbitrarily many stabilizations before they become Legendrian isotopic. Similar new phenomena are observed for transverse knots. To achieve these results we define and study "partially thickenable" tori...
Legendrian and transverse cables of positive torus knots
DEFF Research Database (Denmark)
Etnyre, John; LaFountain, Douglas; Tosun, Bülent
2012-01-01
Thurston-Bennequin invariant is arbitrarily far from maximal. We also exhibit Legendrian knots requiring arbitrarily many stabilizations before they become Legendrian isotopic. Similar new phenomena are observed for transverse knots. To achieve these results we define and study "partially thickenable" tori...
Factorization of differential expansion for antiparallel double-braid knots
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.
Studying uniform thickness II: Transversely nonsimple iterated torus knots
DEFF Research Database (Denmark)
LaFountain, Douglas
2011-01-01
We prove that an iterated torus knot type in the standard contact 3-sphere fails the uniform thickness property (UTP) if and only if it is formed from repeated positive cablings, which is precisely when an iterated torus knot supports the standard contact structure. This is the first complete UTP...
Genetic analysis of root-knot nematode resistance in potato
Draaistra, J.
2006-01-01
The development of potato varieties with resistance towards the potato cyst nematode, allowed a dramatic decrease of the use of nematicides. Subsequently the population of the free living nematodes and the root-knot nematodes ( Meloidogyne spp.) has increased. Among the root-knot nematodes, three Me
Photoelectric properties of cystine-modified nano-TiO{sub 2} with visible-light response
Energy Technology Data Exchange (ETDEWEB)
Cheng Xiuwen [Department of Environmental Science and Engineering, Heilongjiang University, Xuefu Road 74, Nangang District, Harbin 150080, Heilongjiang Province (China); State Key Laboratory of Urban Water Resources and Environment, Harbin Institute of Technology, Huanghe Road 73, Nangang District, Harbin 150090 (China); Department of Environmental Science and Engineering, School of Municipal and Environmental Engineering, Harbin Institute of Technology, Huanghe Road 73, Nangang District, Harbin 150090 (China); Yu Xiujuan, E-mail: yuxjuan@hit.edu.cn [Department of Environmental Science and Engineering, Heilongjiang University, Xuefu Road 74, Nangang District, Harbin 150080, Heilongjiang Province (China); Xing Zipeng [Department of Environmental Science and Engineering, Heilongjiang University, Xuefu Road 74, Nangang District, Harbin 150080, Heilongjiang Province (China)
2012-05-15
Highlights: Black-Right-Pointing-Pointer Cystine modified TiO{sub 2} was prepared by the addition of biomolecule cystine. Black-Right-Pointing-Pointer The growth of crystallite sizes was greatly inhibited by modification with cystine. Black-Right-Pointing-Pointer The light absorption was red shifted to visible region by modification with cystine. Black-Right-Pointing-Pointer The photoinduced charge carriers of TiO{sub 2} were improved by modification with cystine. Black-Right-Pointing-Pointer The photoelectrical property of TiO{sub 2} modification with cystine was discussed. - Abstract: Visible light responsible TiO{sub 2} nano-particles (TiO{sub 2} NPs) were prepared through sol-gel method using tetrabutyl titanate and biomolecule cystine as raw materials. The resulting materials were characterized by X-ray diffraction (XRD), ultraviolet-visible diffuse reflectance spectroscopy (UV-vis DRS), surface photovoltage spectroscopy (SPS) and electric field induced surface photovoltage spectroscopy (EFISPS). The XRD results showed that the addition of cystine could effectively retard the phase transformation of TiO{sub 2} from anatase to rutile and the growth of crystallite sizes. DRS results indicated that the light absorption edge of TiO{sub 2} was significantly red-shifted to visible region with the addition of biomolecule cystine. SPS results exhibited that the separation efficiency of the photoinduced charge carriers of TiO{sub 2} were effectively improved. In addition, EFISPS indicated that TiO{sub 2} nano-particles modification with biomolecule cystine were still n-type semiconductor.
Extended knots and the space of states of quantum gravity
Griego, J R
1996-01-01
In the loop representation the quantum constraints of gravity can be solved. This fact allowed significant progress in the understanding of the space of states of the theory. The analysis of the constraints over loop dependent wavefunctions has been traditionally based upon geometric (in contrast to analytic) properties of the loops. The reason for this preferred way is twofold: for one hand the inherent difficulties associated with the analytic loop calculus, and on the other our limited knowledge about the analytic properties of knots invariants. Extended loops provide a way to overcome the difficulties at both levels. For one hand, a systematic method to construct analytic expressions of diffeomorphism invariants (the extended knots) in terms of the Chern-Simons propagators can be developed. Extended knots are simply related to ordinary knots (at least formally). The analytic expressions of knot invariants could be produced then in a generic way. On the other hand, the evaluation of the Hamiltonian over ex...
Relative symplectic caps, 4-genus and fibered knots
Indian Academy of Sciences (India)
Siddhartha Gadgil; Dheeraj Kulkarni
2016-05-01
We prove relative versions of the symplectic capping theorem and sufficiency of Giroux’s criterion for Stein fillability and use these to study the 4-genus of knots. More precisely, suppose we have a symplectic 4-manifold with convex boundary and a symplectic surface in such that is a transverse knot in . In this paper, we prove that there is a closed symplectic 4-manifold with a closed symplectic surface such that (, ) embeds into (, ) symplectically. As a consequence we obtain a relative version of the symplectic Thom conjecture. We also prove a relative version of the sufficiency part of Giroux’s criterion for Stein fillability, namely, we show that a fibered knot whose mondoromy is a product of positive Dehn twists bounds a symplectic surface in a Stein filling. We use this to study 4-genus of fibered knots in $\\mathbb S^3$. Further, we give a criterion for quasipositive fibered knots to be strongly quasipositive.
Knot Solitons in Spinor Bose-Einstein Condensates
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.
Knot polynomials in the first non-symmetric representation
Anokhina, A.; Mironov, A.; Morozov, A.; Morozov, And.
2014-05-01
We describe the explicit form and the hidden structure of the answer for the HOMFLY polynomial for the figure-8 and some other 3-strand knots in representation [21]. This is the first result for non-torus knots beyond (anti)symmetric representations, and its evaluation is far more complicated. We provide a whole variety of different arguments, allowing one to guess the answer for the figure-8 knot, which can be also partly used in more complicated situations. Finally we report the result of exact calculation for figure-8 and some other 3-strand knots based on the previously developed sophisticated technique of multi-strand calculations. We also discuss a formula for the superpolynomial in representation [21] for the figure-8 knot, which heavily relies on the conjectural form of superpolynomial expansion nearby the special polynomial point. Generalizations and details will be presented elsewhere.
Colored knot polynomials. HOMFLY in representation [2,1
Mironov, A; Morozov, An; Sleptsov, A
2015-01-01
This paper starts a systematic description of colored knot polynomials, beginning from the first non-(anti)symmetric representation R=[2,1]. The project involves several steps: (i) parametrization of big families of knots a la arXiv:1506.00339, (ii) evaluating Racah/mixing matrices for various numbers of strands in various representations a la arXiv:1112.2654, (iii) tabulating and collecting the results at www.knotebook.org. In this paper we discuss only representation R=[2,1] and construct all necessary ingredients that allow one to evaluate knot/links represented by three strand closed parallel braids with inserted double-fat fingers. In particular, it is used to evaluate knots from a 7-parametric family: this family contains over 80% of knots with up to 10 intersections, but does not include mutants.
Majcher, Małgorzata A; Jeleń, Henryk H
2007-07-11
Aromas generated in extruded potato snacks without and with addition of 0.25, 0.5, and 1% (w/w) of flavor precursors, cysteine and cystine, were compared and evaluated by descriptive sensory profiling. The results showed that high addition of cysteine (0.5 and 1%) resulted in the formation of undesirable odor and taste described as mercaptanic/sulfur, onion-like, and bitter; on the contrary, addition of cystine even at high concentration gave product with pleasant odor and taste, slightly changed into breadlike notes. GC/O analysis showed cysteine to be a much more reactive flavor precursor than cystine, stimulating formation of 12 compounds with garlic, sulfury, burnt, pungent/beer, cabbage/mold, meatlike, roasted, and popcorn odor notes. Further analysis performed by the AEDA technique identified 2-methyl-3-furanthiol (FD 2048) as a most potent odorant of extruded potato snacks with 1% addition of cysteine. Other identified compounds with high FD were butanal, 3-methyl-2-butenethiol, 2-methylthiazole, methional, 2-acetyl-1-pyrroline, and 3-hydroxy-4,5-dimethyl-2(5H)-furanone. In the case of cystine addition (1%) the highest FD factors were calculated for butanal, 2-acetyl-1-pyrroline, benzenemethanethiol, methional, phenylacetaldehyde, dimethyltrisulfide, 1-octen-3-ol, 1,5-octadien-3-one, and 2-acetylpyrazine.
Human CD4+ T cells require exogenous cystine for glutathione and DNA synthesis
DEFF Research Database (Denmark)
Levring, Trine B; Kongsbak-Wismann, Martin; Rode, Anna Kathrine Obelitz
2015-01-01
Adaptive immune responses require activation and expansion of antigen-specific T cells. Whereas early T cell activation is independent of exogenous cystine (Cys2), T cell proliferation is dependent of Cys2. However, the exact roles of Cys2 in T cell proliferation still need to be determined. The ...
Slavković, Andjelka; Radovanović, Miladin; Sirić, Zlatko; Vlajković, Marina; Stefanović, Vladisav
2002-01-01
The Siemens Lithostar Litotriptor was used to treat 6 children with cystine nephrolithiasis, previously treated by open surgery. Five children had renal calculi (3 multiple caliceal, 2 pelvis) and one had ureteral calculus. Stone size ranged from 0.2-2.5 cm in diameter, and stone burden was from 0.24 to 10.81 cm3 per kidney. From one to 4 ESWL sessions per unit were applied, with a total of 1,800 to 12,000 shock waves. The stone free rate at 3 months was 50%. A complete elimination was obtained with cystine stones in renal pelvis and ureter, however, up to 4 ESWL treatments failed in caliceal stones. Rather location of cystine calculi than previous surgery was associated with ESWL success rate. Two patients with positive urine cultures were successfully treated with appropriate antibiotics before ESWL was attempted. Perirenal hematoma was major complication demonstrated by radionuclide scintigraphy in one patient, and resolved spontaneously by 3 months. In the combined treatment of cystine urolithiasis in children ESWL, as auxillary procedure, was safe and effective in pelvis stone but failed in caliceal stones. Medical dissolution for retained fragments was found effective.
Smart platform for the time since death determination from vitreous humor cystine.
Ansari, Niha; Lodha, Anand; Menon, Shobhana K
2016-12-15
In this work, we report the smart application of AgNPs based sensors for determination of time since death (TSD) via recognition and quantification of vitreous humor (VH) cystine as well as provide the portability for on spot determination of TSD. The lower detection limit was found to be 7.0ng/ml with prominent selectivity. It was found that there is a linear correlation between the VH cystine concentration and TSD as the concentration of cystine increases up to 96h±3.9h. Further for the first time TSD determination is given a smart approach and it proves to have a great utility up to 24h±2.6h. The linear regression equation between TSD (the dependent variable), RGB intensity of cystine concentration till 24h (the independent variable) was found to be TSD=26.69+-0.05*x. The proposed method gives the smart detection, portability, rapidity, sensitivity, selectivity as well as cost effectiveness for determination of time since death.
Urinary felinine excretion in intact male cats is increased by dietary cystine
Hendriks, W.H.; Rutherfurd-Markwick, K.J.; Weidgraaf, K.; Morton, R.H.; Rogers, Q.R.
2008-01-01
Felinine is a branched-chain sulfur amino acid present in the urine of certain Felidae, including domestic cats. The objective of the present study was to determine if additional cystine and/or dietary N would increase felinine and N-acetylfelinine excretion by intact male cats fed a low-protein (LP
Tiwari, Krishnanand; Shebannavar, Sunil; Kattavarapu, Krishna; Pokalwar, Santosh; Mishra, Maheshwari K; Chauhan, Ugam Kumari
2012-08-01
Granulocyte colony-stimulating factor (G-CSF) is a multifunctional cytokine which is widely used for treating neutropenia in humans. Evaluation of alternative to expensive components of redox buffer (reduced and oxidized glutathione) is an important step in reducing the cost of production of human biotherapeutic proteins. In the present study, refolding of recombinant human G-CSF expressed as inclusion bodies (IBs) in E. coli was optimized using cysteine and cystine redox agents. The refolding to correct native form of G-CSF was assessed by reverse phase high performance liquid chromatography (RP-HPLC). The optimized concentrations of cysteine and cystine for correct refolding of G-CSF were found to be 2 mM and 1 mM, respectively. The correctly refolded G-CSF was detected as early as 4 h of incubation in renaturation buffer containing optimized concentrations of cysteine (2 mM) and cystine (1 mM) redox agents. Refolding of G-CSF in optimized redox system increased with increase in shuffling time. Overall, the results suggested the use of cysteine/cystine redox pair could be an alternative to the costlier redox pairs for successful refolding of G-CSF and possibly other human biotherapeutic proteins of importance.
Iglesias, Diana M; El-Kares, Reyhan; Taranta, Anna; Bellomo, Francesco; Emma, Francesco; Besouw, Martine; Levtchenko, Elena; Toelen, Jaan; van den Heuvel, Lambertus; Chu, Leelee; Zhao, Jing; Young, Yoon Kow; Eliopoulos, Nicoletta; Goodyer, Paul
2012-01-01
Cystinosis is a rare disease caused by homozygous mutations of the CTNS gene, encoding a cystine efflux channel in the lysosomal membrane. In Ctns knockout mice, the pathologic intralysosomal accumulation of cystine that drives progressive organ damage can be reversed by infusion of wildtype bone marrow-derived stem cells, but the mechanism involved is unclear since the exogeneous stem cells are rarely integrated into renal tubules. Here we show that human mesenchymal stem cells, from amniotic fluid or bone marrow, reduce pathologic cystine accumulation in co-cultured CTNS mutant fibroblasts or proximal tubular cells from cystinosis patients. This paracrine effect is associated with release into the culture medium of stem cell microvesicles (100-400 nm diameter) containing wildtype cystinosin protein and CTNS mRNA. Isolated stem cell microvesicles reduce target cell cystine accumulation in a dose-dependent, Annexin V-sensitive manner. Microvesicles from stem cells expressing CTNS(Red) transfer tagged CTNS protein to the lysosome/endosome compartment of cystinotic fibroblasts. Our observations suggest that exogenous stem cells may reprogram the biology of mutant tissues by direct microvesicle transfer of membrane-associated wildtype molecules.
Strict cysteamine dose regimen is required to prevent nocturnal cystine accumulation in cystinosis.
Levtchenko, E.N.; Dael, C.M. van; Graaf-Hess, A.C. de; Wilmer, M.J.G.; Heuvel, L.P.W.J. van den; Monnens, L.A.H.; Blom, H.J.
2006-01-01
Cystinosis is an autosomal recessive disorder, caused by mutations in the lysosomal cystine carrier cystinosin, encoded by the CTNS gene. The disease generally manifests with Fanconi syndrome during the first year of life and progresses towards end stage renal disease before the age of 10 years. Cys
Strict cysteamine dose regimen is required to prevent nocturnal cystine accumulation in cystinosis
Levtchenko, EN; van Dael, CM; de Graaf-Hess, AC; Wilmer, MJG; van den Heuvel, LP; Monnens, LA; Blom, HJ
2006-01-01
Cystinosis is an autosomal recessive disorder, caused by mutations in the lysosomal cystine carrier cystinosin, encoded by the CTNS gene. The disease generally manifests with Fanconi syndrome during the first year of life and progresses towards end stage renal disease before the age of 10 years. Cys
Spectroscopic study of cystine adsorption on pyrite surface: From vacuum to solution conditions
Energy Technology Data Exchange (ETDEWEB)
Sanchez-Arenillas, M.; Mateo-Marti, E., E-mail: mateome@cab.inta-csic.es
2015-09-08
Highlights: • Successful adsorption of cystine on pyrite surface under several conditions. • Detailed XPS spectroscopic characterization of cystine adsorption on pyrite surface. • Spectroscopy evidence, oxidation and anoxic conditions adjust molecular adsorption. • Molecular chemistry on pyrite is driven depending on the surrounding conditions. • The cystine/pyrite(100) model is in good agreement with Wächtershäuser’s theory. - Abstract: We characterized the adsorption of cystine molecules on pyrite surface via X-ray photoelectron spectroscopy. Anoxic conditions were simulated under ultra-high-vacuum conditions. In contrast, to simulate oxidation conditions, the molecules were adsorbed on pyrite surface from solution. A novel comparative analysis revealed remarkable differences with respect to molecular adsorption and surface chemistry induced by environmental conditions. Molecular adsorption under anoxic conditions was observed to be more favorable, concentrating a large number of molecules on the surface and two different chemical species. In contrast, the presence of oxygen induced an autocatalytic oxidation process on the pyrite surface, which facilitated water binding on pyrite surface and partially blocked molecular adsorption. Pyrite is a highly reactive surface and contains two crucial types of surface functional groups that drive molecular chemistry on the surface depending on the surrounding conditions. Therefore, the system explored in this study holds interesting implications for supporting catalyzed prebiotic chemistry reactions.
Directory of Open Access Journals (Sweden)
Diana M Iglesias
Full Text Available Cystinosis is a rare disease caused by homozygous mutations of the CTNS gene, encoding a cystine efflux channel in the lysosomal membrane. In Ctns knockout mice, the pathologic intralysosomal accumulation of cystine that drives progressive organ damage can be reversed by infusion of wildtype bone marrow-derived stem cells, but the mechanism involved is unclear since the exogeneous stem cells are rarely integrated into renal tubules. Here we show that human mesenchymal stem cells, from amniotic fluid or bone marrow, reduce pathologic cystine accumulation in co-cultured CTNS mutant fibroblasts or proximal tubular cells from cystinosis patients. This paracrine effect is associated with release into the culture medium of stem cell microvesicles (100-400 nm diameter containing wildtype cystinosin protein and CTNS mRNA. Isolated stem cell microvesicles reduce target cell cystine accumulation in a dose-dependent, Annexin V-sensitive manner. Microvesicles from stem cells expressing CTNS(Red transfer tagged CTNS protein to the lysosome/endosome compartment of cystinotic fibroblasts. Our observations suggest that exogenous stem cells may reprogram the biology of mutant tissues by direct microvesicle transfer of membrane-associated wildtype molecules.
Taranta, Anna; Bellomo, Francesco; Emma, Francesco; Besouw, Martine; Levtchenko, Elena; Toelen, Jaan; van den Heuvel, Lambertus; Chu, LeeLee; Zhao, Jing; Young, Yoon Kow; Eliopoulos, Nicoletta; Goodyer, Paul
2012-01-01
Cystinosis is a rare disease caused by homozygous mutations of the CTNS gene, encoding a cystine efflux channel in the lysosomal membrane. In Ctns knockout mice, the pathologic intralysosomal accumulation of cystine that drives progressive organ damage can be reversed by infusion of wildtype bone marrow-derived stem cells, but the mechanism involved is unclear since the exogeneous stem cells are rarely integrated into renal tubules. Here we show that human mesenchymal stem cells, from amniotic fluid or bone marrow, reduce pathologic cystine accumulation in co-cultured CTNS mutant fibroblasts or proximal tubular cells from cystinosis patients. This paracrine effect is associated with release into the culture medium of stem cell microvesicles (100–400 nm diameter) containing wildtype cystinosin protein and CTNS mRNA. Isolated stem cell microvesicles reduce target cell cystine accumulation in a dose-dependent, Annexin V-sensitive manner. Microvesicles from stem cells expressing CTNSRed transfer tagged CTNS protein to the lysosome/endosome compartment of cystinotic fibroblasts. Our observations suggest that exogenous stem cells may reprogram the biology of mutant tissues by direct microvesicle transfer of membrane-associated wildtype molecules. PMID:22912749
Urinary felinine excretion in intact male cats is increased by dietary cystine
Hendriks, W.H.; Rutherfurd-Markwick, K.J.; Weidgraaf, K.; Morton, R.H.; Rogers, Q.R.
2008-01-01
Felinine is a branched-chain sulfur amino acid present in the urine of certain Felidae, including domestic cats. The objective of the present study was to determine if additional cystine and/or dietary N would increase felinine and N-acetylfelinine excretion by intact male cats fed a low-protein
Directory of Open Access Journals (Sweden)
Clauber Polese
2012-07-01
Full Text Available The objective of this study was to determine the requirement of digestible methionine + cystine of brown-eggs laying hens from 50 to 66 weeks age at the end of the first production cycle. The design was completely randomized, with 150 Brown Shaver hens, which were distributed in five treatments with six replications of five birds each. Birds received a basal diet with 2857 kcal/kg metabolizable energy and 15.97% crude protein, supplemented with 0.132; 0.174, 0.215, 0.256 and 0.298% DL-methionine (98%, in order to provide 0.572, 0.613, 0.653, 0.693 and 0.734% digestible methionine + cystine. The levels of digestible methionine + digestible cystine followed, respectively, the relations of 67, 72, 77, 81 and 86% with lysine fixed at 0.851%. Feed intake, methionine + cystine intake, feed conversion per dozen eggs, egg weigth and mass, percentage of egg components, internal egg quality and weight gain were evaluated. Methionine + cystine levels showed a quadratic effect on feed conversion per dozen eggs and egg weight, a linear effect on feed conversion per kilogram of eggs and percentage of albumen. There was also a positive linear effect on yolk percentage. The methionine + cystine requirement was estimated at 0.572%, corresponding to 682 mg of digestible methionine + cystine/bird/day.
TcyR regulates L-cystine uptake via the TcyABC transporter in Streptococcus mutans.
Kim, Jennifer; Senadheera, Dilani B; Lévesque, Céline M; Cvitkovitch, Dennis G
2012-03-01
Streptococcus mutans, a primary dental pathogen, has a remarkable capacity to scavenge nutrients from the oral biofilm for its survival. Cystine is an amino acid dimer formed by the oxidation of two cysteine residues that is required for optimal growth of S. mutans, which modulates l-cystine uptake via two recently identified transporters designated TcyABC and TcyDEFGH, which have not been fully characterized. Using a nonpolar tcyABC-deficient mutant (SmTcyABC), here, we report that l-cystine uptake is drastically diminished in the mutant, whereas its ability to grow is severely impaired under l-cystine starvation conditions, relative to wild type. A substrate competition assay showed that l-cystine uptake by the TcyABC transporter was strongly inhibited by dl-cystathionine and l-djenkolic acid and moderately inhibited by S-methyl-l-cysteine and l-cysteine. Using gene expression analysis, we observed that the tcyABC operon was upregulated under cystine starvation. TcyABC has been shown to be positively regulated by the LysR-type transcriptional regulator CysR. We identified another LysR-type transcriptional regulator that negatively regulates TcyABC with homology to the Bacillus subtilis YtlI regulator, which we termed TcyR. Our study enhances the understanding of l-cystine uptake in S. mutans, which allows survival and persistence of this pathogen in the oral biofilm.
Solving Infinite Kolam in Knot Theory
Ishimoto, Yukitaka
2007-01-01
In south India, there are traditional patterns of line-drawings encircling dots, called ``Kolam'', among which one-line drawings or the ``infinite Kolam'' provide very interesting questions in mathematics. For example, we address the following simple question: how many patterns of infinite Kolam can we draw for a given grid pattern of dots? The simplest way is to draw possible patterns of Kolam while judging if it is infinite Kolam. Such a search problem seems to be NP complete. However, it is certainly not. In this paper, we focus on diamond-shaped grid patterns of dots, (1-3-5-3-1) and (1-3-5-7-5-3-1) in particular. By using the knot-theory description of the infinite Kolam, we show how to find the solution, which inevitably gives a sketch of the proof for the statement ``infinite Kolam is not NP complete.'' Its further discussion will be given in the final section.
Decay of trefoil and other magnetic knots
Candelaresi, Simon; Brandenburg, Axel
2010-01-01
Two setups with interlocked magnetic flux tubes are used to study the evolution of magnetic energy and helicity on magnetohydrodynamical (MHD) systems like plasmas. In one setup the initial helicity is zero while in the other it is finite. To see if it is the actual linking or merely the helicity content that influences the dynamics of the system we also consider a setup with unlinked field lines as well as a field configuration in the shape of a trefoil knot. For helical systems the decay of magnetic energy is slowed down by the helicity which decays slowly. It turns out that it is the helicity content, rather than the actual linking, that is significant for the dynamics.
Teaching and Learning of Knot Theory in School Mathematics
Kawauchi, Akio
2012-01-01
This book is the result of a joint venture between Professor Akio Kawauchi, Osaka City University, well-known for his research in knot theory, and the Osaka study group of mathematics education, founded by Professor Hirokazu Okamori and now chaired by his successor Professor Tomoko Yanagimoto, Osaka Kyoiku University. The seven chapters address the teaching and learning of knot theory from several perspectives. Readers will find an extremely clear and concise introduction to the fundamentals of knot theory, an overview of curricular developments in Japan, and in particular a series of teaching
Intraoperative wide bore nasogastric tube knotting: A rare incidence.
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.
Motion of charged particles in a knotted electromagnetic field
Energy Technology Data Exchange (ETDEWEB)
Arrayas, M; Trueba, J L, E-mail: joseluis.trueba@urjc.e [Area de Electromagnetismo, Universidad Rey Juan Carlos, Camino del Molino s/n, 28943 Fuenlabrada, Madrid (Spain)
2010-06-11
In this paper we consider the classical relativistic motion of charged particles in a knotted electromagnetic field. After reviewing how to construct electromagnetic knots from maps between the three-sphere and the two-sphere, we introduce a mean quadratic radius of the energy density distribution in order to study some properties of this field. We study the classical relativistic motion of electrons in the electromagnetic field of the Hopf map, and compute their trajectories. It is observed that these electrons initially at rest are strongly accelerated by the electromagnetic force, becoming ultrarelativistic in a period of time that depends on the knot energy and size.
Pinus pinaster Knot: A Source of Polyphenols against Plasmopara viticola.
Gabaston, Julien; Richard, Tristan; Cluzet, Stéphanie; Palos Pinto, Antonio; Dufour, Marie-Cécile; Corio-Costet, Marie-France; Mérillon, Jean-Michel
2017-09-29
Pine knot extract from Pinus pinaster byproducts was characterized by UHPLC-DAD-MS and NMR. Fourteen polyphenols divided into four classes were identified as follows: lignans (nortrachelogenin, pinoresinol, matairesinol, isolariciresinol, secoisolariciresinol), flavonoids (pinocembrin, pinobanksin, dihydrokaempferol, taxifolin), stilbenes (pinosylvin, pinosylvin monomethyl ether, pterostilbene), and phenolic acids (caffeic acid, ferulic acid). The antifungal potential of pine knot extract, as well as the main compounds, was tested in vitro against Plasmopara viticola. The ethanolic extract showed a strong antimildew activity. In addition, pinosylvins and pinocembrin demonstrated significant inhibition of zoospore mobility and mildew development. These findings strongly suggest that pine knot is a potential biomass that could be used as a natural antifungal product.
Topological Structure of Knotted Vortex Lines in Liquid Crystals
Institute of Scientific and Technical Information of China (English)
DUAN Yi-Shi; ZHAO Li; ZHANG Xin-Hui
2007-01-01
In this paper, a novel decomposition expression for the U(1) gauge field in liquid crystals (LCs) is derived.Using this decomposition expression and the φ-mapping topological current theory,.we investigate the topological structure of the vortex lines in LCs in detail. A topological invariant, i.e., the Chern-Simons (CS) action for the knotted vortex lines is presented, and the CS action is shown to be the total sum of all the self-linking and linking numbers of the knot family. Moreover, it is pointed out that the CS action is preserved in the branch processes of the knotted vortex lines.
... or the flu eating certain foods, such as chocolate or cheese, or additives such as caffeine, nitrites— ... people with cyclic vomiting syndrome. Eating, Diet, and Nutrition During the prodrome and vomiting phases of cyclic ...
Superextensions of cyclic semigroups
Directory of Open Access Journals (Sweden)
V. M. Gavrylkiv
2013-06-01
Full Text Available Given a cyclic semigroup $S$ we study right and left zeros,singleton left ideals, the minimal ideal, left cancelable andright cancelable elements of superextensions $lambda(S$ andcharacterize cyclic semigroups whose superextensions arecommutative.
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].
Cyclic Railway Timetable Optimization
L.W.P. Peeters (Leon)
2003-01-01
textabstractCyclic Railway Timetable Optimization describes mathematical models and solution methods for constructing high quality cyclic railway timetables. In a cyclic timetable, a train for a certain destination leaves a certain station at the same time every cycle time, say every half an hour,
Knots, splices and rope-work an illustrated handbook
Verrill, A Hyatt
2006-01-01
This treasury of practical and ornamental knots ranges from easy half-hitches and bow-lines to intricate rope-work projects, such as rope buckles and cask slings. Detailed instructions accompany the 148 drawings.
Linked and knotted chimera filaments in oscillatory systems.
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.
Topological Aspect of Knotted Vortex Filaments in Excitable Media
Institute of Scientific and Technical Information of China (English)
REN Ji-Rong; ZHU Tao; DUAN Yi-Shi
2008-01-01
Scroll waves exist ubiquitously in three-dimensional excitable media.The rotation centre can be regarded as a topological object called the vortex filament.In three-dimensional space,the vortex filaments usually form closed loops,and can be even linked and knotted.We give a rigorous topological description of knotted vortex filaments.By using the Φ-mapping topological current theory,we rewrite the topological current form of the charge density of vortex filaments,and using this topological current we reveal that the Hopf invariant of vortex filaments is just the sum of the linking and self-linking numbers of the knotted vortex filaments.We think that the precise expression of the Hopf invariant may imply a new topological constraint on knotted vortex filaments.
Tilton, Buck
2008-01-01
Untie the mystery of knot-making with this clever and handy guide. This new compendium presents all the knots you need to know, with brightly colored photographs enabling you to easily follow the instructions. In addition, the book includes copious information on using knots in most popular activities. With its clear step-by-step instructions and friendly tone, this is the one volume you can count on to guide you toward quick success in knot-making.
The beauty of knots at the molecular level.
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.
Chern-Simons Invariants of Torus Knots and Links
Stevan, Sébastien
2010-01-01
We compute the vacuum expectation values of torus knot operators in Chern-Simons theory, and we obtain explicit formulae for all classical gauge groups and for arbitrary representations. We reproduce a known formula for the HOMFLY invariants of torus links and we obtain an analogous formula for Kauffman invariants. We also derive a formula for cable knots. We use our results to test a recently proposed conjecture that relates HOMFLY and Kauffman invariants.
SOME APPLICATIONS OF PLANAR GRAPH IN KNOT THEORY
Institute of Scientific and Technical Information of China (English)
Cheng Zhiyun; Gao Hongzhu
2012-01-01
The relationship between a link diagram and its corresponding planar graph is briefly reviewed.A necessary and sufficient condition is given to detect when a planar graph corresponds to a knot.The relationship between planar graph and almost planar Seifert surface is discussed.Using planar graph,we construct an alternating amphicheiral prime knot with crossing number n for any even number n ≥ 4.This gives an affirmative answer to problem 1.66(B) on Kirby's problem list.
Exact computation of the n-loop invariants of knots
Garoufalidis, Stavros; Scott, Shane
2015-01-01
The loop invariants of Dimofte-Garoufalidis is a formal power series with arithmetically interesting coefficients that conjecturally appears in the asymptotics of the Kashaev invariant of a knot to all orders in $1/N$. We develop methods implemented in SnapPy that compute the first 6 coefficients of the formal power series of a knot. We give examples that illustrate our method and its results.
Many-knot spline technique for approximation of data
Institute of Scientific and Technical Information of China (English)
齐东旭; 李华山
1999-01-01
A class of new fundamental functions with compact support called many-knot spline is introduced. The two-scale relation for the fundamental functions is investigated, and the higher order accuracy spline approximation scheme is constructed by using the available degrees of freedom which come from additional knots. The technique has been efficiently applied to the problems such as time-frequency analysis, computer aided geometric design, and digital signal processing.
Shunt insufficiency due to knot formation in the peritoneal catheter.
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.
Knots in the Helix Nebula found in H2
Matsuura, M; McHunu, B M; Tanaka, I; Wright, N J; Smith, M D; Zijlstra, A A; Viti, S; Wesson, R
2009-01-01
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 micron H2 v=1-0 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' fromthe 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 multi-peaks 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 H2 surface brightness in the inner ring: H2 exists only within the knots. Possible mechanisms which...
DEFF Research Database (Denmark)
Aabech, J; Andersen, J T
1993-01-01
Treatment of cystine stones in the urinary tract can be difficult because of a high frequency of recurrence, resistance to Extracorporeal Shock Wave Lithotripsy (ESWL), difficulty in localization and access to peripheral stones during Percutaneous Nephrolithotripsy (PCNL), and the insufficient...... effect of oral chemolysis. We present two cases of urinary cystine calculi treated with a combination of pyelolithotomy, PCNL, ESWL and percutaneous irrigation chemolysis, using N-acetylcysteine and Tromethamine-E....
Bazin, Dominique; Daudon, Michel; André, Gilles; Matzen, Guy; Véron, Emmanuel
2014-01-01
International audience; With an incidence of 1:7000 births, cystinuria, the most frequent cause of stone formation among genetic diseases, represents a major medical problem. Twentyfive cystine stones randomly selected from cystinuric patients were investigated. From a crystallographic point of view, cystine stones are composed of micrometre size crystallites, which are made up of an aggregation of nanocrystals. Through scanning electron microscopy, the morphology and size of the crystallites...
Wendt-Nordahl, Gunnar; Sagi, Sreedhar; Bolenz, Christian; Alken, Peter; Michel, Maurice Stephan; Knoll, Thomas
2008-02-01
Cystinuria is a rare hereditary disease resulting in recurrent stone formation and the need for repeated invasive interventions. So far, two responsible genes have been identified which encode the two transporters, rBAT and b(0,+)AT forming a heterodimer to transport cystine in proximal tubular cells (PTC) and whose defect results in increased excretion of cystine. A human cell line mimicing the phenotype of cystinuria in vitro is yet to be developed. Human kidney (HK)-2 is a PTC line derived from normal HK. After determining the presence of rBAT gene by RT-PCR and Western blot analysis, radioactively labeled cystine (S(35)) was used to evaluate the functional presence of the amino acid transport in HK-2 cells when cultured in vitro. To achieve a cystinuria type I phenotype in HK-2 cells, the rBAT gene was silenced using antisense oligonucleotides complimentary to human rBAT mRNA. The reduced transport activity of cystine was then determined by radiolabeled cystine uptake measurements. RT-PCR and Western blot confirmed the expression of the rBAT gene in HK-2 cells. Considerable transport of the radio labeled cystine was observed in HK-2 cells and was linearly dependent on the incubation time with the amino acid. The cystine transport in rBAT knockdown cells after incubation with antisense oligonucleotides was significantly lower compared to control (0.76 vs. 0.98%; P=0.0008), proving a transient knock-down of the rBAT gene. This study demonstrates the presence of the b(0,+) amino acid transport system in human proximal tubular HK-2 cells when cultured in vitro. Inhibition of this transport system is possible by using antisense technology. A permanent inhibition of the cystine transport, based on our model, would be useful for the development and evaluation gene therapeutic approaches.
Directory of Open Access Journals (Sweden)
Liang He
2016-01-01
Full Text Available Smart polymer nanogel-assisted drug delivery systems have attracted more and more attention in cancer chemotherapy because of their well-defined morphologies and pleiotropic functions in recent years. In this work, an l-cystine-crosslinked reduction-responsive polypeptide nanogel of methoxy poly(ethylene glycol-poly(l-phenylalanine-co-l-cystine (mPEG-P(LP-co-LC was employed as a smart excipient for RM-1 prostate cancer (PCa chemotherapy. Doxorubicin (DOX, as a regular chemotherapy drug, was embedded in the nanogel. The loading nanogel marked as NG/DOX was shown to exhibit glutathione (GSH-induced swelling and GSH-accelerated DOX release. Subsequently, NG/DOX showed efficient cellular uptake and proliferation inhibition. Furthermore, NG/DOX presented enhanced antitumor efficacy and security in an RM-1 PCa-grafted mouse model in vivo, indicating its great potential for clinical treatment.
One-pot synthesis of one-dimensional CdTe-cystine nanocomposite for humidity sensing
Lu, Zhisong; Wang, Jing; Xie, Jiale; Li, Chang Ming
2014-03-01
Quantum dot (QD)-incorporated one-dimensional (1D) nanocomposites offer great application potential. However, a facile one-step synthesis of the nanocomposites and fabrication of their free-standing film for sensing has not been accomplished. Herein a rod-shaped nanocomposite is one-pot synthesized via an L-cysteine-assisted hydrothermal approach, in which synthesis parameters including L-cysteine amount, temperature and reaction duration are tailored to control the composite nanostructures. CdTe nanocrystals are incorporated into the L-cystine matrices to form the nanorods, which tangle each other to network an intact film structure via a simple drying process. The free-standing CdTe-cystine nanorod film is directly utilized as a humidity sensor. This work provides a one-pot synthesis approach to grow 1D CdTe incorporated nanocomposites, demonstrating their great potential in film sensing applications.
Staghorn cystine stone in a 72-year-old recurrent calcium stone former.
Cupisti, Adamasco; Farnesi, Ilaria; Armillotta, Nicola; Francesca, Francesco
2012-07-01
This case deals with the first diagnosis of Type B cystinuria with cystine nephrolithiasis in a 72-year-old male. Cystinuria is an inherited disease that consists of congenital abnormalities of renal and intestinal transport of dibasic amino acids. It often leads to frequent recurrent stone formation. Cystine stones most frequently occur in the 1st through 3rd decades of life with a decreased incidence in old age. This case shows that the first diagnosis of cystinuria may be made even in the 8th decade, without any family history, and in a patient with a history of recurrent calcium stone disease. Therefore, the chance of cystinuria must be always considered, even in older calcium stone formers.
Inhibition of xc⁻ transporter-mediated cystine uptake by sulfasalazine analogs.
Shukla, Krupa; Thomas, Ajit G; Ferraris, Dana V; Hin, Niyada; Sattler, Rita; Alt, Jesse; Rojas, Camilo; Slusher, Barbara S; Tsukamoto, Takashi
2011-10-15
A series of sulfasalazine analogs were synthesized and tested for their ability to block cystine-glutamate antiporter system xc⁻ using L-[(14)C]cystine as a substrate. Replacement of sulfasalazine's diazo group with an alkyne group led to an equally potent inhibitor, 2-hydroxy-5-((4-(N-pyridin-2-ylsulfamoyl)phenyl)ethynyl)benzoic acid 6. Our SAR studies also revealed that the carboxylate group of sulfasalazine is essential for its inhibitory activity while the phenolic hydroxyl group is dispensable. Truncated analogs lacking an N-pyridin-2-ylsulfamoyl moiety were less potent than sulfasalazine, but may serve as more tractable templates because of their low molecular weight by applying a variety of fragment growing approaches. Given that sulfasalazine is rapidly metabolized through cleavage of the diazo bond, these analogs may possess a more desirable pharmacological profile as system xc- blockers, in particular, for in vivo studies.
Directory of Open Access Journals (Sweden)
Saeed Najafi
2016-09-01
Full Text Available Knots appear frequently in semiflexible (biopolymers, including double-stranded DNA, and their presence can affect the polymer’s physical and functional properties. In particular, it is possible and indeed often the case that multiple knots appear on a single chain, with effects which have only come under scrutiny in the last few years. In this manuscript, we study the interaction of two knots on a stretched semiflexible polymer, expanding some recent results on the topic. Specifically, we consider an idealization of a typical optical tweezers experiment and show how the bending rigidity of the chain—And consequently its persistence length—Influences the distribution of the entanglements; possibly more importantly, we observe and report how the relative chirality of the otherwise identical knots substantially modifies their interaction. We analyze the free energy of the chain and extract the effective interactions between embedded knots, rationalizing some of their pertinent features by means of simple effective models. We believe the salient aspect of the knot–knot interactions emerging from our study will be present in a large number of semiflexible polymers under tension, with important consequences for the characterization and manipulation of these systems—Be they artificial or biologica in origin—And for their technological application.
Shape-controlled assembly of luminescent dumbbell-like CdTe cystine nanocomposites
Bao, Haifeng; Cui, Xiaoqiang; Li, Chang Ming; Zang, Jianfeng
2007-11-01
A shape perfect luminescent dumbbell with size up to several microns was prepared by incorporating CdTe quantum dots (QDs) into locally created L-cystine matrices, and the photoluminescence of the shaped dumbbells can be easily tailored by reaction time. The growth mechanism was thoroughly investigated. This work not only gives a potential application in optical devices, but also gives a deep insight on the assembly mechanism of nanomaterials into micron-size objects.
Shape-controlled assembly of luminescent dumbbell-like CdTe-cystine nanocomposites
Energy Technology Data Exchange (ETDEWEB)
Bao Haifeng; Cui Xiaoqiang; Li Changming; Zang Jianfeng [School of Chemical and Biomedical Engineering, Nanyang Technological University, 70 Nanyang Drive 637457 (Singapore); Center for Advanced Bionanosystems, Nanyang Technological University, 70 Nanyang Drive 637457 (Singapore)
2007-11-14
A shape perfect luminescent dumbbell with size up to several microns was prepared by incorporating CdTe quantum dots (QDs) into locally created L-cystine matrices, and the photoluminescence of the shaped dumbbells can be easily tailored by reaction time. The growth mechanism was thoroughly investigated. This work not only gives a potential application in optical devices, but also gives a deep insight on the assembly mechanism of nanomaterials into micron-size objects.
Directory of Open Access Journals (Sweden)
Ekaterina A Ivanova
Full Text Available Nephropathic cystinosis is a lysosomal storage disorder caused by mutations in the CTNS gene encoding cystine transporter cystinosin that results in accumulation of amino acid cystine in the lysosomes throughout the body and especially affects kidneys. Early manifestations of the disease include renal Fanconi syndrome, a generalized proximal tubular dysfunction. Current therapy of cystinosis is based on cystine-lowering drug cysteamine that postpones the disease progression but offers no cure for the Fanconi syndrome. We studied the mechanisms of impaired reabsorption in human proximal tubular epithelial cells (PTEC deficient for cystinosin and investigated the endo-lysosomal compartments of cystinosin-deficient PTEC by means of light and electron microscopy. We demonstrate that cystinosin-deficient cells had abnormal shape and distribution of the endo-lysosomal compartments and impaired endocytosis, with decreased surface expression of multiligand receptors and delayed lysosomal cargo processing. Treatment with cysteamine improved surface expression and lysosomal cargo processing but did not lead to a complete restoration and had no effect on the abnormal morphology of endo-lysosomal compartments. The obtained results improve our understanding of the mechanism of proximal tubular dysfunction in cystinosis and indicate that impaired protein reabsorption can, at least partially, be explained by abnormal trafficking of endosomal vesicles.
Kasperova, Alena; Cahlikova, Romana; Kunert, Jiri; Sebela, Marek; Novak, Zdenek; Raska, Milan
2014-11-01
Cysteine dioxygenase (CDO) is involved in regulation of intracellular cysteine levels by catabolising the cysteine to sulphite and sulphate. In keratinolytic fungi, sulphite is actively excreted to reduce disulphide bridges in keratin before its enzymatic degradation. The pathogenicity role of CDO was confirmed in cysteine-hypersensitive and growth-defective ΔCdo mutant of Arthroderma benhamiae on hair and nails. We analysed the CDO expression regulation in T. mentagrophytes (anamorph of A. benhamiae) mycelia by determining the Cdo mRNA and CDO protein levels and by analysing the proportion of two molecular forms of CDO in response to l-cystine exposure. Cdo mRNA levels in mycelia lysates were detected by reverse-transcription real-time polymerase chain reaction and CDO protein by western blot using mouse CDO-specific hyperimmune serum. The Cdo mRNA level increased gradually 2.5-4.5 h after exposure of the mycelium to l-cystine. The CDO protein, detected as two bands of different mobility, appeared earlier in comparison to mRNA (1 h) and culminated after 24 h. More mobile form prevailed after 4.5 h. The comparison of the dynamics in the Cdo mRNA and CDO protein levels indicates that T. mentagrophytes responds to l-cystine by increased transcription and apparently decreased degradation of the CDO and by changing towards higher mobility molecular form, similar to previous reports describing mammalian analogue.
Cyclic phosphonium ionic liquids
Directory of Open Access Journals (Sweden)
Sharon I. Lall-Ramnarine
2014-01-01
Full Text Available Ionic liquids (ILs incorporating cyclic phosphonium cations are a novel category of materials. We report here on the synthesis and characterization of four new cyclic phosphonium bis(trifluoromethylsulfonylamide ILs with aliphatic and aromatic pendant groups. In addition to the syntheses of these novel materials, we report on a comparison of their properties with their ammonium congeners. These exemplars are slightly less conductive and have slightly smaller self-diffusion coefficients than their cyclic ammonium congeners.
Optical knots and contact geometry II. From Hopf links to transverse and cosmetic knots
Kholodenko, Arkady L
2014-01-01
In 1985 Moffatt conjectured that in steady incompressible Euler-type fluids the streamlines could have knots/links of all types. Using methods of contact geometry Etnyre and Ghrist in 2000 developed the existence-type proof of the Moffatt conjecture. The alternative proof, also of existence-type, was proposed by Enciso and Peralta -Salas in 2012. In all three papers the Beltrami equation was used as point of departure. However, only work by Etnyre and Ghrist takes full advantage of contact-geometric nature of the Beltrami equation. In this work we propose the constructive proof of the Moffatt conjecture based on ideas and methods of contact geometry. We discuss in sufficient detail various physical processes generating such knotted structures. By employing the correspondence between ideal hydrodynamics and electrodynamics discussed in part I, the Moffatt conjecture is proved for Maxwellian electrodynamics. The potential relevance of the obtained results for source-free Yang-Mills and gravity fields is also br...
Resch, Jon M.; Albano, Rebecca; Liu, XiaoQian; Hjelmhaug, Julie; Lobner, Doug; Baker, David A.; Choi, SuJean
2014-01-01
In the central nervous system, cystine import in exchange for glutamate through system xc− is critical for the production of the antioxidant glutathione by astrocytes, as well as the maintenance of extracellular glutamate. Therefore, regulation of system xc− activity affects multiple aspects of cellular physiology and may contribute to disease states. Pituitary adenylate cyclase-activating polypeptide (PACAP) is a neuronally-derived peptide that has already been demonstrated to modulate multiple aspects of glutamate signaling suggesting PACAP may also target activity of cystine-glutamate exchange via system xc−. In the current study, 24-hour treatment of primary cortical cultures containing neurons and glia with PACAP concentration-dependently increased system xc− function as measured by radiolabeled cystine uptake. Furthermore, the increase in cystine uptake was completely abolished by the system xc− inhibitor, (S)-4-carboxyphenylglycine (CPG), attributing increases in cystine uptake specifically to system xc− activity. Time course and quantitative PCR results indicate that PACAP signaling may increase cystine-glutamate exchange by increasing expression of xCT, the catalytic subunit of system xc−. Furthermore, the potentiation of system xc− activity by PACAP occurs via a PKA-dependent pathway that is not mediated by the PAC1R, but rather the shared vasoactive intestinal polypeptide receptor VPAC1R. Finally, assessment of neuronal, astrocytic, and microglial-enriched cultures demonstrated that only astrocyte-enriched cultures exhibit enhanced cystine uptake following both PACAP and VIP treatment. These data introduce a novel mechanism by which both PACAP and VIP regulate system xc− activity. PMID:25066643
Lim, Julie C; Lam, Leo; Li, Bo; Donaldson, Paul J
2013-11-01
In this study we have sought to identify whether cystine uptake mechanisms previously identified in the rat lens are also found in the human lens. Using a combination of reverse transcriptase PCR, Western blotting and immunohistochemistry, we show that the light chain subunit of the cystine/glutamate exchanger (XC-), xCT, and members of the glutamate transporter family (XAG) which include the Excitatory Amino Acid Transporter 4 (EAAT4) and the Alanine Serine Cysteine Transporter 2 (ASCT2) are all present at the transcript and protein level in human lenses. We demonstrate that in young lenses xCT, EAAT4 and ASCT2 are expressed in all regions indicating that a potential cystine uptake pathway similar to that found in the rat might also exist in human lenses. However, with increasing age, the immunolabeling for all transporters decreases, with no xCT labelling detected in the centre of old donor lenses. Our results show that XC- and EAAT4/ASCT2 may work together to mediate cystine uptake in the lens core of young human lenses. This suggests that the lens contains uptake mechanisms that are capable of accumulating cystine/cysteine in the lens centre where cysteine can be used as an antioxidant or cystine utilised as a source for protein-S-S-cysteine (PSSC) formation to buffer against oxidative stress. With increasing age, transporters in the lens core undergo age dependent post translational modifications. However, despite processing of these transporters with age, our results indicate that this cystine uptake pathway could account for the increased PSSC levels previously observed in the nucleus of older human lenses.
Colored HOMFLY polynomials of knots presented as double fat diagrams
Mironov, A; Morozov, An; Ramadevi, P; Singh, Vivek Kumar
2015-01-01
Many knots and links in S^3 can be drawn as gluing of three manifolds with one or more four-punctured S^2 boundaries. We call these knot diagrams as double fat graphs whose invariants involve only the knowledge of the fusion and the braiding matrices of four-strand braids. Incorporating the properties of four-point conformal blocks in WZNW models, we conjecture colored HOMFLY polynomials for these double fat graphs where the color can be rectangular or non-rectangular representation. With the recent work of Gu-Jockers, the fusion matrices for the non-rectangular [21] representation, the first which involves multiplicity is known. We verify our conjecture by comparing with the [21] colored HOMFLY of many knots, obtained as closure of three braids. The conjectured form is computationally very effective leading to writing [21]-colored HOMFLY polynomials for many pretzel type knots and non-pretzel type knots. In particular, we find class of pretzel mutants which are distinguished and another class of mutants whic...
Knot Invariants from Topological Recursion on Augmentation Varieties
Gu, Jie; Klemm, Albrecht; Soroush, Masoud
2014-01-01
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 annulu...
Decay of helical and non-helical magnetic knots
Candelaresi, Simon
2011-01-01
We present calculations of the relaxation of magnetic field structures that have the shape of particular knots and links. A set of helical magnetic flux configurations is considered, which we call $n$-foil knots of which the trefoil knot is the most primitive member. We also consider two non-helical knots, namely the Borromean rings as well as a single interlocked flux rope that also serves as the logo of the Inter-University Centre for Astronomy and Astrophysics in Pune, India. The field decay characteristics of both configurations is investigated and compared with previous calculations of helical and non-helical triple ring configurations. For the $n$-foil knots the decay is described by power laws that range form $t^{-2/3}$ to $t^{-1/3}$, which can be as slow as the $t^{-1/3}$ behavior for helical triple-ring structures that was seen in earlier work. The two non-helical configurations decay like $t^{-1}$, which is somewhat slower than the previously obtained $t^{-3/2}$ behavior in the decay of interlocked ...
Stewart, Greg; Kuntzleman, Thomas S.; Amend, John R.; Collins, Michael J.
2009-01-01
Cyclic voltammetry is an important component of the undergraduate chemical curriculum. Unfortunately, undergraduate students rarely have the opportunity to conduct experiments in cyclic voltammetry owing to the high cost of potentiostats, which are required to control these experiments. By using MicroLab data acquisition interfaces in conjunction…
Stewart, Greg; Kuntzleman, Thomas S.; Amend, John R.; Collins, Michael J.
2009-01-01
Cyclic voltammetry is an important component of the undergraduate chemical curriculum. Unfortunately, undergraduate students rarely have the opportunity to conduct experiments in cyclic voltammetry owing to the high cost of potentiostats, which are required to control these experiments. By using MicroLab data acquisition interfaces in conjunction…
Millett, Kenneth C; Rawdon, Eric J; Stasiak, Andrzej; Physical and Numerical Models in Knot theory: including Applications to the Life Sciences; Conference on Knots, Random Walks and Biomolecules
2005-01-01
The physical properties of knotted and linked configurations in space have long been of interest to mathematicians. More recently, these properties have become significant to biologists, physicists, and engineers among others. Their depth of importance and breadth of application are now widely appreciated and valuable progress continues to be made each year. This volume presents several contributions from researchers using computers to study problems that would otherwise be intractable. While computations have long been used to analyze problems, formulate conjectures, and search for special structures in knot theory, increased computational power has made them a staple in many facets of the field. The volume also includes contributions concentrating on models researchers use to understand knotting, linking, and entanglement in physical and biological systems. Topics include properties of knot invariants, knot tabulation, studies of hyperbolic structures, knot energies, the exploration of spaces of knots, knot...
Ijjas, Anna
2016-01-01
Cyclic models of the universe have the advantage of avoiding initial conditions problems related to postulating any sort of beginning in time. To date, the only known viable examples of cyclic models have been ekpyrotic. In this paper, we show that the recently proposed anamorphic scenario can also be made cyclic. The key to the cyclic completion is a classically stable, non-singular bounce. Remarkably, even though the bounce construction was originally developed to connect a period of contraction with a period of expansion both described by Einstein gravity, we show here that it can naturally be modified to connect an ordinary contracting phase described by Einstein gravity with a phase of anamorphic smoothing. The paper will present the basic principles and steps in constructing cyclic anamorphic models.
Differential expansion and rectangular HOMFLY for the figure eight knot
Directory of Open Access Journals (Sweden)
A. Morozov
2016-10-01
Full Text Available 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.
Untangling knots via reaction-diffusion dynamics of vortex strings
Maucher, Fabian
2016-01-01
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.
Differential expansion and rectangular HOMFLY for the figure eight knot
Morozov, A
2016-01-01
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 $3_1$ and for the figure eight knot $4_1$. 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 fulfil this program for all rectangular representation $R=[r^s]$, 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.
Differential expansion and rectangular HOMFLY for the figure eight knot
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.
Emission knots and polarization swings of swinging jets
Lyutikov, Maxim
2016-01-01
Knots (emission features in jets of active galactic nuclei) often show non-ballistic dynamics and variable emission/polarization properties. We model these features as emission pattern propagating in a jet that carries helical magnetic field and is launched along a changing direction. The model can reproduce a wide range of phenomena observed in the motion of knots: non-ballistic motion (both smooth and occasional sudden change of direction, and/or oscillatory behavior), variable brightness, confinement of knots' motion within an overlaying envelope. The model also reproduces smooth large polarization angle swings, and at the same time allows for the seemingly random behavior of synchrotron fluxes, polarization fraction and occasional $\\pi/2$ polarization jumps.
Untangling Knots Via Reaction-Diffusion Dynamics of Vortex Strings
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.
Classification of knotted tori in 2-metastable dimension
Cencelj, Matija
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 → Sm. We study the specific case of knotted tori, that is, the embeddings Sp × Sq → Sm. The classification of knotted tori up to isotopy in the metastable dimension range m > p + 3 2 q + 2, p 6 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: Theorem. Assume that p+ 4 3 q +2 < mp+ 3 2 q +2 and m > 2p+q +2. Then the set of isotopy classes of smooth embeddings Sp × Sq → Sm is infinite if and only if either q + 1 or p + q + 1 is divisible by 4. © 2012 RAS(DoM) and LMS.
Erickson, Stephen B; Vrtiska, Terri J; Canzanello, Vincent J; Lieske, John C
2011-06-01
Cystine kidney stones frequently recur because inadequate prevention exists. We recruited documented recurrent cystine kidney stone formers (6 men, 4 women, 44 ± 17 years) into a 2-phased study to assess safety and effectiveness of Cystone®, a herbal treatment used to prevent and facilitate passage of cystine kidney stones. The first phase was a randomized double-blinded 12 weeks crossover study assessing the effect of Cystone® versus placebo (2 tablets BID) on urinary chemistries. The second phase was an open label 1 year study of Cystone® to determine if renal stone burden decreased, as assessed by quantitative and subjective assessment of CT. There was no statistically significant change of urinary composition from baseline short (6 weeks) or long (52 weeks) term on Cystone®, including volume (2525, 2611, 2730 ml), pH (6.7, 6.7, 7.05), and cystine excretion (2770, 2889, 4025 μmol). Pre and post-CT was available in nine patients. Although seven kidneys lost stones spontaneously or surgically, overall stone burden increased in seven kidneys, was unchanged in nine, and fell in only two. Quantitative scoring increased in both the left and right kidneys (1602-1667 and 301-2064 volumetric units, respectively). Therefore, this study does not suggest that Cystone® has a favorable effect on urinary chemistries that could decrease cystine stone formation, nor does it appear to prevent stone growth or promote stone passage over a 1-year period.
Knots and physics: Old wine in new bottles
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.
Excitation of knotted vortex lines in matter waves
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.
Root - knot nematodes on summer vegetables in North Tunisia
Directory of Open Access Journals (Sweden)
Moens, M.
1985-01-01
Full Text Available The influence of different factors on the root-knot nematode infestation and on the yield of tomato have been examined : date of planting, cultivar choice, rotation scheme and soil disinfestation. It was found that the earliest planting date gave the highest yield but also the most severe root galling on susceptible tomato cultivars. A cropping sequence where wheat is alternated with tomatoes was not sufficient for reducing root-knot nematode population to a level permitting the cropping of a susceptible tomato cultivar. Long rotations with non host crops should be used. Soil treatment with certain nematicides significantly reduced the root galling and improved the yield.
Kothari, Hema; Nayak, Ramesh C; Rao, L Vijaya Mohan; Pendurthi, Usha R
2010-05-27
Tissue factor (TF) on cell surfaces resides mostly in a cryptic state. It is not entirely clear how cryptic TF differs from procoagulantly active TF and how deencryption occurs. Here, we critically evaluated the importance of cystine 186-cystine 209 (Cys186-Cys209) bond formation for TF procoagulant activity and its de-encryption. Chinese hamster ovary cells transfected with TF(C186S), TF(C209S), or TF(C186S/C209S) expressed little procoagulant activity at the cell surface. TF monoclonal antibody and activated factor VII (FVIIa) binding studies showed that little TF protein was present at the cell surface in cells expressing mutant TF. Similar data were obtained in human umbilical vein endothelial cells (HUVECs) transduced to express TF(C186S), TF(C209S), or TF(C186S/C209S). Analysis of TF activity in HUVECs expressing similar levels of wild-type TF and TF(C186S/C209S) showed that TF mutant in the presence of saturating concentrations of FVIIa exhibited similar coagulant activity as that of wild-type TF. More importantly, treatment of HUVECs expressing TF(C186S/C209S) with HgCl(2) or ionomycin increased the cell-surface TF activity to the same extent as that of the wild-type TF. Our data provide clear evidence that TF lacking the Cys186-Cys209 bond is coagulantly active once it is complexed with FVIIa, and TF de-encryption does not require Cys186-Cys209 disulfide bond formation.
Successful Treatment of Stent Knot in the Proximal Ureter Using Ureteroscopy and Holmium Laser
Directory of Open Access Journals (Sweden)
Masters M. Richards
2011-01-01
Full Text Available Knotted ureteral stent is rare yet tedious complication that might represent a treatment challenge to the endourologist. Only twelve cases of knotted stent have been reported. Different management options have been reported, including simple traction, ureteroscopy, percutaneous removal, and open surgery. In this paper, we present the successful untying of the knot using ureteroscopy with holmium laser.
The Mental Manipulation of 2-D Representations of Knots as Deformable Structures.
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…
Dissection of mitogenic and neurodegenerative actions of cystine and glutamate in malignant gliomas.
Savaskan, N E; Seufert, S; Hauke, J; Tränkle, C; Eyüpoglu, I Y; Hahnen, E
2011-01-06
Malignant glioma represents one of the most aggressive and lethal human neoplasias. A hallmark of gliomas is their rapid proliferation and destruction of vital brain tissue, a process in which excessive glutamate release by glioma cells takes center stage. Pharmacologic antagonism with glutamate signaling through ionotropic glutamate receptors attenuates glioma progression in vivo, indicating that glutamate release by glioma cells is a prerequisite for rapid glioma growth. Glutamate has been suggested to promote glioma cell proliferation in an autocrine or paracrine manner, in particular by activation of the (RS)-α-amino-3-hydroxy-5-methylisoxazole-4-propionic acid hydrate (AMPA) subtype of glutamate receptors. Here, we dissect the effects of glutamate secretion on glioma progression. Glioma cells release glutamate through the amino-acid antiporter system X(c)(-), a process that is mechanistically linked with cystine incorporation. We show that disrupting glutamate secretion by interfering with the system X(c)(-) activity attenuates glioma cell proliferation solely cystine dependently, whereas glutamate itself does not augment glioma cell growth in vitro. Neither AMPA receptor agonism nor antagonism affects glioma growth in vitro. On a molecular level, AMPA insensitivity is concordant with a pronounced transcriptional downregulation of AMPA receptor subunits or overexpression of the fully edited GluR2 subunit, both of which block receptor activity. Strikingly, AMPA receptor inhibition in tumor-implanted brain slices resulted in markedly reduced tumor progression associated with alleviated neuronal cell death, suggesting that the ability of glutamate to promote glioma progression strictly requires the tumor microenvironment. Concerning a potential pharmacotherapy, targeting system X(c)(-) activity disrupts two major pathophysiological properties of glioma cells, that is, the induction of excitotoxic neuronal cell death and incorporation of cystine required for
Src binds cortactin through an SH2 domain cystine-mediated linkage.
Evans, Jason V; Ammer, Amanda G; Jett, John E; Bolcato, Chris A; Breaux, Jason C; Martin, Karen H; Culp, Mark V; Gannett, Peter M; Weed, Scott A
2012-12-15
Tyrosine-kinase-based signal transduction mediated by modular protein domains is critical for cellular function. The Src homology (SH)2 domain is an important conductor of intracellular signaling that binds to phosphorylated tyrosines on acceptor proteins, producing molecular complexes responsible for signal relay. Cortactin is a cytoskeletal protein and tyrosine kinase substrate that regulates actin-based motility through interactions with SH2-domain-containing proteins. The Src kinase SH2 domain mediates cortactin binding and tyrosine phosphorylation, but how Src interacts with cortactin is unknown. Here we demonstrate that Src binds cortactin through cystine bonding between Src C185 in the SH2 domain within the phosphotyrosine binding pocket and cortactin C112/246 in the cortactin repeats domain, independent of tyrosine phosphorylation. Interaction studies show that the presence of reducing agents ablates Src-cortactin binding, eliminates cortactin phosphorylation by Src, and prevents Src SH2 domain binding to cortactin. Tandem MS/MS sequencing demonstrates cystine bond formation between Src C185 and cortactin C112/246. Mutational studies indicate that an intact cystine binding interface is required for Src-mediated cortactin phosphorylation, cell migration, and pre-invadopodia formation. Our results identify a novel phosphotyrosine-independent binding mode between the Src SH2 domain and cortactin. Besides Src, one quarter of all SH2 domains contain cysteines at or near the analogous Src C185 position. This provides a potential alternative mechanism to tyrosine phosphorylation for cysteine-containing SH2 domains to bind cognate ligands that may be widespread in propagating signals regulating diverse cellular functions.
Bridges, Richard J; Natale, Nicholas R; Patel, Sarjubhai A
2012-01-01
System x(c)(-) is an amino acid antiporter that typically mediates the exchange of extracellular l-cystine and intracellular L-glutamate across the cellular plasma membrane. Studied in a variety of cell types, the import of L-cystine through this transporter is critical to glutathione production and oxidative protection. The exchange-mediated export of L-glutamate takes on added significance within the CNS, as it represents a non-vesicular route of release through which this excitatory neurotransmitter can participate in either neuronal signalling or excitotoxic pathology. When both the import of L-cystine and the export of L-glutamate are taken into consideration, system x(c)(-) has now been linked to a wide range of CNS functions, including oxidative protection, the operation of the blood-brain barrier, neurotransmitter release, synaptic organization, viral pathology, drug addiction, chemosensitivity and chemoresistance, and brain tumour growth. The ability to selectively manipulate system x(c)(-), delineate its function, probe its structure and evaluate it as a therapeutic target is closely linked to understanding its pharmacology and the subsequent development of selective inhibitors and substrates. Towards that goal, this review will examine the current status of our understanding of system x(c)(-) pharmacology and the structure-activity relationships that have guided the development of an initial pharmacophore model, including the presence of lipophilic domains adjacent to the substrate binding site. A special emphasis is placed on the roles of system x(c)(-) within the CNS, as it is these actions that are among the most exciting as potential long-range therapeutic targets.
Wang, Y; Waghorn, G C; Barry, T N; Shelton, I D
1994-12-01
Fresh Lotus corniculatus containing 27 g extractable condensed tannin (CT)/kg dry matter (DM) and 8 g bound CT/kg DM was fed at hourly intervals to sheep held in metabolism cages to study the effects of CT on nutrient digestion and on metabolism of methionine, cystine and inorganic sulphate in plasma. Polyethylene glycol (PEG) was continuously infused into the rumen of half the sheep to remove the effects of CT. Principal measurements in the two groups were plasma irreversible loss (IRL) rate and interconversions of methionine, cystine and inorganic sulphate using 35S labelling. CT in Lotus corniculatus had no effects on the apparent digestion of cellulose and minerals, slightly depressed DM, organic matter and hemicellulose digestion and markedly reduced the apparent digestion of N (P Lotus corniculatus reduced rumen protein degradation and markedly increased utilization of plasma cystine for body synthetic reactions.
Choi, Ae Ran; Kim, Min-Sik; Kang, Sung Gyun; Lee, Hyun Sook
2016-01-01
A variety of microbes grow by respiration with dimethyl sulfoxide (DMSO) as an electron acceptor, and several distinct DMSO respiratory systems, consisting of electron carriers and a terminal DMSO reductase, have been characterized. The heterotrophic growth of a hyperthermophilic archaeon Thermococcus onnurineus NA1 was enhanced by the addition of DMSO, but the archaeon was not capable of reducing DMSO to DMS directly using a DMSO reductase. Instead, the archaeon reduced DMSO via a cysteine-cystine redox shuttle through a mechanism whereby cystine is microbially reduced to cysteine, which is then reoxidized by DMSO reduction. A thioredoxin reductase-protein disulfide oxidoreductase redox couple was identified to have intracellular cystine-reducing activity, permitting recycle of cysteine. This study presents the first example of DMSO reduction via an electron shuttle. Several Thermococcales species also exhibited enhanced growth coupled with DMSO reduction, probably by disposing of excess reducing power rather than conserving energy.
Real Topological Cyclic Homology
DEFF Research Database (Denmark)
Høgenhaven, Amalie
The main topics of this thesis are real topological Hochschild homology and real topological cyclic homology. If a ring or a ring spectrum is equipped with an anti-involution, then it induces additional structure on the topological Hochschild homology spectrum. The group O(2) acts on the spectrum......, where O(2) is the semi-direct product of T, the multiplicative group of complex number of modulus 1, by the group G=Gal(C/R). We refer to this O(2)-spectrum as the real topological Hochschild homology. This generalization leads to a G-equivariant version of topological cyclic homology, which we call...... real topological cyclic homology. The first part of the thesis computes the G-equivariant homotopy type of the real topological cyclic homology of spherical group rings at a prime p with anti-involution induced by taking inverses in the group. The second part of the thesis investigates the derived G...
Spontaneous knot; a rare cause of ventriculoperitoneal shunt blockage.
LENUS (Irish Health Repository)
Mohammed, Wail
2012-02-01
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.
Integrated management of root-knot nematode (Meloidogyne ...
African Journals Online (AJOL)
(p<0.05) the nematode egg hatching as well as juvenile motility over the untreated control. Higher ... the pot house experiment. .... and placed to a drop of glycerine on a clean glass slide with ... knot nematode for subsequent experiments in the.
Knot energy in unstretching ergodic magnetic flux tubes
de Andrade, Garcia
2009-01-01
Recently Titov et al [ApJ \\textbf{693},(2009) and ApJ (2007)] have made use of a covariant model to investigate magnetic reconnection of astrophysical plasmas. Earlier R Ricca [Phys Rev A (1991)] has used another covariant formalism, to investigated vortex filaments and solitons. This formalism, called Ricci rotation coefficients (RRC), is applied here, to the Chui and Moffatt [PRSA (1995)] knotted magnetic flux tube (MFT) Riemann metric in the case of vanishing stretch. It is shown that, the vanishing of some components of the (RRC) leads to unstretching knotted tubes. Computing of magnetic knot energy in terms of the RCC, shows that, uniform, unstretching and constant cross-section tubes leads to a marginal dynamo action over magnetic surfaces. Recent investigation on the role of stretching in plasma dynamo action showed that in diffusive media [Phys Plasma \\textbf{14} (2008)], unstretching unknotted tubes would not support fast dynamo action. This result was generalized here to much more general knotted MF...
Spontaneous knot; a rare cause of ventriculoperitoneal shunt blockage.
LENUS (Irish Health Repository)
Mohammed, Wail
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.
The unique cysteine knot regulates the pleotropic hormone leptin.
Directory of Open Access Journals (Sweden)
Ellinor Haglund
Full Text Available Leptin plays a key role in regulating energy intake/expenditure, metabolism and hypertension. It folds into a four-helix bundle that binds to the extracellular receptor to initiate signaling. Our work on leptin revealed a hidden complexity in the formation of a previously un-described, cysteine-knotted topology in leptin. We hypothesized that this unique topology could offer new mechanisms in regulating the protein activity. A combination of in silico simulation and in vitro experiments was used to probe the role of the knotted topology introduced by the disulphide-bridge on leptin folding and function. Our results surprisingly show that the free energy landscape is conserved between knotted and unknotted protein, however the additional complexity added by the knot formation is structurally important. Native state analyses led to the discovery that the disulphide-bond plays an important role in receptor binding and thus mediate biological activity by local motions on distal receptor-binding sites, far removed from the disulphide-bridge. Thus, the disulphide-bridge appears to function as a point of tension that allows dissipation of stress at a distance in leptin.
True Umbilical Cord Knot Leading to Fetal Demise
African Journals Online (AJOL)
She had onset of labor at a GA of 40 weeks and 5 days following cervical ripening ... the baby. We have reported a case of true umbilical cord knot in Nnewi, South‑East Nigeria. .... Besides, other possible reasons for the fetal demise could not.
Polynomial Invariants of Torus Knots and (p,q)-Calculus
Pavlyuk, Anatoliy M.
2016-01-01
We introduce the deformed fermionic numbers, corresponding to the skein relations, the main characteristics of knots and links. These fermionic numbers allow one to restore the skein relations. For the Alexander (Jones) skein relation we introduce corresponding Alexander (Jones) fermionic q-numbers, and for the HOMFLY skein relation - the HOMFLY deformed (p,q)-numbers with one fermionic parameter.
Factorization of colored knot polynomials at roots of unity
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.
Factorization of colored knot polynomials at roots of unity
Directory of Open Access Journals (Sweden)
Ya. Kononov
2015-07-01
Full Text Available 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⋅Hm 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=e2πi/|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.
Ham, Ji-Young; Lee, Joongul
2016-11-01
We calculate the Chern-Simons invariants of the hyperbolic orbifolds of the knot with Conway's notation C(2n, 3) using the Schläfli formula for the generalized Chern-Simons function on the family of C(2n, 3) cone-manifold structures. We present the concrete and explicit formula of them. We apply the general instructions of Hilden, Lozano, and Montesinos-Amilibia and extend the Ham and Lee's methods. As an application, we calculate the Chern-Simons invariants of cyclic coverings of the hyperbolic C(2n, 3) orbifolds.
Institute of Scientific and Technical Information of China (English)
Wen Chao Guan; Xiang Ying Tang; Li Zhen Huang; Hong Xu
2007-01-01
A novel water-soluble cystine C60 derivative was synthesized in the presence of the catalyst, tetrabutylammonium hydroxide (TBAH). The product was characterized by FT-IR, UV, 1H NMR, 13C NMR, MS and elemental analysis. Furthermore, the that cystine C60 derivative showed an excellent efficiency in eliminating superoxygen anion radical and hydroxyl radical. The 50%inhibition concentration (IC50) for superoxygen anion radical and hydroxyl radical were 0.167 and 0.008 mg/mL, respectively.
Cup products in Hopf cyclic cohomology via cyclic modules I
Rangipour, Bahram
2007-01-01
This is the first one in a series of two papers on the continuation of our study in cup products in Hopf cyclic cohomology. In this note we construct cyclic cocycles of algebras out of Hopf cyclic cocycles of algebras and coalgebras. In the next paper we consider producing Hopf cyclic cocycle from "equivariant" Hopf cyclic cocycles. Our approach in both situations is based on (co)cyclic modules and bi(co)cyclic modules together with Eilenberg-Zilber theorem which is different from the old definition of cup products defined via traces and cotraces on DG algebras and coalgebras.
Roland, Christopher D.; Li, Hong; Abboud, Khalil A.; Wagener, Kenneth B.; Veige, Adam S.
2016-08-01
Cyclic polymers have dramatically different physical properties compared with those of their equivalent linear counterparts. However, the exploration of cyclic polymers is limited because of the inherent challenges associated with their synthesis. Conjugated linear polyacetylenes are important materials for electrical conductivity, paramagnetic susceptibility, optical nonlinearity, photoconductivity, gas permeability, liquid crystallinity and chain helicity. However, their cyclic analogues are unknown, and therefore the ability to examine how a cyclic topology influences their properties is currently not possible. We have solved this challenge and now report a tungsten catalyst supported by a tetraanionic pincer ligand that can rapidly polymerize alkynes to form conjugated macrocycles in high yield. The catalyst works by tethering the ends of the polymer to the metal centre to overcome the inherent entropic penalty of cyclization. Gel-permeation chromatography, dynamic and static light scattering, viscometry and chemical tests are all consistent with theoretical predictions and provide unambiguous confirmation of a cyclic topology. Access to a wide variety of new cyclic polymers is now possible by simply choosing the appropriate alkyne monomer.
Constructing a polynomial whose nodal set is the three-twist knot 52
Dennis, Mark R.; Bode, Benjamin
2017-06-01
We describe a procedure that creates an explicit complex-valued polynomial function of three-dimensional space, whose nodal lines are the three-twist knot 52. The construction generalizes a similar approach for lemniscate knots: a braid representation is engineered from finite Fourier series and then considered as the nodal set of a certain complex polynomial which depends on an additional parameter. For sufficiently small values of this parameter, the nodal lines form the three-twist knot. Further mathematical properties of this map are explored, including the relationship of the phase critical points with the Morse-Novikov number, which is nonzero as this knot is not fibred. We also find analogous functions for other simple knots and links. The particular function we find, and the general procedure, should be useful for designing knotted fields of particular knot types in various physical systems.
Unusual specific heat of almost dry L-cysteine and L-cystine amino acids.
Ishikawa, M S; Lima, T A; Ferreira, F F; Martinho, H S
2015-03-01
A detailed quantitative analysis of the specific heat in the 0.5- to 200-K temperature range for almost dry L-cysteine and its dimer, L-cystine, amino acids is presented. We report the occurrence of a sharp first-order transition at ∼76 K for L-cysteine associated with the thiol group ordering which was successfully modeled with the two-dimensional Ising model. We demonstrated that quantum rotors, two-level systems (TLS), Einstein oscillators, and acoustic phonons (the Debye model) are essential ingredients to correctly describe the overall experimental data. Our analysis pointed out the absence of the TLS contribution to the low temperature specific heat of L-cysteine. This result was similar to that found in other noncrystalline amorphous materials, e.g., amorphous silicon, low density amorphous water, and ultrastable glasses. L-cystine presented an unusual nonlinear acoustic dispersion relation ω(q)=vq0.95 and a Maxwell-Boltzmann-type distribution of tunneling barriers. The presence of Einstein oscillators with ΘE∼70 K was common in both systems and adequately modeled the boson peak contributions.
The structures of complexes of Chromium(III with cystine and ethylglycine
Directory of Open Access Journals (Sweden)
Lina A. Chernushenko
2014-03-01
Full Text Available It has been investigated the electronic spectra of complex compounds of chromium(III with amino acids as bidentate coordinated in compound (I and as monodentate coordinated in compound (II in solution. Three-ethyl glycinate and three-cystinate have the octahedral structure. Two bands of transition were observed in the visible part of the spectrum 4Т1g¬4A2g and 4Т2g¬4A2g, one band of transition was observed in UV- spectrum, 4Т1g(Р¬4A2g. It was submitted the results of calculations of crystal field parameters: Dq = 1790 cm-1, В = 560.57 cm-1 and b = 0.54 for compound (I, Dq = 1786 cm-1, В = 504.53sm-1 and b = 0.49 for compound (II. The computer three-dimensional models of structure of such chromium(III complexes as three-cystinate chromium (III and three-chromium glycinate were created. Quantum-chemical modeling programs Chemcraft and WinGAMESS were used. Angles and bond lengths were calculated.
Dietary cystine level affects metabolic rate and glycaemic control in adult mice.
Elshorbagy, Amany K; Church, Chris; Valdivia-Garcia, Maria; Smith, A David; Refsum, Helga; Cox, Roger
2012-04-01
Plasma total cysteine (tCys) is strongly and independently associated with obesity in large human cohorts, but whether the association is causal is unknown. Dietary cyst(e)ine increases weight gain in some rodent models. We investigated the body composition, metabolic rate and metabolic phenotype of mature C3H/HeH mice assigned to low-cystine (LC) or high-cystine (HC) diets for 12 weeks. Compared to LC mice, HC mice gained more weight (P=.004 for 12-week weight gain %), with increased fat mass and lean mass, and lowered O₂ consumption and CO₂ production by calorimetry. The HC mice had 30% increase in intestinal fat/body weight % (P=.003) and ∼twofold elevated hepatic triglycerides (P=.046), with increased expression of hepatic lipogenic factors, peroxisome proliferator-activated receptor-γ and sterol regulatory element binding protein-1. Gene expression of both basal and catecholamine-stimulated lipolytic enzymes, adipose triglyceride lipase and hormone-sensitive lipase was inhibited in HC mice adipose tissue. The HC mice also had elevated fasting glucose (7.0 vs. 4.5 mmol/L, Pcystine intake promotes adiposity and an adverse metabolic phenotype in mice, indicating that the positive association of plasma tCys with obesity in humans may be causal.
Dixon, Scott J; Patel, Darpan N; Welsch, Matthew; Skouta, Rachid; Lee, Eric D; Hayano, Miki; Thomas, Ajit G; Gleason, Caroline E; Tatonetti, Nicholas P; Slusher, Barbara S; Stockwell, Brent R
2014-05-20
Exchange of extracellular cystine for intracellular glutamate by the antiporter system xc (-) is implicated in numerous pathologies. Pharmacological agents that inhibit system xc (-) activity with high potency have long been sought, but have remained elusive. In this study, we report that the small molecule erastin is a potent, selective inhibitor of system xc (-). RNA sequencing revealed that inhibition of cystine-glutamate exchange leads to activation of an ER stress response and upregulation of CHAC1, providing a pharmacodynamic marker for system xc (-) inhibition. We also found that the clinically approved anti-cancer drug sorafenib, but not other kinase inhibitors, inhibits system xc (-) function and can trigger ER stress and ferroptosis. In an analysis of hospital records and adverse event reports, we found that patients treated with sorafenib exhibited unique metabolic and phenotypic alterations compared to patients treated with other kinase-inhibiting drugs. Finally, using a genetic approach, we identified new genes dramatically upregulated in cells resistant to ferroptosis.DOI: http://dx.doi.org/10.7554/eLife.02523.001.
Cystine-modified biomass for Cd(II) and Pb(II) biosorption
Energy Technology Data Exchange (ETDEWEB)
Yu Junxia [College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072 (China); Tong Mi [Key Laboratory of Analytical Chemistry of the State Ethnic Affairs Commission, College of Chemistry and Materials Science, South-Central University for Nationalities, Wuhan 430074 (China); Sun Xiaomei [Key Laboratory of Analytical Chemistry of the State Ethnic Affairs Commission, College of Chemistry and Materials Science, South-Central University for Nationalities, Wuhan 430074 (China); Li Buhai [College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072 (China) and Key Laboratory of Analytical Chemistry of the State Ethnic Affairs Commission, College of Chemistry and Materials Science, South-Central University for Nationalities, Wuhan 430074 (China)]. E-mail: libuhai@163.com
2007-05-08
The surface of dried biomass of baker's yeast was modified by crosslinking cystine with glutaraldehyde. X-ray photoelectron spectroscopy and microscope were used to characterize the modified biomass. The adsorption capacity of the modified biomass for Cd{sup 2+} and Pb{sup 2+} showed an increase compared with the pristine biomass due to the presence of cystine on the biomass surface. Experimental data showed that the adsorption of the two metal ions increased with time until equilibrium was achieved. The adsorption capacities for Cd{sup 2+} and Pb{sup 2+} were 11.63 and 45.87 mg g{sup -1}, respectively, which were determined from the Langmuir isotherm. The loaded biosorbent was regenerated using HCl solution and could be used repeatedly at six times with little loss of uptake capacity. FTIR spectroscopy revealed that carboxyl, amide, and hydroxyl groups on the biomass surface were involved in the adsorption of Cd{sup 2+} and Pb{sup 2+}.
Unusual specific heat of almost dry L-cysteine and L-cystine amino acids
Ishikawa, M. S.; Lima, T. A.; Ferreira, F. F.; Martinho, H. S.
2015-03-01
A detailed quantitative analysis of the specific heat in the 0.5- to 200-K temperature range for almost dry L-cysteine and its dimer, L-cystine, amino acids is presented. We report the occurrence of a sharp first-order transition at ˜76 K for L-cysteine associated with the thiol group ordering which was successfully modeled with the two-dimensional Ising model. We demonstrated that quantum rotors, two-level systems (TLS), Einstein oscillators, and acoustic phonons (the Debye model) are essential ingredients to correctly describe the overall experimental data. Our analysis pointed out the absence of the TLS contribution to the low temperature specific heat of L-cysteine. This result was similar to that found in other noncrystalline amorphous materials, e.g., amorphous silicon, low density amorphous water, and ultrastable glasses. L-cystine presented an unusual nonlinear acoustic dispersion relation ω (q ) =v q0.95 and a Maxwell-Boltzmann-type distribution of tunneling barriers. The presence of Einstein oscillators with ΘE˜70 K was common in both systems and adequately modeled the boson peak contributions.
Directory of Open Access Journals (Sweden)
Bannai Shiro
2007-09-01
Full Text Available Abstract Background Cystine/glutamate transporter, system xc-, contributes to the maintenance of intracellular glutathione levels and the redox balance in the extracellular space. The main component of the transporter, xCT, is known to be strongly induced by various stimuli like oxidative stress in mammalian cultured cells. We examined the expression of xCT mRNA in vivo in the experimental endotoxemia. Methods Northern blot analysis and in situ hybridization were used to investigate the expression of xCT mRNA in the tissues of the mice exposed to bacterial lipopolysaccharide (LPS. Results Northern blot analysis revealed that xCT mRNA was constitutively expressed in the brain, thymus, and spleen, and that the expression of xCT mRNA was strongly up-regulated in thymus and spleen by the administration of a sublethal dose of LPS. In addition to brain, thymus, and spleen, xCT mRNA was detected also in the bronchiolar epithelium of the lung by the administration of the lethal dose of LPS. Conclusion xCT is induced in some specific tissues by the administration of LPS. The results suggest that cystine/glutamate transporter plays an important role under the inflammatory conditions.
Gurbuz, Nilgun; Park, Margaret A; Dent, Paul; Abdel Mageed, Asim B; Sikka, Suresh C; Baykal, Asli
2015-01-01
Protein kinase C-δ (PKC-δ) and PKC-ε are reported to be effective in cancer prevention via S-thiolation-mediated mechanisms. This may be through stimulation of the pro-apoptotic, tumor-suppressive isozyme PKC-δ and/or inactivation of the growth stimulatory, oncogenic isozyme PKC-ε. We investigated oxidative regulatory responses of PKC-δ and PKC-ε to cystine dimethyl ester (CDME), a metabolic precursor of cystine, which, by inducing release of cellular cystine stimulates apoptosis in different prostate cancer cells, PC3 and LNCaP, compared to normal RWPE1 cells. Treatment of CDME in doses of 0.5mM and 5mM significantly induces apoptosis due to regulation of concentration-dependent PKC-δ stimulation and PKC-ε reduction in these prostate cancer cells. This apoptotic regulation was confirmed by immunoblot analyses and specific PKC enzyme assays in immunoprecipitated samples. Additionally, inhibition of PKC-δ by small interfering RNA (siRNA) proved that CDME-induced cell death was dependent on PKC-δ activity in prostate cancer cells. These data demonstrated that CDME induces apoptosis by cysteinylation of both PKC-δ and PKC-ε in tumorigenic prostate epithelial cells compared to control nontumorigenic cells. Cellular cystine may play a critical role in treatment and/or prevention of prostate cancer by regulating PKC activity.
A method using reversed phase high performance liquid chromtography/electrospray ionization-mass spectrometry (RP-LC/ESI-MS) has been developed to confirm the dientity of dansylated derivatives of cysteine (C) and glutathione (GSH), and their respective dimers, cystine (CSSC) and...
How should patients with cystine stone disease be evaluated and treated in the twenty-first century?
Andreassen, Kim Hovgaard; Pedersen, Katja Venborg; Osther, Susanne Sloth; Jung, Helene Ulrik; Lildal, Søren Kissow; Osther, Palle Joern Sloth
2016-02-01
Cystinuria continues to be one of the most challenging stone diseases. During the latest decades our knowledge of the molecular basis of cystinuria has expanded. Today 160 different mutations in the SLC3A1 gene and 116 in the SLC7A9 gene are listed. The full implications of type A, B or AB status are not yet fully understood but may have implications for prognosis, management and treatment. Despite better understanding of the molecular basis of cystinuria the principles of recurrence prevention have remained essentially the same through decades. No curative treatment of cystinuria exists, and patients will have a life long risk of stone formation, repeated surgery, impaired renal function and quality of life. Therapy to reduce stone formation is directed towards lowering urine cystine concentration and increasing cystine solubility. Different molecules that could play a role in promoting nucleation and have a modulating effect on cystine solubility may represent new targets for cystinuria research. Investigation of newer thiol-containing drugs with fewer adverse effects is also warranted. Determining cystine capacity may be an effective tool to monitor the individual patient's response. Compliance in cystinuric patients concerning both dietary and pharmacological intervention is poor. Frequent clinical follow-up visits in dedicated centres seem to improve compliance. Cystinuric patients should be managed in dedicated centres offering the complete range of minimal invasive treatment modalities, enabling a personalized treatment approach in order to reduce risk and morbidity of multiple procedures.
DEFF Research Database (Denmark)
Lund-Thomsen, E.; Nielsen, S. O.
1972-01-01
Single crystals of cystine dihydrochloride were irradiated at room temperature with monochromatic uv radiation. The optical bandwidth was about 20 Å for each wavelength used. Essentially two ESR centers were observed, the relative yield being approximately 1. One center is identified as the RS...
Generalized Wideband Cyclic MUSIC
Directory of Open Access Journals (Sweden)
Zhang-Meng Liu
2009-01-01
Full Text Available The method of Spectral Correlation-Signal Subspace Fitting (SC-SSF fails to separate wideband cyclostationary signals with coherent second-order cyclic statistics (SOCS. Averaged Cyclic MUSIC (ACM method made up for the drawback to some degree via temporally averaging the cyclic cross-correlation of the array output. This paper interprets ACM from another perspective and proposes a new DOA estimation method by generalizing ACM for wideband cyclostationary signals. The proposed method successfully makes up for the aforementioned drawback of SC-SSF and obtains a more satisfying performance than ACM. It is also demonstrated that ACM is a simplified form of the proposed method when only a single spectral frequency is exploited, and the integration of the frequencies within the signal bandwidth helps the new method to outperform ACM.
The cyclic reduction algorithm
Bini, Dario; Meini, Beatrice
2009-05-01
Cyclic reduction is an algorithm invented by G.H. Golub and R. W. Hockney in the mid 1960s for solving linear systems related to the finite differences discretization of the Poisson equation over a rectangle. Among the algorithms of Gene Golub, it is one of the most versatile and powerful ever created. Recently, it has been applied to solve different problems from different applicative areas. In this paper we survey the main features of cyclic reduction, relate it to properties of analytic functions, recall its extension to solving more general finite and infinite linear systems, and different kinds of nonlinear matrix equations, including algebraic Riccati equations, with applications to Markov chains, queueing models and transport theory. Some new results concerning the convergence properties of cyclic reduction and its applicability are proved under very weak assumptions. New formulae for overcoming breakdown are provided.
Direct observation of DNA knots using a solid-state nanopore
Plesa, Calin; Verschueren, Daniel; Pud, Sergii; van der Torre, Jaco; Ruitenberg, Justus W.; Witteveen, Menno J.; Jonsson, Magnus P.; Grosberg, Alexander Y.; Rabin, Yitzhak; Dekker, Cees
2016-12-01
Long DNA molecules can self-entangle into knots. Experimental techniques for observing such DNA knots (primarily gel electrophoresis) are limited to bulk methods and circular molecules below 10 kilobase pairs in length. Here, we show that solid-state nanopores can be used to directly observe individual knots in both linear and circular single DNA molecules of arbitrary length. The DNA knots are observed as short spikes in the nanopore current traces of the traversing DNA molecules and their detection is dependent on a sufficiently high measurement resolution, which can be achieved using high-concentration LiCl buffers. We study the percentage of molecules with knots for DNA molecules of up to 166 kilobase pairs in length and find that the knotting occurrence rises with the length of the DNA molecule, consistent with a constant knotting probability per unit length. Our experimental data compare favourably with previous simulation-based predictions for long polymers. From the translocation time of the knot through the nanopore, we estimate that the majority of the DNA knots are tight, with remarkably small sizes below 100 nm. In the case of linear molecules, we also observe that knots are able to slide out on application of high driving forces (voltage).
Rosier, Bob T; Lazova, Milena D
2016-01-01
The chemotaxis system enables motile bacteria to search for an optimum level of environmental factors. Salmonella typhimurium senses the amino acid cysteine as an attractant and its oxidized dimeric form, cystine, as a repellent. We investigated the dose-response dependence of changes in chemotactic signaling activity upon exposure to cysteine and cystine of S. typhimurium LT2 using in vivo fluorescence resonance energy transfer (FRET) measurements. The dose-response curve of the attractant response to cysteine had a sigmoidal shape, typical for receptor-ligand interactions. However, in a knockout strain of the chemoreceptor genes tsr and tar, we detected a repellent response to cysteine solutions, scaling linearly with the logarithm of the cysteine concentration. Interestingly, the magnitude of the repellent response to cystine also showed linear dependence to the logarithm of the cystine concentration. This linear dependence was observed over more than four orders of magnitude, where detection started at nanomolar concentrations. Notably, low concentrations of another oxidized compound, benzoquinone, triggered similar responses. In contrast to S. typhimurium 14028, where no response to cystine was observed in a knockout strain of chemoreceptor genes mcpB and mcpC, here we showed that McpB/McpC-independent responses to cystine existed in the strain S. typhimurium LT2 even at nanomolar concentrations. Additionally, knocking out mcpB and mcpC did not affect the linear dose-response dependence, whereas enhanced responses were only observed to solutions that where not pH neutral (>100 μM cystine) in the case of McpC overexpression. We discuss that the linear dependence of the response on the logarithm of cystine concentrations could be a result of a McpB/C-independent redox-sensing pathway that exists in S. typhimurium LT2. We supported this hypothesis with experiments with defined cysteine/cystine mixed solutions, where a transition from repellent to attractant
Kelvin Waves and Dynamic Knots on Perturbative Helical Vortex Lines
Kou, Su-Peng
2016-01-01
Vortex lines are one-dimensional extended objects in three-dimensional superfluids. Vortex lines have many interesting properties, including Kelvin waves, exotic statistics, and possible entanglement. In this paper, an emergent "quantum world" is explored by projecting helical vortex lines. A one-dimensional quantum Fermionic model is developed to effectively describe the local fluctuations of helical vortex lines. The elementary excitations are knots with half winding-number that obey emergent quantum mechanics. The Biot-Savart equation, and its Kelvin wave solutions on helical vortex lines become Schrodinger equation, and the wave functions of probability waves for finding knots, respectively. This work shows an alternative approach to simulating quantum many-body physics based on classical systems.
BPS counting for knots and combinatorics on words
Kucharski, Piotr; Sułkowski, Piotr
2016-11-01
We discuss relations between quantum BPS invariants defined in terms of a product decomposition of certain series, and difference equations (quantum A-polynomials) that annihilate such series. We construct combinatorial models whose structure is encoded in the form of such difference equations, and whose generating functions (Hilbert-Poincaré series) are solutions to those equations and reproduce generating series that encode BPS invariants. Furthermore, BPS invariants in question are expressed in terms of Lyndon words in an appropriate language, thereby relating counting of BPS states to the branch of mathematics referred to as combinatorics on words. We illustrate these results in the framework of colored extremal knot polynomials: among others we determine dual quantum extremal A-polynomials for various knots, present associated combinatorial models, find corresponding BPS invariants (extremal Labastida-Mariño-Ooguri-Vafa invariants) and discuss their integrality.
Mutation on Knots and Whitney's 2-Isomorphism Theorem
Institute of Scientific and Technical Information of China (English)
Zhi Yun CHENG; Hong Zhu GAO
2013-01-01
Whitney's 2-switching theorem states that any two embeddings of a 2-connected planar graph in S2 can be connected via a sequence of simple operations,named 2-switching.In this paper,we obtain two operations on planar graphs from the view point of knot theory,which we will term "twisting" and "2-switching" respectively.With the twisting operation,we give a pure geometrical proof of Whitney's 2-switching theorem.As an application,we obtain some relationships between two knots which correspond to the same signed planar graph.Besides,we also give a necessary and sufficient condition to test whether a pair of reduced alternating diagrams are mutants of each other by their signed planar graphs.
SU(2)/SL(2) knot invariants and KS monodromies
Galakhov, D; Morozov, A
2015-01-01
We review the Reshetikhin-Turaev approach to construction of non-compact knot invariants involving R-matrices associated with infinite-dimensional representations, primarily those made from Faddeev's 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 manipulation with integration contours. We discuss possibilities to extract more explicit and handy expressions which 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, difference equations for colored Jones polynomials should be the same, just in non-compact case the equations are homogeneous, while they have a non-trivial right-hand side for ordinary Jones polynomials.
The Faddeev knots as stable solitons:Existence theorems
Institute of Scientific and Technical Information of China (English)
LIN; Fanghua; YANG; Yisong
2004-01-01
The problem of existence of knot-like solitons as the energy-minimizing configurations in the Faddeev model, topologically characterized by an Hopf invariant, Q, is considered. It is proved that, in the full space situation, there exists an infinite set S of integers so that for any m ∈ S, the Faddeev energy, E, has a minimizer among the class Q = m; in the bounded domain situation, the same existence theorem holds when S is the set of all integers. One of the important technical results is that E and Q satisfy the sublinear inequality E ≤ C|Q|3/4, where C ＞0 is a universal constant, which explains why knotted (clustered soliton) configurations are preferred over widely separated unknotted (multisoliton) configurations when |Q| is sufficiently large.
Towards U(N|M) knot invariant from ABJM theory
Eynard, Bertrand
2014-01-01
We study U(N|M) character expectation value with the supermatrix Chern-Simons theory, known as the ABJM matrix model, with emphasis on its connection to the knot invariant. This average just gives the half BPS circular Wilson loop expectation value in ABJM theory, which shall correspond to the unknot invariant. We derive the determinantal formula, which gives U(N|M) character expectation values in terms of U(1|1) averages for a particular type of character representations. This means that the U(1|1) character expectation value is a building block for all the U(N|M) averages, and in particular, by an appropriate limit, for the U(N) invariants. In addition to the original model, we introduce another supermatrix model obtained through the symplectic transform, which is motivated by the torus knot Chern-Simons matrix model. We obtain the Rosso-Jones-type formula and the spectral curve for this case.
Design and performance of the APPLE-Knot undulator
Energy Technology Data Exchange (ETDEWEB)
Ji, Fuhao [Department of Physics, State Key Laboratory of Surface Physics, and Laboratory of Advanced Materials, Fudan University, 2005 Songhu Road, Shanghai 200438, People’s Republic of (China); Chang, Rui [State Key Laboratory of Functional Materials for Informatics, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, 865 Changning Road, Shanghai 200050, People’s Republic of (China); Zhou, Qiaogen; Zhang, Wei [Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, 239 Zhangheng Road, Shanghai 201204, People’s Republic of (China); Ye, Mao [State Key Laboratory of Functional Materials for Informatics, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, 865 Changning Road, Shanghai 200050, People’s Republic of (China); Sasaki, Shigemi [Hiroshima Synchrotron Radiation Center, Hiroshima University, 2-313 Kagamiyama, Hiroshima 739-0046 (Japan); Qiao, Shan, E-mail: qiaoshan@mail.sim.ac.cn [State Key Laboratory of Functional Materials for Informatics, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, 865 Changning Road, Shanghai 200050, People’s Republic of (China); School of Physical Science and Technology, ShanghaiTech University, 319 Yueyang Road, Shanghai 200031, People’s Republic of (China)
2015-06-09
The design and performance of the Apple-Knot undulator which can generate photons with arbitrary polarization and low on-axis heat load are presented. Along with the development of accelerator technology, synchrotron emittance has continuously decreased. This results in increased brightness, but also causes a heavy heat load on beamline optics. Recently, optical surfaces with 0.1 nm micro-roughness and 0.05 µrad slope error (r.m.s.) have become commercially available and surface distortions due to heat load have become a key factor in determining beamline performance, and heat load has become a serious problem at modern synchrotron radiation facilities. Here, APPLE-Knot undulators which can generate photons with arbitrary polarization, with low on-axis heat load, are reported.
Toward U(N|M) knot invariant from ABJM theory
Eynard, Bertrand; Kimura, Taro
2017-02-01
We study U(N|M) character expectation value with the supermatrix Chern-Simons theory, known as the ABJM matrix model, with emphasis on its connection to the knot invariant. This average just gives the half-BPS circular Wilson loop expectation value in ABJM theory, which shall correspond to the unknot invariant. We derive the determinantal formula, which gives U(N|M) character expectation values in terms of U(1|1) averages for a particular type of character representations. This means that the U(1|1) character expectation value is a building block for the U(N|M) averages and also, by an appropriate limit, for the U(N) invariants. In addition to the original model, we introduce another supermatrix model obtained through the symplectic transform, which is motivated by the torus knot Chern-Simons matrix model. We obtain the Rosso-Jones-type formula and the spectral curve for this case.
BPS counting for knots and combinatorics on words
Kucharski, Piotr
2016-01-01
We discuss relations between quantum BPS invariants defined in terms of a product decomposition of certain series, and difference equations (quantum A-polynomials) that annihilate such series. We construct combinatorial models whose structure is encoded in the form of such difference equations, and whose generating functions (Hilbert-Poincar\\'e series) are solutions to those equations and reproduce generating series that encode BPS invariants. Furthermore, BPS invariants in question are expressed in terms of Lyndon words in an appropriate language, thereby relating counting of BPS states to the branch of mathematics referred to as combinatorics on words. We illustrate these results in the framework of colored extremal knot polynomials: among others we determine dual quantum extremal A-polynomials for various knots, present associated combinatorial models, find corresponding BPS invariants (extremal Labastida-Mari\\~no-Ooguri-Vafa invariants) and discuss their integrality.
The Preon Sector of the SLq(2) (Knot) Model
Finkelstein, Robert J
2013-01-01
We describe a Lagrangian defining the preon sector of the knot model. The preons are the elements of the fundamental representation of SLq(2). They exactly agree with the preons conjectured by Harari and Shupe. The coupling constants and masses required by this Lagrangian are in principle experimentally measurable. There is an alternative formulation of the kinematics permitting possible additional isotopic partners of the quarks.
The Knot Spectrum of Confined Random Equilateral Polygons
Directory of Open Access Journals (Sweden)
Diao Y.
2014-01-01
Full Text Available It is well known that genomic materials (long DNA chains of living organisms are often packed compactly under extreme confining conditions using macromolecular self-assembly processes but the general DNA packing mechanism remains an unsolved problem. It has been proposed that the topology of the packed DNA may be used to study the DNA packing mechanism. For example, in the case of (mutant bacteriophage P4, DNA molecules packed inside the bacteriophage head are considered to be circular since the two sticky ends of the DNA are close to each other. The DNAs extracted from the capsid without separating the two ends can thus preserve the topology of the (circular DNAs. It turns out that the circular DNAs extracted from bacteriophage P4 are non-trivially knotted with very high probability and with a bias toward chiral knots. In order to study this problem using a systematic approach based on mathematical modeling, one needs to introduce a DNA packing model under extreme volume confinement condition and test whether such a model can produce the kind of knot spectrum observed in the experiments. In this paper we introduce and study a model of equilateral random polygons con_ned in a sphere. This model is not meant to generate polygons that model DNA packed in a virus head directly. Instead, the average topological characteristics of this model may serve as benchmark data for totally randomly packed circular DNAs. The difference between the biologically observed topological characteristics and our benchmark data might reveal the bias of DNA packed in the viral capsids and possibly lead to a better understanding of the DNA packing mechanism, at least for the bacteriophage DNA. The purpose of this paper is to provide information about the knot spectrum of equilateral random polygons under such a spherical confinement with length and confinement ratios in a range comparable to circular DNAs packed inside bacteriophage heads.
Zeros of Jones polynomials for families of knots and links
Chang, S.-C.; Shrock, R.
2001-12-01
We calculate Jones polynomials VL( t) for several families of alternating knots and links by computing the Tutte polynomials T( G, x, y) for the associated graphs G and then obtaining VL( t) as a special case of the Tutte polynomial. For each of these families we determine the zeros of the Jones polynomial, including the accumulation set in the limit of infinitely many crossings. A discussion is also given of the calculation of Jones polynomials for non-alternating links.
Colored knot amplitudes and Hall-Littlewood polynomials
Shakirov, Sh
2013-01-01
The amplitudes of refined Chern-Simons (CS) theory, colored by antisymmetric (or symmetric) representations, conjecturally generate the Lambda^r- (or S^r-) colored triply graded homology of (n,m) torus knots. This paper is devoted to the generalization of Rosso-Jones formula to refined amplitudes, that involves non-trivial Gamma-factors -- expansion coefficients in the Macdonald basis. We derive from refined CS theory a linear recursion w.r.t. transformations (n,m) -> (n, n+m) and (n,m) -> (m,-n) that fully determines these factors. Applying this recursion to (n,nk+1) torus knots colored by antisymmetric representations [1^r] we prove that their amplitudes are rectangular [n^r] Hall-Littlewood polynomials under k units of framing (a.k.a. the Garsia-Haiman nabla) operator. For symmetric representations [r], we find the dual -- q-Whittaker -- polynomials. These results confirm and give a colored extension of the observation of arXiv:1201.3339 that triply graded homology of many torus knots has a strikingly simp...
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Cyclic Voltammetry Experiment.
Van Benschoten, James J.; And Others
1983-01-01
Describes a three-part experiment designed to introduce cyclic voltammetry to graduate/undergraduate students. Part 1 demonstrates formal reduction potential, redox electron transfer, diffusion coefficient, and electrochemical reversibility. Part 2 investigates electrochemical behavior of acetaminophen. Part 3 examines such experimental variables…
Wu, Yingquan
2008-01-01
The paper has a threefold purpose. The first purpose is to present an explicit description of expanded cyclic codes defined in $\\GF(q^m)$. The proposed explicit construction of expanded generator matrix and expanded parity check matrix maintains the symbol-wise algebraic structure and thus keeps many important original characteristics. The second purpose of this paper is to identify a class of constant-weight cyclic codes. Specifically, we show that a well-known class of $q$-ary BCH codes excluding the all-zero codeword are constant-weight cyclic codes. Moreover, we show this class of codes achieve the Plotkin bound. The last purpose of the paper is to characterize expanded cyclic codes utilizing the proposed expanded generator matrix and parity check matrix. We analyze the properties of component codewords of a codeword and particularly establish the precise conditions under which a codeword can be represented by a subbasis. With the new insights, we present an improved lower bound on the minimum distance of...
Cyclic Voltammetry Experiment.
Van Benschoten, James J.; And Others
1983-01-01
Describes a three-part experiment designed to introduce cyclic voltammetry to graduate/undergraduate students. Part 1 demonstrates formal reduction potential, redox electron transfer, diffusion coefficient, and electrochemical reversibility. Part 2 investigates electrochemical behavior of acetaminophen. Part 3 examines such experimental variables…
Gopalaswamy, G; Balasubramaniam, N; Kanagasabapathy, A S
1984-12-15
Cystine aminopeptidase (EC 3.4.11.3) enzymes, present in term human placenta and maternal serum, were compared with respect to their behaviour on ion-exchange columns, Km and pH optima, chelator, metal ion and L-methionine effects, Sepharose 6B elution profiles and molecular weights. From placental extracts two activity peaks (CAS I and II) hydrolysing S-benzyl L-cysteine paranitroanilide were separated on DEAE Sephacel. Differences in properties between the two forms were evident. Maternal serum enzyme eluted from the DEAE Sephacel column in a position similar to that of placental CAS I. In addition, the maternal serum enzyme was similar in properties to placental CAS I. It is possible that of all the different cystyl aminopeptidase enzyme systems present in placental tissue, only one appears in maternal blood.
Anbuchezhiyan, M.; Ponnusamy, S.; Muthamizhchelvan, C.
2010-02-01
Single crystal of a new semiorganic nonlinear optical material, L-cystine dihydrobromide, was grown successfully from aqueous solution by slow evaporation method. The grown crystals were characterized by single crystal X-ray diffraction technique to determine the cell parameters. Powder X-ray diffraction analysis also confirms the structure of the grown title compound. The functional groups and vibrational frequencies have been identified using FTIR and FT Raman spectral data. Transmittance of the title compound was analyzed using UV-Vis spectrum. The mechanical strength of the grown crystal was found using Vickers microhardness measurement. The thermal stability of the grown crystal was determined with the aid of thermogravimetric analysis (TGA), differential thermal analysis (DTA) and differential scanning calorimetry (DSC). Second order nonlinear optical behavior of the grown crystal has been confirmed by Kurtz powder second harmonic generation (SHG) test and its SHG efficiency was found as deff=0.38 deff (KDP).
A mild L-cystine-assisted hydrothermal route to metastable γ-MnS multipods
Liu, Meiying; Shan, Nannan; Chen, Linlin; Li, Xiaoqian; Li, Bona; You, Wansheng
2012-08-01
A facile biomolecule-assisted hydrothermal route has been demonstrated to grow γ-MnS multipods at 130 °C for 10 h in distilled water when L-cystine was used as both the sulfur source and complexing agent. The products were characterized by XRD, SEM, TEM and photoluminescence. The results indicate that the as-synthesized γ-MnS multipods are composed of single-crystal, hexagonal and prism-like rods with a size of ca. 300-800 nm and a length of 2-4 μm. The room-temperature photoluminescence spectrum exhibits a peak centered at 419 nm corresponding to the band edge emission when the sample was excited with a wavelength of 358 nm. A possible formation mechanism for the γ-MnS multipods was also discussed based on the time-dependent experiments.
Energy Technology Data Exchange (ETDEWEB)
Anbuchezhiyan, M. [Department of Physics, Valliammai Engineering College, S.R.M. Nagar, Kattankulathur 603 203, Chennai (India); Ponnusamy, S., E-mail: suruponnus@gmail.co [Centre for Material Science and Nano Devices, Department of Physics, SRM University, Kattankulathur 603 203, Chennai (India); Muthamizhchelvan, C. [Centre for Material Science and Nano Devices, Department of Physics, SRM University, Kattankulathur 603 203, Chennai (India)
2010-02-15
Single crystal of a new semiorganic nonlinear optical material, L-cystine dihydrobromide, was grown successfully from aqueous solution by slow evaporation method. The grown crystals were characterized by single crystal X-ray diffraction technique to determine the cell parameters. Powder X-ray diffraction analysis also confirms the structure of the grown title compound. The functional groups and vibrational frequencies have been identified using FTIR and FT Raman spectral data. Transmittance of the title compound was analyzed using UV-Vis spectrum. The mechanical strength of the grown crystal was found using Vickers microhardness measurement. The thermal stability of the grown crystal was determined with the aid of thermogravimetric analysis (TGA), differential thermal analysis (DTA) and differential scanning calorimetry (DSC). Second order nonlinear optical behavior of the grown crystal has been confirmed by Kurtz powder second harmonic generation (SHG) test and its SHG efficiency was found as d{sub eff}=0.38d{sub eff} (KDP).
Liu, Huailei; Zhang, Weiguang; Wang, Kaikai; Wang, Xiaoxiong; Yin, Fei; Li, Chenguang; Wang, Chunlei; Zhao, Boxian; Zhong, Chen; Zhang, Jiakang; Peng, Fei; Bi, Yunke; Shen, Chen; Hou, Xu; Zhang, Daming; Liu, Yaohua; Ai, Jing; Zhao, Shiguang
2015-01-22
Cancer cells are highly dependent on methionine and cystine (Met-Cys) for survival and proliferation. However, the molecular mechanism is not fully clear. The present study is to investigate the effects of Met-Cys deprivation on glioma cells proliferation. The results showed that Met-Cys double deprivation had synergistic action on elevating ROS level, decreased GSH level and inhibition of glioma cell proliferation. Moreover, both of them deprivation triggered autophagy of glioma cells both in vitro and in vivo. Importantly, Met-Cys double restriction diet inhibited growth of glioma. These results provided a new regulation mechanism of Met-Cys metabolism on affecting glioma cell proliferation, suggesting that targeting Met-Cys metabolism may be a potential strategy for glioma therapy.
Spectroscopic study of cystine adsorption on pyrite surface: From vacuum to solution conditions
Sanchez-Arenillas, M.; Mateo-Marti, E.
2015-09-01
We characterized the adsorption of cystine molecules on pyrite surface via X-ray photoelectron spectroscopy. Anoxic conditions were simulated under ultra-high-vacuum conditions. In contrast, to simulate oxidation conditions, the molecules were adsorbed on pyrite surface from solution. A novel comparative analysis revealed remarkable differences with respect to molecular adsorption and surface chemistry induced by environmental conditions. Molecular adsorption under anoxic conditions was observed to be more favorable, concentrating a large number of molecules on the surface and two different chemical species. In contrast, the presence of oxygen induced an autocatalytic oxidation process on the pyrite surface, which facilitated water binding on pyrite surface and partially blocked molecular adsorption. Pyrite is a highly reactive surface and contains two crucial types of surface functional groups that drive molecular chemistry on the surface depending on the surrounding conditions. Therefore, the system explored in this study holds interesting implications for supporting catalyzed prebiotic chemistry reactions.
L-Cystine hydrochloride: A novel semi-organic nonlinear optical material for optical devices
Selvaraju, K.; Valluvan, R.; Kirubavathi, K.; Kumararaman, S.
2007-01-01
A new semi-organic nonlinear optical (NLO) material L-cystine hydrochloride (LCHCl) was grown in large size measuring 19 × 5 × 3 mm 3 by slow solvent evaporation technique for the first time in literature. The cell parameter values were determined by single crystal X-ray diffraction studies. Fourier Transform Infrared spectroscopic analysis was carried out on the grown sample to ascertain the fundamental functional groups. Thermal behavior of the grown LCHCl sample was analyzed by TG & DTA analysis. The mechanical properties of the grown crystals have been studied using Vickers microhardness tester. The optical transmission studies and second harmonic generation (SHG) efficiency studies justified the device quality of the grown crystal and the SHG study reveals that the grown sample has nearly 1.2 times higher efficiency than that of potassium dihydrogen phosphate (KDP), a well known NLO material.
Crystal structure of seleno-l-cystine dihydrochloride
Görbitz, Carl Henrik; Levchenko, Vladimir; Semjonovs, Jevgenijs; Sharif, Mohamed Yusuf
2015-01-01
Numerous crystal structures are available for the dimeric amino acid cystine. In proteins it is formed by oxidation of the –SH thiol groups of two closely spaced cysteine residues, resulting in the formation of a familiar disulfide bridge. The title compound [systematic name: (R,R)-1,1′-dicarboxy-2,2′-(diselanediyl)diethanaminium dichloride], C6H14N2O4Se2 2+·2Cl−, is the first example of a small molecule structure of the biologically important analogue with a —CH2—Se—Se—CH2— bridging unit...
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.
A steered molecular dynamics study on the elastic behaviour of knotted polymer chains
Institute of Scientific and Technical Information of China (English)
Shen Yu; Zhang Lin-Xi
2008-01-01
In this paper the influence of a knot on the structure of a polymethylene (PM) strand in the tensile process is investigated by using the steered molecular dynamics (SMD) method. The gradual increasing of end-to-end distance, R,results in a tighter knot and a more stretched contour. That the break in a knotted rope almost invariably occurs at a point just outside the 'entrance' to the knot, which has been shown in a good many experiments, is further theoretically verified in this paper through the calculation of some structural and thermodynamic parameters. Moreover, it is found that the analyses on bond length, torsion angle and strain energy can facilitate to the study of the localization and the size of a knot in the tensile process. The symmetries of torsion angles, bond lengths and bond angles in the knot result in the whole symmetry of the knot in microstructure, thereby adapting itself to the strain applied. Additionally,the statistical property of the force-dependent average knot size illuminates in detail the change in size of a knot with force f, and therefore the minimum size of the knot in the restriction of the potentials considered in this work for a PM chain is deduced. At the same time, the difference in response to uniaxial strain, between a knotted PM strand and an unknotted one is also investigated. The force-extension profile is easily obtained from the simulation. As expected,for a given f, the knotted chain has an R significantly smaller than that of an unknotted polymer. However, the scaled difference becomes less pronounced for larger values of N, and the results for longer chains approach those of the unknotted chains.
KNOT POINT PLANNING FOR CARTESIAN TRAJECTORY GENERATION BASED ON INHERITANCE BISECTION ALGORITHM
Institute of Scientific and Technical Information of China (English)
Yan Bo; Yan Guozheng
2005-01-01
The computation algorithm of knot point planning for Cartesian trajectory generation of manipulator is investigated. A novel inheritance bisection algorithm (IBA) based on conventional bisection algorithm (BA) is proposed. IBA has two steps. The first step is the 1st knot point planning under lower set position accuracy; the second step is the 2nd knot point planning that inherits the results of the 1st planning under higher set position accuracy. The simulation results reveal that the number of inverse kinematical calculation (IKC) caused by IBA is decreased compared with BA. IBA is more efficient to plan knot points.
Safavieh, Roozbeh; Zhou, Gina Z; Juncker, David
2011-08-07
We present and characterize cotton yarn and knots as building blocks for making microfluidic circuits from the bottom up. The yarn used is made up of 200-300 fibres, each with a lumen. Liquid applied at the extremity of the yarn spontaneously wets the yarn, and the wetted length increases linearly over time in untreated yarn, but progresses according to a square root relationship as described by Washburn's equation upon plasma activation of the yarn. Knots are proposed for combining, mixing and splitting streams of fluids. Interestingly, the topology of the knot controls the mixing ratio of two inlet streams into two outlet yarns, and thus the ratio can be adjusted by choosing a specific knot. The flow resistance of a knot is shown to depend on the force used to tighten it and the flow resistance rapidly increases for single-stranded knots, but remains low for double-stranded knots. Finally, a serial dilutor is made with a web made of yarns and double-stranded overhand knots. These results suggest that yarn and knots may be used to build low cost microfluidic circuits.
Cyclic Voltammograms from First Principles
DEFF Research Database (Denmark)
Karlberg, Gustav; Jaramillo, Thomas; Skulason, Egill
2007-01-01
Cyclic voltammetry is a fundamental experimental tool for characterizing electrochemical surfaces. Whereas cyclic voltammetry is widely used within the field of electrochemistry, a way to quantitatively and directly relate the cyclic voltammogram to ab initio calculations has been lacking, even f...
Zhang, Lijuan; Lu, Biqi; Lu, Chao; Lin, Jin-Ming
2014-01-01
We have demonstrated for the first time the suitability of fluorosurfactant-capped spherical gold nanoparticles as HPLC postcolumn colorimetric reagents for the direct assay of cysteine, homocysteine, cystine, and homocystine. The success of this work was based on the use of an on-line tris(2-carboxyethyl)phosphine reduction column for cystine and homocystine. Several parameters affecting the separation efficiency and the postcolumn colorimetric detection were thoroughly investigated. Under the optimized conditions, cysteine, homocysteine, cystine, and homocystine in human urine and plasma samples were determined. Detection limits for cysteine, homocysteine, cystine, and homocystine ranged from 0.16-0.49 μM. The accuracy in terms of recoveries ranged between 94.0-102.1%. This proposed method was rapid, inexpensive, and simple.
Vulfson, Iosif
2015-01-01
This book focuses on modern methods of oscillation analysis in machines, including cyclic action mechanisms (linkages, cams, steppers, etc.). It presents schematization techniques and mathematical descriptions of oscillating systems, taking into account the variability of the parameters and nonlinearities, engineering evaluations of dynamic errors, and oscillation suppression methods. The majority of the book is devoted to the development of new methods of dynamic analysis and synthesis for cyclic machines that form regular oscillatory systems with multiple duplicate modules. There are also sections examining aspects of general engineering interest (nonlinear dissipative forces, systems with non-stationary constraints, impacts and pseudo-impacts in clearances, etc.) The examples in the book are based on the widely used results of theoretical and experimental studies as well as engineering calculations carried out in relation to machines used in the textile, light, polygraphic and other industries. Particu...
Steinhardt, P J; Steinhardt, Paul J.; Turok, Neil
2004-01-01
The Cyclic Model attempts to resolve the homogeneity, isotropy, and flatness problems and generate a nearly scale-invariant spectrum of fluctuations during a period of slow contraction that precedes a bounce to an expanding phase. Here we describe at a conceptual level the recent developments that have greatly simplified our understanding of the contraction phase and the Cyclic Model overall. The answers to many past questions and criticisms are now understood. In particular, we show that the contraction phase has equation of state w>1 and that contraction with w>1 has a surprisingly similar properties to inflation with w < -1/3. At one stroke, this shows how the model is different from inflation and why it may work just as well as inflation in resolving cosmological problems.
Directory of Open Access Journals (Sweden)
J Gordon Millichap
2002-12-01
Full Text Available In a study at Children’s Hospital, Ann Arbor, MI, and Children’s Memorial Hospital, Chicago, designed primarily to compare cost-effectiveness of three methods of management of cyclic vomiting cases, one group of patients received an extensive diagnostic evaluation, a second was treated with empiric antimigraine drugs for 2 months, and a third an upper GI series with small-bowel follow-through (UGI-SBFT plus empiric therapy.
2009-12-18
analysis of the equilibria based on linearization of the shape dynamics. In [10], the authors extend their analysis to incorporate feedback control...differentiable curves in R2, deriving our dynamics from the natural Frenet frame equations (see, e.g., [5] for details). (A three- dimensional analysis of...cyclic pursuit formulated in terms of the natural Frenet frame equations is a topic of ongoing work.) As is depicted in figure 1, we let ri denote the
Barry, Christopher; Key, Tim; Haddad, Rami; Duncan, Roy
2010-05-28
The reovirus fusion-associated small transmembrane (FAST) proteins are the smallest known viral membrane fusion proteins. With ectodomains of only approximately 20-40 residues, it is unclear how such diminutive fusion proteins can mediate cell-cell fusion and syncytium formation. Contained within the 40-residue ectodomain of the p10 FAST protein resides an 11-residue sequence of moderately apolar residues, termed the hydrophobic patch (HP). Previous studies indicate the p10 HP shares operational features with the fusion peptide motifs found within the enveloped virus membrane fusion proteins. Using biotinylation assays, we now report that two highly conserved cysteine residues flanking the p10 HP form an essential intramolecular disulfide bond to create a cystine loop. Mutagenic analyses revealed that both formation of the cystine loop and p10 membrane fusion activity are highly sensitive to changes in the size and spatial arrangement of amino acids within the loop. The p10 cystine loop may therefore function as a cystine noose, where fusion peptide activity is dependent on structural constraints within the noose that force solvent exposure of key hydrophobic residues. Moreover, inhibitors of cell surface thioreductase activity indicate that disruption of the disulfide bridge is important for p10-mediated membrane fusion. This is the first example of a viral fusion peptide composed of a small, spatially constrained cystine loop whose function is dependent on altered loop formation, and it suggests the p10 cystine loop represents a new class of viral fusion peptides.
Institute of Scientific and Technical Information of China (English)
Zhen Hu; Hai Ping Xing; Zhou Zhu; Wei Wang; Wen Chao Guan
2007-01-01
Oxidative stress has been considered as a major cause of cellular injuries in a variety of clinical abnormalities, especially prominent in neural diseases. One of the usable ways to prevent the reactive oxygen species (ROS)-mediated cellular injury is dietary or pharmaceutical augmentation of some free radical scavenger. Water-soluble amino-fullerene is a novel compound that behaves as a free radical scavenger with excellent biology consistent. In the present study, we have synthesized and characterized a novel cystine C60 derivative for the first time, and investigated the effects on hydrogen peroxide-induced oxidative stress and apoptotic death in cultured rat pheochromocytoma (PC12) cells. PC12 cells treated with hydrogen peroxide underwent apoptotic death as determined by MTT, PI/Hoechst 33342 staining and flow cytometry analysis. These results suggested that cystine C60 derivative has the potential to prevent oxidative stress-induced cell death and has no evident toxicity.
Maruo, Takuya; Kanemaki, Nobuyuki; Onda, Ken; Sato, Reiichiro; Ichihara, Nobuteru; Ochiai, Hideharu
2014-04-01
The cystine transport activity of a lens epithelial cell line originated from a canine mature cataract was investigated. The distinct cystine transport activity was observed, which was inhibited to 28% by extracellular 1 mM glutamate. The cDNA sequences of canine cysteine/glutamate exchanger (xCT) and 4F2hc were determined. The predicted amino acid sequences were 527 and 533 amino acid polypeptides, respectively. The amino acid sequences of canine xCT and 4F2hc showed high similarities (>80%) to those of humans. The expression of xCT in lens epithelial cell line was confirmed by western blot analysis. RT-PCR analysis revealed high level expression only in the brain, and it was below the detectable level in other tissues.
Energy Technology Data Exchange (ETDEWEB)
Lee, Jihun; Blaber, Michael; (FSU)
2010-11-09
The 22 members of the mouse/human fibroblast growth factor (FGF) family of proteins contain a conserved cysteine residue at position 83 (numbering scheme of the 140-residue form of FGF-1). Sequence and structure information suggests that this position is a free cysteine in 16 members and participates as a half-cystine in at least 3 (and perhaps as many as 6) other members. While a structural role as a half-cystine provides a stability basis for possible selective pressure, it is less clear why this residue is conserved as a free cysteine (although free buried thiols can limit protein functional half-life). To probe the structural role of the free cysteine at position 83 in FGF-1, we constructed Ala, Ser, Thr, Val, and Ile mutations and determined their effects on structure and stability. These results show that position 83 in FGF-1 is thermodynamically optimized to accept a free cysteine. A second cysteine mutation was introduced into wild-type FGF-1 at adjacent position Ala66, which is known to participate as a half-cystine with position 83 in FGF-8, FGF-19, and FGF-23. Results show that, unlike position 83, a free cysteine at position 66 destabilizes FGF-1; however, upon oxidation, a near-optimal disulfide bond is formed between Cys66 and Cys83, resulting in {approx} 14 kJ/mol of increased thermostability. Thus, while the conserved free cysteine at position 83 in the majority of the FGF proteins may have a principal role in limiting functional half-life, evidence suggests that it is a vestigial half-cystine.
Cysteine-cystine redox cycling in a gold-gold dual-plate generator-collector microtrench sensor.
Hammond, Jules L; Gross, Andrew J; Estrela, Pedro; Iniesta, Jesus; Green, Stephen J; Winlove, C Peter; Winyard, Paul G; Benjamin, Nigel; Marken, Frank
2014-07-15
Thiols and disulfides are ubiquitous and important analytical targets. However, their redox properties, in particular on gold sensor electrodes, are complex and obscured by strong adsorption. Here, a gold-gold dual-plate microtrench dual-electrode sensor with feedback signal amplification is demonstrated to give well-defined (but kinetically limited) steady-state voltammetric current responses for the cysteine-cystine redox cycle in nondegassed aqueous buffer media at pH 7 down to micromolar concentration levels.
McEvoy, Bernadette; Sumayao, Rodolfo; Slattery, Craig; McMorrow, Tara; Newsholme, Philip
2015-12-01
The pancreatic β-cell has reduced antioxidant defences making it more susceptible to oxidative stress. In cystinosis, a lysosomal storage disorder, an altered redox state may contribute to cellular dysfunction. This rare disease is caused by an abnormal lysosomal cystine transporter, cystinosin, which causes excessive accumulation of cystine in the lysosome. Cystinosis associated kidney damage and dysfunction leads to the Fanconi syndrome and ultimately end-stage renal disease. Following kidney transplant, cystine accumulation in other organs including the pancreas leads to multi-organ dysfunction. In this study, a Ctns gene knockdown model of cystinosis was developed in the BRIN-BD11 rat clonal pancreatic β-cell line using Ctns-targeting siRNA. Additionally there was reduced cystinosin expression, while cell cystine levels were similarly elevated to the cystinotic state. Decreased levels of chronic (24 h) and acute (20 min) nutrient-stimulated insulin secretion were observed. This decrease may be due to depressed ATP generation particularly from glycolysis. Increased ATP production and the ATP/ADP ratio are essential for insulin secretion. Oxidised glutathione levels were augmented, resulting in a lower [glutathione/oxidised glutathione] redox potential. Additionally, the mitochondrial membrane potential was reduced, apoptosis levels were elevated, as were markers of oxidative stress, including reactive oxygen species, superoxide and hydrogen peroxide. Furthermore, the basal and activated phosphorylated forms of the redox-sensitive transcription factor NF-κB were increased in cells with silenced Ctns. From this study, the cystinotic-like pancreatic β-cell model demonstrated that the altered oxidative status of the cell, resulted in depressed mitochondrial function and pathways of ATP production, causing reduced nutrient-stimulated insulin secretion.
Mattox, Mildred L; D'Angelo, June A; Grimes, Zachary M; Fiebiger, Edda; Dickinson, Bonny L
2012-11-30
Indoleamine 2,3-dioxygenase (IDO) is the rate-limiting enzyme in the tryptophan-catabolizing pathway and a key regulator of peripheral immune tolerance. As the suppressive effects of IDO are predominantly mediated by dendritic cells (DCs) and IDO-competent DCs promote long-term immunologic tolerance, a detailed understanding of how IDO expression and activity is regulated in these cells is central to the rational design of therapies to induce robust immune tolerance. We previously reported that the cystine/glutamate antiporter modulates the functional expression of IDO in human monocyte-derived DCs. Specifically, we showed that blocking antiporter uptake of cystine significantly increased both IDO mRNA and IDO enzymatic activity and that this correlated with impaired DC presentation of exogenous antigen to T cells via MHC class II and the cross-presentation pathway. The antiporter regulates intracellular and extracellular redox by transporting cystine into the cell in exchange for glutamate. Intracellular cystine is reduced to cysteine to support biosynthesis of the major cellular antioxidant glutathione and cysteine is exported from the cell where it functions as an extracellular antioxidant. Here we show that antiporter control of IDO expression in DCs is reversible, independent of interferon-γ, regulated by redox, and requires active protein synthesis. These findings highlight a role for antiporter regulation of cellular redox as a critical control point for modulating IDO expression and activity in DCs. Thus, systemic disease and aging, processes that perturb redox homeostasis, may adversely affect immunity by promoting the generation of IDO-competent DCs.
Racah matrices and hidden integrability in evolution of knots
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.
Knots and surfaces a guide to discovering mathematics
Farmer, David W
1995-01-01
In most mathematics textbooks, the most exciting part of mathematics-the process of invention and discovery-is completely hidden from the reader. The aim of Knots and Surfaces is to change all that. By means of a series of carefully selected tasks, this book leads readers to discover some real mathematics. There are no formulas to memorize; no procedures to follow. The book is a guide: its job is to start you in the right direction and to bring you back if you stray too far. Discovery is left to you. Suitable for a one-semester course at the beginning undergraduate level, there are no prerequi
Explorations in topology map coloring, surfaces and knots
Gay, David
2013-01-01
Explorations in Topology, Second Edition, provides students a rich experience with low-dimensional topology (map coloring, surfaces, and knots), enhances their geometrical and topological intuition, empowers them with new approaches to solving problems, and provides them with experiences that will help them make sense of future, more formal topology courses. The book's innovative story-line style models the problem-solving process, presents the development of concepts in a natural way, and engages students in meaningful encounters with the material. The updated end-of-chapter investigation
Punctured torus groups and 2-bridge knot groups
Akiyoshi, Hirotaka; Wada, Masaaki; Yamashita, Yasushi
2007-01-01
This monograph is Part 1 of a book project intended to give a full account of Jorgensen's theory of punctured torus Kleinian groups and its generalization, with application to knot theory. Although Jorgensen's original work was not published in complete form, it has been a source of inspiration. In particular, it has motivated and guided Thurston's revolutionary study of low-dimensional geometric topology. In this monograph, we give an elementary and self-contained description of Jorgensen's theory with a complete proof. Through various informative illustrations, readers are naturally led to an intuitive, synthetic grasp of the theory, which clarifies how a very simple fuchsian group evolves into complicated Kleinian groups.
Knotted Picture of a Quantum Network of Two Nodes
Institute of Scientific and Technical Information of China (English)
QIAN Shang-Wu; GU Zhi-Yu
2004-01-01
This article discusses the variation of the knotted picture of the quantum pure state |X〉 = α| ↑↓〉 + β|↓↑〉with the varintion of the complex coefficients a and β. It is shown that there are three kinds of link that correspond tc three different ranks of the matrix of covariance correlation tensor, i.e., the zero rank corresponds to trivial link, the rank one corresponds to the two-component link with two crossings, and the rank three corresponds to the two-component link with four crossings.
Design and performance of the APPLE-Knot undulator.
Ji, Fuhao; Chang, Rui; Zhou, Qiaogen; Zhang, Wei; Ye, Mao; Sasaki, Shigemi; Qiao, Shan
2015-07-01
Along with the development of accelerator technology, synchrotron emittance has continuously decreased. This results in increased brightness, but also causes a heavy heat load on beamline optics. Recently, optical surfaces with 0.1 nm micro-roughness and 0.05 µrad slope error (r.m.s.) have become commercially available and surface distortions due to heat load have become a key factor in determining beamline performance, and heat load has become a serious problem at modern synchrotron radiation facilities. Here, APPLE-Knot undulators which can generate photons with arbitrary polarization, with low on-axis heat load, are reported.
Sleire, L; Skeie, B S; Netland, I A; Førde, H E; Dodoo, E; Selheim, F; Leiss, L; Heggdal, J I; Pedersen, P-H; Wang, J; Enger, P Ø
2015-12-03
Glioblastomas (GBMs) are aggressive brain tumors that always recur after radiotherapy. Cystine, mainly provided by the system X(c)(-) antiporter, is a requirement for glioma cell synthesis of glutathione (GSH) which has a critical role in scavenging free radicals, for example, after radiotherapy. Thus, we hypothesized that the X(c)(-)-inhibitor sulfasalazine (SAS) could potentiate the efficacy of radiotherapy against gliomas. Here, we show that the catalytic subunit of system X(c)(-), xCT, was uniformly expressed in a panel of 30 human GBM biopsies. SAS treatment significantly reduced cystine uptake and GSH levels, whereas it significantly increased the levels of reactive oxygen species (ROS) in glioma cells in vitro. Furthermore, SAS and radiation synergistically increased DNA double-strand breaks and increased glioma cell death, whereas adding the antioxidant N-acetyl-L-cysteine (NAC) reversed cell death. Moreover, SAS and gamma knife radiosurgery (GKRS) synergistically prolonged survival in nude rats harboring human GBM xenografts, compared with controls or either treatment alone. In conclusion, SAS effectively blocks cystine uptake in glioma cells in vitro, leading to GSH depletion and increased ROS levels, DNA damage and cell death. Moreover, it potentiates the anti-tumor efficacy of GKRS in rats with human GBM xenografts, providing a survival benefit. Thus, SAS may have a role as a radiosensitizer to enhance the efficacy of current radiotherapies for glioma patients.
Totally geodesic Seifert surfaces in hyperbolic knot and link complements II
DEFF Research Database (Denmark)
Adams, Colin; Bennett, Hanna; Davis, Christopher James;
2008-01-01
We generalize the results of Adams–Schoenfeld, finding large classes of totally geodesic Seifert surfaces in hyperbolic knot and link complements, each covering a rigid 2-orbifold embedded in some hyperbolic 3-orbifold. In addition, we provide a uniqueness theorem and demonstrate that many knots ...
First report of the root-knot nematode Meloidogyne ethiopica on tomato in Slovenia
Sirca, S.; Urek, G.; Karssen, G.
2004-01-01
The root-knot nematode Meloidogyne ethiopica Whitehead originally described from Tanzania is also distributed in South Africa, Zimbabwe, and Ethiopia (3). Although this species is a relatively unknown root-knot nematode, M. ethiopica parasitizes several economical important crops, such as tomato, co
Repeat knot formation in a patient with an indwelling ureteral stent
Directory of Open Access Journals (Sweden)
Brian Eisner
2006-06-01
Full Text Available A patient treated for nephrolithiasis formed knots in 2 occasions, in 2 separate indwelling ureteral stents. This rare complication may make stent removal difficult. To our knowledge, this is the first case report of repeat knot formation in a single patient.
Totally geodesic Seifert surfaces in hyperbolic knot and link complements II
DEFF Research Database (Denmark)
Adams, Colin; Bennett, Hanna; Davis, Christopher James
2008-01-01
We generalize the results of Adams–Schoenfeld, finding large classes of totally geodesic Seifert surfaces in hyperbolic knot and link complements, each covering a rigid 2-orbifold embedded in some hyperbolic 3-orbifold. In addition, we provide a uniqueness theorem and demonstrate that many knots...
Onrust, J.; de Fouw, J.; Oudman, T.; van der Geest, M.; Piersma, T.; van Gils, J.A.
2013-01-01
Capsule Context-specific equations are needed to reconstruct diet composition and intake rate of Red Knots by the use of shell fragments retrieved from droppings.Aims To explore whether the method to reconstruct Red Knot diet described by Dekinga & Piersma [Dekinga, A. & Piersma, T. 1993. Reconstruc
Onrust, Jeroen; De Fouw, Jimmy; Oudman, Thomas; Van der Geest, Matthijs; Piersma, Theunis; Van Gils, Jan A.
2013-01-01
Capsule Context-specific equations are needed to reconstruct diet composition and intake rate of Red Knots by the use of shell fragments retrieved from droppings. Aims To explore whether the method to reconstruct Red Knot diet described by Dekinga & Piersma [Dekinga, A. & Piersma, T. 1993. Reconstru
Why do few Afro-Siberian Knots Calidris canutus canutus now visit Britain?
Boyd, H; Piersma, T
2001-01-01
The nominate (Afro-Siberian) subspecies of the Knot Calidris canutus canutus breeds on the Taimyr Peninsula in Siberia and occurs commonly in the westernmost Wadden Sea during migration to West and South Africa. The recoveries and controls of 2045 Knots ringed in Britain and Ireland provide no evide
Expression of almond KNOTTED1 homologue (PdKn1) anticipates adventitious shoot initiation
Background and Aims: The transcription factor encoded by the gene Knotted1 is a nuclear homeodomain protein, regulating meristematic cells at the shoot apical meristem. It has been proven that Knotted1 (KN1) has a role in the switch from an indeterminate to determinate cell fate and as such this gen...
Verboven, N.; Piersma, T.
1995-01-01
To test whether Knot Calidris canutus wintering in the tropics suffer higher rates of water loss through evaporation than do Knot wintering at temperate latitudes, we tried to develop a physically realistic model to predict evaporative heat loss from air temperature, wind and humidity. In separate e
Institute of Scientific and Technical Information of China (English)
Jess G. THOENE
2005-01-01
SUMMARY Nephropathic cystinosis is a lethal inborn error of metabolism that destroys kidney function by age 10 years. It is characterized by lysosomal cystine accumulation. How the cystine causes the phenotype is an open question. We propose that during apoptosis, permeablized lysosomes permit cystine to reach the cytosol where mixed disulfide formation occurs, augmenting apoptosis by interaction with a variety of pro-apoptotic proteins.
Directory of Open Access Journals (Sweden)
Julio Francisco Valiati Marin
2011-09-01
Full Text Available Objetivou-se determinar o melhor nível de metionina mais cistina digestível e a melhor relação metionina mais cistina digestível:lisina digestível em diferentes níveis de proteína para codorna em postura. Foram utilizadas 400 codornas japonesas produtoras de ovos de consumo com 45 dias de idade, em delineamento inteiramente casualizado, num esquema fatorial 2 x 5, dois níveis de proteína bruta (19,5% e 21,5% e cinco níveis de metionina mais cistina digestível (0,60%; 0,67%; 0,74%; 0,81% e 0,88%, com cinco repetições e oito aves por unidade experimental. Foram analisadas as taxas de postura (%, peso médio dos ovos (g, massa de ovos (g de ovos/ave/dia, consumo de ração (g/ave/dia, conversão alimentar (g de ração/g de ovos, peso e porcentagem de gema (g e %, peso e porcentagem de clara (g e % e peso e porcentagem de casca (g e %. Para o nível de 19,5% de proteína 0,60% de metionina mais cistina digestível e relação metionina mais cistina digestível:lisina digestível de 0,66% foram suficientes para otimizar a produção. Para o nível de 21,5% de proteína 0,851% de metionina mais cistina digestível com relação metionina mais cistina digestível:lisina digestível de 0,935% com consumo diário de 223,3mg/ave levou a uma melhor produção de ovos de codornas.This research had the purpose to determine the best level of digestible methionine plus cystine and the best relation of digestible methionine plus cystine:digestible lysine in different levels of protein for laying Japanese quails. 400 laying Japanese quails, with 45 days of age were used in a completely randomized design, with a factorial 2 x 5, two crude protein levels (19,5% and 21,5% and five levels of digestible methionine plus cystine (0,60%; 0,67%; 0,74%; 0,81% e 0,88%, with five replicates and eight quails per experimental unity. There were analysis of the posture rate (%, egg average weight (g egg mass (egg grams/bird/day, feed intake (g/bird/day, feed
Knot Physics -- an Ultimate Unified Theory of Matter and its Motion
Kou, Su-Peng
2016-01-01
A Theory of Everything (TOE) is physics theory that unifies all the fundamental interactions of nature: gravitation, strong interaction, weak interaction, and electromagnetism.\\ Now, TOE becomes the Holy Grail of modern physics. In this paper, knot physics becomes a new candidate of TOE that not only unified all the fundamental interactions but also explores the underline physics of quantum mechanics. In knot physics, our universe is a standard knot-crystal, a particular periodic entanglement-pattern between two 3-branes (three dimensional branes/manifolds), of which the low energy effective theory not only reproduces the Standard model -- an SU(3)*SU(2)*U(1) gauge theory but also leads to the physics of general relativity. The collective motions of the standard knot-crystal are described by fermionic elementary particles and gauge fields. Fermionic elementary particles are topological excitations that correspond to different types of knots.
Two-stage directed self-assembly of a cyclic [3]catenane
Wood, Christopher S.; Ronson, Tanya K.; Belenguer, Ana M.; Holstein, Julian J.; Nitschke, Jonathan R.
2015-04-01
Interlocked molecules possess properties and functions that depend upon their intricate connectivity. In addition to the topologically trivial rotaxanes, whose structures may be captured by a planar graph, the topologically non-trivial knots and catenanes represent some of chemistry's most challenging synthetic targets because of the three-dimensional assembly necessary for their construction. Here we report the synthesis of a cyclic [3]catenane, which consists of three mutually interpenetrating rings, via an unusual synthetic route. Five distinct building blocks self-assemble into a heteroleptic triangular framework composed of two joined FeII3L3 circular helicates. Subcomponent exchange then enables specific points in the framework to be linked together to generate the cyclic [3]catenane product. Our method represents an advance both in the intricacy of the metal-templated self-assembly procedure and in the use of selective imine exchange to generate a topologically complex product.
Knots on a Torus: A Model of the Elementary Particles
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Jack S. Avrin
2012-02-01
Full Text Available Two knots; just two rudimentary knots, the unknot and the trefoil. That’s all we need to build a model of the elementary particles of physics, one with fermions and bosons, hadrons and leptons, interactions weak and strong and the attributes of spin, isospin, mass, charge, CPT invariance and more. There are no quarks to provide fractional charge, no gluons to sequester them within nucleons and no “colors” to avoid violating Pauli’s principle. Nor do we require the importation of an enigmatic Higgs boson to confer mass upon the particles of our world. All the requisite attributes emerge simply (and relativistically invariant as a result of particle conformation and occupation in and of spacetime itself, a spacetime endowed with the imprimature of general relativity. Also emerging are some novel tools for systemizing the particle taxonomy as governed by the gauge group SU(2 and the details of particle degeneracy as well as connections to Hopf algebra, Dirac theory, string theory, topological quantum field theory and dark matter. One exception: it is found necessary to invoke the munificent geometry of the icosahedron in order to provide, as per the group “flavor” SU(3, a scaffold upon which to organize the well-known three generations—no more, no less—of the particle family tree.
A Knot Model Sugugested by the Standard Electroweak Theory
Finkelstein, R J
2004-01-01
We attempt to go beyond the standard electroweak theory by replacing the underlying Lie algebra with its q-deformation: SU_q(2) x SU(1). This step introduces new degrees of freedom that we interpret as indicative of non-locality and as a possible basis for a solitonic model of the elementary particles. The solitons are conjectured to be knotted flux tubes labelled by the irreducible representations of SU_q(2), an algebra which is not only closely related to the standard theory but also plays a role in the description of knots. Each of the four families of elementary fermions is conujectured to be represented by one of the four possible trefoils. The three individual fermions belonging to any family then occupy the three lowest states in the excitation spectrum of the trefoil for that family. The dimensionless deformation parameter, q, is assumed to be a function of the Higgs field and to be an effective measure of the influence of the new degrees of freedom introduced by the deformation of SU(2). One finds a ...
Plasma cysteine/cystine redox couple disruption in animal models of temporal lobe epilepsy
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Li-Ping Liang
2016-10-01
Full Text Available Currently the field of epilepsy lacks peripheral blood-based biomarkers that could predict the onset or progression of chronic seizures following an epileptogenic injury. Thiol/disulfide ratios have been shown to provide a sensitive means of assessing the systemic redox potential in tissue and plasma. In this study, we utilized a rapid, simple and reliable method for simultaneous determination of several thiol-containing amino acids in plasma using HPLC with electrochemical detection in kainic acid (KA and pilocarpine rat models of epilepsy. In contrast to GSH and GSSG levels, the levels of cysteine (Cys were decreased by 42% and 62% and cystine (Cyss were increased by 46% and 23% in the plasma of KA- and pilocarpine-injected rats, respectively after 48 h. In chronically epileptic rats, plasma cysteine was decreased by 40.4% and 37.7%, and plasma GSSG increased by 33.8% and 35.0% following KA and pilocarpine, respectively. Treatment of rats with a catalytic antioxidant, 60 min after KA or pilocarpine significant attenuated the decrease of plasma Cys/Cyss ratios at the 48 h time point in both models. These observations suggest that the decreased cysteine and ratio of Cys/Cyss in plasma could potentially serve as redox biomarkers in temporal lobe epilepsy.
Human CD4+ T cells require exogenous cystine for glutathione and DNA synthesis.
Levring, Trine B; Kongsbak, Martin; Rode, Anna K O; Woetmann, Anders; Ødum, Niels; Bonefeld, Charlotte Menné; Geisler, Carsten
2015-09-08
Adaptive immune responses require activation and expansion of antigen-specific T cells. Whereas early T cell activation is independent of exogenous cystine (Cys2), T cell proliferation is dependent of Cys2. However, the exact roles of Cys2 in T cell proliferation still need to be determined. The aim of this study was to elucidate why activated human T cells require exogenous Cys2 in order to proliferate. We activated purified naïve human CD4+ T cells and found that glutathione (GSH) levels and DNA synthesis were dependent on Cys2 and increased in parallel with increasing concentrations of Cys2. Vice-versa, the GSH synthesis inhibitor L-buthionine-sulfoximine (BSO) and inhibition of Cys2 uptake with glutamate inhibited GSH and DNA synthesis in parallel. We further found that thioredoxin (Trx) can partly substitute for GSH during DNA synthesis. Finally, we show that GSH or Trx is required for the activity of ribonucleotide reductase (RNR), the enzyme responsible for generation of the deoxyribonucleotide DNA building blocks. In conclusion, we show that activated human T cells require exogenous Cys2 to proliferate and that this is partly explained by the fact that Cys2 is required for production of GSH, which in turn is required for optimal RNR-mediated deoxyribonucleotide synthesis and DNA replication.
Pandey, Chandra Mouli; Sumana, Gajjala; Tiwari, Ida
2014-11-15
Here, we report a simple and reproducible method for large scale fabrication of novel flower and palm-leaf like 3D cystine microstructures (CMs) with high uniformity having a size of 50 µm and 10 µm respectively, through a facile aqueous solution route as a function of pH and concentration. In a proof-of-concept study, the 3D CMs have been further explored to fabricate a label-free high-performance electrochemical immunosensor by immobilizing monoclonal antibodies. Electrochemical methods were employed to study the stepwise modification of the system and the electronic transduction for the detection. The fabricated immunosensor design demonstrates high performance with enhanced sensitivity (4.70 cfu ml(-1)) and linear sensing range from 10 to 3 x 10(9) cfu ml(-1) a long shelf-life (35 days) and high selectivity over other bacterial pathogens. The enhanced performance originates from a novel nanostructuring in which the CMs provide higher surface coverage for the immobilization of antibodies providing excellent electronic/ionic conductivity which result in the enhanced sensitivity.
Bifunctional redox flow battery - 2. V(III)/V(II)-L-cystine(O{sub 2}) system
Energy Technology Data Exchange (ETDEWEB)
Wen, Y.H.; Xun, Y. [Research Institute of Chemical Defense, Beijing 100083 (China); Cheng, J.; Yang, Y.S. [Research Institute of Chemical Defense, Beijing 100083 (China); Beijing Science and Technology University, Beijing 100083 (China); Ma, P.H. [Full Cell R and D Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023 (China)
2008-08-20
A new bifunctional redox flow battery (BRFB) system, V(III)/V(II) - L-cystine(O{sub 2}), was systematically investigated by using different separators. It is shown that during charge, water transfer is significantly restricted with increasing the concentration of HBr when the Nafion 115 cation exchange membrane is employed. The same result can be obtained when the gas diffusion layer (GDL) hot-pressed separator is used. The organic electro-synthesis is directly correlated with the crossover of vanadium. When employing the anion exchange membrane, the electro-synthesis efficiency is over 96% due to a minimal crossover of vanadium. When the GDL hot-pressed separator is applied, the crossover of vanadium and water transfer are noticeably prevented and the electro-synthesis efficiency of over 99% is obtained. Those impurities such as vanadium ions and bromine can be eliminated through the purification of organic electro-synthesized products. The purified product is identified to be L-cysteic acid by IR spectrum. The BRFB shows a favorable discharge performance at a current density of 20 mA cm{sup -2}. Best discharge performance is achieved by using the GDL hot-pressed separator. The coulombic efficiency of 87% and energy efficiency of about 58% can be obtained. The cause of major energy losses is mainly associated with the cross-contamination of anodic and cathodic active electrolytes. (author)
The kinetics of β-elimination of cystine and the formation of lanthionine in gliadin.
Lagrain, Bert; De Vleeschouwer, Kristel; Rombouts, Ine; Brijs, Kristof; Hendrickx, Marc E; Delcour, Jan A
2010-10-13
When gliadin, a mixture of wheat storage proteins containing only intramolecular disulfide (SS) bonds, is heated at high temperatures and preferably at alkaline pH, the SS bonds are cleaved by β-elimination reactions leading to decreased cystine levels and the generation of dehydroalanine (DHA) and free sulfhydryl (SH) groups. DHA and the free SH group of cysteine can further react to form the irreversible cross-link lanthionine (LAN). The kinetics of this reaction were studied by heating model systems containing gliadin at different pH values (pH 6.0, 8.0 and 11.0) at temperatures up to 120 °C. Multiresponse modeling was applied to simultaneously describe the course of the reaction partners, intermediates and products. The estimated kinetic parameters indicate that the reaction rate constant for the elimination reaction increases with temperature and pH. Moreover, the predominant reaction consuming the intermediary DHA is the cross-link with cysteine to form LAN following second-order reaction kinetics. The corresponding reaction rate constant is less dependent on temperature and pH. Use of the proposed kinetic model to estimate reaction product concentrations in cereal-based foods allowed us to conclude that the β-elimination reaction may be less important during, e.g., bread making, but may well contribute to gluten network formation during the production of soft wheat products. It may also well be relevant in the production of bioplastics made from gluten.
Selektivitas Medium Cystine Tellurite Blood Agar (CTBA terhadap Beberapa Isolat Bakteri
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Kambang Sariadji
2015-05-01
Full Text Available Cystine tellurite blood agar (CTBA medium is a selective medium for Corynebacterium diphtheriae culture. The presence of tellurite is a selectivity of this medium to inhibit the others bacteria. Others medium were used as a selective medium for the culture of Corynebacterium diphtheriae were tinsdale and Hoyle medium, but was recommended by the World Health Organization (WHO were CTBA and hoyle medium. However, information about the selectivity of medium was recommended by WHO is still limited. The aims of study to determine the selectivity of medium against a number of others species bacteria on CTBA. A number of 24 isolates contains of different species Corynebacterium spp and others species were regrown, then all isolates were cultured in CTBA medium, incubated for 24 – 48 haours at 37°C. The growthing of colony in CTBA were observed. The results showed that 7 isolates for Corynebacterium species can grow well on medium CTBA, 5 isolates from different species showed growth in CTBA medium including Staphylococcus aureus, Streptococcus pneumoniae, Enterobacter sakazakii , Klebsiella pneumoniae and Candida albicans. Meanwhile the rest 12 isolates showed no growthing on CTBA medium. Therefore it can be concluded that the selectivity of the CTBA medium has limited capabilities.
Ekpyrotic and Cyclic Cosmology
Lehners, Jean-Luc
2008-01-01
Ekpyrotic and cyclic cosmologies provide theories of the very early and of the very late universe. In these models, the big bang is described as a collision of branes - and thus the big bang is not the beginning of time. Before the big bang, there is an ekpyrotic phase with equation of state w=P/rho >> 1 (where P is the average pressure and rho the average energy density) during which the universe slowly contracts. This phase resolves the standard cosmological puzzles and generates a nearly scale-invariant spectrum of cosmological perturbations containing a significant non-gaussian component. At the same time it produces small-amplitude gravitational waves with a blue spectrum. The dark energy dominating the present-day cosmological evolution is reinterpreted as a small attractive force between our brane and a parallel one. This force eventually induces a new ekpyrotic phase and a new brane collision, leading to the idea of a cyclic universe. This review discusses the detailed properties of these models, thei...
Ekpyrotic and cyclic cosmology
Energy Technology Data Exchange (ETDEWEB)
Lehners, Jean-Luc [Princeton Center for Theoretical Science, Jadwin Hall, Princeton University, Princeton NJ 08544 (United States)], E-mail: jlehners@princeton.edu
2008-09-15
Ekpyrotic and cyclic cosmologies provide theories of the very early and of the very late universe. In these models, the big bang is described as a collision of branes - and thus the big bang is not the beginning of time. Before the big bang, there is an ekpyrotic phase with equation of state w=P/({rho}) >>1 (where P is the average pressure and {rho} the average energy density) during which the universe slowly contracts. This phase resolves the standard cosmological puzzles and generates a nearly scale-invariant spectrum of cosmological perturbations containing a significant non-Gaussian component. At the same time it produces small-amplitude gravitational waves with a blue spectrum. The dark energy dominating the present-day cosmological evolution is reinterpreted as a small attractive force between our brane and a parallel one. This force eventually induces a new ekpyrotic phase and a new brane collision, leading to the idea of a cyclic universe. This review discusses the detailed properties of these models, their embedding in M-theory and their viability, with an emphasis on open issues and observational signatures.
[Asthma and cyclic neutropenia].
Salazar Cabrera, A N; Berrón Pérez, R; Ortega Martell, J A; Onuma Takane, E
1996-01-01
We report a male with history of recurrent infections (recurrent oral aphtous disease [ROAD], middle ear infections and pharyngo amigdalitis) every 3 weeks since he was 7 months old. At the age of 3 years cyclic neutropenia was diagnosed with cyclic fall in the total neutrophil count in blood smear every 21 days and prophylactic antimicrobial therapy was indicated. Episodic events every 3 weeks of acute asthma and allergic rhinitis were detected at the age of 6 years old and specific immunotherapy to Bermuda grass was given during 3 years with markedly improvement in his allergic condition but not in the ROAD. He came back until the age of 16 with episodic acute asthma and ROAD. The total neutrophil count failed to 0 every 21 days and surprisingly the total eosinophil count increased up to 2,000 at the same time, with elevation of serum IgE (412 Ul/mL). Specific immunotherapy to D.pt. and Aller.a. and therapy with timomodulin was indicated. After 3 months we observed clinical improvement in the asthmatic condition and the ROAD disappeared, but the total neutrophil count did not improve. We present this case as a rare association between 2 diseases with probably no etiological relationship but may be physiopatological that could help to understand more the pathogenesis of asthma.
Richard, Lenaïg; Vachot, Christiane; Surget, Anne; Rigolet, Vincent; Kaushik, Sadasivam J; Geurden, Inge
2011-09-01
This 35-d feeding experiment examined in juvenile shrimp Penaeus monodon (3·3 g initial body weight) the effects of methionine (Met), choline and cystine on protein accretion and the activity of two key enzymes of remethylation (betaine-homocysteine methyltransferase; BHMT) and trans-sulfuration (cystathionine β-synthase; CBS). The interaction between Met and choline was tested using semi-purified diets either adequate or limiting (30 or 50 %) in total sulphur amino acid (SAA) content with a constant cystine:Met ratio. The diets contained either basal or excess choline (3 v. 7 g/kg feed). Cystine was added to two other 30 and 50 % Met-limiting diets to adjust the SAA supply to that of the control diet in order to evaluate the interaction between Met and cystine. As expected, N accretion was significantly lower with the SAA-limiting diets but increased back to control levels by the extra choline or cystine, demonstrating their sparing effect on Met utilisation for protein accretion. We show, for the first time, the activities of BHMT and CBS in shrimp hepatopancreas. Only BHMT responded to the SAA deficiencies, whereas the extra choline and cystine did not stimulate remethylation or down-regulate trans-sulfuration. Our data also suggest the capacity of P. monodon to synthesise taurine, being significantly affected by the cystine level in the 30 % SAA-limiting diets. Further research is warranted to better understand the metabolic regulation of taurine synthesis in shrimp and of the observed Met-sparing effects.
Bridges, Richard; Lutgen, Victoria; Lobner, Doug; Baker, David A
2012-07-01
System x(c)(-) represents an intriguing target in attempts to understand the pathological states of the central nervous system. Also called a cystine-glutamate antiporter, system x(c)(-) typically functions by exchanging one molecule of extracellular cystine for one molecule of intracellular glutamate. Nonvesicular glutamate released during cystine-glutamate exchange activates extrasynaptic glutamate receptors in a manner that shapes synaptic activity and plasticity. These findings contribute to the intriguing possibility that extracellular glutamate is regulated by a complex network of release and reuptake mechanisms, many of which are unique to glutamate and rarely depicted in models of excitatory signaling. Because system x(c)(-) is often expressed on non-neuronal cells, the study of cystine-glutamate exchange may advance the emerging viewpoint that glia are active contributors to information processing in the brain. It is noteworthy that system x(c)(-) is at the interface between excitatory signaling and oxidative stress, because the uptake of cystine that results from cystine-glutamate exchange is critical in maintaining the levels of glutathione, a critical antioxidant. As a result of these dual functions, system x(c)(-) has been implicated in a wide array of central nervous system diseases ranging from addiction to neurodegenerative disorders to schizophrenia. In the current review, we briefly discuss the major cellular components that regulate glutamate homeostasis, including glutamate release by system x(c)(-). This is followed by an in-depth discussion of system x(c)(-) as it relates to glutamate release, cystine transport, and glutathione synthesis. Finally, the role of system x(c)(-) is surveyed across a number of psychiatric and neurodegenerative disorders.
Fragmentations of protonated cyclic-glycylglycine and cyclic-alanylalanine
Shek, P. Y. I.; Lau, J. K. C.; Zhao, J. F.; Grzetic, J.; Verkerk, U. H.; Oomens, J.; Hopkinson, A. C.; Siu, K. W. M.
2012-01-01
Collision-induced dissociation has been used to study the fragmentations of two protonated diketopiperazines, protonated cyclic-glycylglycine and cyclic-alanylalanine. Protonated cyclo-AA lost CO and (CO + NH3) at low collision energies, channels attributed to dissociation of the O-protonated
On the Braids for 810 Knot = 810 Düğümünün Örgüsü Hakkında
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Ahmet KÜÇÜK
2001-06-01
Full Text Available This paper is concerned with 810 knots and its braids. The braids structure is very important role in Knots Theory. In view of this structure, we obtained braids for that knot and we will give the representations of Artin and we examine Garside Word problem. And then we will examine the positivity structure for these knots.
Some Sufficient Conditions for Tunnel Numbers of Connected Sum of Two Knots Not to Go Down
Institute of Scientific and Technical Information of China (English)
Guo Qiu YANG; Feng Chun LEI
2011-01-01
In this paper,we show the following result:Let Ki be a knot in a closed orientable 3-manifold Mi such that (Mi,Ki) is not homeomorphic to (S2 × S1,x0 × S1),i =1,2.Suppose that the Euler Characteristic of any meridional essential surface in each knot complement E(Ki) is less than the difference of one and twice of the tunnel number of Ki.Then the tunnel number of their connected sum will not go down.If in addition that the distance of any minimal Heegaard splitting of each knot complement is strictly more than 2,then the tunnel number of their connected sum is super additive.We further show that if the distance of a Heegaard splitting of each knot complement is strictly bigger than twice the tunnel number of the knot (twice the sum of the tunnel number of the knot and one,respectively),then the tunnel number of connected sum of two such knots is additive (super additive,respectively).
Effects of horseshoe crab harvest in delaware bay on red knots: Are harvest restrictions working?
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.
Köhler, P; Belitz, H D; Wieser, H
1993-03-01
Glutenin was prepared from gluten of the wheat variety Rektor by extraction of gliadin with aqueous ethanol. It was cleaved successively into soluble peptides by the enzymes trypsin and thermolysin. Separation of the peptide mixtures was performed by gel permeation chromatography (GPC) on Sephadex G25 and reversed phase high performance liquid chromatography (RP-HPLC) on ODS-Hypersil. Cystine peptides were detected by differential chromatography of the samples prior to and after reduction. After isolation by multi-step RP-HPLC, the cystine peptides were reduced. The resulting cysteine peptides were alkylated with 4-vinylpyridine, separated by RP-HPLC and sequenced by means of the Edman degradation. The isolated cystine peptides represented a considerable portion of the total cysteine in glutenin: four out of seven cysteine residues of HMW subunits, and eight out of nine cysteine residues of LMW subunits are documented by at least one cystine peptide. Most of the peptides corresponded to known sequences of gluten protein components. From the structures of some tryptic peptides, inter- and intramolecular disulphide bonds for HMW subunits of glutenin have been proven. Cystine peptides from the thermolytic digest have been assigned to LMW subunits of glutenin and to gamma-gliadins. Other peptides have been closely related to partial sequences of these protein components. The results have allowed several conclusions about the arrangement of intra- and intermolecular disulphide bridges in gluten proteins.
Lazova, Milena D; Butler, Mitchell T; Shimizu, Thomas S; Harshey, Rasika M
2012-05-01
Chemoreceptors McpB and McpC in Salmonella enterica have been reported to promote chemotaxis in LB motility-plate assays. Of the chemicals tested as potential effectors of these receptors, the only response was towards L-cysteine and its oxidized form, L-cystine. Although enhanced radial migration in plates suggested positive chemotaxis to both amino acids, capillary assays failed to show an attractant response to either, in cells expressing only these two chemoreceptors. In vivo fluorescence resonance energy transfer (FRET) measurements of kinase activity revealed that in wild-type bacteria, cysteine and cystine are chemoeffectors of opposing sign, the reduced form being a chemoattractant and the oxidized form a repellent. The attractant response to cysteine was mediated primarily by Tsr, as reported earlier for Escherichia coli. The repellent response to cystine was mediated by McpB/C. Adaptive recovery upon cystine exposure required the methyl-transferase/-esterase pair, CheR/CheB, but restoration of kinase activity was never complete (i.e. imperfect adaptation). We provide a plausible explanation for the attractant-like responses to both cystine and cysteine in motility plates, and speculate that the opposing signs of response to this redox pair might afford Salmonella a mechanism to gauge and avoid oxidative environments.
The arabidopsis cyclic nucleotide interactome
Donaldson, Lara
2016-05-11
Background Cyclic nucleotides have been shown to play important signaling roles in many physiological processes in plants including photosynthesis and defence. Despite this, little is known about cyclic nucleotide-dependent signaling mechanisms in plants since the downstream target proteins remain unknown. This is largely due to the fact that bioinformatics searches fail to identify plant homologs of protein kinases and phosphodiesterases that are the main targets of cyclic nucleotides in animals. Methods An affinity purification technique was used to identify cyclic nucleotide binding proteins in Arabidopsis thaliana. The identified proteins were subjected to a computational analysis that included a sequence, transcriptional co-expression and functional annotation analysis in order to assess their potential role in plant cyclic nucleotide signaling. Results A total of twelve cyclic nucleotide binding proteins were identified experimentally including key enzymes in the Calvin cycle and photorespiration pathway. Importantly, eight of the twelve proteins were shown to contain putative cyclic nucleotide binding domains. Moreover, the identified proteins are post-translationally modified by nitric oxide, transcriptionally co-expressed and annotated to function in hydrogen peroxide signaling and the defence response. The activity of one of these proteins, GLYGOLATE OXIDASE 1, a photorespiratory enzyme that produces hydrogen peroxide in response to Pseudomonas, was shown to be repressed by a combination of cGMP and nitric oxide treatment. Conclusions We propose that the identified proteins function together as points of cross-talk between cyclic nucleotide, nitric oxide and reactive oxygen species signaling during the defence response.
Cyclic cohomology of Hopf algebras
Crainic, M.
2001-01-01
We give a construction of ConnesMoscovicis cyclic cohomology for any Hopf algebra equipped with a character Furthermore we introduce a noncommutative Weil complex which connects the work of Gelfand and Smirnov with cyclic cohomology We show how the Weil complex arises naturally when looking at Hopf
Helicity, Topology and Kelvin Waves in reconnecting quantum knots
di Leoni, P Clark; Brachet, M E
2016-01-01
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 and solar physics, in fluid dynamics, in atmospheric sciences, and in 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 vortex lines can be downright impossible to apply in complex and turbulent scenarios. We present a new definition of helicity which overcomes these problems. With it, we show that only certain reconnection events conserve helicity. In other cases helicity can change abruptly during reconnection. Furthermore, we show that these events can also excite Kelvin waves, which slowly deplete helicity as they interact nonlinearly, thus linking the theory of vortex knots with observations of quantum turbulence.
Material Properties of Wire for the Fabrication of Knotted Fences
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Dirk J. Pons
2014-01-01
Full Text Available This paper describes the materials properties of galvanised fencing wire, as used in the fabrication of knotted wire fences. A range of physical properties are investigated: tensile strength, ductility in tension, Young’s modulus, three-point bending, and bending span. A range of commercially available wire products were tested. The results show that most, but not all, high tensile wire samples met the minimum tensile and ductility requirements. Young’s modulus results failed to provide any meaningful insights into wire quality. Flexural modulus results also failed to provide any insight into wire quality issues, with no statistically significant differences existing between acceptable and problematic wire batches. The implications are that premature fence failures are unlikely to be caused solely by reduced tensile properties. Existing test methods, including tensile strength and ductility, are somewhat incomplete, perhaps even unreliable, as measures of wire quality.
Disciplinary Knots and Learning Problems in Waves Physics
Di Renzone, Simone; Montalbano, Vera
2012-01-01
An investigation on student understanding of waves is performed during an optional laboratory realized in informal extracurricular way with few, interested and talented pupils. The background and smart intuitions of students rendered the learning path very dynamic and ambitious. The activities started by investigating the basic properties of waves by means of a Shive wave machine. In order to make quantitative observed phenomena, the students used a camcorder and series of measures were obtained from the captured images. By checking the resulting data, it arose some learning difficulties especially in activities related to the laboratory. This experience was the starting point for a further analysis on disciplinary knots and learning problems in the physics of waves in order to elaborate a teaching-learning proposal on this topic.
Rectangular superpolynomials for the figure-eight knot
Kononov, Ya
2016-01-01
We rewrite the recently proposed differential expansion formula for HOMFLY polynomials of the knot $4_1$ in arbitrary rectangular representation $R=[r^s]$ as a sum over all Young sub-diagrams $\\lambda$ of $R$ with extraordinary simple coefficients $D_{\\lambda^{tr}}(r)\\cdot D_\\lambda(s)$ in front of the $Z$-factors. Somewhat miraculously, these coefficients are made from quantum dimensions of symmetric representations of the groups $SL(r)$ and $SL(s)$ and restrict summation to diagrams with no more than $s$ rows and $r$ columns. They possess a natural $\\beta$-deformation to Macdonald dimensions and produces positive Laurent polynomials, which can be considered as plausible candidates for the role of the rectangular superpolynomials. Both polynomiality and positivity are non-evident properties of arising expressions, still they are true. This extends the previous suggestions for symmetric and antisymmetric representations (when $s=1$ or $r=1$ respectively) to arbitrary rectangular representations. As usual for ...
Numerical simulation of the knotted nylon netting panel
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Li Yuwei
2016-01-01
Full Text Available A piece of netting, consists of the 8 8 meshes, fixed on a square frame, was simulated and the tensions and their distribution, the positions of knots and netting shape were calculated by means of MATLAB in computer. The dynamic mathematic model was developed based on lumped mass method, the netting was treated as spring-mass system, the Runge-Kutta fifth-order and sixth-order method was used to solve the differential equations for every step, then the displacement and tension of each mass point were obtained. For verify this model, the tests have been carried out in a flume tank. The results of the numerical simulation fully agreed with the experiments.
Racah matrices and hidden integrability in evolution of knots
Mironov, A; Morozov, An; Sleptsov, A
2016-01-01
We construct a general procedure to extract the exclusive Racah matrices S and \\bar S 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 \\bar S relate respectively the maps (R\\otimes R)\\otimes \\bar R\\longrightarrow R with R\\otimes (R \\otimes \\bar R) \\longrightarrow R and (R\\otimes \\bar R) \\otimes R \\longrightarrow R with R\\otimes (\\bar R \\otimes R) \\longrightarrow 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.
Symmetric alteration of four knots of B-spline and NURBS surfaces
Institute of Scientific and Technical Information of China (English)
LI Ya-juan; WANG Guo-zhao
2006-01-01
Modifying the knots ofa B-spline curve, the shape of the curve will be changed. In this paper, we present the effect of the symmetric alteration of four knots of the B-spline and the NURBS surfaces, i.e., symmetrical alteration of the knots of surface,the extended paths of points of the surface will converge to a point which should be expressed with several control points. This theory can be used in the constrained shape modification of B-spline and NURBS surfaces.
Knot detection in X-ray images of wood planks using dictionary learning
DEFF Research Database (Denmark)
Hansson, Nils Mattias; Enescu, Alexandru; Brandt, Sami Sebastian
2015-01-01
This paper considers a novel application of x-ray imaging of planks, for the purpose of detecting knots in high quality furniture wood. X-ray imaging allows the detection of knots invisible from the surface to conventional cameras. Our approach is based on texture analysis, or more specifically......, discriminative dictionary learning. Experiments show that the knot detection and segmentation can be accurately performed by our approach. This is a promising result and can be directly applied in industrial processing of furniture wood....
Multiple folding pathways of proteins with shallow knots and co-translational folding
Chwastyk, Mateusz
2015-01-01
We study the folding process in the shallowly knotted protein MJ0366 within two variants of a structure-based model. We observe that the resulting topological pathways are much richer than identified in previous studies. In addition to the single knot-loop events, we find novel, and dominant, two-loop mechanisms. We demonstrate that folding takes place in a range of temperatures and the conditions of most successful folding are at temperatures which are higher than those required for the fastest folding. We also demonstrate that nascent conditions are more favorable to knotting than off-ribosome folding.
Successful retrieval of a knotted pulmonary artery catheter trapped in the tricuspid valve apparatus
Muhammad Ishaq; Nicki Alexander; David H. T. Scott
2013-01-01
We report the case of a 64-year-old patient in whom a pulmonary artery catheter formed a knot fixed within the right ventricle in the region of the tricuspid valve apparatus. Knot formation is a recognized complication associated with pulmonary artery catheters (PAC) insertion. This problem is usually dealt with by simply withdrawing the PAC until the knot impacts onto the introducer and after enlarging the puncture site by a small skin incision removing the introducer-PAC as one unit. Howeve...
Nematicides and nonconventional soil amendments in the management of root-knot nematode on cotton.
Jorgenson, E C
1984-04-01
Granular and liquid commercial humates, with micronutrients, and a microbial fermentation product were compared in several combinations with nematicides for their effects on cotton lint yield and root-knot nematode suppression. Fumigant nematicides effectively reduced cotton root galling caused by root-knot nematodes, and cotton lint yields increased. Organophosphates and carbamates were not effective. Occasionally, cotton lint yields were increased or maintained with combination treatments o f humates, micronutrients, and a microbial fermentation product, but galling o f cotton roots by root-knot nematodes was usually not reduced by these treatments.
Levels of lysine and methionine+cystine for growing New Zealand White rabbits
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Ana Carolina Monteiro-Motta
2013-12-01
Full Text Available Two experiments were carried out to evaluate, respectively, nitrogen balance (NB and the productive performance of 31-to-50-day-old rabbits subjected to different levels of lysine and methionine+cystine (met+cys. Seventy-five animals were randomly distributed in 5 × 3 blocks (five levels of lysine: 5.5, 6.5, 7.5, 8.5 and 9.5 g/kg combined with three levels of met+cys: 5.0, 6.0 and 7.0 g/kg, with 15 treatments and five replications for the NB assay. The assay lasted 14 days: 10 days for acclimatization and four days for feces and urine collection. Increasing met+cys levels had a quadratic effect on the nitrogen excreted in urine (NU: the lowest excretion was found at the dietary level of 5.9 g/kg met+cys. Increasing lysine levels also affected NU and nitrogen retained daily (NR: the lowest NU was obtained at the dietary level of 7.28 g/kg lysine, and maximum NR was found at 7.24 g/kg lysine. Increases in met+cys levels in the diets affected neither performance nor carcass characteristics of rabbits up to 50 days of age. On the other hand, body weight at 50 days, daily weight gain and feed conversion of rabbits slaughtered at 50 days had a quadratic effect as the lysine levels increased. The best results were found at 7.5, 7.38 and 7.36 g/kg lysine. Lysine and met+cys levels of 7.4 and 5.0 g/kg in the diet are recommended for 31-to-50-day-old rabbits.
Response of laying hens to methionine + cystine intake by dilution technique
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Hilda Cristina Palma Bendezu
2015-01-01
Full Text Available The objective of this study was to measure the response of Dekalb White laying hens to different intakes of digestible methionine + cystine (met+cys to optimise their performance. Two hundred eighty-eight Dekalb White laying hens, ranging in age from 33 to 48 weeks, were used in the study. The birds were randomly allocated into eight treatment (levels of met+cys and the control treatment groups with six replicates of six hens per unit. The experimental diets consisted of seven increasing levels of met+cys (1.37, 2.75, 4.14, 5.51, 6.89, 7.92 and 8.95 g kg−1 and were prepared using a dilution technique. A control treatment was used to confirm that the limiting response was due to met+cys intake. Egg production, feed intake, egg weight, egg mass and feed conversion per mass were measured. The data were analysed with repeated measures and regression analyses using Broken Line and Quadratic models, as well as using the combination of both models. The different met+cys intakes influenced the studied variables; all the variables except feed conversion per mass were significantly different between the periods and levels. The digestible met+cys intakes based on the association of the Broken Line and Quadratic models to optimise the birds' response to egg mass are 671 mg/bird d for 33 to 36 weeks, 728 mg/bird d for 37 to 40 weeks, 743 mg/bird d for 41 to 44 weeks, and 770 mg/bird d for 45 to 48 weeks.
PredSTP: a highly accurate SVM based model to predict sequential cystine stabilized peptides.
Islam, S M Ashiqul; Sajed, Tanvir; Kearney, Christopher Michel; Baker, Erich J
2015-07-05
Numerous organisms have evolved a wide range of toxic peptides for self-defense and predation. Their effective interstitial and macro-environmental use requires energetic and structural stability. One successful group of these peptides includes a tri-disulfide domain arrangement that offers toxicity and high stability. Sequential tri-disulfide connectivity variants create highly compact disulfide folds capable of withstanding a variety of environmental stresses. Their combination of toxicity and stability make these peptides remarkably valuable for their potential as bio-insecticides, antimicrobial peptides and peptide drug candidates. However, the wide sequence variation, sources and modalities of group members impose serious limitations on our ability to rapidly identify potential members. As a result, there is a need for automated high-throughput member classification approaches that leverage their demonstrated tertiary and functional homology. We developed an SVM-based model to predict sequential tri-disulfide peptide (STP) toxins from peptide sequences. One optimized model, called PredSTP, predicted STPs from training set with sensitivity, specificity, precision, accuracy and a Matthews correlation coefficient of 94.86%, 94.11%, 84.31%, 94.30% and 0.86, respectively, using 200 fold cross validation. The same model outperforms existing prediction approaches in three independent out of sample testsets derived from PDB. PredSTP can accurately identify a wide range of cystine stabilized peptide toxins directly from sequences in a species-agnostic fashion. The ability to rapidly filter sequences for potential bioactive peptides can greatly compress the time between peptide identification and testing structural and functional properties for possible antimicrobial and insecticidal candidates. A web interface is freely available to predict STP toxins from http://crick.ecs.baylor.edu/.
Thioredoxin-related protein of 14 kDa is an efficient L-cystine reductase and S-denitrosylase.
Pader, Irina; Sengupta, Rajib; Cebula, Marcus; Xu, Jianqiang; Lundberg, Jon O; Holmgren, Arne; Johansson, Katarina; Arnér, Elias S J
2014-05-13
Thioredoxin-related protein of 14 kDa (TRP14, also called TXNDC17 for thioredoxin domain containing 17, or TXNL5 for thioredoxin-like 5) is an evolutionarily well-conserved member of the thioredoxin (Trx)-fold protein family that lacks activity with classical Trx1 substrates. However, we discovered here that human TRP14 has a high enzymatic activity in reduction of l-cystine, where the catalytic efficiency (2,217 min(-1)⋅µM(-1)) coupled to Trx reductase 1 (TrxR1) using NADPH was fivefold higher compared with Trx1 (418 min(-1)⋅µM(-1)). Moreover, the l-cystine reduction with TRP14 was in contrast to that of Trx1 fully maintained in the presence of a protein disulfide substrate of Trx1 such as insulin, suggesting that TRP14 is a more dedicated l-cystine reductase compared with Trx1. We also found that TRP14 is an efficient S-denitrosylase with similar efficiency as Trx1 in catalyzing TrxR1-dependent denitrosylation of S-nitrosylated glutathione or of HEK293 cell-derived S-nitrosoproteins. Consequently, nitrosylated and thereby inactivated caspase 3 or cathepsin B could be reactivated through either Trx1- or TRP14-catalyzed denitrosylation reactions. TRP14 was also, in contrast to Trx1, completely resistant to inactivation by high concentrations of hydrogen peroxide. The oxidoreductase activities of TRP14 thereby complement those of Trx1 and must therefore be considered for the full understanding of enzymatic control of cellular thiols and nitrosothiols.
Lewerenz, Jan; Hewett, Sandra J; Huang, Ying; Lambros, Maria; Gout, Peter W; Kalivas, Peter W; Massie, Ann; Smolders, Ilse; Methner, Axel; Pergande, Mathias; Smith, Sylvia B; Ganapathy, Vadivel; Maher, Pamela
2013-02-10
The antiporter system x(c)(-) imports the amino acid cystine, the oxidized form of cysteine, into cells with a 1:1 counter-transport of glutamate. It is composed of a light chain, xCT, and a heavy chain, 4F2 heavy chain (4F2hc), and, thus, belongs to the family of heterodimeric amino acid transporters. Cysteine is the rate-limiting substrate for the important antioxidant glutathione (GSH) and, along with cystine, it also forms a key redox couple on its own. Glutamate is a major neurotransmitter in the central nervous system (CNS). By phylogenetic analysis, we show that system x(c)(-) is a rather evolutionarily new amino acid transport system. In addition, we summarize the current knowledge regarding the molecular mechanisms that regulate system x(c)(-), including the transcriptional regulation of the xCT light chain, posttranscriptional mechanisms, and pharmacological inhibitors of system x(c)(-). Moreover, the roles of system x(c)(-) in regulating GSH levels, the redox state of the extracellular cystine/cysteine redox couple, and extracellular glutamate levels are discussed. In vitro, glutamate-mediated system x(c)(-) inhibition leads to neuronal cell death, a paradigm called oxidative glutamate toxicity, which has successfully been used to identify neuroprotective compounds. In vivo, xCT has a rather restricted expression pattern with the highest levels in the CNS and parts of the immune system. System x(c)(-) is also present in the eye. Moreover, an elevated expression of xCT has been reported in cancer. We highlight the diverse roles of system x(c)(-) in the regulation of the immune response, in various aspects of cancer and in the eye and the CNS.
Energy Technology Data Exchange (ETDEWEB)
Schmiegelow, P.; Puschmann, M.; Giese, U.
1984-01-16
Clinical experience has obviously shown a positive effect of application of sulfated amino acids on degenerative cartilage diseases. L-Cystin, presumed to be of therapeutic effect, was autoradiographically localized in articular, columnar and intervertebral cartilage as well as in skeletal musculature. In 10 days old NMRI-mice, we had shown a dose-dependent incorporation of the radioactively labelled /sup 35/S-Cystin in hair follicle. These statistically significant differences had been measured by quantitative autoradiographical microscope photometry. The sulfated amino acids are also proven in nail matrix, nail hyponychium as well as in cartilage and skeletal musculature. Besides a localization of radioactively labelled L-Cystin in tissues, presumed as target organs of a therapeutic effect, there is still lacking an experimental proof of efficacy on cell proliferation and functional metabolism e.g. in arthrosis by suitable animal models.
Weirich, W; Frohneberg, D; Ackermann, D; Alken, P
1984-03-01
In 18 patients (20 kidneys) with struvite/apatite-, uric acid- and cystine stones antegrade local chemolysis was performed via percutaneous or operative nephrostomy. Complete stone dissolution was achieved in 11 kidneys, while in six kidneys partial dissolution of stones was performed. In these six cases added instrumental manipulations shortened the time of therapy. In three cases chemolysis was unsuccessful. Average irrigation time was 21 days per renal unit. Only minor complications like dysuria and skin rashes were seen. Due to long time of irrigation we recommend chemolitholysis mainly as an additional form of therapy in case of residual stones after operative or percutaneous nephrolithotomy.
Bulut, Haydar; Moniot, Sebastien; Licht, Anke; Scheffel, Frank; Gathmann, Stephanie; Saenger, Wolfram; Schneider, Erwin
2012-01-20
ATP-binding cassette (ABC) transporters are integral membrane proteins that carry a variety of substrates across biological membranes at the expense of ATP. The here considered prokaryotic canonical importers consist of three entities: an extracellular solute receptor, two membrane-intrinsic proteins forming a translocation pathway, and two cytoplasmic ATP-binding subunits. The ngo0372-74 and ngo2011-14 gene clusters from the human pathogen Neisseria gonorrhoeae were predicted by sequence homology as ABC transporters for the uptake of cystine and cysteine, respectively, and chosen for structural characterization. The structure of the receptor component Ngo0372 was obtained in a ligand-free "open" conformation and in a "closed" conformation when co-crystallized with L-cystine. Our data provide the first structural information of an L-cystine ABC transporter. Dissociation constants of 21 and 33 nM for L-cystine and L-selenocystine, respectively, were determined by isothermal titration calorimetry. In contrast, L-cystathionine and L-djenkolic acid are weak binders, while no binding was detectable for S-methyl-L-cysteine. Mutational analysis of two residues from the binding pocket, Trp97 and Tyr59, revealed that the latter is crucial for L-cystine binding. The structure of the Ngo2014 receptor was obtained in closed conformation in complex with co-purified L-cysteine. The protein binds L-cysteine with a K(d) of 26 nM. Comparison of the structures of both receptors and analysis of the ligand binding sites shed light on the mode of ligand recognition and provides insight into the tight binding of both substrates. Moreover, since L-cystine limitation leads to reduction in virulence of N. gonorrhoeae, Ngo0372 might be suited as target for an antimicrobial vaccine.
US Fish and Wildlife Service, Department of the Interior — This FY2014 progress report documents project activity for determining critical wintering sites and migration routes for juvenile red knots. Project goals, expected...
Knot numbers used as labels for identifying subject matter of a khipu
Directory of Open Access Journals (Sweden)
Alberto Saez-Rodriguez
2013-03-01
Full Text Available This investigation presents a new way to look at the numerical khipu, a knotted-string recording device from Pachacamac (Peru, and the types of information it contains. In addition to celestial coordinates, khipu knots apparently pertain to an early form of double-entry accounting. This study hypothesizes that the khipu sample has the recording capacity needed to register double-entry-like accounts. After the identification of its subject matter, the khipu sample was studied in an attempt to ascertain whether the knot values could represent instructions from the Inca state administration to a local accounting center. The results indicate that the numerical information in the pairing quadrants (determined by the distribution of S- and Z-knots should be read from top to bottom along the full length of the string and can then provide certain complementary details regarding the projected corn stocks of the Inca stat
PRESENCE OF RED KNOT (CALIDRIS CANUTUS IN ITE WETLANDS, TACNA, PERU
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Jhonson K. Vizcarra
2012-06-01
Full Text Available The presence of Red Knot (Calidris canutus, Linnaeus 1758 in Ite Wetlands, Tacna, Peru is documented. Two individuals were observed in October 2011. This species had only one occurrence without details in this area.
The algebraic crossing number and the braid index of knots and links
Kawamuro, Keiko
2009-01-01
It has been conjectured that the algebraic crossing number of a link is uniquely determined in minimal braid representation. This conjecture is true for many classes of knots and links. The Morton-Franks-Williams inequality gives a lower bound for braid index. And sharpness of the inequality on a knot type implies the truth of the conjecture for the knot type. We prove that there are infinitely many examples of knots and links for which the inequality is not sharp but the conjecture is still true. We also show that if the conjecture is true for K and L, then it is also true for the (p,q)-cable of K and for the connect sum of K and L.
Some Dimensions of Spaces of Finite Type Invariants of Virtual Knots
Bar-Natan, Dror; Leung, Louis; Roukema, Fionntan
2009-01-01
We compute many dimensions of spaces of finite type invariants of virtual knots (of several kinds) and the dimensions of the corresponding spaces of "weight systems", finding everything to be in agreement with the conjecture that "every weight system integrates".
Biocontrol (Formulation of Bacillus firmus (BioNem)) of Root-knot ...
African Journals Online (AJOL)
Key words: Bacillus firmus, Biological control, Meloidogyne incognita, Tomato. Introduction ... levels of biocontrol formulation, BioNem on root-knot nematode infestation and plant ...... Journal of invertebrate Pathology 100 (2009)94-99.
Folding of small knotted proteins: Insights from a mean field coarse-grained model
Energy Technology Data Exchange (ETDEWEB)
Najafi, Saeed; Potestio, Raffaello, E-mail: potestio@mpip-mainz.mpg.de [Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz (Germany)
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.
On the species status of the root-knot nematode Meloidogyne mayaguensis Rammah & Hirschmann, 1988
Karssen, G.; Liao, J.; Kan, Z.; Heese, van E.; Nijs, L.J.M.F.
2012-01-01
Holo- and paratypes of the root-knot nematodes Meloidogyne mayaguensis Rammah & Hirschmann, 1988 and M. enterolobii Yang & Eisenback, 1983 were morphometrically and morphologically compared. All observed female, male and second-stage juvenile morphometrical and morphological characters are i
Ishaq, Muhammad; Alexander, Nicki; Scott, David H T
2013-04-01
We report the case of a 64-year-old patient in whom a pulmonary artery catheter formed a knot fixed within the right ventricle in the region of the tricuspid valve apparatus. Knot formation is a recognized complication associated with pulmonary artery catheters (PAC) insertion. This problem is usually dealt with by simply withdrawing the PAC until the knot impacts onto the introducer and after enlarging the puncture site by a small skin incision removing the introducer-PAC as one unit. However, we recently encountered a situation where the PAC was knotted around the tricuspid valve apparatus and could not be withdrawn. An interventional radiologist was able to unknot the catheter and release it from the tricuspid valve. We reviewed the literature related to this topic. We believe our experience could be of use to others.
Successful retrieval of a knotted pulmonary artery catheter trapped in the tricuspid valve apparatus
Directory of Open Access Journals (Sweden)
Muhammad Ishaq
2013-01-01
Full Text Available We report the case of a 64-year-old patient in whom a pulmonary artery catheter formed a knot fixed within the right ventricle in the region of the tricuspid valve apparatus. Knot formation is a recognized complication associated with pulmonary artery catheters (PAC insertion. This problem is usually dealt with by simply withdrawing the PAC until the knot impacts onto the introducer and after enlarging the puncture site by a small skin incision removing the introducer-PAC as one unit. However, we recently encountered a situation where the PAC was knotted around the tricuspid valve apparatus and could not be withdrawn. An interventional radiologist was able to unknot the catheter and release it from the tricuspid valve. We reviewed the literature related to this topic. We believe our experience could be of use to others.
Broughton, S Allen
2010-01-01
A cyclic $n$-gonal surface is a compact Riemann surface $X$ of genus $g\\geq 2$ admitting a cyclic group of conformal automorphisms $C$ of order $n$ such that the quotient space $X/C$ has genus 0. In this paper, we provide an overview of ongoing research into automorphism groups of cyclic $n$-gonal surfaces. Much of the paper is expository or will appear in forthcoming papers, so proofs are usually omitted. Numerous explicit examples are presented illustrating the computational methods currently being used to study these surfaces.
Martin, L; Gardner, L B
2015-08-06
SLC7A11 encodes a subunit of the xCT cystine/glutamate amino-acid transport system and has a critical role in the generation of glutathione and the protection of cells from oxidative stress. Expression of SLC7A11 promotes tumorigenesis and chemotherapy resistance, but while SLC7A11 has been previously noted to be upregulated in hypoxic cells, its regulation has not been fully delineated. We have recently shown that nonsense-mediated RNA decay (NMD) is inhibited by cellular stresses generated by the tumor microenvironment, including hypoxia, and augments tumorigenesis. Here we demonstrate that the inhibition of NMD by various cellular stresses leads to the stabilization and upregulation of SLC7A11 mRNA and protein. The inhibition of NMD and upregulation of SLC7A11 augments intracellular cystine transport and increases intracellular levels of cysteine and glutathione. Accordingly, the inhibition of NMD protects cells against oxidative stress via SLC7A11 upregulation. Together our studies identify a mechanism for the dynamic regulation of SLC7A11, through the stress-inhibited regulation of NMD, and add to the growing evidence that the inhibition of NMD is an adaptive response.
Directory of Open Access Journals (Sweden)
Wilson Massamitu Furuya
2004-12-01
Full Text Available Este estudo foi realizado para determinar a exigência de metionina + cistina para alevinos de tilápia do Nilo (2,61 ± 0,14g. Foi utilizado o modelo em blocos ao acaso, com seis tratamentos, três repetições e cinco peixes por unidade experimental. Foi utilizada ração basal contendo 28% de proteína bruta e 3173kcal ED kg-1 de ração, suplementada com DL-metionina, resultando em rações com 0,87; 0,95; 1,03; 1,11; 1,19 e 1,27% de metionina + cistina. As rações foram fornecidas à vontade durante 41 dias. Não foram observados efeitos (P>0,05 dos níveis de metionina + cistina sobre a taxa de sobrevivência e índice hepato-somático. Foi observado efeito quadrático (PThis study was carried out to determine the methionine + cystine requirement for Nile tilápia, fingerlings (2.61 ± 0.14g. A randomized block designs, with six treatments, three replicates and five fish by experimental unit was used. Basal diet was utilized with 28% crude protein and 3173DE kcal kg-1 of digestible energy, supplemented with DL-methionine, resulting in diets with 0.87; 0.95; 1.03; 1.11; 1.19 and 1.27% of methionine + cystine. Diets were fed to satiation during 41 days. No effects (P>0.05 of methionine + cystine levels on survival rate and hepatosomatic index were observed. A quadratic effect (P<0.05 for weight gain was observed, which increased up to 1.22% methionine + cystine in the diet. Feed conversion ratio and protein efficiency ratio increased (P<0.05 up to 1.00% of methionine + cystine. A quadratic effect (P<0.05 of methionine + cystine level on carcass yield was observed, which increased up to 1.13% of methionine + cystine. The concentration of 1.00% methionine + cystine corresponding to 3.54% crude protein, in the presence of 0.54% methionine in the diet, showed the best njperformance.
Knots: attractive places with high path tortuosity in mouse open field exploration.
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Anna Dvorkin
2010-01-01
Full Text Available When introduced into a novel environment, mammals establish in it a preferred place marked by the highest number of visits and highest cumulative time spent in it. Examination of exploratory behavior in reference to this "home base" highlights important features of its organization. It might therefore be fruitful to search for other types of marked places in mouse exploratory behavior and examine their influence on overall behavior.Examination of path curvatures of mice exploring a large empty arena revealed the presence of circumscribed locales marked by the performance of tortuous paths full of twists and turns. We term these places knots, and the behavior performed in them-knot-scribbling. There is typically no more than one knot per session; it has distinct boundaries and it is maintained both within and across sessions. Knots are mostly situated in the place of introduction into the arena, here away from walls. Knots are not characterized by the features of a home base, except for a high speed during inbound and a low speed during outbound paths. The establishment of knots is enhanced by injecting the mouse with saline and placing it in an exposed portion of the arena, suggesting that stress and the arousal associated with it consolidate a long-term contingency between a particular locale and knot-scribbling.In an environment devoid of proximal cues mice mark a locale associated with arousal by twisting and turning in it. This creates a self-generated, often centrally located landmark. The tortuosity of the path traced during the behavior implies almost concurrent multiple views of the environment. Knot-scribbling could therefore function as a way to obtain an overview of the entire environment, allowing re-calibration of the mouse's locale map and compass directions. The rich vestibular input generated by scribbling could improve the interpretation of the visual scene.
An eddy-current-based sensor for preventing knots in metallic wire drawing processes
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.
The volume conjecture, perturbative knot invariants, and recursion relations for topological strings
Dijkgraaf, Robbert; Fuji, Hiroyuki; Manabe, Masahide
2011-08-01
We study the relation between perturbative knot invariants and the free energies defined by topological string theory on the character variety of the knot. Such a correspondence between SL(2;C) Chern-Simons gauge theory and the topological open string theory was proposed earlier on the basis of the volume conjecture and AJ conjecture. In this paper we discuss this correspondence beyond the subleading order in the perturbative expansion on both sides. In the computation of the perturbative invariants for the hyperbolic 3-manifold, we adopt the state integral model for the hyperbolic knots, and the factorized AJ conjecture for the torus knots. On the other hand, we iteratively compute the free energies on the character variety using the Eynard-Orantin topological recursion relation. We discuss the correspondence for the figure eight knot complement and the once punctured torus bundle over S with the monodromy LR up to the fifth order. For the torus knots, we find trivial the recursion relations on both sides.
The volume conjecture, perturbative knot invariants, and recursion relations for topological strings
Energy Technology Data Exchange (ETDEWEB)
Dijkgraaf, Robbert, E-mail: r.h.dijkgraaf@uva.n [Institute for Theoretical Physics and KdV Institute for Mathematics, University of Amsterdam, Spui 21, 1012 WX Amsterdam (Netherlands); Fuji, Hiroyuki, E-mail: fuji@th.phys.nagoya-u.ac.j [Department of Physics, Nagoya University, Nagoya 464-8602 (Japan); Manabe, Masahide, E-mail: d07002p@math.nagoya-u.ac.j [Graduate School of Mathematics, Nagoya University, Nagoya 464-8602 (Japan)
2011-08-01
We study the relation between perturbative knot invariants and the free energies defined by topological string theory on the character variety of the knot. Such a correspondence between SL(2;C) Chern-Simons gauge theory and the topological open string theory was proposed earlier on the basis of the volume conjecture and AJ conjecture. In this paper we discuss this correspondence beyond the subleading order in the perturbative expansion on both sides. In the computation of the perturbative invariants for the hyperbolic 3-manifold, we adopt the state integral model for the hyperbolic knots, and the factorized AJ conjecture for the torus knots. On the other hand, we iteratively compute the free energies on the character variety using the Eynard-Orantin topological recursion relation. We discuss the correspondence for the figure eight knot complement and the once punctured torus bundle over S{sup 1} with the monodromy L{sup 2}R up to the fifth order. For the torus knots, we find trivial the recursion relations on both sides.
The Volume Conjecture, Perturbative Knot Invariants, and Recursion Relations for Topological Strings
Dijkgraaf, Robbert; Manabe, Masahide
2010-01-01
We study the relation between perturbative knot invariants and the free energies defined by topological string theory on the character variety of the knot. Such a correspondence between SL(2;C) Chern-Simons gauge theory and the topological open string theory was proposed earlier on the basis of the volume conjecture and AJ conjecture. In this paper we discuss this correspondence beyond the subleading order in the perturbative expansion on both sides. In the computation of the perturbative invariants for the hyperbolic 3-manifold, we adopt the state integral model for the hyperbolic knots, and the factorized AJ conjecture for the torus knots. On the other hand, we iteratively compute the free energies on the character variety using the Eynard-Orantin topological recursion relation. We check the correspondence for the figure eight knot complement and the once punctured torus bundle over S^1 with the holonomy L^2R up to the fourth order. For the torus knots, we find trivial the recursion relations on both sides.
Condensates and instanton - torus knot duality. Hidden Physics at UV scale
Gorsky, A
2014-01-01
We establish the duality between the torus knot superpolynomials or the Poincare polynomials of the Khovanov homology and particular condensates in Omega-deformed 5D supersymmetric QED compactified on a circle with 5d Chern-Simons(CS) term. This is the generalization of the Witten's recipe of the evaluation of the knot polynomials via Wilson loops in 3d CS theory for case of the torus knots. It is explicitly shown that $n$-instanton contribution to the condensate of the massless flavor in the background of four-observable, which can be associated with some composite defect, exactly coincides with the superpolynomial of the T(n,nk+1) torus knot where k - is the level of CS term. In contrast to the previously known results, the particular torus knot corresponds not to the partition function of the gauge theory but to the particular instanton contribution and summation over the knots has to be performed in order to obtain the complete answer. The instantons are sitting almost at the top of each other and the phy...
The X-ray emission from the knots in 3C 120
Institute of Scientific and Technical Information of China (English)
无
2010-01-01
3C 120 is a Seyfert galaxy with a well detected X-ray jet.We investigate the X-ray emission of its five jet knots and fit their spectral energy distributions(SEDs) from the radio to the X-ray bands with a single-zone lepton model.We find that the SEDs of knots k7,s2,and s3 can be explained by synchrotron radiation,and the X-rays are the simple extension of the radio-optical emission component,but that of the inner knot k4 requires the IC/CMB model,in which the X-rays are due to the inverse Compton scattering of the cosmic microwave background photons by relativistic electrons in the jet with a beaming factor δ-14.The outer knot k25 is resolved into a three-part sub-structure.It is shown that the fitting of the X-rays from this knot with the IC/CMB model needs an extraordinary beaming factor δ-15-25 for a jet at the kpc scale.If the X-rays of knot k25 are produced by synchrotron radiation similar to k7,s2,and s3,they may be contributed by a relativistic electron population whose radiations in other wavelengths are not detected.
Knotted Vortices: Entropic Lattice Boltzmann Method for Simulation of Vortex dynamics
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.
Freely Expanding X-ray Ejecta Knots in Kepler's Supernova Remnant
Hughes, John Patrick; Sato, Toshiki
2017-08-01
Using archival data from the Chandra X-ray Observatory, we measure the proper motions and radial velocities of compact X-ray bright knots in Kepler's supernova remnant (SNR). The high speed ejecta knots are morphologically and kinematically distinct from the rest of the ejecta and appear only in specific, limited locations. The highest speed knots show both large proper motions and high radial velocities with estimated space velocities of 10,000 km/s, similar to the typical Si velocity seen in Type Ia supernovae near maximum light. The proper motions of five knots extrapolate back over the age of the remnant to a consistent central position, defining a kinematic center for Kepler's SNR. Our new explosion center agrees well with previous determinations, but suffers less from systematic uncertainty. These five knots are expanding at close to the free expansion rate (expansion indices of 0.75 speeds and expansion indices consistent with decelerated ejecta knots. The differences in the expansion rates are likely a function of differences in the ambient medium density surrounding Kepler’s SNR.
A DECADE-BASELINE STUDY OF THE PLASMA STATES OF EJECTA KNOTS IN CASSIOPEIA A
Energy Technology Data Exchange (ETDEWEB)
Rutherford, John; Dewey, Daniel; Figueroa-Feliciano, Enectali; Heine, Sarah N. T.; Canizares, C. R.; Bastien, Fabienne A.; Sato, Kosuke, E-mail: enectali@mit.edu, E-mail: jmrv@mit.edu [Department of Physics and Kavli Institute for Astrophysics and Space Research, Massachusetts Institute of Technology, Cambridge, MA 02139 (United States)
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.
Prognosis of Cyclic Vomiting Syndrome
Directory of Open Access Journals (Sweden)
J. Gordon Millichap
2016-03-01
Full Text Available Investigators from Teikyo University School of Medicine, Tokyo, Japan, evaluated the clinical features, prognosis, and prophylaxis of cyclic vomiting syndrome and the relationship between the syndrome and levels of adrenocorticotropic/antidiuretic hormones (ACTH/ADH.
National Research Council Canada - National Science Library
Piao, Yun-Song
2010-01-01
Recently, it has been noticed that the amplification of the amplitude of curvature perturbation cycle by cycle can lead to a cyclic multiverse scenario, in which the number of universes increases cycle by cycle...
Algebraic curves of maximal cyclicity
Caubergh, Magdalena; Dumortier, Freddy
2006-01-01
The paper deals with analytic families of planar vector fields, studying methods to detect the cyclicity of a non-isolated closed orbit, i.e. the maximum number of limit cycles that can locally bifurcate from it. It is known that this multi-parameter problem can be reduced to a single-parameter one, in the sense that there exist analytic curves in parameter space along which the maximal cyclicity can be attained. In that case one speaks about a maximal cyclicity curve (mcc) in case only the number is considered and of a maximal multiplicity curve (mmc) in case the multiplicity is also taken into account. In view of obtaining efficient algorithms for detecting the cyclicity, we investigate whether such mcc or mmc can be algebraic or even linear depending on certain general properties of the families or of their associated Bautin ideal. In any case by well chosen examples we show that prudence is appropriate.
Tsai, Wei-Yuan; Tsai, Ru-Yin; Liu, Chih-Chung; Wu, Jia-Lin; Wong, Chih-Shung
2016-04-01
We had previously demonstrated that excitatory amino acid glutamate plays a role in the progression and severity of knee osteoarthritis (OA), and early hyaluronic acid injection attenuates the OA progression by attenuation of knee joint glutamate level, which was also related to the cystine/glutamate antiporter system X (system XC-) expression. System XC- uptakes cystine into chondrocytes for glutathione (GSH) synthesis, but the role of system XC- in OA is rarely addressed. Sulfasalazine (SSZ) is a system XC- inhibitor; SSZ was applied intra-articularly to study the function of system XC- in the development of OA in rats subjected to anterior cruciate ligament transection and medial meniscectomy (ACLT + MMx). Moerover, the system XC- activator N-acetylcysteine (NAC) was also applied to verify the role of system XC-. The intra-articular injection of SSZ significantly attenuated knee swelling and cartilage destruction in the knees of ACLT + MMx rats and this effect was blocked by NAC. The results showed that inhibition of system XC- function can attenuate ACLT + MMx-induced cartilage destruction. In the present study, system XC- inhibitor SSZ was shown to reduce glutamate content in synovial fluid and GSH in chondrocytes. It was also showed SSZ could attenuate ACLT + MMx-induced cartilage destruction, and treatment of NAC reversed the protective effect of SSZ.
Change of Cystine/Glutamate Antiporter Expression in Ethanol-Dependent Rats
Directory of Open Access Journals (Sweden)
Alessandra Tiziana Peana
2014-10-01
Full Text Available Background: Some drugs of abuse down regulate the expression of cystine/glutamate (xCT antiporter in the nucleus accumbens (Acb after extinction or withdrawal. The altered level of xCT exchanger in Acb, a structure involved in ethanol reinforcement, may contribute to the pathological glutamatergic signalling, linked to addiction. We hypothesised that the expression of xCT may be changed in Acb and whole brain also in non-dependent (occasional drinkers, ethanol-dependent rats, as well as, during ethanol withdrawal.Methods: Wistar rats were made ethanol-dependent by chronic exposure to an alcoholic milk beverage (from 2.4 to 7.2% v/v ethanol. Ethanol non-dependent rats were exposed to a similar, but non-alcoholic liquid diet and self-administered ethanol (10% twice a week. Withdrawal in ethanol-dependent rats was studied at 12 hours after the last ethanol-enriched diet exposure. Immediately after the measurement of somatic signs of withdrawal, Western blot analysis with a polyclonal antibody against xCT was carried out in a naïve control group, non-dependent and ethanol-dependent rats as well as withdrawal rats, in order to study the level of xCT expression in Acb and whole brain. Results. Non-dependent rats self-administered an average dose of 1.21±0.02 g/kg per session (30 min. Daily ethanol consumption during chronic exposure to the alcoholic beverage ranged from 6.30±0.16 to 13.99±0.66 g/kg. Ethanol dependent rats after suspension of the ethanol-enriched diet have shown significant somatic signs of withdrawal. Western blotting analysis of Acb lysates revealed that xCT was over expressed in ethanol-dependent rats whereas in whole brain preparations xCT was over expressed in both non-dependent and ethanol-dependent rats compared to control group. On the contrary, xCT expression during withdrawal was down regulated in Acb and restored to control level in whole brain preparations. Conclusions: The changes of xCT expression in both Acb and
Cyclic Cushing's syndrome: an overview.
Albiger, Nora Maria Elvira; Scaroni, Carla M; Mantero, Franco
2007-11-01
Cyclic Cushing's syndrome (CS) is a disorder in which glucocorticoid levels are alternately normal and high, the latter occurring in episodes that can last from a few days to several months. It is more common in children than in adults. Cyclic CS may be either of the two different forms of CS (ACTH-dependent or -independent CS). Clinically, it may present with one or many symptoms, depending on the duration of disease activity and the timing of the fluctuations. A serotoninergic influence, cyclic changes in central dopaminergic tone, spontaneous episodic hemorrhage in the tumor, and the action of inflammatory cytokines with antitumor properties are some of the mechanisms suggested to explain the physiopathology of this phenomenon but the exact mechanism remains to be clarified. The cyclic pattern of hypercortisolism can delay the final diagnosis of CS and make it difficult to interpret the results of dynamic tests. Patients may have paradoxical responses to dexamethasone that can reflect increasing or decreasing levels of endogenous activity. Hormone assessments have to be repeated periodically when a diagnosis of CS is suspected. The cyclic pattern can also interfere with medical treatment because patients may show unexpected clinical and biochemical signs of hypocortisolism when cortisol secretion cyclically returns to normal, so an accurate follow-up is mandatory in these patients.
Transitive oriented 3-Hypergraphs of cyclic orders
2012-01-01
In this paper we introduce the definition of transitivity for oriented 3-hypergraphs in order to study partial and complete cyclic orders. This definition allow us to give sufficient conditions on a partial cyclic order to be totally extendable. Furthermore, we introduce the 3-hypergraph associated to a cyclic permutation and characterize it in terms of cyclic comparability 3-hypergraphs.
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.
Optical vortex knots – one photon at a time
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
Optical vortex knots - one photon at a time
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.
Helicity, topology, and Kelvin waves in reconnecting quantum knots
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.
Park, Jong Taek; Cho, Dong Woo; Lee, Young Bok
2017-01-01
Epidural block is achieved either by single injection of local anesthetic through an epidural needle or as a continuous block by infusion pump through an epidural catheter. Complications associated with epidural catheters include breakage, entrapment, and knotting. Knotting of epidural catheters is very rare, but knotting in lumbar epidural catheters has been reported in a number of studies, and most of these cases involved removal difficulty. We report a case in which we inserted a cervical epidural catheter in a patient who was experiencing severe post-herpetic neuralgia and then removed the knotted catheter without complications. PMID:28261560
Lee, Jaepil
2015-01-01
In the bordered Floer theory, gluing thickened torus of positive meridional Dehn twist to the boundary of a knot complement result in the knot complement of increased framing. For a fixed knot K, we construct a direct system of positively framed knot complements and study the direct limit. We also study the morphism space between two type-DD modules, and derive type-DA morphisms from DD morphisms to derive the direct system maps. In addition, we introduce a direct limit invariant from the dir...
Institute of Scientific and Technical Information of China (English)
顾之雨; 钱尚武
2015-01-01
The GHZ states and W states are two fundamental types of three qubits quantum entangled states. For finding the knotted pictures of three nodes W states, on the one side, we empty any one node, thus obtaining three degenerated two-node W states, then we find the nonzero submatrix of the corresponding covariance correlation tensor in quantum network theory. On the other side, excepting the linkage 41 corresponding to Bell bases, we conjecture that the another one possible oriented link (which is composed of two-component knots entangled with each other and has four crossings) would be the required knotted pictures of the two nodes W states, thence obtain the nonzero submatrix of the Alexander relation matrix in the theory of knot crystals for these knotted pictures. The equality of the two nonzero submatrices of different kinds thus verify the exactness of our conjecture. The superposition of three knotted pictures of two-node W states from different choices of the emptied node gives the knotted pictures of three-node W states, thus shows the correspondence between three-node W states in quantum network theory and the oriented links in knot theory. Finally we point out that there is an intimate and simple relationship between the knotted pictures of GHZ states and W states.
Manual for Cyclic Triaxial Test
DEFF Research Database (Denmark)
Shajarati, Amir; Sørensen, Kris Wessel; Nielsen, Søren Kjær
/dynamic triaxial cell is overall constructed in the same way as the static triaxial cell at Aalborg University, but with the ability to apply any kind of load sequence to the test sample. When conducting cyclic triaxial tests, it is recommended that the manual is followed very tediously since there are many steps...... and if they are done improperly or in the wrong order there is a risk of destroying the test sample or obtaining invalid results.......This manual describes the different steps that is included in the procedure for conducting a cyclic triaxial test at the geotechnical Laboratory at Aalborg University. Furthermore it contains a chapter concerning some of the background theory for the static triaxial tests. The cyclic...